WorldWideScience

Sample records for bovin phylogeny accomplishments

  1. CDBG Accomplishment Data

    Data.gov (United States)

    Department of Housing and Urban Development — Community Planning and Development (CPD) has developed profiles that display accomplishments for selected housing, economic development, public improvement, and...

  2. Life Sciences Accomplishments 1994

    Science.gov (United States)

    Burnell, Mary Lou (Editor)

    1993-01-01

    proposals for ground-based and flight research for all programs. Areas of particular interest to NASA were defined Proposals due April 29, 1994, will be peer reviewed - externally for scientific merit. This annual NRA process is now the mechanism for recruiting both extramural and intramural investigations. As an overview of LBSAD activities in 1993, this accomplishments document covers each of the major organizational components of the Division and the accomplishments of each. The second section is a review of the Space Life Sciences Research programs Space Biology, Space Physiology and Countermeasures, Radiation Health, Environmental Health, Space Human Factors, Advanced Life Support, and Global Monitoring and Disease Prediction, The third section, Research in Space Flight, describes the substantial contributions of the Spacelab Life Sciences 2 (SLS-2) mission to life sciences research and the significant contributions of the other missions flown in 1993, along with plans for future missions. The Division has greatly expanded and given high priority to its Education and Outreach Programs, which are presented in the fourth section. The fifth and final section, Partners for Space, shows the Divisions Cooperative efforts with other national and international agencies to achieve common goals, along with the accomplishments of joint research and analysis programs.

  3. EFRC CMSNF Major Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    D. Hurley; Todd R. Allen

    2014-09-01

    The mission of the Center for Material Science of Nuclear Fuels (CMSNF) has been to develop a first-principles-based understanding of thermal transport in the most widely used nuclear fuel, UO2, in the presence of defect microstructure associated with radiation environments. The overarching goal within this mission was to develop an experimentally validated multiscale modeling capability directed toward a predictive understanding of the impact of radiation and fission-product induced defects and microstructure on thermal transport in nuclear fuel. Implementation of the mission was accomplished by integrating the physics of thermal transport in crystalline solids with microstructure science under irradiation through multi institutional experimental and computational materials theory teams from Idaho National Laboratory, Oak Ridge National Laboratory, Purdue University, the University of Florida, the University of Wisconsin, and the Colorado School of Mines. The Center’s research focused on five major areas: (i) The fundamental aspects of anharmonicity in UO2 crystals and its impact on thermal transport; (ii) The effects of radiation microstructure on thermal transport in UO2; (iii) The mechanisms of defect clustering in UO2 under irradiation; (iv) The effect of temperature and oxygen environment on the stoichiometry of UO2; and (v) The mechanisms of growth of dislocation loops and voids under irradiation. The Center has made important progress in each of these areas, as summarized below.

  4. Developing Accomplished Teaching and Teachers

    OpenAIRE

    Forde, C

    2010-01-01

    This paper discusses the question of the development of accomplished teachers and teaching in Scotland and examines a number of emerging issues including the definition of accomplished teaching, the enhancement of teaching quality, the role of accomplished teachers including chartered teachers in schools, the contribution of accomplished teachers and impact on pupil learning, the question of teacher agency and enhanced professionalism and opportunities to engage with the wider social and educ...

  5. The phylogeny of Arthrotardigrada

    DEFF Research Database (Denmark)

    Hansen, Jesper Guldberg

    2011-01-01

    The order Arthrotardigrada, or water bears, constitutes a small group of 160 species of marine, microscopical invertebrates, within the phylum Tardigrada. Although the position of tardigrades in the Animal Kingdom has received much attention focusing on the metazoan phylogeny, the phylogenetic...... arthrotardigrade phylogeny based on combined morphological and molecular data. As a first step to reach this goal, detailed examinations of more than 100 species and thorough revisions of various arthrotardigrade genera were conducted to uncover their taxonomic diversity and morphological disparity, generating new...... Faroestygarctus nov. gen. belonging to the families Coronarctidae, Halechiniscidae (Euclavarctinae, Florarctinae), Renaudarctidae and Stygarctidae (Megastygarctidinae, Stygarctinae). In addition, diagnostic characters are given for 8 species of Archechiniscus and 3 species of Florarctinae nov. gen. Phylogenies of...

  6. Genetics of bovine vaccination

    OpenAIRE

    Leach, Richard Jonathan

    2011-01-01

    Infectious disease is an important issue for animal breeders, farmers and governments. Solutions to control infectious disease are needed and research focused on the genetic loci determining variation in immune-related traits has the potential to deliver solutions. The primary aim of this thesis is to discover regions of the bovine genome which influence the immune response post immunisation. To accomplish this two types of immunising agents, a Foot-and-Mouth Disease Virus (FMD...

  7. Fossils and decapod phylogeny

    NARCIS (Netherlands)

    Schram, Frederick R.; Dixon, Christopher

    2003-01-01

    An expanded series of morphological characters developed for a cladistic analysis of extant decapods has yielded a new hypothesis for the phylogeny of the group. Application of this database to selected fossil genera produces some interesting results and demonstrates the feasibility of treating foss

  8. Building a Twig Phylogeny

    Science.gov (United States)

    Flinn, Kathryn M.

    2015-01-01

    In this classroom activity, students build a phylogeny for woody plant species based on the morphology of their twigs. Using any available twigs, students can practice the process of cladistics to test evolutionary hypotheses for real organisms. They identify homologous characters, determine polarity through outgroup comparison, and construct a…

  9. Mapping Mutations on Phylogenies

    DEFF Research Database (Denmark)

    Nielsen, Rasmus

    2005-01-01

    This chapter provides a short review of recent methodologies developed for mapping mutations on phylogenies. Mapping of mutations, or character changes in general, using the maximum parsimony principle has been one of the most powerful tools in phylogenetics, and it has been used in a variety of...

  10. Constructing computer virus phylogenies

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, L.A. [Warwick Univ., Coventry (United Kingdom) Dept. of Computer Science; Goldberg, P.W. [Aston Univ., Birmingham (United Kingdom) Dept. of Applied Mathematics; Phillips, C.A. [Sandia National Labs., Albuquerque, NM (United States); Sorkin, G.B. [International Business Machines Corp., Yorktown Heights, NY (United States). Thomas J. Watson Research Center

    1996-03-01

    There has been much recent algorithmic work on the problem of reconstructing the evolutionary history of biological species. Computer virus specialists are interested in finding the evolutionary history of computer viruses--a virus is often written using code fragments from one or more other viruses, which are its immediate ancestors. A phylogeny for a collection of computer viruses is a directed acyclic graph whose nodes are the viruses and whose edges map ancestors to descendants and satisfy the property that each code fragment is ``invented`` only once. To provide a simple explanation for the data, we consider the problem of constructing such a phylogeny with a minimal number of edges. In general, this optimization problem cannot be solved in quasi-polynomial time unless NQP=QP; we present positive and negative results for associated approximated problems. When tree solutions exist, they can be constructed and randomly sampled in polynomial time.

  11. Molecular Phylogeny of Acanthamoeba

    OpenAIRE

    Kong, Hyun Hee

    2009-01-01

    After morphological grouping of Acanthamoeba by Pussard and Pons, phylogeny of the genus has been always a big topic to the researchers. Because of the variability of morphological characteristics, unchangeable and stable characters have been investigated for phylogenic criteria. Isoenzyme and mitochondrial DNA RFLP (Mt DNA RFLP) analyses revealed different patterns among strains assigned to a same species. Therefore, these characteristics would be considered as tools for strain discriminatio...

  12. Advanced Fuels Campaign 2012 Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed

    2012-11-01

    The Advanced Fuels Campaign (AFC) under the Fuel Cycle Research and Development (FCRD) program is responsible for developing fuels technologies to support the various fuel cycle options defined in the DOE Nuclear Energy Research and Development Roadmap, Report to Congress, April 2010. The fiscal year 2012 (FY 2012) accomplishments are highlighted below. Kemal Pasamehmetoglu is the National Technical Director for AFC.

  13. The shape of mammalian phylogeny

    DEFF Research Database (Denmark)

    Purvis, Andy; Fritz, Susanne A; Rodríguez, Jesús;

    2011-01-01

    six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within...... an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions...... of geographical or niche space....

  14. Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

    Directory of Open Access Journals (Sweden)

    Suchard Marc A

    2007-03-01

    Full Text Available Abstract Background Phylogenies of rapidly evolving pathogens can be difficult to resolve because of the small number of substitutions that accumulate in the short times since divergence. To improve resolution of such phylogenies we propose using insertion and deletion (indel information in addition to substitution information. We accomplish this through joint estimation of alignment and phylogeny in a Bayesian framework, drawing inference using Markov chain Monte Carlo. Joint estimation of alignment and phylogeny sidesteps biases that stem from conditioning on a single alignment by taking into account the ensemble of near-optimal alignments. Results We introduce a novel Markov chain transition kernel that improves computational efficiency by proposing non-local topology rearrangements and by block sampling alignment and topology parameters. In addition, we extend our previous indel model to increase biological realism by placing indels preferentially on longer branches. We demonstrate the ability of indel information to increase phylogenetic resolution in examples drawn from within-host viral sequence samples. We also demonstrate the importance of taking alignment uncertainty into account when using such information. Finally, we show that codon-based substitution models can significantly affect alignment quality and phylogenetic inference by unrealistically forcing indels to begin and end between codons. Conclusion These results indicate that indel information can improve phylogenetic resolution of recently diverged pathogens and that alignment uncertainty should be considered in such analyses.

  15. Predicting microbial traits with phylogenies.

    Science.gov (United States)

    Goberna, Marta; Verdú, Miguel

    2016-04-01

    Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbial ecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogenies and limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists. PMID:26371406

  16. GESAMP: Two decades of accomplishments

    International Nuclear Information System (INIS)

    Many of the uses of the oceans by society may lead potentially to the degradation of the marine environment. Human activities on land lead to the inadvertent or deliberate input of contaminants to the oceans which also may result in marine environmental degradation on local, regional or global scales. Potential impacts on the marine environment of human activities on land and the potential conflicts of society's utilization of the oceans require ongoing global evaluation from a multidisciplinary scientific perspective. This has been recognized for some time by the community of United Nations organizations, eight of which jointly sponsor an interdisciplinary groups of scientists to provide independent advice on existing and potential marine pollution problems. This Group of Experts on the Scientific Aspects of Marine Pollution (GESAMP) was formed two decades ago to serve as a mechanism for encouraging coordination, collaboration and harmonization of activities related to marine pollution of common interest to the co-sponsoring bodies. More recently, GESAMP has expanded its programme to include consideration of the impacts of other human activities, such as coastal development, on the marine environment. The purpose of this booklet is to briefly describe what GESAMP is, how it operates and what it accomplishes

  17. ADVANCED FUELS CAMPAIGN 2013 ACCOMPLISHMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed

    2013-10-01

    The mission of the Advanced Fuels Campaign (AFC) is to perform Research, Development, and Demonstration (RD&D) activities for advanced fuel forms (including cladding) to enhance the performance and safety of the nation’s current and future reactors; enhance proliferation resistance of nuclear fuel; effectively utilize nuclear energy resources; and address the longer-term waste management challenges. This includes development of a state-of-the art Research and Development (R&D) infrastructure to support the use of “goal-oriented science-based approach.” In support of the Fuel Cycle Research and Development (FCRD) program, AFC is responsible for developing advanced fuels technologies to support the various fuel cycle options defined in the Department of Energy (DOE) Nuclear Energy Research and Development Roadmap, Report to Congress, April 2010. Accomplishments made during fiscal year (FY) 2013 are highlighted in this report, which focuses on completed work and results. The process details leading up to the results are not included; however, the technical contact is provided for each section.

  18. Phylogeny of filamentous ascomycetes

    Science.gov (United States)

    Lumbsch, H. T.

    Phylogenetic studies of higher ascomycetes are enhanced by the introduction of molecular markers. Most studies employed sequences of the SSU rRNA gene, but recently data from additional genes (RPB2, LSU rRNA) have become available. Several groups defined by their ascoma-type, such as Pyrenomycetes, are supported while others, like the Discomycetes, appear to be paraphyletic. The Pezizales with operculate asci are basal to other eu-ascomycetes, while other Discomycetes appear to be derived eu-ascomycetes. The re-evaluation of classical characters using molecular data is discussed using three examples. Ascus types are often regarded as being of major importance in ascomycete systematics, but prototunicate asci were found to be of poor taxonomic value, since ascomycetes with prototunicate asci are polyphyletic. The independence of the Agyriales, assumed from their morphological characters, is supported by sequence data but the relationship to supposed sister groups remains dubious. The phylogeny of ascolocularous fungi and their circumscription requires further study. While a circumscription based on bitunicate asci can be rejected, it remains unclear whether fungi with ascolocularous ascoma development represent a monophyletic entity.

  19. MYRRHA Draft-2 Design accomplishments

    International Nuclear Information System (INIS)

    One of the main SCK-CEN research facility, namely the Materials Testing Reactor (MTR) BR2, is nowadays in operation for more than 40 years. The need for a safe and economic operation of the European nuclear park for preserving the natural resources, demand the start-up of one or more new MTRs in a very near future. On the other hand the closing of the fuel cycle as well as the development of future energy systems request clearly the use of fast spectrum irradiation facilities. The MYRRHA project started at SCK-CEN in this context, the concept of a new irradiation and testing facility to replace BR2. MYRRHA, being a fast neutron facility, would be a complementary project to the thermal MTR Jules Horowitz Reactor in France. That would give Europe a full research capacity in terms of nuclear research and development for Generation III and IV reactors. At mid-2002, a first pre-design file of MYRRHA (namely the ''MYRRHA Draft - 1'' file with a core nominal power of 30 MWth) has been submitted to an International Technical Guidance Committee (ITGC) for reviewing. No show stopper has been identified in the project. Nevertheless, the ITGC members have recommended: (1) to give more attention to safety studies and iterate to the pre-design before entering the detailed engineering phase; (2) to address some RandD topics to avoid bottlenecks such as fuel pin and assembly development and qualification; (3) to make a decision on the accelerator option (cyclotron or LINAC) and possibly revisit the beam parameters that were already at that moment fixed to 350 MeV*5 mA but mainly derived from the cyclotron technology possibilities. The objective of this effort in the period 2003-2005 was to update and progress the MYRRHA Draft-1 design based on the ITGC evaluation results, the consequences of the safety studies that had to be accomplished on basis of the Draft-1 design and holding the initial objectives of the MYRRHA facility. This resulted at mid-2005 in producing the MYRRHA Draft

  20. Space Biophysics: Accomplishments, Trends, Challenges

    Science.gov (United States)

    Smith, Jeffrey D.

    2015-01-01

    the protective environment of Earth, the biophysical properties underlying these changes must be studied, characterized and understood. This lecture reviews the current state of NASA biophysics research accomplishments and identifies future trends and challenges for biophysics research on the International Space Station and beyond.

