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Sample records for gen agxt r197q

  1. In vivo evidence that Agxt2 can regulate plasma levels of dimethylarginines in mice.

    PubMed

    Kittel, Anja; Maas, Renke; König, Jörg; Mieth, Maren; Weiss, Norbert; Jarzebska, Natalia; Hohenstein, Bernd; Martens-Lobenhoffer, Jens; Bode-Böger, Stefanie M; Rodionov, Roman N

    2013-01-01

    Elevated plasma concentrations of the asymmetric (ADMA) and symmetric (SDMA) dimethylarginine have repeatedly been linked to adverse cardiovascular clinical outcomes. Both dimethylarginines can be degraded by alanine-glyoxylate aminotransferase 2 (Agxt2), which is also the key enzyme responsible for the degradation of endogenously formed β-aminoisobutyrate (BAIB). In the present study we wanted to investigate the effect of BAIB on Agxt2 expression and Agxt2-mediated metabolism of dimethylarginines. We infused BAIB or saline intraperitoneally for 7days in C57/BL6 mice via minipumps. Expression of Agxt2 was determined in liver and kidney. The concentrations of BAIB, dimethylarginines and the Agxt2-specific ADMA metabolite α-keto-δ-(N(G),N(G)-dimethylguanidino)valeric acid (DMGV) was determined by LC-MS/MS in plasma and urine. As compared to controls systemic administration of BAIB increased plasma and urine BAIB levels by a factor of 26.5 (p<0.001) and 25.8 (p<0.01), respectively. BAIB infusion resulted in an increase of the plasma ADMA and SDMA concentrations of 27% and 31%, respectively, (both p<0.05) and a 24% decrease of plasma DMGV levels (p<0.05), while expression of Agxt2 was not different. Our data demonstrate that BAIB can inhibit Agxt2-mediated metabolism of dimethylarginines and show for the first time that endogenous Agxt2 is involved in the regulation of systemic ADMA, SDMA and DMGV levels. The effect of BAIB excess on endogenous dimethylarginine levels may have direct clinical implications for humans with the relatively common genetic trait of hyper-β-aminoisobutyric aciduria.

  2. A novel mutation in the AGXT gene causing primary hyperoxaluria type I: genotype-phenotype correlation.

    PubMed

    M'Dimegh, Saoussen; Aquaviva-Bourdain, Cécile; Omezzine, Asma; M'Barek, Ibtihel; Souche, Geneviéve; Zellama, Dorsaf; Abidi, Kamel; Achour, Abdelattif; Gargah, Tahar; Abroug, Saoussen; Bouslama, Ali

    2016-09-01

    Primary hyperoxaluria type I (PH1) is an autosomal recessive metabolic disorder caused by inherited mutations in the AGXT gene encoding liver peroxisomal alanine : glyoxylate aminotransferase (AGT) which is deficient or mistargeted to mitochondria. PH1 shows considerable phenotypic and genotypic heterogeneity. The incidence and severity of PH1 varies in different geographic regions. DNA samples of the affected members from two unrelated Tunisian families were tested by amplifying and sequencing each of the AGXT exons and intron-exon junctions. We identified a novel frameshift mutation in the AGXT gene, the c.406_410dupACTGC resulting in a truncated protein (p.Gln137Hisfs*19). It is found in homozygous state in two nonconsanguineous unrelated families from Tunisia. These molecular findings provide genotype/phenotype correlations in the intrafamilial phenotypic and permit accurate carrier detection, and prenatal diagnosis. The novel p.Gln137Hisfs*19 mutation detected in our study extend the spectrum of known AGXT gene mutations in Tunisia. PMID:27659337

  3. Mutational analysis of AGXT in two Chinese families with primary hyperoxaluria type 1

    PubMed Central

    2014-01-01

    Background Primary hyperoxaluria type 1 is a rare autosomal recessive disease of glyoxylate metabolism caused by a defect in the liver-specific peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT) that leads to hyperoxaluria, recurrent urolithiasis, and nephrocalcinosis. Methods Two unrelated patients with recurrent urolithiasis, along with members of their families, exhibited mutations in the AGXT gene by PCR direct sequencing. Results Two heterozygous mutations that predict truncated proteins, p.S81X and p.S275delinsRAfs, were identified in one patient. The p.S81X mutation is novel. Two heterozygous missense mutations, p.M1T and p.I202N, were detected in another patient but were not identified in her sibling. These four mutations were confirmed to be of paternal and maternal origin. Conclusions These are the first cases of primary hyperoxaluria type 1 to be diagnosed by clinical manifestations and AGXT gene mutations in mainland China. The novel p.S81X and p.I202N mutations detected in our study extend the spectrum of known AGXT gene mutations. PMID:24934730

  4. Alanine-glyoxylate aminotransferase 2 (AGXT2) polymorphisms have considerable impact on methylarginine and β-aminoisobutyrate metabolism in healthy volunteers.

    PubMed

    Kittel, Anja; Müller, Fabian; König, Jörg; Mieth, Maren; Sticht, Heinrich; Zolk, Oliver; Kralj, Ana; Heinrich, Markus R; Fromm, Martin F; Maas, Renke

    2014-01-01

    Elevated plasma concentrations of asymmetric (ADMA) and symmetric (SDMA) dimethylarginine have repeatedly been linked to adverse clinical outcomes. Both methylarginines are substrates of alanine-glyoxylate aminotransferase 2 (AGXT2). It was the aim of the present study to simultaneously investigate the functional relevance and relative contributions of common AGXT2 single nucleotide polymorphisms (SNPs) to plasma and urinary concentrations of methylarginines as well as β-aminoisobutyrate (BAIB), a prototypic substrate of AGXT2. In a cohort of 400 healthy volunteers ADMA, SDMA and BAIB concentrations were determined in plasma and urine using HPLC-MS/MS and were related to the coding AGXT2 SNPs rs37369 (p.Val140Ile) and rs16899974 (p.Val498Leu). Volunteers heterozygous or homozygous for the AGXT2 SNP rs37369 had higher SDMA plasma concentrations by 5% and 20% (p = 0.002) as well as higher BAIB concentrations by 54% and 146%, respectively, in plasma and 237% and 1661%, respectively, in urine (both p<0.001). ADMA concentrations were not affected by both SNPs. A haplotype analysis revealed that the second investigated AGXT2 SNP rs16899974, which was not significantly linked to the other AGXT2 SNP, further aggravates the effect of rs37369 with respect to BAIB concentrations in plasma and urine. To investigate the impact of the amino acid exchange p.Val140Ile, we established human embryonic kidney cell lines stably overexpressing wild-type or mutant (p.Val140Ile) AGXT2 protein and assessed enzyme activity using BAIB and stable-isotope labeled [²H₆]-SDMA as substrate. In vitro, the amino acid exchange of the mutant protein resulted in a significantly lower enzyme activity compared to wild-type AGXT2 (p<0.05). In silico modeling of the SNPs indicated reduced enzyme stability and substrate binding. In conclusion, SNPs of AGXT2 affect plasma as well as urinary BAIB and SDMA concentrations linking methylarginine metabolism to the common genetic trait of hyper

  5. Caenorhabditis elegans AGXT-1 is a mitochondrial and temperature-adapted ortholog of peroxisomal human AGT1: New insights into between-species divergence in glyoxylate metabolism.

    PubMed

    Mesa-Torres, Noel; Calvo, Ana C; Oppici, Elisa; Titelbaum, Nicholas; Montioli, Riccardo; Miranda-Vizuete, Antonio; Cellini, Barbara; Salido, Eduardo; Pey, Angel L

    2016-09-01

    In humans, glyoxylate is an intermediary product of metabolism, whose concentration is finely balanced. Mutations in peroxisomal alanine:glyoxylate aminotransferase (hAGT1) cause primary hyperoxaluria type 1 (PH1), which results in glyoxylate accumulation that is converted to toxic oxalate. In contrast, glyoxylate is used by the nematode Caenorhabditis elegans through a glyoxylate cycle to by-pass the decarboxylation steps of the tricarboxylic acid cycle and thus contributing to energy production and gluconeogenesis from stored lipids. To investigate the differences in glyoxylate metabolism between humans and C. elegans and to determine whether the nematode might be a suitable model for PH1, we have characterized here the predicted nematode ortholog of hAGT1 (AGXT-1) and compared its molecular properties with those of the human enzyme. Both enzymes form active PLP-dependent dimers with high specificity towards alanine and glyoxylate, and display similar three-dimensional structures. Interestingly, AGXT-1 shows 5-fold higher activity towards the alanine/glyoxylate pair than hAGT1. Thermal and chemical stability of AGXT-1 is lower than that of hAGT1, suggesting temperature-adaptation of the nematode enzyme linked to the lower optimal growth temperature of C. elegans. Remarkably, in vivo experiments demonstrate the mitochondrial localization of AGXT-1 in contrast to the peroxisomal compartmentalization of hAGT1. Our results support the view that the different glyoxylate metabolism in the nematode is associated with the divergent molecular properties and subcellular localization of the alanine:glyoxylate aminotransferase activity.

  6. Caenorhabditis elegans AGXT-1 is a mitochondrial and temperature-adapted ortholog of peroxisomal human AGT1: New insights into between-species divergence in glyoxylate metabolism.

    PubMed

    Mesa-Torres, Noel; Calvo, Ana C; Oppici, Elisa; Titelbaum, Nicholas; Montioli, Riccardo; Miranda-Vizuete, Antonio; Cellini, Barbara; Salido, Eduardo; Pey, Angel L

    2016-09-01

    In humans, glyoxylate is an intermediary product of metabolism, whose concentration is finely balanced. Mutations in peroxisomal alanine:glyoxylate aminotransferase (hAGT1) cause primary hyperoxaluria type 1 (PH1), which results in glyoxylate accumulation that is converted to toxic oxalate. In contrast, glyoxylate is used by the nematode Caenorhabditis elegans through a glyoxylate cycle to by-pass the decarboxylation steps of the tricarboxylic acid cycle and thus contributing to energy production and gluconeogenesis from stored lipids. To investigate the differences in glyoxylate metabolism between humans and C. elegans and to determine whether the nematode might be a suitable model for PH1, we have characterized here the predicted nematode ortholog of hAGT1 (AGXT-1) and compared its molecular properties with those of the human enzyme. Both enzymes form active PLP-dependent dimers with high specificity towards alanine and glyoxylate, and display similar three-dimensional structures. Interestingly, AGXT-1 shows 5-fold higher activity towards the alanine/glyoxylate pair than hAGT1. Thermal and chemical stability of AGXT-1 is lower than that of hAGT1, suggesting temperature-adaptation of the nematode enzyme linked to the lower optimal growth temperature of C. elegans. Remarkably, in vivo experiments demonstrate the mitochondrial localization of AGXT-1 in contrast to the peroxisomal compartmentalization of hAGT1. Our results support the view that the different glyoxylate metabolism in the nematode is associated with the divergent molecular properties and subcellular localization of the alanine:glyoxylate aminotransferase activity. PMID:27179589

  7. Two novel AGXT mutations identified in primary hyperoxaluria type-1 and distinct morphological and structural difference in kidney stones.

    PubMed

    Wang, Cui; Lu, Jingru; Lang, Yanhua; Liu, Ting; Wang, Xiaoling; Zhao, Xiangzhong; Shao, Leping

    2016-01-01

    Primary hyperoxaluria type 1 (PH1) is a rare genetic disease characterized by excessive oxalate accumulation in plasma and urine, resulting in various phenotypes because of allelic and clinical heterogeneity. This study aimed to detect disease-associated genetic mutations in three PH1 patients in a Chinese family. All AGXT exons and 3 common polymorphisms which might synergistically interact with mutations, including P11L, I340 M and IVSI+74 bp were analyzed by direct sequencing in all family members. It demonstrated that in each of three patients, a previously reported nonsense mutation p.R333(*) was in cis with a novel missense mutation p.M49L in the minor allele characterized by the polymorphism of 74-bp duplication in intron 1, while the other novel missense mutation p.N72I was in trans with both p.R333(*) and P.M49L in the major allele. Kidney stones from two sibling patients were also observed though stereomicroscopic examination and scanning electron microscopy. Distinct morphological and inner-structure differences in calculi were noticed, suggesting clinical heterozygosity of PH1 to a certain extent. In brief, two novel missense mutations were identified probably in association with PH1, a finding which should provide an accurate tool for prenatal diagnosis, genetic counseling and screening for potential presymptomatic individuals. PMID:27644547

  8. Two novel AGXT mutations identified in primary hyperoxaluria type-1 and distinct morphological and structural difference in kidney stones

    PubMed Central

    Wang, Cui; Lu, Jingru; Lang, Yanhua; Liu, Ting; Wang, Xiaoling; Zhao, Xiangzhong; Shao, Leping

    2016-01-01

    Primary hyperoxaluria type 1 (PH1) is a rare genetic disease characterized by excessive oxalate accumulation in plasma and urine, resulting in various phenotypes because of allelic and clinical heterogeneity. This study aimed to detect disease-associated genetic mutations in three PH1 patients in a Chinese family. All AGXT exons and 3 common polymorphisms which might synergistically interact with mutations, including P11L, I340 M and IVSI+74 bp were analyzed by direct sequencing in all family members. It demonstrated that in each of three patients, a previously reported nonsense mutation p.R333* was in cis with a novel missense mutation p.M49L in the minor allele characterized by the polymorphism of 74-bp duplication in intron 1, while the other novel missense mutation p.N72I was in trans with both p.R333* and P.M49L in the major allele. Kidney stones from two sibling patients were also observed though stereomicroscopic examination and scanning electron microscopy. Distinct morphological and inner-structure differences in calculi were noticed, suggesting clinical heterozygosity of PH1 to a certain extent. In brief, two novel missense mutations were identified probably in association with PH1, a finding which should provide an accurate tool for prenatal diagnosis, genetic counseling and screening for potential presymptomatic individuals. PMID:27644547

  9. Using GenBank.

    PubMed

    Sayers, Eric W; Karsch-Mizrachi, Ilene

    2016-01-01

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

  10. GenBank.

    PubMed

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

    1994-09-01

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

  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. Mapping from GenBank to MEDLINE.

    PubMed Central

    Bicknell, E J; Rada, R; Davidson, S; Stander, R

    1988-01-01

    GenBank has been based largely on literature that provides nucleic acid sequences. To find additional literature that is relevant to a given sequence, a search of MEDLINE can prove helpful. This paper documents some of the similarities between GenBank and MEDLINE that facilitate retrieval of documents from MEDLINE. In particular, techniques and examples are presented which take GenBank information and lead to MEDLINE information that supplements the GenBank information. PMID:3281141

  13. 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

  14. 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.

  15. 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.

  16. Unleashing Gen Y: Marketing Mars to Millennials

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

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

  17. 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

  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. 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...

  20. 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

  1. 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.

  2. 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.

  3. GEN3D Ver. 1.37

    2012-01-04

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

  4. 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

  5. TidGen Power System Commercialization Project

    SciTech Connect

    Sauer, Christopher R.; McEntee, Jarlath

    2013-12-30

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

  6. Gen IV Materials Handbook Functionalities and Operation

    SciTech Connect

    Ren, Weiju

    2009-12-01

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

  7. 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.

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

    ERIC Educational Resources Information Center

    Lichy, Jessica

    2012-01-01

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

  9. Hoja informativa de pruebas genéticas

    Cancer.gov

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

  10. 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. 

  11. GenVisR: Genomic Visualizations in R

    PubMed Central

    Skidmore, Zachary L.; Wagner, Alex H.; Lesurf, Robert; Campbell, Katie M.; Kunisaki, Jason; Griffith, Obi L.; Griffith, Malachi

    2016-01-01

    Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor. Availability and Implementation: GenVisR is an R package available via Bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website. Contacts: obigriffith@wustl.edu or mgriffit@wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27288499

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. GenR, an IclR-type regulator, activates and represses the transcription of gen genes involved in 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum.

    PubMed

    Chao, Hongjun; Zhou, Ning-Yi

    2013-04-01

    The genes required for 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum are closely clustered in three operons. GenR, an IclR-type regulator, can activate the transcription of genKH and genDFM operons in response to 3-hydroxybenzoate and gentisate, and it can repress its own expression. Footprinting analyses demonstrated that GenR bound to four sites with different affinities. Two GenR-binding sites (DFMn01 and DFMn02) were found to be located between positions --41 and --84 upstream of the --35 and --10 regions of the genDFM promoter, which was involved in positive regulation of genDFM transcription. The GenR binding site R-KHn01 (located between positions --47 and --16) overlapped the --35 region of the genKH promoter sequence and is involved in positive regulation of its transcription. The binding site R-KHn02, at which GenR binds to its own promoter, was found within a footprint extending from position --44 to --67. It appeared to be involved in negative regulation of the activity of the genR promoter. A consensus motif with a 5-bp imperfect palindromic sequence [ATTCC-N(7(5))-GGAAT] was identified among all four GenR binding sites and found to be necessary to GenR regulation through site-directed mutagenesis. The results reveal a new regulatory function of the IclR family in the catabolism of aromatic compounds.

  17. 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

  18. 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

  19. EPCGen2 pseudorandom number generators: analysis of J3Gen.

    PubMed

    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

  20. 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

  1. 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).

  2. 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

  3. 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

  4. Training trust in automation within a NextGen environment

    NASA Astrophysics Data System (ADS)

    Higham, Tiana-Lynn M.

    The projected increase in air traffic density has led to the development of NextGen that is expected to revolutionize the way the NAS is currently functioning. For NextGen to be implemented successfully, it is important to understand the humanautomation relationship within a complex system. Controllers will have to rely on automated tools to successfully manage aircraft in their sector. Increasing human trust in automation can lead to an increase in automation acceptance and its proper use. However, we are not aware of any research studies that have attempted to directly train individuals to trust automation. We report on an attempt to train 8 novice air traffic controllers to trust the automated NextGen tools in a radar internship course. Although the results were not statistically significant, the trend in the data suggests that it may be possible to train trust in automation.

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

    PubMed

    Riley, M; Space, D B

    1996-01-01

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

  6. GenR, an IclR-Type Regulator, Activates and Represses the Transcription of gen Genes Involved in 3-Hydroxybenzoate and Gentisate Catabolism in Corynebacterium glutamicum

    PubMed Central

    Chao, Hongjun

    2013-01-01

    The genes required for 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum are closely clustered in three operons. GenR, an IclR-type regulator, can activate the transcription of genKH and genDFM operons in response to 3-hydroxybenzoate and gentisate, and it can repress its own expression. Footprinting analyses demonstrated that GenR bound to four sites with different affinities. Two GenR-binding sites (DFMn01 and DFMn02) were found to be located between positions −41 and −84 upstream of the −35 and −10 regions of the genDFM promoter, which was involved in positive regulation of genDFM transcription. The GenR binding site R-KHn01 (located between positions −47 and −16) overlapped the −35 region of the genKH promoter sequence and is involved in positive regulation of its transcription. The binding site R-KHn02, at which GenR binds to its own promoter, was found within a footprint extending from position −44 to −67. It appeared to be involved in negative regulation of the activity of the genR promoter. A consensus motif with a 5-bp imperfect palindromic sequence [ATTCC-N7(5)-GGAAT] was identified among all four GenR binding sites and found to be necessary to GenR regulation through site-directed mutagenesis. The results reveal a new regulatory function of the IclR family in the catabolism of aromatic compounds. PMID:23354754

  7. 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.

  8. 77 FR 54648 - Seventh Meeting: RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-05

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

  9. 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,...

  10. 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:...

  11. 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:...

  12. 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...

  13. 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…

  14. 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…

  15. 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.

  16. 78 FR 8108 - NextGen Solutions Vendors Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ... Organization's (ICAO) Aviation System Block Upgrade (ASBU) initiative. The NextGen solutions address the ICAO..., this request seeks responses from (e) the knowledge and service providers who can facilitate these... Efficiency through the initial application of Data Link En-Route (e) Knowledge and service providers...

  17. ORPC RivGen controller performance raw data - Igiugig 2015

    SciTech Connect

    Jarlath McEntee

    2015-12-18

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

  18. 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.

  19. 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.

  20. GenNet: A Platform for Hybrid Network Experiments.

    PubMed

    Kispersky, Tilman J; Economo, Michael N; Randeria, Pratik; White, John A

    2011-01-01

    We describe General Network (GenNet), a software plugin for the real time experimental interface (RTXI) dynamic clamp system that allows for straightforward and flexible implementation of hybrid network experiments. This extension to RTXI allows for hybrid networks that contain an arbitrary number of simulated and real neurons, significantly improving upon previous solutions that were limited, particularly by the number of cells supported. The benefits of this system include the ability to rapidly and easily set up and perform scalable experiments with hybrid networks and the ability to scan through ranges of parameters. We present instructions for installing, running and using GenNet for hybrid network experiments and provide several example uses of the system.

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

    PubMed

    Smith, S

    2001-04-01

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

  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. 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

  4. 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)

  5. PowerGen Plc -- A commercial user of Orimulsion

    SciTech Connect

    Tombs, R.; Jones, A.

    1996-12-31

    PowerGen has been operating two power stations commercially on Orimulsion fuel since 1991. Prior to the conversions, both power stations, Ince and Richborough, experienced low load factors caused by the inconsistent, but on average, high fuel oil prices. Orimulsion provided an opportunity of economic operation at both power stations if it could be proved that the fuel could be burnt safely, efficiently and cleanly. Consequently, a series of trials was organized at both plants and these commenced in 1988. Ince was the first plant to use Orimulsion when single burner trials were conducted with the objective of selecting a suitable burner system for subsequent full boiler trials. Having developed burners which would ensure stable and clean combustion, full scale boiler trials were undertaken at both power stations in 1989. The key objectives of these trials were to establish the impact on the plant of handling and burning the fuel, to define hardware modifications that would be required for commercial operation and for the operators to gain experience with Orimulsion. Following different levels of plant modification at Ince and Richborough Power Stations, judged necessary as a result of the trials, commercial operation was begun. Since late 1991, PowerGen has consumed about 1.3m tonnes of Orimulsion each year. PowerGen has been able to develop a unique knowledge on all aspects of handling and burning Orimulsion. The intent of this paper is to provide an update of their experience under commercial operation.

  6. The GenABEL Project for statistical genomics.

    PubMed

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

    2016-01-01

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

  7. The GenABEL Project for statistical genomics.

    PubMed

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

    2016-01-01

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

  8. 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.

  9. 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.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  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. Meloneis Gen. Nov., a New Epipsammic Genus of Rhaphoneidaceae (Bacillariophyceae)

    PubMed Central

    Louvrou, Ioanna; Danielidis, Daniel B.; Economou-Amilli, Athena

    2012-01-01

    The diatom family Rhaphoneidaceae is characterized by high generic diversity and low species diversity with most genera known to have long stratigraphic ranges. The genera within this family are neritic marine, and mostly epipsammic. A new modern and epipsammic genus, Meloneis gen. nov., is described herein and is compared to all genera within Rhaphoneidaceae and especially to Rhaphoneis Ehrenberg s.l. Within Meloneis three new species and one variety are distinguished and described herein: M. mimallis sp. nov., M. mimallis var. zephyria var. nov., M. akytos sp. nov., and M. gorgis sp. nov. PMID:22442663

  14. Frigitilla gen. nov., a new genus of Amazonian Mutillidae (Hymenoptera).

    PubMed

    Bartholomay, Pedro R; Williams, Kevin A; Luz, David R; Morato, Elder F

    2015-01-01

    Mutilla frigidula Cresson, 1902 was transferred to Tobantilla by Williams et al. (2011), based on morphological similarities with females of that genus. Discovery of the male of this species indicated significant morphological differences from Tobantilla. We therefore erect the genus, Frigitilla gen. nov., for Mutilla frigidula. Herein, we describe the male of F. frigidula (Cresson, 1902), comb. nov., associate it with its host (Trypoxylon spp.), and discuss its relations to other mutillid genera. The impact of collecting method and specimen age on the integumental coloration of specimens is discussed, emphasizing the need to diagnose species on consistent structural features rather than differences in color pattern.

  15. 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.

  16. Nuclear Data Needs for the Assessment of Gen IV Systems

    NASA Astrophysics Data System (ADS)

    Rimpault, Gerald

    2006-04-01

    Four of the six nuclear systems identified by the Gen-IV international forum are relying in fast reactors. The high performance required from these future FR's calls for very innovative core characteristics compared with conventional fast reactor designs, which in turns give rise to new challenges for the available neutronics methods and data. The ERANOS “formulaire” was developed for reliable, precise and efficient calculations of sodium-cooled fast neutron reactor cores. Such a “formulaire” enables the prediction of all the neutronic quantities of interest for reactor design, operation and safety studies, along with their corresponding uncertainties. Given its achievement in terms of accuracy for existing sodium cooled reactors, the way the ERANOS “formulaire” has been designed should be looked as an example for developing similar tools for GENIV fast cores. The methodology for defining nuclear data needs is briefly covered. Target accuracies for GEN-IV neutronic characteristics is an important point to start with. The covariance data is of significant importance for quantifying the needs and evaluators should provide them with their nuclear data. Hence, nuclear data requests should be associated to uncertainty values. Integral experiments have a complementary role to differential measurements for meeting some nuclear data needs (for instance Pu239 fission). High Priority Level Requests should include those nuclides accessible with current differential measurement technology and should include less important nuclides A list of potential requests is existing, quantifying their uncertainties remain a significant effort particularly when looking at fuel cycle quantities.

  17. Next gen wavelets down-sampling preserving statistics

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

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

  18. GenDecoder: genetic code prediction for metazoan mitochondria.

    PubMed

    Abascal, Federico; Zardoya, Rafael; Posada, David

    2006-07-01

    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 http://darwin.uvigo.es/software/gendecoder.html.

  19. Genetic code prediction for metazoan mitochondria with GenDecoder.

    PubMed

    Abascal, Federico; Zardoya, Rafael; Posada, David

    2009-01-01

    There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating its protein-coding genes. Such characterization is particularly important in the case of metazoan mitochondrial genomes for two reasons: first, many variant codes occur in them and second, mitochondrial data is frequently used for evolutionary studies. Variant codes are usually found by comparative sequence analyses. Given a protein alignment, if a particular codon for a given species occurs at positions in which a particular amino acid is frequently found in other species, then the most likely hypothesis is that the codon is translated as that particular amino acid in that species. Previously, we have shown that this method can be very reliable provided that enough taxa and positions are included in the comparisons and have implemented it in the web-ser GenDecoder (http://darwin.uvigo.es/software/gendecoder.html). In this chapter we describe the rationale of the method used by GenDecoder and its usage through worked examples, highlighting the potential problems that can arise during the analysis.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. 76 FR 3931 - Second Meeting RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION 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...

  2. 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...

  3. How Gen Y and Boomers will reshape your agenda.

    PubMed

    Hewlett, Sylvia Ann; Sherbin, Laura; Sumberg, Karen

    2009-01-01

    When it comes to workplace preferences, Generation Y workers closely resemble Baby Boomers. Because these two huge cohorts now coexist in the workforce, their shared values will hold sway in the companies that hire them. The authors, from the Center for Work-Life Policy, conducted two large-scale surveys that reveal those values. Gen Ys and Boomers are eager to contribute to positive social change, and they seek out workplaces where they can do that. They expect flexibility and the option to work remotely, but they also want to connect deeply with colleagues. They believe in employer loyalty but desire to embark on learning odysseys. Innovative firms are responding by crafting reward packages that benefit both generations of workers--and their employers.

  4. 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.

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

    PubMed

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

    2010-11-01

    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_2519delAAGTT, 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

  6. 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

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

    NASA Astrophysics Data System (ADS)

    Kappes, Alexander

    2016-04-01

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

  8. 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

  9. 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

  10. 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.

  11. GenIE: an intelligent system for writing genetic counseling patient letters.

    PubMed

    Green, Nancy

    2005-01-01

    We are developing GenIE, a prototype intelligent system to create first drafts of genetic counseling patient letters. GenIE will apply natural language generation techniques to construct the first draft of a letter for subsequent review and editing, if needed, by the genetic counselor. For purposes of knowledge acquisition, we have been analyzing a corpus of patient letters. Based on the corpus analysis we are developing a knowledge base and text generation strategies.

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

    PubMed

    Riley, M

    1997-01-01

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

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

    PubMed

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

    2016-08-01

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

  14. 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). PMID:26828023

  15. Modelling of advanced structural materials for GEN IV reactors

    NASA Astrophysics Data System (ADS)

    Samaras, M.; Hoffelner, W.; Victoria, M.

    2007-09-01

    The choice of suitable materials and the assessment of long-term materials damage are key issues that need to be addressed for the safe and reliable performance of nuclear power plants. Operating conditions such as high temperatures, irradiation and a corrosive environment degrade materials properties, posing the risk of very expensive or even catastrophic plant damage. Materials scientists are faced with the scientific challenge to determine the long-term damage evolution of materials under service exposure in advanced plants. A higher confidence in life-time assessments of these materials requires an understanding of the related physical phenomena on a range of scales from the microscopic level of single defect damage effects all the way up to macroscopic effects. To overcome lengthy and expensive trial-and-error experiments, the multiscale modelling of materials behaviour is a promising tool, bringing new insights into the fundamental understanding of basic mechanisms. This paper presents the multiscale modelling methodology which is taking root internationally to address the issues of advanced structural materials for Gen IV reactors.

  16. 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).

  17. 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.

  18. 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.

  19. 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

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

    PubMed

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

    2016-03-01

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

  1. Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater.

    PubMed

    Vaidya, Bhumika; Kumar, Ravinder; Sharma, Gunjan; Srinivas, Tanuku Naga Radha; Kumar, Pinnaka Anil

    2015-11-01

    A novel Gram-stain-negative, rod-shaped, yellow-pigmented, non-sporulating, non-motile bacterium, designated strain AK20T, was isolated from seawater collected from Kochi city, Kerala state, India. Colonies on marine agar were circular, yellow, shiny, translucent, 2-3 mm in diameter, convex and with entire margin. Flexirubin-type pigment was present. The fatty acids were dominated by iso-branched units with a high abundance of iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and iso-C15:0 3-OH. Polar lipids included phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and four unidentified lipids. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The DNA G+C content of strain AK20T was 38.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK20T was closely related to Formosa spongicola A2T and Bizionia paragorgiae KMM 6029T (pair-wise sequence similarities of 95.9 and 95.7%, respectively), forming a distinct branch within the family Flavobacteriaceae and clustering with the clade comprising species of the genus Bizionia. Based on phenotypic and chemotaxonomic characteristics and phylogenetic analysis, strain AK20T is different from the existing genera in the family Flavobacteriaceae, and is therefore considered to represent a novel species of a new genus, for which the name Xanthomarina gelatinilytica gen. nov., sp. nov. is proposed. The type strain of Xanthomarina gelatinilytica is AK20T ( = MTCC 11705T = JCM 18821T). PMID:26956595

  2. Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment.

    PubMed

    Wang, Zong-Jie; Xie, Zhi-Hong; Wang, Chao; Du, Zong-Jun; Chen, Guan-Jun

    2014-10-01

    A novel Gram-stain-negative, rod-to-spiral-shaped, oxidase- and catalase- positive and facultatively aerobic bacterium, designated HS6(T), was isolated from marine sediment of Yellow Sea, China. It can reduce nitrate to nitrite and grow well in marine broth 2216 (MB, Hope Biol-Technology Co., Ltd) with an optimal temperature for growth of 30-33 °C (range 12-45 °C) and in the presence of 2-3% (w/v) NaCl (range 0.5-7%, w/v). The pH range for growth was pH 6.2-9.0, with an optimum at 6.5-7.0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel isolate was 93.3% similar to the type strain of Neptunomonas antarctica, 93.2% to Neptunomonas japonicum and 93.1% to Marinobacterium rhizophilum, the closest cultivated relatives. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown lipids. Major cellular fatty acids were summed feature 3 (C(16:1) ω7c/iso-C15:0 2-OH), C(18:1) ω7c and C(16:0) and the main respiratory quinone was Q-8. The DNA G+C content of strain HS6(T) was 61.2 mol%. Based on the phylogenetic, physiological and biochemical characteristics, strain HS6(T) represents a novel genus and species and the name Motiliproteus sediminis gen. nov., sp. nov., is proposed. The type strain is HS6(T) (=ATCC BAA-2613(T)=CICC 10858(T)).

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-10-01

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

  5. Marinirhabdus gelatinilytica gen. nov., sp. nov., isolated from seawater.

    PubMed

    Wu, Yue-Hong; Xamxidin, Maripat; Meng, Fan-Xu; Zhang, Xin-Qi; Wang, Chun-Sheng; Tohty, Dilbar; Xu, Xue-Wei

    2016-08-01

    A Gram-stain-negative, aerobic and slightly halophilic bacterium was isolated from the South China Sea, and was subjected to characterization using a polyphasic taxonomic approach. Cells of the isolate, designated NH83T, were non-motile and rod-shaped. On the basis of 16S rRNA gene sequence analysis, strain NH83Twas closely related to members of the genera Aureisphaera (with sequence similarity of 92.9 %), Jejudonia (92.8 %), Marixanthomonas (92.6 %), Altuibacter (92.6 %), Ulvibacter (91.5-91.9 %), Gilvibacter (91.8 %) and Aequorivita (89.6-91.2 %), all of which belong to the family Flavobacteriaceae. Phylogenetic analysis indicated that it represented an independent lineage and its closest relatives belonged to the genus Marixanthomonas. The sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, two aminolipids, one aminophospholipid and one unidentified lipid. The principal fatty acids were branched fatty acids, including iso-C15 : 0, iso-C17 : 0 3-OH, iso-C16 : 0, iso-C15 : 1 G and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The genomic DNA G+C content was 41.0 mol%. Strain NH83T was positive for hydrolysis of aesculin, gelatin and Tween 60. Phylogenetic distinctiveness and chemotaxonomic differences, together with differential phenotypic properties, revealed that strain NH83T could be differentiated from closely related genera. Therefore, it is proposed that strain NH83T represents a novel species in a new genus, for which the name Marinirhabdus gelatinilytica gen. nov., sp. nov. (type strain NH83T=CGMCC 1.15462T=DSM 101478T) is proposed.

  6. Analysis and Improvement of a Pseudorandom Number Generator for EPC Gen2 Tags

    NASA Astrophysics Data System (ADS)

    Melia-Segui, J.; Garcia-Alfaro, J.; Herrera-Joancomarti, J.

    The EPC Gen2 is an international standard that proposes the use of Radio Frequency Identification (RFID) in the supply chain. It is designed to balance cost and functionality. The development of Gen2 tags faces, in fact, several challenging constraints such as cost, compatibility regulations, power consumption, and performance requirements. As a consequence, security on board of Gen2 tags is often minimal. It is, indeed, mainly based on the use of on board pseudorandomness. This pseudorandomness is used to blind the communication between readers and tags; and to acknowledge the proper execution of password-protected operations. Gen2 manufacturers are often reluctant to show the design of their pseudorandom generators. Security through obscurity has always been ineffective. Some open designs have also been proposed. Most of them fail, however, to prove their correctness. We analyze a recent proposal presented in the literature and demonstrate that it is, in fact, insecure. We propose an alternative mechanism that fits the Gen2 constraints and satisfies the security requirements.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Halopolyspora alba gen. nov., sp. nov., isolated from sediment.

    PubMed

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

    2014-08-01

    A novel halophilic, filamentous actinomycete, designated strain AFM 10251(T), was isolated from a sediment sample collected from the Dead Sea, Israel. The isolate grew with 10-35% multi-salts, and did not grow without NaCl or MgCl2. The isolate formed a white aerial mycelium, and long chains of arthrospores with more than 10 spores per chain. The spores were spherical or oval with warty surfaces, and sterile mycelium was present between individual spores. The isolate contained meso-diaminopimelic acid and a small proportion of LL-diaminopimelic acid as cell-wall diamino acids, and galactose and arabinose as whole-cell sugars. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and three unknown phospholipids. Major fatty acids were iso-C(16 : 0), iso-C(17 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content of strain AFM 10251(T) was 66.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM 10251(T) and the genus Actinopolyspora formed a distinct lineage. Analysis of the secondary structures of variable areas of the 16S rRNA gene showed that strain AFM 10251(T) was different from all recognized species of the genus Actinopolyspora and members of the family Pseudonocardiaceae. Analysis of the signature nucleotides of the 16S rRNA gene showed that strain AFM 10251(T) and Actinopolyspora halophila formed a single group, but with base pair differences at positions 127 : 234 and 183 : 194. On the basis of analysis of chemical and molecular characteristics, strain AFM 10251(T) is considered to represent a novel species of a new genus in the family Actinopolysporaceae, for which the name Halopolyspora alba gen. nov., sp. nov. is proposed. The type strain of Halopolyspora alba is AFM 10251(T) ( = DSM 45976(T) = CGMCC 4.7114(T)). PMID:24860112

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

    PubMed

    2003-01-01

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

  14. Scintigraphy of the salivary glands in Sjögen's syndrome.

    PubMed Central

    Arrago, J P; Rain, J D; Brocheriou, C; Rocher, F

    1987-01-01

    Scintigraphy of the salivary glands with technetium-sodium pertechnetate (99mTc) was undertaken on 320 patients with oral dryness or connective tissue disease using a computer assisted method that gave quantitative results about the major salivary gland function. Compared with clinical and histological data, scintigraphy provides a sensitive method, even though it is not specific, for detecting minimal injuries to salivary glands in patients suspected of having Sjögen's syndrome. Moreover, it might differentiate between the Sjögen-like syndrome and the sequelae of radiotherapy in patients with bone marrow graft. Scintigraphy of the major salivary glands could therefore form part of the routine investigation of patients with Sjögen's syndrome. PMID:2828435

  15. 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.

  16. 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.

  17. 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

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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…

  3. 75 FR 1052 - Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-08

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of Filing December 30, 2009. Take notice that on December 24, 2009, Terra-Gen...

  4. 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...

  5. Complete cDNAs from Brachymyrmex patagonicus (Hymenoptera: Formicidae). --GenBank accession numbers: GU582126-GU582140.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    15 new gene sequences were identified from workers of Brachymyrmex patagonicus, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU582126-GU582140. This information will provide scientists with genetic tools to study the development and the p...

  6. 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.

  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. PMID:27567715

  8. 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.

  9. 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

  10. 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…

  11. 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

  12. Balancing Formative and Summative Science Assessment Practices: Year One of the GenScope Assessment Project.

    ERIC Educational Resources Information Center

    Hickey, Daniel T.; Kruger, Ann Cale; Fredrick, Laura D.; Schafer, Nancy Jo; Kindfield, Ann C. H.

    This paper describes the GenScope Assessment Project, a project that is exploring ways of using multimedia computers to teach complex science content, refining sociocultural views of assessment and motivation, and considering different ways of reconciling the differences between these newer views and prior behavioral and cognitive views. The…

  13. Sinolatindia petila gen. n. and sp. n. from China (Blattodea, Corydiidae, Latindiinae).

    PubMed

    Qiu, Lu; Che, Yanli; Wang, Zongqing

    2016-01-01

    Sinolatindia petila gen. n. and sp. n. (Blattodea: Corydiidae: Latindiinae) is reported from Yunnan Province, China. Description, illustrations and a distribution map of the new taxon are provided. Comparisons with the type genus Latindia Stål, 1860 and the genus Homopteroidea Shelford, 1906 are given.

  14. Sinolatindia petila gen. n. and sp. n. from China (Blattodea, Corydiidae, Latindiinae)

    PubMed Central

    Qiu, Lu; Che, Yanli; Wang, Zongqing

    2016-01-01

    Abstract Sinolatindia petila gen. n. and sp. n. (Blattodea: Corydiidae: Latindiinae) is reported from Yunnan Province, China. Description, illustrations and a distribution map of the new taxon are provided. Comparisons with the type genus Latindia Stål, 1860 and the genus Homopteroidea Shelford, 1906 are given. PMID:27408574

  15. GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap

    PubMed Central

    Xing, Eric P.; Curtis, Ross E.; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  16. 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

  17. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    PubMed Central

    Liu, Yijin; Freeman, Alasdair D.J.; Déclais, Anne-Cécile; Wilson, Timothy J.; Gartner, Anton; Lilley, David M.J.

    2015-01-01

    Summary We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction. PMID:26686639

  18. 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.

  19. 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.

  20. GWAS in a box: statistical and visual analytics of structured associations via GenAMap.

    PubMed

    Xing, Eric P; Curtis, Ross E; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  1. Extending Validated Human Performance Models to Explore NextGen Concepts

    NASA Technical Reports Server (NTRS)

    Gore, Brian Francis; Hooey, Becky Lee; Mahlstedt, Eric; Foyle, David C.

    2012-01-01

    To meet the expected increases in air traffic demands, NASA and FAA are researching and developing Next Generation Air Transportation System (NextGen) concepts. NextGen will require substantial increases in the data available to pilots on the flight deck (e.g., weather,wake, traffic trajectory predictions, etc.) to support more precise and closely coordinated operations (e.g., self-separation, RNAV/RNP, and closely spaced parallel operations, CSPOs). These NextGen procedures and operations, along with the pilot's roles and responsibilities, must be designed with consideration of the pilot's capabilities and limitations. Failure to do so will leave the pilots, and thus the entire aviation system, vulnerable to error. A validated Man-machine Integration and design Analysis System (MIDAS) v5 model was extended to evaluate anticipated changes to flight deck and controller roles and responsibilities in NextGen approach and Land operations. Compared to conditions when the controllers are responsible for separation on decent to land phase of flight, the output from these model predictions suggest that the flight deck response time to detect the lead aircraft blunder will decrease, pilot scans to the navigation display will increase, and workload will increase.

  2. 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.

  3. 77 FR 25524 - Sixth Meeting: RTCA, NextGen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-30

    ... implementation 10:45-11:15 Break 11:15-12:15 Best Equipped Best Served A facilitated discussion of an important principle for NextGen implementation 12:15-1:00 Lunch Break 1:00-1:20 Review and Approve Recommendation...

  4. GWAS in a box: statistical and visual analytics of structured associations via GenAMap.

    PubMed

    Xing, Eric P; Curtis, Ross E; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap.

  5. GEN1 promotes Holliday junction resolution by a coordinated nick and counter-nick mechanism

    PubMed Central

    Chan, Ying Wai; West, Stephen

    2015-01-01

    Holliday junctions (HJs) that physically link sister chromatids or homologous chromosomes are formed as intermediates during DNA repair by homologous recombination. Persistent recombination intermediates are acted upon by structure-selective endonucleases that are required for proper chromosome segregation at mitosis. Here, we have purified full-length human GEN1 protein and show that it promotes Holliday junction resolution by a mechanism that is analogous to that exhibited by the prototypic HJ resolvase E. coli RuvC. We find that GEN1 cleaves HJs by a nick and counter-nick mechanism involving dual co-ordinated incisions that lead to the formation of ligatable nicked duplex products. As observed with RuvC, cleavage of the first strand is rate limiting, while second strand cleavage is rapid. In contrast to RuvC, however, GEN1 is largely monomeric in solution, but dimerizes on the HJ. Using HJs containing non-cleavable phosphorothioate-containing linkages in one strand, we show that the two incisions can be uncoupled and that the first nick occurs upon GEN1 dimerization at the junction. These results indicate that the mechanism of HJ resolution is largely conserved from bacteria to man, despite a lack of sequence homology between the resolvases. PMID:26578604

  6. Introduction of Orimulsion{sup R} fuel into PowerGen PLC (UK)

    SciTech Connect

    Tombs, R.

    1995-09-01

    PowerGen has 4GW of oil fired plant comprising three power stations. Whilst burning fuel oil the load factor has been very low at between 3 and 20% because of the variable fuel price. Orimulsion, which is a bitumen-in-water emulsion, was seen as a candidate substitute fuel because of its stable cost. Because Orimulsion has very different characteristics to those of fuel oil, before committing itself to the fuel PowerGen decided to conduct full boiler trials to establish the effect of the fuel on the plant, the modifications that would be necessary to convert to full commercial operation and the environmental implications. This paper describes the outcome of the early trials that took place at each of the three power stations and the modifications that were necessary to convert plant at two of the stations. PowerGen is currently the world`s largest user of Orimulsion, consuming up to 1.5 m tonnes each year at two sites and the operational experience at each site since the start of commercial operation is summarized. Because of its unique experience with the use of Orimulsion, PowerGen can assist potential users in addressing the key conversion issues that need to be considered through consultancy services. A typical example of the issues addressed at a European utility is discussed in this paper.

  7. 76 FR 15039 - RTCA Government/Industry NextGen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION Federal Aviation Administration RTCA Government/Industry NextGen Advisory Committee AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice of RTCA Charter Renewal. SUMMARY: The FAA is...

  8. 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

  9. Overview of NASA's Next Generation Air Transportation System (NextGen) Research

    NASA Technical Reports Server (NTRS)

    Swenson, Harry N.

    2009-01-01

    This slide presentation is an overview of the research for the Next Generation Air Transportation System (NextGen). Included is a review of the current air transportation system and the challenges of air transportation research. Also included is a review of the current research highlights and significant accomplishments.

  10. Phanurus oligoovus gen. et sp. nov. (Digenea: Waretrematidae) from Liza carinatus from the South China Sea.

    PubMed

    Liu, Sheng-fa; Yang, Ting-bao

    2002-04-01

    The species Phanurus oligoovus gen. et sp. nov. is described from the intestine of Liza carinatus (Cuvier et Valencienne) from the South China Sea. From the general internal anatomy, it belongs to the Waretrematidae and is distinguished from the other known species of the Waretrematidae by the tail appendage. A new subfamily, Phanurunae, is proposed for the genus Phanurus.

  11. 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…

  12. GenColors: annotation and comparative genomics of prokaryotes made easy.

    PubMed

    Romualdi, Alessandro; Felder, Marius; Rose, Dominic; Gausmann, Ulrike; Schilhabel, Markus; Glöckner, Gernot; Platzer, Matthias; Sühnel, Jürgen

    2007-01-01

    GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293

  13. Transduction of Photoreceptors With Equine Infectious Anemia Virus Lentiviral Vectors: Safety and Biodistribution of StarGen for Stargardt Disease

    PubMed Central

    Binley, Katie; Widdowson, Peter; Loader, Julie; Kelleher, Michelle; Iqball, Sharifah; Ferrige, Georgina; de Belin, Jackie; Carlucci, Marie; Angell-Manning, Diana; Hurst, Felicity; Ellis, Scott; Miskin, James; Fernandes, Alcides; Wong, Paul; Allikmets, Rando; Bergstrom, Christopher; Aaberg, Thomas; Yan, Jiong; Kong, Jian; Gouras, Peter; Prefontaine, Annick; Vezina, Mark; Bussieres, Martin; Naylor, Stuart; Mitrophanous, Kyriacos A.

    2013-01-01

    Purpose. StarGen is an equine infectious anemia virus (EIAV)-based lentiviral vector that expresses the photoreceptor-specific adenosine triphosphate (ATP)-binding cassette transporter (ABCA4) protein that is mutated in Stargardt disease (STGD1), a juvenile macular dystrophy. EIAV vectors are able to efficiently transduce rod and cone photoreceptors in addition to retinal pigment epithelium in the adult macaque and rabbit retina following subretinal delivery. The safety and biodistribution of StarGen following subretinal delivery in macaques and rabbits was assessed. Methods. Regular ophthalmic examinations, IOP measurements, ERG responses, and histopathology were carried out in both species to compare control and vector-treated eyes. Tissue and fluid samples were obtained to evaluate the persistence, biodistribution, and shedding of the vector following subretinal delivery. Results. Ophthalmic examinations revealed a slightly higher level of inflammation in StarGen compared with control treated eyes in both species. However, inflammation was transient and no overt toxicity was observed in StarGen treated eyes and there were no abnormal clinical findings. There was no StarGen-associated rise in IOP or abnormal ERG response in either rabbits or macaques. Histopathologic examination of the eyes did not reveal any detrimental changes resulting from subretinal administration of StarGen. Although antibodies to StarGen vector components were detected in rabbit but not macaque serum, this immunologic response did not result in any long-term toxicity. Biodistribution analysis demonstrated that the StarGen vector was restricted to the ocular compartment. Conclusions. In summary, these studies demonstrate StarGen to be well tolerated and localized following subretinal administration. PMID:23620430

  14. 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

  15. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

    PubMed

    Parks, Donovan H; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S; Armanini, David G; Baird, Donald J; Langille, Morgan G I; Beiko, Robert G

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  16. 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.

  17. 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.

  18. Griveaudus gen. nov. (Hemiptera: Fulgoromorpha: Flatidae) from Tsaratanana Massif supports the biodiversity of montane flatids in Madagascar.

    PubMed

    Stroiński, Adam; Świerczewski, Dariusz

    2014-09-11

    The paper describes a new flatid genus, Griveaudus gen. nov., comprising two species G. issidiformis sp. nov. and G. tsarantananae sp. nov. from Madagascar. Additionally, the illustrations of the female internal genital structures are provided. 

  19. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.

    PubMed

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory).

  20. 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....

  1. 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.

  2. 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.

  3. 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.

  4. 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.

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

    PubMed Central

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

    2015-01-01

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

  6. Revision of J3Gen and Validity of the Attacks by Peinado et al.

    PubMed

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

    2015-01-01

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

  7. 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.

  8. Two New Freshwater Woloszynskioids Asulcocephalium miricentonis gen. et sp. nov. and Leiocephalium pseudosanguineum gen. et sp. nov. (Suessiaceae, Dinophyceae) Lacking an Apical Furrow Apparatus.

    PubMed

    Takahashi, Kazuya; Moestrup, Øjvind; Jordan, Richard W; Iwataki, Mitsunori

    2015-12-01

    Two new woloszynskioid dinoflagellates, Asulcocephalium miricentonis gen. et sp. nov. and Leiocephalium pseudosanguineum gen. et sp. nov., are described from Japanese freshwater ponds on the basis of bright field and fluorescence light microscopy, scanning and transmission electron microscopy, and molecular phylogeny inferred from rDNA sequences. Asulcocephalium miricentonis has a spherical anterior nucleus and chloroplast with a pyrenoid penetrated by the cytoplasm. This species has 9-12 latitudinal series of amphiesmal vesicles (AVs), including an apparently large AV on the right ventral side of the epicone. Leiocephalium pseudosanguineum has a U-shaped nucleus in the epicone and chloroplasts without a pyrenoid. This species has at least 24 latitudinal series of AVs. The characteristic features of both species were brick-like material (type E) in the eyespot and the lack of an apical furrow. These features coincide with those of Polarella glacialis, but the two species differ in cell shape, number and arrangement of AVs, shape of resting cysts, and habitats; i.e., P. glacialis has been reported only from marine cold waters. Molecular phylogeny revealed that A. miricentonis and L. pseudosanguineum were positioned in the Suessiaceae and closely related to Piscinoodinium sp., but their relationship to Polarella and other reported taxa was not supported. PMID:26599726

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

    PubMed Central

    Breider, Sven; Scheuner, Carmen; Schumann, Peter; Fiebig, Anne; Petersen, Jörn; Pradella, Silke; Klenk, Hans-Peter; Brinkhoff, Thorsten; Göker, Markus

    2014-01-01

    Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended. PMID:25157246

  10. 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)).

  11. Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture.

    PubMed

    Foesel, Bärbel U; Drake, Harold L; Schramm, Andreas

    2011-11-01

    Three Gram-negative bacterial strains were isolated from the biofilter of a recirculating marine aquaculture. They were non-pigmented rods, mesophiles, moderately halophilic, and showed chemo-organoheterotrophic growth on various sugars, fatty acids, and amino acids, with oxygen as electron acceptor; strains D9-3(T) and D11-58 were in addition able to denitrify. Phototrophic or fermentative growth could not be demonstrated. Phylogenetic analysis of the 16S rRNA gene sequences placed D9-3(T) and D11-58, and D1-19(T) on two distinct branches within the alpha-3 proteobacterial Rhodobacteraceae, affiliated with, but clearly separate from, the genera Rhodobacter, Rhodovulum, and Rhodobaca. Based on morphological, physiological, and 16S rRNA-based phylogenetic characteristics, the isolated strains are proposed as new species of two novel genera, Defluviimonas denitrificans gen. nov., sp. nov. (type strain D9-3(T)=DSM 18921(T)=ATCC BAA-1447(T); additional strain D11-58=DSM19039=ATCC BAA-1448) and Pararhodobacter aggregans gen. nov., sp. nov (type strain D1-19(T)=DSM 18938(T)=ATCC BAA-1446(T)).

  12. 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)). PMID:25487949

  13. 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.

  14. Description of Distorhabditis poonchiana n. gen., n. sp. (Nematoda: Rhabditidae) from Jammu and Kashmir, India.

    PubMed

    Shah, Ali Asghar; Vaid, Shavish; Hussain, Abid; Ahmad, Rakeeb

    2015-12-01

    Distorhabditis poonchiana n. gen., n. sp. from humus in Jammu and Kashmir, India, is described and illustrated. The new genus is characterized by a small body; slightly setoff labial region; long tubular gymnostom; prominently cuticularized cheilostom; absence of glottoid apparatus; monoprodelphic reproductive system; vulva (V) = 81 to 84; spicules with trifurcated distal ends, simple gubernaculum, peloderan bursa with eight pairs of bursal papillae arranged in 1 + 1 + 1 + 2 + 1 + 2 arrangement. PMID:26941466

  15. Description of Distorhabditis poonchiana n. gen., n. sp. (Nematoda: Rhabditidae) from Jammu and Kashmir, India.

    PubMed

    Shah, Ali Asghar; Vaid, Shavish; Hussain, Abid; Ahmad, Rakeeb

    2015-12-01

    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.

  16. 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

  17. A mechanism for maintaining an up-to-date GenBank database via Usenet.

    PubMed

    Smith, R H; Gottesman, S; Hobbs, B; Lear, E; Kristofferson, D; Benton, D; Smith, P R

    1991-01-01

    In this paper, we describe an automated system for distributing updates to the GenBank nucleic acid sequence database, using the Usenet news system as the underlying transport mechanism. Our system allows new loci to be distributed as soon as the sequences are available, over existing networks, using existing Usenet software and infrastructure currently available on a wide range of computer systems. PMID:2004268

  18. 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

  19. 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.

  20. 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.

  1. Papiliocoelotes gen. n., a new genus of Coelotinae (Araneae, Agelenidae) spiders from the Wuling Mountains, China

    PubMed Central

    Zhao, Zhe; Li, Shuqiang

    2016-01-01

    Abstract One new genus of the spider subfamily Coelotinae, Papiliocoelotes gen. n., with five new species is described for both sexes: Papiliocoelotes guanyinensis sp. n., Papiliocoelotes guitangensis sp. n., Papiliocoelotes jiepingensis sp. n., Papiliocoelotes meiyuensis sp. n., Papiliocoelotes yezhouensis sp. n. All new species were collected from caves in the Wuling Mountains of Hubei and Hunan Provinces, China. DNA barcodes were obtained for future use. PMID:27199603

  2. 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.

  3. NQRS Data for C8H20Br3GeN (Subst. No. 1129)

    NASA Astrophysics Data System (ADS)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume A `Substances Containing Ag … C10H15' of Volume 48 `Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III `Condensed Matter'. It contains an extract of Section `3.2 Data tables' of the Chapter `3 Nuclear quadrupole resonance data' providing the NQRS data for C8H20Br3GeN (Subst. No. 1129)

  4. 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

  5. Papiliocoelotes gen. n., a new genus of Coelotinae (Araneae, Agelenidae) spiders from the Wuling Mountains, China.

    PubMed

    Zhao, Zhe; Li, Shuqiang

    2016-01-01

    One new genus of the spider subfamily Coelotinae, Papiliocoelotes gen. n., with five new species is described for both sexes: Papiliocoelotes guanyinensis sp. n., Papiliocoelotes guitangensis sp. n., Papiliocoelotes jiepingensis sp. n., Papiliocoelotes meiyuensis sp. n., Papiliocoelotes yezhouensis sp. n. All new species were collected from caves in the Wuling Mountains of Hubei and Hunan Provinces, China. DNA barcodes were obtained for future use. PMID:27199603

  6. Erection of a new genus Biura gen. nov., of the subtribe Aolina (Hemiptera: Cicadidae: Cicadinae: Dundubiini).

    PubMed

    Lee, Young June; Sanborn, Allen F

    2015-11-20

    A new genus, Biura gen. nov., is erected within the subtribe Aolina Boulard, 2012, designating Haphsa bicolora Sanborn, 2009 as the type species. This new genus is distinguished from all other genera in Aolina by the light-colored body lacking prominent markings, non-infuscated wings, very small and short male operculum, thin and long uncal lobes, and distinctly prominent basal lobes of the pygofer.

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

    PubMed

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

    2015-01-01

    A new genus is proposed based on a new species from Iran, Ephemerotoma skarzynskii gen. et sp. nov., and three known species: E. huadongensis (Chen, 1985) comb. nov., E. multituberculata (Martynova, 1971) comb. nov. and E. porcella (Ellis, 1976) comb. nov. The genus shares the characters of Subisotoma Stach and Proctostephanus Börner and is distributed in southern areas of Eurasia (Eastern Mediterranean, Iran, Tajikistan, China). Ephemerotoma gen. nov. belongs to the Proisotoma-complex and is characterized by a simple maxillary palp, only 4 guards on labial papilla E and 2 prelabral chaetae. Four s-chaetae on Abd.V are arranged in two rows, two anterior and two posterior chaetae. All members of Ephemerotoma gen. nov. are redescribed or discussed based on type or fresh material, and a key to species of the genus is given. Scutisotoma potapovi Xie & Chen, 2008 is considered a synonym of E. huadongensis, while Proisotoma anopolitana is moved to the genus Proctostephanus. Sexual dimorphism is described for three species. PMID:26701434

  8. 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

  9. 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.

  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. 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.

  13. 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.

  14. 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.

  15. GenAge: a genomic and proteomic network map of human ageing.

    PubMed

    de Magalhães, João Pedro; Toussaint, Olivier

    2004-07-30

    The aim of this work was to provide an overview of the genetics of human ageing to gain novel insights about the mechanisms involved. By incorporating findings from model organisms to humans, such as mutations that either delay or accelerate ageing in mice, we constructed the gene networks previously related to ageing: namely, the network related to DNA metabolism and the network involving the GH/IGF-1 axis. Gathering data about the interacting partners of these proteins allowed us to suggest the involvement in ageing of a number of proteins through a "guilt-by-association" methodology. To organize our data, we developed the first curated database of genes related to human ageing: GenAge. With over 200 entries, GenAge may serve as a reference database of genes related to human ageing. Moreover, we rendered the first proteomic network map of human ageing, which suggests a relationship between the genetics of development and the genetics of ageing. Our work serves as a framework upon which a systems-biology understanding of ageing can be developed. GenAge is freely available for academic purposes at: http://genomics.senescence.info/genes/.

  16. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    DOE PAGES

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; USA, Richland Washington; Bonneville, Alain; USA, Richland Washington; Sullivan, E. Charlotte; USA, Richland Washington; Johnson, Tim C.; USA, Richland Washington; et al

    2014-12-31

    A comprehensive monitoring program will be needed in order to assess the effectiveness of carbon sequestration at the FutureGen 2.0 carbon capture and storage (CCS) field-site. Geophysical monitoring methods are sensitive to subsurface changes that result from injection of CO2 and will be used for: (1) tracking the spatial extent of the free phase CO2 plume, (2) monitoring advancement of the pressure front, (3) identifying or mapping areas where induced seismicity occurs, and (4) identifying and mapping regions of increased risk for brine or CO2 leakage from the reservoir. Site-specific suitability and cost effectiveness were evaluated for a number ofmore » geophysical monitoring methods including: passive seismic monitoring, reflection seismic imaging, integrated surface deformation, time-lapse gravity, pulsed neutron capture logging, cross-borehole seismic, electrical resistivity tomography, magnetotellurics and controlled source electromagnetics. The results of this evaluation indicate that CO2 injection monitoring using reflection seismic methods would likely be difficult at the FutureGen 2.0 site. Electrical methods also exhibited low sensitivity to the expected CO2 saturation changes and would be affected by metallic infrastructure at the field site. Passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture monitoring were selected for implementation as part of the FutureGen 2.0 storage site monitoring program.« less

  17. 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. PMID:24644371

  18. 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

  19. 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.

  20. Processing the Loblolly Pine PtGen2 cDNA Microarray

    PubMed Central

    Lorenz, W. Walter; Yu, Yuan-Sheng; Simões, Marta; Dean, Jeffrey F. D.

    2009-01-01

    PtGen2 is a 26,496 feature cDNA microarray containing amplified loblolly pine ESTs. The array is produced in our laboratory for use by researchers studying gene expression in pine and other conifer species. PtGen2 was developed as a result of our gene discovery efforts in loblolly pine, and is comprised of sequences identified primarily from root tissues, but also from needle and stem.1,2 PtGen2 has been tested by hybridizing different Cy-dye labeled conifer target cDNAs, using both amplified and non-amplified indirect labeling methods, and also tested with a number of hybridization and washing conditions. This video focuses on the handling and processing of slides before and after pre-hybridization, as well as after hybridization, using some modifications to procedures developed previously.3,4 Also included, in text form only, are the protocols used for the generation, labeling and clean up of target cDNA s, as well as information on software used for downstream data processing. PtGen2 is printed with a proprietary print buffer that contains high concentrations of salt that can be difficult to remove completely. The slides are washed first in a warm SDS solution prior to pre-hybridization. After pre-hybridization, the slides are washed vigorously in several changes of water to complete removal of remaining salts. LifterSlips™ are then cleaned and positioned on the slides and labeled cDNA is carefully loaded onto the microarray by way of capillary action which provides for even distribution of the sample across the slide, and reduces the chance of bubble incorporation. Hybridization of targets to the array is done at 48°C in high humidity conditions. After hybridization, a series of standard washes are done at 53°C and room temperature for extended times. Processing PtGen2 slides using this technique reduces salt and SDS-derived artifacts often seen when the array is processed less rigorously. Hybridizing targets derived from several different conifer RNA

  1. Processing the loblolly pine PtGen2 cDNA microarray.

    PubMed

    Lorenz, W Walter; Yu, Yuan-Sheng; Simões, Marta; Dean, Jeffrey F D

    2009-01-01

    PtGen2 is a 26,496 feature cDNA microarray containing amplified loblolly pine ESTs. The array is produced in our laboratory for use by researchers studying gene expression in pine and other conifer species. PtGen2 was developed as a result of our gene discovery efforts in loblolly pine, and is comprised of sequences identified primarily from root tissues, but also from needle and stem. PtGen2 has been tested by hybridizing different Cy-dye labeled conifer target cDNAs, using both amplified and non-amplified indirect labeling methods, and also tested with a number of hybridization and washing conditions. This video focuses on the handling and processing of slides before and after pre-hybridization, as well as after hybridization, using some modifications to procedures developed previously. Also included, in text form only, are the protocols used for the generation, labeling and clean up of target cDNA s, as well as information on software used for downstream data processing. PtGen2 is printed with a proprietary print buffer that contains high concentrations of salt that can be difficult to remove completely. The slides are washed first in a warm SDS solution prior to pre-hybridization. After pre-hybridization, the slides are washed vigorously in several changes of water to complete removal of remaining salts. LifterSlips are then cleaned and positioned on the slides and labeled cDNA is carefully loaded onto the microarray by way of capillary action which provides for even distribution of the sample across the slide, and reduces the chance of bubble incorporation. Hybridization of targets to the array is done at 48 degrees C in high humidity conditions. After hybridization, a series of standard washes are done at 53 degrees C and room temperature for extended times. Processing PtGen2 slides using this technique reduces salt and SDS-derived artifacts often seen when the array is processed less rigorously. Hybridizing targets derived from several different conifer RNA

  2. 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

  3. Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov.

    PubMed

    Kaur, Sukhpreet; Yawar, Mir; Kumar, P Anil; Suresh, K

    2014-03-01

    A Gram-stain-positive, rod-shaped, spore-forming and strictly anaerobic bacterium, designated UB-B.2(T), was isolated from an industrial effluent anaerobic digester sample. It grew optimally at 30 °C and pH 7.0. Comparative analysis of the 16S rRNA gene sequence confirmed that strain UB-B.2(T) was closely related to Clostridium hathewayi DSM 13479(T) (97.84% similarity), a member of rRNA gene cluster XIVa of the genus Clostridium, and formed a coherent cluster with other related members of the Blautia (Clostridium) coccoides rRNA group in phylogenetic analyses. The end products of glucose fermentation by strain UB-B.2(T) were acetate and propionate. The G+C content of the DNA was 51.4 mol%. Although strain UB-B.2(T) showed 97.8% 16S rRNA gene sequence identity to the type strain of C. hathewayi, it exhibited only 38.4% relatedness at the whole-genome level. It also showed differences from its closest phylogenetic relative, C. hathewayi DSM 13479(T), in phenotypic characteristics such as hydrolysis of aesculin, starch and urea and fermentation end products. Both strains showed phenotypic differences from the members of rRNA gene cluster XIVa of the genus Clostridium. Based on these differences, C. hathewayi DSM 13479(T) and strain UB-B.2(T) were identified as representatives of a new genus of the family Clostridiaceae. Thus, we propose the reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov., the type species of the new genus (type strain DSM 13479(T) = CCUG 43506(T) = MTCC 10951(T)). Strain UB-B.2(T) ( = MTCC 11101(T) = DSM 24995(T)) is assigned to the novel species Hungatella effluvii gen. nov., sp. nov as the type strain.

  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. 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.

  6. MetaPopGen: an r package to simulate population genetics in large size metapopulations.

    PubMed

    Andrello, Marco; Manel, Stéphanie

    2015-09-01

    Population genetics simulation models are useful tools to study the effects of demography and environmental factors on genetic variation and genetic differentiation. They allow for studying species and populations with complex life histories, spatial distribution and many other complicating factors that make analytical treatment impracticable. Most simulation models are individual-based: this poses a limitation to simulation of very large populations because of the limits in computer memory and long computation times. To overcome these limitations, we propose an intermediate approach that allows modelling of very complex demographic scenarios, which would be intractable with analytical models, and removes the limitations imposed by large population size, which affect individual-based simulation models. We implement this approach in a software package for the r environment, MetaPopGen. The innovative concept of this approach with respect to the other population genetic simulators is that it focuses on genotype numbers rather than on individuals. Genotype numbers are iterated through time by using random number generators for appropriate probabilistic distributions to reproduce the stochasticity inherent to Mendelian segregation, survival, dispersal and reproduction. Features included in the model are age structure, monoecious and dioecious (or separate sexes) life cycles, mutation, dispersal and selection. The model simulates only one locus at a time. All demographic parameters can be genotype-, sex-, age-, deme- and time-dependent. MetaPopGen is therefore indicated to study large populations and very complex demographic scenarios. We illustrate the capabilities of MetaPopGen by applying it to the case of a marine fish metapopulation in the Mediterranean Sea. PMID:25585533

  7. 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.

  8. iGen 0.1: the automated generation of a parameterisation of entrainment in marine stratocumulus

    NASA Astrophysics Data System (ADS)

    Tang, D. F.; Dobbie, S.

    2011-09-01

    In a previous paper we described a new technique for automatically generating parameterisations using a program called iGen. iGen generates parameterisations by analysing the source code of a~high resolution model that resolves the physics to be parameterised. In order to demonstrate that this technique scales up to deal with models of realistic complexity we have used iGen to generate a parameterisation of entrainment in marine stratocumulus. We describe how iGen was used to analyse the source code of an eddy resolving model (ERM) and generate a parameterisation of entrainment velocity in marine stratocumulus in terms of the large-scale state of the boundary layer. The parameterisation was tested against results from the DYCOMS-II intercomparison of ERM models and iGen's parameterisation of mean entrainment velocity was found to be 5.27 × 10-3 ± 0.62 × 10-3 m s-1 compared to 5.2 × 10-3 ± 0.8 × 10-3 m s-1 for the DYCOMS-II ensemble of large eddy simulation (LES) models.

  9. 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.

  10. 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).

  11. 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.

  12. 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.

  13. Cyathoshiva amaleshi gen. n. sp. n. (Nematoda: Cyatholaimidae) from the coast of India.

    PubMed

    Datta, Tridip Kumar; Miljutin, Dmitry M; Chakraborty, Susanta Kumar; Mohapatra, Anil

    2016-01-01

    A new genus, Cyathoshiva, of free-living marine nematodes from the subfamily Cyatholaiminae (family Cyatholaimidae, order Chromadorida), is described from the Indian coast. The new genus differs from other known Cyatholaiminae genera in having a unique combination of morphological characters: buccal cavity with well-developed dorsal tooth and two subventral teeth, proximally unpaired gubernaculum and non-cup shaped supplements. The type species Cyathoshiva amaleshi gen. n. sp. n. is characterized by having multispiral amphids with 4.5 turns, punctated cuticle with a weak lateral differentiation, a conical tail, three supplements possessing both tubular and setoid parts, and a gubernaculum with a serrated and dentate distal end. PMID:27395607

  14. 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

  15. 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.

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

    PubMed

    Hoppmann, Anselm S; Schlosser, Pascal; Backofen, Rolf; Lausch, Ekkehart; Köttgen, Anna

    2016-01-01

    Genome-wide association studies (GWAS) evaluate associations between genetic variants and a trait or disease of interest free of prior biological hypotheses. GWAS require stringent correction for multiple testing, with genome-wide significance typically defined as association p-value <5*10-8. This study presents a new tool that uses external information about genes to prioritize SNP associations (GenToS). For a given list of candidate genes, GenToS calculates an appropriate statistical significance threshold and then searches for trait-associated variants in summary statistics from human GWAS. It thereby allows for identifying trait-associated genetic variants that do not meet genome-wide significance. The program additionally tests for enrichment of significant candidate gene associations in the human GWAS data compared to the number expected by chance. As proof of principle, this report used external information from a comprehensive resource of genetically manipulated and systematically phenotyped mice. Based on selected murine phenotypes for which human GWAS data for corresponding traits were publicly available, several candidate gene input lists were derived. Using GenToS for the investigation of candidate genes underlying murine skeletal phenotypes in data from a large human discovery GWAS meta-analysis of bone mineral density resulted in the identification of significantly associated variants in 29 genes. Index variants in 28 of these loci were subsequently replicated in an independent GWAS replication step, highlighting that they are true positive associations. One signal, COL11A1, has not been discovered through GWAS so far and represents a novel human candidate gene for altered bone mineral density. The number of observed genes that contained significant SNP associations in human GWAS based on murine candidate gene input lists was much greater than the number expected by chance across several complex human traits (enrichment p-value as low as 10-10). Gen

  17. 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.

  18. 'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lung.

    PubMed

    Du, Yina; Guo, Minzhe; Whitsett, Jeffrey A; Xu, Yan

    2015-11-01

    We developed LungGENS (Lung Gene Expression iN Single-cell), a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables. LungGENS will be broadly applicable in respiratory research, providing a cell-specific RNA expression resource at single-cell resolution. LungGENS is freely available for non-commercial use at https://research.cchmc.org/pbge/lunggens/default.html.

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

    DOE PAGES

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

    2015-06-26

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

  20. Structural materials for Gen-IV nuclear reactors: Challenges and opportunities

    NASA Astrophysics Data System (ADS)

    Murty, K. L.; Charit, I.

    2008-12-01

    Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses and extremely corrosive environment, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This paper presents a summary of various Gen-IV reactor concepts, with emphasis on the structural materials issues depending on the specific application areas. This paper also discusses the challenges involved in using the existing materials under both service and off-normal conditions. Tasks become increasingly complex due to the operation of various fundamental phenomena like radiation-induced segregation, radiation-enhanced diffusion, precipitation, interactions between impurity elements and radiation-produced defects, swelling, helium generation and so forth. Further, high temperature capability (e.g. creep properties) of these materials is a critical, performance-limiting factor. It is demonstrated that novel alloy and microstructural design approaches coupled with new materials processing and fabrication techniques may mitigate the challenges, and the optimum system performance may be achieved under much demanding conditions.

  1. Gen-2 Hand-Held Optical Imager towards Cancer Imaging: Reflectance and Transillumination Phantom Studies

    PubMed Central

    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. PMID:22438743

  2. PubAngioGen: a database and knowledge for angiogenesis and related diseases.

    PubMed

    Li, Peng; Liu, Yongrui; Wang, Huan; He, Yuan; Wang, Xue; He, Yundong; Lv, Fang; Chen, Huaqing; Pang, Xiufeng; Liu, Mingyao; Shi, Tieliu; Yi, Zhengfang

    2015-01-01

    Angiogenesis is the process of generating new blood vessels based on existing ones, which is involved in many diseases including cancers, cardiovascular diseases and diabetes mellitus. Recently, great efforts have been made to explore the mechanisms of angiogenesis in various diseases and many angiogenic factors have been discovered as therapeutic targets in anti- or pro-angiogenic drug development. However, the resulted information is sparsely distributed and no systematical summarization has been made. In order to integrate these related results and facilitate the researches for the community, we conducted manual text-mining from published literature and built a database named as PubAngioGen (http://www.megabionet.org/aspd/). Our online application displays a comprehensive network for exploring the connection between angiogenesis and diseases at multilevels including protein-protein interaction, drug-target, disease-gene and signaling pathways among various cells and animal models recorded through text-mining. To enlarge the scope of the PubAngioGen application, our database also links to other common resources including STRING, DrugBank and OMIM databases, which will facilitate understanding the underlying molecular mechanisms of angiogenesis and drug development in clinical therapy.

  3. A Precision Optical Calibration Module (POCAM) for IceCube-Gen2

    NASA Astrophysics Data System (ADS)

    Jurkovič, M.; Abraham, K.; Holzapfel, K.; Krings, K.; Resconi, E.; Veenkamp, J.

    2016-04-01

    We present here a new concept of an in-situ self-calibrated isotropic light source for the future IceCube-Gen2 neutrino detector called the Precision Optical Calibration Module (POCAM). IceCube-Gen2 will be a matrix of light sensors buried deep in the ice at the geographic South Pole. The timing, the location, and the amount of Cherenkov light deposited by the secondary charged particles are used to reconstruct the properties of the incident neutrinos. The reconstruction relies on a detailed detector model that includes the response of optical modules to the Cherenkov light, as well as the optical properties of the detector medium - the natural Antarctic ice. To understand these properties, both natural, and artificial light sources are already used for calibration. New calibration devices are being developed in order to improve the precision of these measurements, and reduce systematic errors. The POCAM concept is based on the principle of an inverted integrating sphere. The main components are LEDs emitting light at several wavelengths and solid-state light sensors e.g. calibrated photodiode or silicon photomultipliers to monitor the emitted light intensity. We report on the current status of the POCAM R&D.

  4. [Tribuliphorus salilotae gen. et spec. nov., a new representative of the monogena].

    PubMed

    Mamaev, J L

    1977-02-01

    Belonging to the Monogenean family Diclidophoridae, Tribuliphorus salitotae nov. gen. nov. spec. is described from a gadiform fish, Salilota australia (family Moridae). Its specific characteristics are: big and sharp clasps at the anterior lateral and the posterior lateral plates of the adhesing valves. All 8 valves are structured in the same manner, but they differ in their situation and size: the first 3 pairs are smaller and are inverted (180 degrees to the body's length exis) the hind pair is twice as big and situated normally. --In respect to its morphology, Tribuliphorus nov. gen. could belong to the lowes (most primitive) genera of the subfamily Diclidophorinae, which parasitize the Macruriformes. On the other side, the genus shows affinities to Anchophorus, whose only representative (A. sinensis Bychovsky & Nagibina, 1958) has been found on cynoglossids (an apart group of the Pleuronectiformes), and which has been put in a monotypic family Anchophoridae. By this, the parasitological data again support the previously expressed view (by one of the authors) regarding the relationship of the Pleuronectiformes to the Gadiformes and Goryphaenoididae = Macruriformes).

  5. 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.

  6. Flight Deck Technologies to Enable NextGen Low Visibility Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J.; Kramer, Lynda J.; Norman, Robert M.; Bailey, Randall E.; Jones, Denise R.; Karwac, Jerry R., Jr.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2013-01-01

    Many key capabilities are being identified to enable Next Generation Air Transportation System (NextGen), including the concept of Equivalent Visual Operations (EVO) . replicating the capacity and safety of today.s visual flight rules (VFR) in all-weather conditions. NASA is striving to develop the technologies and knowledge to enable EVO and to extend EVO towards a Better-Than-Visual operational concept. This operational concept envisions an .equivalent visual. paradigm where an electronic means provides sufficient visual references of the external world and other required flight references on flight deck displays that enable Visual Flight Rules (VFR)-like operational tempos while maintaining and improving safety of VFR while using VFR-like procedures in all-weather conditions. The Langley Research Center (LaRC) has recently completed preliminary research on flight deck technologies for low visibility surface operations. The work assessed the potential of enhanced vision and airport moving map displays to achieve equivalent levels of safety and performance to existing low visibility operational requirements. The work has the potential to better enable NextGen by perhaps providing an operational credit for conducting safe low visibility surface operations by use of the flight deck technologies.

  7. Aliterella atlantica gen. nov., sp. nov., and Aliterella antarctica sp. nov., novel members of coccoid Cyanobacteria.

    PubMed

    Rigonato, Janaina; Gama, Watson Arantes; Alvarenga, Danillo Oliveira; Branco, Luis Henrique Zanini; Brandini, Frederico Pereira; Genuário, Diego Bonaldo; Fiore, Marli Fatima

    2016-09-01

    Two Cyanobacteria isolated from South Atlantic Ocean continental shelf deep water and from a marine green algae inhabiting the Admiralty Bay, King George Island, Antarctica were investigated based on morphological and ultrastructural traits, phylogeny of 16S rRNA gene sequences, secondary structure of the 16S-23S internal transcribed spacer regions and phylogenomic analyses. The majority of these evaluations demonstrated that both strains differ from the genera of cyanobacteria with validly published names and, therefore, supported the description of the novel genus as Aliterella gen. nov. The identity and phylogeny of 16S rRNA gene sequences, together with the secondary structure of D1D1' and BoxB intergenic regions, further supported the two strains representing distinct species: Aliterella atlantica gen. nov., sp. nov. (type SP469036, strain CENA595T) and Aliterella antarctica sp. nov. (type SP469035, strain CENA408T). The phylogenomic analysis of A. atlantica sp. nov. CENA595T, based on 21 protein sequences, revealed that this genus belongs to the cyanobacterial order Chroococcidiopsidales. The isolation and cultivation of two geographically distant unicellular members of a novel cyanobacterial genus and the sequenced genome of the type strain bring new insights into the current classification of the coccoid group, and into the reconstruction of their evolutionary history. PMID:27054834

  8. 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.

  9. 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.

  10. Competition between supercluster and stuffed cage structures in medium-sized Gen (n=30-39) clusters

    NASA Astrophysics Data System (ADS)

    Wang, Lu; Zhao, Jijun

    2008-01-01

    We have performed an unbiased global search for the geometries of low-lying Gen clusters in the size range of 30⩽n⩽39 using genetic algorithm incorporated with a tight-binding model. Density functional theory calculations were carried out to further optimize the isomer structures. Gen (n=30-39) clusters prefer the motif of supercluster structures stacked by several stable subunits such as Ge10 and Ge6, connecting via a few bridging atoms. Size-dependent cluster properties such as binding energy, HOMO-LUMO gaps, and ionization potentials were discussed and compared with experiments.

  11. Memoan ciceroi gen. et sp. nov., a remarkable new firefly genus and species from the Atlantic Rainforest (Coleoptera: Lampyridae).

    PubMed

    Da Silveira, Luiz Felipe Lima; Mermudes, José Ricardo M

    2013-01-01

    A species of firefly discovered in a fragile and rapidly disappearing Atlantic Rainforest biome in Brazil does not fit into any of the existing subfamilies nor described generic categories in the Lampyridae and is described here as Memoan ciceroi gen. et sp. nov. and classed as Lampyridae Incertae sedis, as it exhibits features of both the Amydetinae and Lampyrinae. An overview of subfamily arrangements and relevant generic characters is given to support this action. Memoan gen. nov. can be distinguished by its alveolate pronotum and elytra; subserrate antennae, antenommeres II-IX compressed, antennal sockets obliquely inserted on tubercles; labial palp one-segmented and obconic, and by its conspicuous pleuroventral suture.

  12. Application of part-whole training methods to evaluate when to introduce NextGen air traffic management tools to students.

    PubMed

    Vu, Kim-Phuong L; Kiken, Ariana; Chiappe, Dan; Strybel, Thomas Z; Battiste, Vernol

    2013-01-01

    The Next Generation Air Transportation System (NextGen) will use advanced technologies and new concepts of operation to accommodate projected increases in air travel over the next few decades. Use of NextGen tools requires air traffic controllers (ATCos) to use different procedures than those required to manage NextGen-unequipped aircraft, and ATCos will need to integrate the 2 skill sets when managing a sector consisting of NextGen-equipped and unequipped aircraft. The goal of the present study was to determine the effectiveness of 2 procedures in the training of student controllers to manage both equipage types. We applied a variant of the part-whole training paradigm in the present study. Using a quasi-experimental design, we trained students from 2 different labs of an internship course to manage air traffic with potential NextGen tools concurrent with their traditional training (whole-task group) or after they had time to learn traditional air traffic management skills (part-whole group). Participants were then tested in their ability to manage a simulated sector consisting of different percentages of NextGen-equipped and unequipped aircraft at the mid-term and after the final week of their internship. Results showed that it is better to train students in manual ATCo skills before introducing NextGen tools, unless the students are of higher aptitude. For more skilled students, simultaneously introducing NextGen and manual tools into their curriculum had little negative impact. PMID:24455810

  13. A Phocus on Phenotyping: opportunities and challenges in local and centralized trait evaluation from the VitisGen experience

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The integration of relevant genetic resources, robust phenotypes, and cutting-edge genotypic data is a challenge that individual scientists rarely overcome successfully. In the USDA-NIFA VitisGen project ( www.vitisgen.org ) for grapevine cultivar improvement, our research team has pursued a shared ...

  14. Rationale and Design of the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) Registry

    PubMed Central

    2010-01-01

    Background Although the management of thoracic aortic aneurysms (TAAs) has improved significantly, patients presenting with aortic dissections, rupture or other acute complications of TAAs continue to suffer high rates of morbidity and mortality. Accumulating data have indicated that many TAAs are due to underlying gene mutations. A comprehensive approach to the study of TAAs resulting from genetic mutations is needed to translate this information into advances in treatment. Objective The National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) was established to provide a biospecimen inventory and bioinformatics infrastructure to enable research to advance the clinical management of genetically-triggered TAAs and related complications. Methods The GenTAC Registry is a longitudinal observational cohort study enrolling patients with conditions related to genetically-induced TAAs from five regional clinical centers in the United States. Results Over 700 subjects with associated clinical histories, physical examinations, imaging data, and biospecimens have been enrolled in the Registry to date. Enrollment is expected to continue until September 2010. Total enrollment of nearly 3,000 subjects is expected. No interim analysis has yet been undertaken. Conclusions GenTAC has been established to facilitate studies by GenTAC investigators and others that will advance multiple scientific frontiers in thoracic aortic disease. Genotypic, proteomic, clinical, and imaging data will be integrated systematically with outcomes data to determine the optimal clinical management of patients suffering from genetically-induced TAAs. PMID:19185640

  15. Gene expression profiling of RNA extracted from FFPE tissues: NuGEN technologies' whole-transcriptome amplification system.

    PubMed

    Turner, Leah; Heath, Joe Don; Kurn, Nurith

    2011-01-01

    Gene expression profiling of RNA isolated from formalin fixed, paraffin-embedded (FFPE) tissue samples has been historically challenging. Yet FFPE samples are sought-after because of the in-depth retrospective records typically associated with them rendering these samples a valuable resource for translational medicine studies. Extensive degradation, chemical modifications, and cross-linking have made it difficult to isolate RNA of sufficient quality required for large-scale gene expression profiling studies. NuGEN Technologies' WT-Ovation™ FFPE System linearly amplifies RNA from FFPE samples through a robust and simple whole-transcriptome approach using as little as 50 ng total RNA isolated from FFPE samples. The amplified material may be labeled with validated kits and/or protocols from NuGEN for analysis on any of the major gene expression microarray platforms, including: Affymetrix, Agilent, and Illumina gene expression arrays. Results compare well with those obtained using RNA from fresh-frozen samples. RNA quality from FFPE samples varies significantly and neither sample age nor sample size analysis via gel electrophoresis or the Agilent Bioanalyzer system accurately predict materials suitable for amplification. Therefore, NuGEN has validated a correlative qPCR-based analytical method for the RNA derived from FFPE samples which effectively predicts array results. The NuGEN approach enables fast and successful analysis of samples previously thought to be too degraded for gene expression analysis.

  16. An update on VitisGen: recent advances in using DNA marker technologies in U.S. grape breeding programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-NIFA VitisGen project involves a multidisciplinary team of 25 co-PIs at 11 institutions aiming to optimize grape cultivar improvement. To this end, an impressive collection of phenotypic data and high-resolution genetic maps has been developed for seventeen F1 families. Here, we will prese...

  17. 75 FR 5780 - Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of Complaint January 28, 2010. Take notice that on January 25, 2010, Green Borders Geothermal, LLC (Green Borders) filed...

  18. 77 FR 52352 - Notice of Intent To Prepare an Environmental Impact Statement for the Rio Mesa Gen-Tie Project...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-29

    ... Gen-Tie Project and Possible Land Use Plan Amendment, Riverside County, CA AGENCY: Bureau of Land..., special management areas, land use, noise, paleontological resources, public health, socioeconomic, soils.... If a land use plan amendment is necessary, the BLM will integrate the land use planning process...

  19. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.

    PubMed

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

  20. Enhancement of the acute phase response to lipopolysaccharide in feedlot steers supplemented with OmniGen-AF

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was designed to determine the effect of supplementing feedlot steers with OmniGen-AF on the acute phase response to a lipopolysaccharide (LPS) challenge. Steers (n = 18; 270 ± 5 kilograms body weight) were separated into two treatment groups (n=9/treatment): one group was fed a standard ...

  1. Modulation of the metabolic response to an endotoxin challenge in Brahman heifers through OmniGen-AF supplementation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the metabolic response of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 183±5 kilograms) from the Texas AgriLife Research Center in Overton, TX, were separated into 2...

  2. OmniGen-AF supplementation modulated the physiological and acute phase responses of Brahman heifers to an endotoxin challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the physiological and acute phase responses (APR) of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 183±5 kilograms) from the Texas AgriLife Research Center in Overton...

  3. The Generic Spacecraft Analyst Assistant (GenSAA): A tool for automating spacecraft monitoring with expert systems

    NASA Technical Reports Server (NTRS)

    Hughes, Peter M.; Luczak, Edward C.

    1991-01-01

    Flight Operations Analysts (FOAs) in the Payload Operations Control Center (POCC) are responsible for monitoring a satellite's health and safety. As satellites become more complex and data rates increase, FOAs are quickly approaching a level of information saturation. The FOAs in the spacecraft control center for the COBE (Cosmic Background Explorer) satellite are currently using a fault isolation expert system named the Communications Link Expert Assistance Resource (CLEAR), to assist in isolating and correcting communications link faults. Due to the success of CLEAR and several other systems in the control center domain, many other monitoring and fault isolation expert systems will likely be developed to support control center operations during the early 1990s. To facilitate the development of these systems, a project was initiated to develop a domain specific tool, named the Generic Spacecraft Analyst Assistant (GenSAA). GenSAA will enable spacecraft analysts to easily build simple real-time expert systems that perform spacecraft monitoring and fault isolation functions. Lessons learned during the development of several expert systems at Goddard, thereby establishing the foundation of GenSAA's objectives and offering insights in how problems may be avoided in future project, are described. This is followed by a description of the capabilities, architecture, and usage of GenSAA along with a discussion of its application to future NASA missions.

  4. Evaluation of Mixed-Mode Data-Link Communications for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or NextGen. Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research examining data-link communications during 4DT and equivalent visual surface operations.

  5. Gen Green: Changes in Australian Apprentices' and Trainees' Experience of Skills and Sustainability from 2008 to 2011

    ERIC Educational Resources Information Center

    Sack, Fabian

    2012-01-01

    The Gen Green research in 2008 and 2011 indicates that skills for sustainability public policy and business initiatives are having an impact, but that young skilled Australians' high level of interest in sustainability skills is confounded by a lack of guidance and incentives from employers, the market and educators. The research indicates that,…

  6. Protosclerogibba australis gen. et sp. nov., new genus and species of sclerogibbid wasps (Hymenoptera: Sclerogibbidae) from South Africa.

    PubMed

    Olmi, Massimo; Marletta, Alessandro; Guglielmino, Adalgisa; Speranza, Stefano

    2016-01-01

    Protosclerogibba australis Olmi, Marletta, Guglielmino & Speranza, gen. et sp. nov. is described and illustrated from specimens collected in Kimberley (Northern Cape Province, South Africa). The female of the new taxon is the first micropterous sclerogibbid. Females of other extant Sclerogibbidae are always apterous, whereas fossil females can be apterous or macropterous. PMID:27394292

  7. A review of Chinese tribe Achilini (Hemiptera: Fulgoromorpha: Achilidae), with descriptions of Paracatonidia webbeda gen. & sp. nov.

    PubMed

    Long, Jian-Kun; Yang, Lin; Chen, Xiang-Sheng

    2015-12-02

    Planthoppers of the tribe Achilini (Hemiptera: Fulgoromorpha: Achilidae) from China, are reviewed. A key to the three genera of Chinese Achilini is given. A new genus and species of the tribe from southwestern China: Paracatonidia webbeda gen. & sp. nov., is described. A new genus and species record for China, Cixidia kasparyani Anufriev, is also given.

  8. A New Deep-branching Stramenopile, Platysulcus tardus gen. nov., sp. nov.

    PubMed

    Shiratori, Takashi; Nakayama, Takeshi; Ishida, Ken-ichiro

    2015-07-01

    A novel free-living heterotrophic stramenopile, Platysulcus tardus gen. nov., sp. nov. was isolated from sedimented detritus on a seaweed collected near the Ngeruktabel Island, Palau. P. tardus is a gliding flagellate with tubular mastigonemes on the anterior short flagellum and a wide, shallow ventral furrow. Although the flagellar apparatus of P. tardus is typical of stramenopiles, it shows novel ultrastructural combinations that are not applied to any groups of heterotrophic stramenopiles. Phylogenetic analysis using SSU rRNA genes revealed that P. tardus formed a clade with stramenopiles with high support. However, P. tardus did not form a subclade with any species or environmental sequences within the stramenopiles, and no close relative was suggested by the phylogenetic analysis. Therefore, we concluded that P. tardus should be treated as a new genus and species of stramenopiles and have proposed a new family, Platysulcidae fam. nov., for this phylogenetically distinct organism. PMID:26070192

  9. Development of Distributed Generic Simulator (GenSim) through Invention of Simulated Network (simNetwork)

    NASA Astrophysics Data System (ADS)

    Koo, Cheol-Hea; Lee, Hoon-Hee; Cheon, Yee-Jin

    2011-09-01

    A simulated network protocol provides the capability of distributed simulation to a generic simulator. Through this, full coverage of management of data and service handling among separated simulators is achieved. The distributed simulation environment is much more conducive to handling simulation load balancing and hazard treatment than a standalone computer. According to the simulated network protocol, one simulator takes on the role of server and the other simulators take on the role of client, and client is controlled by server. The purpose of the simulated network protocol is to seamlessly connect multiple simulator instances into a single simulation environment. This paper presents the development of a simulated network (simNetwork) that provides the capability of distributed simulation to a generic simulator (GenSim), which is a software simulator of satellites that has been developed by the Korea Aerospace Research Institute since 2010, to use as a flight software! validation bench for future satellite development.

  10. Combresomyces cornifer gen. sp. nov., an endophytic peronosporomycete in Lepidodendron from the Carboniferous of central France.

    PubMed

    Dotzler, Nora; Krings, Michael; Agerer, Reinhard; Galtier, Jean; Taylor, Thomas N

    2008-09-01

    Structurally preserved periderm of the lycophyte Lepidodendron rhodumnense from the Visean (Mississippian) of central France contains a peronosporomycete (Combresomyces cornifer gen. sp. nov.) that occurs in the form of pyriform to subglobose terminal oogonia. On the surface is a conspicuous ornamentation, which may have formed through condensation of a mucilaginous extra-oogonial wall secretion. Some oogonia contain thin-walled spherules, which may represent (walled) oospheres or spores of an endoparasitic fungus (?chytrid), whereas single, large spheres in the interior are interpreted as oospores. Antheridia adpressed to several of the specimens are clavate and paragynous. This discovery sheds light on the morphology and biology of peronosporomycetes in a terrestrial ecosystem some 330My ago. Although the organism occurs exclusively in the periderm of L. rhodumnense, it is not known whether it represents a symptomless endophyte, pathogen, or saprotroph. PMID:18692373

  11. Coynema gen. n., a new genus of nematode (Thelastomatoidea, Hystrignathidae) parasites of Passalidae (Coleoptera) from Cuba

    PubMed Central

    Rodríguez, Jans Morffe; Rodríguez, Nayla García

    2011-01-01

    Abstract The new genus Coynema gen. n. is described as parasite of the two passalid beetles from Cuba: Passalus interstitialis Escholtz, 1829 (type host) and Passalus pertyi Kaup, 1869. Females are characterized by the shape of their cephalic end, cervical cuticle unarmed, a sub-cylindrical procorpus with its base abruptly dilated, fore region of intestine dilated as a sac-like structure, genital system didelphic-amphidelphic and eggs markedly ovoid and smooth-shelled. Males have a digestive system similar to females, tail sharply pointed, bearing a Y-like thickening of the dorsal cuticle. They also present a big, median, mammiform pre-cloacal papillae and a pair of small, sub-dorsal pre-cloacal papillae anterior to the cuticular thickening of the tail. PMID:21594137

  12. Sandrewia, n. gen., a problematical plant from the Lower Permian of Texas and Kansas

    USGS Publications Warehouse

    Mamay, S.H.

    1975-01-01

    Sandrewia, n. gen., monotypified by S. texana, n. sp., is a plant from Lower Permian beds of north-central Texas and east-central Kansas. It is characterized by stout axes with spirally disposed, laxly inserted, petiolate leaves; the laminae are broadly flabelliform with coarse, open venation. The leaves are reminiscent of the vojnovskyalean Nephropsis, of the Permian Petchora Basin, U.S.S.R., but biologic relationships are only speculative because of limited material. However, leaf characteristics render Sandrewia easily identifiable. Its presently limited stratigraphic range, along with floristic associations, indicates it may be a useful guide fossil and supports the author's beliefs regarding important times and places in Paleozoic plant evolution. ?? 1975.

  13. Enhanced Vision for All-Weather Operations Under NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.

    2010-01-01

    Recent research in Synthetic/Enhanced Vision technology is analyzed with respect to existing Category II/III performance and certification guidance. The goal is to start the development of performance-based vision systems technology requirements to support future all-weather operations and the NextGen goal of Equivalent Visual Operations. This work shows that existing criteria to operate in Category III weather and visibility are not directly applicable since, unlike today, the primary reference for maneuvering the airplane is based on what the pilot sees visually through the "vision system." New criteria are consequently needed. Several possible criteria are discussed, but more importantly, the factors associated with landing system performance using automatic and manual landings are delineated.

  14. Eremonidiopsis aggregata, gen. n., sp. n. from Cuba, the third West Indian Dioptinae (Lepidoptera, Notodontidae)

    PubMed Central

    Aguila, Rayner Núñez

    2013-01-01

    Abstract A new genus and species of Dioptinae (Lepidoptera, Noctuoidea, Notodontidae) is described from Cuba, this being the third taxon of the subfamily known from the West Indies. Eremonidiopsis aggregata, gen. n., sp. n., appears to be closely related to Eremonidia mirifica Rawlins & Miller from Hispaniola among members of the tribe Dioptini. Eremonidiopsis aggregata is known from two localities in the middle and western portions of the northeastern Cuban mountain range, Nipe–Sagua–Baracoa. The species inhabits low elevations (300–400 m) covered by lowland rainforest and sclerophyll rainforest. The six known specimens, all males, were part of small swarms flying near the top of an unidentified tree during the day at both collecting sites. These localities are included within protected areas, the “Pico Cristal” National Park in the West and the “Alexander von Humbolt” National Park in the East. PMID:24146561

  15. Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Agogué, Hélène; Intertaglia, Laurent; Lesongeur, Françoise; Lebaron, Philippe

    2008-11-01

    A novel aerobic, Gram-negative bacterial strain, designated 5IX/A01/131(T), was isolated from waters in the coastal north-western Mediterranean Sea. The cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine 2216 agar. The G+C content of the genomic DNA was 57 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, strain 5IX/A01/131(T) represents a novel genus and species, for which the name Melitea salexigens gen. nov., sp. nov. is proposed. The type strain of Melitea salexigens is 5IX/A01/131(T) (=DSM 19753(T) =CIP 109757(T) =MOLA 225(T)).

  16. Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Intertaglia, Laurent; Lesongeur, Françoise; Lebaron, Philippe

    2008-05-01

    A novel aerobic, Gram-negative bacterium, designated 3X/A02/235T, was isolated from the surface of coastal waters in the north-western Mediterranean Sea. Cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 61 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria and within the family Alteromonadaceae. On the basis of 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, this isolate represents a novel species of a novel genus, for which the name Haliea salexigens gen. nov., sp. nov. is proposed. The type strain of Haliea salexigens is 3X/A02/235T (=DSM 19537T =CIP 109602T =MOLA 286T).

  17. Life cycle of Schizochytriodinium calani nov. gen. nov. spec., a dinoflagellate parasitizing copepod eggs

    NASA Astrophysics Data System (ADS)

    Elbrächter, Malte

    1988-09-01

    During the Polarstern-cruise ARK IV/2 June 1987, in the Fram Strait, dinophytes parasitizing copepod eggs were observed. In the laboratory on board, vegetative reproduction was documented and re-infection of Calanus glacialis and C. hyperboreus eggs was experimentally established. During food uptake, a primary cyst produces successively several secondary cysts, all separating immediately after formation from the primary cyst. In every one of these free floating secondary cysts up to 256 dinospores are formed by palintomy. Re-infection only occurred after a “maturation time” of at least 2 days after formation of the dinospores. The life cycle is compared to that of other similar parasitic dinophyte genera: Apodinium Chatton, Chytriodinium Chatton, Dissodinium Klebs in Pascher and Myxodinium Cachon, Cachon & Bouquaheux. As the taxon under discussion does not fit in with any species or genus known so far, it is described as Schizochytriodinium calani nov. gen. nov. spec.

  18. GenASiS Basics: Object-oriented utilitarian functionality for large-scale physics simulations

    DOE PAGES

    Cardall, Christian Y.; Budiardja, Reuben D.