  1. NPAR program - Status and accomplishments

    International Nuclear Information System (INIS)

    Upon completing the early scoping studies, the US NRC Office of Nuclear Regulatory Research took a lead worldwide in 1985 by publishing a comprehensive program plan for Nuclear Plant aging Research (NPAR). The plan identified significant technical safety issues related to plant aging; discussed a phased approach to aging and life assessment of components systems, and structures; and recommended the utilization of research results for, (i) the selection and the prioritization of components and structures, (ii) where to focus inspection and maintenance, (iii) what type of data collection and record keeping would be useful, (iv) how to perform technical evaluation of mothballed units for reactivation, (v) the determination of risk significance of aging, (vi) the development of technical bases for license renewal and extended plant life considerations, (vii) the ongoing regulatory issues, and (viii) recommendations to the national codes and standards groups involved in activities related to aging. Since the publication of the NPAR program plan in 1985 significant progress has been made in completing the initial phase of the NPAR activities and substantial new initiatives have been undertaken expanding the overall scope. Also, by recognizing the NRC's leadership role for emphasizing the need for aging management significant developments are taking place worldwide in implementing dedicated programs related to understanding and managing aging in older operating nuclear power plants. In fact, in some countries, aging management programs are being implemented now for relatively new plants so as to eventually realize the potential benefits of extended plant life beyond the originally conceived design and service life. This paper briefly describe the major elements of the NPAR program, its status and results or accomplishments. In the process the author emphasizes the need for total industry commitment and participation in implementing programs for understanding and managing

  2. Research on assessment system of accomplishment

    Institute of Scientific and Technical Information of China (English)

    Fu Zhimin; Li Hanling

    2006-01-01

    Project assessment of accomplishment is a complicated process of system engineering management. This paper is based on the examination of project management achievement. A system analysis of accomplishment examination has been made from the implication, content, style, method, aim, principle, procedure, kind to restriction, psychology effect of accomplishment examination. The purpose of aforementioned all is for the establishment of whole system and thought in the study, foundation and implement of project accomplishment assessment.

  3. Summary of Laurasiatheria (Mammalia) Phylogeny

    Institute of Scientific and Technical Information of China (English)

    Jingyang HU; Yaping ZHANG; Li YU

    2012-01-01

    Laurasiatheria is one of the richest and most diverse superorders of placental mammals.Because this group had a rapid evolutionary radiation,the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open.Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation.We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic,morphological and molecular data,and discuss the controversies of its phylogenetic relationship.This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.

  4. Molecular phylogeny of Daucus (Apiaceae)

    Science.gov (United States)

    We studied the phylogeny of 22 accessions of Daucus: D. broteri, D. capillifolius, D. carota, D. carota subsp. carota, D. carota subsp. commutatus, D. carota subsp. commutatus, D. carota subsp. drepanensis, D. carota subsp. gadecaei, D. carota subsp. gummifer, D. carota subsp. halophilius, D. carota...

  5. Transmutation Fuels Campaign FY-09 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Lori Braase

    2009-09-01

    This report summarizes the fiscal year 2009 (FY-08) accomplishments for the Transmutation Fuels Campaign (TFC). The emphasis is on the accomplishments and relevance of the work. Detailed description of the methods used to achieve the highlighted results and the associated support tasks are not included in this report.

  6. Antiviral effects of bovine interferons on bovine respiratory tract viruses.

    OpenAIRE

    Fulton, R W; Downing, M M; Cummins, J M

    1984-01-01

    The antiviral effects of bovine interferons on the replication of bovine respiratory tract viruses were studied. Bovine turbinate monolayer cultures were treated with bovine interferons and challenged with several bovine herpesvirus 1 strains, bovine viral diarrhea virus, parainfluenza type 3 virus, goat respiratory syncytial virus, bovine respiratory syncytial virus, bovine adenovirus type 7, or vesicular stomatitis virus. Treatment with bovine interferons reduced viral yield for each of the...

  7. High-Performance Phylogeny Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Tiffani L. Williams

    2004-11-10

    Under the Alfred P. Sloan Fellowship in Computational Biology, I have been afforded the opportunity to study phylogenetics--one of the most important and exciting disciplines in computational biology. A phylogeny depicts an evolutionary relationship among a set of organisms (or taxa). Typically, a phylogeny is represented by a binary tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. The task of phylogenetics is to infer this tree from observations upon present-day organisms. Reconstructing phylogenies is a major component of modern research programs in many areas of biology and medicine, but it is enormously expensive. The most commonly used techniques attempt to solve NP-hard problems such as maximum likelihood and maximum parsimony, typically by bounded searches through an exponentially-sized tree-space. For example, there are over 13 billion possible trees for 13 organisms. Phylogenetic heuristics that quickly analyze large amounts of data accurately will revolutionize the biological field. This final report highlights my activities in phylogenetics during the two-year postdoctoral period at the University of New Mexico under Prof. Bernard Moret. Specifically, this report reports my scientific, community and professional activities as an Alfred P. Sloan Postdoctoral Fellow in Computational Biology.

  8. Wind Energy Program: Top 10 Program Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    None

    2009-01-18

    Brochure on the top accomplishments of the Wind Energy Program, including the development of large wind machines, small machines for the residential market, wind tunnel testing, computer codes for modeling wind systems, high definition wind maps, and successful collaborations.

  9. Planning and Accomplishment Narrative Fiscal Year 1973

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This narrative report for Bombay Hook National Wildlife Refuge outlines Refuge accomplishments during the 1973 fiscal year. The report begins with a Refuge...

  10. Pollution Prevention Accomplishments Hanford Site FY2001

    International Nuclear Information System (INIS)

    In Fiscal Year 2001, the Hanford Site Prime Contractors, Bechtel Hanford Inc. (BHI), CH2M Hill hanford Group (CHG), Fluor Hanford Inc. (FH), and Pacific Northwest National Laboratory (PNNL) achieved over $32 million in cost savings/avoidance. The total cost savings/avoidance includes accomplishments reported to DOE Headquarters and additional accomplishments achieved on the Hanford Site. This accomplishment report highlights the major successes totaling over $5.5 million in cost savings/avoidance. The following summarizes the FY 2001 waste reduced, and cost savings/avoidance by waste category for accomplishments documented in this report. Additionally, this accomplishment report documents the hanford site Return on Investment (ROI) projects completed or in progress during FY 2001. The ROI projects continue to show excellent results this past year. The ROI program funds waste minimization projects that provide a high return on investment. The funding is available to all Hanford contractors for pollution prevention projects. This accomplishment report highlights 7 ROI projects implemented and 6 projects that were in progress during FY 2001. The annual cost savings of the ROI projects completed and in progress is over $53.5 million. The Hanford Site continues to be the leader in pollution prevention and waste minimization across the DOE complex. This was evidenced by meeting aggressive Hanford Site waste generation goals and operating an outstanding recycling program. Additionally, waste streams are continuously evaluated and reduced through effective analysis and implementation via Pollution Prevention Opportunity Assessments

  11. Phylogeny and subgeneric taxonomy of Aspergillus

    DEFF Research Database (Denmark)

    Peterson, S.W.; Varga, Janos; Frisvad, Jens Christian;

    2008-01-01

    The phylogeny of the genus Aspergillus and its teleomorphs is discussed based on multilocus sequence data. DNA sequence analysis was used to formulate a nucleotide sequence framework of the genus and to analyze character changes in relationship to the phylogeny hypothesized from the DNA sequence...

  12. Phylogeny Constructed by Using Dsing Diversity Increment

    Institute of Scientific and Technical Information of China (English)

    Shi Feng; Li Na-na; Li Yuan-xiang; Zhou Huai-bei

    2003-01-01

    A new approach based on the concept of the diversity increment is applied to reconstruct a phylogeny. The phylogeny of the Eutherian orders use concatenated H-stranded amino acid sequences, and the result is consistent with the commonly accepted one for the Eutherians.

  13. Engineering Accomplishments in the Construction of NCSX

    Energy Technology Data Exchange (ETDEWEB)

    G. H. Neilson; P.J. Heitzenroeder; B.E. Nelson; W.T. Reiersen; A. Brooks; T.G. Brown; J.H. Chrzanowski; M.J. Cole; F. Dahlgren; T. Dodson; L.E. Dudek; R.A. Ellis; H.M. Fan; P.J. Fogarty; K.D. Freudenberg; P.L. Goranson; J.H. Harris; M.R. Kalish; G. Labik; J.F. Lyon; N. Pomphrey; C.D. Priniski; S. Raftopoulos; D.J. Rej; W.R. Sands; R.T. Simmons; B.E. Stratton; R.L. Strykowsky; M.E. Viola; D.E. Williamson; M.C. Zarnstorff

    2008-09-01

    The National Compact Stellarator Experiment (NCSX) was designed to test a compact, quasiaxisymmetric stellarator configuration. Flexibility and accurate realization of its complex 3D geometry were key requirements affecting the design and construction. While the project was terminated before completing construction, there were significant engineering accomplishments in design, fabrication, and assembly. The design of the stellarator core device was completed. All of the modular coils, toroidal field coils, and vacuum vessel sectors were fabricated. Critical assembly steps were demonstrated. Engineering advances were made in the application of CAD modeling, structural analysis, and accurate fabrication of complex-shaped components and subassemblies. The engineering accomplishments of the project are summarized

  14. 77 FR 29914 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2012-05-21

    ... RIN 0579-AC68 Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products AGENCY... live bovines and products derived from bovines with regard to bovine spongiform encephalopathy. This.... SUPPLEMENTARY INFORMATION: On March 16, 2012, we published in the Federal Register (77 FR 15848-15913, Docket...

  15. Reconstruction of Nansan Oil Store Accomplished

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ On June 15th 2005, Russian crude oil unloading reconstruction project of Nansan oil store, which has drawn much attention of the state, China National Petroleum Corporation (CNPC) and Daqing Oilfield, was successfully accomplished and put into operation, marking the start of large scale import of Russian crude and opening up a new era for Daqing Oilfield to involve in foreign crude trade.

  16. Accomplished Teachers Implementation of Quality Teaching Practices

    Science.gov (United States)

    Chen, Weiyun; Hammond-Bennett, Austin; Upton, Ashely; Mason, Steve

    2014-01-01

    The purpose of this study was to describe how accomplished teachers implement the quality of teaching practices in their daily lessons. The participants were four elementary physical education teachers (one male, three female). The data sources consisted of videotape of the teachers teaching 12 lessons, transcription of the taped lessons,…

  17. Biomass Program 2007 Accomplishments - Full Report

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2009-10-27

    The Office of Energy Efficiency and Renewable Energy's (EERE’s) Biomass Program works with industry, academia and its national laboratory partners on a balanced portfolio of research in biomass feedstocks and conversion technologies. This document provides Program accomplishments for 2007.

  18. Overview of LAMPF and its accomplishments

    International Nuclear Information System (INIS)

    The report presented is from a talk given at a Los Alamos Scientific Laboratory colloquium on October 4, 1977, in which the history, technological accomplishments, present status, and scientific program at the Clinton P. Anderson Meson Physics Facility (LAMPF) were reviewed

  19. Advanced Fuels Campaign FY 2011 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed

    2011-11-01

    One of the major research and development (R&D) areas under the Fuel Cycle Research and Development (FCRD) program is advanced fuels development. The Advanced Fuels Campaign (AFC) has the responsibility to develop advanced fuel technologies for the Department of Energy (DOE) using a science-based approach focusing on developing a microstructural understanding of nuclear fuels and materials. Accomplishments made during fiscal year (FY 20) 2011 are highlighted in this report, which focuses on completed work and results. The process details leading up to the results are not included; however, the technical contact is provided for each section. The order of the accomplishments in this report is consistent with the AFC work breakdown structure (WBS).

  20. The discursive accomplishment of regimes of automobility

    DEFF Research Database (Denmark)

    Lindegaard, Laura Bang

    2016-01-01

    the chapter adds a widely acknowledged yet underdeveloped perspective to already existing research on automobility: a perspective that enquires into how rationalities of automobility are accomplished in discursive interaction at the vulgar everyday level. In more detail, the chapter reports on a qualitative...... conceptualisation of mobility, I address impacts of thought schemes and structures on current social and political discourses of mobility as I discuss and demonstrate how rationalities of advanced liberalism co-constitute a car-dependent way of living. Drawing on both studies of governmentality and ethnomethodology...... case study in a decentralised Danish village that demonstrates how citizens accomplish the rationalities that co-constitute their car-dependent mobility in discursive interaction. During the time of the case study (2010-11), the village was engaged in an energy village project, and the study...

  1. Sandia Technology engineering and science accomplishments

    International Nuclear Information System (INIS)

    This document presents recent accomplishments in engineering and science at Sandia National Laboratories. Commercial-scale parabolic troughs at the National Solar Thermal Test Facility are used for such applications as heating water, producing steam for industrial processes, and driving absorption air conditioning systems. Computerized-aided design, superconductor technology, radar imaging, soldering technology, software development breakthroughs are made known. Defense programs are exhibited. And microchip engineering applications in test chips, flow sensors, miniature computers, integrated circuits, and microsensors are presented

  2. Effective mass spectrometer. [History and accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Ayres, D.

    1979-10-12

    The history and major accomplishments of the Effective Mass Spectrometer (EMS) are described. In the eight years since the EMS turned on, 21 experiments have been completed by groups from nine institutions in 32 months of operation. Over 400 million triggers have been recorded on magnetic tape, resulting in 29 journal publications to date. A list of experimental proposals for the EMS and a sampling of results are presented. 12 figures, 4 tables.

  3. Enhanced surveillance program FY1998 accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Kass, J

    1998-10-01

    This report highlights the accomplishments of the Enhanced Surveillance Program (ESP), the highest-priority research and development effort in stockpile management today. This is volume one of eleven, the unclassified summary of selected program highlights. These highlights fall into the following focus areas: pits, high explosives, organics, dynamics, diagnostics, systems, secondaries, materials-aging models, non-nuclear components, and routine surveillance testing system upgrades. Principal investigators from around the DOE complex contributed to this report.

  4. NASA total quality management 1989 accomplishments report

    Science.gov (United States)

    1990-01-01

    Described here are the accomplishments of NASA as a result of the use of Total Quality Management (TQM). The principles in practice which led to these process refinements are important cultural elements to any organization's productivity and quality efforts. The categories of TQM discussed here are top management leadership and support, strategic planning, focus on the customer, employee training and recognition, employee empowerment and teamwork, measurement and analysis, and quality assurance.

  5. NASA total quality management 1990 accomplishments report

    Science.gov (United States)

    1991-01-01

    NASA's efforts in Total Quality Management are based on continuous improvement and serve as a foundation for NASA's present and future endeavors. Given here are numerous examples of quality strategies that have proven effective and efficient in a time when cost reduction is critical. These accomplishment benefit our Agency and help to achieve our primary goal, keeping American in the forefront of the aerospace industry.

  6. Basic Energy Sciences: Summary of Accomplishments

    Science.gov (United States)

    1990-05-01

    For more than four decades, the Department of Energy, including its predecessor agencies, has supported a program of basic research in nuclear- and energy-related sciences, known as Basic Energy Sciences. The purpose of the program is to explore fundamental phenomena, create scientific knowledge, and provide unique user'' facilities necessary for conducting basic research. Its technical interests span the range of scientific disciplines: physical and biological sciences, geological sciences, engineering, mathematics, and computer sciences. Its products and facilities are essential to technology development in many of the more applied areas of the Department's energy, science, and national defense missions. The accomplishments of Basic Energy Sciences research are numerous and significant. Not only have they contributed to Departmental missions, but have aided significantly the development of technologies which now serve modern society daily in business, industry, science, and medicine. In a series of stories, this report highlights 22 accomplishments, selected because of their particularly noteworthy contributions to modern society. A full accounting of all the accomplishments would be voluminous. Detailed documentation of the research results can be found in many thousands of articles published in peer-reviewed technical literature.