    2015-06-11

    Aside from numerical algorithms and problem setup, large-scale physics simulations on distributed-memory supercomputers require more basic utilitarian functionality, such as physical units and constants; display to the screen or standard output device; message passing; I/O to disk; and runtime parameter management and usage statistics. Here we describe and make available Fortran 2003 classes furnishing extensible object-oriented implementations of this sort of rudimentary functionality, along with individual `unit test' programs and larger example problems demonstrating their use. Lastly, these classes compose the Basics division of our developing astrophysics simulation code GenASiS (General Astrophysical Simulation System), but their fundamental nature makes themmore » useful for physics simulations in many fields.« less

  19. Microstructure stability of candidate stainless steels for Gen-IV SCWR fuel cladding application

    NASA Astrophysics Data System (ADS)

    Li, Jian; Zheng, W.; Penttilä, S.; Liu, P.; Woo, O. T.; Guzonas, D.

    2014-11-01

    In the past few years, significant progress has been made in materials selection for Gen-IV SCWR fuel cladding applications. Current studies indicate that austenite stainless steels such as 310H are promising candidates for in-core applications. Alloys in this group are promising for their corrosion resistance, SCC resistance, high temperature mechanical properties and creep resistance at temperatures up to 700 °C. However, one under-studied area of this alloy is the long-term microstructure stability under the proposed reactor operating condition. Unstable microstructure not only results in embrittlement but also has the potential to reduce their resistance to corrosion or stress-corrosion cracking. In this study, stainless steels 310H and 304H were tested for their SCWR corrosion resistance and microstructure stability.

  20. Application of constitutive model considering nonlinear unloading behavior for Gen.3 AHSS

    NASA Astrophysics Data System (ADS)

    Sun, Li; Wagoner, R. H.

    2013-05-01

    Nonlinear unloading behavior has been reported as an important factor for accurate springback prediction. In this study, a newly proposed special component of strain: "Quasi-Plastic-Elastic" ("QPE") strain was utilized to study the springback behavior of Advanced High Strength Steels (AHSS). Several types of steels, including IF steel, DP780, TRIP780, DP980, TWIP980 and QP980 were considered in this research. The results showed that all the tested steels have following behavior: 1) QPE strain is recoverable, like elastic deformation. 2) It dissipates work, like plastic deformation. A 3-D constitutive model considering QPE behavior was implemented in Abaqus/Standard with shell element and applied to draw-bend springback test for Gen. 3 AHSS, QP980. Predictions for springback using the QPE model were more accurate compared with standard elastic-plastic models.

  1. Similascarophis n. gen. n. spp. (Nematoda: Cystidicolidae) parasitizing marine fishes off the Chilean coast.

    PubMed

    Muñoz, Gabriela; González, María Teresa; George-Nascimento, Mario

    2004-08-01

    Similascarophis (Cystidicolidae) n. gen. is proposed. In the mouth of specimens of this genus, submedial labia are absent and pseudolabia do not have any part projecting toward the central oral opening. These nematodes were obtained from the alimentary tract of 7 marine fish species along the coast of Chile: Bovichthys chilensis Regan, Eleginops maclovinus (Cuvier), Pinguipes chilensis (Valenciennes), Cilus gilberti (Abbott), Cheilodactylus variegatus Valenciennes, Girella laevifrons (Tschudi), and Graus nigra Philippi. Morphology and morphometry are compared between 2 new Similascarophis species: Similascarophis maulensis n. sp. and S. chilensis n. sp., which differ in the presence of sublabia and in the length of the glandular esophagus and left spicule. We also recorded Similascarophis sp. in 2 other host species, which showed some distinct proportional measurements, although these differences were not sufficiently clear to identify them as a new species.

  2. Uktena riparia n. gen., n. sp. (Annelida, Clitellata, Lumbriculidae), a new spermatophore-producing oligochaete.

    PubMed

    Fend, Steven V; Rodriguez, Pilar; Lenat, David R

    2015-01-01

    Uktena riparia n. gen., n. sp. has been collected in hyporheic habitats at several sites in North Carolina, southeastern USA. The genus is defined by unusual characters related to reproductive structures, including the formation of encapsulated spermatophores for sperm transfer and large bundles of genital chaetae, both previously unknown in the Lumbriculidae. The simultaneous occurrence of both spermatophores and spermathecae is rare in the microdrile oligochaetes. Uktena spermatophores appear more similar to those reported in leeches than to those in other microdrile oligochaete families. Possible synapomorphies associating Uktena with the genera Kincaidiana and Guestphalinus include a filiform, ringed proboscis, a forward shift of reproductive organs relative to the usual position in the family, and spermathecae in the atrial segment. The new species adds to the already diverse, endemic lumbriculid fauna of the North Carolina Sandhills ecoregion. PMID:26250281

  3. Combresomyces cornifer gen. sp. nov., an endophytic peronosporomycete in Lepidodendron from the Carboniferous of central France.

    PubMed

    Dotzler, Nora; Krings, Michael; Agerer, Reinhard; Galtier, Jean; Taylor, Thomas N

    2008-09-01

    Structurally preserved periderm of the lycophyte Lepidodendron rhodumnense from the Visean (Mississippian) of central France contains a peronosporomycete (Combresomyces cornifer gen. sp. nov.) that occurs in the form of pyriform to subglobose terminal oogonia. On the surface is a conspicuous ornamentation, which may have formed through condensation of a mucilaginous extra-oogonial wall secretion. Some oogonia contain thin-walled spherules, which may represent (walled) oospheres or spores of an endoparasitic fungus (?chytrid), whereas single, large spheres in the interior are interpreted as oospores. Antheridia adpressed to several of the specimens are clavate and paragynous. This discovery sheds light on the morphology and biology of peronosporomycetes in a terrestrial ecosystem some 330My ago. Although the organism occurs exclusively in the periderm of L. rhodumnense, it is not known whether it represents a symptomless endophyte, pathogen, or saprotroph.

  4. Multimodal information Management: Evaluation of Auditory and Haptic Cues for NextGen Communication Displays

    NASA Technical Reports Server (NTRS)

    Begault, Durand R.; Bittner, Rachel M.; Anderson, Mark R.

    2012-01-01

    Auditory communication displays within the NextGen data link system may use multiple synthetic speech messages replacing traditional ATC and company communications. The design of an interface for selecting amongst multiple incoming messages can impact both performance (time to select, audit and release a message) and preference. Two design factors were evaluated: physical pressure-sensitive switches versus flat panel "virtual switches", and the presence or absence of auditory feedback from switch contact. Performance with stimuli using physical switches was 1.2 s faster than virtual switches (2.0 s vs. 3.2 s); auditory feedback provided a 0.54 s performance advantage (2.33 s vs. 2.87 s). There was no interaction between these variables. Preference data were highly correlated with performance.

  5. Thalassomonas viridans gen. nov., sp. nov., a novel marine gamma-proteobacterium.

    PubMed

    Macián, M C; Ludwig, W; Schleifer, K H; Garay, E; Pujalte, M J

    2001-07-01

    A new genus and species are proposed for two halophilic, strictly aerobic, chemo-organotrophic, marine bacterial strains. These bacteria are gram-negative, motile rods isolated from oysters cultivated off the Mediterranean coast at Valencia (Spain). They produce green/blue-green diffusible pigment. The G+C content of the DNA of the proposed type strain (XOM25T) is 48.4 mol %. A 16S rRNA gene sequence analysis of the two strains has shown that the new isolates represent a branch within the gamma-Proteobacteria, close to the genus Colwellia. The type species of the new genus is Thalassomonas viridans gen. nov., sp. nov., with the type strain XOM25T (= CECT 5083T = DSM 13754T).

  6. Enhanced vision for all-weather operations under NextGen

    NASA Astrophysics Data System (ADS)

    Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.

    2010-04-01

    Recent research in Synthetic/Enhanced Vision technology is analyzed with respect to existing Category II/III performance and certification guidance. The goal is to start the development of performance-based vision systems technology requirements to support future all-weather operations and the NextGen goal of Equivalent Visual Operations. This work shows that existing criteria to operate in Category III weather and visibility are not directly applicable since, unlike today, the primary reference for maneuvering the airplane is based on what the pilot sees visually through the "vision system." New criteria are consequently needed. Several possible criteria are discussed, but more importantly, the factors associated with landing system performance using automatic and manual landings are delineated.

  7. Mrakiella cryoconiti gen. nov., sp. nov., a psychrophilic, anamorphic, basidiomycetous yeast from alpine and arctic habitats.

    PubMed

    Margesin, Rosa; Fell, Jack W

    2008-12-01

    A novel psychrophilic basidiomycetous species is described in a new anamorphic genus as Mrakiella cryoconiti gen. nov., sp. nov.; the type strain of Mrakiella cryoconiti is strain A15(T) (=CBS 10834(T) =DSM 21094(T)). Two representatives were isolated from alpine glacier cryoconite and from northern Siberian sediment. Physiological and biochemical properties are similar to characteristics shared by members of the genus Mrakia, although sexual reproduction is absent. Mrakiella cryoconiti strains are psychrophilic and produce cold-active pectate lyase. Sequence analyses of the ITS and 26S rRNA D1/D2 regions indicated that these strains represent a distinct taxon within the Mrakia clade of the order Cystofilobasidiales, class Tremellomycetes and phylum Basidiomycota. On the basis of phenotypic and genotypic characteristics, Cryptococcus aquaticus (a member of the Mrakia clade) is transferred to the newly described genus as Mrakiella aquatica comb. nov.

  8. Rugosothynnus gen. nov. (Hymenoptera: Tiphiidae: Thynninae: Rhagigasterini), a newly recognised Australian genus.

    PubMed

    Brown, Graham

    2015-01-01

    Rugosothynnus gen. nov. (type species Rhagigaster corrugatus Turner, 1910) is erected for 12 Rhagigaster-like species. Nine species are described and illustrated from Australia: R. brunneus sp. nov., R. clypeatus sp. nov., R. confusus sp. nov., R. depressus sp. nov., R. fulvescens sp. nov., R. houstoni sp. nov., R. monteithae sp. nov., R. neocorrugatus sp. nov. and R. schichai sp. nov. New combinations are proposed for R. burnsi (Given, 1959), comb. nov., R. corrugatus (Turner, 1910), comb. nov. and R. tristis (Smith, 1859), comb. nov. (all previously from genus Rhagigaster Guérin-Ménéville, 1838). A key to both sexes of all species is provided except for the females of R. clypeatus sp. nov., R. depressus sp. nov., R. neocorrugatus sp. nov. and R. schichai sp. nov. which are unknown.

  9. NASA System-Level Design, Analysis and Simulation Tools Research on NextGen

    NASA Technical Reports Server (NTRS)

    Bardina, Jorge

    2011-01-01

    A review of the research accomplished in 2009 in the System-Level Design, Analysis and Simulation Tools (SLDAST) of the NASA's Airspace Systems Program is presented. This research thrust focuses on the integrated system-level assessment of component level innovations, concepts and technologies of the Next Generation Air Traffic System (NextGen) under research in the ASP program to enable the development of revolutionary improvements and modernization of the National Airspace System. The review includes the accomplishments on baseline research and the advancements on design studies and system-level assessment, including the cluster analysis as an annualization standard of the air traffic in the U.S. National Airspace, and the ACES-Air MIDAS integration for human-in-the-loop analyzes within the NAS air traffic simulation.

  10. Metulocladosporiella gen. nov. for the causal organism of Cladosporium speckle disease of banana.

    PubMed

    Crous, Pedro W; Schroers, Hans-Josef; Groenewald, Johannes Z; Braun, Uwe; Schubert, Konstanze

    2006-03-01

    Cladosporium musae, a widespread leaf-spotting hyphomycete on Musa spp., is genetically and morphologically distinct from Cladosporium s. str. (Davidiella anamorphs, Mycosphaerellaceae, Dothideales). DNA sequence data derived from the ITS and LSU gene regions of C. musae isolates show that this species is part of a large group of hyphomycetes in the Chaetothyriales with dematiaceous blastoconidia in acropetal chains. Cladosporium adianticola, a foliicolous hyphomycete known from leaf litter in Cuba is also a member of this clade and is closely related to C. musae. A comparison with other genera in the Cladosporium complex revealed that C. musae belongs to a lineage for which no generic name is currently available, and for which the genus Metulocladosporiella gen. nov. is proposed. Two species of Metulocladosporiella are currently known, namely M. musae, which is widely distributed, and M. musicola sp. nov., which is currently known from Africa.

  11. GenASiS Basics: Object-oriented utilitarian functionality for large-scale physics simulations

    SciTech Connect

    Cardall, Christian Y.; Budiardja, Reuben D.

    2015-06-11

    Aside from numerical algorithms and problem setup, large-scale physics simulations on distributed-memory supercomputers require more basic utilitarian functionality, such as physical units and constants; display to the screen or standard output device; message passing; I/O to disk; and runtime parameter management and usage statistics. Here we describe and make available Fortran 2003 classes furnishing extensible object-oriented implementations of this sort of rudimentary functionality, along with individual `unit test' programs and larger example problems demonstrating their use. Lastly, these classes compose the Basics division of our developing astrophysics simulation code GenASiS (General Astrophysical Simulation System), but their fundamental nature makes them useful for physics simulations in many fields.

  12. Description of Groenewaldozyma gen. nov. for placement of Candida auringiensis, Candida salmanticensis and Candida tartarivorans.

    PubMed

    Kurtzman, Cletus P

    2016-07-01

    DNA sequence analyses have demonstrated that species of the polyphyletic anamorphic ascomycete genus Candida may be members of described teleomorphic genera, members of the Candida tropicalis clade upon which the genus Candida is circumscribed, or members of isolated clades that represent undescribed genera. From phylogenetic analysis of gene sequences from nuclear large subunit rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II, Candida auringiensis (NRRL Y-17674(T), CBS 6913(T)), Candida salmanticensis (NRRL Y-17090(T), CBS 5121(T)), and Candida tartarivorans (NRRL Y-27291(T), CBS 7955(T)) were shown to be members of an isolated clade and are proposed for reclassification in the genus Groenewaldozyma gen. nov. (MycoBank MB 815817). Neighbouring taxa include species of the Wickerhamiella clade and Candida blankii. PMID:27142089

  13. Ascidiimonas aurantiaca gen. nov., sp. nov., a member of Flavobacteriaceae isolated from a sea squirt.

    PubMed

    Yoon, Jaewoo; Oku, Naoya; Kasai, Hiroaki

    2016-04-01

    A Gram-stain negative, strictly aerobic, chemoheterotrophic, tangerine orange pigmented, curved-rod shaped bacterium, designated N5DA8-2C(T), was isolated from a sea squirt by use of a bait-streaked agar technique. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared high (92.6 %) sequence similarity with Frondibacter aureus A5Q-67(T). The strain could be differentiated phenotypically from the related members of the family Flavobacteriaceae. The major fatty acids of strain N5DA8-2C(T) were iso-C15:1 G, iso-C17:0 3-OH, iso-C15:0 and C16:1 ω7c and/or C16:1 ω6c. A polar lipid profile was present consisting of phosphatidylethanolamine and three unidentified amino lipids. The DNA G+C content of the strain was determined to be 41 mol% and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Ascidiimonas aurantiaca gen. nov., sp. nov. is proposed. The type strain of A. aurantiaca gen. nov., sp. nov. is N5DA8-2C(T) (= KCTC 32992(T) = NBRC 110020(T)). PMID:26800666

  14. GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments.

    PubMed

    Groß, Lynn; Herrmann, Carmen

    2016-09-30

    Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 2016 Wiley Periodicals, Inc. PMID:27416879

  15. Gymnoxanthella radiolariae gen. et sp. nov. (Dinophyceae), a dinoflagellate symbiont from solitary polycystine radiolarians.

    PubMed

    Yuasa, Tomoko; Horiguchi, Takeo; Mayama, Shigeki; Takahashi, Osamu

    2016-02-01

    The symbiotic dinoflagellate Gymnoxanthella radiolariae T. Yuasa et T. Horiguchi gen. et sp. nov. isolated from polycystine radiolarians is described herein based on light, scanning and transmission electron microscopy as well as molecular phylogenetic analyses of SSU and LSU rDNA sequences. Motile cells of G. radiolariae were obtained in culture, and appeared to be unarmored. The cells were 9.1-11.4 μm long and 5.7-9.4 μm wide, and oval to elongate oval in the ventral view. They possessed an counterclockwise horseshoe-shaped apical groove, a nuclear envelope with vesicular chambers, cingulum displacement with one cingulum width, and the nuclear fibrous connective; all of these are characteristics of Gymnodinium sensu stricto (Gymnodinium s.s.). Molecular phylogenetic analyses also indicated that G. radiolariae belongs to the clade of Gymnodinium s.s. However, in our molecular phylogenetic trees, G. radiolariae was distantly related to Gymnodinium fuscum, the type species of Gymnodinium. Based on the consistent morphological, genetic, and ecological divergence of our species with the other genera and species of Gymnodinium s.s., we considered it justified to erect a new, separate genus and species G. radiolariae gen. et sp. nov. As for the peridinioid symbiont of radiolarians, Brandtodinium has been erected as a new genus instead of Zooxanthella, but the name Zooxanthella is still valid. Brandtodinium is a junior synonym of Zooxanthella. Our results suggest that at least two dinoflagellate symbiont species, peridinioid Zooxanthella nutricula and gymnodinioid G. radiolariae, exist in radiolarians, and that they may have been mixed and reported as "Z. nutricula" since the 19th century. PMID:26987091

  16. Gymnoxanthella radiolariae gen. et sp. nov. (Dinophyceae), a dinoflagellate symbiont from solitary polycystine radiolarians.

    PubMed

    Yuasa, Tomoko; Horiguchi, Takeo; Mayama, Shigeki; Takahashi, Osamu

    2016-02-01

    The symbiotic dinoflagellate Gymnoxanthella radiolariae T. Yuasa et T. Horiguchi gen. et sp. nov. isolated from polycystine radiolarians is described herein based on light, scanning and transmission electron microscopy as well as molecular phylogenetic analyses of SSU and LSU rDNA sequences. Motile cells of G. radiolariae were obtained in culture, and appeared to be unarmored. The cells were 9.1-11.4 μm long and 5.7-9.4 μm wide, and oval to elongate oval in the ventral view. They possessed an counterclockwise horseshoe-shaped apical groove, a nuclear envelope with vesicular chambers, cingulum displacement with one cingulum width, and the nuclear fibrous connective; all of these are characteristics of Gymnodinium sensu stricto (Gymnodinium s.s.). Molecular phylogenetic analyses also indicated that G. radiolariae belongs to the clade of Gymnodinium s.s. However, in our molecular phylogenetic trees, G. radiolariae was distantly related to Gymnodinium fuscum, the type species of Gymnodinium. Based on the consistent morphological, genetic, and ecological divergence of our species with the other genera and species of Gymnodinium s.s., we considered it justified to erect a new, separate genus and species G. radiolariae gen. et sp. nov. As for the peridinioid symbiont of radiolarians, Brandtodinium has been erected as a new genus instead of Zooxanthella, but the name Zooxanthella is still valid. Brandtodinium is a junior synonym of Zooxanthella. Our results suggest that at least two dinoflagellate symbiont species, peridinioid Zooxanthella nutricula and gymnodinioid G. radiolariae, exist in radiolarians, and that they may have been mixed and reported as "Z. nutricula" since the 19th century.

  17. Pharmacogenetic Association of Hypertension Candidate Genes with Fasting Glucose in the GenHAT Study

    PubMed Central

    Irvin, Marguerite R.; Lynch, Amy I.; Kabagambe, Edmond K.; Tiwari, Hemant K.; Barzilay, Joshua I.; Eckfeldt, John H.; Boerwinkle, Eric; Davis, Barry R.; Ford, Charles E.; Arnett, Donna K.

    2010-01-01

    Several clinical studies report increased risk of diabetes mellitus (DM) with pharmacologic treatment for hypertension (HTN). HTN genes may modify glycemic response to antihypertensive treatment. The current study examined the association of 24 single nucleotide polymorphisms (SNPs) in 11 HTN candidate genes with fasting glucose measured at 2, 4, and 6 years after treatment initiation. The study sample included participants free of diabetes at baseline in the Genetics of Hypertension Associated Treatment (GenHAT) study (N=9,309). GenHAT participants were randomized to receive treatment with a diuretic (chlorthalidone), calcium channel blocker (amlodipine), or ACE inhibitor (lisinopril). Mixed models for repeated measures were employed to test for gene and pharmacogenetic associations with fasting glucose during follow-up. Fasting glucose at year 2 increased on average 6.8 mg/dL, 4.8 mg/dL and 3.0 mg/dL from baseline in the chlorthalidone, amlodipine and lisinopril groups, respectively. Carrying the I allele (rs1799752) of the angiotensin-converting enzyme (ACE) I/D polymorphism was associated with lower fasting glucose levels (P=0.02). Additionally, an ACE promoter polymorphism (−262, rs4291) was associated with lower fasting glucose for the model AA/AT vs. TT which remained significant after correction for multiple testing (P=0.001). Finally, a SNP in the α-subunit of the amiloride-sensitive epithelial sodium channel (SCNN1A, rs2228576) modified the association of amlodipine versus chlorthalidone treatment with fasting glucose (P<0.001). Further examination of these genes and their relationships with cardiometabolic disease could foster development of pharmacogenetic guidelines aimed to prevent increases in fasting glucose during antihypertensive treatment. PMID:20577119

  18. Evaluating SoilGen2 as a tool for projecting soil evolution induced by global change.

    PubMed

    Keyvanshokouhi, Saba; Cornu, Sophie; Samouëlian, Anatja; Finke, Peter

    2016-11-15

    To protect soils against threats, it is necessary to predict the consequences of human activities and global change on their evolution on a ten to hundred year time scale. Mechanistic modelling of soil evolution is then a useful tool. We analysed the ability of the SoilGen model to be used for projections of soil characteristics associated to various soil threats: vertical distributions of <2μm fraction, organic carbon content (OC), bulk density and pH. This analysis took the form of a functional sensitivity analysis in which we varied the initial conditions (parent material properties) and boundary conditions (co-evolution of precipitation and temperature; type and amount of fertilization and tillage as well as duration of agriculture). The simulated scenario variants comprised anthroposequences in Luvisols at two sites with one default scenario, six variants for initial conditions and 12 variants for boundary conditions. The variants reflect the uncertainties to our knowledge of parent material properties or reconstructed boundary conditions. We demonstrated a sensitivity of the model to climate and agricultural practices for all properties. We also conclude that final model results are not significantly affected by the uncertainties of boundary conditions for long simulations runs, although influenced by uncertainties on initial conditions. The best results were for organic carbon, although improvements can be reached through calibration or by incorporating a dynamic vegetation growth module in SoilGen. Results were poor for bulk density due to a fixed-volume assumption in the model, which is not easily modified. The <2μm fraction depth patterns are reasonable but the process of clay new formation needs to be added to obtain the belly shape of the Bt horizon. After calibration for organic carbon under agriculture, the model is suitable for producing soil projections due to global change. PMID:27470670

  19. Metahyphopichia laotica gen. nov., sp. nov., a polymorphic yeast related to Hyphopichia.

    PubMed

    Sipiczki, Matthias; Pfliegler, Walter P; Safar, Silvana V B; Morais, Paula B; Rosa, Carlos A

    2016-07-01

    Four strains alternating between yeast and filamentous growth morphologies were isolated from flowers in two regions of Laos. In liquid environment the isolates propagated by budding and developed irregularly shaped pseudohyphae. On solid media, their yeast cells switched to hyphal growth which could return to the yeast phase by developing lateral blastoconidia. The sequences of the D1/D2 domains of the large subunit (LSU) 26S rRNA genes, the internal transcribed spacer (ITS) regions and the small subunit (SSU) 18S rRNA genes were identical in the four strains and differed from the corresponding sequences of other yeast species available in databases by at least 11 % (D1/D2), 13 % (ITS) and 7 % (SSU). In an independent project, two strains with D1/D2 and ITS sequences very similar to those of the Laotian strains were found in bark samples collected in Brazil. The six strains also differed from the closest yeast species in physiological properties, indicating that they represented a hitherto undescribed species. Phylogenetic analysis of the D1/D2 sequences, and the concatenated sequences of the SSU rRNA genes, D1/D2 domains of LSU rRNA genes as well as the protein-encoding genes ACT1 and TEF1 placed thestrains close to Hyphopichia. To reflect this position, the novel genus name Metahyphopichia gen. nov. and the novel species name Metahyphopichia laotica gen. nov., sp. nov. are proposed for them. The type strain of the type species is 11-1006T(=CBS 13022T=CCY 092-001-001T=NCAIM Y.02126T) and was isolated in Luang Prabang (Laos). MycoBank registration numbers are MB 808253 (Metahyphopichia) and MB 808254 (Metahyphopichia laotica).

  20. Towards an improved modeling of chemical weathering in the SoilGen soil evolution model

    NASA Astrophysics Data System (ADS)

    Opolot, Emmanuel; Finke, Peter

    2014-05-01

    As the need for soil information particularly in the fields of agriculture, land evaluation, hydrology, biogeochemistry and climate change keeps increasing, models for soil evolution are increasingly becoming valuable tools to provide such soil information. Although still limited, such models are progressively being developed. The SoilGen model is one of such models with capabilities to provide soil information such as soil texture, pH, base saturation, organic carbon, CEC, etc over multi-millennia time scale. SoilGen is a mechanistic water flow driven pedogenetic model describing soil forming processes such as carbon cycling, clay migration, decalcification, bioturbation, physical weathering and chemical weathering. The model has been calibrated and confronted with field measurements in a number of case studies, giving plausible results. Discrepancies between measured and simulated soil properties as concluded from case studies have been mainly attributed to (i) the simple chemical weathering system (ii) poor estimates of initial data inputs such as bulk density and element fluxes, and (iii) incorrect values of variables that describe boundary conditions such as precipitation and potential evapotranspiration. This study focuses on extending the chemical weathering system, such that it can deal with a more heterogeneous composition of primary minerals and includes more elements such as Fe and Si. We propose and discuss here an extended description of chemical weathering in the model that is based on more primary minerals, taking into account the role of the specific area of these minerals, and the effect of physical weathering on these specific areas over time. In the initial stage, the proposed chemical weathering mechanism is also implemented in PHREEQC (a widely applied geochemical code with capabilities to simulate equilibrium reactions involving water and minerals, surface complexes and ion exchangers, etc.) to facilitate comparison with the model results

  1. A method for establishing class III medical device equivalence: sodium hyaluronate (GenVisc 850) for the treatment of knee osteoarthritis

    PubMed Central

    Doros, Gheorghe; Lavin, Philip T; Daley, Michael; Miller, Larry E

    2016-01-01

    Although the concept of equivalence for drugs (generics) and biologics (biosimilars) has been readily adopted, the concept of equivalence or indistinguishable characteristics for class III medical devices has yet to be specifically addressed regarding a defined regulatory approval process in the US. In September 2015, GenVisc 850® (sodium hyaluronate), a hyaluronic acid approved for the treatment of knee osteoarthritis, was approved by the US Food and Drug Administration (FDA) based upon indistinguishable characteristics in comparison to an approved branded hyaluronic acid (Supartz®/Supartz FX™). The purpose of this paper is to review the methodology and report the main outcomes used to demonstrate clinical comparability of GenVisc 850 with Supartz/Supartz FX. The FDA approval was collectively attained using prospectively defined methods for preclinical, physical, and chemical testing, as well as noninferiority in clinical performance comparisons. Evidence from five randomized controlled studies of Supartz/Supartz FX vs saline control injections (used for Supartz approval), two randomized controlled trials of GenVisc 850 vs saline control injections, and one randomized controlled study of GenVisc 850 vs Supartz/Supartz FX provided evidence of safety for GenVisc 850. Efficacy was further assessed based on assessment of the same Supartz studies and three prospectively identified GenVisc 850 studies. A Bayesian network meta-analysis was used to demonstrate that the clinical efficacy of GenVisc 850 was noninferior to Supartz/Supartz FX and superior to saline control. Overall, safety of GenVisc 850 was similar to that of Supartz/Supartz FX and saline control injections, while efficacy of GenVisc 850 was noninferior to that of Supartz/Supartz FX and superior to saline control injections. PMID:27471412

  2. A method for establishing class III medical device equivalence: sodium hyaluronate (GenVisc 850) for the treatment of knee osteoarthritis.

    PubMed

    Doros, Gheorghe; Lavin, Philip T; Daley, Michael; Miller, Larry E

    2016-01-01

    Although the concept of equivalence for drugs (generics) and biologics (biosimilars) has been readily adopted, the concept of equivalence or indistinguishable characteristics for class III medical devices has yet to be specifically addressed regarding a defined regulatory approval process in the US. In September 2015, GenVisc 850® (sodium hyaluronate), a hyaluronic acid approved for the treatment of knee osteoarthritis, was approved by the US Food and Drug Administration (FDA) based upon indistinguishable characteristics in comparison to an approved branded hyaluronic acid (Supartz®/Supartz FX™). The purpose of this paper is to review the methodology and report the main outcomes used to demonstrate clinical comparability of GenVisc 850 with Supartz/Supartz FX. The FDA approval was collectively attained using prospectively defined methods for preclinical, physical, and chemical testing, as well as noninferiority in clinical performance comparisons. Evidence from five randomized controlled studies of Supartz/Supartz FX vs saline control injections (used for Supartz approval), two randomized controlled trials of GenVisc 850 vs saline control injections, and one randomized controlled study of GenVisc 850 vs Supartz/Supartz FX provided evidence of safety for GenVisc 850. Efficacy was further assessed based on assessment of the same Supartz studies and three prospectively identified GenVisc 850 studies. A Bayesian network meta-analysis was used to demonstrate that the clinical efficacy of GenVisc 850 was noninferior to Supartz/Supartz FX and superior to saline control. Overall, safety of GenVisc 850 was similar to that of Supartz/Supartz FX and saline control injections, while efficacy of GenVisc 850 was noninferior to that of Supartz/Supartz FX and superior to saline control injections. PMID:27471412

  3. Measurement of the neutron's electric form factor G(E)(n) via doubly polarized, quasi-elastic scattering at Jefferson Lab

    SciTech Connect

    Frank Wesselmann

    2004-11-01

    We determined the electric form factor of the neutron GEn via the reaction d(e,e?n)p using a longitudinally polarized electron beam and a frozen, polarized 15ND3 target at Jefferson Lab. The knocked out neutrons were detected in a segmented plastic scintillator in coincidence with the quasi-elastically scattered electrons which were tracked in Hall C's High Momentum Spectrometer. To extract GEn, we compared the experimental beam-target asymmetry with theoretical calculations based on different GEn models. We report the results of the fall 2001 run at Q2=0.5 and 1.0 (GeV/c)2.

  4. Evaluation of safety and efficacy of NexGen – an ultrathin strut and hybrid cell design cobalt-chromium bare metal stent implanted in a real life patient population – the Polish NexGen Registry

    PubMed Central

    Milewski, Krzysztof; Gąsior, Paweł; Samborski, Stefan; Buszman, Piotr P.; Błachut, Aleksandra; Młodziankowski, Adam; Mendyk, Artur; Król, Marek; Wojakowski, Wojciech; Buszman, Paweł E.

    2016-01-01

    Introduction Despite the dominance of drug-eluting stents in modern interventional cardiology, there is still a niche for bare metal stents. Aim The aim of the Polish NexGen registry was to evaluate the safety and efficacy of a new generation cobalt-chromium NexGen stent in a real life patient population. Material and methods A prospective multi-center registry was conducted in five clinical sites of American Heart of Poland. Three hundred and eighty-three patients who underwent percutaneous coronary intervention (PCI) with NexGen stent implantation were included. Clinical follow-up was performed at 1, 6 and 12 months. Additionally, a group of 42 randomly selected patients underwent control angiography at 6 months (10.96% of study population). The primary endpoint was occurrence of target vessel revascularization (TVR) at 6-month follow-up. Angiographic endpoints included rates of binary restenosis and late lumen loss at 6-month follow-up based on QCA analysis. Multivessel disease was present in more than 70% of patients, and 52.4% of lesions were complex. The main indications for angiography were non-ST elevation acute coronary syndromes (54.8%) and ST elevation myocardial infarction (34.99%). Results At 6-month follow-up 47 (12.7%) patients reached the primary endpoint of TVR. The composite of major acute cardiac event rates at 30-day and 6- and 12-month follow-up was 6.01% (n = 23), 18.5% (n = 69) and 25.21% (n = 92) respectively. Control angiography performed after 6 months showed in-stent late loss of 0.66 ±0.71 mm and a binary restenosis rate of 16.7%. Conclusions Our study showed that PCI with the NexGen stent is safe and effective at 6- and 12-month follow-up. Angiographic results showed a satisfactory restenosis rate and low late lumen loss. PMID:27625684

  5. Evaluation of safety and efficacy of NexGen – an ultrathin strut and hybrid cell design cobalt-chromium bare metal stent implanted in a real life patient population – the Polish NexGen Registry

    PubMed Central

    Milewski, Krzysztof; Gąsior, Paweł; Samborski, Stefan; Buszman, Piotr P.; Błachut, Aleksandra; Młodziankowski, Adam; Mendyk, Artur; Król, Marek; Wojakowski, Wojciech; Buszman, Paweł E.

    2016-01-01

    Introduction Despite the dominance of drug-eluting stents in modern interventional cardiology, there is still a niche for bare metal stents. Aim The aim of the Polish NexGen registry was to evaluate the safety and efficacy of a new generation cobalt-chromium NexGen stent in a real life patient population. Material and methods A prospective multi-center registry was conducted in five clinical sites of American Heart of Poland. Three hundred and eighty-three patients who underwent percutaneous coronary intervention (PCI) with NexGen stent implantation were included. Clinical follow-up was performed at 1, 6 and 12 months. Additionally, a group of 42 randomly selected patients underwent control angiography at 6 months (10.96% of study population). The primary endpoint was occurrence of target vessel revascularization (TVR) at 6-month follow-up. Angiographic endpoints included rates of binary restenosis and late lumen loss at 6-month follow-up based on QCA analysis. Multivessel disease was present in more than 70% of patients, and 52.4% of lesions were complex. The main indications for angiography were non-ST elevation acute coronary syndromes (54.8%) and ST elevation myocardial infarction (34.99%). Results At 6-month follow-up 47 (12.7%) patients reached the primary endpoint of TVR. The composite of major acute cardiac event rates at 30-day and 6- and 12-month follow-up was 6.01% (n = 23), 18.5% (n = 69) and 25.21% (n = 92) respectively. Control angiography performed after 6 months showed in-stent late loss of 0.66 ±0.71 mm and a binary restenosis rate of 16.7%. Conclusions Our study showed that PCI with the NexGen stent is safe and effective at 6- and 12-month follow-up. Angiographic results showed a satisfactory restenosis rate and low late lumen loss.

  6. Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments.

    PubMed

    Vaishampayan, Parag; Moissl-Eichinger, Christine; Pukall, Rüdiger; Schumann, Peter; Spröer, Cathrin; Augustus, Angela; Roberts, Anne Hayden; Namba, Greg; Cisneros, Jessica; Salmassi, Tina; Venkateswaran, Kasthuri

    2013-07-01

    Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MA(T) and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with Arthrobacter crystallopoietes ATCC 15481(T), Arthrobacter luteolus ATCC BAA-272(T), Arthrobacter tumbae DSM 16406(T) and Arthrobacter subterraneus DSM 17585(T). In contrast with previously described Arthrobacter species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod-coccus life cycle typically observed in nearly all Arthrobacter species, except A. agilis. The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related Arthrobacter species. Based on these observations, the authors propose that strains 1P05MA(T) and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MA(T) and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MA(T) ( = NRRL B-59547(T) = DSM 30849(T)).

  7. Aggregicoccus edonensis gen. nov., sp. nov., an unusually aggregating myxobacterium isolated from a soil sample.

    PubMed

    Sood, Sakshi; Awal, Ram Prasad; Wink, Joachim; Mohr, Kathrin I; Rohde, Manfred; Stadler, Marc; Kämpfer, Peter; Glaeser, Stefanie P; Schumann, Peter; Garcia, Ronald; Müller, Rolf

    2015-03-01

    A novel myxobacterium, MCy1366(T) (Ar1733), was isolated in 1981 from a soil sample collected from a region near Tokyo, Japan. It displayed general myxobacterial features like Gram-negative-staining, rod-shaped vegetative cells, gliding on solid surfaces, microbial lytic activity, fruiting-body-like aggregates and myxospore-like structures. The strain was mesophilic, aerobic and showed a chemoheterotrophic mode of nutrition. It was resistant to many antibiotics such as cephalosporin C, kanamycin, gentamicin, hygromycin B, polymyxin and bacitracin, and the key fatty acids of whole cell hydrolysates were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 0 2-OH. The genomic DNA G+C content of the novel strain was 65.6 mol%. The 16S rRNA gene sequence showed highest similarity (97.60 %) to 'Stigmatella koreensis' strain KYC-1019 (GenBank accession no. EF112185). Phylogenetic analysis based on 16S rRNA gene sequences and MALDI-TOF MS data revealed a novel branch in the family Myxococcaceae. DNA-DNA hybridization showed only 28 % relatedness between the novel strain and the closest recognized species, Corallococcus exiguus DSM 14696(T) (97 % 16S rRNA gene sequence similarity). A recent isolate from a soil sample collected in Switzerland, MCy10622, displayed 99.9 % 16S rRNA gene sequence similarity with strain MCy1366(T) and showed almost the same characteristics. Since some morphological features like fruiting-body-like aggregates were barely reproducible in the type strain, the newly isolated strain, MCy10622, was also intensively studied. On the basis of a comprehensive taxonomic study, we propose a novel genus and species, Aggregicoccus edonensis gen. nov., sp. nov., for strains MCy1366(T) and MCy10622. The type strain of the type species is MCy1366(T) ( = DSM 27872(T) = NCCB 100468(T)).

  8. Digyalum oweni, gen. nov., sp. nov., a new and unusual gregarin protozoan from the gut of mollusc Littorina obtusata (Prosobranchia: Gastropoda).

    PubMed

    Koura, E A; Grahame, J; Owen, R W; Kamel, E G

    1990-06-01

    Digyalum oweni, gen. nov., sp. nov., is described from the gut of the gastropod mollusc Littorina obtusata. The gregarine has the unusual features of transverse orientation of the epicyte folds and two anterior pouch-like hollows. PMID:2110230

  9. AN EXPLORATION OF DIVERSITY AMONG THE OSTERTAGIINAE: AFRICANASTRONGYLUS BUCEROS GEN. NOV. ET SP. NOV. (NEMATODA: TRICHOSTRONGYLOIDEA) IN AFRICAN BUFFALO (SYNCERUS CAFFER).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Abomasal nematodes (Ostertagiine: Trichostrongyloidea) representing a previously unrecognized genus and species are reported in African Buffalo (Syncerus caffer caffer) from Kenya, Uganda and South Africa. Africanastrongylus buceros gen. nov. et sp. nov. is characterized by a symmetrical tapering ...

  10. A new family, genus and species of freshwater amphipod Australomicroprotopus megacoxa gen. nov. sp. nov. (Senticaudata, Corophiidea, Microprotopoidea, Australomicroprotopidae fam. nov.) from Australia.

    PubMed

    Myers, Alan A; Lowry, James K; Billingham, Zac

    2016-01-01

    A new species of fresh-water amphipod is described from Australia. Australomicroprotopus megacoxa gen. nov. sp. nov. It is placed in a new family, the Australomicroprotopidae fam. nov. and is fully described and figured. PMID:27615940

  11. 'Urinacoccus massiliensis' gen. nov. sp. nov., identified in urine sample of a 7-year-old boy hospitalized for dental care under general anaesthesia.

    PubMed

    Morand, A; Cornu, F; Tsimaratos, M; Cadoret, F; Lagier, J-C; Fournier, P E; Raoult, D

    2016-11-01

    We report here the main characteristics of 'Urinacoccus massiliensis' gen. nov. sp. nov., strain FC2 (CSURP1992). This strain was isolated from the urine of an asymptomatic 7-year-old boy. PMID:27668082

  12. 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

  13. Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes.

    PubMed

    Katz, Laura A; Grant, Jessica; Parfrey, Laura Wegener; Gant, Anastasia; O'Kelly, Charles J; Anderson, O Roger; Molestina, Robert E; Nerad, Thomas

    2011-11-01

    While a large number of aerobic free-living protists have been described within the last decade, the number of new anaerobic or microaerophilic microbial eukaryotic taxa has lagged behind. Here we describe a microaerophilic genus and species of amoeboflagellate isolated from a near-shore marine site off the coast at Plymouth, Massachusetts: Subulatomonas tetraspora nov. gen. nov. sp. This taxon is closely related to Breviata anathema based on both microscopical features and phylogenetic analyses of sequences of three genes: SSU-rDNA, actin, and alpha-tubulin. However, Subulatomonas tetraspora nov. gen. nov. sp. and B. anathema are morphologically distinctive, differ by 14.9% at their SSU-rDNA locus, and were isolated from marine and 'slightly brackish' environments, respectively. Phylogenetic analyses of these two taxa plus closely related sequences from environmental surveys provide support for a novel clade of eukaryotes that is distinct from the major clades including the Opisthokonta, Excavata, Amoebozoa and 'SAR' (Stramenopile, Alveolate, Rhizaria).

  14. Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1

    PubMed Central

    Blanco, Miguel G.; Matos, Joao

    2015-01-01

    Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs) act upon recombining joint molecules (JMs) to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs – MUS81 and Yen1/GEN1– uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM-processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions. PMID:26284109

  15. Chemopreventive activity of GEN-27, a genistein derivative, in colitis-associated cancer is mediated by p65-CDX2-β-catenin axis

    PubMed Central

    Wang, Hong; Fan, Huimin; Li, Yan; Wang, Jianing; Zhang, Xu; Lu, Jinrong; Ji, Hui; Hu, Rong

    2016-01-01

    Nonresolving inflammation in the intestine predisposes individuals to colitis-associated colorectal cancer (CAC), which leads to high morbidity and mortality. Here we show that genistein-27 (GEN-27), a derivative of genistein, inhibited proliferation of human colorectal cancer cells through inhibiting β-catenin activity. Our results showed that GEN-27 increased expressions of adenomatous polyposis coli (APC) and axis inhibition protein 2 (AXIN2), and reduced β-catenin nuclear localization, which resulted from the inhibition of NF-κB/p65 nuclear localization and up-regulation of caudal-related homeobox transcription factor 2 (CDX2). Furthermore, GEN-27 decreased binding of p65 to the silencer region of CDX2 and increased binding of CDX2 to the promoter regions of APC and AXIN2, thus inhibiting the activation of β-catenin induced by TNF-α. Importantly, GEN-27 protected mice from azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colon carcinogenesis, with reduced mortality, tumor number and tumor volume. Histopathology, immunohistochemistry and flow cytometry revealed that dietary GEN-27 significantly decreased secretion of proinflammatory cytokines and macrophage infiltration. Moreover, GEN-27 inhibited AOM/DSS-induced p65 and β-catenin nuclear translocation, while promoted the expression of CDX2, APC, and AXIN2. Taken together, our findings demonstrate that the anti-proliferation effect of GEN-27 in vitro and the prevention of CAC in vivo is mediated by p65-CDX2-β-catenin axis via inhibiting β-catenin target genes. Our results imply that GEN-27 could be a promising candidate for the chemoprevention of CAC. PMID:26910375

  16. Praecocilenchus rhaphidophorus n. gen., n. sp. (Nematoda: Aphelenchoidea) Parasitizing Rhynchophorus bilineatus (Montrouzier) (Coleoptera: Curculionidae) in New Britain

    PubMed Central

    Poinar, G. O.

    1969-01-01

    Praecocilenchus rhaphidophorus n. gen., n. sp. is described as a new endoparasitic aphelenchoid nematode parasitizing adults of the palm weevil, Rhynchophorus bilineatus (Montrouzier). P. rhaphidophorus is unusual in that juveniles develop to maturity within the female uterus and thin, needle-shaped crystals form in the intestines of mature parasitic females. Hundreds of parasitic female nematodes were found in the body cavity of infected hosts. The role of this parasite as a biological control agent of Rhynchophorus weevils is discussed. PMID:19325682

  17. Genome Sequences of Oblitimonas alkaliphila gen. nov. sp. nov. (Proposed), a Novel Bacterium of the Pseudomonadaceae Family

    PubMed Central

    Lauer, Ana C.; Humrighouse, Ben W.; Emery, Brian; Drobish, Adam; Juieng, Phalasy; Loparev, Vladimir; McQuiston, John R.

    2015-01-01

    Results obtained through 16S rRNA gene sequencing and phenotypic testing of eight related, but unidentified, isolates located in a historical collection at the Centers for Disease Control and Prevention suggested that these isolates belong to a novel genera of bacteria. The genomes of the bacteria, to be named Oblitimonas alkaphilia gen. nov. sp. nov., were sequenced using Illumina technology. Closed genomes were produced for all eight isolates. PMID:26679585

  18. Potamostoma shizunaiense gen. et sp. nov. (Nemertea: Hoplonemertea: Monostilifera): a new brackish-water nemertean from Japan.

    PubMed

    Kajihara, Hiroshi; Gibson, Ray; Mawatari, Shunsuke F

    2003-04-01

    Potamostoma shizunaiense gen. et sp. nov. (Nemertea: Hoplonemertea: Monostilifera) is described from the mouth of the River Shizunai, Hokkaido, Japan. This genus is readily distinguished from other monostiliferans by an oesophagus opening far anteriorly into the rhynchodaeum, a well developed excretory system extending the whole body length, terminals of the excretory collecting tubules situated between the body wall circular muscle layer and the dermis, and bilobed testes in males.

  19. Quisarctus yasumurai gen. et sp. nov. (Arthrotardigrada: Halechiniscidae) from a submarine cave, off Iejima, Ryukyu Islands, Japan.

    PubMed

    Fujimoto, Shinta

    2015-01-01

    Quisarctus yasumurai gen. et sp. nov. (Arthrotardigrada: Halechiniscidae) is described from the submarine cave 'Daidokutsu', off Iejima, Okinawa Islands, Ryukyu Islands, Japan. It is characterised by a cylindrical body, long primary clava and shorter lateral cirrus inserted on a common cirrophore, and simple digits of unequal lengths (without folds, peduncles, proximal pads, pretarsi, or wrinkles) that terminate in a sheathed, small, crescent-shaped claw with a minute calcar. Quisarctinae subfam. nov. is erected for this unique new genus. PMID:25947769

  20. Surface Map Traffic Intent Displays and Net-Centric Data-link Communications for NextGen

    NASA Technical Reports Server (NTRS)

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

    2009-01-01

    By 2025, U.S. air traffic is predicted to increase three fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research, conducted at National Aeronautics and Space Administration (NASA) Langley Research Center, examining data-link communications and traffic intent data during envisioned four-dimensional trajectory (4DT)-based and equivalent visual (EV) surface operations. Overall, the results suggest that controller pilot data-link communications (CPDLC) with the use of mandatory pilot read-back of all clearances significantly enhanced situation awareness for 4DT and EV surface operations. The depiction of graphical traffic state and intent information on the surface map display further enhanced off-nominal detection and pilot qualitative reports of safety and awareness.

  1. Meeting Air Transportation Demand in 2025 by Using Larger Aircraft and Alternative Routing to Complement NextGen Operational Improvements

    NASA Technical Reports Server (NTRS)

    Smith, Jeremy C.; Guerreiro, Nelson M.; Viken, Jeffrey K.; Dollyhigh, Samuel M.; Fenbert, James W.

    2010-01-01

    A study was performed that investigates the use of larger aircraft and alternative routing to complement the capacity benefits expected from the Next Generation Air Transportation System (NextGen) in 2025. National Airspace System (NAS) delays for the 2025 demand projected by the Transportation Systems Analysis Models (TSAM) were assessed using NASA s Airspace Concept Evaluation System (ACES). The shift in demand from commercial airline to automobile and from one airline route to another was investigated by adding the route delays determined from the ACES simulation to the travel times used in the TSAM and re-generating new flight scenarios. The ACES simulation results from this study determined that NextGen Operational Improvements alone do not provide sufficient airport capacity to meet the projected demand for passenger air travel in 2025 without significant system delays. Using larger aircraft with more seats on high-demand routes and introducing new direct routes, where demand warrants, significantly reduces delays, complementing NextGen improvements. Another significant finding of this study is that the adaptive behavior of passengers to avoid congested airline-routes is an important factor when projecting demand for transportation systems. Passengers will choose an alternative mode of transportation or alternative airline routes to avoid congested routes, thereby reducing delays to acceptable levels for the 2025 scenario; the penalty being that alternative routes and the option to drive increases overall trip time by 0.4% and may be less convenient than the first-choice route.

  2. The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome.

    PubMed

    Sjödin, Andreas; Street, Nathaniel Robert; Sandberg, Göran; Gustafsson, Petter; Jansson, Stefan

    2009-06-01

    Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at www.popgenie.org or via www.populusgenome.info.

  3. Proposal of Ancylothrix gen. nov., a new genus of Phormidiaceae (Cyanobacteria, Oscillatoriales) based on a polyphasic approach.

    PubMed

    Martins, Mariellen Dornelles; Rigonato, Janaina; Taboga, Sebastião Roberto; Branco, Luis Henrique Zanini

    2016-06-01

    During a study about the diversity of Phormidioideae (Phormidiaceae, Oscillatoriales) in Brazil, seven strains from southern and southeastern regions were isolated in monospecifc cultures and submitted to polyphasic evaluation (morphological, ecological, cytological and molecular studies). The populations studied were found to be morphologically similar to Kamptonema (filaments narrowed and bent at the end) and cytologically different (thylakoids' arrangement - radial distribution in Brazilian strains and parietal distribution in Kamptonema). The original habitats were very diverse among the Brazilian strains (freshwater, wet soil and barks of trees). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains were placed together in a very distinctive and highly supported clade. Thus, the set of characteristics of the strains resulted in the recognition of the new genus Ancylothrix Martins et Branco gen. nov. with two species [Ancylothrix rivularis gen. nov., sp. nov. (type species) and Ancylothrix terrestris sp. nov.], distinguishable by differences in genetic and ecological characteristics and described under the provisions of the International Code of Nomenclature for algae, fungi and plants. Secondary structures of D1-D1', box-B and V3 regions were conserved in A. rivularis gen. nov. sp. nov. and more variable in A. terrestris sp. nov.

  4. Hardware and Software Design of FPGA-based PCIe Gen3 interface for APEnet+ network interconnect system

    NASA Astrophysics Data System (ADS)

    Ammendola, R.; Biagioni, A.; Frezza, O.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Paolucci, P. S.; Pastorelli, E.; Rossetti, D.; Simula, F.; Tosoratto, L.; Vicini, P.

    2015-12-01

    In the attempt to develop an interconnection architecture optimized for hybrid HPC systems dedicated to scientific computing, we designed APEnet+, a point-to-point, low-latency and high-performance network controller supporting 6 fully bidirectional off-board links over a 3D torus topology. The first release of APEnet+ (named V4) was a board based on a 40 nm Altera FPGA, integrating 6 channels at 34 Gbps of raw bandwidth per direction and a PCIe Gen2 x8 host interface. It has been the first-of-its-kind device to implement an RDMA protocol to directly read/write data from/to Fermi and Kepler NVIDIA GPUs using NVIDIA peer-to-peer and GPUDirect RDMA protocols, obtaining real zero-copy GPU-to-GPU transfers over the network. The latest generation of APEnet+ systems (now named V5) implements a PCIe Gen3 x8 host interface on a 28 nm Altera Stratix V FPGA, with multi-standard fast transceivers (up to 14.4 Gbps) and an increased amount of configurable internal resources and hardware IP cores to support main interconnection standard protocols. Herein we present the APEnet+ V5 architecture, the status of its hardware and its system software design. Both its Linux Device Driver and the low-level libraries have been redeveloped to support the PCIe Gen3 protocol, introducing optimizations and solutions based on hardware/software co-design.

  5. The National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC): Results from Phase I and Scientific Opportunities in Phase II

    PubMed Central

    Kroner, Barbara L.; Tolunay, H. Eser; Basson, Craig T.; Pyeritz, Reed E.; Holmes, Kathryn; Maslen, Cheryl L.; Milewicz, Dianna M.; LeMaire, Scott A.; Hendershot, Tabitha; Desvigne-Nickens, Patrice; Devereux, Richard B.; Dietz, Harry C.; Song, Howard; Ringer, Danny; Mitchell, Megan; Weinsaft, Jonathan W.; Ravekes, William; Menashe, Victor; Eagle, Kim A.

    2011-01-01

    Background Genetically triggered thoracic aortic conditions (GenTAC) represent an important problem for patients and their families. Accordingly, the National Heart, Lung and Blood Institute (NHLBI) established the first phase of its national GenTAC Registry in 2006. Enrollment and Diagnoses Between 2007 and 2010, six enrolling centers established the GenTAC I Registry consisting of 2,046 patients [(Marfan syndrome 576 (28.2%); bicuspid aortic valve disease 504 (24.6%), aneurysm or dissection age <50 years 369 (18%), and others.] Biologic samples for DNA analyses (WBC’s or saliva) are available in 97% and stored plasma is available in 60% of enrollees. Results Initial scientific inquiry using the GenTAC Registry has included validation studies of genetic causes for aortic syndromes, potential usefulness of TGFB blood levels in Marfan subjects, and current surgical approaches to ascending aortic conditions. Future Opportunity GenTAC II will allow biannual follow-up of GenTAC I enrollees for up to nine years, enrollment of an additional 1,500 subjects, further integration of imaging findings with clinical and genetic data through utilization of an imaging core lab, important validation of phenotype-genotype correlations through a phenotyping core lab, and integration of a scientific advisory committee to help define the full range and depth of the Registry’s scientific capabilities. The registry resources are available to the external scientific community through an application process accessible at https://gentac.rti.org. PMID:21982653

  6. Indirubin, a component of Ban-Lan-Gen, activates CYP3A4 gene transcription through the human pregnane X receptor.

    PubMed

    Kumagai, Takeshi; Aratsu, Yusuke; Sugawara, Ryosuke; Sasaki, Takamitsu; Miyairi, Shinichi; Nagata, Kiyoshi

    2016-04-01

    Ban-Lan-Gen is the common name for the dried roots of indigo plants, including Polygonum tinctorium, Isatis indigotica, Isatis tinctoria, and Strobilanthes cusia. Ban-Lan-Gen is frequently used as an anti-inflammatory and an anti-viral for the treatment of hepatitis, influenza, and various types of inflammation. One of the cytochrome P450 (CYP) enzymes, CYP3A4, is responsible for the metabolism of a wide variety of xenobiotics, including an estimated 60% of all clinically used drugs. In this study, we investigated the effect of Ban-Lan-Gen on the transcriptional activation of the CYP3A4 gene. Ban-Lan-Gen extract increased CYP3A4 gene reporter activity in a dose-dependent manner. Indirubin, one of the biologically active ingredients in the Ban-Lan-Gen, also dose-dependently increased CYP3A4 gene reporter activity. Expression of short hairpin RNA for the human pregnane X receptor (hPXR-shRNA) inhibited CYP3A4 gene reporter activity, and overexpression of human PXR increased indirubin- and rifampicin-induced CYP3A4 gene reporter activity. Furthermore, indirubin induced CYP3A4 mRNA expression in HepG2 cells. Taken together, these results indicate that indirubin, a component of Ban-Lan-Gen, activated CYP3A4 gene transcription through the activation of the human PXR. PMID:26987505

  7. Indirubin, a component of Ban-Lan-Gen, activates CYP3A4 gene transcription through the human pregnane X receptor.

    PubMed

    Kumagai, Takeshi; Aratsu, Yusuke; Sugawara, Ryosuke; Sasaki, Takamitsu; Miyairi, Shinichi; Nagata, Kiyoshi

    2016-04-01

    Ban-Lan-Gen is the common name for the dried roots of indigo plants, including Polygonum tinctorium, Isatis indigotica, Isatis tinctoria, and Strobilanthes cusia. Ban-Lan-Gen is frequently used as an anti-inflammatory and an anti-viral for the treatment of hepatitis, influenza, and various types of inflammation. One of the cytochrome P450 (CYP) enzymes, CYP3A4, is responsible for the metabolism of a wide variety of xenobiotics, including an estimated 60% of all clinically used drugs. In this study, we investigated the effect of Ban-Lan-Gen on the transcriptional activation of the CYP3A4 gene. Ban-Lan-Gen extract increased CYP3A4 gene reporter activity in a dose-dependent manner. Indirubin, one of the biologically active ingredients in the Ban-Lan-Gen, also dose-dependently increased CYP3A4 gene reporter activity. Expression of short hairpin RNA for the human pregnane X receptor (hPXR-shRNA) inhibited CYP3A4 gene reporter activity, and overexpression of human PXR increased indirubin- and rifampicin-induced CYP3A4 gene reporter activity. Furthermore, indirubin induced CYP3A4 mRNA expression in HepG2 cells. Taken together, these results indicate that indirubin, a component of Ban-Lan-Gen, activated CYP3A4 gene transcription through the activation of the human PXR.

  8. Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil.

    PubMed

    Okamura, Keiko; Hisada, Takayoshi; Kanbe, Toshio; Hiraishi, Akira

    2009-02-01

    A photoorganotrophic alphaproteobacterium designated strain G2-11(T) was isolated from submerged paddy soil. This bacterium had relatively large, oval to rod-shaped cells (2.0-3.0x3.0-10 microm). Cells were motile by means of single polar flagella. The color of phototrophically growing cultures was reddish-brown. The cell extract had absorption maxima at 375, 465, 492, 529, 592, 804, and 844 nm, indicating the presence of bacteriochlorophyll a and carotenoides of the spirilloxanthin series. Vesicular intracytoplasmic membranes were present. The main component of cellular fatty acids was C(18:1)omega7c. Ubiquinone-10 and rhodoquinone-10 were the major quinones. A 16S rRNA gene sequence analysis revealed that the isolate is closest to the acidophilic aerobic photosynthetic bacterium Acidisphaera rubrifaciens strain HS-AP3(T) (93.3% similarity). The G+C content of genomic DNA is 67.8 mol%. The name Rhodovastum atsumiense gen. nov., sp. nov. is proposed for the novel isolate. The type strain is strain G2-11(T) (=NBRC 104268(T)=KCTC 5708(T)).

  9. Sinocoelotes gen. n., a new genus of the subfamily Coelotinae (Araneae, Agelenidae) from Southeast Asia.

    PubMed

    Chen, Lu; Zhao, Zhe; Li, Shuqiang

    2016-01-01

    A new genus of the spider subfamily Coelotinae, Sinocoelotes gen. n., with nine new species, is described from Yunnan and Sichuan Provinces in southern China. The new species are: Sinocoelotes cangshanensis sp. n. (♀), Sinocoelotes hehuaensis sp. n. (♂♀), Sinocoelotes luoshuiensis sp. n. (♀), Sinocoelotes mangbangensis sp. n. (♀) from Yunnan; Sinocoelotes kangdingensis sp. n. (♀), Sinocoelotes ludingensis sp. n. (♂♀), Sinocoelotes mahuanggouensis sp. n. (♀), Sinocoelotes muliensis sp. n. (♀), and Sinocoelotes yanyuanensis sp. n. (♂) from Sichuan. In addition, six Coelotes species are transferred to the new genus: Sinocoelotes acicularis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀), Sinocoelotes forficatus (Liu & Li, 2010), comb. n. (♂♀), Sinocoelotes guangxian (Zhang, Yang, Zhu & Song, 2003), comb. n. (♂♀), Sinocoelotes pseudoterrestris (Schenkel, 1963), comb. n. (♂♀), Sinocoelotes pseudoyunnanensis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀) and Sinocoelotes thailandensis (Dankittipakul & Wang, 2003), comb. n. (♂♀). DNA barcodes of all the species were documented for future use. PMID:27667932

  10. Phocaeicola abscessus gen. nov., sp. nov., an anaerobic bacterium isolated from a human brain abscess sample.

    PubMed

    Al Masalma, Mouhamad; Raoult, Didier; Roux, Véronique

    2009-09-01

    A strictly anaerobic bacterial strain, 7401987T, was isolated from a human brain abscess sample. Cells were Gram-negative, non-spore-forming, coccoid to rod-shaped and motile by flagella in a lophotrichous arrangement. The isolate was asaccharolytic and the major cellular fatty acids were anteiso-C15:0 (28.2%), C16:0 (18.0%), iso-C15:0 (12.3%) and iso-C17:0 3-OH (11.7%). 16S rRNA gene sequence comparisons showed that the isolate was distantly related to members of the genera Bacteroides (<83.6% similarity), Parabacteroides (<79.9% similarity), Tannerella (<79.8% similarity), Dysgonomonas (<79.6% similarity), Porphyromonas (<79.3% similarity) and Prevotella (<78.9% similarity). The low 16S rRNA gene sequence similarity values and physiological and biochemical characteristics differentiated strain 7401987T from all known species and indicate that our isolate represents a novel species in a new genus within the phylum Bacteroidetes. The name Phocaeicola abscessus gen. nov., sp. nov. is proposed; the type strain of Phocaeicola abscessus is 7401987T (=CCUG 55929T=CSUR P22T=DSM 21584T). PMID:19620382

  11. Kretzoiarctos gen. nov., the oldest member of the giant panda clade.

    PubMed

    Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint.

  12. Myceligenerans xiligouense gen. nov., sp. nov., a novel hyphae-forming member of the family Promicromonosporaceae.

    PubMed

    Cui, Xiaolong; Schumann, Peter; Stackebrandt, Erko; Kroppenstedt, Reiner M; Pukall, Rüdiger; Xu, Lihua; Rohde, Manfred; Jiang, Chenglin

    2004-07-01

    Strain XLG9A10.2T was isolated from an alkaline salt marsh soil in western China. 16S rRNA gene sequence analysis indicated that strain XLG9A10.2T constitutes a distinct lineage within the family Promicromonosporaceae, sharing 94.8-95.1% gene similarity with members of the genus Promicromonospora and 94.4-95.7% similarity with those of Xylanimonas and related genera. The general colony and cell morphology of strain XLG9A10.2T is similar to that of members of Promicromonospora, but differs from members of the genus Xylanimonas in forming a well-developed branching mycelium and production of coccoid spores. Strain XLG9A10.2T shows the peptidoglycan type A4alpha (L-lys<--L-thr<--D-Glu), contains glucose, mannose and galactose as whole cell sugars and has MK-9(H4) and MK-9(H6) as major menaquinones, while phospholipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, three unidentified phospholipids and one unidentified glycolipid. The DNA base composition is 71.9 mol% G+C. On the basis of morphological, chemotaxonomic, metabolic and phylogenetic differences from other species of Promicromonosporaceae, a new genus and species, Myceligenerans xiligouense gen. nov., sp. nov., is proposed. The type strain is XLG9A10.2T (=DSM 15700T=CGMCC 1.3458T.)

  13. Acidomelania panicicola gen. et sp. nov. from switchgrass roots in acidic New Jersey pine barrens.

    PubMed

    Walsh, Emily; Luo, Jing; Zhang, Ning

    2014-01-01

    A new genus, Acidomelania, is described based on molecular phylogenetic analyses and ecological and morphological characters. Isolated from switchgrass roots in acidic and oligotrophic New Jersey pine barrens in this study, Acidomelania likely has a global distribution because its internal transcribed spacer (ITS) sequence has high similarity with a number of GenBank sequences resulted from various ecological studies. Apparently these samples all were from roots of plants that lived in acidic, nutrient-poor environments. Phylogenetic analyses based on ITS, LSU and ACT sequence data strongly supported the fact that Acidomelania isolates formed a monophyletic clade in Helotiales, distinct from any known taxa. Phylogenetically Acidomelania is closely related to Loramyces, Mollisia and Phialocephala fortinii, Acephala applanata species complex (PAC), the dark septate endophytes. Acidomelania also can be distinguished from Loramyces and Mollisia by its association with living grass roots. While taxa in PAC also are root endophytes, they have more complex phialid arrangement than Acidomelania. Results from this work will facilitate ecological and evolutionary studies on root-associated fungi. PMID:24891423

  14. Functional Allocation for Ground-Based Automated Separation Assurance in NextGen

    NASA Technical Reports Server (NTRS)

    Prevot, Thomas; Mercer, Joey; Martin, Lynne; Homola, Jeffrey; Cabrall, Christopher; Brasil, Connie

    2010-01-01

    As part of an ongoing research effort into functional allocation in a NextGen environment, a controller-in-the-loop study on ground-based automated separation assurance was conducted at NASA Ames' Airspace Operations Laboratory in February 2010. Participants included six FAA front line managers, who are currently certified professional controllers and four recently retired controllers. Traffic scenarios were 15 and 30 minutes long where controllers interacted with advanced technologies for ground-based separation assurance, weather avoidance, and arrival metering. The automation managed the separation by resolving conflicts automatically and involved controllers only by exception, e.g., when the automated resolution would have been outside preset limits. Results from data analyses show that workload was low despite high levels of traffic, Operational Errors did occur but were closely tied to local complexity, and safety acceptability ratings varied with traffic levels. Positive feedback was elicited for the overall concept with discussion on the proper allocation of functions and trust in automation.

  15. GenSAA: A tool for advancing satellite monitoring with graphical expert systems

    NASA Technical Reports Server (NTRS)

    Hughes, Peter M.; Luczak, Edward C.

    1993-01-01

    During numerous contacts with a satellite each day, spacecraft analysts must closely monitor real time data for combinations of telemetry parameter values, trends, and other indications that may signify a problem or failure. As satellites become more complex and the number of data items increases, this task is becoming increasingly difficult for humans to perform at acceptable performance levels. At the NASA Goddard Space Flight Center, fault-isolation expert systems have been developed to support data monitoring and fault detection tasks in satellite control centers. Based on the lessons learned during these initial efforts in expert system automation, a new domain-specific expert system development tool named the Generic Spacecraft Analyst Assistant (GenSAA) is being developed to facilitate the rapid development and reuse of real-time expert systems to serve as fault-isolation assistants for spacecraft analysts. Although initially domain-specific in nature, this powerful tool will support the development of highly graphical expert systems for data monitoring purposes throughout the space and commercial industry.

  16. Bandoniozyma gen. nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species

    PubMed Central

    Landell, Melissa Fontes; Crestani, Juliana; Pagnocca, Fernando Carlos; Sette, Lara Durães; Passarini, Michel Rodrigo Zambrano; Rosa, Carlos Augusto; Brandão, Luciana R.; Pimenta, Raphael S.; Ribeiro, José Roberto; Garcia, Karina Marques; Lee, Ching-Fu; Suh, Sung-Oui; Péter, Gábor; Dlauchy, Dénes; Fell, Jack W.; Scorzetti, Gloria; Theelen, Bart; Vainstein, Marilene H.

    2012-01-01

    Background Independent surveys across the globe led to the proposal of a new basidiomycetous yeast genus within the Bulleromyces clade of the Tremellales, Bandoniozyma gen. nov., with seven new species. Methodology/Principal Findings The species were characterized by multiple methods, including the analysis of D1/D2 and ITS nucleotide sequences, and morphological and physiological/biochemical traits. Most species can ferment glucose, which is an unusual trait among basidiomycetous yeasts. Conclusions/Significance In this study we propose the new yeast genus Bandoniozyma, with seven species Bandoniozyma noutii sp. nov. (type species of genus; CBS 8364T  =  DBVPG 4489T), Bandoniozyma aquatica sp. nov. (UFMG-DH4.20T  =  CBS 12527T  =  ATCC MYA-4876T), Bandoniozyma complexa sp. nov. (CBS 11570T  =  ATCC MYA-4603T  =  MA28aT), Bandoniozyma fermentans sp. nov. (CBS 12399T  =  NU7M71T  =  BCRC 23267T), Bandoniozyma glucofermentans sp. nov. (CBS 10381T  =  NRRL Y-48076T  =  ATCC MYA-4760T  =  BG 02-7-15-015A-1-1T), Bandoniozyma tunnelae sp. nov. (CBS 8024T  =  DBVPG 7000T), and Bandoniozyma visegradensis sp. nov. (CBS 12505T  =  NRRL Y-48783T  =  NCAIM Y.01952T). PMID:23056233

  17. Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Kramer, Lynda J.; Ellis,Kyle K.; Rehfeld, Sherri A.

    2012-01-01

    The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SEVS operational and system-level performance capabilities. Nine test flights (38 flight hours) were conducted over the summer and fall of 2011. The evaluations were flown in Gulfstream.s G450 flight test aircraft outfitted with the SEVS technology under very low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 ft to 2400 ft visibility) into various airports from Louisiana to Maine. In-situ flight performance and subjective workload and acceptability data were collected in collaboration with ground simulation studies at LaRC.s Research Flight Deck simulator.

  18. Racemicystis crocea gen. nov., sp. nov., a soil myxobacterium in the family Polyangiaceae.

    PubMed

    Awal, Ram Prasad; Garcia, Ronald; Müller, Rolf

    2016-06-01

    A novel bacterial strain designated MSr9521T was isolated in 2014 from a soil sample collected in 1986 from the Philippines. The novel bacterium shows myxobacterial characteristics that include pseudoplasmodial swarming, fruiting body formation and predatory ability to lyse microorganisms. The strain is chemoheterotrophic, mesophilic and aerobic. Major fatty acids are C18:1, C17:1 2-OH and iso-C15:0, and also contains trace amounts of omega-3/-6 polyunsaturated fatty acids. The G+C content of the genomic DNA is 70.4 mol%. The 16S rRNA gene sequence shows 95-96 % closest similarity to Sorangium cellulosum DSM 14627T, Polyangium fumosum Pl fu5T, Jahnella thaxteri Pl t4T and Byssovorax cruenta By c2T. The molecular phylogenetic analysis shows that the novel isolate forms a novel branch in the family Polyangiaceae, suborder Sorangiineae. Polyphasic taxonomic characterization suggests that the strain MSr9521T represents a novel species of a new genus in the family Polyangiaceae, for which the name Racemicystis crocea gen. nov., sp. nov. is proposed. The type strain of Racemicystis crocea is MSr9521T (=DSM 100773T=NCCB 100574T).

  19. Sinocoelotes gen. n., a new genus of the subfamily Coelotinae (Araneae, Agelenidae) from Southeast Asia

    PubMed Central

    Chen, Lu; Zhao, Zhe; Li, Shuqiang

    2016-01-01

    Abstract A new genus of the spider subfamily Coelotinae, Sinocoelotes gen. n., with nine new species, is described from Yunnan and Sichuan Provinces in southern China. The new species are: Sinocoelotes cangshanensis sp. n. (♀), Sinocoelotes hehuaensis sp. n. (♂♀), Sinocoelotes luoshuiensis sp. n. (♀), Sinocoelotes mangbangensis sp. n. (♀) from Yunnan; Sinocoelotes kangdingensis sp. n. (♀), Sinocoelotes ludingensis sp. n. (♂♀), Sinocoelotes mahuanggouensis sp. n. (♀), Sinocoelotes muliensis sp. n. (♀), and Sinocoelotes yanyuanensis sp. n. (♂) from Sichuan. In addition, six Coelotes species are transferred to the new genus: Sinocoelotes acicularis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀), Sinocoelotes forficatus (Liu & Li, 2010), comb. n. (♂♀), Sinocoelotes guangxian (Zhang, Yang, Zhu & Song, 2003), comb. n. (♂♀), Sinocoelotes pseudoterrestris (Schenkel, 1963), comb. n. (♂♀), Sinocoelotes pseudoyunnanensis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀) and Sinocoelotes thailandensis (Dankittipakul & Wang, 2003), comb. n. (♂♀). DNA barcodes of all the species were documented for future use.

  20. Kretzoiarctos gen. nov., the oldest member of the giant panda clade.

    PubMed

    Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

  1. Eionea nigra gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Intertaglia, Laurent; Lesongeur, Françoise; Lebaron, Philippe

    2011-07-01

    A novel aerobic, gram-negative bacterial strain, designated 17X/A02/237(T), was isolated from waters of the coastal north-western Mediterranean Sea. Cells were motile straight rods and formed dark-grey colonies on marine agar medium. Strain 17X/A02/237(T) contained ubiquinone Q-8 and its major fatty acids were C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH, C(18 : 1)ω7c, C(16 : 0), C(18 : 0) and C(10 : 0) 3-OH. The G+C content of the genomic DNA was 47.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. Based on 16S rRNA gene sequence data, as well as physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name of Eionea nigra gen. nov., sp. nov. is proposed. The type strain is 17X/A02/237(T) ( = DSM 19752(T) = CIP 109759(T) = MOLA 288(T)).

  2. Celoporthe dispersa gen. et sp. nov. from native Myrtales in South Africa

    PubMed Central

    Nakabonge, Grace; Gryzenhout, Marieka; Roux, Jolanda; Wingfield, Brenda D.; Wingfield, Michael J.

    2006-01-01

    In a survey for Cryphonectria and Chrysoporthe species on Myrtales in South Africa, a fungus resembling the stem canker pathogen Chrysoporthe austroafricana was collected from native Syzygium cordatum near Tzaneen (Limpopo Province), Heteropyxis canescens near Lydenburg (Mpumalanga Province) and exotic Tibouchina granulosa in Durban (KwaZulu-Natal Province). The fungus was associated with dying branches and stems on S. cordatum, H. canescens and T. granulosa. However, morphological differences were detected between the unknown fungus from these three hosts and known species of Chrysoporthe. The aim of this study was to characterise the fungus using DNA sequence comparisons and morphological features. Pathogenicity tests were also conducted to assess its virulence on Eucalyptus (ZG 14 clones), H. natalensis and T. granulosa. Plants of H. canescens were not available for inoculation. Results showed distinct morphological differences between the unknown fungus and Chrysoporthe spp. Phylogenetic analysis showed that isolates reside in a clade separate from Chrysoporthe and other related genera. Celoporthe dispersa gen. et sp. nov. is, therefore, described to accommodate this fungus. Pathogenicity tests showed that C. dispersa is not pathogenic to H. natalensis, but that it is a potential pathogen of Eucalyptus and Tibouchina spp. PMID:18490984

  3. Neoceratium gen. nov., a new genus for all marine species currently assigned to Ceratium (Dinophyceae).

    PubMed

    Gómez, Fernando; Moreira, David; López-García, Purificación

    2010-01-01

    The dinoflagellate genus Ceratium contains marine and freshwater species. Freshwater species possess six cingular plates, thick plates in the concave ventral area and usually develop a third hypothecal horn. The marine Ceratium species (>62 species) possess five cingular plates and thin plates in the concave ventral area; a third hypothecal horn is atypical. Resting cysts, a common feature in the freshwater species, are unreported in marine species. We illustrate for the first time resting cysts in marine Ceratium species (C. furca and C. candelabrum). We obtained small subunit ribosomal RNA gene (SSU rDNA) sequences of 23 Ceratium species (more than one third of the total marine species described so far), with representatives of the four acknowledged subgenera. Phylogenetic analyses including the type species, the freshwater C. hirundinella, showed that the four available sequences of freshwater species formed a strongly supported subclade, very distant from the marine cluster. Our data support the splitting of Ceratium sensu lato into two genera. Ceratium sensu stricto should be reserved for freshwater species possessing six cingular plates (three cingular plates in dorsal view). The new genus name, Neoceratium gen. nov. should be applied to the marine species of Ceratium sensu lato that possess five cingular plates (two cingular plates in dorsal view).

  4. Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile.

    PubMed

    Takeda, Minoru; Kamagata, Yoichi; Ghiorse, William C; Hanada, Satoshi; Koizumi, Jun-ichi

    2002-05-01

    A poly(3-hydroxybutyrate) (PHB)-degrading, gram-negative, aerobic bacterium, strain HS(T), was isolated from a hot spring and chemotaxonomically and phylogenetically characterized. The oxidase-positive, weakly catalase-positive, non-pigmented cells (0.6 x 2.6 microm) exhibited a single polar flagellum and accumulated PHB granules. Strain HS(T) was capable of manganese oxidation. Highest growth rate was attained at 50 degrees C. The optimum pH for growth was 7-8. The major respiratory quinone was ubiquinone-8 and major cellular fatty acids were C16:0, C16:1 and C18:1. The G+C content of the DNA was 66.2 mol%. Comparative 16S rDNA analysis indicated that strain HS(T) is related to the Rubrivivax subgroup and the family Comamonadaceae. The nearest phylogenetic relatives were Ideonella dechloratans (92.1% similarity), Leptothrix discophora (93.6%), Roseateles depolymerans (92.4%) and Rubrivivax gelatinosus (92.2%). On the basis of its phylogenetic and phenotypic properties, it is proposed that this isolate be designated Caldimonas manganoxidans gen. nov., sp. nov.; the type strain is HS(T) (= JCM 10698T = IFO 16448T = ATCC BAA-369T). PMID:12054255

  5. Lombardia GENS: a collaborative registry for monogenic diseases associated with stroke

    PubMed Central

    Bersano, Anna; Baron, Pierluigi; Lanfranconi, Silvia; Trobia, Nadia; Sterzi, Roberto; Motto, Cristina; Comi, Giancarlo; Sessa, Maria; Martinelli-Boneschi, Filippo; Micieli, Giuseppe; Ferrarese, Carlo; Santoro, Patrizia; Parati, Eugenio; Boncoraglio, Giorgio; Padovani, Alessandro; Pezzini, Alessandro; Candelise, Livia

    2012-01-01

    Summary The Italian region of Lombardy, with its existing stroke centers and high-technology laboratories, provides a favorable context for studying monogenic diseases associated with stroke. The Lombardia GENS project was set up to create a regional network for the diagnosis of six monogenic diseases associated with stroke: CADASIL, Fabry disease, MELAS, familial and sporadic hemiplegic migraine, hereditary cerebral amyloid angiopathy and Marfan syndrome. The network comprises 36 stroke centers and seven high-technology laboratories, performing molecular analysis. In this context, all stroke/TIA patients fulfilling clinical criteria for monogenic diseases are currently being included in an ongoing study. Demographic, clinical and family data and diagnostic criteria are collected using standardized forms. On the basis of stroke incidence in Lombardy and the reported prevalence of the diseases considered, we expect, during the course of the study, to collect datasets and DNA samples from more than 200 stroke patients suspected of having monogenic diseases. This will allow evaluation of the regional burden and better phenotype characterization of monogenic diseases associated with stroke. PMID:23158583

  6. Salisediminibacterium halotolerans gen. nov., sp. nov., a halophilic bacterium from soda lake sediment.

    PubMed

    Jiang, Feng; Cao, Shu-Juan; Li, Zhao-Hu; Fan, Hua; Li, Hai-Feng; Liu, Wei-Jie; Yuan, Hong-Li

    2012-09-01

    An orange-pigmented, Gram-reaction-positive, non-spore-forming, halophilic, alkali-tolerant rod, designated strain halo-2(T), was isolated from sediment of Xiarinaoer soda lake, in China's Inner Mongolia Autonomous Region. Strain halo-2(T) grew in a complex medium with 3-30 % (w/v) NaCl and at pH 5-10. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids were anteiso-C(15 : 0) (43.6 %), anteiso-C(17 : 0) (14.8 %) and iso-C(15 : 0) (6.8 %) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of the novel strain was 48.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain halo-2(T) was most closely related to Bacillus agaradhaerens DSM 8721(T) (93.9 % sequence similarity). However, strain halo-2(T) could be clearly differentiated from its closest phylogenetic relatives on the basis of several phenotypic, genotypic and chemotaxonomic characteristics. Strain halo-2(T) therefore represents a novel species in a new genus for which the name Salisediminibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of the type species is halo-2(T) (= CGMCC 1.7654(T) = NBRC 104935(T)). PMID:22039006

  7. Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2015-02-01

    A facultatively anaerobic, Gram-stain negative, golden-yellow pigmented, non-motile and rod-shaped bacterium, designated strain A5Q-67(T) was isolated from leaf litter collected at the mangrove estuary of Nakama River, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (94.2 %) to Imtechella halotolerans K1(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain A5Q-67(T) were identified as iso-C17:0 3-OH, summed feature 1 (iso-C15:1 H and/or C13:0 3-OH) and iso-C15:0 as defined by the MIDI system. The DNA G+C content was determined to be 36.7 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Frondibacter aureus gen. nov., sp. nov. is proposed. The type strain of F. aureus is A5Q-67(T) (=KCTC 32991(T) = NBRC 110021(T)). PMID:25385000

  8. Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota.

    PubMed

    Liu, Min-Jiao; Zhu, Wen-Yong; Li, Jie; Zhao, Guo-Zhen; Xiong, Zhi; Park, Dong-Jin; Hozzein, Wael N; Kim, Chang-Jin; Li, Wen-Jun

    2015-08-01

    An actinomycete strain, designated YIM 690008T, was isolated from Daucus carota collected from South Korea and its taxonomic position was investigated by using a polyphasic approach. The strain grew well on most media tested and no diffusible pigment was produced. The aerial mycelium formed wrinkled single spores and short spore chains, some of which were branched. The whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, mannose, ribose, galactose and rhamnose. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-10(H2). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, some unknown phospholipids, glycolipids and polar lipids. The major fatty acids were i-C16 : 0, ai-C17 : 0 and C18 : 1ω9c. The DNA G+C content of the genomic DNA was 63.1 mol%. Phylogenetic analysis indicated that the isolate belongs to the family Nocardiopsaceae. However, based on phenotypic, chemotaxonomic and genotypic data, it was concluded that strain YIM 690008T represents a novel genus and novel species of the family Nocardiopsaceae, for which the name Actinorugispora endophytica gen. nov., sp. nov. (type strain YIM 690008T = DSM 46770T = JCM 30099T = KCTC 29480T) is proposed.

  9. Sergey gen. n., a new doryctine genus from temperate forests of Mexico and Cuba (Hymenoptera, Braconidae).

    PubMed

    Martínez, Juan José; Lázaro, Rubi Nelsi Meza; Pedraza-Lara, Carlos; Zaldívar-Riverón, Alejandro

    2016-01-01

    The new doryctine genus Sergey gen. n. is described with four new species (Sergey cubaensis Zaldívar-Riverón & Martínez, sp. n., Sergey coahuilensis Zaldívar-Riverón & Martínez, sp. n., Sergey tzeltal Martínez & Zalídivar-Riverón, sp. n., Sergey tzotzil Martínez & Zalídivar-Riverón, sp. n.) from temperate forests of Mexico and Cuba. Similar to many other doryctine taxa, the new genus has a considerably elongated, petiolate basal sternal plate of the first metasomal tergite, although it can be distinguished from these by having the mesoscutum sharply declivous anteriorly with sharp anterolateral edges. The described species have been characterised molecularly based on two mitochondrial (COI, cyt b) and one nuclear (28S) gene markers. Based on the mitochondrial gene genealogies reconstructed, the evidence suggests the existence of incomplete lineage sorting or hybridization in the populations from Chiapas and Oaxaca assigned to Sergey tzeltal sp. n. PMID:27408539

  10. Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch.

    PubMed

    Kim, Myung Kyum; Im, Wan-Taek; Shin, Yong Kook; Lim, Ju Hyoung; Kim, Sung-Hye; Lee, Byung Chul; Park, Mi-Yeoun; Lee, Ki Young; Lee, Sung-Taik

    2004-11-01

    Gram-negative, non-spore-forming, rod-shaped, yellow-pigmented bacteria isolated from a freshwater stream in Korea were investigated to determine their taxonomic position. Complete 16S rRNA gene sequence analysis indicated that the organisms should be placed in the Chryseobacterium-Bergeyella-Riemerella branch in the family Flavobacteriaceae. Phylogenetically, the strains were most closely related to Chryseobacterium balustinum ATCC 33487(T) and Chryseobacterium scophthalmum LMG 13028(T) (94.3 and 94.1 % 16S rRNA gene sequence similarity, respectively) and they clustered on a separate well-supported branch. The strains contained menaquinone MK-6 as the predominant respiratory quinone and showed higher G+C contents (41.7 mol%) than other species in the Chryseobacterium-Bergeyella-Riemerella branch and i-C(15 : 0) as a major fatty acid (47-52 %). The phylogenetic distances from any species with validly published names and their phenotypic properties confirmed that the strains constitute a separate species in a new genus, for which the name Kaistella koreensis gen. nov., sp. nov. is proposed (type strain Chj707(T)=KCTC 12107(T)=IAM 15050(T)).

  11. Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees.

    PubMed

    Kwong, Waldan K; Moran, Nancy A

    2016-03-01

    Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29-31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T).

  12. GenInfoGuard—A Robust and Distortion-Free Watermarking Technique for Genetic Data

    PubMed Central

    Khan, Sharifullah; Anwar, Zahid; Kamran, Muhammad

    2015-01-01

    Genetic data, in digital format, is used in different biological phenomena such as DNA translation, mRNA transcription and protein synthesis. The accuracy of these biological phenomena depend on genetic codes and all subsequent processes. To computerize the biological procedures, different domain experts are provided with the authorized access of the genetic codes; as a consequence, the ownership protection of such data is inevitable. For this purpose, watermarks serve as the proof of ownership of data. While protecting data, embedded hidden messages (watermarks) influence the genetic data; therefore, the accurate execution of the relevant processes and the overall result becomes questionable. Most of the DNA based watermarking techniques modify the genetic data and are therefore vulnerable to information loss. Distortion-free techniques make sure that no modifications occur during watermarking; however, they are fragile to malicious attacks and therefore cannot be used for ownership protection (particularly, in presence of a threat model). Therefore, there is a need for a technique that must be robust and should also prevent unwanted modifications. In this spirit, a watermarking technique with aforementioned characteristics has been proposed in this paper. The proposed technique makes sure that: (i) the ownership rights are protected by means of a robust watermark; and (ii) the integrity of genetic data is preserved. The proposed technique—GenInfoGuard—ensures its robustness through the “watermark encoding” in permuted values, and exhibits high decoding accuracy against various malicious attacks. PMID:25689741

  13. GenInfoGuard--a robust and distortion-free watermarking technique for genetic data.

    PubMed

    Iftikhar, Saman; Khan, Sharifullah; Anwar, Zahid; Kamran, Muhammad

    2015-01-01

    Genetic data, in digital format, is used in different biological phenomena such as DNA translation, mRNA transcription and protein synthesis. The accuracy of these biological phenomena depend on genetic codes and all subsequent processes. To computerize the biological procedures, different domain experts are provided with the authorized access of the genetic codes; as a consequence, the ownership protection of such data is inevitable. For this purpose, watermarks serve as the proof of ownership of data. While protecting data, embedded hidden messages (watermarks) influence the genetic data; therefore, the accurate execution of the relevant processes and the overall result becomes questionable. Most of the DNA based watermarking techniques modify the genetic data and are therefore vulnerable to information loss. Distortion-free techniques make sure that no modifications occur during watermarking; however, they are fragile to malicious attacks and therefore cannot be used for ownership protection (particularly, in presence of a threat model). Therefore, there is a need for a technique that must be robust and should also prevent unwanted modifications. In this spirit, a watermarking technique with aforementioned characteristics has been proposed in this paper. The proposed technique makes sure that: (i) the ownership rights are protected by means of a robust watermark; and (ii) the integrity of genetic data is preserved. The proposed technique-GenInfoGuard-ensures its robustness through the "watermark encoding" in permuted values, and exhibits high decoding accuracy against various malicious attacks.

  14. Sinocoelotes gen. n., a new genus of the subfamily Coelotinae (Araneae, Agelenidae) from Southeast Asia

    PubMed Central

    Chen, Lu; Zhao, Zhe; Li, Shuqiang

    2016-01-01

    Abstract A new genus of the spider subfamily Coelotinae, Sinocoelotes gen. n., with nine new species, is described from Yunnan and Sichuan Provinces in southern China. The new species are: Sinocoelotes cangshanensis sp. n. (♀), Sinocoelotes hehuaensis sp. n. (♂♀), Sinocoelotes luoshuiensis sp. n. (♀), Sinocoelotes mangbangensis sp. n. (♀) from Yunnan; Sinocoelotes kangdingensis sp. n. (♀), Sinocoelotes ludingensis sp. n. (♂♀), Sinocoelotes mahuanggouensis sp. n. (♀), Sinocoelotes muliensis sp. n. (♀), and Sinocoelotes yanyuanensis sp. n. (♂) from Sichuan. In addition, six Coelotes species are transferred to the new genus: Sinocoelotes acicularis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀), Sinocoelotes forficatus (Liu & Li, 2010), comb. n. (♂♀), Sinocoelotes guangxian (Zhang, Yang, Zhu & Song, 2003), comb. n. (♂♀), Sinocoelotes pseudoterrestris (Schenkel, 1963), comb. n. (♂♀), Sinocoelotes pseudoyunnanensis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀) and Sinocoelotes thailandensis (Dankittipakul & Wang, 2003), comb. n. (♂♀). DNA barcodes of all the species were documented for future use. PMID:27667932

  15. Cochleicola gelatinilyticus gen. nov., sp. nov., Isolated from a Marine Gastropod, Reichia luteostoma.

    PubMed

    Shin, Su-Kyoung; Kim, Eunji; Choi, Sungmi; Yi, Hana

    2016-08-28

    A yellow, rod-shaped, non-motile, gram-negative, and strictly aerobic bacterial strain, designated LPB0005(T), was isolated from a marine gastropod, Reichia luteostoma. Here the genome sequence was determined, which comprised 3,395,737 bp with 2,962 protein-coding genes. The DNA G+C content was 36.3 mol%. The 16S rRNA gene sequence analysis indicated that the isolate represents a novel genus and species in the family Flavobacteriaceae, with relatively low sequence similarities to other closely related genera. The isolate showed chemotaxonomic properties within the range reported for the family Flavobacteriaceae, but possesses many physiological and biochemical characteristics that distinguished it from species in the closely related genera Ulvibacter, Jejudonia, and Aureitalea. Based on phylogenetic, phenotypic, and genomic analyses, strain LPB0005(T) represents a novel genus and species, for which the name Cochleicola gelatinilyticus gen. nov., sp. nov. is proposed. The type strain is LPB0005(T) (= KACC 18693(T) = JCM 31218(T)). PMID:27197669

  16. Accelerating Our Understanding of Supernova Explosion Mechanism via Simulations and Visualizations with GenASiS

    SciTech Connect

    Budiardja, R. D.; Cardall, Christian Y; Endeve, Eirik

    2015-01-01

    Core-collapse supernovae are among the most powerful explosions in the Universe, releasing about 1053 erg of energy on timescales of a few tens of seconds. These explosion events are also responsible for the production and dissemination of most of the heavy elements, making life as we know it possible. Yet exactly how they work is still unresolved. One reason for this is the sheer complexity and cost of a self-consistent, multi-physics, and multi-dimensional core-collapse supernova simulation, which is impractical, and often impossible, even on the largest supercomputers we have available today. To advance our understanding we instead must often use simplified models, teasing out the most important ingredients for successful explosions, while helping us to interpret results from higher fidelity multi-physics models. In this paper we investigate the role of instabilities in the core-collapse supernova environment. We present here simulation and visualization results produced by our code GenASiS.

  17. Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

    PubMed Central

    Abella, Juan; Alba, David M.; Robles, Josep M.; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

  18. Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae.

    PubMed

    Ivanova, Elena P; Alexeeva, Yulia V; Flavier, Sébastien; Wright, Jonathan P; Zhukova, Natalia V; Gorshkova, Natalia M; Mikhailov, Valery V; Nicolau, Dan V; Christen, Richard

    2004-05-01

    Four light-yellow-pigmented, Gram-negative, short-rod-shaped, non-motile isolates were obtained from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The isolates studied were chemo-organotrophic, alkalitolerant and mesophilic. Polar lipids were analysed and phosphatidylethanolamine was the only phospholipid identified. The predominant cellular fatty acids were 15 : 0, i15 : 0, ai15 : 0, i15 : 1 and 15 : 1(n-6). The DNA G+C contents of the four strains were 34.0-34.4 mol%. The level of DNA relatedness of the four isolates was conspecific (88-98 %), indicating that they belong to the same species. The 16S rDNA sequence of strain KMM 3553(T) was determined. Phylogenetic analysis revealed that KMM 3553(T) formed a distinct phyletic line in the phylum Bacteroidetes, class Flavobacteria in the family Flavobacteriaceae and that, phylogenetically, this strain could be placed almost equidistant from the genera Gelidibacter and Psychroserpens (16S rRNA gene sequence similarities of 94 %). On the basis of significant differences in phenotypic and chemotaxonomic characteristics, it is suggested that the isolates represent a novel species in a new genus; the name Formosa algae gen. nov., sp. nov. is proposed. The type strain is KMM 3553(T) (=CIP 107684(T)).

  19. Decay Heat Removal in GEN IV Gas-Cooled Fast Reactors

    DOE PAGES

    Cheng, Lap-Yan; Wei, Thomas Y. C.

    2009-01-01

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

  20. Emergency Decay Heat Removal in a GEN-IV Gas-Cooled Fast Reactor

    SciTech Connect

    Cheng, Lap Y.; Ludewig, Hans; Jo, Jae

    2006-07-01

    A series of transient analyses using the system code RELAP5-3d has been performed to confirm the efficacy of a proposed hybrid active/passive combination approach to the decay heat removal for an advanced 2400 MWt GEN-IV gas-cooled fast reactor. The accident sequence of interest is a station blackout simultaneous with a small break (10 sq.inch/0.645 m{sup 2}) in the reactor vessel. The analyses cover the three phases of decay heat removal in a depressurization accident: (1) forced flow cooling by the power conversion unit (PCU) coast down, (2) active forced flow cooling by a battery powered blower, and (3) passive cooling by natural circulation. The blower is part of an emergency cooling system (ECS) that by design is to sustain passive decay heat removal via natural circulation cooling 24 hours after shutdown. The RELAP5 model includes the helium-cooled reactor, the ECS (primary and secondary side), the PCU with all the rotating machinery (turbine and compressors) and the heat transfer components (recuperator, pre-cooler and inter-cooler), and the guard containment that surrounds the reactor and the PCU. The transient analysis has demonstrated the effectiveness of passive decay heat removal by natural circulation cooling when the guard containment pressure is maintained at or above 800 kPa. (authors)

  1. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

    PubMed Central

    Rambaut, Andrew; Lam, Tommy T.; Max Carvalho, Luiz; Pybus, Oliver G.

    2016-01-01

    Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data. Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression approach to explore the association between genetic divergence through time and sampling dates. TempEst can be used to (1) assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and (2) identify sequences whose genetic divergence and sampling date are incongruent. Examination of the latter can help identify data quality problems, including errors in data annotation, sample contamination, sequence recombination, or alignment error. We recommend that all users of the molecular clock models implemented in BEAST first check their data using TempEst prior to analysis. PMID:27774300

  2. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide

    USGS Publications Warehouse

    Schaefer, J.K.; Goodwin, K.D.; McDonald, I.R.; Murrell, J.C.; Oremland, R.S.

    2002-01-01

    A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the ??-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov.

  3. Palaeoanellus dimorphus gen. et sp. nov. (Deuteromycotina): a Cretaceous predatory fungus.

    PubMed

    Schmidt, Alexander R; Dörfelt, Heinrich; Perrichot, Vincent

    2008-10-01

    In habitats where nitrogen is the limiting factor, carnivorous fungi gain an advantage by preying on nematodes and other microorganisms. These fungi are abundant in modern terrestrial ecosystems, but they are not predestined for preservation as fossils. Conclusions on their evolutionary history are therefore mainly based on molecular studies that are generally limited to those taxa that have survived until today. Here we present a fossil dimorphic fungus that was found in Late Albian amber from southwestern France. This fungus possessed unicellular hyphal rings as trapping devices and formed blastospores from which a yeast stage developed. The fossil probably represents an anamorph of an ascomycete and is described as Palaeoanellus dimorphus gen. et sp. nov. Because predatory fungi with regular yeast stages are not known from modern ecosystems, the fungus is assumed to not be related to any Recent carnivorous fungus and to belong to an extinct lineage of carnivorous fungi. The inclusions represent the only record of fossil fungi that developed trapping devices, so far. The fungus lived c. 100 million years ago in a limnetic-terrestrial microhabitat, and it was a part of a highly diverse biocenosis at the forest floor of a Cretaceous coastal amber forest. PMID:21632336

  4. Parasaccharibacter apium, gen. nov., sp. nov., Improves Honey Bee (Hymenoptera: Apidae) Resistance to Nosema.

    PubMed

    Corby-Harris, V; Snyder, L; Meador, C A D; Naldo, R; Mott, B; Anderson, K E

    2016-04-01

    The honey bee, Apis mellifera L., is host to a variety of microorganisms. The bacterial community that occupies the adult worker gut contains a core group of approximately seven taxa, while the hive environment contains its own distribution of bacteria that is in many ways distinct from the gut. Parasaccharibacter apium, gen. nov., sp. nov., is a hive bacterium found in food stores and in larvae, worker jelly, worker hypopharyngeal glands, and queens. Parasaccharibacter apium increases larval survival under laboratory conditions. To determine if this benefit is extended to colonies in the field, we tested if P. apium 1) survives and reproduces in supplemental pollen patty, 2) is distributed throughout the hive when added to pollen patty, 3) benefits colony health, and 4) increases the ability of bees to resist Nosema. Parasaccharibacter apium survived in supplemental diet and was readily consumed by bees. It was distributed throughout the hive under field conditions, moving from the pollen patty to hive larvae. While P. apium did not significantly increase colony brood production, food stores, or foraging rates, it did increase resistance to Nosema infection. Our data suggest that P. apium may positively impact honey bee health.

  5. A new tardigrade, Mutaparadoxipus duodigifinis gen. nov., sp. nov. (Heterotardigrada: Arthrotardigrada), from the Southeastern United States.

    PubMed

    Gross, Vladimir; Miller, William R; Hochberg, Rick

    2014-07-10

    A new genus and species of Arthrotardigrada is described from Florida, USA based on its unique adhesive pad/claw combinations. Mutaparadoxipus duodigifinis gen. nov., sp. nov., is characterized by well-developed, ventral secondary clavae that are adjacent to the mouth, pointed lateral and caudal alae, seminal receptacles with coiled ducts opening lateral to the gonopore, and all legs with digits bearing proximal adhesive pads. Distal claws are present on digits I-III of legs I-III, but are missing from digit IV. On leg IV, distal claws are present only on digits II & III. A single accessory point is present on claws II & III only. This is the fourth species discovered to date with proximal adhesive pads, increasing support for a clade of adhesive-padded arthrotardigrades, and is likely the sister taxon of Paradoxipus orzeliscoides. The incomplete set of claws may represent an evolutionary step in a progressive loss of claws hypothesized to have occurred within the Halechiniscidae. The subfamily Orzeliscinae is amended as a result.