  7. Sandia technology engineering and science accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    1993-03-01

    Sandia is a DOE multiprogram engineering and science laboratory with major facilities at Albuquerque, New Mexico, and Livermore, California, and a test range near Tonapah, Nevada. We have major research and development responsibilities for nuclear weapons, arms control, energy, the environment, economic competitiveness, and other areas of importance to the needs of the nation. Our principal mission is to support national defense policies by ensuring that the nuclear weapon stockpile meets the highest standards of safety, reliability, security, use control, and military performance. Selected unclassified technical activities and accomplishments are reported here. Topics include advanced manufacturing technologies, intelligent machines, computational simulation, sensors and instrumentation, information management, energy and environment, and weapons technology.

  8. Advanced Fuels Campaign FY 2015 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Braase, Lori Ann [Idaho National Lab. (INL), Idaho Falls, ID (United States); Carmack, William Jonathan [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-10-29

    The mission of the Advanced Fuels Campaign (AFC) is to perform research, development, and demonstration (RD&D) activities for advanced fuel forms (including cladding) to enhance the performance and safety of the nation’s current and future reactors; enhance proliferation resistance of nuclear fuel; effectively utilize nuclear energy resources; and address the longer-term waste management challenges. This report is a compilation of technical accomplishment summaries for FY-15. Emphasis is on advanced accident-tolerant LWR fuel systems, advanced transmutation fuels technologies, and capability development.

  9. Accomplishments and needs in safety research

    International Nuclear Information System (INIS)

    My purpose today is to review recent accomplishments in water reactor safety research and to point out important tasks that remain to be done. I will also comment on the changes of focus that I see ahead in reactor safety research. I speak from a U.S. perspective on the subject, but note that the program of the U.S. Nuclear Regulatory Commission and also that of the U.S. industry's Electric Power Research Institute include many international collaborative research efforts. Without any doubt, nuclear safety research today is international in scope, and the collaborative movement is gaining in strength

  10. Advanced Fuels Campaign FY 2010 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Lori Braase

    2010-12-01

    The Fuel Cycle Research and Development (FCRD) Advanced Fuels Campaign (AFC) Accomplishment Report documents the high-level research and development results achieved in fiscal year 2010. The AFC program has been given responsibility to develop advanced fuel technologies for the Department of Energy (DOE) using a science-based approach focusing on developing a microstructural understanding of nuclear fuels and materials. The science-based approach combines theory, experiments, and multi-scale modeling and simulation aimed at a fundamental understanding of the fuel fabrication processes and fuel and clad performance under irradiation. The scope of the AFC includes evaluation and development of multiple fuel forms to support the three fuel cycle options described in the Sustainable Fuel Cycle Implementation Plan4: Once-Through Cycle, Modified-Open Cycle, and Continuous Recycle. The word “fuel” is used generically to include fuels, targets, and their associated cladding materials. This document includes a brief overview of the management and integration activities; but is primarily focused on the technical accomplishments for FY-10. Each technical section provides a high level overview of the activity, results, technical points of contact, and applicable references.

  11. Mobile Genetic Elements Provide Evidence for a Bovine Origin of Clonal Complex 17 of Streptococcus agalactiae▿

    OpenAIRE

    Héry-Arnaud, Geneviève; Bruant, Guillaume; Lanotte, Philippe; Brun, Stella; Picard, Bertrand; Rosenau, Agnès; Van Ver Mee-Marquet, Nathalie; Rainard, Pascal; Quentin, Roland; Mereghetti, Laurent

    2007-01-01

    International audience We sought an explanation for epidemiological changes in Streptococcus agalactiae infections by investigating the link between ecological niches of the bacterium by determining the prevalence of 11 mobile genetic elements. The prevalence of nine of these elements differed significantly according to the human or bovine origin of the isolate. Correlating this distribution with the phylogeny obtained by multilocus sequence analysis, we observed that human isolates harbor...

  12. 77 FR 20319 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2012-04-04

    ...; ] DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service 9 CFR Part 93 RIN 0579-AC68 Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products Correction In proposed rule...

  13. 78 FR 73993 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2013-12-10

    ... Health Inspection Service 9 CFR Parts 92, 93, 94, 95, 96, and 98 RIN 0579-AC68 Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products Corrections In rule document 2013-28228 appearing...

  14. NASA total quality management 1989 accomplishments report

    Science.gov (United States)

    Tai, Betty P. (Editor); Stewart, Lynne M. (Editor)

    1990-01-01

    NASA and contractor employees achieved many notable improvements in 1989. The highlights of those improvements, described in this seventh annual Accomplishments Report, demonstrate that the people who support NASA's activities are getting more involved in quality and continuous improvement efforts. Their gains solidly support NASA's and this Nation's goal to remain a leader in space exploration and in world-wide market competition, and, when communicated to others through avenues such as this report, foster improvement efforts across government and industry. The principles in practice which led to these process refinements are important cultural elements to any organization's productivity and quality efforts. The categories in this report reflect NASA principles set forth in the 1980's and are more commonly known today as Total Quality Management (TQM): top management leadership and support; strategic planning; focus on the customer; employee training and recognition; employee empowerment and teamwork; measurement and analysis; and quality assurance.

  15. New accomplishments of Ambiente & Agua scientific journal

    Directory of Open Access Journals (Sweden)

    Getulio Teixeira Batista

    2009-04-01

    Full Text Available Ambiente & Água – An Interdisciplinary Journal of Applied Science (Ambi-Agua was classified as B2 in the Interdisciplinary Area, the major thematic area of this journal, by CAPES classification system known as "Qualis". Also, the journal was registered in the Digital Object Identifier (DOI® System. Three other facts were accomplished: 1 all published articles since April, 2008 have the submitted and accepted dates stamped; 2 long-term preservation will be now secured in association with DOAJ - Lund University Libraries and the e-Depot of the National Library of the Netherlands (KB; and 3 we entered into an electronic licensing relationship with EBSCO Publishing to have full text of our journal in EBSCO Publishing's databases in the near future.

  16. Molecular phylogeny of Duvenhage virus

    Directory of Open Access Journals (Sweden)

    Louis H. Nel

    2011-11-01

    Full Text Available The Duvenhage virus (DUVV constitutes one of the 11 species in the Lyssavirus genus and causes fatal rabies encephalitis. The virus is associated with insectivorous bat species and three human cases have been reported, all of which were linked to contact with bats. Few of these isolates have been studied and thus little is known about the phylogeny and epidemiology of this lyssavirus. Until 2007, when an isolate was made from the East African country of Kenya, all isolations of this virus had been from southern Africa. This discovery led to many questions regarding the spread and diversity of this lyssavirus. Phylogenetic analysis indicated that the DUVV isolates constitute two different lineages, in which the southern African isolates group together to form one lineage and the more recent isolate from Kenya constitutes a new, second lineage. We found that the new isolate has a genetic variation that has not yet been seen for DUVV. Not only is our lack of knowledge regarding the geographical distribution of this uniquely African virus emphasised, but we have also demonstrated the potential diversity within this genotype.

  17. Unlocking the bovine genome

    Science.gov (United States)

    The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

  18. Camel and bovine chymosin

    DEFF Research Database (Denmark)

    Langholm Jensen, Jesper; Mølgaard, Anne; Navarro Poulsen, Jens Christian;

    2013-01-01

    Bovine and camel chymosin are aspartic peptidases that are used industrially in cheese production. They cleave the Phe105-Met106 bond of the milk protein κ-casein, releasing its predominantly negatively charged C-terminus, which leads to the separation of the milk into curds and whey. Despite...... having 85% sequence identity, camel chymosin shows a 70% higher milk-clotting activity than bovine chymosin towards bovine milk. The activities, structures, thermal stabilities and glycosylation patterns of bovine and camel chymosin obtained by fermentation in Aspergillus niger have been examined...... interactions arising from variation in the surface charges and the greater malleability both in domain movements and substrate binding contribute to the better milk-clotting activity of camel chymosin towards bovine milk....

  19. Juvenile morphology in baleen whale phylogeny

    Science.gov (United States)

    Tsai, Cheng-Hsiu; Fordyce, R. Ewan

    2014-09-01

    Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.

  20. The phylogeny of Orussidae (Insecta: Hymenoptera) revisited

    DEFF Research Database (Denmark)

    Vilhelmsen, Lars

    2007-01-01

    The phylogeny of the parasitic wasp family Orussidae is analyzed with a slightly expanded version of a previously published data set. The basal splitting events in the family between two fossil taxa and the extant members are not unambiguously resolved. Intergeneric relationships in general are...... poorly supported and change under different analytical conditions. This corroborates earlier fi ndings regarding the phylogeny of the family. A resumé of the evolutionary history of the Orussidae is provided. Leptorussus madagascarensis sp.n. is described. Udgivelsesdato: 7/12...

  1. The phylogeny graphs of doubly partial orders

    CERN Document Server

    Park, Boram

    2011-01-01

    The competition graph of a doubly partial order is known to be an interval graph. The CCE graph and the niche graph of a doubly partial order are also known to be interval graphs if the graphs do not contain a cycle of length four and three as an induced subgraph, respectively. Phylogeny graphs are variant of competition graphs. The phylogeny graph $P(D)$ of a digraph $D$ is the (simple undirected) graph defined by $V(P(D)):=V(D)$ and $E(P(D)):=\\{xy \\mid N^+_D(x) \\cap N^+_D(y) \

  2. Molecular data and phylogeny of family

    International Nuclear Information System (INIS)

    Family Smilacaceae's higher order taxonomy remained disputed for many years. It was treated as an order 'Smilacales' and was also placed under Liliales by several taxonomists. Even some considered as part of family Liliacaeae. In present paper, we investigated the family's higher order phylogeny and also compared its rbcL gene sequence data with related taxa to elucidate its phylogeny. The data suggests that its family stature is beyond dispute because of its advanced karyotype, woody climbing habit and DNA sequence data. The data suggest that Smilacaceae may be a sister group of order Liliales and it forms a clear clade with the order. (author)

  3. Bovine Herpesvirus 4 infections and bovine mastitis

    NARCIS (Netherlands)

    Wellenberg, Gerardus Johannus

    2002-01-01

    Mastitis is an often occurring disease in dairy cattle with an enormous economic impact for milk producers worldwide. Despite intensive research, which is historically based on the detection of bacterial udder pathogens, still around 20-35% of clinical cases of bovine mastitis have an unknown aetiol

  4. Planning and accomplishment narrative: Northwest Montana Waterfowl Production Area [1973

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This planning and accomplishments narrative report for Northwest Montana Wetland Management District outlines Refuge accomplishments during the 1973 calendar year....

  5. Light Water Reactor Sustainability Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    McCarthy, Kathryn A. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-02-01

    Welcome to the 2014 Light Water Reactor Sustainability (LWRS) Program Accomplishments Report, covering research and development highlights from 2014. The LWRS Program is a U.S. Department of Energy research and development program to inform and support the long-term operation of our nation’s commercial nuclear power plants. The research uses the unique facilities and capabilities at the Department of Energy national laboratories in collaboration with industry, academia, and international partners. Extending the operating lifetimes of current plants is essential to supporting our nation’s base load energy infrastructure, as well as reaching the Administration’s goal of reducing greenhouse gas emissions to 80% below 1990 levels by the year 2050. The purpose of the LWRS Program is to provide technical results for plant owners to make informed decisions on long-term operation and subsequent license renewal, reducing the uncertainty, and therefore the risk, associated with those decisions. In January 2013, 104 nuclear power plants operated in 31 states. However, since then, five plants have been shut down (several due to economic reasons), with additional shutdowns under consideration. The LWRS Program aims to minimize the number of plants that are shut down, with R&D that supports long-term operation both directly (via data that is needed for subsequent license renewal), as well indirectly (with models and technology that provide economic benefits). The LWRS Program continues to work closely with the Electric Power Research Institute (EPRI) to ensure that the body of information needed to support SLR decisions and actions is available in a timely manner. This report covers selected highlights from the three research pathways in the LWRS Program: Materials Aging and Degradation, Risk-Informed Safety Margin Characterization, and Advanced Instrumentation, Information, and Control Systems Technologies, as well as a look-ahead at planned activities for 2015. If you

  6. Lunabotics Mining Competition: Inspiration Through Accomplishment

    Science.gov (United States)

    Mueller, Robert P.

    2011-01-01

    NASA's Lunabotics Mining Competition is designed to promote the development of interest in space activities and STEM (Science, Technology, Engineering, and Mathematics) fields. The competition uses excavation, a necessary first step towards extracting resources from the regolith and building bases on the moon. The unique physical properties of lunar regolith and the reduced 1/6th gravity, vacuum environment make excavation a difficult technical challenge. Advances in lunar regolith mining have the potential to significantly contribute to our nation's space vision and NASA space exploration operations. The competition is conducted annually by NASA at the Kennedy Space Center Visitor Complex. The teams that can use telerobotic or autonomous operation to excavate a lunar regolith geotechnical simulant, herein after referred to as Black Point-1 (or BP-1) and score the most points (calculated as an average of two separate 10-minute timed competition attempts) will eam points towards the Joe Kosmo Award for Excellence and the scores will reflect ranking in the on-site mining category of the competition. The minimum excavation requirement is 10.0 kg during each competition attempt and the robotic excavator, referred to as the "Lunabot", must meet all specifications. This paper will review the achievements of the Lunabotics Mining Competition in 2010 and 2011, and present the new rules for 2012. By providing a framework for robotic design and fabrication, which culminates in a live competition event, university students have been able to produce sophisticated lunabots which are tele-operated. Multi-disciplinary teams are encouraged and the extreme sense of accomplishment provides a unique source of inspiration to the participating students, which has been shown to translate into increased interest in STEM careers. Our industrial sponsors (Caterpillar, Newmont Mining, Harris, Honeybee Robotics) have all stated that there is a strong need for skills in the workforce related

  7. Multilocus phylogeny of Sciurini tree squirrels

    Czech Academy of Sciences Publication Activity Database

    Pečnerová, P.; Martínková, Natália

    Brno : Akademické nakladatelství CERM, 2012 - (Budinská, E.; Popovici, V.), s. 55-63 ISBN 978-80-7204-804-5. [Summer School on Computational Biology /8./. Mikulov (CZ), 12.09.2012-15.09.2012] Institutional support: RVO:68081766 Keywords : phylogeny * supermatrix * supertree * squirrels Subject RIV: EG - Zoology

  8. The Binary Perfect Phylogeny with Persistent characters

    CERN Document Server

    Braghin, Chiara; Trucco, Gabriella; Bonizzoni, Paola

    2011-01-01

    The near-perfect phylogeny over binary set of characters has been proposed as an extension of the too restrictive model of the perfect phylogeny in order to model biological events such as homoplasy. However the model appears to be too general to model some situations and is computationally inefficient on some instances. In this paper we consider the problem of reconstructing a near-perfect phylogeny where only a type of homoplasy is allowed in the tree: we consider back mutations according to notion of {\\em persistency}, that is characters can be gained and lost at most once. The notion of persistency leads to the problem of the Persistent Perfect Phylogeny (referred as P-PPH). By exploring combinatorial properties of the problem we develop an exact algorithm for solving the P-PPH problem that in the worst case runs in time that is exponential in the number of characters, but is polynomial in the number of species. Indeed, we show that the P-PPH problem can be restated as a special case of the Incomplete Per...