  6. Using Game Theoretic Models to Predict Pilot Behavior in NextGen Merging and Landing Scenario

    NASA Technical Reports Server (NTRS)

    Yildiz, Yildiray; Lee, Ritchie; Brat, Guillaume

    2012-01-01

    In this paper, we present an implementation of the Semi Network-Form Game framework to predict pilot behavior in a merging and landing scenario. In this scenario, two aircraft are approaching to a freeze horizon with approximately equal distance when they become aware of each other via an ADS-B communication link that will be available in NextGen airspace. Both pilots want to gain advantage over the other by entering the freeze horizon earlier and obtain the first place in landing. They re-adjust their speed accordingly. However, they cannot simply increase their speed to the maximum allowable values since they are concerned with safety, separation distance, effort, possibility of being vectored-off from landing and possibility of violating speed constraints. We present how to model these concerns and the rest of the system using semi network-from game framework. Using this framework, based on certain assumptions on pilot utility functions and on system configuration, we provide estimates of pilot behavior and overall system evolution in time. We also discuss the possible employment of this modeling tool for airspace design optimization. To support this discussion, we provide a case where we investigate the effect of increasing the merging point speed limit on the commanded speed distribution and on the percentage of vectored aircraft.

  7. Investigating contact toxicity of Geranium and Artemisia essential oils on Bemisia tabaci Gen.

    PubMed Central

    Yarahmadi, Fatemeh; Rajabpour, Ali; Zandi Sohani, Nooshin; Ramezani, Leila

    2013-01-01

    Objective: Sweet potato whitefly, Bemisia tabaci Gen. (B. tabaci), is one of the most important pests of various greenhouse crops in Iran. Nowadays, chemical insecticides are broadly used for control of the pests that causes risk to consumer's health. For the first time, contact toxicity of Pelargonium roseum Andrews and Artemisia sieberi Besser essential oils on B. tabaci and its possible application against the whitefly was evaluated in 2012. Materials and Methods: Essential oil with concentrations of 2500, 1250, 125, and 12 ppm were used. Infested leaves of greenhouse cucumber were treated by mentioned concentrations. After 24 hours, mortality of B. tabaci was recorded and compared after correcting by Abbot's formula. Results: Results showed that all concentrations of the essential oil could significantly reduce population of B. tabaci compared with the control treatment. Phytotoxicity of the treated leaves were recorded after 24, 48, and 72 hours and compared with the control. Concentrations of 2500, 1250, and 125 ppm caused severe phytotoxicity on greenhouse cucumber leaves and therefore are not suitable for greenhouse application. Phytotoxicity of 12 ppm was relatively low. Conclusions: This data implicated suitable protective effects of the essential oils to the pest infestation. Therefore, essential oils distillated from Geranium and Artemisia could be applied to control B. tabaci in greenhouse cucumber at V/V 12 ppm. PMID:25050264

  8. Aquisphaera giovannonii gen. nov., sp. nov., a planctomycete isolated from a freshwater aquarium.

    PubMed

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

    2011-12-01

    As part of a study of the diversity of planctomycetes, two novel strains, designated OJF2(T) and OJF8, were isolated from the sediments of a freshwater aquarium. The organisms were chemoheterotrophic, spherical and pink-pigmented, had an optimum growth temperature of about 30-35 °C and an optimum pH for growth of around 7.5-8.5. The predominant fatty acids were C(18:1)ω9c and C(16:0). The two strains were able to assimilate several sugars and organic acids. 16S rRNA gene sequence analysis confirmed the affiliation of these organisms to the phylum 'Planctomycetes'; they showed highest similarity to the type strains of Singulisphaera acidiphila (92.4%) and Isosphaera pallida (91.9%). On the basis of physiological, biochemical and chemotaxonomic characteristics, strains OJF2(T) and OJF8 are considered to represent a novel species of a new genus of the order Planctomycetales, for which the name Aquisphaera giovannonii gen. nov., sp. nov. is proposed. The type strain of Aquisphaera giovannonii is OJF2(T) (=CECT 7510(T) =DSM 22561(T)). PMID:21239565

  9. Development of Complexity Science and Technology Tools for NextGen Airspace Research and Applications

    NASA Technical Reports Server (NTRS)

    Holmes, Bruce J.; Sawhill, Bruce K.; Herriot, James; Seehart, Ken; Zellweger, Dres; Shay, Rick

    2012-01-01

    The objective of this research by NextGen AeroSciences, LLC is twofold: 1) to deliver an initial "toolbox" of algorithms, agent-based structures, and method descriptions for introducing trajectory agency as a methodology for simulating and analyzing airspace states, including bulk properties of large numbers of heterogeneous 4D aircraft trajectories in a test airspace -- while maintaining or increasing system safety; and 2) to use these tools in a test airspace to identify possible phase transition structure to predict when an airspace will approach the limits of its capacity. These 4D trajectories continuously replan their paths in the presence of noise and uncertainty while optimizing performance measures and performing conflict detection and resolution. In this approach, trajectories are represented as extended objects endowed with pseudopotential, maintaining time and fuel-efficient paths by bending just enough to accommodate separation while remaining inside of performance envelopes. This trajectory-centric approach differs from previous aircraft-centric distributed approaches to deconfliction. The results of this project are the following: 1) we delivered a toolbox of algorithms, agent-based structures and method descriptions as pseudocode; and 2) we corroborated the existence of phase transition structure in simulation with the addition of "early warning" detected prior to "full" airspace. This research suggests that airspace "fullness" can be anticipated and remedied before the airspace becomes unsafe.

  10. Molecular and morphological characterization of Veleshkinema iranicum n. gen., n. sp. (Nematoda: Hexatylina, Sphaerularioidea) from Iran.

    PubMed

    Miraeiz, Esmaeil; Heydari, Ramin; Álvarez-Ortega, Sergio; Pedram, Majid; Atighi, Mohammad Reza

    2015-08-19

    Veleshkinema  iranicum n. gen., n. sp. is described and illustrated based on morphological, morphometric and molecular characters. The new genus is characterized by having slender females and males, stylet with asymmetrical knobs, dorsal gland orifice just posterior to subventral knob, lip region with flattened apex and eight sectors, pharynx with a non-muscular and non-valvular median bulb, pharyngeal glands slightly overlapping intestine dorsally, visible cellular cardia, female with a single gonad having a quadricolumellate crustaformeria with 8-10 cells in each column, no postvulval uterine sac and rounded and offset spermatheca containing spheroid sperm cells, males with arcuate tylenchoid spicules and subterminal bursa. The new genus is morphologically compared with four genera: Abursanema, Deladenus, Prothallonema and Sphaerularia. Molecular phylogenetic studies of the new genus using 808 bp partial sequences of SSU ribosomal RNA gene placed the new genus in a clade with Sphaerularia spp. In phylogenetic analyses using 756 bp partial sequences of the 28S ribosomal RNA gene (D2-D3 segments), the new genus formed a monophyletic group with Abursanema iranicum and Sphaerularia spp.

  11. Phylogeny of Thiobacillus cuprinus and other mixotrophic thiobacilli: proposal for Thiomonas gen. nov.

    PubMed

    Moreira, D; Amils, R

    1997-04-01

    The complete 5S and 16S ribosomal DNA (rDNA) sequences of the facultatively chemolithotrophic bacterium Thiobacillus cuprinus and results of a comparison of these sequences with homologous sequences from several proteobacterial species supported affiliation of T. cuprinus with the beta 1 subgroup of the Proteobacteria. T. cuprinus, Thiobacillus intermedius, Thiobacillus perometabolis, and Thiobacillus thermosulfatus form a phylogenetic cluster that comprises some of the thiobacilli capable of mixotrophic growth. This cluster is related to some pseudomonads and Alcaligenes species belonging to the beta subclass. In addition, a low-frequency restriction fragment analysis (LFRFA) of some mixotrophic thiobacilli and some related species was carried out by using pulsed-field gel electrophoresis (PFGE) to determine the SpeI and XbaI macrorestriction patterns and genome sizes of these organisms. The correlation of the LFRFA results and the 16S rDNA analysis results and the usefulness of the two analyses are discussed. The PFGE fingerprints suggested that Thiobacillus sp. strain ATCC 27793 is related to T. intermedius rather than to T. perometabolis, as described previously. The distinctive characteristics of the mixotrophic species analyzed in this work, their phylogenetic relatedness, and their physiological differences from other groups belonging to the Proteobacteria, including other thiobacilli, suggest that these organisms should be transferred to a new genus, the genus Thiomonas gen. nov.

  12. Aquisphaera giovannonii gen. nov., sp. nov., a planctomycete isolated from a freshwater aquarium.

    PubMed

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

    2011-12-01

    As part of a study of the diversity of planctomycetes, two novel strains, designated OJF2(T) and OJF8, were isolated from the sediments of a freshwater aquarium. The organisms were chemoheterotrophic, spherical and pink-pigmented, had an optimum growth temperature of about 30-35 °C and an optimum pH for growth of around 7.5-8.5. The predominant fatty acids were C(18:1)ω9c and C(16:0). The two strains were able to assimilate several sugars and organic acids. 16S rRNA gene sequence analysis confirmed the affiliation of these organisms to the phylum 'Planctomycetes'; they showed highest similarity to the type strains of Singulisphaera acidiphila (92.4%) and Isosphaera pallida (91.9%). On the basis of physiological, biochemical and chemotaxonomic characteristics, strains OJF2(T) and OJF8 are considered to represent a novel species of a new genus of the order Planctomycetales, for which the name Aquisphaera giovannonii gen. nov., sp. nov. is proposed. The type strain of Aquisphaera giovannonii is OJF2(T) (=CECT 7510(T) =DSM 22561(T)).

  13. Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water.

    PubMed

    Fernandes, Chantal; Rainey, Fred A; Nobre, M Fernanda; Pinhal, Isabel; Folhas, Fátima; da Costa, Milton S

    2005-09-01

    Several yellowish-pigmented bacteria with an optimum growth temperature of about 30 degrees C, were recovered from the source (borehole) of bottled mineral water in the Serra da Estrela in Eastern Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strains S-94T , S-97, S-99 and S-92 indicated that these organisms represent a new species of the Betaproteobacteria that is not closely related to any other known species. The major fatty acids of the strains are 16:1 omega7c and 16:0. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. The new strains only assimilated organic acids, glycine and alanine. Casamino acids and a mixture of all natural amino acids are not used as sole carbon and nitrogen sources; these are used as nitrogen source in the presence of organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we are of the opinion that strains S-94T, S-97, S-99 and S-92 represent a new species of a novel genus for which we propose the name Herminiimonas fonticola gen. nov., sp. nov.

  14. Nicola gen. nov. with redescription of Nicola tetela (Borojevic & Peixinho, 1976) (Porifera: Calcarea: Calcinea: Clathrinida).

    PubMed

    Cóndor-Luján, B; Klautau, M

    2016-04-13

    Guancha tetela was originally described as a species having a peduncle and a skeleton exclusively composed of sagittal triactines. Therefore, according to the most recent phylogeny of Clathrinida, it should be placed in the genus Clathrina. This species was collected on the Northeastern Brazilian coast in 1968 and it was not collected again until 2011 in Curaçao. In this study, we reanalyzed the type material and the new specimens from Curaçao under a morphological-molecular approach. Morphological analysis revealed the presence of tetractines in the skeleton of all the studied specimens, including a slide of the holotype. In the molecular phylogeny G. tetela grouped with genera containing tetractines, but as an independent new lineage, different from all the other genera of Clathrinida. Based on these results, we propose the erection of a new genus, Nicola gen. nov., to include species whose body is composed of tubes without anastomosis nor branches but that run in parallel and coalesce at the apical and basal regions. Moreover, the skeleton is exclusively composed of sagittal triactines and tetractines.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  16. Diddensiella caesifluorescens gen. nov., sp. nov., a riboflavin-producing yeast species of the family Trichomonascaceae.

    PubMed

    Péter, Gábor; Dlauchy, Dénes; Price, Neil P J; Kurtzman, Cletus P

    2012-12-01

    Four strains of a novel heterothallic yeast species were isolated from rotten wood collected in or near the Pilis Mountains in Hungary. The strains produced riboflavin in liquid culture. Analysis of gene sequences for the D1/D2 domains of the LSU nuclear rRNA, as well as analysis of concatenated gene sequences for the D1/D2 nuclear LSU rRNA, mitochondrial SSU rRNA and cytochrome oxidase II placed the novel species in a small clade including only two recognized species, Candida santjacobensis and Candida transvaalensis, in the family Trichomonascaceae. DNA sequence analyses demonstrated that the novel species was distinct from all currently recognized teleomorphic yeast genera. The name Diddensiella caesifluorescens gen nov., sp. nov. is proposed to accommodate the novel genus and species. The new genus proposed here can be recognized only from gene sequence analysis, because the characters of its asexual reproduction and ascospore formation are shared by several members of the genera Trichomonascus, Sugiyamaella and Spencermartinsiella. The type and isotype strains of D. caesifluorescens are NCAIM Y.01949(T) ( = NRRL Y-48781(T) = CBS 12613(T)) and NCAIM Y.01956(I) ( = NRRL Y-48782(I) = CBS 12614(I)), respectively. In view of their close relatedness to D. caesifluorescens, C. santjacobensis and C. transvaalensis are transferred to the genus Diddensiella as new combinations in accordance with changes in the International Code of Nomenclature for algae, fungi and plants. PMID:22843712

  17. Thermogladius shockii gen. nov., sp. nov., a hyperthermophilic crenarchaeote from Yellowstone National Park, USA.

    PubMed

    Osburn, Magdalena R; Amend, Jan P

    2011-01-01

    A hyperthermophilic heterotrophic archaeon (strain WB1) was isolated from a thermal pool in the Washburn hot spring group of Yellowstone National Park, USA. WB1 is a coccus, 0.6-1.2 μm in diameter, with a tetragonal S-layer, vacuoles, and occasional stalk-like protrusions. Growth is optimal at 84°C (range 64-93°C), pH 5-6 (range 3.5-8.5), and <1 g/l NaCl (range 0-4.6 g/l NaCl). Tests of metabolic properties show the isolate to be a strict anaerobe that ferments complex organic substrates. Phylogenetic analysis of the 16S rRNA gene sequence places WB1 in a clade of previously uncultured Desulfurococcaceae and shows it to have ≤ 96% 16S rRNA sequence identity to Desulfurococcus mobilis, Staphylothermus marinus, Staphylothermus hellenicus, and Sulfophobococcus zilligii. The 16S rRNA gene contains a large insertion similar to homing endonuclease introns reported in Thermoproteus and Pyrobaculum species. Growth is unaffected by the presence of S(0) or SO(4)(2-), thereby differentiating the isolate from its closest relatives. Based on phylogenetic and physiological differences, it is proposed that isolate WB1 represents the type strain of a novel genus and species within the Desulfurococcaceae, Thermogladius shockii gen. nov., sp. nov. (RIKEN = JCM-16579, ATCC = BAA-1607, Genbank 16S rRNA gene = EU183120).

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

    PubMed

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

    2014-08-01

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

  19. Sapocribrum chincoteaguense n. gen. n. sp.: A Small, Scale-bearing Amoebozoan with Flabellinid Affinities.

    PubMed

    Lahr, Daniel J G; Grant, Jessica; Molestina, Robert; Katz, Laura A; Anderson, O Roger

    2015-01-01

    The isolate American Type Culture Collection (ATCC)® 50979™ is a small amoebozoan whose actin gene was previously characterized, but did not allow a stable phylogenetic placement. This isolate was originally mis-identified upon deposition, and subsequently mis-illustrated in a recent publication. Here, we provide both a detailed morphological description as well as additional molecular analyses in order to clarify the isolate's phylogenetic relationships. The amoeba is minute (less than 5 μm), and presents the behavior of staying in a fixed location, while emitting one or two thin pseudopods. Transmission electron microscopy reveals that the cell is covered in a layer with embedded scales, giving the cell an armored appearance. Molecular phylogenetic analyses of data (actin, alpha- and beta-tubulin, elongation factor 2, and 14-3-3) from transcriptomes of this and four other isolates reveals that ATCC® 50979(™) is closely related to the recently described Squamamoeba japonica and in a novel, stable clade. Due to the unique nature of the scale covering, as well as other gross morphological characters and the molecular phylogenetic analyses, we formally describe the isolate as Sapocribrum chincoteaguense n. gen. n. sp.

  20. Constrictibacter antarcticus gen. nov., sp. nov., a cryptoendolithic micro-organism from Antarctic white rock.

    PubMed

    Yamada, Kozo; Fukuda, Wakao; Kondo, Yuka; Miyoshi, Yuki; Atomi, Haruyuki; Imanaka, Tadayuki

    2011-08-01

    A Gram-negative, non-spore-forming, ovoid to rod-shaped aerobic or microaerobic bacterium, strain 262-8(T), was isolated from a cavity within white rock collected in Antarctica. Strain 262-8(T) grew at 5-30 °C (optimum 25 °C), at pH 6-8 (optimum approximately pH 7) and with 0.1-2.0 % (w/v) NaCl (optimum 0.5 % NaCl). The addition of tryptone or yeast extract was essential for growth. Strain 262-8(T) was able to utilize organic compounds such as ribose, pyruvate and succinate in the presence of a low concentration of tryptone. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C(18 : 1), C(16 : 0) and C(18 : 0). The G+C content of the genomic DNA was 69.8 mol%. Comparative analyses of 16S rRNA gene sequences and physiological characteristics indicated that strain 262-8(T) was a phylogenetically novel bacterium that should be classified in a new genus of the family Rhodospirillaceae, for which the name Constrictibacter antarcticus gen. nov., sp. nov. is proposed. The type strain of the type species is 262-8(T) ( = JCM 16422(T) = ATCC BAA-1906(T)).

  1. Zhizhongheella caldifontis gen. nov., sp. nov., a novel member of the family Comamonadaceae.

    PubMed

    Dong, Lei; Ming, Hong; Liu, Lan; Zhou, En-Min; Yin, Yi-Rui; Duan, Yan-Yan; Nie, Guo-Xing; Feng, Hui-Geng; Li, Wen-Jun

    2014-04-01

    An alkalitolerant, thermotolerant, strictly aerobic and Gram-staining negative bacterial strain, designated YIM 78140(T), was isolated from a water sample in Hehua hot spring, Tengchong, Yunnan province, south-west China. The colonies were light brown, convex and circular. Phylogenetic analysis of the 16S rRNA gene sequence of strain YIM 78140(T) indicated that it was clustered with members of β-Proteobacteria (with the similarity from 96.9 to 93.6 %). Good growth occurred at 40-50 °C, pH 8.0-9.0 and in the presence of 0-3 % (w/v) NaCl. The predominant ubiquinones were Q-8 and Q-9. The major fatty acids were C16:0, C17:0 cyclo, C18:1 ω7c and summed feature 3. The G+C content of genomic DNA was 70.8 mol%. The results of physiological and biochemical characteristics, phylogenetic analysis allowed the phenotypic and genotypic differentiation of strain YIM 78140(T) from its closest phylogenetic neighbours. Therefore, the strain YIM 78140(T) represents a novel genus of the family Comamonadaceae, for which the name Zhizhongheella caldifontis gen. nov., sp. nov. is proposed. The type strain is YIM 78140(T) (= BCRC 80649(T) = KCTC 32557(T)).

  2. Acidomelania panicicola gen. et sp. nov. from switchgrass roots in acidic New Jersey pine barrens.

    PubMed

    Walsh, Emily; Luo, Jing; Zhang, Ning

    2014-01-01

    A new genus, Acidomelania, is described based on molecular phylogenetic analyses and ecological and morphological characters. Isolated from switchgrass roots in acidic and oligotrophic New Jersey pine barrens in this study, Acidomelania likely has a global distribution because its internal transcribed spacer (ITS) sequence has high similarity with a number of GenBank sequences resulted from various ecological studies. Apparently these samples all were from roots of plants that lived in acidic, nutrient-poor environments. Phylogenetic analyses based on ITS, LSU and ACT sequence data strongly supported the fact that Acidomelania isolates formed a monophyletic clade in Helotiales, distinct from any known taxa. Phylogenetically Acidomelania is closely related to Loramyces, Mollisia and Phialocephala fortinii, Acephala applanata species complex (PAC), the dark septate endophytes. Acidomelania also can be distinguished from Loramyces and Mollisia by its association with living grass roots. While taxa in PAC also are root endophytes, they have more complex phialid arrangement than Acidomelania. Results from this work will facilitate ecological and evolutionary studies on root-associated fungi.

  3. Nicola gen. nov. with redescription of Nicola tetela (Borojevic & Peixinho, 1976) (Porifera: Calcarea: Calcinea: Clathrinida).

    PubMed

    Cóndor-Luján, B; Klautau, M

    2016-01-01

    Guancha tetela was originally described as a species having a peduncle and a skeleton exclusively composed of sagittal triactines. Therefore, according to the most recent phylogeny of Clathrinida, it should be placed in the genus Clathrina. This species was collected on the Northeastern Brazilian coast in 1968 and it was not collected again until 2011 in Curaçao. In this study, we reanalyzed the type material and the new specimens from Curaçao under a morphological-molecular approach. Morphological analysis revealed the presence of tetractines in the skeleton of all the studied specimens, including a slide of the holotype. In the molecular phylogeny G. tetela grouped with genera containing tetractines, but as an independent new lineage, different from all the other genera of Clathrinida. Based on these results, we propose the erection of a new genus, Nicola gen. nov., to include species whose body is composed of tubes without anastomosis nor branches but that run in parallel and coalesce at the apical and basal regions. Moreover, the skeleton is exclusively composed of sagittal triactines and tetractines. PMID:27394730

  4. Hypnocyclicus thermotrophus gen. nov., sp. nov. isolated from a microbial mat in a hydrothermal vent field.

    PubMed

    Roalkvam, Irene; Bredy, Florian; Baumberger, Tamara; Pedersen, Rolf-B; Steen, Ida Helene

    2015-12-01

    The bacterial strain, IR-2T, was isolated from a microbial mat sampled near a hydrothermal vent in the Greenland Sea. Phylogenetic analysis, based on the 16S rRNA gene, showed that the closest relatives of IR-2T were Ilyobacter tartaricus, Ilyobacter insuetus, Propionigenium modestum and Fusobacterium varium (91 % 16S rRNA gene sequence similarity). The cells of the novel strain were Gram-stain-negative and pleomorphic; changing from long motile rods to non-motile ring structures during the growth cycle. Growth occurred at 20-55 °C (optimally at 48 °C), with 1-6 % (w/v) NaCl (optimally with 2 %), and at pH 5.3-8.0 (optimally at pH 6.0-8.0). The strain had obligate fermentative growth on various sugars and yeast extract. The DNA G+C content of strain IR-2T was 25.7 mol%. The cell sugars comprised mainly ribose, mannose and glucose, while the main polar lipids were glycolipids, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. The fatty acid content of strain IR-2 was dominated by saturated and unsaturated iso-branched or anteiso-branched forms. Strain IR-2 represents a novel genus and species, for which the name Hypnocyclicus thermotrophus gen. nov., sp. nov. is proposed. The type strain is IR-2T ( = DSM 100055 = JCM 30901). PMID:26373292

  5. Maeridae from the Indo-Pacific: Elasmopus, Leeuwinella gen. nov., Maeropsis, Pseudelasmopus and Quadrimaera (Amphipoda: Crustacea).

    PubMed

    Hughes, Lauren E

    2015-01-01

    Twenty-two species of Maeridae including the new genus, Leeuwinella, and eight new species are described from Indo-Pacific waters. Leeuwinella mistakensis gen. et sp. nov. from southern Western Australia has dorsal carinae and serrate epimeral margins on pleonites 1-3 and mandibular palp article 3 concave; this significant combination of characters justifies erection of a new genus. Elasmopus coxacallus sp. nov., with a castelloserrate posterior margin of pereopod 7 presents a novel character for the genus, which contains over 100 described species. Elasmopus incomptus sp. nov. and E. norfolkensis sp. nov. are also described from Norfolk Island, South Pacific, while new distribution records are provided for E. gracilis Schellenberg, 1938, E. integer Myers, 1989, and E. molokai J.L. Barnard, 1970 from northwestern Australia, and E. souillacensis Appadoo & Myers, 2003, from the Kermadec Islands. New distribution records for Maeropsis griffini (Berents, 1983) from Bedout Island in Western Australia are the first of the species outside the Queensland type locality and new records of M. thetis (Lowry & Springthorpe, 2005) from mainland Australia to Tasmania and across the Tasman Sea extending its range. Pseudelasmopus walkerae sp. nov. is described from Norfolk Island, and is the second species recorded in the genus, previously known only from Mauritius. Lastly, three new Quadrimaera species, Q. gregoryi, Q. brownorum and Q. vallaris, along with eight known Quadrimaera species, are reported from various locations extending their distributions in the Indo-Pacific. PMID:26701562

  6. Sergey gen. n., a new doryctine genus from temperate forests of Mexico and Cuba (Hymenoptera, Braconidae).

    PubMed

    Martínez, Juan José; Lázaro, Rubi Nelsi Meza; Pedraza-Lara, Carlos; Zaldívar-Riverón, Alejandro

    2016-01-01

    The new doryctine genus Sergey gen. n. is described with four new species (Sergey cubaensis Zaldívar-Riverón & Martínez, sp. n., Sergey coahuilensis Zaldívar-Riverón & Martínez, sp. n., Sergey tzeltal Martínez & Zalídivar-Riverón, sp. n., Sergey tzotzil Martínez & Zalídivar-Riverón, sp. n.) from temperate forests of Mexico and Cuba. Similar to many other doryctine taxa, the new genus has a considerably elongated, petiolate basal sternal plate of the first metasomal tergite, although it can be distinguished from these by having the mesoscutum sharply declivous anteriorly with sharp anterolateral edges. The described species have been characterised molecularly based on two mitochondrial (COI, cyt b) and one nuclear (28S) gene markers. Based on the mitochondrial gene genealogies reconstructed, the evidence suggests the existence of incomplete lineage sorting or hybridization in the populations from Chiapas and Oaxaca assigned to Sergey tzeltal sp. n.

  7. The hemimastigophora (Hemimastix amphikineta nov. gen., nov. spec.), a new protistan phylum from gondwanian soils.

    PubMed

    Foissner, W; Blatterer, H; Foissner, I

    1988-10-01

    The morphology, morphogenesis and ultrastructure of Hemimastix amphikineta nov. gen., nov. spec, are described. This species occurred in some Australian and in 1 Chilean soil, but was absent from more than 1000 soil samples from Laurasian localities. Thus, it has probably a restricted Gondwanian distribution. Hemimastix amphikineta is a small (14-20 × 7-10 μn), colourless organism that looks distinctly Ciliophora-like because of its posteriorly located contractile vacuole and its 2 longitudinal somatic kineties each composed of about 12 cilia-like flagella. These 2 kineties are interposed between 2 large plicated and microtubule-bearing pellicular plates which are arranged inversely mirror-image like ("diagonal symmetry"). Hemimastix amphikineta has saccular to tubular mitochondrial cristae and complex extrusomes. It has 2 microtubular systems and a membranous sac associated with each kinetid. The nucleolus persists throughout nuclear division. A permanent cytostome-cytopharyngeal complex, pharyngeal rods, striated fibres, mastigonemes, and a paraflagellar rod are absent. This unique combination of characters dictates a very separate position for H. amphikineta within the known protists. Thus, the phylum Hemimastigophora nov. phylum (Hemimastigea nov. cl. and Hemimastigida nov. ord.), is established to include H. amphikineta and possibly Spironema multiciliatum Klebs, 1892. The structure of the pellicle and the nuclear apparatus of H. amphikineta indicate some relationship with the Euglenophyta. However, clear evidence for a certain affinity is lacking. Thus, the Hemimastigophora are placed in an incertae sedis position within the kingdom Protista Haeckel, 1866.

  8. Katatopygia gen. n., a monophyletic branch segregated from Boletina (Diptera, Mycetophilidae)

    PubMed Central

    Martinsson, Svante; Kjærandsen, Jostein

    2012-01-01

    Abstract The genus Katatopygia gen. n. is proposed for the Boletina erythropyga/punctus-group that was first introduced by Garrett (1924, 1925) and currently comprises eight described species. Molecular studies have strongly indicated that this group forms a monophyletic sister-group to a clade consisting of all other Boletina, Coelosia and Gnoriste, and its monophyly is supported by morphological data as well. The new genus includes the following species: Katatopygia antoma (Garrett, 1924), comb. n., Katatopygia antica (Garrett, 1924), comb. n., Katatopygia erythropyga (Holmgren, 1883), comb. n.,Katatopygia hissarica (Zaitzev & Polevoi, 2002), comb. n., Katatopygia magna (Garrett, 1925), comb. n., Katatopygia laticauda (Saigusa, 1968), comb. n., Katatopygia neoerythropyga (Zaitzev & Polevoi, 2002), comb. n. andKatatopygia sahlbergi (Lundström, 1906), comb. n., all transferred from Boletina. Katatopygia sahlbergi is found to be a senior synonym of Boletina punctus Garrett, 1925, syn. n. A phylogeny based on morphological data and using parsimony analysis yielded four most parsimonious trees where the new genus is retrieved as monophyletic with high support. Katatopygia neoerythropyga is found to be the sister-taxon to all other species that form two clades, one with Katatopygia sahlbergi-like species and one with Katatopygia erythropyga-like species. A key to males of Katatopygia is provided. PMID:22451790

  9. A new tardigrade, Mutaparadoxipus duodigifinis gen. nov., sp. nov. (Heterotardigrada: Arthrotardigrada), from the Southeastern United States.

    PubMed

    Gross, Vladimir; Miller, William R; Hochberg, Rick

    2014-01-01

    A new genus and species of Arthrotardigrada is described from Florida, USA based on its unique adhesive pad/claw combinations. Mutaparadoxipus duodigifinis gen. nov., sp. nov., is characterized by well-developed, ventral secondary clavae that are adjacent to the mouth, pointed lateral and caudal alae, seminal receptacles with coiled ducts opening lateral to the gonopore, and all legs with digits bearing proximal adhesive pads. Distal claws are present on digits I-III of legs I-III, but are missing from digit IV. On leg IV, distal claws are present only on digits II & III. A single accessory point is present on claws II & III only. This is the fourth species discovered to date with proximal adhesive pads, increasing support for a clade of adhesive-padded arthrotardigrades, and is likely the sister taxon of Paradoxipus orzeliscoides. The incomplete set of claws may represent an evolutionary step in a progressive loss of claws hypothesized to have occurred within the Halechiniscidae. The subfamily Orzeliscinae is amended as a result. PMID:25081448

  10. Maeridae from the Indo-Pacific: Elasmopus, Leeuwinella gen. nov., Maeropsis, Pseudelasmopus and Quadrimaera (Amphipoda: Crustacea).

    PubMed

    Hughes, Lauren E

    2015-12-22

    Twenty-two species of Maeridae including the new genus, Leeuwinella, and eight new species are described from Indo-Pacific waters. Leeuwinella mistakensis gen. et sp. nov. from southern Western Australia has dorsal carinae and serrate epimeral margins on pleonites 1-3 and mandibular palp article 3 concave; this significant combination of characters justifies erection of a new genus. Elasmopus coxacallus sp. nov., with a castelloserrate posterior margin of pereopod 7 presents a novel character for the genus, which contains over 100 described species. Elasmopus incomptus sp. nov. and E. norfolkensis sp. nov. are also described from Norfolk Island, South Pacific, while new distribution records are provided for E. gracilis Schellenberg, 1938, E. integer Myers, 1989, and E. molokai J.L. Barnard, 1970 from northwestern Australia, and E. souillacensis Appadoo & Myers, 2003, from the Kermadec Islands. New distribution records for Maeropsis griffini (Berents, 1983) from Bedout Island in Western Australia are the first of the species outside the Queensland type locality and new records of M. thetis (Lowry & Springthorpe, 2005) from mainland Australia to Tasmania and across the Tasman Sea extending its range. Pseudelasmopus walkerae sp. nov. is described from Norfolk Island, and is the second species recorded in the genus, previously known only from Mauritius. Lastly, three new Quadrimaera species, Q. gregoryi, Q. brownorum and Q. vallaris, along with eight known Quadrimaera species, are reported from various locations extending their distributions in the Indo-Pacific.

  11. Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses.

    PubMed

    da Silva Malone, Camila Francieli; Rigonato, Janaína; Laughinghouse, Haywood Dail; Schmidt, Éder Carlos; Bouzon, Zenilda Laurita; Wilmotte, Annick; Fiore, Marli Fátima; Sant'Anna, Célia Leite

    2015-09-01

    For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus analyses). Using a multifaceted approach, we propose a new, well-defined genus, Cephalothrix gen. nov., by analysing seven filamentous strains that are morphologically 'intermediate' between gas-vacuolated taxa and Phormidium. Furthermore, we characterize two novel species: Cephalothrix komarekiana sp. nov. (strains CCIBt 3277, CCIBt 3279, CCIBt 3523, CCALA 155, SAG 75.79 and UTEX 1580) and Cephalothrix lacustris sp. nov. (strain CCIBt 3261). The generic name and specific epithets are proposed under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants.

  12. Sergey gen. n., a new doryctine genus from temperate forests of Mexico and Cuba (Hymenoptera, Braconidae)

    PubMed Central

    Martínez, Juan José; Lázaro, Rubi Nelsi Meza; Pedraza-Lara, Carlos; Zaldívar-Riverón, Alejandro

    2016-01-01

    Abstract The new doryctine genus Sergey gen. n. is described with four new species (Sergey cubaensis Zaldívar-Riverón & Martínez, sp. n., Sergey coahuilensis Zaldívar-Riverón & Martínez, sp. n., Sergey tzeltal Martínez & Zalídivar-Riverón, sp. n., Sergey tzotzil Martínez & Zalídivar-Riverón, sp. n.) from temperate forests of Mexico and Cuba. Similar to many other doryctine taxa, the new genus has a considerably elongated, petiolate basal sternal plate of the first metasomal tergite, although it can be distinguished from these by having the mesoscutum sharply declivous anteriorly with sharp anterolateral edges. The described species have been characterised molecularly based on two mitochondrial (COI, cyt b) and one nuclear (28S) gene markers. Based on the mitochondrial gene genealogies reconstructed, the evidence suggests the existence of incomplete lineage sorting or hybridization in the populations from Chiapas and Oaxaca assigned to Sergey tzeltal sp. n. PMID:27408539

  13. Auraticoccus monumenti gen. nov., sp. nov., an actinomycete isolated from a deteriorated sandstone monument.

    PubMed

    Alonso-Vega, Pablo; Carro, Lorena; Martínez-Molina, Eustoquio; Trujillo, Martha E

    2011-05-01

    A Gram-type-positive, strictly aerobic actinobacterium, designated strain MON 2.2(T), was isolated from the surface of a sandstone monument. Cells with a coccoid shape, arranged in pairs or clusters, were non-motile and did not produce spores. The 10 closest 16S rRNA gene sequence matches (~95 % similarity) found in the public databases were uncultured actinobacteria, while the closest cultured members indicated a phylogenetic relationship with members of the family Propionibacteriaceae (92-95 % similarity). Subsequent phylogenetic analysis placed the new isolate within the radiation of the genera Friedmanniella and Microlunatus, but forming an independent branch. Chemotaxonomic markers were consistent with the classification of strain MON 2.2(T) in the family Propionibacteriaceae, amongst the genera containing ll-diaminopimelic acid in their peptidoglycan. Characteristic fatty acids iso-C(15 : 0) and anteiso-C(15 : 0) also supported its affiliation to this taxon; however, polar lipid and menaquinone compositions clearly differentiated strain MON 2.2(T) from other genera in the family. On the basis of these results and additional physiological data obtained in the present study, it is proposed that strain MON 2.2(T) be classified in a novel species in a new genus, for which the name Auraticoccus monumenti gen. nov., sp. nov. is proposed. The type strain of Auraticoccus monumenti is MON 2.2(T) ( = CECT 7672(T)  = DSM 23257(T)  = LMG 25551(T)).

  14. Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium.

    PubMed

    Inoue, Kentaro; Itoh, Takashi; Ohkuma, Moriya; Kogure, Kazuhiro

    2011-04-01

    A novel halophilic archaeon, strain KeC-11(T), was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0-8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11(T) were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis Gabara(T) (91 % sequence similarity). The strain contained C(20)C(20) and C(20)C(25) diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data support the placement of isolate KeC-11(T) in a novel species in a new genus within the family Halobacteriaceae, for which the name Halomarina oriensis gen. nov., sp. nov. is proposed; the type strain is KeC-11(T) ( = JCM 16495(T)  = KCTC 4074(T)).

  15. Sapocribrum chincoteaguense n. gen. n. sp.: A Small, Scale-bearing Amoebozoan with Flabellinid Affinities.

    PubMed

    Lahr, Daniel J G; Grant, Jessica; Molestina, Robert; Katz, Laura A; Anderson, O Roger

    2015-01-01

    The isolate American Type Culture Collection (ATCC)® 50979™ is a small amoebozoan whose actin gene was previously characterized, but did not allow a stable phylogenetic placement. This isolate was originally mis-identified upon deposition, and subsequently mis-illustrated in a recent publication. Here, we provide both a detailed morphological description as well as additional molecular analyses in order to clarify the isolate's phylogenetic relationships. The amoeba is minute (less than 5 μm), and presents the behavior of staying in a fixed location, while emitting one or two thin pseudopods. Transmission electron microscopy reveals that the cell is covered in a layer with embedded scales, giving the cell an armored appearance. Molecular phylogenetic analyses of data (actin, alpha- and beta-tubulin, elongation factor 2, and 14-3-3) from transcriptomes of this and four other isolates reveals that ATCC® 50979(™) is closely related to the recently described Squamamoeba japonica and in a novel, stable clade. Due to the unique nature of the scale covering, as well as other gross morphological characters and the molecular phylogenetic analyses, we formally describe the isolate as Sapocribrum chincoteaguense n. gen. n. sp. PMID:25515047

  16. A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China.

    PubMed

    Reisz, Robert R; Liu, Jun; Li, Jin-Ling; Müller, Johannes

    2011-05-01

    Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent.

  17. Gynuella sunshinyii gen. nov., sp. nov., an antifungal rhizobacterium isolated from a halophyte, Carex scabrifolia Steud.

    PubMed

    Chung, Eu Jin; Park, Jeong Ae; Jeon, Che Ok; Chung, Young Ryun

    2015-03-01

    An antifungal bacterial strain, designated YC6258(T), was isolated from the rhizosphere of a halophyte (Carex scabrifolia Steud.) growing in a tidal flat area of Namhae Island, Korea. Cells of the strain were Gram-stain-negative, facultatively anaerobic, moderately halophilic, rod-shaped and motile by a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YC6258(T) formed a phyletic lineage distinct from members of the most closely related genera, Saccharospirillum and Reinekea, with less than 91.2 % sequence similarities. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and Summed feature 3 (C16 : 1ω7c/ C16 : 1ω6c). The quinone system of strain YC6258(T) consisted mainly of ubiquinone Q-8. The polar lipid profile exhibited phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unknown lipids. The DNA G+C content was 48.9 mol%. Based on the phylogenetic and phenotypic characteristics, strain YC6258(T) should be classified as a representative of a novel species in a novel genus for which the name Gynuella sunshinyii gen. nov., sp. nov. is proposed. The type strain is YC6258(T) (KCCM 43015(T) = NBRC 109345(T)).

  18. Melghiribacillus thermohalophilus gen. nov., sp. nov., a novel filamentous, endospore-forming, thermophilic and halophilic bacterium.

    PubMed

    Addou, Nariman Ammara; Schumann, Peter; Spröer, Cathrin; Ben Hania, Wajdi; Hacene, Hocine; Fauque, Guy; Cayol, Jean-Luc; Fardeau, Marie-Laure

    2015-04-01

    A novel filamentous, endospore-forming, thermophilic and moderately halophilic bacterium designated strain Nari2A(T) was isolated from soil collected from an Algerian salt lake, Chott Melghir. The novel isolate was Gram-staining-positive, aerobic, catalase-negative and oxidase-positive. Optimum growth occurred at 50-55 °C, 7-10% (w/v) NaCl and pH 7-8. The strain exhibited 95.4, 95.4 and 95.2% 16S rRNA gene sequence similarity to Thalassobacillus devorans G19.1(T), Sediminibacillus halophilus EN8d(T) and Virgibacillus kekensis YIM-kkny16(T), respectively. The major menaquinone was MK-7. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three unknown phosphoglycolipids and two unknown phospholipids. The predominant cellular fatty acids were iso-C(15 : 0) and iso-C(17 : 0). The DNA G+C content was 41.9 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain Nari2A(T) is considered to represent a novel species of a new genus in the family Bacillaceae , order Bacillales , for which the name Melghiribacillus thermohalophilus gen. nov., sp. nov. is proposed. The type strain of Melghiribacillus thermohalophilus is Nari2A(T) ( = DSM 25894(T) = CCUG 62543(T)). PMID:25604343

  19. Compostibacillus humi gen. nov., sp. nov., a member of the family Bacillaceae, isolated from sludge compost.

    PubMed

    Yu, Zhen; Wen, Junlin; Yang, Guiqin; Liu, Jing; Zhou, Shungui

    2015-02-01

    Two novel Gram-staining-positive, rod-shaped, endospore-forming and moderately thermophilic bacteria, designated strains DX-3(T) and GIESS002, were isolated from sludge composts from Guangdong Province, China. Analysis of 16S rRNA gene sequences revealed that the isolates were closely related to each other with extremely high similarity (99.6 %), and were members of the family Bacillaceae. However, these two isolates formed a novel phylogenetic branch within this family. Their closest relatives were the members of the genera Ornithinibacillus, Oceanobacillus and Virgibacillus. Cells of both strains were facultatively anaerobic and catalase- and oxidase-positive. The cell-wall peptidoglycan type was A1γ (meso-diaminopimelic acid direct). The predominant isoprenoid quinone was MK-7. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acid was iso-C15 : 0. The DNA G+C content was 43.2-43.7 mol%. The results of a polyphasic taxonomic study indicated that strains DX-3(T) and GIESS002 represent a novel species in a new genus in the family Bacillaceae, order Bacillales, for which the name Compostibacillus humi gen. nov., sp. nov. is proposed. The type strain is DX-3(T) ( = KCTC 33104(T) = CGMCC 1.12360(T)). PMID:25358510

  20. Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water.

    PubMed

    Poroshina, Maria N; Trotsenko, Yuri A; Doronina, Nina V

    2015-04-01

    An aerobic halotolerant restricted facultatively methylotrophic bacterium was isolated from a saline hot spring in Pamukkale, Turkey, and designated strain PK2(T). The cells of this strain were Gram-stain-negative, asporogenous, motile short rods multiplying by binary fission. They utilized methanol, methylamine and mannitol as carbon and energy sources. The organism grew optimally at 30 °C in media containing 85 mM NaCl and at pH 7.5-8.0. C1 compounds were assimilated via the isocitrate-lyase-positive variant of the serine pathway. Poly-β-hydroxybutyrate and the compatible solute ectoine were found in the cells. The dominant phospholipids were phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The major cellular fatty acids of methanol-grown cells were C(18 : 1)ω7 and C(16 : 1)ω7c. The main ubiquinone was Q-10. The DNA G+C content was 67.9 mol% (T(m)). The 16S rRNA gene sequence suggests that strain PK2(T) is affiliated with the order Rhizobiales within the class Alphaproteobacteria , being most closely related to Mesorhizobium gobiense CCBAU 83330(T) (94% similarity). A novel genus and species, Methylobrevis pamukkalensis gen. nov., sp. nov., is proposed on the basis of phenotypic and genotypic data, with PK2(T) (VKM B-2849(T) = JCM 30229(T)) as the type strain. PMID:25667389

  1. Haloglycomyces albus gen. nov., sp. nov., a halophilic, filamentous actinomycete of the family Glycomycetaceae.

    PubMed

    Guan, Tong-Wei; Tang, Shu-Kun; Wu, Jin-Yuan; Zhi, Xiao-Yang; Xu, Li-Hua; Zhang, Li-Li; Li, Wen-Jun

    2009-06-01

    A novel halophilic actinobacterium, designated YIM 92370(T), was isolated from a hypersaline habitat in Xinjiang Province, north-west China. The strain was aerobic, Gram-positive-staining and halophilic, with an optimum NaCl concentration for growth of 8-12 % (w/v). The whole-cell sugar pattern consisted of ribose, xylose and glucose. The predominant menaquinone was MK-9(H(4)) and the major fatty acids were iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0). The phospholipid pattern consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phosphoglycolipids and one unknown phospholipid. The G+C content of the genomic DNA was 60.8 mol%. Phylogenetic analysis showed that strain YIM 92370(T) can be distinguished from representatives of Glycomyces and Stackebrandtia, the two existing genera in the family Glycomycetaceae, by low 16S rRNA gene sequence similarities (<93.7 %). Strain YIM 92370(T) therefore represents a novel genus and species of the family Glycomycetaceae, for which the name Haloglycomyces albus gen. nov., sp. nov. is proposed. The type strain of Haloglycomyces albus is YIM 92370(T) (=DSM 45210(T) =KCTC 19481(T)). PMID:19502305

  2. Tubulideres seminoli gen. et sp. nov. and Zelinkaderes brightae sp. nov. (Kinorhyncha, Cyclorhagida) from Florida

    NASA Astrophysics Data System (ADS)

    Sørensen, Martin V.; Heiner, Iben; Ziemer, Ole; Neuhaus, Birger

    2007-12-01

    One new kinorhynch genus and species and one new species from the genus Zelinkaderes are described from sandy sediment off Fort Pierce, Florida. The new genus and species, Tubulideres seminoli gen. et sp. nov. is characterized by the presence of the first trunk segment consisting of a closed ring, the second segment of a bent tergal plate with a midventral articulation and the following nine segments consisting of a tergal and two sternal plates. Cuspidate spines are not present, but flexible tubules are located on several segments, and in particular concentrated on the ventral side of the second segment. Middorsal spines are present on all trunk segments and are alternatingly offset to a position slightly lateral to the middorsal line. Zelinkaderes brightae nov. sp. is characterized by its spine formula in having middorsal spines on trunk segments 4, 6 and 8-11, lateroventral acicular spines on segment 2, lateral accessory cuspidate spines on segments 2 and 8, ventrolateral cuspidate spines on segments 4-6 and 9, lateroventral acicular spines present on segments 8 and 9, and midterminal, lateral terminal and lateral terminal accessory spines on segment 11. The spine formula of Z. brightae nov. sp. places it in a position in between Z. submersus and a clade consisting of Z. klepali and Z. floridensis. The new findings on Z. brightae nov. sp. have led us to propose an emended diagnosis for the genus.

  3. Spongiispira norvegica gen. nov., sp. nov., a marine bacterium isolated from the boreal sponge Isops phlegraei.

    PubMed

    Kaesler, Ines; Graeber, Ingeborg; Borchert, Martin S; Pape, Thomas; Dieckmann, Ralf; von Döhren, Hans; Nielsen, Preben; Lurz, Rudi; Michaelis, Walter; Szewzyk, Ulrich

    2008-08-01

    The bacterial strain Gp_4_7.1T, isolated from the marine sponge Isops phlegraei collected at the Sula Ridge off the Norwegian coast, was characterized. The isolate was a motile spirillum that was monopolarly and monotrichously flagellated. It was aerobic, Gram-negative, oxidase-positive and catalase-negative. Optimal growth occurred between 20 and 30 degrees C, at pH 7-8 and with a salt concentration of 2-3 % (w/v). The isolate showed a relatively restricted nutritional profile. Substrate utilization tests were only positive for arabinose. Enzyme tests were positive for esterase lipase C8, lipase C14, leucine arylamidase and naphthol-AS-BI-phosphohydrolase. The strain was not able to reduce nitrate. The major cellular fatty acids were C16:1 omega7 and C16:0. The DNA G+C content was 62.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison classified the strain as a member of the order Oceanospirillales in the class Gammaproteobacteria. Strain Gp_4_7.1T formed a distinct phyletic line with less than 94 % 16S rRNA gene sequence similarity to its closest relatives with validly published names. Based on the determined data, it is proposed that the strain represents a novel species in a new genus, Spongiispira norvegica gen. nov., sp. nov.; the type strain of Spongiispira norvegica is Gp_4_7.1T (=DSM 17749T =NCIMB 14401T).

  4. Ornithinibacter aureus gen. nov., sp. nov., a novel member of the family Intrasporangiaceae.

    PubMed

    Xiao, Chuan; Huang, Huiqin; Ye, Jianjun; Wu, Xiaopeng; Zhu, Jun; Zhan, Baolin; Bao, Shixiang

    2011-03-01

    A novel strain of the class Actinobacteria was isolated from a seawater sample collected in the South China Sea using modified R2A agar plates. The strain was a Gram-stain-positive, nonmotile, non-spore-forming, catalase-positive, irregular rod-shaped bacterium. The strain grew at 4-45 °C and pH 5.0-10.2, and tolerated 5% (w/v) NaCl. Based on its 16S rRNA gene sequence, the organism was related phylogenetically to members of the genera Fodinibacter (96.7% similarity), Lapillicoccus (96.5 %), Knoellia (95.0-95.8 %), Oryzihumus (95.6 %) and Humibacillus (95.6 %). The cell-wall contained L-ornithine as the major diagnostic diamino acid in the peptidoglycan. MK-8(H₄) was the predominant menaquinone. Major cellular fatty acids were iso-C₁₈:₁ω9c, iso-C₁₆:₀, iso-C₁₅:₀ and C₁₇:₀. The G+C content of the DNA was 69.6 mol%. Phenotypic and phylogenetic data revealed that this strain represents a novel species in a new genus of the family Intrasporangiaceae, for which the name Ornithinibacter aureus gen. nov., sp. nov. is proposed; the type strain of Ornithinibacter aureus is HB09001(T) (=CGMCC 1.10341(T) =DSM 23364(T)).