  9. Bayesian inference of the metazoan phylogeny

    DEFF Research Database (Denmark)

    Glenner, Henrik; Hansen, Anders J; Sørensen, Martin V;

    2004-01-01

    Metazoan phylogeny remains one of evolutionary biology's major unsolved problems. Molecular and morphological data, as well as different analytical approaches, have produced highly conflicting results due to homoplasy resulting from more than 570 million years of evolution. To date, parsimony has...

  10. Bovine Herpesvirus 4 infections and bovine mastitis

    OpenAIRE

    Wellenberg, Gerardus Johannus

    2002-01-01

    Mastitis is an often occurring disease in dairy cattle with an enormous economic impact for milk producers worldwide. Despite intensive research, which is historically based on the detection of bacterial udder pathogens, still around 20-35% of clinical cases of bovine mastitis have an unknown aetiology. Due to the high number of unknown causes of clinical mastitis, studies were undertaken to gain more insight into the role of viruses in this important disease. For the first time, we found tha...

  11. Cartilage (Bovine and Shark) (PDQ)

    Science.gov (United States)

    ... Ask about Your Treatment Research Cartilage (Bovine and Shark) (PDQ®)–Patient Version Overview Go to Health Professional ... 8 ). Questions and Answers About Cartilage (Bovine and Shark) What is cartilage? Cartilage is a type of ...

  12. Phylogeny and subgeneric taxonomy of Aspergillus

    DEFF Research Database (Denmark)

    Peterson, S.W.; Varga, Janos; Frisvad, Jens Christian; Samson, Robert A.

    The phylogeny of the genus Aspergillus and its teleomorphs is discussed based on multilocus sequence data. DNA sequence analysis was used to formulate a nucleotide sequence framework of the genus and to analyze character changes in relationship to the phylogeny hypothesized from the DNA sequence...... analysis. The sequence data used to delimitate subgeneric taxa included partial calmodulin, rDNA and RNA polymerase gene sequences. In our phylogenic structure of Aspergillus extrolite data of the various Aspergillus taxa collected from ex-type cultures and numerous other isolates are also discussed. A new...... subgeneric classification is proposed which includes 8 subgenera and 22 sections within the Aspergillus genus. Characteristics of these taxa are shortly discussed in this chapter....

  13. Measuring Asymmetry in Time-Stamped Phylogenies.

    OpenAIRE

    Dearlove, Bethany L.; Simon D W Frost

    2015-01-01

    Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of ‘core groups’ with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the phylo...

  14. Mammalian phylogeny reveals recent diversification rate shifts

    OpenAIRE

    Stadler, Tanja

    2011-01-01

    Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous–Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveal...

  15. Measuring Asymmetry in Time-Stamped Phylogenies

    OpenAIRE

    Dearlove, Bethany L; Frost, Simon D. W.

    2015-01-01

    Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of ‘core groups’ with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the phylo...

  16. Whole genome phylogenies for multiple Drosophila species

    Directory of Open Access Journals (Sweden)

    Seetharam Arun

    2012-12-01

    Full Text Available Abstract Background Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees. Results An unfiltered whole genome analysis (193,622 predicted proteins strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. Similar results were obtained when just the melanogaster subgroup was analyzed. Conclusions These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between

  17. Bovine milk exosome proteome

    Science.gov (United States)

    Exosomes are 40-100 nm membrane vesicles of endocytic origin and are found in blood, urine, amniotic fluid, bronchoalveolar lavage (BAL) fluid, as well as human and bovine milk. Exosomes are extracellular organelles important in intracellular communication/signaling, immune function, and biomarkers ...

  18. Bovine Spongiform Encephalopathy

    Science.gov (United States)

    Bovine spongiform encephalopathy (BSE), also referred to as “mad cow disease” is a chronic, non-febrile, neuro-degenerative disease affecting the central nervous system. The transmissible spongiform encephalopathies (TSEs) of domestic animals, of which BSE is a member includes scrapie of sheep...

  19. BOVINE VIRAL DIARRHEA VIRUSES

    Science.gov (United States)

    Bovine viral diarrhea virus (BVDV) is an umbrella term for two species of viruses, BVDV1 and BVDV2, within the Pestivirus genus of the Flavivirus family. BVDV viruses are further subclassified as cytopathic and noncytopathic based on their activity in cultured epithelial cells. Noncytopathic BVDV p...

  20. Genotyping bovine coronaviruses.

    Science.gov (United States)

    Bovine coronaviruses (BoCV) are enveloped, single-stranded, positive-sense RNA viruses of the Coronaviridae family. Infection is associated with enteritis and pneumonia in calves and Winter Dysentery in adult cattle. Strains, isolated more than 50 years ago, are used in vaccines and as laboratory ...

  1. Accomplishments in 2007 in the Adjuvant Treatment of Colorectal Cancer

    OpenAIRE

    de Gramont, Aimery; Haller, Daniel G.

    2008-01-01

    Overview of the Disease IncidencePrognosisCurrent General Standards and Regional Variations Colon Cancer Stage IIIStage IIRectal CancerAccomplishments (or Lack of Accomplishments) During the Year TherapyMethodologyPsycho-oncologyBasic Science: BiomarkersWhat Needs To Be Done Controversies and DisagreementsFuture Directions Comments on ResearchObstacles to Progress

  2. Molecular phylogeny of intracellular symbiotic Gammaproteobacteria in insects

    OpenAIRE

    HUSNÍK, Filip

    2010-01-01

    Many groups of insects harbor mutualistic intracellular bacteria. These bacteria originated mainly from two bacterial phyla: Bacteroidetes and Proteobacteria. The thesis is focused on phylogeny of Enterobacteriaceae - the most diverse group of endosymbiotic bacteria within Gammaproteobacteria. The study brings new phylogenetical data on "primary" symbionts and summarizes the current state of knowledge on their phylogeny, evolution and diversity.

  3. Chromosomal phylogeny and evolution of gibbons (Hylobatidae).

    Science.gov (United States)

    Müller, Stefan; Hollatz, Melanie; Wienberg, Johannes

    2003-11-01

    Although human and gibbons are classified in the same primate superfamily (Hominoidae), their karyotypes differ by extensive chromosome reshuffling. To date, there is still limited understanding of the events that shaped extant gibbon karyotypes. Further, the phylogeny and evolution of the twelve or more extant gibbon species (lesser apes, Hylobatidae) is poorly understood, and conflicting phylogenies have been published. We present a comprehensive analysis of gibbon chromosome rearrangements and a phylogenetic reconstruction of the four recognized subgenera based on molecular cytogenetics data. We have used two different approaches to interpret our data: (1) a cladistic reconstruction based on the identification of ancestral versus derived chromosome forms observed in extant gibbon species; (2) an approach in which adjacent homologous segments that have been changed by translocations and intra-chromosomal rearrangements are treated as discrete characters in a parsimony analysis (PAUP). The orangutan serves as an "outgroup", since it has a karyotype that is supposed to be most similar to the ancestral form of all humans and apes. Both approaches place the subgenus Bunopithecus as the most basal group of the Hylobatidae, followed by Hylobates, with Symphalangus and Nomascus as the last to diverge. Since most chromosome rearrangements observed in gibbons are either ancestral to all four subgenera or specific for individual species and only a few common derived rearrangements at subsequent branching points have been recorded, all extant gibbons may have diverged within relatively short evolutionary time. In general, chromosomal rearrangements produce changes that should be considered as unique landmarks at the divergence nodes. Thus, molecular cytogenetics could be an important tool to elucidate phylogenies in other species in which speciation may have occurred over very short evolutionary time with not enough genetic (DNA sequence) and other biological divergence to

  4. Le complexe respiratoire bovin

    OpenAIRE

    Lekeux, Pierre

    1996-01-01

    Les maladies respiratoires des bovins sont, partout dans le monde, la cause principale de mortalité chez les jeunes bovins. Plusieurs facteurs favorisent l'apparition de ce syndrome : des facteurs propres à l'animal, comme l'âge, l'état général et le statut immunitaire; d'autres relatifs à l'environnement, comme les stress engendrés par les changements de régime alimentaire, de température et d'humidité; d'autres encore, liés à la présence d'agents infectieux, comme des bactéries, des virus e...

  5. Waubay National Wildlife Refuge : Annual Summary of Accomplishments

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This narrative report for Waubay National Wildlife Refuge outlines Refuge accomplishments for fiscal year 1943. The report begins by summarizing the wildlife, water...

  6. Waubay National Wildlife Refuge : Annual Summary of Accomplishments [1944

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This narrative report for Waubay National Wildlife Refuge outlines Refuge accomplishments for fiscal year 1944. The report begins by summarizing the wildlife, water...

  7. Planning and accomplishment narrative: FY - 1975: Mingo National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This annual narrative report for Mingo National Wildlife Refuge outlines Refuge accomplishments during the 1975 fiscal year. The report begins by summarizing the...

  8. Planning and accomplishment narrative: National Bison Range: [Fiscal year: 1973

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This annual narrative report for National Bison Range outlines Refuge accomplishments during the 1973 fiscal year. The report begins by summarizing the weather...

  9. Idaho National Laboratory Mission Accomplishments, Fiscal Year 2015

    Energy Technology Data Exchange (ETDEWEB)

    Allen, Todd Randall [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wright, Virginia Latta [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-09-01

    A summary of mission accomplishments for the research organizations at the Idaho National Laboratory for FY 2015. Areas include Nuclear Energy, National and Homeland Security, Science and Technology Addressing Broad DOE Missions; Collaborations; and Stewardship and Operation of Research Facilities.

  10. Enhanced surveillance program FY97 accomplishments. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Mauzy, A. [ed.; Laake, B. [comp.

    1997-10-01

    This annual report is one volume of the Enhanced Surveillance Program (ESP) FY97 Accomplishments. The complete accomplishments report consists of 11 volumes. Volume 1 includes an ESP overview and a summary of selected unclassified FY97 program highlights. Volume 1 specifically targets a general audience, reflecting about half of the tasks conducted in FY97 and emphasizing key program accomplishments and contributions. The remaining volumes of the accomplishments report are classified, organized by program focus area, and present in technical detail the progress achieved in each of the 104 FY97 program tasks. Focus areas are as follows: pits; high explosives; organics; dynamics; diagnostics; systems; secondaries; nonnuclear materials; nonnuclear components; and Surveillance Test Program upgrades.

  11. Vitrification of Bovine Oocytes

    OpenAIRE

    Anchamparuthy, Vahida Muhammed Ismail

    2007-01-01

    Cryopreservation of oocytes is a challenge. Studies were conducted to vitrify mouse zygotes and cumulus-intact bovine oocytes from follicles of different diameters, small (â ¤ 4 mm) and medium (4 to 10 mm), using nylon mesh. The specific goals were to assess changes in apoptotic gene expression (Fas-FasL, Bax, Bcl-2, and survivin) in conjunction with terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and caspase assays. Mouse zygotes were exposed to increasing concentrations...

  12. Business accomplishments, gender and entrepreneurial self-image

    OpenAIRE

    Thurik, Roy; Verheul, Ingrid; Uhlaner, Lorraine

    2003-01-01

    textabstractDrawing on Bem’s psychological theory of self-perception, this paper presents and tests a model that examines the impact of business accomplishments and gender on entrepreneurial self-image and explores the definition of entrepreneurship according to Vesper’s Entrepreneurial Typology. Regression techniques are used to identify those business accomplishments that university alumni associate with self-perceptions of entrepreneurship. Experience as a small business person (founding, ...

  13. A supertree approach to shorebird phylogeny

    Directory of Open Access Journals (Sweden)

    Thomas Gavin H

    2004-08-01

    Full Text Available Abstract Background Order Charadriiformes (shorebirds is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species. Here we use the matrix representation with parsimony method to produce the first fully inclusive supertree of Charadriiformes. We also provide preliminary estimates of ages for all nodes in the tree. Results Three main lineages are revealed: i the plovers and allies; ii the gulls and allies; and iii the sandpipers and allies. The relative position of these clades is unresolved in the strict consensus tree but a 50% majority-rule consensus tree indicates that the sandpiper clade is sister group to the gulls and allies whilst the plover group is placed at the base of the tree. The overall topology is highly consistent with recent molecular hypotheses of shorebird phylogeny. Conclusion The supertree hypothesis presented herein is (to our knowledge the only complete phylogenetic hypothesis of all extant shorebirds. Despite concerns over the robustness of supertrees (see Discussion, we believe that it provides a valuable framework for testing numerous evolutionary hypotheses relating to the diversity of behaviour, ecology and life-history of the Charadriiformes.

  14. Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach

    OpenAIRE

    Gusfield, Dan

    2015-01-01

    The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely investigated in recent years. In this paper, we explore two alternative approaches to the persistent-phylogeny problem that grow out of our previous work on perfect phylogeny, and on galled trees. We develop an integer programming solution to the Persistent-...

  15. Partitional Classification: A Complement to Phylogeny

    Science.gov (United States)

    Salomon, Marc; Dassy, Bruno

    2016-01-01

    The tree of life is currently an active object of research, though next to vertical gene transmission non vertical gene transfers proved to play a significant role in the evolutionary process. To overcome this difficulty, trees of life are now constructed from genes hypothesized vital, on the assumption that these are all transmitted vertically. This view has been challenged. As a frame for this discussion, we developed a partitional taxonomical system clustering taxa at a high taxonomical rank. Our analysis (1) selects RNase P RNA sequences of bacterial, archaeal, and eucaryal genera from genetic databases, (2) submits the sequences, aligned, to k-medoid analysis to obtain clusters, (3) establishes the correspondence between clusters and taxa, (4) constructs from the taxa a new type of taxon, the genetic community (GC), and (5) classifies the GCs: Archaea–Eukaryotes contrastingly different from the six others, all bacterial. The GCs would be the broadest frame to carry out the phylogenies. PMID:27346943

  16. Bovine Virus Diarrhea (BVD)

    OpenAIRE

    Hoar, Bruce R.

    2004-01-01

    Bovine virus diarrhea (BVD) is a complicated disease to discuss as it can result in a wide variety of disease problems from very mild to very severe. BVD can be one of the most devastating diseases cattle encounter and one of the hardest to get rid of when it attacks a herd. The viruses that cause BVD have been grouped into two genotypes, Type I and Type II. The disease syndrome caused by the two genotypes is basically the same, however disease caused by Type II infection is often more severe...

  17. Proteomic Analysis of Bovine Nucleolus

    Institute of Scientific and Technical Information of China (English)

    Amrutlal K.Patel; Doug Olson; Suresh K. Tikoo

    2010-01-01

    Nucleolus is the most prominent subnuclear structure, which performs a wide variety of functions in the eu-karyotic cellular processes. In order to understand the structural and functional role of the nucleoli in bovine cells,we analyzed the proteomie composition of the bovine nueleoli. The nucleoli were isolated from Madin Darby bo-vine kidney cells and subjected to proteomie analysis by LC-MS/MS after fractionation by SDS-PAGE and strongcation exchange chromatography. Analysis of the data using the Mascot database search and the GPM databasesearch identified 311 proteins in the bovine nucleoli, which contained 22 proteins previously not identified in theproteomic analysis of human nucleoli. Analysis of the identified proteins using the GoMiner software suggestedthat the bovine nueleoli contained proteins involved in ribosomal biogenesis, cell cycle control, transcriptional,translational and post-translational regulation, transport, and structural organization.

  18. Accomplishments and challenges of the severe accident research

    International Nuclear Information System (INIS)

    This paper describes the progress of the severe accident research since 1980, in terms of the accomplishments made so far and the challenges that remain. Much has been accomplished: many important safety issues have been resolved and consensus is near on some others. However, some of the previously identified safety issues remain as challenges, while some new ones have arisen due to the shift in focus from containment integrity to vessel integrity. New reactor designs have also created some new challenges. In general, the regulatory demands in new reactor designs are much stricter, thereby requiring much greater attention to the safety issues concerned with the containment design of the new large reactors

  19. Phylogeny and Species Diversity of Gulf of California Oysters

    Data.gov (United States)

    U.S. Environmental Protection Agency — Dataset of DNA sequence data from two mitochondrial loci (COI and 16S) used to infer the phylogeny of oysters in the genus Ostrea along the Pacific coast of North...

  20. A MOLECULAR PHYLOGENY FOR THE PROTOSTRONGYLIDAE (NEMATODA: METASTRONGYLINA)

    Science.gov (United States)

    Protostrongylids, a putative monophyletic group among the lungworms (Metastrongylina: Metastrongyloidea), are economically important pathogens infecting domestic and free-ranging ungulate and leporid hosts throughout the world. Here, we reconstruct a molecular phylogeny based on ribosomal DNA (28S) ...

  1. 78 FR 72979 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2013-12-04

    ... risks of other livestock diseases, such as bovine viral diarrhea, foot-and-mouth disease, infectious... Products Derived from Bovines,'' published in the Federal Register on September 18, 2007 (72 FR 53314-53379..., 2012, we published in the Federal Register (77 FR 15848-15913, Docket No. APHIS-2008-0010) a...

  2. Phylogeny And Biogeography of the Carnivorous Plant Family Sarraceniaceae

    OpenAIRE

    Davis, Charles Cavender; Ellison, Aaron M.; Butler, Elena D.; Hicks, Emily Jean; Calie, Patrick J.; Bell, Charles D.; Naczi, Robert F. C.

    2012-01-01

    The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniacea...

  3. Phylogeny reconstruction based on protein phylogenetic profiles of organisms

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    With the coming of the Post Genomic Era, more and more genomes have been sequenced and it has become possible to study phylogeny reconstruction at genome level. The concept of protein phylogenetic profiles of organisms is defined in this work which is used in phylogeny reconstruction by proteome comparisons. This method is more stable than the prevailing molecular systematics methods and can be used widely. It will develop very fast with the rapid progress in genome sequencing.

  4. Viral infections and bovine mastitis: a review

    NARCIS (Netherlands)

    Wellenberg, G.J.; Poel, van der W.H.M.; Oirschot, van J.T.

    2002-01-01

    This review deals with the role of viruses in the aetiology of bovine mastitis. Bovine herpesvirus 1, bovine herpesvirus 4, foot-and-mouth disease virus, and parainfluenza 3 virus have been isolated from milk from cows with clinical mastitis. Intramammary inoculations of bovine herpesvirus 1 or para

  5. Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida).

    Science.gov (United States)

    Cornils, Astrid; Blanco-Bercial, Leocadio

    2013-12-01

    The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters. PMID:23831457

  6. Business accomplishments, gender and entrepreneurial self-image

    NARCIS (Netherlands)

    A.R. Thurik (Roy); I. Verheul (Ingrid); L.M. Uhlaner (Lorraine)

    2003-01-01

    textabstractDrawing on Bem’s psychological theory of self-perception, this paper presents and tests a model that examines the impact of business accomplishments and gender on entrepreneurial self-image and explores the definition of entrepreneurship according to Vesper’s Entrepreneurial Typology. Re

  7. China Accomplished Its First Space Rendezvous and Docking

    Institute of Scientific and Technical Information of China (English)

    Chen Xiaoli

    2011-01-01

    At 1:36 am on November 3,China's Shenzhou 8 unmanned spaceship and Tiangong 1 space lab spacecraft accomplished the country's first space docking procedure and coupling in space at more than 343km above Earth's surface,marking a great leap in China's space program.

  8. Research accomplishments in particle physics: Annual progress report

    International Nuclear Information System (INIS)

    This document presents our report of the research accomplishments of Boston University researchers in six projects in high energy physics research: Colliding Beams Physics; Proton Decay; Monopole Detection with MACRO; Precision Muon G-2 Experiment; Accelerator Design Physics; and Theoretical Physics

  9. Knowledge translation in health care as a multimodal interactional accomplishment

    DEFF Research Database (Denmark)

    Kjær, Malene

    2014-01-01

    of their education where they are in clinical practice. The analysis is made possible through video recordings of how student nurses translate their theoretical knowledge into a professional situational conduct in everyday interactional accomplishments among supervisors and patients. The analysis shows how some...

  10. Bootstrapping phylogenies inferred from rearrangement data

    Directory of Open Access Journals (Sweden)

    Lin Yu

    2012-08-01

    Full Text Available Abstract Background Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. Results We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Conclusions Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its

  11. Bovine Rhinitis Viruses Are Common in U.S. Cattle with Bovine Respiratory Disease

    OpenAIRE

    Hause, Ben M.; Collin, Emily A.; Anderson, Joe; Hesse, Richard A.; Anderson, Gary

    2015-01-01

    Bovine rhinitis viruses (BRV) are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1) has been identified while bovine rhinitis A virus 2 (BRAV2) and bovine rhinitis B virus (BRBV) were previously only identified in England and Japan, respectively. Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD) ...

  12. FY 1995 research highlights: PNL accomplishments in OER programs

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    Pacific Northwest Laboratory (PNL) conducts fundamental and applied research in support of the US Department of Energy`s (DOE) core missions in science and technology, environmental quality, energy resources, and national security. Much of this research is funded by the program offices of DOE`s Office of Energy Research (DOE-ER), primarily the Office of Basic Energy Sciences (BES) and the Office of Health and Environmental Research (OHER), and by PNL`s Laboratory Directed Research and Development (LDRD) Program. This document is a collection of research highlights that describe PNL`s accomplishments in DOE-ER funded programs during Fiscal Year 1995. Included are accomplishments in research funded by OHER`s Analytical Technologies, Environmental Research, Health Effects, General Life Sciences, and Carbon Dioxide Research programs; BES`s Materials Science, Chemical Sciences, Engineering and Geoscience, and Applied Mathematical Sciences programs; and PNL`s LDRD Program. Summaries are given for 70 projects.

  13. Abstract and research accomplishments of University Coal Research Projects

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    The Principal Investigators of the grants supported by the University Coal Research Program were requested to submit abstracts and highlight accomplishments of their respective projects in time for distribution at a conference on June 13--14, 1995 at Tennessee State University in Nashville, Tennessee. This book is a compilation of the material received in response to that request. For convenience, the 70 grants reported in this book are stored into eight technical areas, Coal Science, Coal Surface Science, Reaction Chemistry, Advanced Process Concepts, Engineering Fundamentals and Thermodynamics, Environmental Science, high Temperature Phenomena, and Special topics. Indexes are provided for locating projects by subject, principal investigators, and contracting organizations. Each extended abstract describes project objectives, work accomplished, significance to the Fossil Energy Program, and plans for the next year.

  14. Abstracts and research accomplishments of university coal research projects

    International Nuclear Information System (INIS)

    The Principal Investigators of the grants supported by the University Coal Research Program were requested to submit abstracts and highlight accomplishments of their projects in time for distribution at a grantees conference. This book is a compilation of the material received in response to the request. Abstracts discuss the following area: coal science, coal surface science, reaction chemistry, advanced process concepts, engineering fundamentals and thermodynamics, environmental science

  15. NGNP Process Heat Applications: Hydrogen Production Accomplishments for FY2010

    Energy Technology Data Exchange (ETDEWEB)

    Charles V Park

    2011-01-01

    This report summarizes FY10 accomplishments of the Next Generation Nuclear Plant (NGNP) Engineering Process Heat Applications group in support of hydrogen production technology development. This organization is responsible for systems needed to transfer high temperature heat from a high temperature gas-cooled reactor (HTGR) reactor (being developed by the INL NGNP Project) to electric power generation and to potential industrial applications including the production of hydrogen.

  16. The Teacher-Student Data Link Project: Three Lasting Accomplishments

    OpenAIRE

    Cassie Pickens Jewell; Kristin Hallgren; Sarah Wissel

    2014-01-01

    In 2010, the Bill & Melinda Gates Foundation invited five states and three pilot districts in each state to participate in the Teacher-Student Data Link (TSDL) project. Mathematica developed a report presenting findings from 2011, the project’s first year of implementation. Building on that report, this brief articulates three lasting accomplishments of the TSDL project, and presents additional resources and best practices for initiatives like TSDL that intend to bolster linked teacher-stud...

  17. Abstracts and research accomplishments of university coal research projects

    Energy Technology Data Exchange (ETDEWEB)

    1991-06-01

    The Principal Investigators of the grants supported by the University Coal Research Program were requested to submit abstracts and highlight accomplishments of their projects in time for distribution at a grantees conference. This book is a compilation of the material received in response to the request. Abstracts discuss the following area: coal science, coal surface science, reaction chemistry, advanced process concepts, engineering fundamentals and thermodynamics, environmental science.

  18. The eighth NASA total quality management accomplishments report, 1990

    Science.gov (United States)

    1990-01-01

    The eighth annual accomplishments report provides numerous examples of quality strategies that have proven effective and efficient in a time when cost reduction is critical. NASA's continuous improvement efforts can provide insight for others to succeed in their own endeavors. The report covers: top management leadership and support, strategic planning, focus on the customer, employee training and recognition, employee empowerment and teamwork, measurement and analysis, and quality assurance.

  19. Chemical Research Projects Office: Functions, accomplishments, and programs

    Science.gov (United States)

    Kourtides, D. A.; Parker, J. A.

    1972-01-01

    The purpose, technical accomplishments, and related activities of the Chemical Research Project Group are outlined. Data cover efforts made to: (1) identify chemical research and technology required for solutions to problems of national urgency, synchronous with aeronautics and space effort; (2) conduct basic and applied interdisciplinary research on chemical problems in the areas of macromolecular science and fire research, and (3) provide productive liason with the engineering community and effective transfer of technology to other agencies and industry.

  20. Health and Environmental Research: summary of accomplishments. Volume 2

    Energy Technology Data Exchange (ETDEWEB)

    1986-08-01

    This is an account of some of the accomplishments of the health and environmental research program performed in national laboratories, universities, and research institutes. Both direct and indirect societal benefits emerged from the new knowledge provided by the health and environmental research program. In many cases, the private sector took this knowledge and applied it well beyond the mission of supporting the defense and energy needs of the Nation. Industrial and medical applications, for example, have in several instances provided annual savings to society of $100 million or more. The form of this presentation is, in fact, through ''snapshots'' - examples of significant, tangible accomplishments in each of the areas at certain times to illustrate the role and impact of the research program. The program's worth is not necessarily confined to such accomplishments; it extends, rather, to its ability to identify and help solve potential health and environmental problems before they become critical. This anticipatory mission has been pursued with an approach that combines applied problem solving with a commitment to fundamental research that is long-term and high-risk. The narrative of this research program concludes with a perspective of its past and a prospectus on its future.

  1. Health and Environmental Research: summary of accomplishments. Volume 2

    International Nuclear Information System (INIS)

    This is an account of some of the accomplishments of the health and environmental research program performed in national laboratories, universities, and research institutes. Both direct and indirect societal benefits emerged from the new knowledge provided by the health and environmental research program. In many cases, the private sector took this knowledge and applied it well beyond the mission of supporting the defense and energy needs of the Nation. Industrial and medical applications, for example, have in several instances provided annual savings to society of $100 million or more. The form of this presentation is, in fact, through ''snapshots'' - examples of significant, tangible accomplishments in each of the areas at certain times to illustrate the role and impact of the research program. The program's worth is not necessarily confined to such accomplishments; it extends, rather, to its ability to identify and help solve potential health and environmental problems before they become critical. This anticipatory mission has been pursued with an approach that combines applied problem solving with a commitment to fundamental research that is long-term and high-risk. The narrative of this research program concludes with a perspective of its past and a prospectus on its future

  2. Phylogeny based discovery of regulatory elements

    Directory of Open Access Journals (Sweden)

    Cohen Barak A

    2006-05-01

    Full Text Available Abstract Background Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences. Results We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose. Conclusion The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs.

  3. Bacterial phylogeny structures soil resistomes across habitats

    Science.gov (United States)

    Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

    2014-05-01

    Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.

  4. Molecular epidemiology, phylogeny and evolution of Legionella.

    Science.gov (United States)

    Khodr, A; Kay, E; Gomez-Valero, L; Ginevra, C; Doublet, P; Buchrieser, C; Jarraud, S

    2016-09-01

    Legionella are opportunistic pathogens that develop in aquatic environments where they multiply in protozoa. When infected aerosols reach the human respiratory tract they may accidentally infect the alveolar macrophages leading to a severe pneumonia called Legionnaires' disease (LD). The ability of Legionella to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Although Legionella is a large genus comprising nearly 60 species that are worldwide distributed, only about half of them have been involved in LD cases. Strikingly, the species Legionella pneumophila alone is responsible for 90% of all LD cases. The present review summarizes the molecular approaches that are used for L. pneumophila genotyping with a major focus on the contribution of whole genome sequencing (WGS) to the investigation of local L. pneumophila outbreaks and global epidemiology studies. We report the newest knowledge regarding the phylogeny and the evolution of Legionella and then focus on virulence evolution of those Legionella species that are known to have the capacity to infect humans. Finally, we discuss the evolutionary forces and adaptation mechanisms acting on the Dot/Icm system itself as well as the role of mobile genetic elements (MGE) encoding T4ASSs and of gene duplications in the evolution of Legionella and its adaptation to different hosts and lifestyles. PMID:27180896

  5. Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae).