  5. Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment.

    PubMed

    Kim, Wonduck; Lee, Jung-Hyun; Kwon, Kae Kyoung

    2016-05-01

    A Gram-staining-negative, thin rod-shaped, anaerobic bacterium designated MCWD3(T) was isolated from sediment of the deep sea in Ulleung Basin, East Sea, Korea. The ranges of temperature, pH and NaCl for growth of this strain were 15-40°C (optimum 29°C), 5.0-10.0 (optimum pH 6.5), and 1-5%, respectively. The major fatty acids were iso-C(15:0) (30%) and iso-C(15:0) dimethyl acetal (17%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipids, phospholipids, and aminolipids. The fermentation product from yeast extract was acetate. Phylogenetic analysis based on 16S rRNA genes indicated that the isolate was related to Sporosalibacterium faouarense (92.8% sequence identity), Clostridiisalibacter paucivorans (92.6%), and Brassicibacter mesophilus (92.4%). However, the isolate was differentiated from these genera by both physiological and chemotaxonomical properties. On the basis of a polyphasic taxonomic analysis, we propose that MCWD3(T) represents a novel taxon with the name Abyssisolibacter fermentans gen. nov. sp. nov. PMID:27095453

  6. Methods for Estimating Environmental Effects and Constraints on NexGen: High Density Case Study

    NASA Technical Reports Server (NTRS)

    Augustine, S.; Ermatinger, C.; Graham, M.; Thompson, T.

    2010-01-01

    This document provides a summary of the current methods developed by Metron Aviation for the estimate of environmental effects and constraints on the Next Generation Air Transportation System (NextGen). This body of work incorporates many of the key elements necessary to achieve such an estimate. Each section contains the background and motivation for the technical elements of the work, a description of the methods used, and possible next steps. The current methods described in this document were selected in an attempt to provide a good balance between accuracy and fairly rapid turn around times to best advance Joint Planning and Development Office (JPDO) System Modeling and Analysis Division (SMAD) objectives while also supporting the needs of the JPDO Environmental Working Group (EWG). In particular this document describes methods applied to support the High Density (HD) Case Study performed during the spring of 2008. A reference day (in 2006) is modeled to describe current system capabilities while the future demand is applied to multiple alternatives to analyze system performance. The major variables in the alternatives are operational/procedural capabilities for airport, terminal, and en route airspace along with projected improvements to airframe, engine and navigational equipment.

  7. Anaerosalibacter bizertensis gen. nov., sp. nov., a halotolerant bacterium isolated from sludge.

    PubMed

    Rezgui, Raja; Maaroufi, Abderrazak; Fardeau, Marie-Laure; Ben Ali Gam, Zouhaier; Cayol, Jean-Luc; Ben Hamed, Saïd; Labat, Marc

    2012-10-01

    A strictly anaerobic, halotolerant and thermotolerant strain, designated C5BEL(T), was isolated in north Tunisia from storage tanks holding waste generated by the recycling of discarded motor oils. Cells of strain C5BEL(T) were Gram-stain-positive, motile by laterally inserted flagella, straight, and spore-forming. Their two major fatty acids were iso-C(15 : 0) and iso-C(15 : 0) dimethyl acetal. Growth was observed at temperatures of 25-55 °C (optimum, 40 °C) and at pH 6-9 (optimum, pH 7.5). The salinity range for growth was 0-100 g l(-1) NaCl (optimum, 5 g l(-1)). Yeast extract was required for growth. Strain C5BEL(T) was heterotrophic, able to use glucose, pyruvate, succinate, yeast extract, bio-trypticase and peptone, but unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content of strain C5BEL(T) was 31.1 mol%. 16S rRNA gene sequence analysis indicated that strain C5BEL(T) was a member of the family Clostridiaceae, class Clostridia, phylum Firmicutes and was most closely related to Sporanaerobacter acetigenes Lup33(T) ( = DSM 13106(T)) (92.4 % similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain C5BEL(T) can be classified as a novel species in a new genus, for which the name Anaerosalibacter bizertensis gen. nov., sp. nov. is proposed. The type strain of the type species is C5BEL(T) ( = DSM 23801(T) = JCM 17239(T)).

  8. Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir.

    PubMed

    Grabowski, Agnès; Tindall, Brian J; Bardin, Véronique; Blanchet, Denis; Jeanthon, Christian

    2005-05-01

    A mesophilic, anaerobic, fermentative bacterium, strain BN3(T), was isolated from a producing well of a biodegraded oil reservoir in Canada. Cells were Gram-negative, non-motile rods that did not form spores. The temperature range for growth was 15-40 degrees C, with optimum growth at 37-40 degrees C. The strain grew with up 4 % NaCl, with optimum growth in the absence of NaCl. Tryptone was required for growth. Yeast extract and elemental sulfur stimulated growth. Growth was also enhanced during fermentation of glucose, arabinose, galactose, maltose, mannose, rhamnose, lactose, ribose, fructose, sucrose, cellobiose, lactate, mannitol and glycerol. Acetate, hydrogen and CO(2) were produced during glucose fermentation. Elemental sulfur and nitrate were used as electron acceptors and were reduced to sulfide and ammonium, respectively. The G + C content of the genomic DNA was 40.8 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was a member of the phylum 'Bacteroidetes', distantly related to the genera Bacteroides and Tannerella (similarity values of less than 90 %). The chemotaxonomic data (fatty acids, polar lipids and quinones composition) also indicated that strain BN3(T) could be clearly distinguished from its closest cultivated relatives. This novel organism possesses phenotypic, chemotaxonomic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, it is proposed that this isolate should be described as a member of a novel species of a new genus, Petrimonas gen. nov., of which Petrimonas sulfuriphila sp. nov. is the type species. The type strain is BN3(T) (= DSM 16547(T) = JCM 12565(T)). PMID:15879242

  9. Cryptanaerobacter phenolicus gen. nov., sp. nov., an anaerobe that transforms phenol into benzoate via 4-hydroxybenzoate.

    PubMed

    Juteau, Pierre; Côté, Valérie; Duckett, Marie-France; Beaudet, Réjean; Lépine, François; Villemur, Richard; Bisaillon, Jean-Guy

    2005-01-01

    An anaerobic bacterium that transforms phenol and 4-hydroxybenzoate (4-OHB) into benzoate, strain LR7.2T, was isolated from a culture originating from a mixture of swamp water, sewage sludge, swine waste and soil. Cells of strain LR7.2T are Gram-positive short rods (1 x 2 microm) that are electron-dense when observed by electron microscopy. The optimum pH and temperature for growth and transformation activity of 4-OHB are 7.5-8.0 and 30-37 degrees C, respectively. The bacterium does not use sulphate, thiosulphate, nitrate, nitrite, FeCl3, fumarate or arsenate as an electron acceptor. It does not normally use sulphite, although stimulation of growth and 4-OHB transformation activity at a low concentration (up to 2 mM) has been reported previously under different culture conditions. The presence of 4-OHB or phenol is essential for growth; transformation of 4-OHB or phenol into benzoate is used to produce energy for growth. Using [6D]-phenol, 4-OHB was shown to be an intermediate in the transformation of phenol into benzoate. No spore was observed. The bacterium has a DNA G+C content of 51 mol% and its major membrane fatty acid is anteiso-C(15 : 0). The 16S rRNA gene sequence of strain LR7.2T shows only 90 % similarity to its closest relative (Pelotomaculum thermopropionicum). From these results, a new taxon is proposed: Cryptanaerobacter phenolicus gen. nov., sp. nov. The type strain is LR7.2T (=ATCC BAA-820T=DSM 15808T). PMID:15653882

  10. Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen.

    PubMed

    Zhang, Kegui; Song, Lei; Dong, Xiuzhu

    2010-09-01

    Two strictly anaerobic, proteolytic bacterial strains, designated strain D3RC-2(T) and D3RC-3r, were isolated from a cellulose-degrading mixed culture enriched from yak rumen content. The strains were Gram-stain negative and non-spore-forming with cell sizes of 0.5-0.8 x 0.6-2.0 mum. The temperature range for growth was 24-46 degrees C (optimum 38-39 degrees C) and the pH range was between 5.6 and 8.7 (optimum 7.0-7.3). Both strains used soya peptone, tryptone, l-phenylalanine, l-leucine, l-methionine, l-serine, l-valine, l-threonine and l-histidine as carbon and nitrogen sources, but did not use any of the saccharides tested. The major fermentation products from PY medium were acetate, propionate and iso-butyrate. The DNA G+C contents of strains D3RC-2(T) and D3RC-3r were 41.0+/-0.1 mol% and 41.3+/-0.1 mol% (HPLC), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains represented a new phyletic sublineage within the family Clostridiaceae, with <93.8 % 16S rRNA gene sequence similarity to recognized species. On the basis of the phenotypic, genotypic and physiological evidence, strains D3RC-2(T) and D3RC-3r are proposed as representing a novel species of a new genus, for which the name Proteiniclasticum ruminis gen. nov., sp. nov. is proposed. The type strain of the type species is D3RC-2(T) (=AS 1.5057(T)=JCM 14817(T)).

  11. Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent.

    PubMed

    Felföldi, Tamás; Vengring, Anita; Kéki, Zsuzsa; Márialigeti, Károly; Schumann, Peter; Tóth, Erika M

    2014-06-01

    A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16 : 0), C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(14 : 0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) ( = DSM 25520(T) = NCAIM B 02512(T)).

  12. Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons.

    PubMed

    Yakimov, Michail M; Giuliano, Laura; Denaro, Renata; Crisafi, Ermanno; Chernikova, Tatiana N; Abraham, Wolf-Rainer; Luensdorf, Heinrich; Timmis, Kenneth N; Golyshin, Peter N

    2004-01-01

    An aerobic, heterotrophic, Gram-negative, curved bacterial strain, designated MIL-1T, was isolated by extinction dilution from an n-tetradecane enrichment culture that was established from sea water/sediment samples collected in the harbour of Milazzo, Italy. In the primary enrichment, the isolate formed creamy-white, medium-sized colonies on the surface of the agar. The isolate did not grow in the absence of NaCl; growth was optimal at 2.7% NaCl. Only a narrow spectrum of organic compounds, including aliphatic hydrocarbons (C7-C20), their oxidized derivatives and acetate, were used as growth substrates. The isolate was not able to grow under denitrifying conditions. The DNA G+C content and genome size of strain MIL-1T were estimated to be 53.2 mol% and 2.2 Mbp, respectively. The major cellular and phospholipid fatty acids were palmitoleic, palmitic and oleic acids (33.5, 29.5 and 11.0% and 18, 32 and 31%, respectively). 3-hydroxy lauric acid was the only hydroxy fatty acid detected. Thirteen different compounds that belonged to two types of phospholipid (phosphatidylethylamine and phosphatidylglycerol) were identified. 16S rRNA gene sequence analysis revealed that this isolate represents a distinct phyletic lineage within the gamma-Proteobacteria and has about 94.4% sequence similarity to Oceanobacter kriegii (the closest bacterial species with a validly published name). The deduced protein sequence of the putative alkane hydrolase, AlkB, of strain MIL-1T is related to the corresponding enzymes of Alcanivorax borkumensis and Pseudomonas oleovorans (81 and 80% similarity, respectively). On the basis of the analyses performed, Thalassolituus oleivorans gen. nov., sp. nov. is described. Strain MIL-1T (=DSM 14913T=LMG 21420T) is the type and only strain of T. oleivorans. PMID:14742471

  13. Allohumibacter endophyticus gen. nov., sp. nov., isolated from the root of wild Artemisia princeps (mugwort).

    PubMed

    Ri Kim, Yu; Kim, Tae-Su; Han, Ji-Hye; Joung, Yochan; Park, Jisun; Kim, Seung Bum

    2016-04-01

    A novel actinobacterium designated strain MWE-A11T was isolated from the root of wild Artemisia princeps (mugwort). The isolate was aerobic, Gram-stain-positive and short rod-shaped, and the colonies were yellow and circular with entire margin. Strain MWE-A11T grew at 15-37 °C and pH 6.0-8.0. The predominant isoprenoid quinones were MK-11 and MK-10. The predominant fatty acids were anteiso-C15:0 and iso-C16:0, and the DNA G+C content was 68.8 mol%. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The peptidoglycan contained 2,4-diaminobutyric acid as the diagnostic diamino acid, and the acyl type was glycolyl. Phylogenetic analyses based on 16S rRNA gene sequence comparisons indicated that strain MWE-A11T was affiliated with the family Microbacteriaceae, and was most closely related to the type strains of Humibacter antri (96.4% 16S rRNA gene sequence similarity), Herbiconiux moechotypicola (96.3%), Leifsonia soli (96.3%), Leifsonia lichenia (96.2%), Leifsonia xyli subsp. cynodontis (96.1%), Microbacterium testaceum (96.0%) and Humibacter albus (96.0%). However, the combination of chemotaxonomic properties clearly distinguished strain MWE-A11T from the related taxa at genus level. Accordingly, Allohumibacter endophyticus gen. nov., sp. nov. is proposed to accommodate a new member of the family Microbacteriaceae. The type strain of the type species is MWE-A11T (=JCM 19371T=KCTC 29232T). PMID:26842896

  14. Visual Advantage of Enhanced Flight Vision System During NextGen Flight Test Evaluation

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K.

    2014-01-01

    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. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

  15. Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture

    SciTech Connect

    Edelstein, P.H.

    1986-03-01

    A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with /sup 125/I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture.

  16. Pseudocollinia brintoni gen. nov., sp. nov. (Apostomatida: Colliniidae), a parasitoid ciliate infecting the euphausiid Nyctiphanes simplex.

    PubMed

    Gómez-Gutiérrez, J; Strüder-Kypke, M C; Lynn, D H; Shaw, T C; Aguilar-Méndez, M J; López-Cortés, A; Martínez-Gómez, S; Robinson, C J

    2012-05-15

    A novel parasitoid ciliate, Pseudocollinia brintoni gen. nov., sp. nov. was discovered infecting the subtropical sac-spawning euphausiid Nyctiphanes simplex off both coasts of the Baja California peninsula, Mexico. We used microscopic, and genetic information to describe this species throughout most of its life cycle. Pseudocollinia is distinguished from other Colliniidae genera because it exclusively infects euphausiids, has a polymorphic life cycle, and has a small cone-shaped oral cavity whose left wall has a field of ciliated kinetosomes and whose opening is surrounded on the left and right by 2 'oral' kineties (or ciliary rows) that terminate at its anterior border. Two related species that infect different euphausiid species from higher latitudes in the northeastern Pacific Ocean, Collinia beringensis Capriulo and Small, 1986, briefly redescribed herein, and Collinia oregonensis Gómez-Gutiérrez, Peterson, and Morado, 2006, are transferred to the genus Pseudocollinia. P. brintoni has between 12 and 18 somatic kineties, and its oral cavity has only 2 oral kineties, while P. beringensis comb. nov. has more somatic kineties, including 3 oral kineties. P. oregonensis comb. nov. has an intermediate number of somatic kineties. P. beringensis comb. nov. also infects Thysanoessa raschi (a new host species). SSU rRNA and cox1 gene sequences demonstrated that Pseudocollinia ciliates are apostome ciliates and that P. brintoni is different from P. beringensis comb. nov. High densities of rod-shaped bacteria (1.7 µm length, 0.2 to 0.5 µm diameter) were associated with P. brintoni. After euphausiid rupture, high concentrations of P. brintoni and bacteria cluster to form 3 to 6 cm long filaments where tomites encyst and transform to the phoront stage; this is a novel place for encystation. P. brintoni may complete its life cycle when the euphausiids feed on these filaments. PMID:22585303

  17. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

    PubMed

    Derrien, Muriel; Vaughan, Elaine E; Plugge, Caroline M; de Vos, Willem M

    2004-09-01

    The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T).

  18. Halotia gen. nov., a phylogenetically and physiologically coherent cyanobacterial genus isolated from marine coastal environments.

    PubMed

    Genuário, Diego Bonaldo; Vaz, Marcelo Gomes Marçal Vieira; Hentschke, Guilherme Scotta; Sant'Anna, Célia Leite; Fiore, Marli Fátima

    2015-02-01

    Nostoc is a common and well-studied genus of cyanobacteria and, according to molecular phylogeny, is a polyphyletic group. Therefore, revisions of this genus are urged in an attempt to clarify its taxonomy. Novel strains isolated from underexplored environments and assigned morphologically to the genus Nostoc are not genetically related to the 'true Nostoc' group. In this study, four strains isolated from biofilms collected in Antarctica and five strains originated from Brazilian mangroves were evaluated. Despite their morphological similarities to other morphotypes of Nostoc, these nine strains differed from other morphotypes in ecological, physiological and genetic aspects. Based on the phylogeny of the 16S rRNA gene, the Antarctic sequences were grouped together with the sequences of the Brazilian mangrove isolates and Nostoc sp. Mollenhauer 1 : 1-067 in a well-supported cluster (74 % bootstrap value, maximum-likelihood). This novel cluster was separated phylogenetically from the 'true Nostoc' clade and from the clades of the morphologically similar genera Mojavia and Desmonostoc. The 16S rRNA gene sequences generated in this study exhibited 96 % similarity to sequences from the nostocacean genera mentioned above. Physiologically, these nine strains showed the capacity to grow in a salinity range of 1-10 % NaCl, indicating their tolerance of saline conditions. These results provide support for the description of a new genus, named Halotia gen. nov., which is related morphologically to the genera Nostoc, Mojavia and Desmonostoc. Within this new genus, three novel species were recognized and described based on morphology and internal transcribed spacer secondary structures: Halotia branconii sp. nov., Halotia longispora sp. nov. and Halotia wernerae sp. nov., under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants.

  19. Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae.

    PubMed

    Zhou, En-Min; Yu, Tian-Tian; Liu, Lan; Ming, Hong; Yin, Yi-Rui; Dong, Lei; Tseng, Min; Nie, Guo-Xing; Li, Wen-Jun

    2014-09-01

    Strains YIM 77562(T) and YIM 77580, two novel Gram-staining-positive, filamentous bacterial isolates, were recovered from the Rehai geothermal field, Tengchong, Yunnan province, south-west China. Good growth was observed at 50-55 °C and pH 7.0. Aerial mycelium was absent on all media tested. Substrate mycelium was well-developed, long and moderately flexuous, and formed abundant, single, warty, ornamented endospores. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains indicated that they belong to the family Thermoactinomycetaceae. Similarity levels between the 16S rRNA gene sequences of the two strains and those of type strains of members of the Thermoactinomycetaceae were 88.33-93.24 %; the highest sequence similarity was with Hazenella coriacea DSM 45707(T). In both strains, the predominant menaquinone was MK-7, the diagnostic diamino acid was meso-diaminopimelic acid and the major cellular fatty acids were iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids and unidentified phospholipids. The genomic DNA G+C contents of strains YIM 77562(T) and YIM 77580 were 45.5 and 44.2 mol%, respectively. DNA-DNA relatedness data suggest that the two isolates represent a single species. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that the two strains represent a single novel species in a new genus, Geothermomicrobium terrae gen. nov., sp. nov. The type strain of Geothermomicrobium terrae is YIM 77562(T) ( = CCTCC AA 2011022(T) = JCM 18057(T)).

  20. Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye.

    PubMed

    Hirota, Kikue; Aino, Kenichi; Yumoto, Isao

    2016-06-01

    Facultatively alkaliphilic strains, designated as strains IEB3T and IEB14, were isolated as indigo-reducing strains from a fermented Polygonum indigo (Polygonum tinctorium Lour) liquor sample prepared in our laboratory using a medium containing an indigo fermentation liquor as a sole substrate. The 16S rRNA gene sequence phylogeny and similarity suggested that strains IEB3T and IEB14 exhibit distinctive positions among the members of the genus Bacillus, and their closest neighbour was Bacillus nanhaiisediminis NH3T (similarity: 97.4 %) among the species with validly published names. The 16S rRNA sequence of strain IEB3Twas identical to that of strain IEB14. The cells of the isolates stained Gram-positive and were facultatively anaerobic, straight rods that were motile by a pair of subpolar flagella. Strains IEB3T and IEB14 grew at temperatures between 12 and 40 °C with optimum growth at 30‒33 °C and in the range of pH 7.5-12. Menaquinone-7 (MK-7) was detected as the major isoprenoid quinone. The DNA G+C contents of strains IEB3T and IEB14 were 49.1 and 49.9 mol%, respectively. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C14:0, iso-C15:0 and anteiso-C15:0. DNA-DNA hybridization revealed a low relatedness value between strain IEB3T and the phylogenetically most closely related species, Bacillus nanhaiisediminis JCM 16507T (<7 % ). On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, the isolates represent a novel species within a novel genus, for which the name Fermentibacillus polygoni gen. nov., sp. nov. is proposed. The type strain is IEB3T (=JCM 30817T=NCIMB 14984T). PMID:26971318

  1. Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

    NASA Technical Reports Server (NTRS)

    Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Matsa, M. E.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

  2. Lutibaculum baratangense gen. nov., sp. nov., a proteobacterium isolated from a mud volcano.

    PubMed

    Kumar, P Anil; Srinivas, T N R; Manasa, P; Madhu, S; Shivaji, S

    2012-08-01

    A novel Gram-negative, oval to rod-shaped, motile bacterium, strain AMV1(T), was isolated from a soil sample collected from a mud volcano of Baratang Island, Andamans, India. The predominant fatty acids were C(16:0) (5.7%), C(18:1)ω7c (78.6%) and C(19:0) cyclo ω8c (6.3%). Strain AMV1(T) contained ubiquinone 10 (Q-10) as the major respiratory quinone and minor quantities of ubiquinone 9 (Q-9). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified lipids, one unidentified phospholipid and one unidentified aminolipid. 16S rRNA gene sequence analysis indicated that strain AMV1(T) was related most closely to the type strains of Tepidamorphus gemmatus, Bauldia consociata, Afifella pfennigii and Amorphus coralli, four members of the order Rhizobiales (class Alphaproteobacteria), with pairwise sequence similarities of 95.0, 94.5, 94.4 and 94.0%, respectively; it shared <94% 16S rRNA gene sequence similarity with all the other members of the order Rhizobiales. Phylogenetic analyses indicated that strain AMV1(T) clustered with Tepidamorphus gemmatus and with species of the genera Amorphus, Rhodobium and Afifella. Phenotypic and phylogenetic characteristics thus suggest that strain AMV1(T) is a representative of a novel species of a new genus, for which the name Lutibaculum baratangense gen. nov., sp. nov. is proposed. The type strain of Lutibaculum baratangense is AMV1(T) ( = KCTC 22669(T) = NBRC 105799(T) = CCUG 58046(T)).

  3. Frederiksenia canicola gen. nov., sp. nov. isolated from dogs and human dog-bite wounds.

    PubMed

    Korczak, Bożena M; Bisgaard, Magne; Christensen, Henrik; Kuhnert, Peter

    2014-04-01

    Polyphasic analysis was done on 24 strains of Bisgaard taxon 16 from five European countries and mainly isolated from dogs and human dog-bite wounds. The isolates represented a phenotypically and genetically homogenous group within the family Pasteurellaceae. Their phenotypic profile was similar to members of the genus Pasteurella. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry clearly identified taxon 16 and separated it from all other genera of Pasteurellaceae showing a characteristic peak combination. Taxon 16 can be further separated and identified by a RecN protein signature sequence detectable by a specific PCR. In all phylogenetic analyses based on 16S rRNA, rpoB, infB and recN genes, taxon 16 formed a monophyletic branch with intraspecies sequence similarity of at least 99.1, 90.8, 96.8 and 97.2 %, respectively. Taxon 16 showed closest genetic relationship with Bibersteinia trehalosi as to the 16S rRNA gene (95.9 %), the rpoB (89.8 %) and the recN (74.4 %), and with Actinobacillus lignieresii for infB (84.9 %). Predicted genome similarity values based on the recN gene sequences between taxon 16 isolates and the type strains of known genera of Pasteurellaceae were below the genus level. Major whole cell fatty acids for the strain HPA 21(T) are C14:0, C16:0, C18:0 and C16:1 ω7c/C15:0 iso 2OH. Major respiratory quinones are menaquinone-8, ubiquinone-8 and demethylmenaquinone-8. We propose to classify these organisms as a novel genus and species within the family of Pasteurellaceae named Frederiksenia canicola gen. nov., sp. nov. The type strain is HPA 21(T) (= CCUG 62410(T) = DSM 25797(T)).

  4. Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments.

    PubMed

    Hirayama, Hisako; Fuse, Hiroyuki; Abe, Mariko; Miyazaki, Masayuki; Nakamura, Takamichi; Nunoura, Takuro; Furushima, Yasuo; Yamamoto, Hiroyuki; Takai, Ken

    2013-03-01

    Two aerobic methane-oxidizing bacterial strains were isolated from distinct marine environments in Japan. Strains IT-4(T) and T2-1 were Gram-stain-negative, aerobic, motile, plump short rods or oval-shaped bacteria with a single polar flagellum and type I intracytoplasmic membranes. They were obligate methanotrophs that grew only on methane or methanol. Each strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. The strains grew best at 37 °C, and did not grow at 45 °C. NaCl was required for growth within a concentration range of 1-8 % (w/v). The major phospholipid fatty acids were C16 : 0, C16 : 1ω7c, and C16 : 1ω5t. The major isoprenoid quinone was MQ-8. The DNA G+C content was 50.9-51.7 mol%. The 16S rRNA gene sequences of the strains showed 99.4 % similarity to each other, and DNA-DNA hybridization analysis indicated that the strains were representatives of the same species. The 16S rRNA gene sequences were highly similar to some marine environmental sequences (94.0-97.7 % similarity), but did not show similarities more than 94 % with sequences of members of other related genera, such as Methylomicrobium, Methylobacter, Methylomonas and Methylosarcina. Phylogenies based on 16S rRNA gene sequences and deduced partial PmoA sequences, and the physiological and chemotaxonomic characteristics revealed that strains IT-4(T) and T2-1 represent a novel species of a new genus in the family Methylococcaceae, for which the name Methylomarinum vadi gen. nov., sp. nov. is proposed. The type strain is IT-4(T) ( = JCM 13665(T) = DSM 18976(T)).

  5. Imtechella halotolerans gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from estuarine water.

    PubMed

    Surendra, Vikram; Bhawana, Pant; Suresh, Korpole; Srinivas, T N R; Kumar, Pinnaka Anil

    2012-11-01

    A novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1(T), was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0-2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1(T) was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H(2)S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C(15:0), iso-C(15:1) G and iso-C(17:0) 3-OH; MK-6 (64%) and MK-7 (34%) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1(T) was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1(T) was related most closely to the type strain of Zhouia amylolytica (pairwise sequence similarity of 93.0%). Phylogenetic analysis showed that strain K1(T) formed a distinct branch within the family Flavobacteriaceae and clustered with the clade comprising species of the genera Zhouia, Coenonia and Capnocytophaga, being phylogenetically most closely related to the type strain of Zhouia amylolytica at a distance of 9.2% (90.8% similarity). Other species of the genera within the same clade were related to strain K1(T) at distances of 15.0-23.1%. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1(T) is considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1(T) (=MTCC 11055(T)=JCM 17677(T)).

  6. Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae.

    PubMed

    Hamada, Moriyuki; Shibata, Chiyo; Nurkanto, Arif; Ratnakomala, Shanti; Lisdiyanti, Puspita; Tamura, Tomohiko; Suzuki, Ken-ichiro

    2015-05-01

    Two novel Gram-stain positive actinobacteria, designated PS-14-16(T) and RS-7-1, were isolated from the rhizosphere of a mangrove and sea sediment, respectively, and their taxonomic positions were investigated by a polyphasic approach. Both strains were observed to form vegetative hyphae in the early phase of growth but the hyphae eventually fragment into short rods to coccoid cells. The peptidoglycan type of both strains was found to be A4α. Their predominant menaquinone was identified as MK-9(H4) and the major fatty acid as anteiso-C(15:0). The DNA G+C content was determined to be 68.4-68.5 mol%. 16S rRNA gene sequencing revealed that strains PS-14-16(T) and RS-7-1 were related to members of the family Cellulomonadaceae. Their nearest phylogenetic neighbour was found to be Sediminihabitans luteus, which is currently the only species of the genus Sediminihabitans, with a similarity of 97.94%. However, strains PS-14-16(T) and RS-7-1 were distinguishable from the members of the genus Sediminihabitans and the other genera within the family Cellulomonadaceae in terms of chemotaxonomic characteristics and phylogenetic relationship. The results of DNA-DNA hybridization experiments indicated that strains PS-14-16(T) and RS-7-1 belong to the same species. Strains PS-14-16(T) and RS-7-1 are concluded to represent a novel genus and species of the family Cellulomonadaceae, for which the name Tropicihabitans flavus gen. nov., sp. nov. is proposed. The type strain of T. flavus is PS-14-16(T) (=NBRC 110109(T) = IanCC A 516(T)). [corrected].

  7. Pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic Mediterranean zone.

    PubMed

    Kimes, Nikole E; López-Pérez, Mario; Flores-Félix, José David; Ramírez-Bahena, Martha-Helena; Igual, José M; Peix, Alvaro; Rodriguez-Valera, Francisco; Velázquez, Encarna

    2015-07-01

    Two novel Alphaproteobacteria strains, R1-200B4(T) and R2-400B4, were isolated from the Mediterranean Sea off the coast of Alicante in Spain. The phylogenetic analysis of the 16S rRNA gene showed that they are related to members of Family Rhizobiaceae. The 16S rRNA gene sequence of strain R1-200B4(T) presents 97.0% and 95.6% similarity with respect to the type strains of the type species from genera Neorhizobium and Rhizobium, Neorhizobium galegae HAMBI 540(T) and Rhizobium leguminosarum USDA 2370(T), respectively. The remaining genera of family Rhizobiaceae showed similarities lower than 95%. The recA and atpD gene sequences of strain R1-200B4(T) showed, respectively, 90% and 88.6% similarity with respect to N. galegae HAMBI 540(T) and 87% and 86% with respect to R. leguminosarum USDA 2370(T). The calculated ANI values between the genomes of the strain R1-200B4(T) and those of N. galegae HAMBI 540(T) and R. leguminosarum 3841 are 75.9% and 74.0%, respectively. The major fatty acids are those from summed feature 8 (C18:1 ω6c/C18:1 ω7c) and the C16:0. Catalase and oxidase were positive. Nitrate reduction and aesculin hydrolysis were positive. Production of β-galactosidase and urease was positive. The production of indol, arginine dehydrolase or gelatinase was negative. Growth was observed in presence of 7% NaCl. Therefore, based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, we propose to classify the strains isolated in this study in a new genus named Pseudorhizobium gen. nov. and a new species named Pseudorhizobium pelagicum sp. nov. with the type strain R1-200B4(T) (=LMG 28314(T)=CECT 8629(T)).

  8. Thermotunica guangxiensis gen. nov., sp. nov., isolated from mushroom residue compost.

    PubMed

    Wu, Hao; Lian, Yunpeng; Liu, Bin; Ren, Yanling; Qin, Peisheng; Huang, Fuchang

    2014-05-01

    A novel thermophilic actinomycete, designated AG2-7T, was isolated from mushroom residue compost in Guangxi University, Nanning, China. The strain grew optimally at 45-60 °C, at pH 7.0 and with 0-3.0% (w/v) NaCl. Vegetative mycelia were branched and whitish to pale yellow without fragmentation. Aerial mycelium was abundant, whitish and differentiated into long chains of spores, with a membranous structure or tunica partially covering the surface of aerial hyphae. The non-motile spores were oval in shape with a ridged surface. Strain AG-27T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were galactose and ribose. Major fatty acids were iso-C16:0 (27.51%), iso-C17:0 (10.47%) and anteiso-C17:0 (12.01%). MK-9(H4) was the predominant menaquinone. The polar phospholipids were diphosphatidylglycerol, ninhydrin-positive glycophospholipid, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unknown phospholipid and unknown glucosamine-containing phospholipids. The G+C content of the genomic DNA was 63.6 mol%. 16S rRNA gene sequence analysis showed that the organism belonged to the family Pseudonocardiaceae, suborder Pseudonocardineae and showed more than 5% divergence from other members of the family. Based on the phenotypic and phylogenetic data, strain AG2-7T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Thermotunica guangxiensis gen. nov., sp. nov. is proposed. The type strain of the type species is AG2-7T (=ATCC BAA-2499T=CGMCC 4.7099T). PMID:24488931

  9. NextGen Flight Deck Surface Trajectory-Based Operations (STBO): Contingency Holds

    NASA Technical Reports Server (NTRS)

    Bakowski, Deborah Lee; Hooey, Becky Lee; Foyle, David C.; Wolter, Cynthia A.; Cheng, Lara W. S.

    2013-01-01

    The purpose of this pilot-in-the-loop taxi simulation was to investigate a NextGen Surface Trajectory-Based Operations (STBO) concept called "contingency holds." The contingency-hold concept parses a taxi route into segments, allowing an air traffic control (ATC) surface traffic management (STM) system to hold an aircraft when necessary for safety. Under nominal conditions, if the intersection or active runway crossing is clear, the hold is removed, allowing the aircraft to continue taxiing without slowing, thus improving taxi efficiency, while minimizing the excessive brake use, fuel burn, and emissions associated with stop-and-go taxi. However, when a potential traffic conflict exists, the hold remains in place as a fail-safe mechanism. In this departure operations simulation, the taxi clearance included a required time of arrival (RTA) to a specified intersection. The flight deck was equipped with speed-guidance avionics to aid the pilot in safely meeting the RTA. On two trials, the contingency hold was not released, and pilots were required to stop. On two trials the contingency hold was released 15 sec prior to the RTA, and on two trials the contingency hold was released 30 sec prior to the RTA. When the hold remained in place, all pilots complied with the hold. Results also showed that when the hold was released at 15-sec or 30-sec prior to the RTA, the 30-sec release allowed pilots to maintain nominal taxi speed, thus supporting continuous traffic flow; whereas, the 15-sec release did not. The contingency-hold concept, with at least a 30-sec release, allows pilots to improve taxiing efficiency by reducing braking, slowing, and stopping, but still maintains safety in that no pilots "busted" the clearance holds. Overall, the evidence suggests that the contingency-hold concept is a viable concept for optimizing efficiency while maintaining safety.

  10. Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales.

    PubMed

    Bao, Zhihua; Sato, Yoshinori; Fujimura, Reiko; Ohta, Hiroyuki

    2014-03-01

    A thallium-tolerant, aerobic bacterium, designated strain SK200a-9(T), isolated from a garden soil sample was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain SK200a-9(T) was affiliated with an uncultivated lineage within the Alphaproteobacteria and the nearest cultivated neighbours were bacteria in genera in the family Methylocystaceae (93.3-94.4% 16S rRNA gene sequence similarity) and the family Beijerinckiaceae (92.3-93.1%) in the order Rhizobiales. Cells of strain SK200a-9(T) were Gram-stain-negative, non-motile, non-spore-forming, poly-β-hydroxybutyrate-accumulating rods. The strain was a chemo-organotrophic bacterium, which was incapable of growth on C1 substrates. Catalase and oxidase were positive. Atmospheric nitrogen fixation and nitrate reduction were negative. The strain contained ubiquinone Q-10 and cellular fatty acids C18 : 1ω7c, C18 : 0, C16 : 1ω7c and C16 : 0 as predominant components. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 64.8 mol%. On the basis of the information described above, strain SK200a-9(T) is considered to represent a novel species of a new genus in the order Rhizobiales, for which the name Alsobacter metallidurans gen. nov., sp. nov. is proposed. The type strain of Alsobacter metallidurans is SK200a-9(T) ( = NBRC 107718(T) = CGMCC 1.12214(T)).

  11. Crenalkalicoccus roseus gen. nov., sp. nov., a thermophilic bacterium isolated from alkaline hot springs.

    PubMed

    Ming, Hong; Duan, Yan-Yan; Yin, Yi-Rui; Meng, Xiao-Lin; Li, Shuai; Zhou, En-Min; Huang, Jian-Rong; Nie, Guo-Xing; Li, Wen-Jun

    2016-06-01

    Two closely related thermophilic bacterial strains, designated YIM 78023T and YIM 78058, were isolated from samples collected from two alkaline hot springs in Tengchong county, Yunnan province, south-west China. The novel isolates were Gram-stain-negative, non-motile, aerobic ovoid- to coccoid-shaped and non-spore-forming. Strain YIM 78023T grew at 20-60 ºC and pH 6.0-9.0 with optimal growth observed at 40-50 ºC and pH 8.0, while strain YIM 78058 grew at 25-60 ºC and pH 6.0-10.0 with optimal growth at 45-50 ºC and pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences affiliated these two isolates within the family Acetobacteraceae with high sequence similarities to members of the genera Roseomonas and Belnapia (all sequence similarities <94.5 %). In addition to the above two genera, these strains also clustered with the genera Craurococcus and Paracraurococcus (having sequence similarities <93.3 %) in the phylogenetic tree, but with a distinct lineage within the family Acetobacteraceae. The major ubiquinone was Q-10 and the major fatty acids observed were C18:1ω7c, summed feature 4 and C16:0. The genomic DNA G+C contents observed for strains YIM 78023T and YIM 78058 were 74.3 and 74.0 mol%, respectively. Morphological, phylogenetic and chemotaxonomic results suggest that strains YIM 78023T and YIM 78058 are representatives of a novel species of a new genus within the family Acetobacteraceae, for which the name Crenalkalicoccus roseus gen. nov., sp. nov. is proposed. The type strain of Crenalkalicoccus roseus is YIM 78023T (=JCM 19657T=KACC 17825T). PMID:27001292

  12. Finding genome-transcriptome-phenome association with structured association mapping and visualization in GenAMap.

    PubMed

    Curtis, Ross E; Yin, Junming; Kinnaird, Peter; Xing, Eric P

    2012-01-01

    Despite the success of genome-wide association studies in detecting novel disease variants, we are still far from a complete understanding of the mechanisms through which variants cause disease. Most of previous studies have considered only genome-phenome associations. However, the integration of transcriptome data may help further elucidate the mechanisms through which genetic mutations lead to disease and uncover potential pathways to target for treatment. We present a novel structured association mapping strategy for finding genome-transcriptome-phenome associations when SNP, gene-expression, and phenotype data are available for the same cohort. We do so via a two-step procedure where genome-transcriptome associations are identified by GFlasso, a sparse regression technique presented previously. Transcriptome-phenome associations are then found by a novel proposed method called gGFlasso, which leverages structure inherent in the genes and phenotypic traits. Due to the complex nature of three-way association results, visualization tools can aid in the discovery of causal SNPs and regulatory mechanisms affecting diseases. Using wellgrounded visualization techniques, we have designed new visualizations that filter through large three-way association results to detect interesting SNPs and associated genes and traits. The two-step GFlasso-gGFlasso algorithmic approach and new visualizations are integrated into GenAMap, a visual analytics system for structured association mapping. Results on simulated datasets show that our approach has the potential to increase the sensitivity and specificity of association studies, compared to existing procedures that do not exploit the full structural information of the data. We report results from an analysis on a publically available mouse dataset, showing that identified SNP-gene-trait associations are compatible with known biology.

  13. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine.

    PubMed

    Kläring, Karoline; Hanske, Laura; Bui, Nam; Charrier, Cédric; Blaut, Michael; Haller, Dirk; Plugge, Caroline M; Clavel, Thomas

    2013-12-01

    A Gram-positive, spore-forming, non-motile, strictly anaerobic rod-shaped bacterium was isolated from the caecal content of a TNF(deltaARE) mouse. The isolate, referred to as strain SRB-521-5-I(T), was originally cultured on a reduced agar medium containing yeast extract, rumen fluid and lactic acid as main energy and carbon sources. Phylogenetic analysis of partial 16S rRNA genes revealed that the species most closely related to strain SRB-521-5-I(T) were Flavonifractor plautii and Pseudoflavonifractor capillosus (<95 % sequence similarity; 1436 bp). In contrast to F. plautii and P. capillosus, strain SRB-521-5-I(T) contained a substantial amount of C18 : 0 dimethylacetal. Additional major fatty acids were C14 : 0 methyl ester, C16 : 0 dimethylacetal and C18 : 0 aldehyde. Strain SRB-521-5-I(T) differed in its enzyme profile from F. plautii and P. capillosus by being positive for dextrin, maltotriose, turanose, dl-lactic acid and d-lactic acid methyl ester but negative for d-fructose. In reduced Wilkins-Chalgren-Anaerobe broth, strain SRB-521-5-I(T) produced approximately 8 mM butyrate and 4 mM acetate. In contrast to F. plautii, the strain did not metabolize flavonoids. It showed intermediate resistance towards the antibiotics ciprofloxacin, colistin and tetracycline. Based on genotypic and phenotypic characteristics, we propose the name Intestinimonas butyriciproducens gen. nov., sp. nov. to accommodate strain SRB-521-5-I(T) ( = DSM 26588(T) = CCUG 63529(T)) as the type strain. PMID:23918795

  14. Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil.

    PubMed

    Nunes, Inês; Tiago, Igor; Pires, Ana Luísa; da Costa, Milton S; Veríssimo, António

    2006-08-01

    A Gram-positive bacterium, designated B22(T), was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 degrees C and pH 8.0-8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0-8 % NaCl. The cell wall peptidoglycan is of the A4alpha type with a cross-linkage containing d-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22(T) formed a new branch within the family Bacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the genera Salinibacillus, Virgibacillus, Oceanobacillus and Lentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22(T) exhibited 16S rRNA gene pairwise sequence similarity values of 94.7-94.3 % with members of the genus Salinibacillus, 95.1-92.8 % with members of the genus Virgibacillus, 94.7-93.2 % with members of the genus Oceanobacillus and 93.1-92.3 % with members of the genus Lentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22(T) represents a novel species in a new genus, Paucisalibacillus globulus gen. nov., sp. nov. Strain B22(T) (=LMG 23148(T)=CIP 108857(T)) is the type strain of Paucisalibacillus globulus.

  15. 'Candidatus glomeribacter gigasporarum' gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi.

    PubMed

    Bianciotto, Valeria; Lumini, Erica; Bonfante, Paola; Vandamme, Peter

    2003-01-01

    Arbuscular mycorrhizal fungi are obligate endosymbionts that colonize the roots of almost 80 % of land plants. The present paper describes morphological and molecular data on a bacterial endosymbiont living in the cytoplasm of dormant or germinating spores and symbiotic mycelia of the fungal species Gigaspora margarita, Scutellospora persica and Scutellospora castanea. PCR amplification of almost the entire 16S rRNA gene of the Gigaspora margarita BEG 34 endosymbiont, using universal bacterial primers, and subsequent sequence analysis demonstrated that this organism occupies a very distinct phylogenetic position within the beta-Proteobacteria, with the genera Burkholderia, Pandoraea and Ralstonia as its closest neighbours. Primers specific to the 16S rDNA of the endosymbiotic bacteria of BEG 34 allowed amplification of spore DNA from endosymbionts of Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea, but not from the Gigaspora gigantea endosymbiont (which was morphologically different) or from the cytoplasm of Gigaspora rosea (which did not contain endosymbiotic bacteria). These specific primers were successfully used as a probe for the in-situ hybridization of endobacteria in Gigaspora margarita spores. The overall rod-shaped morphology of the Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea endosymbionts was similar, and amplification and sequence analysis of the almost-complete 16S rRNA genes of several Gigaspora margarita, S. persica and S. castanea endosymbionts revealed over 98% sequence similarity. These morphological and genomic characteristics were used to assign the endosymbionts of these three species (five isolates) of arbuscular mycorrhizal fungi as 'Candidatus Glomeribacter gigasporarum' gen. nov., sp. nov.

  16. Neostasina gen. nov., a new genus of huntsman spiders from the Neotropical region (Araneae, Sparassidae, Sparianthinae).

    PubMed

    Rheims, Cristina Anne

    2016-01-01

    Neostasina gen. nov. is proposed to include the type species, Neostasina macleayi (Bryant, 1940) comb. nov., and four other described species: N. lucasi (Bryant, 1940) comb. nov. and N. saetosa (Bryant, 1948) comb. nov., transferred from Stasina Simon, 1877, N. bicolor (Banks, 1914) comb. nov., from Olios Walckenaer, 1837, and N. antiguensis (Bryant, 1923) comb. nov., from Pseudosparianthis Simon, 1887. Stasina portoricensis Petrunkevitch, 1930 and Olios darlingtoni Bryant, 1942 are considered junior synonyms of N. bicolor comb. nov. All species are redescribed and illustrated. Twenty-two new species are described, namely: N. baoruco sp. nov. (♀), N. bermudezi sp. nov. (♂, ♀) and N. cachote sp. nov. (♀) from the Dominican Republic, N. bryantae sp. nov. (♂, ♀), N. granpiedra sp. nov. (♂, ♀), N. iberia sp. nov. (♂, ♀), N. montegordo sp. nov. (♀), N. siempreverde sp. nov. (♂) and N. turquino sp. nov. (♀) from Cuba, N. croix sp. nov. (♂) from the Island of St. Croix and N. virginensis sp. nov. (♀) from the Island of St. John, both U.S. Virgin Islands, N. guanaboa sp. nov. (♂), N. gunboat sp. nov. (♂), N. jamaicana sp. nov. (♀), N. liguanea sp. nov. (♂, ♀), N. lucea sp. nov. (♀), N. mammee sp. nov. (♂, ♀), and N. maroon sp. nov. (♂, ♀) from Jamaica, N. ouali sp. nov. (♂, ♀) from Nevis Island, N. amalie sp. nov. (♂, ♀) from U.S. (St. John and St. Thomas Islands) and British Virgin Islands (Peter Island and Sandy Cay), and N. taino sp. nov. (♂, ♀) from Puerto Rico and Dominican Republic. An identification key and distribution maps are provided for all known species. PMID:27396008

  17. Feasibility of a Networked Air Traffic Infrastructure Validation Environment for Advanced NextGen Concepts

    NASA Technical Reports Server (NTRS)

    McCormack, Michael J.; Gibson, Alec K.; Dennis, Noah E.; Underwood, Matthew C.; Miller,Lana B.; Ballin, Mark G.

    2013-01-01

    Abstract-Next Generation Air Transportation System (NextGen) applications reliant upon aircraft data links such as Automatic Dependent Surveillance-Broadcast (ADS-B) offer a sweeping modernization of the National Airspace System (NAS), but the aviation stakeholder community has not yet established a positive business case for equipage and message content standards remain in flux. It is necessary to transition promising Air Traffic Management (ATM) Concepts of Operations (ConOps) from simulation environments to full-scale flight tests in order to validate user benefits and solidify message standards. However, flight tests are prohibitively expensive and message standards for Commercial-off-the-Shelf (COTS) systems cannot support many advanced ConOps. It is therefore proposed to simulate future aircraft surveillance and communications equipage and employ an existing commercial data link to exchange data during dedicated flight tests. This capability, referred to as the Networked Air Traffic Infrastructure Validation Environment (NATIVE), would emulate aircraft data links such as ADS-B using in-flight Internet and easily-installed test equipment. By utilizing low-cost equipment that is easy to install and certify for testing, advanced ATM ConOps can be validated, message content standards can be solidified, and new standards can be established through full-scale flight trials without necessary or expensive equipage or extensive flight test preparation. This paper presents results of a feasibility study of the NATIVE concept. To determine requirements, six NATIVE design configurations were developed for two NASA ConOps that rely on ADS-B. The performance characteristics of three existing in-flight Internet services were investigated to determine whether performance is adequate to support the concept. Next, a study of requisite hardware and software was conducted to examine whether and how the NATIVE concept might be realized. Finally, to determine a business case

  18. Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring.

    PubMed

    Dong, Lei; Ming, Hong; Zhou, En-Min; Yin, Yi-Rui; Liu, Lan; Feng, Hui-Geng; Xian, Wen-Dong; Nie, Guo-Xing; Li, Wen-Jun

    2015-01-01

    A slightly thermophilic, Gram-staining-negative and strictly aerobic bacteria, designated strain YIM 78141(T), was isolated from a sediment sample collected at Hehua hot spring, Tengchong, Yunnan province, south-west China. Cells of the strain were short-rod-shaped and colonies were yellowish and circular. The strain grew at pH 6.0-10.0 (optimum, pH 8.0-9.0) and 10-55 °C (optimum, 40-50 °C). Phylogenetic analyses based on 16S rRNA gene sequence comparison demonstrated that strain YIM 78141(T) belongs to the family Neisseriaceae, and strain YIM 78141(T) also showed low levels of 16S rRNA gene sequence similarity (below 93.4%) with all other genera in this family. The only quinone was ubiquinone 8 and the genomic DNA G+C content was 67.3 mol%. Major fatty acids (>5%) were C12:0, C16:0, C18:1ω7c and summed feature 3. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phospholipids of unknown structure containing aminoglycophospholipid and three unidentified polar lipids. On the basis of the morphological, physiological and biochemical characteristics as well as genotypic data, this strain should be classified as a representative of a novel genus and species of the family Neisseriaceae, for which the name Crenobacter luteus gen. nov., sp. nov. is proposed. The type strain is YIM 78141(T) ( =BCRC 80650(T) =KCTC 32558(T) =DSM 27258(T)).