    Science.gov (United States)

    Tang, Kevin L; Agnew, Mary K; Chen, Wei-Jen; Vincent Hirt, M; Raley, Morgan E; Sado, Tetsuya; Schneider, Leah M; Yang, Lei; Bart, Henry L; He, Shunping; Liu, Huanzhang; Miya, Masaki; Saitoh, Kenji; Simons, Andrew M; Wood, Robert M; Mayden, Richard L

    2011-10-01

    The members of the cyprinid subfamily Gobioninae, commonly called gudgeons, form one of the most well-established assemblages in the family Cyprinidae. The subfamily is a species-rich group of fishes, these fishes display diverse life histories, appearances, and behavior. The phylogenetic relationships of Gobioninae are examined using sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. This investigation produced a data matrix of 4114 bp for 162 taxa that was analyzed using parsimony, maximum likelihood, and Bayesian inference methods. The phylogenies our analyses recovered corroborate recent studies on the group. The subfamily Gobioninae is monophyletic and composed of three major lineages. We find evidence for a Hemibarbus-Squalidus group, and the tribes Gobionini and Sarcocheilichthyini, with the Hemibarbus-Squalidus group sister to a clade of Gobionini-Sarcocheilichthyini. The Hemibarbus-Squalidus group includes those two genera; the tribe Sarcocheilichthyini includes Coreius, Coreoleuciscus, Gnathopogon, Gobiocypris, Ladislavia, Paracanthobrama, Pseudorasbora, Pseudopungtungia, Pungtungia, Rhinogobio, and Sarcocheilichthys; the tribe Gobionini includes Abbottina, Biwia, Gobio, Gobiobotia, Huigobio, Microphysogobio, Platysmacheilus, Pseudogobio, Romanogobio, Saurogobio, and Xenophysogobio. The monotypic Acanthogobio is placed into the synonymy of Gobio. We tentatively assign Belligobio to the Hemibarbus-Squalidus group and Mesogobio to Gobionini; Paraleucogobio and Parasqualidus remain incertae sedis. Based on the topologies presented, the evolution of swim bladder specializations, a distinctive feature among cyprinids, has occurred more than once within the subfamily. PMID:21672635

  6. Molecular phylogeny of euthyneura (mollusca: gastropoda).

    Science.gov (United States)

    Grande, Cristina; Templado, José; Cervera, J Lucas; Zardoya, Rafael

    2004-02-01

    A new phylogenetic hypothesis for Euthyneura is proposed based on the analysis of primary sequence data (mitochondrial cox1, trnV, rrnL, trnL(cun), trnA, trnP, nad6, and nad5 genes) and the phylogenetic utility of two rare genomic changes (the relative position of the mitochondrial trnP gene, and an insertion/deletion event in a conserved region of the mitochondrial Cox1 protein) is addressed. Both sources of phylogenetic information clearly rejected the monophyly of pulmonates, a group of gastropods well supported so far by morphological evidence. The marine basommatophoran pulmonate Siphonaria was placed within opisthobranchs and shared with them the insertion of a Glycine in the Cox 1 protein. The marine systellommatophoran pulmonate Onchidella was recovered at the base of the opisthobranch + Siphonaria clade. Opisthobranchs, Siphonaria, and Onchidella shared the relative position of the mitochondrial trnP gene between the mitochondrial trnA and nad6 genes. The land snails and slugs (stylommatophoran pulmonates) were recovered as an early split in the phylogeny of advanced gastropods. The monophyly of the Euthyneura (Opisthobranchia + Pulmonata) was rejected by the inclusion of the heterostrophan Pyramidella. PMID:14660702

  7. Phylogeny and diversification patterns among vesicomyid bivalves.

    Directory of Open Access Journals (Sweden)

    Carole Decker

    Full Text Available Vesicomyid bivalves are among the most abundant and diverse symbiotic taxa in chemosynthetic-based ecosystems: more than 100 different vesicomyid species have been described so far. In the present study, we investigated the phylogenetic positioning of recently described vesicomyid species from the Gulf of Guinea and their western Atlantic and Pacific counterparts using mitochondrial DNA sequence data. The maximum-likelihood (ML tree provided limited support for the recent taxonomic revision of vesicomyids based on morphological criteria; nevertheless, most of the newly sequenced specimens did not cluster with their morphological conspecifics. Moreover, the observed lack of geographic clustering suggests the occurrence of independent radiations followed by worldwide dispersal. Ancestral character state reconstruction showed a significant correlation between the characters "depth" and "habitat" and the reconstructed ML phylogeny suggesting possible recurrent events of 'stepwise speciation' from shallow to deep waters in different ocean basins. This is consistent with genus or species bathymetric segregation observed from recent taxonomic studies. Altogether, our results highlight the need for ongoing re-evaluation of the morphological characters used to identify vesicomyid bivalves.

  8. On simulated annealing phase transitions in phylogeny reconstruction.

    Science.gov (United States)

    Strobl, Maximilian A R; Barker, Daniel

    2016-08-01

    Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. PMID:27150349

  9. Bovine placental lactogen: isolation purification and measurement in biological fluids

    International Nuclear Information System (INIS)

    Studies were conducted to isolate and purify bovine placental lactogen (bPL) and to develop a radioimmunoassay to this protein. Bovine placental lactogen was isolated from culture medium after a 24 hr culture of fetal cotyledonary tissue. Cotyledonary explants were stimulated to secrete bPL by either addition of bovine growth hormone (NIH-B8) to the medium or co-culture of cotyledon and caruncular tissue. Production of bPL was greatly affected by explant size and 70% of that produced in a 48 hr culture was released in the first 12 hr. Purification of bPL was accomplished using a column chromatographic scheme that involved gel filtration, ion exchange and chromatofocusing chromatography. A radioimmunoassay to bPL was developed using an antibody raised at the USDA Beltsville (F56). Dose response curves of amniotic or allantoic fluid or fetal and maternal serum were parallel to the standard curve and bPL was quantitatively recovered at from 82-125%. Using the radioimmunoassay, samples of amniotic and allantoic fluids and fetal and maternal serum were measured for bPL. Concentrations of bPL ranged from undetectable to 50 ng/ml, with fetal blood having the highest concentrations and amniotic fluid the lowest

  10. Multilocus sequence types of Finnish bovine Campylobacter jejuni isolates and their attribution to human infections

    Directory of Open Access Journals (Sweden)

    Corander Jukka

    2010-07-01

    Full Text Available Abstract Background Campylobacter jejuni is the most common bacterial cause of human gastroenteritis worldwide. Due to the sporadic nature of infection, sources often remain unknown. Multilocus sequence typing (MLST has been successfully applied to population genetics of Campylobacter jejuni and mathematical modelling can be applied to the sequence data. Here, we analysed the population structure of a total of 250 Finnish C. jejuni isolates from bovines, poultry meat and humans collected in 2003 using a combination of Bayesian clustering (BAPS software and phylogenetic analysis. Results In the first phase we analysed sequence types (STs of 102 Finnish bovine C. jejuni isolates by MLST and found a high diversity totalling 50 STs of which nearly half were novel. In the second phase we included MLST data from domestic human isolates as well as poultry C. jejuni isolates from the same time period. Between the human and bovine isolates we found an overlap of 72.2%, while 69% of the human isolates were overlapping with the chicken isolates. In the BAPS analysis 44.3% of the human isolates were found in bovine-associated BAPS clusters and 45.4% of the human isolates were found in the poultry-associated BAPS cluster. BAPS reflected the phylogeny of our data very well. Conclusions These findings suggest that bovines and poultry were equally important as reservoirs for human C. jejuni infections in Finland in 2003. Our results differ from those obtained in other countries where poultry has been identified as the most important source for human infections. The low prevalence of C. jejuni in poultry flocks in Finland could explain the lower attribution of human infection to poultry. Of the human isolates 10.3% were found in clusters not associated with any host which warrants further investigation, with particular focus on waterborne transmission routes and companion animals.

  11. Space robotics: Recent accomplishments and opportunities for future research

    Science.gov (United States)

    Montgomery, Raymond C.; Buttrill, Carey S.; Dorsey, John T.; Juang, Jer-Nan; Lallman, Frederick J.; Moerder, Daniel D.; Scott, Michael A.; Troutman, Patrick; Williams, Robert L., II

    1992-01-01

    The Langley Guidance, Navigation, and Control Technical Committee (GNCTC) was one of six technical committees created in 1991 by the Chief Scientist, Dr. Michael F. Card. During the kickoff meeting Dr. Card charged the chairmen to: (1) establish a cross-Center committee; (2) support at least one workshop in a selected discipline; and (3) prepare a technical paper on recent accomplishments in the discipline and on opportunities for future research. The Guidance, Navigation, and Control Committee was formed and selected for focus on the discipline of Space robotics. This report is a summary of the committee's assessment of recent accomplishments and opportunities for future research. The report is organized as follows. First is an overview of the data sources used by the committee. Next is a description of technical needs identified by the committee followed by recent accomplishments. Opportunities for future research ends the main body of the report. It includes the primary recommendation of the committee that NASA establish a national space facility for the development of space automation and robotics, one element of which is a telerobotic research platform in space. References 1 and 2 are the proceedings of two workshops sponsored by the committee during its June 1991, through May 1992 term. The focus of the committee for the June 1992 - May 1993 term will be to further define to the recommended platform in space and to add an additional discipline which includes aircraft related GN&C issues. To the latter end members performing aircraft related research will be added to the committee. (A preliminary assessment of future opportunities in aircraft-related GN&C research has been included as appendix A.)

  12. Ontogeny tends to recapitulate phylogeny in digital organisms.

    Science.gov (United States)

    Clune, Jeff; Pennock, Robert T; Ofria, Charles; Lenski, Richard E

    2012-09-01

    Biologists have long debated whether ontogeny recapitulates phylogeny and, if so, why. Two plausible explanations are that (i) changes to early developmental stages are selected against because they tend to disrupt later development and (ii) simpler structures often precede more complex ones in both ontogeny and phylogeny if the former serve as building blocks for the latter. It is difficult to test these hypotheses experimentally in natural systems, so we used a computational system that exhibits evolutionary dynamics. We observed that ontogeny does indeed recapitulate phylogeny; traits that arose earlier in a lineage's history also tended to be expressed earlier in the development of individuals. The relative complexity of traits contributed substantially to this correlation, but a significant tendency toward recapitulation remained even after accounting for trait complexity. This additional effect provides evidence that selection against developmental disruption also contributed to the conservation of early stages in development. PMID:22854085

  13. Gene order phylogeny and the evolution of methanogens.

    Directory of Open Access Journals (Sweden)

    Haiwei Luo

    Full Text Available Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets revealed that methanogens can be grouped into two classes, "Class I" and "Class II". However, some deep relationships were not resolved. For instance, the monophyly of "Class I" methanogens, which consist of Methanopyrales, Methanobacteriales and Methanococcales, is disputable due to weak statistical support. In this study, we use MSOAR to identify common orthologous genes from eight methanogen species and a Thermococcale species (outgroup, and apply GRAPPA and FastME to compute distance-based gene order phylogeny. The gene order phylogeny supports two classes of methanogens, but it differs from the original classification of methanogens by placing Methanopyrales and Methanobacteriales together with Methanosarcinales in Class II rather than with Methanococcales. This study suggests a new classification scheme for methanogens. In addition, it indicates that gene order phylogeny can complement traditional sequence-based methods in addressing taxonomic questions for deep relationships.

  14. [Summary of phylogeny in family Felidae of Carnivora].

    Science.gov (United States)

    Wang, Jin-Feng; Zhang, Ya-Ping; Yu, Li

    2012-11-01

    Felidae (cats) is one of the strict carnivorous groups in the order Carnivora, many of which are most familiar and spectacular to us. They are the top predators in the world. Thirty-six of 37 living cat species are considered as either "endangered" or "threatened". The relationships among species of the family Felidae, which evolved recently and rapidly, are difficult to resolve, and have been the subject of debate. Construction of a reliable Felidae phylogeny will be of evolutionarily significance and conservation value. In this paper, we summarized phylogeny of Felidae, including cytological, morphological and molecular evidence, and pointed out the existing phylogenetic problems. This review is expected to guide future researches of Felidae phylogeny, and to lay a theoretic foundation for the protection of this animal group. PMID:23208134

  15. Bayesian phylogeny analysis via stochastic approximation Monte Carlo

    KAUST Repository

    Cheon, Sooyoung

    2009-11-01

    Monte Carlo methods have received much attention in the recent literature of phylogeny analysis. However, the conventional Markov chain Monte Carlo algorithms, such as the Metropolis-Hastings algorithm, tend to get trapped in a local mode in simulating from the posterior distribution of phylogenetic trees, rendering the inference ineffective. In this paper, we apply an advanced Monte Carlo algorithm, the stochastic approximation Monte Carlo algorithm, to Bayesian phylogeny analysis. Our method is compared with two popular Bayesian phylogeny software, BAMBE and MrBayes, on simulated and real datasets. The numerical results indicate that our method outperforms BAMBE and MrBayes. Among the three methods, SAMC produces the consensus trees which have the highest similarity to the true trees, and the model parameter estimates which have the smallest mean square errors, but costs the least CPU time. © 2009 Elsevier Inc. All rights reserved.

  16. Inference of Large Phylogenies Using Neighbour-Joining

    DEFF Research Database (Denmark)

    Simonsen, Martin; Mailund, Thomas; Pedersen, Christian Nørgaard Storm

    2011-01-01

    The neighbour-joining method is a widely used method for phylogenetic reconstruction which scales to thousands of taxa. However, advances in sequencing technology have made data sets with more than 10,000 related taxa widely available. Inference of such large phylogenies takes hours or days using...... the Neighbour-Joining method on a normal desktop computer because of the O(n^3) running time. RapidNJ is a search heuristic which reduce the running time of the Neighbour-Joining method significantly but at the cost of an increased memory consumption making inference of large phylogenies infeasible....... We present two extensions for RapidNJ which reduce the memory requirements and \\makebox{allows} phylogenies with more than 50,000 taxa to be inferred efficiently on a desktop computer. Furthermore, an improved version of the search heuristic is presented which reduces the running time of RapidNJ on...

  17. Bovine Tuberculosis, A Zoonotic Disease

    Directory of Open Access Journals (Sweden)

    Tarmudji

    2008-12-01

    Full Text Available Bovine tuberculosis is caused by the infection of Mycobacterium tuberculosis var. bovis (M. bovis. This species is one of Mycobacterium tuberculosis complex, can infect wide range of hosts: cattle and other domesticated animals, wild mammals and humans (zoonotic. M. bovis bacterium from infected hosts can be transmitted to other susceptible animals and humans through respiratory excretes and secretion materials. Humans can be infected with M. bovis by ingested M. bovis contaminated animal products, unpasteurised milk from tuberculosis cows or through respiratory route of contaminated aerosol. Bovine tuberculosis at the first stage does not show any clinical sign but as the disease progress in the next stage which may take several months or years, clinical signs may arise, suh as: fluctuative body temperature, anorexia, lost body weight, coughing, oedema of lymph nodes, increased respiratory frequencies. Pathological lesion of bovine tuberculosis is characterised by the formation of granulomas (tubercles, in which bacterial cells have been localised, most in lymph nodes and pulmonum, but can occur in other organs. The granulomas usually arise in small nodules or tubercles appear yellowish either caseus, caseo-calcareus or calcified. In Indonesia, bovine tuberculosis occurred in dairy cattle since 1905 through the imported dairy cows from Holland and Australian. It was unfortunate that until recently, there were not many research and surveilances of bovine tuberculosis conducted in this country, so the distribution of bovine tuberculosis is unknown. Early serological diagnosis can be done on live cattle by means of tuberculin tests under field conditions. Confirmation can be done by isolation and identification of excreted and secreted samples from the slaughter house. Antibiotic treatment and vaccination were uneffective, therefore the effective control of bovine tuberculosis is suggested by tuberculin tests and by slaughtering the selected

  18. Accomplishments of the Oak Ridge National Laboratory Seed Money program

    Science.gov (United States)

    1986-09-01

    In 1974, a modest program for funding new, innovative research was initiated at ORNL. It was called the "Seed Money" program and has become part of a larger program, called Exploratory R and D, which is being carried out at all DOE national laboratories. This report highlights 12 accomplishments of the Seed Money Program: nickel aluminide, ion implantation, laser annealing, burn meter, Legionnaires' disease, whole-body radiation counter, the ANFLOW system, genetics and molecular biology, high-voltage equipment, microcalorimeter, positron probe, and atom science. (DLC)

  19. Environmental Measurements Laboratory fiscal year 1998: Accomplishments and technical activities

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, M.D.

    1999-01-01

    The Environmental Measurements Laboratory (EML) is government-owned, government-operated, and programmatically under the DOE Office of Environmental Management. The Laboratory is administered by the Chicago Operations Office. EML provides program management, technical assistance and data quality assurance for measurements of radiation and radioactivity relating to environmental restoration, global nuclear nonproliferation, and other priority issues for the Department of Energy, as well as for other government, national, and international organizations. This report presents the technical activities and accomplishments of EML for Fiscal Year 1998.

  20. toward a phylogeny of the kukri snakes, genus oligodon

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    the south and southeast asian snake genus oligodon,known for its egg-eating feeding behavior,has been a taxonomically and systematically challenging group.this work provides the first phylogenetic hypothesis for the genus.we use approximately 1900 base pairs of mitochondrial dna sequence data to infer the relationships of these snakes,and we examine congruence between the phylogeny and hemipenial characters.a hypothesis for the position of oligodon within the colubridae is also proposed.we discuss the implications of the phylogeny for previous taxonomic groupings,and consider the usefulness of the trees in analysis of behavior and biogeography of this genus.

  1. Material Recovery and Waste Form Development FY 2015 Accomplishments Report

    International Nuclear Information System (INIS)

    The Material Recovery and Waste Form Development (MRWFD) Campaign under the U.S. Department of Energy (DOE) Fuel Cycle Technologies (FCT) Program is responsible for developing advanced separation and waste form technologies to support the various fuel cycle options defined in the DOE Nuclear Energy Research and Development Roadmap, Report to Congress, April 2010. The FY 2015 Accomplishments Report provides a highlight of the results of the research and development (R&D) efforts performed within the MRWFD Campaign in FY-14. Each section contains a high-level overview of the activities, results, technical point of contact, applicable references, and documents produced during the fiscal year. This report briefly outlines campaign management and integration activities, but primarily focuses on the many technical accomplishments made during FY-15. The campaign continued to utilize an engineering driven-science-based approach to maintain relevance and focus. There was increased emphasis on development of technologies that support near-term applications that are relevant to the current once-through fuel cycle.

  2. Material Recovery and Waste Form Development FY 2015 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Todd, Terry Allen [Idaho National Lab. (INL), Idaho Falls, ID (United States); Braase, Lori Ann [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-11-01

    The Material Recovery and Waste Form Development (MRWFD) Campaign under the U.S. Department of Energy (DOE) Fuel Cycle Technologies (FCT) Program is responsible for developing advanced separation and waste form technologies to support the various fuel cycle options defined in the DOE Nuclear Energy Research and Development Roadmap, Report to Congress, April 2010. The FY 2015 Accomplishments Report provides a highlight of the results of the research and development (R&D) efforts performed within the MRWFD Campaign in FY-14. Each section contains a high-level overview of the activities, results, technical point of contact, applicable references, and documents produced during the fiscal year. This report briefly outlines campaign management and integration activities, but primarily focuses on the many technical accomplishments made during FY-15. The campaign continued to utilize an engineering driven-science-based approach to maintain relevance and focus. There was increased emphasis on development of technologies that support near-term applications that are relevant to the current once-through fuel cycle.

  3. Twenty years of ABACC: Accomplishments, lessons learnt and future perspectives

    International Nuclear Information System (INIS)

    From the inception of the implementation of the Quadripartite Agreement (INFCIRC/435), in 1991, ABACC has had an important role at the non-proliferation agenda and has also been an active player in the international safeguards. It was necessary for ABACC to develop a technical capacity to face the challenges to be a safeguards agency and to gain credibility in the nuclear safeguards world. This capacity means to develop and implement safeguards systems in the technical area, in the inspection framework, in the conceptual analysis of processes and approaches and in the political scenario. These tasks conducted the strategic plan of ABACC on the last 20 years. Among the accomplishments, ABACC has been involved in the application of safeguards to sensitive and complex installations, in developing safeguards instrumentation, in establishing a technical and trained inspectorate, in constructing a cooperative and coordinate environment with IAEA for safeguards application. Other challenges as R and D of equipment and quality assurance systems were also managed during all these years. ESARDA is one forum that ABACC is involved and always shares experience and ideas. On July 18th, 2011 ABACC will formally complete 20 years. This paper summarizes the accomplishments, lessons learnt and future actions for strengthen the ABACC safeguards role. It also addresses the collaboration of ABACC with other organizations in the non-proliferation and international safeguards arena.

  4. Northeast Regional Biomass Program: Mission, accomplishments, prospects, 1991

    International Nuclear Information System (INIS)

    This 1991 Report contains an update on the mission, goals and accomplishments of the Northeast Regional Biomass Program (NRBP). It describes the activities conducted during the past two years and incorporates the information contained in the 1989 publication of the NRBP Five Year Report. It describes the biomass projects conducted by the individual states of the Northeast Region, and summarizes the results from the Program's technical studies. Publications from both the state and regional projects are listed as well. An appendix lists the biomass-fired electricity generating stations planned or in operation in the region. The NRBP began in 1983 by developing a five year plan to guide its work. Within that time frame, the NRBP undertook over 20 applied research and technology transfer projects, and supported and guided the work of its eleven member states. During and since that period, the NRBP has brought together public and private sector organizations to promote the use in the Northeast of biomass and municipal waste energy resources and technologies. The NRBP's long-range plan was updated in 1990. In light of the accomplishments of the NRBP and the remaining challenges, this Report considers directions for future efforts. The Northeast has abundant biomass resources and markets for their use as energy. Meeting this potential will contribute to reducing the atmospheric greenhouse effect and dependence on imported oil. 49 refs

  5. Bovine respiratory disease model based on dual infections with infection with bovine viral diarrhea virus and bovine corona virus

    Science.gov (United States)

    Bovine respiratory disease complex (BRDC) is the leading cause of economic loss in the U.S. cattle industry. BRDC likely results from simultaneous or sequential infections with multiple pathogens including both viruses and bacteria. Bovine viral diarrhea virus (BVDV) and bovine corona virus (BoCV...

  6. Association of Bovine Viral Diarrhea Virus with Multiple Viral Infections in Bovine Respiratory Disease Outbreaks

    OpenAIRE

    Richer, Lisette; Marois, Paul; Lamontagne, Lucie

    1988-01-01

    We investigated eleven outbreaks of naturally occurring bovine respiratory diseases in calves and adult animals in the St-Hyacinthe area of Quebec. Specific antibodies to bovine herpesvirus-1, bovine viral diarrhea virus, respiratory syncytial virus, parainfluenza type 3 virus, reovirus type 3, and serotypes 1 to 7 of bovine adenovirus were found in paired sera from diseased animals. Several bovine viruses with respiratory tropism were involved concomitantly in herds during an outbreak of bov...

  7. Cementitious Barriers Partnership Accomplishments And Relevance To The DOE Complex

    International Nuclear Information System (INIS)

    The Cementitious Barriers Partnership (CBP) was initiated to reduce risk and uncertainties in the performance assessments that directly impact U.S. Department of Energy (DOE) environmental cleanup and closure programs. The CBP is supported by the DOE Office of Environmental Management (DOE-EM) and has been specifically addressing the following critical EM program needs: (i) the long-term performance of cementitious barriers and materials in nuclear waste disposal facilities and (ii) increased understanding of contaminant transport behavior within cementitious barrier systems to support the development and deployment of adequate closure technologies. To accomplish this, the CBP has two initiatives: (1) an experimental initiative to increase understanding of changes in cementitious materials over long times (> 1000 years) over changing conditions and (2) a modeling initiative to enhance and integrate a set of computational tools validated by laboratory and field experimental data to improve understanding and prediction of the long-term performance of cementitious barriers and waste forms used in nuclear applications. In FY10, the CBP developed the initial phase of an integrated modeling tool that would serve as a screening tool which could help in making decisions concerning disposal and tank closure. The CBP experimental programs are underway to validate this tool and provide increased understanding of how CM changes over time and under changing conditions. These initial CBP products that will eventually be enhanced are anticipated to reduce the uncertainties of current methodologies for assessing cementitious barrier performance and increase the consistency and transparency of the DOE assessment process. These tools have application to low activity waste forms, high level waste tank closure, D and D and entombment of major nuclear facilities, landfill waste acceptance criteria, and in-situ grouting and immobilization of vadose zone contamination. This paper

  8. The US Advanced Fuel Cycle Programme: Objectives and Accomplishments

    International Nuclear Information System (INIS)

    For approximately a decade, the United States Department of Energy has been conducting an advanced fuel cycle programme, presently named the Fuel Cycle R and D Program, devoted to lessening both the environmental burden of nuclear energy and the proliferation risk of accumulating used nuclear fuel. Currently, the programme is being redirected towards a science based, goal oriented focus with the objective of deploying successfully demonstrated technology in the 2040-2050 time frame. The present paper reports the key considerations of the science based research approach, the elements of the technical programme and the accomplishments in fast reactor research and development, the goal of which is to improve the primary issues that have inhibited fast reactor introduction in the past, namely, economics and safety. (author)

  9. Geotrap: radionuclide migration in geologic, heterogeneous media. Summary of accomplishments

    International Nuclear Information System (INIS)

    GEOTRAP - the OECD/NEA Project on Radionuclide Migration in Geologic, Heterogeneous Media - was carried out in the context of site evaluation and safety assessment of deep repository systems for long-lived radioactive waste. The project was created in 1996 with the aim of developing an understanding of, and modelling capability for, potential radionuclide migration. This report provides an overview of the project's main findings and accomplishments over its five-year life. This summary should help make the valuable information collected and generated by the GEOTRAP project accessible to a wide readership both within and outside the radioactive waste community.It is a reflection of the careful attention paid by this community to the question of radionuclide transport. (authors)

  10. Research accomplishments and future goals in particle physics

    International Nuclear Information System (INIS)

    This report presents the research accomplishments and ongoing activities of Boston University researchers in high energy physics. We are active in eight principal areas which are discussed in this report: Colliding Beams - physics of electron-positron annihilation; Accelerator Design Physics - advanced accelerator design; Monopole/ Neutrino - searchers for magnetic monopoles and for neutrino oscillations; Proton Decay - search for nucleon instability and study of nonaccelarator physics; Particle Theory - theoretical high energy particles physics; Muon G-2 - an experiment to measure the anomalous magnetic moment of the muon with a factor of 20 better precision than currently achieved; SSSintcal - scintillating fiber calorimetry for the SSC; and SSC Muon Detectors - development of muon detectors for the GEM Experiment at the SSC

  11. Accomplishments and challenges in development of an autonomous operation system

    International Nuclear Information System (INIS)

    The authors are studying an autonomous operation system for nuclear power plants in which AI plays key roles as an alternative of plant operators and traditional controllers. In contrast with past studies dedicated to assist the operators, the ultimate target of development of the autonomous operation system is to operate the nuclear plants by AI. To realize humanlike decision-making process by means of AI, the authors used a model-based approach from multiple viewpoints and methodology diversity. A hierarchical distributed cooperative multi-agent system configuration is adopted to allow to incorporate diversified methodologies and to dynamically reorganize system functions. In the present paper, accomplishments to date in the course of the development are described. Challenges for developing methodologies to attain dynamic reorganization are also addressed. (author)

  12. IMHEX fuel cell repeat component manufacturing continuous improvement accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Jakaitis, L.A.; Petraglia, V.J.; Bryson, E.S. [M-C Power Corp., Burr Ridge, IL (United States)] [and others

    1996-12-31

    M-C Power is taking a power generation technology that has been proven in the laboratory and is making it a commercially competitive product. There are many areas in which this technology required scale up and refinement to reach the market entry goals for the IMHEX{reg_sign} molten carbonate fuel cell power plant. One of the primary areas that needed to be addressed was the manufacturing of the fuel cell stack. Up to this point, the fuel cell stack and associated components were virtually hand made for each system to be tested. M-C Power has now continuously manufactured the repeat components for three 250 kW stacks. M-C Power`s manufacturing strategy integrated both evolutionary and revolutionary improvements into its comprehensive commercialization effort. M-C Power`s objectives were to analyze and continuously improve stack component manufacturing and assembly techniques consistent with established specifications and commercial scale production requirements. Evolutionary improvements are those which naturally occur as the production rates are increased and experience is gained. Examples of evolutionary (learning curve) improvements included reducing scrap rates and decreasing raw material costs by buying in large quantities. Revolutionary improvements result in significant design and process changes to meet cost and performance requirements of the market entry system. Revolutionary changes often involve identifying new methods and developing designs to accommodate the new process. Based upon our accomplishments, M-C Power was able to reduce the cost of continuously manufactured fuel cell repeat components from the first to third 250 kW stack by 63%. This paper documents the continuous improvement accomplishments realized by M-C Power during IMHEX{reg_sign} fuel cell repeat component manufacturing.

  13. Relationships within phylogeny of vespertilionid bats (Chiroptera: Vespertilionidae)

    Czech Academy of Sciences Publication Activity Database

    Dolinay, M.; Martínková, Natália

    Brno: Ústav biologie obratlovců AV ČR, 2013 - (Bryja, J.; Řehák, Z.; Zukal, J.). s. 56-57 ISBN 978-80-87189-14-6. [Zoologické dny. 07.02.2013-08.02.2013, Brno] Institutional support: RVO:68081766 Keywords : bats * phylogeny Subject RIV: EG - Zoology

  14. Ecological interaction and phylogeny, studying functionality on composed networks

    Science.gov (United States)

    Cruz, Claudia P. T.; Fonseca, Carlos Roberto; Corso, Gilberto

    2012-02-01

    We study a class of composed networks that are formed by two tree networks, TP and TA, whose end points touch each other through a bipartite network BPA. We explore this network using a functional approach. We are interested in how much the topology, or the structure, of TX (X=A or P) determines the links of BPA. This composed structure is a useful model in evolutionary biology, where TP and TA are the phylogenetic trees of plants and animals that interact in an ecological community. We make use of ecological networks of dispersion of fruits, which are formed by frugivorous animals and plants with fruits; the animals, usually birds, eat fruits and disperse their seeds. We analyse how the phylogeny of TX determines or is correlated with BPA using a Monte Carlo approach. We use the phylogenetic distance among elements that interact with a given species to construct an index κ that quantifies the influence of TX over BPA. The algorithm is based on the assumption that interaction matrices that follows a phylogeny of TX have a total phylogenetic distance smaller than the average distance of an ensemble of Monte Carlo realisations. We find that the effect of phylogeny of animal species is more pronounced in the ecological matrix than plant phylogeny.

  15. Molecular phylogeny of Neotropical monogeneans (Platyhelminthes: Monogenea) from catfishes (Siluriformes)

    Czech Academy of Sciences Publication Activity Database

    Mendoza-Palmero, Carlos Alonso; Blasco-Costa, I.; Scholz, Tomáš

    2015-01-01

    Roč. 8, MAR 18 2015 (2015), s. 164. ISSN 1756-3305 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Phylogeny * Monogenea * Dactylogyridae * Neotropical region * Diversity * Siluriformes * 28S rRNA Subject RIV: EG - Zoology Impact factor: 3.430, year: 2014

  16. Phylogeny of not-yet-cultured spirochetes from termite guts

    DEFF Research Database (Denmark)

    Paster, B.J.; Dewhirst, F.E.; Cooke, S.M.;

    1996-01-01

    Comparisons of 16S rDNA sequences were used to determine the phylogeny of not-yet-cultured spirochetes from hindguts of the African higher termite, Nasutitermes lujae (Wasmann). The 16S rRNA genes were amplified directly from spirochete-rich hindguts by using universal primers, and the amplified...