  19. Thermocatellispora tengchongensis gen. nov., sp. nov., a new member of the family Streptosporangiaceae.

    PubMed

    Zhou, En-Min; Yang, Ling-Ling; Song, Zhao-Qi; Yu, Tian-Tian; Nie, Guo-Xing; Ming, Hong; Zhou, Yu; Tang, Shu-Kun; Li, Wen-Jun

    2012-10-01

    A novel Gram-positive, aerobic, spore-forming, thermophilic actinomycete, designated strain YIM 77521(T), was isolated from a sandy soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. The strain formed branched substrate mycelia and no fragmentation was found. Masses of short, straight or irregular chains of three to eight warty ornamented spores were borne from aerial mycelia. The strain contained meso-diaminopimelic acid in the cell wall and the whole-cell sugars contained mannose, galactose, glucose and ribose. The predominant menaquinones were MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)). The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylmonomethylethanolamine and N-acetylglucosamine-containing phospholipids. The major fatty acids were iso-C(16 : 0), C(17 : 0) 10-methyl and C(18 : 0). The DNA G+C content of strain YIM 77521(T) was 73.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 77521(T) fell within the radiation of the suborder Streptosporangineae and formed a distinct monophyletic lineage adjacent to the family Streptosporangiaceae with a high bootstrap value. On the basis of combined data from the phenotypic and phylogenetic analyses, strain YIM 77521(T) represents a novel genus and species within the family Streptosporangiaceae, for which the name Thermocatellispora tengchongensis gen. nov., sp. nov. is proposed. The type strain is YIM 77521(T) ( = DSM 45615(T)  = CCTCC AA 2011013(T)).

  20. Crenalkalicoccus roseus gen. nov., sp. nov., a thermophilic bacterium isolated from alkaline hot springs.

    PubMed

    Ming, Hong; Duan, Yan-Yan; Yin, Yi-Rui; Meng, Xiao-Lin; Li, Shuai; Zhou, En-Min; Huang, Jian-Rong; Nie, Guo-Xing; Li, Wen-Jun

    2016-06-01

    Two closely related thermophilic bacterial strains, designated YIM 78023T and YIM 78058, were isolated from samples collected from two alkaline hot springs in Tengchong county, Yunnan province, south-west China. The novel isolates were Gram-stain-negative, non-motile, aerobic ovoid- to coccoid-shaped and non-spore-forming. Strain YIM 78023T grew at 20-60 ºC and pH 6.0-9.0 with optimal growth observed at 40-50 ºC and pH 8.0, while strain YIM 78058 grew at 25-60 ºC and pH 6.0-10.0 with optimal growth at 45-50 ºC and pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences affiliated these two isolates within the family Acetobacteraceae with high sequence similarities to members of the genera Roseomonas and Belnapia (all sequence similarities <94.5 %). In addition to the above two genera, these strains also clustered with the genera Craurococcus and Paracraurococcus (having sequence similarities <93.3 %) in the phylogenetic tree, but with a distinct lineage within the family Acetobacteraceae. The major ubiquinone was Q-10 and the major fatty acids observed were C18:1ω7c, summed feature 4 and C16:0. The genomic DNA G+C contents observed for strains YIM 78023T and YIM 78058 were 74.3 and 74.0 mol%, respectively. Morphological, phylogenetic and chemotaxonomic results suggest that strains YIM 78023T and YIM 78058 are representatives of a novel species of a new genus within the family Acetobacteraceae, for which the name Crenalkalicoccus roseus gen. nov., sp. nov. is proposed. The type strain of Crenalkalicoccus roseus is YIM 78023T (=JCM 19657T=KACC 17825T).

  1. Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil.

    PubMed

    Tirandaz, Hassan; Dastgheib, Seyed Mohammad Mehdi; Amoozegar, Mohammad Ali; Shavandi, Mahmoud; de la Haba, Rafael R; Ventosa, Antonio

    2015-12-01

    Strain RIPI 110T was isolated from a soil sample collected from an oil-contaminated site on Siri Island, Persian Gulf, Iran. Cells of the novel isolate were Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped. Cells divided asymmetrically by budding and formed rosette-like clusters. The optimum pH and temperature for growth were pH 7 and 30 °C, while the strain was able to grow at pH 5.5-8 and 15-35 °C. Strain RIPI 110T utilized only complex carbon sources and pyruvate as the sole carbon source and could not grow under photoautotrophic conditions. The highest 16S rRNA gene sequence similarities, 93.9, 93.9 and 93.5 %, were obtained with Variibacter gotjawalensis GJW-30T, Rhodoplanes roseus 941T and Rhodoplanes elegans AS130T, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and C19 : 0 cyclo ω8c. Polar lipid analyses revealed that strain RIPI 110T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid and four unknown phospholipids. Ubiquinone-10 was the predominant quinone component. The DNA G+C content was 59.4 mol%. On the basis of the 16S rRNA gene sequence analysis, in combination with chemotaxonomic and physiological data, the novel isolate could not be classified in any recognized genera. Strain RIPI 110T is thus considered to represent a novel species of a new genus within the order Rhizobiales, for which the name Pseudorhodoplanes sinuspersici gen. nov., sp. nov. is proposed. The type strain of the type species is RIPI 110T ( = IBRC-M 10770T = CECT 8374T). PMID:26420766

  2. Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae.

    PubMed

    Menes, Rodolfo Javier; Viera, Claudia Elizabeth; Farías, María Eugenia; Seufferheld, Manfredo J

    2016-01-01

    A Gram-negative, halophilic, heterotrophic, rod-shaped, non-spore-forming bacterium (SV525T) was isolated from the sediment of a hypersaline lake located at 4600 m above sea level (Laguna Vilama, Argentina). Strain SV525T was strictly aerobic and formed pink-to-magenta colonies. Growth occurred at 10–35 °C (optimum 25–30 °C), at pH levels 6.0–8.5 (optimum 7.0) and at NaCl concentrations of 7.5–25 % (w/v) with an optimum at 10–15 % (w/v). The strain required sodium and magnesium but not potassium ions for growth. Grows with tryptone, or Bacto Peptone as sole carbon and energy source and requires yeast extract for growth. It produced catalase and oxidase. The predominant ubiquinone was Q-8 and the major fatty acids comprised C18:1 ω7c, C16:0 and C18:0. The DNA G+C content was 60.4 mol% and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene indicated that strain SV525T belongs to the family Ectothiorhodospiraceae within the class Gammaproteobacteria. On the basis of phylogenetic and phenotypic data, SV525T represents a novel genus and species, for which the name Halopeptonella vilamensis gen. nov., sp. nov. is proposed. The type strain is SV525T (=DSM 21056T =JCM 16388T =NCIMB 14596T). PMID:26475627

  3. Canaleparolina darwiniensis, gen. nov., sp. nov., and other pillotinaceous spirochetes from insects.

    PubMed

    Wier, A; Ashen, J; Margulis, L

    2000-12-01

    We describe two new pillotinaceous spirochetes (Canaleparolina darwiniensis, Diplocalyx cryptotermitidis) and identify for the first time Hollandina pterotermitidis from both the subterranean termite Cryptotermes cavifrons and the wood-eating cockroach Cryptocercus punctulatus based on morphometric analysis of transmission electron micrographic thin sections. C. darwiniensis, gen. nov., sp. nov., limited to near Darwin, Australia, invariably is present on the surface of the treponeme-studded trichomonad Mixotricha paradoxa, a consistent inhabitant of the hindgut of healthy termite Mastotermes darwiniensis. The spirochete both attached to the surface of protists and free-swimming in the paunch (hindgut) lumen of the insect has 16 periplasmic flagella (16:32:16) and imbricated wall structures that resemble flattened crenulations of Pillotina. The flagella surround half the protoplasmic cylinder. C. darwiniensis is the largest (0.5 microm diameter x 25 microm length) of the three epibiotic bacteria (two spirochetes, one rod) that comprise the complex cortex of its host Mixotricha paradoxa. Several criteria distinguish Diplocalyx cryptotermitidis sp. nov. isolated from Cryptotermes cavifrons intestine: smaller diameter, fewer flagella, absence of inner and outer coats of the outer membrane, wider angle subtended by its flagella and, most notably, cytoplasmic tubule-associated centers, which are periodic electron dense spheres within the protoplasmic cylinder from which emanate cytoplasmic tubules up to 24 nm in diameter. This is also the first report of abundant populations of Hollandina in Cryptotermes cavifrons (those populations belong to the species H. pterotermitidis). Morphometric analysis of the first thin sections of any spirochetes (published nearly 40 years ago by A.V. Grimstone) permits us to identify the large (0.9 microm diameter) free-swimming intestinal symbiont of Cryptocercus punctulatus also as Hollandina pterotermitidis.

  4. Visual advantage of enhanced flight vision system during NextGen flight test evaluation

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2014-06-01

    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. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

  5. Nitropelagi marinus gen. nov., sp. nov., Isolated From Seawater, Je-bu island, South Korea.

    PubMed

    Jeong, Sun Hwan; Lee, Sang Seob

    2016-09-01

    A Gram-stain-negative, non-spore forming, non-motile and aerobic strain, designated JB22(T), was isolated from seawater, Je-bu Island, South Korea. Strain JB22(T) was catalase and oxidase positive. Optimal growth of JB22(T) was observed at 30 °C and pH 7.0. NaCl tolerance range was 1-9 % (w/v) with an optimum of 2.0 % concentration. The phylogenetic analysis based on 16S rRNA gene sequence of strain JB22(T) showed the highest sequence similarity to those of Pelagicola litorisediminis D1-W8(T) (95.8 %), Roseovarius litoreus GSW-M15(T) (95.2 %), Roseovarius aestuarii SMK-122(T) (95.0 %), Donghicola eburmeus SW-277(T) (95.0 %), and Roseovarius halotolerans HJ50(T) (94.9 %). It contained ubiquine-10 as the major respiratory quinone and C18:1 ω7c (69.3 %), :0 (9.9 %), C18:1 ω7c 11-methyl (9.6 %) as the major fatty acid. The polar lipid profile included phosphatidylcholine, phosphatidylglycerol, and unidentified aminolipid. The DNA G+C content of the strain JB22(T) was 47 mol  %. Based on physiological and chemotaxonomic characteristics, strain JB22(T) should be regarded as a new genus of the family Rhodobacteraceae, for which the Nitropelagi marinus gen. nov., sp. nov. is proposed. The type strain is JB22(T) (= KEMB 3001-101(T) = JCM 30822(T)). PMID:27246498

  6. Hydrogenispora ethanolica gen. nov., sp. nov., an anaerobic carbohydrate-fermenting bacterium from anaerobic sludge.

    PubMed

    Liu, Yi; Qiao, Jiang-Tao; Yuan, Xian-Zheng; Guo, Rong-Bo; Qiu, Yan-Ling

    2014-05-01

    An anaerobic, spore-forming, ethanol-hydrogen-coproducing bacterium, designated LX-BT, was isolated from an anaerobic sludge treating herbicide wastewater. Cells of strain LX-BT were non-motile rods (0.3-0.5×3.0-18.0 µm). Spores were terminal with a bulged sporangium. Growth occurred at 20-50 °C (optimum 37-45 °C), pH 5.0-8.0 (optimum pH 6.0-7.7) and 0-2.5% (w/v) NaCl. The strain could grow fermentatively on glucose, maltose, arabinose, fructose, xylose, ribose, galactose, mannose, raffinose, sucrose, pectin, starch, glycerol, fumarate, tryptone and yeast extract. The major end-products of glucose fermentation were acetate, ethanol and hydrogen. Yeast extract was not required but stimulated growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, anthraquinone-2,6-disulfonate, fumarate and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The G+C content of the genomic DNA was 56.1 mol%. The major cellular fatty acids were anteiso-C15:0, iso-C14:0 and C16:0. The most abundant polar lipids of strain LX-BT were diphosphatidylglycerol and phosphatidylglycerol. 16S rRNA gene sequence analysis revealed that it belongs to an as-yet-unidentified taxon at the order- or class-level (OPB54) within the phylum Firmicutes, showing 86.5% sequence similarity to previously described species of the Desulfotomaculum cluster. The name Hydrogenispora ethanolica gen. nov., sp. nov. is proposed to accommodate strain LX-BT (=DSM 25471T=JCM 18117T=CGMCC 1.5175T) as the type strain.

  7. Analysis of first proximity voltage on the property of GEN Ⅲ image intensifier

    NASA Astrophysics Data System (ADS)

    Zhang, Ni; Zhu, Yu-feng; Li, Dan; Nie, Jing; Zhang, Tai-min; Liu, Xiao-jian; Liu, Zhao-lu; Cheng, Wei; Fu, Ling-yun

    2013-08-01

    First proximity voltage is the voltage between the cathode of Low Light Level image intensifier and the input surface of Micro-channel plate(MCP). There are so many factors influencing the image intensifier performance, and the first proximity voltage is one of the most important factors that can not be ignored. Based on the theory analysis and test of different proximity voltage on the gain、signal-to-noise ratio and equivalent background noise, this test has studied on the important performance of Gen III image intensifier effected by the proximity voltage. By the experimental study, the increase of first proximity voltage to a certain extent can improve gain、signal-to-noise ratio and equivalent background noise at the same time. The main cause of this phenomenon is that the increase of proximity voltage can enlarge the incident electron energy, and then improve the quantum efficiency of the incident electron; meantime, stray electron produced by field emission at the action of the electric field of filmed-MCP will lead to equivalent background deterioration. Ultimately we conclude that: 1) Signal to noise is proportional to the square of he cathode sensitivity, increases with the first collision energy of the incident electron, especially at 200-500ev. 2)In the increasing process of voltage from 300v to 800v, the gain of filmed-MCP increases rapidly, but lower again when Upk increases further because of gain self-saturation; lgG and lgUpk are linear relationship, thus the curve can intuitively demonstrate the relationship between them. 3) Stray electron produced by field emission at the action of the electric field of filmed-MCP will lead to equivalent background deterioration, but will not exceed the requirements of technical specifications(2.5×10-7lx).

  8. Unarmoured dinoflagellates with a small hyposome: Torodinium and Lebouridinium gen. nov. for Katodinium glaucum (Gymnodiniales, Dinophyceae)

    PubMed Central

    Gómez, Fernando; Takayama, Haruyoshi; Moreira, David; López-García, Purificación

    2016-01-01

    We investigated the morphology and evolutionary relationships of Torodinium spp. and Katodinium glaucum, unarmoured dinoflagellates characterized by a small hyposome. An emended generic description of Torodinium was proposed based on light and scanning electron microscopy. Torodinium exhibited a unique combination of morphological features including a minute hyposome, a long episome with longitudinal ribs and a canal of unknown function on the dextro-lateral side. Unlike any known dinoflagellate both cingulum and sulcus extended in the episome. The apex surface showed ribs that converged in a bill-like projection. The shape of the apical groove was a circular spiral that extended around the apex running in 2.5 turns in an anticlockwise direction. The type species T. teredo was usually longer than T. robustum. The longitudinal outline of T. teredo was linear, with almost parallel margins, a circular transversal section, a relatively large hyposome and a conspicuous bill-like projection. The longitudinal outline of T. robustum was oblong, widened in the middle, with an ellipsoidal transversal section, a small hyposome and a less prominent bill-like projection. Several morphological features of Katodinium glaucum (=Gyrodinium glaucum) resembled Gyrodinium, such as the cingular displacement, longitudinal ribs, trichocysts, rod-shaped and refractile bodies and a capsule that surrounded the spherical nucleus. Distinctive features of K. glaucum were the horseshoeshaped apical groove under a tongue-shaped notch pointed towards the dorsal side, and a bifurcated proximal end of the cingulum. Phylogenetic analysis revealed that Torodinium spp. and K. glaucum formed two independent lineages with no close relationships with other known dinoflagellates. The morphology of K. glaucum was distant from the type species of Katodinium. We propose the new genus and combination Lebouridinium glaucum gen. nov., comb. nov. for the species Katodinium glaucum. PMID:27284214

  9. Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes.

    PubMed

    Nogi, Yuichi; Yoshizumi, Masaki; Hamana, Koei; Miyazaki, Masayuki; Horikoshi, Koki

    2014-08-01

    Polyvinyl-alcohol-degrading bacteria were isolated from the fruit of a grape in Yokosuka, Japan. The isolated strain, Zumi 37(T), was a Gram-stain-negative, rod-shaped, motile, non-spore-forming and strictly aerobic chemo-organotroph, showing optimal growth at pH 7.5, 30 °C and 0.1% (w/v) NaCl. The major respiratory quinone was Q-8. The predominant fatty acids were iso-C(15 : 0), C(16 : 0) and C(16 : 1)ω7c. The major polyamines were homospermidine and putrescine. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of the novel strain was 64.2 mol%. 16S rRNA gene sequence comparison revealed that strain Zumi 37(T) belongs to the family Sinobacteraceae within the class Gammaproteobacteria. Steroidobacter denitrificans DSM 18526(T) was the most closely related species with a validly published name, with 98.0% similarity based on 16S rRNA gene sequence comparison (and showed less than 87.5% sequence similarity to members of the genera Alkanibacter, Fontimonas, Hydrocarboniphaga, Nevskia and Solimonas with known 16S rRNA gene sequences). Phenotypes for growth under aerobic conditions and on complex media and major fatty acid composition, differed greatly from those of with comparatively high 16S rRNA gene sequence similarity. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain Zumi 37(T) represents a novel species in a new genus for which the name Povalibacter uvarum gen. nov., sp. nov. is proposed. The type strain of the type species is Zumi 37(T) ( = JCM 18749(T) = DSM 26723(T)). PMID:24844263

  10. Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil.

    PubMed

    Nunes, Inês; Tiago, Igor; Pires, Ana Luísa; da Costa, Milton S; Veríssimo, António

    2006-08-01

    A Gram-positive bacterium, designated B22(T), was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 degrees C and pH 8.0-8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0-8 % NaCl. The cell wall peptidoglycan is of the A4alpha type with a cross-linkage containing d-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22(T) formed a new branch within the family Bacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the genera Salinibacillus, Virgibacillus, Oceanobacillus and Lentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22(T) exhibited 16S rRNA gene pairwise sequence similarity values of 94.7-94.3 % with members of the genus Salinibacillus, 95.1-92.8 % with members of the genus Virgibacillus, 94.7-93.2 % with members of the genus Oceanobacillus and 93.1-92.3 % with members of the genus Lentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22(T) represents a novel species in a new genus, Paucisalibacillus globulus gen. nov., sp. nov. Strain B22(T) (=LMG 23148(T)=CIP 108857(T)) is the type strain of Paucisalibacillus globulus. PMID:16902018

  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)). PMID:24801155

  12. Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov.

    PubMed

    Mayr, R; Busse, H-J; Worliczek, H L; Ehling-Schulz, M; Scherer, S

    2006-06-01

    A Gram-positive, aerobic, rod-shaped, motile, endospore-forming bacterium was isolated from pasteurized milk from Bavaria, Germany. 16S rRNA gene sequence similarities indicated that strain WSBC 24001(T) was most closely related to Virgibacillus species (95.3-96.1 %), Oceanobacillus species (95.6-95.7 %), Bacillus firmus IAM 12464(T) (95.5 %) and Bacillus niacini IFO 15566(T) (95.2 %). However, strain WSBC 24001(T) showed the highest level of sequence similarity to an unnamed strain, MB-9(T) (97.6 %), which was isolated from coastal surface sediments in California. Hence, this strain was included in our study. The genomic DNA G + C contents of strains WSBC 24001(T) and MB-9(T) were 36.4 mol and 40.8 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-7 and the peptidoglycan type was A4beta (L-orn<--D-Asp). The polar lipid profiles of these strains contained a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol, an unknown phospholipid and an unknown aminophospholipid. However, strain WSBC 24001(T) could be distinguished from strain MB-9(T) by the presence of an unknown lipid. The fatty acid profiles of the two strains comprised mainly iso- and anteiso-branched acids, but showed some significant quantitative differences in the amounts of certain acids. The DNA-DNA relatedness value (15.5 %) clearly demonstrated that strains WSBC 24001(T) and MB-9(T) are representatives of two different species. On the basis of their phylogenetic position and morphological, physiological and chemotaxonomic properties, a novel genus is proposed, Ornithinibacillus gen. nov., with two novel species, the type species Ornithinibacillus bavariensis sp. nov. (type strain WSBC 24001(T) = DSM 15681(T) = CCM 7096(T)) and Ornithinibacillus californiensis sp. nov. (type strain MB-9(T) = DSM 16628(T) = CCM 7237(T)). PMID:16738118

  13. Ferrovibrio denitrificans gen. nov., sp. nov., a novel neutrophilic facultative anaerobic Fe(II)-oxidizing bacterium.

    PubMed

    Sorokina, Anna Y; Chernousova, Elena Y; Dubinina, Galina A

    2012-10-01

    A neutrophilic Fe(II)-oxidizing bacterium was isolated from the redox zone of a low-salinity spring in Krasnodar krai (Russia), at the FeS-Fe(OH)(3) interface deposited at the sediment surface. The cells of strain Sp-1 were short, thin motile vibrioids with one polar flagellum dividing by binary fission. The optimal values and ranges for pH and temperature were pH 6.2 (5.5-8) and 35 °C (5-45 °C), respectively. The organism was a facultative anaerobe. Strain Sp-1 was capable of organotrophic, lithoheterotrophic and mixotrophic growth with Fe(II) as an electron donor. The denitrification chain was 'disrupted'. Oxidation of Fe(II) was coupled to reduction of NO3 - to NO2 - or of N(2) O to N(2) , as well as under microaerobic conditions, with O(2) as an electron acceptor. The DNA G+C content was 64.2 mol%. According to the results of phylogenetic analysis, the strain was 10.6-12% remote from the closest relatives, members of the genera Sneathiella, Inquilinus, Oceanibaculum and Phaeospirillum within the Alphaproteobacteria. Based on its morphological, physiological and taxonomic characteristics, together with the results of phylogenetic analysis, strain Sp-1 is described as a member of a new genus Ferrovibrio gen. nov., with the type species Ferrovibrio denitrificans sp. nov. and the type strain Sp-1(T) (= LMG 25817(T)  = VKM B-2673(T) ). PMID:22765162

  14. Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea.

    PubMed

    Liu, Xiupian; Li, Guangyu; Lai, Qiliang; Sun, Fengqin; Du, Yaping; Shao, Zongze

    2015-04-01

    A new aerobic, Gram stain-negative, oxidase- and catalase- positive, ovoid or rod-shaped bacterial strain, designated HTCJW17(T), was isolated from a sediment collected from the South China Sea and subjected to a polyphasic taxonomic characterization. The isolate forms small, creamy-white, opaque and circular colonies on agar plates. Growth occurs between 15 and 45 °C, 1-7 % (w/v) NaCl and pH 6-9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HTCJW17(T) belongs to the family Kordiimonadaceae of the order Kordiimonadales, with highest sequence similarity to Kordiimonas gwangyangensis GW14-5(T) (91.1 %). The major fatty acids were identified to be summed feature 8 (C18:1 ω7c/ω6c; 56.6 %), C14:0 (8.5 %), C14:0 2-OH (8.4 %), summed feature 3 (C16:1 ω7c/C16:1 ω6c; 6.2 %), and C16:0 (5.2 %). The polar lipids were determined to be phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, six unidentified glycolipids and two unidentified phospholipids. The respiratory quinone was identified as ubiquinone Q-10. The genomic DNA G+C content was determined to be 56.3 mol%. On the basis of genotypic, chemotaxonomic and phenotypic distinctness, we propose a novel genus, Emcibacter gen. nov., with Emcibacter nanhaiensis sp. nov. as the type species. The type strain is HTCJW17(T) (=CGMCC 1.12471(T) = LMG 27419(T) = MCCC 1A06723(T)).

  15. Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment.

    PubMed

    Xu, Ying; Tian, Xin-Peng; Liu, Yu-Juan; Li, Jie; Kim, Chang-Jin; Yin, Hao; Li, Wen-Jun; Zhang, Si

    2013-03-01

    A marine bacterium, designated SCSIO 03483(T), was isolated from a marine sediment sample collected from the Nansha Islands in the South China Sea. The strain produced roundish colonies with diffusible yellow-coloured pigment on nutrient agar medium or marine agar 2216. Optimal growth occurred in the presence of 0-4 % (w/v) NaCl, at pH 7.0 and a temperature range of 28-37 °C. 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flavobacteriaceae and showed relatively high sequence similarity with Imtechella halotolerans K1(T) (92.7 %). Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the isolate shared a lineage with members of the genera Imtechella, Joostella and Zhouia. Phospholipids were phosphatidylethanolamine, two unidentified aminolipids and three unknown polar lipids. The major respiratory quinone was MK-6 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). The DNA G+C content of strain SCSIO 03483(T) was 38.4 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, strain SCSIO 03483(T) represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Sinomicrobium oceani gen. nov., sp. nov. is proposed. The type strain of Sinobacterium oceani is SCSIO 03483(T) ( = KCTC 23994(T) = CGMCC 1.12145(T)).

  16. Oceanitalea nanhaiensis gen. nov., sp. nov., an actinobacterium isolated from seawater.

    PubMed

    Fu, Yingnan; Li, Qipei; Liu, Keshao; Xu, Yongle; Wang, Yanan; Jiao, Nianzhi

    2012-10-01

    A Gram-positive, motile, short-rod-shaped bacterium, designated strain JLT1488(T), was isolated from the South China Sea and investigated in a taxonomic study using a polyphasic approach. The peptidoglycan type determined for strain JLT1488(T) was A4α with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of L-Lys-L-Glu. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unknown glycolipid and an unknown phospholipid. The only detected menaquinone was MK-8(H(4)), and the major fatty acids were summed feature 8 (C(18 : 1)ω7c/C(18 : 1)ω6c) , C(16 : 0) and summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c); significant amounts of C(12 : 0) 3-OH, C(10 : 0) and C(19 : 0) cyclo ω8c were also present. The G+C content of the genomic DNA was 62.3 mol%. Comparison of the 16S rRNA gene sequence of strain JLT1488(T) with those of related type strains demonstrated that it represented a novel lineage within the family Bogoriellaceae, suborder Micrococcineae, being closely related to species of the genera Georgenia, Bogoriella and Cellulomonas (94.6-96.8 % sequence similarity). These results demonstrate that strain JLT1488(T) is a member of a new genus, for which the name Oceanitalea nanhaiensis gen. nov., sp. nov. is proposed. The type strain of the type species is JLT1488(T) ( = JCM 17755(T) = CGMCC 1.10826(T)).

  17. Dactylogyrids (Platyhelminthes: Monogenoidea) parasitizing butterfly fishes (Teleostei: Chaetodontidae) from the coral reefs of Palau, Moorea, Wallis, New Caledonia, and Australia: species of Euryhaliotrematoides n. gen. and Aliatrema n. gen.

    PubMed

    Plaisance, Laetitia; Kritsky, Delane C

    2004-04-01

    Seven species of Euryhaliotrematoides n. gen. and 1 species of Aliatrema n. gen. (Monogenoidea; Dactylogyridae) are described and reported from the gills of 15 species of butterfly fishes (Chaetodontidae) from the coral reefs of Moorea (French Polynesia), Wallis (Wallis and Futuna), Heron and Lizard (Australia), Palau (Micronesia), and New Caledonia: Aliatrema cribbi n. sp. from Chaetodon auriga, Chaetodon lunula, Chaetodon trifasciatus, Chaetodon ulietensis, Chaetodon vagabundus, Forcipiger flavisissimus, and Heniochus chrysostomus; Euryhaliotrematoides annulocirrus n. comb. from C. auriga, C. lunula, and C. vagabundus; Euryhaliotrematoides aspistis n. sp. from C. auriga, Chaetodon citrinellus, C. lunula, Chaetodon reticulatus, C. ulietensis, and C. vagabundus; Euryhaliotrematoides berenguelae n. sp. from C. citrinellus, Chaetodon ornatissimus, and F. flavisissimus; Euryhaliotrematoides grandis n. comb. from C. auriga, C. citrinellus, Chaetodon ephippium, Chaetodon kleinii, Chaetodon lineolatus, C. lunula, C. ornatissimus, C. trifasciatus, C. vagabundus, and H. chrysostomus; Euryhaliotrematoides microphallus n. comb. from C. auriga, C. citrinellus, C. ephippium, C. kleinii, C. lunula, C. ornatissimus, C. reticulatus, Chaetodon trifascialis, C. trifasciatus, C. vagabundus, F. flavisissimus, and H. chrysostomus; Euryhaliotrematoides pirulum n. sp. from C. auriga, C. citrinellus, C. lunula, C. trifasciatus, and C. vagabundus; and Euryhaliotrematoides triangulovagina n. comb. from C. auriga, C. citrinellus, C. kleinii, C. lunula, C. ornatissimus, C. vagabundus, F. flavisissimus, H. chrysostomus, and Hemitaurichthys polylepis. All reports of previously described species are new locality records. With exceptions of E. grandis and E. annulocirrus on C. auriga and C. lunula and E. triangulovagina and E. microphallus on C. auriga, all reports are new host records. Haliotrema hainanensis and H. affinis are considered junior subjective synonyms of E. triangulovagina and E

  18. Surgical Treatment of Patients Enrolled in the National Registry of Genetically Triggered Thoracic Aortic Conditions (GenTAC)

    PubMed Central

    Song, Howard K.; Bavaria, Joseph E.; Kindem, Mark W.; Holmes, Kathryn W.; Milewicz, Dianna M.; Maslen, Cheryl L.; Pyeritz, Reed E.; Basson, Craig T.; Eagle, Kim; Tolunay, H. Eser; Kroner, Barbara L.; Dietz, Hal; Menashe, Victor; Devereux, Richard B.; Desvigne-Nickens, Patrice; Ravekes, William; Weinsaft, Jonathan W.; Brambilla, Donald; Stylianou, Mario P.; Hendershot, Tabitha; Mitchell, Megan S.; LeMaire, Scott A.

    2011-01-01

    Background Genetic disorders are an important cause of thoracic aortic aneurysms (TAAs) in young patients. Despite advances in the treatment of genetically triggered TAAs, the optimal syndrome-specific treatment approach remains undefined. We used data from the NIH-funded, multicenter National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) to characterize the contemporary surgical treatment of patients with genetically triggered TAAs. Methods GenTAC’s aim is to collect longitudinal clinical data and banked biospecimens from 2800 patients with genetically triggered TAAs. We analyzed data from all patients enrolled in GenTAC to date whose clinical data were available (n=606; mean age, 37.5 years). Results The patients’ primary diagnoses included Marfan syndrome (35.8%), bicuspid aortic valve with aneurysm (29.2%), and familial TAAs and dissections (10.7%). More than half of patients (56.4%) had undergone at least 1 operation; the most common indications were aneurysm (85.7%), valve dysfunction (65.8%), and dissection (25.4%). Surgical procedures included replacement of the aortic root (50.6%), ascending aorta (64.8%), aortic arch (27.9%), and descending or thoracoabdominal aorta (12.4%). Syndrome-specific differences in age, indications for surgery, and procedure type were identified. Conclusions Patients with genetically transmitted TAAs evaluated in tertiary care centers frequently undergo surgery. Aneurysm repairs most commonly involve the aortic root and ascending aorta; distal repairs are less common. Like TAAs themselves, complications of TAAs, including dissection and aortic valve dysfunction, are important indications for surgery. Future studies will focus on syndrome- and gene-specific phenotypes, biomarkers, treatments, and outcomes to improve the treatment of patients with TAAs. PMID:19699898

  19. Assessment of Response to Lithium Maintenance Treatment in Bipolar Disorder: A Consortium on Lithium Genetics (ConLiGen) Report

    PubMed Central

    Manchia, Mirko; Adli, Mazda; Akula, Nirmala; Ardau, Raffaella; Aubry, Jean-Michel; Backlund, Lena; Banzato, Claudio EM.; Baune, Bernhard T.; Bellivier, Frank; Bengesser, Susanne; Biernacka, Joanna M.; Brichant-Petitjean, Clara; Bui, Elise; Calkin, Cynthia V.; Cheng, Andrew Tai Ann; Chillotti, Caterina; Cichon, Sven; Clark, Scott; Czerski, Piotr M.; Dantas, Clarissa; Zompo, Maria Del; DePaulo, J. Raymond; Detera-Wadleigh, Sevilla D.; Etain, Bruno; Falkai, Peter; Frisén, Louise; Frye, Mark A.; Fullerton, Jan; Gard, Sébastien; Garnham, Julie; Goes, Fernando S.; Grof, Paul; Gruber, Oliver; Hashimoto, Ryota; Hauser, Joanna; Heilbronner, Urs; Hoban, Rebecca; Hou, Liping; Jamain, Stéphane; Kahn, Jean-Pierre; Kassem, Layla; Kato, Tadafumi; Kelsoe, John R.; Kittel-Schneider, Sarah; Kliwicki, Sebastian; Kuo, Po-Hsiu; Kusumi, Ichiro; Laje, Gonzalo; Lavebratt, Catharina; Leboyer, Marion; Leckband, Susan G.; López Jaramillo, Carlos A.; Maj, Mario; Malafosse, Alain; Martinsson, Lina; Masui, Takuya; Mitchell, Philip B.; Mondimore, Frank; Monteleone, Palmiero; Nallet, Audrey; Neuner, Maria; Novák, Tomás; O’Donovan, Claire; Ösby, Urban; Ozaki, Norio; Perlis, Roy H.; Pfennig, Andrea; Potash, James B.; Reich-Erkelenz, Daniela; Reif, Andreas; Reininghaus, Eva; Richardson, Sara; Rouleau, Guy A.; Rybakowski, Janusz K.; Schalling, Martin; Schofield, Peter R.; Schubert, Oliver K.; Schweizer, Barbara; Seemüller, Florian; Grigoroiu-Serbanescu, Maria; Severino, Giovanni; Seymour, Lisa R.; Slaney, Claire; Smoller, Jordan W.; Squassina, Alessio; Stamm, Thomas; Steele, Jo; Stopkova, Pavla; Tighe, Sarah K.; Tortorella, Alfonso; Turecki, Gustavo; Wray, Naomi R.; Wright, Adam; Zandi, Peter P.; Zilles, David; Bauer, Michael; Rietschel, Marcella; McMahon, Francis J.

    2013-01-01

    Objective The assessment of response to lithium maintenance treatment in bipolar disorder (BD) is complicated by variable length of treatment, unpredictable clinical course, and often inconsistent compliance. Prospective and retrospective methods of assessment of lithium response have been proposed in the literature. In this study we report the key phenotypic measures of the “Retrospective Criteria of Long-Term Treatment Response in Research Subjects with Bipolar Disorder” scale currently used in the Consortium on Lithium Genetics (ConLiGen) study. Materials and Methods Twenty-nine ConLiGen sites took part in a two-stage case-vignette rating procedure to examine inter-rater agreement [Kappa (κ)] and reliability [intra-class correlation coefficient (ICC)] of lithium response. Annotated first-round vignettes and rating guidelines were circulated to expert research clinicians for training purposes between the two stages. Further, we analyzed the distributional properties of the treatment response scores available for 1,308 patients using mixture modeling. Results Substantial and moderate agreement was shown across sites in the first and second sets of vignettes (κ = 0.66 and κ = 0.54, respectively), without significant improvement from training. However, definition of response using the A score as a quantitative trait and selecting cases with B criteria of 4 or less showed an improvement between the two stages (ICC1 = 0.71 and ICC2 = 0.75, respectively). Mixture modeling of score distribution indicated three subpopulations (full responders, partial responders, non responders). Conclusions We identified two definitions of lithium response, one dichotomous and the other continuous, with moderate to substantial inter-rater agreement and reliability. Accurate phenotypic measurement of lithium response is crucial for the ongoing ConLiGen pharmacogenomic study. PMID:23840348

  20. New data on two remarkable Antarctic species Amblydorylaimus isokaryon (Loof, 1975) Andrássy, 1998 and Pararhyssocolpus paradoxus (Loof, 1975), gen. n., comb. n. (Nematoda, Dorylaimida)

    PubMed Central

    Elshishka, Milka; Lazarova, Stela; Radoslavov, Georgi; Hristov, Petar; Peneva, Vlada K.

    2015-01-01

    Abstract The taxonomic position of two antarctic dorylaimid species Amblydorylaimus isokaryon (Loof, 1975) Andrássy, 1998 and Pararhyssocolpus paradoxus (Loof, 1975), gen. n., comb. n. are discussed on the basis of morphological, including SEM study, morphometric, postembryonic and sequence data of 18S rDNA and the D2-D3 expansion fragments of large subunit rDNA. The evolutionary trees inferred from 18S sequences show insufficient resolution to determine the assignment of the two species to particular families, moreover Pararhyssocolpus paradoxus gen. n., comb. n. (=Rhyssocolpus paradoxus) previously regarded as a member of Nordiidae or Qudsianematidae, showed distant relationship both to Rhyssocolpus vinciguerrae and Eudorylaimus spp. The phylogram inferred from 28S sequences revealed that Amblydorylaimus isokaryon is a member of a well-supported group comprised of several Aporcelaimellus spp., while, no close relationships could be revealed for the Pararhyssocolpus paradoxus gen. n., comb. n. to any nematode genus. On the basis of molecular data and morphological characteristics, some taxonomic changes are proposed. Amblydorylaimus isokaryon is transferred from family Qudsianematidae to family Aporcelaimidae, and a new monotypic genus Pararhyssocolpus gen. n. is proposed, attributed to Pararhyssocolpidae fam. n. The diagnosis of the new family is provided together with emended diagnosis of the genera Amblydorylaimus and Pararhyssocolpus gen. n. Data concerning distribution of these endemic genera in the Antarctic region are also given. PMID:26257550

  1. Rhizonema sequoiae n.gen. n.sp. from Coast Redwood Sequoia sempervirens (D.Don) Endl.

    PubMed

    Del Prado Vera, I C; Lownsbery, B F; Maggenti, A R

    1983-07-01

    Rhizonema sequoiae n.gen, u. sp. is described from the roots of Coast Redwood, Sequoia sempervirens (D. Don) Endl., growing near Lake Lagunitas, Marin County, California. Rhizonema females are annulated over their entire bodies, are wholly embedded in host tissue, and secrete an abundant amount of gel material. Mature females do not form a cyst. The vulva is located on a large posterior terminal cone, and the anus is on the dorsal vulval lip. Esophageal glands of the second-stage larvae fill more than half of the body cavity. Tails of the vermiform males are blunt, and a cloacal tubus is present.

  2. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform.

    PubMed

    Chen, Rui; Im, Hogune; Snyder, Michael

    2015-07-01

    Multiple platforms are available for whole-exome enrichment and sequencing (WES). This protocol is based on the Roche NimbleGen SeqCap EZ Exome Library SR platform, which enriches for ∼44 Mb of the human exonic regions. The SeqCap system uses 55- to 105-base DNA probes to capture known coding DNA sequences (CDS) from the NCBI Consensus CDS Database, RefSeq, and Sanger miRBase. The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.

  3. Genome sequence and description of Desnuesiella massiliensis gen. nov., sp. nov. a new member of family Clostridiaceae

    PubMed Central

    Hadjadj, L.; Tidjani Alou, M.; Sokhna, C.; Lagier, J.-C.; Raoult, D.; Rolain, J.-M.

    2016-01-01

    Desnuesiella massiliensis, strain MT10T gen. nov., sp. nov. is a newly proposed genus within the family Clostridiaceae, isolated from the digestive microbiota of a child suffering from kwashiorkor. Desnuesiella massiliensis is a facultatively anaerobic, Gram-positive rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5 503 196-bp long genome (one chromosome but no plasmid) contains 5227 protein-coding and 81 RNA genes, including 14 rRNA genes. PMID:27158511

  4. Direct detection of Mycobacterium tuberculosis complex in nonrespiratory specimens by Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test.

    PubMed Central

    Gamboa, F; Manterola, J M; Viñado, B; Matas, L; Giménez, M; Lonca, J; Manzano, J R; Rodrigo, C; Cardona, P J; Padilla, E; Domínguez, J; Ausina, V

    1997-01-01

    The Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (AMTDT) was adapted for the detection of Mycobacterium tuberculosis complex in 224 nonrespiratory specimens from 188 patients. The sensitivity and specificity of the AMTDT for such specimens, after resolution of discrepant results, were 85.7 and 100%, respectively. Pretreatment of nonrespiratory specimens with sodium dodecyl (lauryl) sulfate is mandatory to obtain consistent and reproducible AMTDT results. The use of 500 microliters of decontaminated specimen improves the sensitivity of the test. Because the AMTDT detects stable rRNA from noncultivable bacilli, it is not useful for monitoring patients receiving treatment. PMID:8968935

  5. A new member of troglobitic Carychiidae, Koreozospeum nodongense gen. et sp. n. (Gastropoda, Eupulmonata, Ellobioidea) is described from Korea

    PubMed Central

    Jochum, Adrienne; Prozorova, Larisa; Sharyi-ool, Mariana; Páll-Gergely, Barna

    2015-01-01

    Abstract A new genus of troglobitic Carychiidae Jeffreys, 1830 is designated from Nodong Cave, North Chungcheong Province, Danyang, South Korea. This remarkable find represents a great range extension and thus, a highly distant distribution of troglobitic Carychiidae in Asia. The Zospeum-like, carychiid snails were recently included, without a formal description, in records documenting Korean malacofauna. The present paper describes Koreozospeum Jochum & Prozorova, gen. n. and illustrates the type species, Koreozospeum nodongense Lee, Prozorova & Jochum, sp. n. using novel Nano-CT images, including a video, internal shell morphology, SEM and SEM-EDX elemental compositional analysis of the shell. PMID:26312456

  6. Phase Stability under Irradiation of Precipitates and Solid Solutions in Model ALloys and in ODS Alloys Relevant for Gen IV

    SciTech Connect

    Arthur T. Motta; Robert C. Birtcher

    2007-10-17

    The overall objective of this program is to investigate the irradiation-altered phase stability of oxide precipitates in ODS steels and of model alloy solid solutions of associated systems. This information can be used to determine whether the favorable mechanical propertiies of these steels are maintained under irradiation, thus addressing one of the main materials research issues for this class of steels as identified by the GenIV working groups. The research program will also create fundamental understanding of the irradiation precipitation/dissolution problem by studying a "model" system in which the variables can be controlled and their effects understood individually.

  7. Accuracy evaluation of ClimGen weather generator and daily to hourly disaggregation methods in tropical conditions

    NASA Astrophysics Data System (ADS)

    Safeeq, Mohammad; Fares, Ali

    2011-12-01

    Daily and sub-daily weather data are often required for hydrological and environmental modeling. Various weather generator programs have been used to generate synthetic climate data where observed climate data are limited. In this study, a weather data generator, ClimGen, was evaluated for generating information on daily precipitation, temperature, and wind speed at four tropical watersheds located in Hawai`i, USA. We also evaluated different daily to sub-daily weather data disaggregation methods for precipitation, air temperature, dew point temperature, and wind speed at Mākaha watershed. The hydrologic significance values of the different disaggregation methods were evaluated using Distributed Hydrology Soil Vegetation Model. MuDRain and diurnal method performed well over uniform distribution in disaggregating daily precipitation. However, the diurnal method is more consistent if accurate estimates of hourly precipitation intensities are desired. All of the air temperature disaggregation methods performed reasonably well, but goodness-of-fit statistics were slightly better for sine curve model with 2 h lag. Cosine model performed better than random model in disaggregating daily wind speed. The largest differences in annual water balance were related to wind speed followed by precipitation and dew point temperature. Simulated hourly streamflow, evapotranspiration, and groundwater recharge were less sensitive to the method of disaggregating daily air temperature. ClimGen performed well in generating the minimum and maximum temperature and wind speed. However, for precipitation, it clearly underestimated the number of extreme rainfall events with an intensity of >100 mm/day in all four locations. ClimGen was unable to replicate the distribution of observed precipitation at three locations (Honolulu, Kahului, and Hilo). ClimGen was able to reproduce the distributions of observed minimum temperature at Kahului and wind speed at Kahului and Hilo. Although the weather

  8. Garicola koreensis gen. nov., sp. nov., isolated from saeu-jeot, traditional Korean fermented shrimp.

    PubMed

    Lo, Naysim; Lee, Se Hee; Jin, Hyun Mi; Jung, Ji Young; Schumann, Peter; Jeon, Che Ok

    2015-03-01

    A novel Gram-staining-positive, non-endospore-forming, aerobic bacterium, designated strain SJ5-4(T), was isolated from seau-jeot, a traditional food that is made by fermentation of highly salted [approximately 25 % (w/v)] shrimp in Korea. Cells were moderately halophilic, non-motile cocci or short rods that showed catalase- and oxidase-positive reactions. Growth of strain SJ5-4(T) was observed at 15-40 °C (optimum, 30 °C), at pH 6.0-9.5 (optimum, pH 6.5-7.0) and in the presence of 1-17 % (w/v) NaCl (optimum, 6 %). The major cellular fatty acids of strain SJ5-4(T) were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid, three glycolipids and an unidentified lipid were detected as the polar lipids. Strain SJ5-4(T) belonged to the exceptionally small group of strains within the order Micrococcales that show a peptidoglycan cross-linked according to the A-type but containing 2,4-diaminobutyric acid. The G+C content of the genomic DNA was 61.8 mol%. MK-7, MK-8 and MK-9 were detected as the isoprenoid quinones. Strain SJ5-4(T) was most closely related to members of the genus Nesterenkonia, with 16S rRNA gene sequence similarities of 93.1-94.8 %. However, phylogenetic inference based on 16S rRNA gene sequences showed that strain SJ5-4(T) formed a phyletic lineage distinct from members of the genus Nesterenkonia within the family Micrococcaceae. On the basis of its phenotypic and molecular features, strain SJ5-4(T) represents a novel genus and species of the family Micrococcaceae, for which the name Garicola koreensis gen. nov., sp. nov. is proposed. The type strain of Garicola koreensis is SJ5-4(T) ( = KACC 16909(T) = JCM 18572(T) = DSM 28238(T)). PMID:25563923

  9. Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae.

    PubMed

    Chen, Shaoxing; Liu, Hong-Can; Zhou, Jian; Xiang, Hua

    2016-06-01

    Two extremely halophilic archaeal strains, DYS4T and Y2, were isolated from rock salt of the Jiangcheng Salt Mine, Yunnan province, China. Cells of the two strains were non-motile, pleomorphic rods and Gram-stain-negative. The cells produced light red-pigmented colonies. Strains DYS4T and Y2 required 2.6-3.4 M NaCl, pH 7.5- 8.0 and 42 ºC in aerobic conditions for optimal growth. Mg2+ was required for growth. The major polar lipids of both strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. An unidentified minor glycolipid spot was present for strains DYS4T and Y2, which differentiates them from the closely related species of the genera Halorubrum and Halopenitus. The lipid core of the glycolipid was sn-2,3-diphytanylglycerol (C20C20). The sequence similarity of the 16S rRNA gene demonstrated that the closest relatives of strains DYS4T and Y2 were Halorubrum aidingense 31-hongT (94.1 % and 93.6 % 16S rRNA gene sequence similarity to DYS4T and Y2, respectively) and Halopenitus salinus SKJ47T (93.4% and 93.1%). Phylogenetic analysis of the 16S rRNA gene and the rpoB' gene revealed that strains DYS4T and Y2 formed an independent lineage closely related to the genera Halorubrum and Halopenitus. The DNA G+C contents of strains DYS4T and Y2 were 68.2 and 67.0 mol%, respectively. The DNA-DNA relatedness value between strains DYS4T and Y2 was 90.0 ± 0.5%, while that between strain DYS4T and other closest relatives was less than 26 % (19 ± 0.7 % for Halorubrum aidingense 31-hongT and 25 ± 0.3% for Halopenitus salinus SKJ47T). The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains DYS4T and Y2 (=CGMCC 1.15000=JCM 30892) represent a novel species of a new genus within the family Haloferacaceae, for which the name Haloparvum sedimenti gen. nov., sp. nov. is proposed. The type strain of the type species is DYS4T (=CGMCC 1.14998T=JCM 30891T

  10. Desmozoon lepeophtherii n. gen., n. sp., (Microsporidia: Enterocytozoonidae) infecting the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)

    PubMed Central

    2009-01-01

    diplokaryotic stage and a merogonial plasmodium that divides to yield uninucleate sporonts instead of transforming into a sporogonial syncitium, are features not currently associated with the family. Yet, analyses of DNA sequence data clearly place the microsporidian within the Enterocytozoonidae. Therefore, due to the novelty of the copepod host, the ultrastructural findings and the robust nature of the phylogenetic analyses, a new genus should be created within the Enterocytozoonide; Desmozoon lepeophtherii n. gen. n. sp. is proposed. PMID:19943930

  11. Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample.

    PubMed

    Nupur; Tanuku, Naga Radha Srinivas; Shinichi, Takaichi; Pinnaka, Anil Kumar

    2015-08-01

    A novel brown-coloured, Gram-negative-staining, rod-shaped, motile, phototrophic, purple sulfur bacterium, designated strain AK40T, was isolated in pure culture from a sediment sample collected from Coringa mangrove forest, India. Strain AK40T contained bacteriochlorophyll a and carotenoids of the rhodopin series as major photosynthetic pigments. Strain AK40T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically and did not utilize sulfide or thiosulfate as electron donors. Thiamine and riboflavin were required for growth. The dominant fatty acids were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile of strain AK40T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and eight unidentified lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK40T was 65.5 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae within the class Gammaproteobacteria. 16S rRNA gene sequence analysis indicated that strain AK40T was closely related to Phaeochromatium fluminis, with 95.2% pairwise sequence similarity to the type strain; sequence similarity to strains of other species of the family was 90.8-94.8%. Based on the sequence comparison data, strain AK40T was positioned distinctly outside the group formed by the genera Phaeochromatium, Marichromatium, Halochromatium, Thiohalocapsa, Rhabdochromatium and Thiorhodovibrio. Distinct morphological, physiological and genotypic differences from previously described taxa supported the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeobacterium nitratireducens gen. nov., sp. nov. is proposed. The type strain of Phaeobacterium nitratireducens is AK40T ( = JCM 19219T = MTCC 11824T

  12. Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.

    PubMed

    Ogg, Christopher D; Patel, Bharat K C

    2010-06-01

    sequence comparisons and physiological characteristics, strain AeB(T) is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeB(T) (=JCM 15555(T)=KCTC 5667(T)).

  13. A graph based algorithm for adaptable dynamic airspace configuration for NextGen

    NASA Astrophysics Data System (ADS)

    Savai, Mehernaz P.

    The National Airspace System (NAS) is a complicated large-scale aviation network, consisting of many static sectors wherein each sector is controlled by one or more controllers. The main purpose of the NAS is to enable safe and prompt air travel in the U.S. However, such static configuration of sectors will not be able to handle the continued growth of air travel which is projected to be more than double the current traffic by 2025. Under the initiative of the Next Generation of Air Transportation system (NextGen), the main objective of Adaptable Dynamic Airspace Configuration (ADAC) is that the sectors should change to the changing traffic so as to reduce the controller workload variance with time while increasing the throughput. Change in the resectorization should be such that there is a minimal increase in exchange of air traffic among controllers. The benefit of a new design (improvement in workload balance, etc.) should sufficiently exceed the transition cost, in order to deserve a change. This leads to the analysis of the concept of transition workload which is the cost associated with a transition from one sectorization to another. Given two airspace configurations, a transition workload metric which considers the air traffic as well as the geometry of the airspace is proposed. A solution to reduce this transition workload is also discussed. The algorithm is specifically designed to be implemented for the Dynamic Airspace Configuration (DAC) Algorithm. A graph model which accurately represents the air route structure and air traffic in the NAS is used to formulate the airspace configuration problem. In addition, a multilevel graph partitioning algorithm is developed for Dynamic Airspace Configuration which partitions the graph model of airspace with given user defined constraints and hence provides the user more flexibility and control over various partitions. In terms of air traffic management, vertices represent airports and waypoints. Some of the major

  14. Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost.

    PubMed

    Sakai, Masao; Deguchi, Daigo; Hosoda, Akifumi; Kawauchi, Tomohiro; Ikenaga, Makoto

    2015-02-01

    A thermophilic, agar-degrading bacterium, strain FAB2(T), was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2(T) belonged to the family Paenibacillaceae within the phylum Firmicutes. However, FAB2(T) was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus, 91.8 % for Paenibacillus barengoltzii, 89.4 % for Cohnella lupini, 90.1 % for Fontibacillus aquaticus, and 89.0 % for Saccharibacillus sacchari. Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50-65 °C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 °C and pH 8.0-8.6. Growth was inhibited at pH≤7.0 and NaCl concentrations ≥2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2(T) ( = NBRC 109510(T) = KCTC 33130(T)) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae, for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed.

  15. Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Wang, Fang; Zhou, Yu-Guang; Liu, Hong-Can; Liu, Zhi-Pei

    2015-12-01

    A Gram-stain-negative bacterium, strain TS-T30T, was isolated from a saline lake (Lake Tuosu) in Qaidam basin, Qinghai province, China, and its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, non-motile, 0.8-1.4 μm wide and 1.9-4.0 μm long. Strain TS-T30T was strictly heterotrophic and aerobic. Catalase- and oxidase-positive. Growth was observed in the presence of 0.5-11.0 % (w/v) NaCl (optimum 3.0 %), and at 10-35 °C (optimum 25 °C) and pH 6.5-10.0 (optimum pH 8.5). Strain TS-T30T contained C18 : 1ω7c as the only predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content was 62 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T30T formed a distinct lineage that was independent of other most closely related genera: Lutimaribacter (95.2-95.9 % 16S rRNA gene sequence similarities), Poseidonocella (95.4 %), Ruegeria (92.8-94.9 %), Marivita (93.6-94.9 %), Seohaeicola (94.7 %), Sediminimonas (94.7 %), Shimia (93.9-94.7 %), Oceanicola (92.6-94.5 %) and Roseicyclus (94.5 %). The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and an unknown aminolipid; phosphatidylcholine was not detected. These data demonstrated that strain TS-T30T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Lacimonas salitolerans gen. nov., sp. nov. is proposed. The type strain of the type species is TS-T30T ( = CGMCC 1.12477T = NBRC 110969T).

  16. Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

    PubMed

    Hahn, Martin W; Schmidt, Johanna; Taipale, Sami J; Doolittle, W Ford; Koll, Ulrike

    2014-09-01

    A pure culture of an actinobacterium previously described as 'Candidatus Rhodoluna lacicola' strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)).

  17. Conducting Safe and Efficient Airport Surface Operations in a NextGen Environment

    NASA Technical Reports Server (NTRS)

    Jones, Denise R.; Prinzel, Lawrence J., III; Bailey, Randall E.; Arthur, Jarvis J., III; Barnes, James R.

    2016-01-01

    The Next Generation Air Transportation System (NextGen) vision proposes many revolutionary operational concepts, such as surface trajectory-based operations (STBO) and technologies, including display of traffic information and movements, airport moving maps (AMM), and proactive alerts of runway incursions and surface traffic conflicts, to deliver an overall increase in system capacity and safety. A piloted simulation study was conducted at the National Aeronautics and Space Administration (NASA) Langley Research Center to evaluate the ability of a flight crew to conduct safe and efficient airport surface operations while utilizing an AMM. Position accuracy of traffic was varied, and the effect of traffic position accuracy on airport conflict detection and resolution (CD&R) capability was measured. Another goal was to evaluate the crew's ability to safely conduct STBO by assessing the impact of providing traffic intent information, CD&R system capability, and the display of STBO guidance to the flight crew on both head-down and head-up displays (HUD). Nominal scenarios and off-nominal conflict scenarios were conducted using 12 airline crews operating in a simulated Memphis International Airport terminal environment. The data suggest that all traffic should be shown on the airport moving map, whether qualified or unqualified, and conflict detection and resolution technologies provide significant safety benefits. Despite the presence of traffic information on the map, collisions or near-collisions still occurred; when indications or alerts were generated in these same scenarios, the incidents were averted. During the STBO testing, the flight crews met their required time-of-arrival at route end within 10 seconds on 98 percent of the trials, well within the acceptable performance bounds of 15 seconds. Traffic intent information was found to be useful in determining the intent of conflicting traffic, with graphical presentation preferred. The CD&R system was only

  18. Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands

    PubMed Central

    Kulichevskaya, Irina S.; Serkebaeva, Yulia M.; Kim, Yongkyu; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Liesack, Werner; Dedysh, Svetlana N.

    2012-01-01

    Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T = VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0–7.0 (optimum pH 5.0–5.5) and at 6–30°C (optimum 20–26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (≤0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1ω5c, C18:1ω5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9–10 double bonds) and C30:1/C32:1 (ω-1) hydroxy fatty acids. The G + C content of the DNA is 58.5–59.0 mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov. PMID

  19. Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.

    PubMed

    Huang, Zhaobin; Dong, Chunming; Shao, Zongze

    2016-09-01

    A novel Gram-stain-negative bacterium, named strain NSCS20N07DT, was isolated from surface seawater of the South China Sea. Cells of this strain contained poly-β-hydroxybutyrate granules. Growth was observed at 15-35 °C with optimum of 30 °C, at a salinity range of 1-6 % (w/v) NaCl with optimum of 3 % and at pH 5-8 with optimum of pH 5. The full-length 16S rRNA gene sequence of strain NSCS20N07DT showed highest similarity to Photobacterium iliopiscarium ATCC 51760T of 96.0 %, followed by Photobacterium kishitanii pjapo.1.1T, Photobacterium phosphoreum ATCC 11040T and Photobacterium aquimaris LC2-065T of 96.0, 95.8 and 95.7 %, respectively. Phylogenetic analysis showed that strain NSCS20N07DT formed a separate clade distinct from species of the genus Photobacterium and other genera within the family Vibrionaceae, indicating that strain NSCS20N07DT represented a novel genus affiliated with this family. The genome size of strain NSCS20N07DT was 2.5 Mb, which was much smaller than those of related species in the family Vibrionaceae. The predominant fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, C18 : 0 and summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I). The respiratory quinone was Q-8. The polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and four unidentified lipids. The DNA G+C content was 30.7 mol%. Combined, these results suggest that strain NSCS20N07DT represents a novel species of a new genus, for which the name Paraphotobacterium marinum gen. nov., sp. nov. is proposed. The type strain of Paraphotobacterium marinum is NSCS20N07DT (=KCTC 52126T=MCCC 1A01886T=CIP 111031T). PMID:27154455

  20. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species.

  1. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species. PMID:25336723

  2. Halovulum dunhuangense gen. nov., sp. nov., isolated from a saline terrestrial spring.

    PubMed

    Sun, Fengqin; Du, Yaping; Liu, Xiupian; Lai, Qiliang; Shao, Zongze

    2015-09-01

    dunhuangense gen. nov., sp. nov. is proposed. The type strain of Halovulum dunhuangense is YYQ-30(T) ( = LMG 27418(T) = MCCC 1A06483(T)). PMID:26025945

  3. Tatumella ptyseos gen. nov., sp. nov., a member of the family Enterobacteriaceae found in clinical specimens.

    PubMed Central

    Hollis, D G; Hickman, F W; Fanning, G R; Farmer, J J; Weaver, R E; Brenner, D J

    1981-01-01

    The name Tatumella ptyseos gen. nov., sp. nov., is proposed for a group of organisms (previously called group EF-9) isolated from clinical sources in the United States, Canada, and Puerto Rico. A total of 68% of these isolates were from sputum specimens. T. ptyseos strains are gram-negative, oxidase-negative, fermentative rods that grow on MacConkey agar. The distinctive biochemical characteristics of 44 T. ptyseos isolates were as follows: acid but no gas from D-glucose, sucrose, and, usually (71%), D-xylose (62% delayed); no acid from lactose, maltose, or D-mannitol; negative tests for indole, urea, methyl red, gelatin, L-lysine decarboxylase, and L-ornithine decarboxylase; L-arginine dihydrolase variable; phenylalanine deaminase positive; Voges-Proskauer positive by the Coblentz method but negative by the O'Meara method; nonmotile at 36 degrees C but 66% weakly motile (30% delayed) at 25 degrees C; Simmons citrate positive at 25 degrees C (89%) but Simmons citrate negative at 36 degrees C. Deoxyribonucleic acid-deoxyribonucleic acid relatedness studies on 26 T. ptyseos strains showed that they were 80 to 100% related at 60 degrees C, which indicated that they comprise a single species. The deoxyribonucleic acid relatedness to other species within the Enterobacteriaceae was 7 to 38%. This is evidence that this species belongs in this family, is distinct from all described species and is best placed in a new genus. The T. ptyseos isolates studied were susceptible to all of the antimicrobial agents tested by broth dilution; these antimicrobial agents were amikacin, ampicillin, cephalothin, chloramphenicol, gentamicin, kanamycin, tetracycline, and tobramycin. Three striking differences between T. ptyseos and other members of the Enterobacteriaceae were its large zone of inhibition around penicillin (mean diameter 24 mm), its tendency to die on some laboratory media (such as blood agar) within 7 days, and its small number (usually one) of flagella. Strain H36 (=ATCC

  4. Halovulum dunhuangense gen. nov., sp. nov., isolated from a saline terrestrial spring.

    PubMed

    Sun, Fengqin; Du, Yaping; Liu, Xiupian; Lai, Qiliang; Shao, Zongze

    2015-09-01

    dunhuangense gen. nov., sp. nov. is proposed. The type strain of Halovulum dunhuangense is YYQ-30(T) ( = LMG 27418(T) = MCCC 1A06483(T)).

  5. Mangroviflexus xiamenensis gen. nov., sp. nov., a member of the family Marinilabiliaceae isolated from mangrove sediment.

    PubMed

    Zhao, Chao; Gao, Zhaoming; Qin, Qiwei; Ruan, Lingwei

    2012-08-01

    A Gram-negative, obligately anaerobic, non-spore-forming, long rod-shaped bacterium strain P2(T) was isolated from the offshore mangrove sediment of the South China Sea. Growth was observed at between 22 and 39 °C, with an optimum at 35 °C. The pH range for growth was 5.0-8.5, with an optimum around pH 7.0-7.5. Salt tolerance was determined between 0.2 and 3.5% (w/v), optimum at 0.5-1.0%. Catalase and oxidase activities were negative. Strain P2(T) utilized cysteine, lactate, pyruvate, yeast extract or H(2)/CO(2)+acetate as electron donors, and sulfate or sulfite as electron acceptors. Metabolism was strictly fermentative. The main organic fermentation products were propionate, acetate and succinate. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P2(T) formed a distinct evolutionary lineage within the family Marinilabiliaceae. Strain P2(T) was most closely related to members of the genera Alkaliflexus (92.0% 16S rRNA gene sequence similarity), Marinilabilia (91.7%) and Anaerophaga (89.9%) of the family Marinilabiliaceae. The DNA G+C content of the novel strain was 44.2 ± 1.0 mol%. The dominant fatty acids of strain P2(T) were iso-C(15:0) (33.5%), anteiso-C(15:0) (18.9%), C(16:0) (5.4%), C(16:0) 3-OH (7.7%) and iso-C(17:0) 3-OH (13.3%). The respiratory quinone was menaquinone 7 (100% of total quinone) and the major polar lipid was phosphatidylethanolamine. Strain P2(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of phylogenetic, phenotypic and physiological evidence, a novel genus, Mangroviflexus, is proposed to harbour strain P2(T) ( = CGMCC 1.5167(T) = DSM 24214(T)) which is described as the type strain of a novel species, Mangroviflexus xiamenensis gen. nov., sp. nov.

  6. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater.

    PubMed

    Zhang, Xin-Qi; Sun, Cong; Wang, Chun-Sheng; Zhang, Xin; Zhou, Xiang; Wu, Yue-Hong; Xu, Xue-Wei; Wu, Min

    2015-10-01

    Two aerobic, rod-shaped, non-motile, non-sporulating and Gram-staining-negative bacterial strains, namely NH6-24T and Za3-11, were isolated from the surface seawater of the South China Sea and the estuary of the Yangtze River, respectively. The two isolates grew at 14–44 °C (optimum 37–40 °C) and pH 6.0–8.5 (optimum pH 7.0–7.5). The sea salt ranges for growth were 0.5–10 % (w/v) (optimum 1–2.5 %) for strain NH6-24T and 0–12 % (w/v) (optimum 0.5–4.5 %) for strain Za3-11.Both strains could grow in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates showed closest affinity to the genera Fontimonas (96.0 %) and Solimonas (94.1–95.1 %) and formed a single lineage in the cluster of the family Solimonadaceae. The predominant isoprenoid quinone was ubiquinone-8.The major fatty acids were C18 : 1ω7c, iso-C16 : 0 and C16 : 0.The dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 65 mol%. Based on the polyphasic taxonomic characterization, strains NH6-24T and Za3-11 are considered to represent a novel species of a novel genus, for which the name Sinimarinibacterium flocculans gen. nov., sp. nov. is proposed. The type strain of the type species is NH6-24T ( = CGMCC 1.10815T = JCM 17607T) and an additional strain is Za3-11 ( = CGMCC 1.10816 = JCM 17606).

  7. Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.

    PubMed

    Huang, Zhaobin; Dong, Chunming; Shao, Zongze

    2016-09-01

    A novel Gram-stain-negative bacterium, named strain NSCS20N07DT, was isolated from surface seawater of the South China Sea. Cells of this strain contained poly-β-hydroxybutyrate granules. Growth was observed at 15-35 °C with optimum of 30 °C, at a salinity range of 1-6 % (w/v) NaCl with optimum of 3 % and at pH 5-8 with optimum of pH 5. The full-length 16S rRNA gene sequence of strain NSCS20N07DT showed highest similarity to Photobacterium iliopiscarium ATCC 51760T of 96.0 %, followed by Photobacterium kishitanii pjapo.1.1T, Photobacterium phosphoreum ATCC 11040T and Photobacterium aquimaris LC2-065T of 96.0, 95.8 and 95.7 %, respectively. Phylogenetic analysis showed that strain NSCS20N07DT formed a separate clade distinct from species of the genus Photobacterium and other genera within the family Vibrionaceae, indicating that strain NSCS20N07DT represented a novel genus affiliated with this family. The genome size of strain NSCS20N07DT was 2.5 Mb, which was much smaller than those of related species in the family Vibrionaceae. The predominant fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, C18 : 0 and summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I). The respiratory quinone was Q-8. The polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and four unidentified lipids. The DNA G+C content was 30.7 mol%. Combined, these results suggest that strain NSCS20N07DT represents a novel species of a new genus, for which the name Paraphotobacterium marinum gen. nov., sp. nov. is proposed. The type strain of Paraphotobacterium marinum is NSCS20N07DT (=KCTC 52126T=MCCC 1A01886T=CIP 111031T).

  8. Oceanirhabdus sediminicola gen. nov., sp. nov., an anaerobic bacterium isolated from sea sediment.

    PubMed

    Pi, Ruo-Xi; Zhang, Wen-Wu; Fang, Ming-Xu; Zhang, Yan-Zhou; Li, Tian-Tian; Wu, Min; Zhu, Xu-Fen

    2013-11-01

    A novel anaerobic bacterium, designated NH-JN4(T) was isolated from a sediment sample collected in the South China Sea. Cells were Gram-stain-positive, spore-forming, peritrichous and rod-shaped (0.5-1.2×2.2-7 µm). The temperature and pH ranges for growth were 22-42 °C and pH 6.0-8.5. Optimal growth occurred at 34-38 °C and pH 6.5-7.0. The NaCl concentration range for growth was 0.5-6 % (w/v) with an optimum of 2.5 %. Catalase and oxidase were not produced. Substrates which could be utilized were peptone, tryptone, yeast extract, beef extract and glycine. Main fermentation products from PYG medium were formate, acetate, butyrate and ethanol. Strain NH-JN4(T) could utilize sodium sulfite as an electron acceptor. No respiratory quinone was detected. The predominant fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0 DMA. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The DNA G+C content was 35.8 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain NH-JN4(T) was a member of family Clostridiaceae, and was most closely related to Clostridium limosum ATCC 25620(T), Clostridium proteolyticum DSM 3090(T), Clostridium histolyticum ATCC 19401(T) and Clostridium tepidiprofundi SG 508(T), showing 94.0, 93.0, 92.9 and 92.3 % sequence similarity, respectively. On the basis of phenotypic, genotypic and chemotaxonomic properties, strain NH-JN4(T) represents a novel species of a new genus in the family Clostridiaceae, for which the name Oceanirhabdus sediminicola gen. nov., sp. nov. is proposed. The type strain of the type species is NH-JN4(T) ( = JCM 18501(T) = CCTCC AB 2013103(T) = KCTC 15322(T)).

  9. Ultrastructure and 18S rDNA phylogeny of Apoikia lindahlii comb. nov. (Chrysophyceae) and its epibiontic protists, Filos agilis gen. et sp. nov. (Bicosoecida) and Nanos amicus gen. et sp. nov. (Bicosoecida).

    PubMed

    Kim, Eunsoo; Yubuki, Naoji; Leander, Brian S; Graham, Linda E

    2010-04-01

    Three heterotrophic stramenopiles--Apoikia lindahlii comb. nov. (Chrysophyceae), Filos agilis gen. et sp. nov. (Bicosoecida), and Nanos amicus gen. et sp. nov. (Bicosoecida)--were isolated from acidic peat bogs. The biflagellate A. lindahlii forms loose irregular colonies from which swimming cells may detach, and produces extensive mucilaginous material containing bacterial cells. Phylogenetic analyses of small subunit rDNA sequences demonstrated that A. lindahlii branches within the Chrysophyceae. While A. lindahlii is an obligate heterotroph, ultrastructural observations revealed a leukoplast in the perinuclear region. The pico-sized uniflagellates F. agilis and N. amicus were isolated from separate lakes and within the mucilage of A. lindahlii, suggesting their close associations in natural habitats. In SSU rDNA phylogenies, F. agilis and N. amicus were closely related to the bicosoecids Adriamonas, Siluania, Paramonas, and Nerada. While Filos, Nanos, and Siluania are similar in light microscopic features, their SSU rDNA gene sequences differed significantly (>8% differences) and were not monophyletic. Both F. agilis and N. amicus have a cytostome/cytopharynx particle ingestion apparatus. Bacterial cells and material similar to the mucilage of A. lindahlii occurred within the food vacuole of F. agilis and N. amicus. The nature of association between A. lindahlii and its epibiontic bicosoecids is discussed.

  10. Anatoliacodium gen. nov. (Halimedaceae, Green algae) from the Ilerdian-Cuisian in the Eskişehir region (Western Central Turkey)

    NASA Astrophysics Data System (ADS)

    Erdem, Nazire Özgen; Radoicic, Rajka

    2009-08-01

    A new genus Anatoliacodium (Halimedaceae, Green algae) is described from the Ilerdian-Cuisian shallow-water sediments of Eskişehir region, central-western Turkey. These sequences consist of limestones, clayey limestones, sandy limestones and claystones. Anatoliacodium gen. nov. is characterized by erected calcareous segments with well differentiated inner structure: prevailing with large medulla of more or less densely set parallel filaments and cortical zone of prevailing horizontal to subhorizontal cortical filaments, once branching and without constriction. It is supposed that poorly and rarely preserved noncalcareous structures on the skeleton surface could be reproductive structures. The type species of the new genus is Anatoliacodium xinanmui gen. nov. sp. nov. A further new species is also described: Anatoliacodium merici gen. nov. sp. nov. Finally Gymnocodium nummuliticum Pfender, 1966 is emended and transferred to the genus Anatoliacodium.

  11. High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae

    PubMed Central

    2014-01-01

    The family Rickettsiaceae currently includes two genera: Orientia that contains one species, Orientiatsutsugamushi, and Rickettsia that contains 28 species. Occidentia massiliensis gen. nov., sp. nov. strain OS118T is the type strain of O. massiliensis gen. nov., sp. nov., the type species of the new genus Occidentia gen. nov. within the family Rickettsiaceae. This strain, whose genome is described here, was isolated in France from the soft tick Ornithodoros sonrai collected in Senegal. O. massiliensis is an aerobic, rod-shaped, Gram-negative, obligate intracellular bacillus that may be cultivated in BME/CTVM2 cells. Here we describe the features of O. massiliensis, together with the complete genomic sequencing and annotation. The 1,469,252 bp long genome (1 chromosome but no plasmid) contains 1,670 protein-coding and 41 RNA genes, including one rRNA operon. PMID:25780502

  12. Modeling and Evaluating Pilot Performance in NextGen: Review of and Recommendations Regarding Pilot Modeling Efforts, Architectures, and Validation Studies

    NASA Technical Reports Server (NTRS)

    Wickens, Christopher; Sebok, Angelia; Keller, John; Peters, Steve; Small, Ronald; Hutchins, Shaun; Algarin, Liana; Gore, Brian Francis; Hooey, Becky Lee; Foyle, David C.

    2013-01-01

    NextGen operations are associated with a variety of changes to the national airspace system (NAS) including changes to the allocation of roles and responsibilities among operators and automation, the use of new technologies and automation, additional information presented on the flight deck, and the entire concept of operations (ConOps). In the transition to NextGen airspace, aviation and air operations designers need to consider the implications of design or system changes on human performance and the potential for error. To ensure continued safety of the NAS, it will be necessary for researchers to evaluate design concepts and potential NextGen scenarios well before implementation. One approach for such evaluations is through human performance modeling. Human performance models (HPMs) provide effective tools for predicting and evaluating operator performance in systems. HPMs offer significant advantages over empirical, human-in-the-loop testing in that (1) they allow detailed analyses of systems that have not yet been built, (2) they offer great flexibility for extensive data collection, (3) they do not require experimental participants, and thus can offer cost and time savings. HPMs differ in their ability to predict performance and safety with NextGen procedures, equipment and ConOps. Models also vary in terms of how they approach human performance (e.g., some focus on cognitive processing, others focus on discrete tasks performed by a human, while others consider perceptual processes), and in terms of their associated validation efforts. The objectives of this research effort were to support the Federal Aviation Administration (FAA) in identifying HPMs that are appropriate for predicting pilot performance in NextGen operations, to provide guidance on how to evaluate the quality of different models, and to identify gaps in pilot performance modeling research, that could guide future research opportunities. This research effort is intended to help the FAA

  13. Gen-2 RFID compatible, zero down-time, programmable mechanical strain-monitors and mechanical impact detectors

    NASA Astrophysics Data System (ADS)

    Chakrabartty, Shantanu; Feng, Tao; Aono, Kenji

    2013-04-01

    A key challenge in structural health monitoring (SHM) sensors embedded inside civil structures is that elec- tronics need to operate continuously such that mechanical events of interest can be detected and appropriately analyzed. Continuous operation however requires a continuous source of energy which cannot be guaranteed using conventional energy scavenging techniques. The paper describes a hybrid energy scavenging SHM sensor which experiences zero down-time in monitoring mechanical events of interest. At the core of the proposed sensor is an analog floating-gate storage technology that can be precisely programmed at nano-watt and pico- watt power levels. This facilitates self-powered, non-volatile data logging of the mechanical events of interest by scavenging energy directly from the mechanical events itself. Remote retrieval of the stored data is achieved using a commercial off-the-shelf Gen-2 radio-frequency identification (RFID) reader which periodically reads an electronic product code (EPC) that encapsulates the sensor data. The Gen-2 interface also facilitates in simultaneous remote access to multiple sensors and also facilitates in determining the range and orientation of the sensor. The architecture of the sensor is based on a token-ring topology which enables sensor channels to be dynamically added or deleted through software control.

  14. Using the PhenoGen Website for “In Silico” Analysis of Morphine-Induced Analgesia: Identifying Candidate Genes

    PubMed Central

    Hoffman, Paula L.; Bennett, Beth; Saba, Laura M.; Bhave, Sanjiv V.; Carosone-Link, Phyllis J.; Hornbaker, Cheryl K.; Kechris, Katerina J.; Williams, Robert W.; Tabakoff, Boris

    2010-01-01

    The identification of genes that contribute to polygenic (complex) behavioral phenotypes is a key goal of current genetic research. One approach to this goal is to combine gene expression information with genetic information, i.e., to map chromosomal regions that regulate gene expression levels. This approach has been termed “genetical genomics”, and, when used in conjunction with the identification of genomic regions (QTLs) that regulate the complex physiological trait under investigation, provides a strong basis for candidate gene discovery. In this paper, we describe the implementation of the genetical genomic/phenotypic approach to identify candidate genes for sensitivity to the analgesic effect of morphine in BXD recombinant inbred mice. Our analysis was performed “in silico”, using an online interactive resource called PhenoGen (http://phenogen.ucdenver.edu). We describe in detail the use of this resource, which identified a set of candidate genes, some of whose products regulate the cellular localization and activity of the mu opiate receptor. The results demonstrate how PhenoGen can be used to identify a novel set of genes that can be further investigated for their potential role in pain, morphine analgesia and/or morphine tolerance. PMID:21054686

  15. A Controller-in-the Loop Simulation of Ground-Based Automated Separation Assurance in a NextGen Environment

    NASA Technical Reports Server (NTRS)

    Homola, J.; Prevot, Thomas; Mercer, Joey S.; Brasil, Connie L.; Martin, Lynne Hazel; Cabrall, C.

    2010-01-01

    A controller-in-the-loop simulation was conducted in the Airspace Operations Laboratory (AOL) at the NASA Ames Research Center to investigate the functional allocation aspects associated with ground-based automated separation assurance in a far-term NextGen environment. In this concept, ground-based automation handled the detection and resolution of strategic and tactical conflicts and alerted the controller to deferred situations. The controller was responsible for monitoring the automation and managing situations by exception. This was done in conditions both with and without arrival time constraints across two levels of traffic density. Results showed that although workload increased with an increase in traffic density, it was still manageable in most situations. The number of conflicts increased similarly with a related increase in the issuance of resolution clearances. Although over 99% of conflicts were resolved, operational errors did occur but were tied to local sector complexities. Feedback from the participants revealed that they thought they maintained reasonable situation awareness in this environment, felt that operations were highly acceptable at the lower traffic density level but were less so as it increased, and felt overall that the concept as it was introduced here was a positive step forward to accommodating the more complex environment envisioned as part of NextGen.

  16. Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria.

    PubMed

    Roldán, M; Ramírez, M; del Campo, J; Hernández-Mariné, M; Komárek, J

    2013-06-01

    This work characterizes a unicellular cyanobacterium with nearly spherical cells and thin-outlined sheaths that divide irregularly, forming small packets immersed in a diffluent mucilaginous layer. It was isolated growing on calcite speleothems and walls in a show cave in Collbató (Barcelona, Spain). Spectral confocal laser and transmission electron microscopy were used to describe the morphology, fine structure and thylakoid arrangement. The pigments identified were phycoerythrin, phycocyanin, allophycocyanin and chlorophyll a. Three-dimensional reconstructions, generated from natural fluorescence z-stacks, revealed a large surface area of nearly flat, arm-like thylakoidal membranes connected to each other and forming a unified structure in a way that, to our knowledge, has never been described before. Phylogenetic analyses using the 16S rRNA gene sequence showed 95% similarity to strain Chroococcus sp. JJCM (GenBank accession no. AM710384). The diacritical phenotypic features do not correspond to any species currently described, and the genetic traits support the strain being classified as the first member of an independent genus in the order Chroococcales and the family Chroococcaceae. Hence, we propose the name Chalicogloea cavernicola gen. nov., sp. nov. under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. The type strain of Chalicogloea cavernicola is COLL 3(T) (=CCALA 975(T) =CCAP 1424/1(T)).

  17. Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data

    PubMed Central

    Breinholt, Jesse W.; Kawahara, Akito Y.

    2013-01-01

    Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions. PMID:24148944

  18. Lanfrediella amphicirrus gen. nov. sp. nov. Nematotaeniidae (Cestoda: Cyclophyllidea), a tapeworm parasite of Rhinella marina (Linnaeus, 1758) (Amphibia: Bufonidae).

    PubMed

    Melo, Francisco Tiago de Vasconcelos; Giese, Elane Guerreiro; Furtado, Adriano Penha; Soares, Maurílio José; Gonçalves, Evonnildo Costa; Vallinoto, Antonio Carlos Rosário; Santos, Jeannie Nascimento dos

    2011-09-01

    The family Nematotaeniidae, tapeworms commonly found in the small intestines of amphibians and reptiles, includes 27 recognised species distributed among four genera: Bitegmen Jones, Cylindrotaenia Jewell, Distoichometra Dickey and Nematotaenia Lühe. The taxonomy of these cestodes is poorly defined, due in part to the difficulties of observing many anatomical traits. This study presents and describes a new genus and species of nematotaeniid parasite found in cane toads (Rhinella marina) from eastern Brazilian Amazonia. The cestodes were collected during the necropsy of 20 hosts captured in the urban area of Belém, Pará. The specimens were fixed and processed for light microscopy, scanning electron microscopy (SEM) and three-dimensional (3D) reconstruction. Samples were also collected for molecular analyses. The specimens presented a cylindrical body, two testes and paruterine organs. However, they could not be allocated to any of the four existing nematotaeniid genera due to the presence of two each of dorsal compact medullary testes, cirri, cirrus pouches, genital pores, ovaries and vitelline glands per mature segment. Lanfrediella amphicirrus gen. nov. sp. nov. is the first nematotaeniid studied using Historesin analysis, SEM and 3D reconstruction, and it is the second taxon for which molecular data have been deposited in GenBank.

  19. A new anaerobic fungus (Oontomyces anksri gen. nov., sp. nov.) from the digestive tract of the Indian camel (Camelus dromedarius).

    PubMed

    Dagar, Sumit S; Kumar, Sanjay; Griffith, Gareth W; Edwards, Joan E; Callaghan, Tony M; Singh, Rameshwar; Nagpal, Ashok K; Puniya, Anil K

    2015-08-01

    Two cultures of anaerobic fungi were isolated from the forestomach of an Indian camel (Camelus dromedarius). Phylogenetic analysis using both the internal transcribed spacer (ITS) and large-subunit (LSU) regions of the rRNA locus demonstrated that these isolates were identical and formed a distinct clade within the anaerobic fungi (phylum Neocallimastigomycota). Morphological examination showed that these fungi formed monocentric thalli with filamentous rhizoids and uniflagellate zoospores, broadly similar to members of the genus Piromyces. However, distinctive morphological features were observed, notably the pinching of the cytoplasm in the sporangiophore and the formation of intercalary rhizoidal swellings. Since genetic analyses demonstrated this fungus was only distantly related to Piromyces spp. and closer to the polycentric Anaeromyces clade, we have assigned it to a new genus and species Oontomyces anksri gen. nov., sp. nov. Interrogation of the GenBank database identified several closely related ITS sequences, which were all environmental sequences obtained from camels, raising the possibility that this fungus may be specific to camelids. PMID:26228561

  20. New Australian stiletto flies: revision of Manestella Metz and description of Medomega gen. n. (Diptera, Therevidae, Agapophytinae)

    PubMed Central

    Winterton, Shaun L.; Lambkin, Christine L.

    2012-01-01

    Abstract The previously monotypic genus Manestella Metz, 2003 is revised with a single species, Manestella tristriata (Mann, 1933), redescribed and an additional 14 new species described: Manestella caesia sp. n., Manestella campestris sp. n., Manestella canities sp. n., Manestella cooloola sp. n., Manestella fumosa sp. n., Manestella incompleta sp. n., Manestella nubis sp. n., Manestella obscura sp. n., Manestella ocellaris sp. n., Manestella persona sp. n., Manestella poecilothorax sp. n., Manestella umbrapennis sp. n., Manestella vasta sp. n. and Manestella vespera sp. n. The putative sister genus to Manestella, Medomega gen. n., is described containing six new species: Medomega averyi sp. n., Medomega bailmeup sp. n., Medomega chlamydos sp. n., Medomega danielsi sp. n., Medomega gigasathe sp. n., and Medomega nebrias sp. n. Complete taxonomic descriptions were generated from a character matrix developed in Lucid Builder from which natural language descriptions (NLD) were parsed. Images of all species of Manestella and Medomega gen. n. are included, along with dichotomous keys to species. PMID:23226714

  1. Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae

    PubMed Central

    Mishra, Ajay Kumar; Lagier, Jean-Christophe; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Timonella senegalensis strain JC301T gen. nov., sp. nov. is the type strain of T. senegalensis gen. nov., sp. nov., a new species within the newly proposed genus Timonella. This bacterial strain was isolated from the fecal flora of a healthy Senegalese patient. In this report, we detail the features of this organism, together with the complete genome sequence and annotation. Timonella senegalensis strain JC301T exhibits the highest 16S rRNA similarity (95%) with Sanguibacter marinus, the closest validly published bacterial species. The genome of T. senegalensis strain JC301T is 3,010,102-bp long, with one chromosome and no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes, including 5 rRNA genes. The genomic annotation revealed that T. senegalensis strain JC301T possesses the complete complement of enzymes necessary for the de novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin), as well as the enzymes involved in the metabolism of various carbon sources, chaperone genes, and genes involved in the regulation of polyphosphate and glycogen levels. PMID:23991262

  2. The NextGen Model Atmosphere Grid for 3000{le}T{sub eff}{le}10,000 K

    SciTech Connect

    Hauschildt, P.H.; Allard, F.; Baron, E.

    1999-02-01

    We present our NextGen Model Atmosphere grid for low-mass stars for effective temperatures larger than 3000 K. These LTE models are calculated with the same basic model assumptions and input physics as the VLMS part of the NextGen grid so that the complete grid can be used, e.g., for consistent stellar evolution calculations and for internally consistent analysis of cool star spectra. This grid is also the starting point for a large grid of detailed NLTE model atmospheres for dwarfs and giants. The models were calculated from 3000 to 10,000 K (in steps of 200 K) for 3.5{le}logthinspg{le}5.5 (in steps of 0.5) and metallicities of {minus}4.0{le}[M/H]{le}0.0. We discuss the results of the model calculations and compare our results to the Kurucz grid. Some comparisons to standard stars like Vega and the Sun are presented and compared with detailed NLTE calculations. {copyright} {ital {copyright} 1999.} {ital The American Astronomical Society}

  3. 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.

  4. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

    PubMed Central

    2013-01-01

    Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search Gen

  5. Description of Auriculotrema lechneri n. gen., n. sp. (Digenea: Choanocotylidae), a parasite of freshwater turtles (Testudines: Pleurodira: Chelidae) from Queensland, Australia.

    PubMed

    Platt, Thomas R

    2003-02-01

    Auriculotrema lechneri n. gen., n. sp. is described from the small intestine of Emydura krefftii and Elseya latisternum from northern Queensland, Australia. The new species strongly resembles species of Choanocotyle in body shape, ventral incision of the oral sucker, structure of the cirrus sac, and location of the genital pore. The distinctive taxonomic feature is the presence of 2 winglike projections extending beyond the lateral margins of the oral sucker, in contrast to the extremely large, expanded oral sucker diagnostic of Choanocotyle spp. Auriculotrema n. gen. is the second genus included in the formerly monotypic Choanocotylidae Jue Sue and Platt, 1998. PMID:12659317

  6. Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov.

    PubMed

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

    2014-02-01

    novel genus and species and that strain GRS42(T) represents a novel species in the family Microbacteriaceae. The genus Galbitalea gen. nov. is proposed, with strain KIS82-1(T) ( = KACC 15520(T) = NBRC 108727(T)) as the type strain of the type species, Galbitalea soli sp. nov. Strain GRS42(T) ( = KACC 15521(T) = NBRC 108728(T)) is proposed as the type strain of Frondihabitans sucicola sp. nov. PMID:24132916

  7. Progress reports for Gen IV sodium fast reactor activities FY 2007.

    SciTech Connect

    Cahalan, J. E.; Tentner, A. M.; Nuclear Engineering Division

    2007-10-04

    for prevention of progression into severe accident conditions (prevention of core melting) or for mitigation of severe accident consequences (mitigation of the impact of core melting to protect public health and safety). Because design measures for severe accident prevention and mitigation are beyond the normal design basis, established regulatory guidelines and codes do not provide explicit identification of the design performance requirements for severe accident accommodation. The treatment of severe accidents is one of the key issues of R&D plans for the Gen IV systems in general, and for the Sodium Fast Reactor (SFR) in particular. Despite the lack of an unambiguous definition of safety approach applicable for severe accidents, there is an emerging consensus on the need for their consideration for the design. The US SFR program and Argonne National Laboratory (ANL) in particular have actively studied the potential scenarios and consequences of Hypothetical Core Disruptive Accidents (HCDA) for SFRs with oxide fuel during the Fast Flux Test Facility (FFTF) and Clinch River Breeder Reactor Plant (CRBRP) programs in the 70s and 80s. Later, the focus of the US SFR safety R&D activities shifted to the prevention of all HCDAs through passive safety features of the SFRs with metal fuel in the Integral Fast Reactor (IFR) program, and the study of severe accident consequences was de-emphasized. The goal of this paper is to provide an overview of the current SFR safety approach and the role of severe accidents in Japan and France, in preparation for an expected and more active collaboration in this area between the US, Japan, and France.

  8. Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial Vaginosis.

    PubMed

    Maheux, Andrée F; Bérubé, Ève; Boudreau, Dominique K; Raymond, Frédéric; Corbeil, Jacques; Roy, Paul H; Boissinot, Maurice; Omar, Rabeea F

    2016-01-01

    Criibacterium bergeronii gen. nov., sp. nov., CCRI-22567 is the type strain of the new genus Criibacterium The strain was isolated from a woman with bacterial vaginosis. The genome assembly comprised 2,384,460 bp, with 34.4% G+C content. This is the first genome announcement of a strain belonging to the genus Criibacterium. PMID:27587833

  9. El NCI inicia un estudio para evaluar la utilidad de la secuenciación genética para mejorar los resu

    Cancer.gov

    El Instituto Nacional del Cáncer (NCI) lanzará este mes un estudio clínico piloto denominado M-PACT con la finalidad de evaluar si el tratamiento asignado según mutaciones genéticas específicas puede brindar beneficios a pacientes con tumores sólidos meta

  10. Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial Vaginosis

    PubMed Central

    Maheux, Andrée F.; Bérubé, Ève; Boudreau, Dominique K.; Raymond, Frédéric; Corbeil, Jacques; Roy, Paul H.

    2016-01-01

    Criibacterium bergeronii gen. nov., sp. nov., CCRI-22567 is the type strain of the new genus Criibacterium. The strain was isolated from a woman with bacterial vaginosis. The genome assembly comprised 2,384,460 bp, with 34.4% G+C content. This is the first genome announcement of a strain belonging to the genus Criibacterium. PMID:27587833

  11. 75 FR 27332 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources, LLC; Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources... Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC, and Eagle Creek Land Resources, LLC.... For the transferee: Mr. Paul Ho, Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC,...

  12. 77 FR 13592 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC, Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-07

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources... Power, LLC, Eagle Creek Water Resources, LLC, and Eagle Creek Land Resources, LLC (transferees) filed an...) 805-1469. Transferees: Mr. Bernard H. Cherry, Eagle Creek Hydro Power, LLC, Eagle Creek...

  13. Position of the dentifera-group in the Coronatella-branch and its relocation to a new genus: Magnospina gen. n. (Crustacea, Chydoridae, Aloninae)

    PubMed Central

    Sousa, Francisco Diogo R.; Elmoor-Loureiro, Lourdes Maria Abdu; Santos, Sandro

    2016-01-01

    Abstract Magnospina gen. n. was created to relocate species of the dentifera-group from Alona sensu lato (Crustacea: Cladocera) and include Magnospina dentifera comb. n. and Magnospina siamensis comb. n. The synapomorphies of the Magnospina gen. n. are (1) basal spines longer than 2/3 of the postabdominal claw, (2) presence of 1–4 large denticles, broad at their bases, protruding downwards, without setules between them. Morphological traits such as habitus, rostrum and postabdomen shape, armature of IDL setae, number of setae on the exopod of limb III are also important in the distinction between Magnospina gen. n. and other genera from the Coronatella-branch. The morphology of Magnospina dentifera comb. n. male confirms the closer relationship with the clade composed by the elgans-group from Alona sensu lato, Ovalona and Leberis, but the external morphology, morphology of the postabdominal claw, basal spine and setae 2–3 of IDL support their separation from any of the group cited. It is concluded that the Coronatella-lineage of Aloninae is composed of the genera Coronatella, Anthalona, Karualona, Bergamina, Extremalona, Ovalona, Celsinotum, Leberis and Magnospina gen. n. The elegans-group from Alona sensu lato also belongs to Coronatella-lineage, but still need formal allocation. PMID:27199609

  14. Film and Language Learning in Victorian Schools: A Study of the 2009 Next Gen Program of the "Melbourne International Film Festival"

    ERIC Educational Resources Information Center

    Lo Bianco, Hana

    2010-01-01

    This article investigates the role of film in language education based on a study of the 2009 "Melbourne International Film Festival" (MIFF). It is structured around a literature review and results from surveys of students and teachers who participated in the young people's section of the program, Next Gen. The article argues that film can provide…

  15. Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma)

    PubMed Central

    Liu, Alexander G.; Matthews, Jack J.; Menon, Latha R.; McIlroy, Duncan; Brasier, Martin D.

    2014-01-01

    Muscle tissue is a fundamentally eumetazoan attribute. The oldest evidence for fossilized muscular tissue before the Early Cambrian has hitherto remained moot, being reliant upon indirect evidence in the form of Late Ediacaran ichnofossils. We here report a candidate muscle-bearing organism, Haootia quadriformis n. gen., n. sp., from approximately 560 Ma strata in Newfoundland, Canada. This taxon exhibits sediment moulds of twisted, superimposed fibrous bundles arranged quadrilaterally, extending into four prominent bifurcating corner branches. Haootia is distinct from all previously published contemporaneous Ediacaran macrofossils in its symmetrically fibrous, rather than frondose, architecture. Its bundled fibres, morphology, and taphonomy compare well with the muscle fibres of fossil and extant Cnidaria, particularly the benthic Staurozoa. Haootia quadriformis thus potentially provides the earliest body fossil evidence for both metazoan musculature, and for Eumetazoa, in the geological record. PMID:25165764

  16. Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef.

    PubMed

    Oborník, Miroslav; Modrý, David; Lukeš, Martin; Cernotíková-Stříbrná, Eva; Cihlář, Jaromír; Tesařová, Martina; Kotabová, Eva; Vancová, Marie; Prášil, Ondřej; Lukeš, Julius

    2012-03-01

    Chromerida are photoautotrophic alveolates so far only isolated from corals in Australia. It has been shown that these secondary plastid-containing algae are closely related to apicomplexan parasites and share various morphological and molecular characters with both Apicomplexa and Dinophyta. So far, the only known representative of the phylum was Chromera velia. Here we provide a formal description of another chromerid, Vitrella brassicaformis gen. et sp. nov., complemented with a detailed study on its ultrastructure, allowing insight into its life cycle. The novel alga differs significantly from the related chromerid C. velia in life cycle, morphology as well as the plastid genome. Analysis of photosynthetic pigments on the other hand demonstrate that both chromerids lack chlorophyll c, the hallmark of phototrophic chromalveolates. Based on the relatively high divergence between C. velia and V. brassicaformis, we propose their classification into distinct families Chromeraceae and Vitrellaceae. Moreover, we predict a hidden and unexplored diversity of the chromerid algae. PMID:22055836

  17. Third-Party Evaluation of Petro Tex Hydrocarbons, LLC, ReGen Lubricating Oil Re-refining Process

    SciTech Connect

    Compere, A L; Griffith, William {Bill} L

    2009-04-01

    This report presents an assessment of market, energy impact, and utility of the PetroTex Hydrocarbons, LLC., ReGen process for re-refining used lubricating oil to produce Group I, II, and III base oils, diesel fuel, and asphalt. PetroTex Hydrocarbons, LLC., has performed extensive pilot scale evaluations, computer simulations, and market studies of this process and is presently evaluating construction of a 23 million gallon per year industrial-scale plant. PetroTex has obtained a 30 acre site in the Texas Industries RailPark in Midlothian Texas. The environmental and civil engineering assessments of the site are completed, and the company has been granted a special use permit from the City of Midlothian and air emissions permits for the Texas Commission on Environmental Quality.

  18. Leptohelia flexibilis gen. nov. et sp. nov., a remarkable deep-sea stylasterid (Cnidaria: Hydrozoa: Stylasteridae) from the southwest Pacific.

    PubMed

    Lindner, Alberto; Cairns, Stephen D; Zibrowius, Helmut

    2014-01-01

    Leptohelia flexibilis gen. nov. et sp. nov., the first stylasterid with a combined calcified and non-calcified skeleton, is described from seamounts and the slope off the islands of New Caledonia, in the southwestern Pacific. The new species is distinguished from all other species of the family Stylasteridae by having a non-calcified organic axis, internal to the basal portion of the calcified corallum. The internal axis is flexible and enclosed by a series of up to 10 calcified annuli, allowing passive lateral bending of the colony. Molecular phylogenetic analyses confirm that Leptohelia flexibilis is a stylasterid coral and reveal that the species is closely related to Leptohelia microstylus comb. nov., a southwestern Pacific stylasterid that lacks an internal axis. PMID:25543758

  19. A new genus of Strepsiptera, Rozenia gen. n. (Stylopidae), a parasite of bee genera Acamptopoeum and Calliopsis (Andrenidae, Panurginae, Calliopsini).

    PubMed

    Straka, Jakub; Jůzová, Katerina; Batelka, Jan

    2014-01-01

    A new Strepsiptera genus from South America is described, Rozenia gen. n., with three new species: Rozeniacalliopsidis sp. n. (type species), Rozeniaperuana sp. n. and Rozeniaplaticephala sp. n. These three new species are parasites of bees belonging to the tribe Calliopsini (Andrenidae, Panurginae). Rozeniacalliopsidis sp. n. is a parasite of the bee genus Calliopsis Smith, 1853 and Rozeniaperuana sp. n. and Rozeniaplaticephala sp. n. are parasites of the bee genus Acamptopoeum Cockerell, 1905. Diagnoses and descriptions of female puparia are presented for all three species. Diagnoses and descriptions of first instars (triungulinids) are presented for Rozeniacalliopsidis sp. n. and Rozeniaplaticephala sp. n. The first case of increased number of setae on the body of the first instars and augmentation of chaetotaxy of Strepsiptera are discussed. PMID:25349488

  20. Thalassobacter stenotrophicus gen. nov., sp. nov., a novel marine alpha-proteobacterium isolated from Mediterranean sea water.

    PubMed

    Macián, M C; Arahal, D R; Garay, E; Ludwig, W; Schleifer, K H; Pujalte, M J

    2005-01-01

    A Gram-negative, slightly halophilic, strictly aerobic, chemo-organotrophic bacterium was isolated from Mediterranean sea water near Valencia (Spain). 16S rRNA gene sequence comparisons showed that the isolate represented a separate branch within the alpha-3 subclass of the Proteobacteria, now included within the order 'Rhodobacterales'. Jannaschia helgolandensis was the closest relative, but their low sequence similarity and other features indicated that they were not related at the genus level. Isolate 5SM22T produced bacteriochlorophyll a and grew on solid media as regular salmon-pink colonies. Cells are motile rods, with polar flagella. The DNA G+C content is 59.1 mol%. Morphological, physiological and genotypic differences from related, thus far known genera support the description of Thalassobacter stenotrophicus gen. nov., sp. nov. with strain 5SM22T (=CECT 5294T=DSM 16310T) as the type strain.