  17. Ontogeny and Phylogeny from an Epigenetic Point of View.

    Science.gov (United States)

    Lovtrup, Soren

    1984-01-01

    The correlation between ontogeny and phylogeny is analyzed through the discussion of four theories on the reality, history, epigenetic, and ecological aspects of the mechanism of evolution. Also discussed are historical and creative aspects of evolution and three epigenetic mechanisms instantiated in the case of the amphibian embryo. (Author/RH)

  18. Low frequency of paleoviral infiltration across the avian phylogeny

    DEFF Research Database (Denmark)

    Cui, Jie; Zhao, Wei; Huang, Zhiyong;

    2014-01-01

    endogenous viral element evolution.Results: Through a systematic screening of the genomes of 48 species sampled across the avian phylogeny we reveal that birds harbor a limited number of endogenous viral elements compared to mammals, with only five viral families observed: Retroviridae, Hepadnaviridae...

  19. A large phylogeny of turtles (Testudines) using molecular data

    NARCIS (Netherlands)

    Guillon, J.-M.; Guéry, L.; Hulin, V.; Girondot, M.

    2012-01-01

    Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA

  20. The genus Gloriosa (Colchicaceae) : ethnobotany, phylogeny and taxonomy

    NARCIS (Netherlands)

    Maroyi, A.

    2012-01-01

    This thesis focuses on the ethnobotany, phylogeny and taxonomy of the genus Gloriosa L. over its distributional range. Some Gloriosa species are known to have economic and commercial value, but the genus is also well known for its complex alpha taxonomy. An appropriate taxonomy for this group is of

  1. Phylogeny predicts future habitat shifts due to climate change.

    Directory of Open Access Journals (Sweden)

    Matjaž Kuntner

    Full Text Available BACKGROUND: Taxa may respond differently to climatic changes, depending on phylogenetic or ecological effects, but studies that discern among these alternatives are scarce. Here, we use two species pairs from globally distributed spider clades, each pair representing two lifestyles (generalist, specialist to test the relative importance of phylogeny versus ecology in predicted responses to climate change. METHODOLOGY: We used a recent phylogenetic hypothesis for nephilid spiders to select four species from two genera (Nephilingis and Nephilengys that match the above criteria, are fully allopatric but combined occupy all subtropical-tropical regions. Based on their records, we modeled each species niche spaces and predicted their ecological shifts 20, 40, 60, and 80 years into the future using customized GIS tools and projected climatic changes. CONCLUSIONS: Phylogeny better predicts the species current ecological preferences than do lifestyles. By 2080 all species face dramatic reductions in suitable habitat (54.8-77.1% and adapt by moving towards higher altitudes and latitudes, although at different tempos. Phylogeny and life style explain simulated habitat shifts in altitude, but phylogeny is the sole best predictor of latitudinal shifts. Models incorporating phylogenetic relatedness are an important additional tool to predict accurately biotic responses to global change.

  2. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    Science.gov (United States)

    Next generation sequencing is helping to solve the data insufficiency problem hindering well-resolved dominant gene phylogenies. We used Roche 454 technology to obtain DNA sequences from 93 nuclear orthologs, dispersed throughout all linkage groups of Daucus. Of these 93 orthologs, ten were designed...

  3. Molecular phylogeny and evolution of mosquito parasitic Microsporidia (Microsporidia: Amblyosporidae)

    Czech Academy of Sciences Publication Activity Database

    Vossbrinck, C. R.; Andreadis, T.; Vávra, Jiří; Becnel, J. J.

    2004-01-01

    Roč. 51, č. 1 (2004), s. 88-95. ISSN 1066-5234 Institutional research plan: CEZ:AV0Z6022909 Keywords : Microsporidia * molecular phylogeny * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.403, year: 2004

  4. Phylogeny and adaptation shape the teeth of insular mice.

    Science.gov (United States)

    Ledevin, Ronan; Chevret, Pascale; Ganem, Guila; Britton-Davidian, Janice; Hardouin, Emilie A; Chapuis, Jean-Louis; Pisanu, Benoit; da Luz Mathias, Maria; Schlager, Stefan; Auffray, Jean-Christophe; Renaud, Sabrina

    2016-02-10

    By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation. PMID:26842576

  5. Angiosperm phylogeny inferred from sequences of four mitochondrial genes

    Institute of Scientific and Technical Information of China (English)

    Yin-Long QIU; Zhi-Duan CHEN; Libo LI; Bin WANG; Jia-Yu XUE; Tory A. HENDRY; Rui-Qi LI; Joseph W. BROWN; Yang LIU; Geordan T. HUDSON

    2010-01-01

    An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atpl, matR, had5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales-Oxalidales-Malpighiales) clade is sister to malvids (or rosid Ⅱ), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.

  6. Enterotoxemia em bovino Bovine enterotoxaemia

    Directory of Open Access Journals (Sweden)

    F.C.F. Lobato

    2006-10-01

    Full Text Available This report describes a case of bovine enterotoxaemia in Morro da Garça, Minas Gerais, Brazil. Clostridium perfringens type D was isolated in pure culture and was characterized by biochemical reactions and PCR. By the mouse neutralization test, the presence of epsilon toxin from intestinal content was detected.

  7. Enterotoxemia em bovino Bovine enterotoxaemia

    OpenAIRE

    F.C.F. Lobato; R.A. Assis; V.L.V. Abreu; M.F. Souza Jr.; C.G.R.D. Lima; F.M. Salvarani

    2006-01-01

    This report describes a case of bovine enterotoxaemia in Morro da Garça, Minas Gerais, Brazil. Clostridium perfringens type D was isolated in pure culture and was characterized by biochemical reactions and PCR. By the mouse neutralization test, the presence of epsilon toxin from intestinal content was detected.

  8. Bovine Staphylococcus aureus: Subtyping, evolution, and zoonotic transfer.

    Science.gov (United States)

    Boss, R; Cosandey, A; Luini, M; Artursson, K; Bardiau, M; Breitenwieser, F; Hehenberger, E; Lam, Th; Mansfeld, M; Michel, A; Mösslacher, G; Naskova, J; Nelson, S; Podpečan, O; Raemy, A; Ryan, E; Salat, O; Zangerl, P; Steiner, A; Graber, H U

    2016-01-01

    Staphylococcus aureus is globally one of the most important pathogens causing contagious mastitis in cattle. Previous studies using ribosomal spacer (RS)-PCR, however, demonstrated in Swiss cows that Staph. aureus isolated from bovine intramammary infections are genetically heterogeneous, with Staph. aureus genotype B (GTB) and GTC being the most prominent genotypes. Furthermore, Staph. aureus GTB was found to be contagious, whereas Staph. aureus GTC and all the remaining genotypes were involved in individual cow disease. In addition to RS-PCR, other methods for subtyping Staph. aureus are known, including spa typing and multilocus sequence typing (MLST). They are based on sequencing the spa and various housekeeping genes, respectively. The aim of the present study was to compare the 3 analytic methods using 456 strains of Staph. aureus isolated from milk of bovine intramammary infections and bulk tanks obtained from 12 European countries. Furthermore, the phylogeny of animal Staph. aureus was inferred and the zoonotic transfer of Staph. aureus between cattle and humans was studied. The analyzed strains could be grouped into 6 genotypic clusters, with CLB, CLC, and CLR being the most prominent ones. Comparing the 3 subtyping methods, RS-PCR showed the highest resolution, followed by spa typing and MLST. We found associations among the methods but in many cases they were unsatisfactory except for CLB and CLC. Cluster CLB was positive for clonal complex (CC)8 in 99% of the cases and typically positive for t2953; it is the cattle-adapted form of CC8. Cluster CLC was always positive for tbl 2645 and typically positive for CC705. For CLR and the remaining subtypes, links among the 3 methods were generally poor. Bovine Staph. aureus is highly clonal and a few clones predominate. Animal Staph. aureus always evolve from human strains, such that every human strain may be the ancestor of a novel animal-adapted strain. The zoonotic transfer of IMI- and milk-associated strains

  9. EarthScope Education and Outreach: Accomplishments and Emerging Opportunities

    Science.gov (United States)

    Robinson, S.; Ellins, K. K.; Semken, S. C.; Arrowsmith, R.

    2014-12-01

    EarthScope's Education and Outreach (E&O) program aims to increase public awareness of Earth science and enhance geoscience education at the K-12 and college level. The program is distinctive among major geoscience programs in two ways. First, planning for education and public engagement occurred in tandem with planning for the science mission. Second, the NSF EarthScope program includes funding support for education and outreach. In this presentation, we highlight key examples of the program's accomplishments and identify emerging E&O opportunities. E&O efforts have been collaboratively led by the EarthScope National Office (ESNO), IRIS, UNAVCO, the EarthScope Education and Outreach Subcommittee (EEOSC) and PI-driven EarthScope projects. Efforts by the EEOSC, guided by an EarthScope Education and Outreach Implementation Plan that is periodically updated, focus EarthScope E&O. EarthScope demonstrated early success in engaging undergraduate students (and teachers) in its mission through their involvement in siting USArray across the contiguous U.S. Funded E&O programs such as TOTLE, Illinois EarthScope, CEETEP (for K-12), InTeGrate and GETSI (for undergraduates) foster use of freely available EarthScope data and research findings. The Next Generation Science Standards, which stress science and engineering practices, offer an opportunity for alignment with existing EarthScope K-12 educational resources, and the EEOSC recommends focusing efforts on this task. The EEOSC recognizes the rapidly growing use of mobile smart devices by the public and in formal classrooms, which bring new opportunities to connect with the public and students. This will capitalize on EarthScope's already prominent social media presence, an effort that developed to accomplish one of the primary goals of the EarthScope E&O Implementation Plan to "Create a high-profile public identity for EarthScope" and to "Promote science literacy and understanding of EarthScope among all audiences through

  10. Evolution and accomplishments of the radiation therapy oncology group

    International Nuclear Information System (INIS)

    Purpose: The Radiation Therapy Oncology Group (RTOG) recently completed its first quarter century as a cooperative clinical cancer research organization. It is timely and appropriate to document its origins, evolution, and accomplishments. Methods and Materials: The historical review of the RTOG called upon written and oral documentation. Results: The RTOG is the most enduring product of the Committee for Radiation Therapy Studies (CRTS). Although not one of the original 17 clinical trials groups developed by the National Cancer Institute in 1956, the RTOG has pursued trials suggested by laboratory findings including the oxygen effect, intrinsic radiosensitivity, proliferation kinetics of normal and tumor cells, and interactions with other cytotoxic agents. Improvements in survival have been demonstrated for patients with carcinoma of the esophagus and cervix, and nonsmall cell carcinomas of the lung. The national and international radiation oncology communities have benefited from standards and quality control/assurance guidelines for established and new modalities. A growing number of institutions in North America participate in RTOG trials. Conclusion: The RTOG is an important clinical research resource, which has contributed to improved outcome for patients with many forms of cancer. It has become increasingly productive and widely adopted and endorsed by oncologists throughout North America

  11. Research accomplishments and future goals in particle physics

    International Nuclear Information System (INIS)

    This document presents a report of the research accomplishments of Boston University researchers in six projects in high energy physics research: Study of high energy electron-positron annihilation, using the ASP and SLD detectors at SLAC; Search for proton decay and neutrinos from point astrophysical sources, as well as the study of cosmic ray muons and neutrinos in the IMB detector; Development of a new underground detector facility in the Gran Sasso Laboratory in Italy for magnetic monopoles and to study astrophysical muons and neutrinos; Preparation of an experiment to measure the anomalous magnetic moment of the muon in a new superconducting storage ring and detector system at BNL; Development of new concepts for particle accelerator components, including design and prototyping of high-precision electrostatic and magnetic elements; and Study of theoretical particle physics, including lattice gauge theories, string theories, phenomenology of the Standard Model and its extensions, and application of particle physics concepts to the early universe, cosmology and astrophysics, as well as the extension of these techniques into computational physics

  12. 77 FR 15847 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2012-03-16

    ... been fed ruminant protein, other than milk protein, during their lifetime; The bovines from which the... from animals that are not known to have been fed ruminant protein, other than milk protein, during... March 16, 2012 Part II Department of Agriculture Animal and Plant Health Inspection Service 9 CFR...

  13. Astrobiology at Arizona State University: An Overview of Accomplishments

    Science.gov (United States)

    Farmer, Jack

    2005-01-01

    During our five years as an NAI charter member, Arizona State University sponsored a broadly-based program of research and training in Astrobiology to address the origin, evolution and distribution of life in the Solar System. With such a large, diverse and active team, it is not possible in a reasonable space, to cover all details of progress made over the entire five years. The following paragraphs provide an overview update of the specific research areas pursued by the Arizona State University (ASU) Astrobiology team at the end of Year 5 and at the end of the 4 month and subsequent no cost month extensions. for a more detailed review, the reader is referred to the individual annual reports (and Executive Summaries) submitted to the NAI at the end of each of our five years of membership. Appended in electronic form is our complete publication record for all five years, plus a tabulation of undergraduates, graduate students and post-docs supported by our program during this time. The overarching theme of ASU s Astrobiology program was "Exploring the Living Universe: Studies of the Origin, Evolution and Distribution of Life in the Solar System". The NAi-funded research effort was organized under three basic sub- themes: 1. Origins of the Basic Building Blocks of Life. 2. Early Biosphere Evolution. and 3. Exploring for Life in the Solar System. These sub-theme areas were in turn, subdivided into Co-lead research modules. In the paragraphs that follow, accomplishments for individual research modules are briefly outlined, and the key participants presented in tabular form. As noted, publications for each module are appended in hard copy and digital formats, under the name(s) of lead co-Is.

  14. Delta-like 1 homolog in Capra hircus: molecular characteristics, expression pattern and phylogeny.

    Science.gov (United States)

    Hu, Jiangtao; Zhao, Wei; Zhan, Siyuan; Xiao, Ping; Zhou, Jingxuan; Wang, Linjie; Li, Li; Zhang, Hongping; Niu, Lili; Zhong, Tao

    2016-06-01

    To research the molecular characteristics, expression pattern and phylogeny of the Delta-like 1 homolog gene (Dlk1) in goats. Dlk1 transcripts were identified in the Jianyang Da'er goats by reverse-transcription polymerase chain reaction (RT-PCR). Phylogenetic trees were constructed by Bayesian inference and neighbor-joining methods. Quantitative real-time PCR (qPCR), western blotting and in situ hybridization were performed to analyze the expression pattern of Dlk1. Five alternatively transcripts were identified in different tissues and designated as Dlk1-AS1, 2, 3, 4 and 5. Compared with the normal transcript Dlk1-AS1, Dlk1-AS4 and Dlk1-AS5 retained the identical open reading frame (ORF) and encoded proteins with truncated epidermal-growth-factor like repeats of 121 and 83 amino acids, respectively. Using the Bayesian inference method, the consensus phylogenetic tree indicated that caprine Dlk1 had a closer relationship with bovine Dlk1 than with Dlk1 from pigs, humans and mice. qPCR revealed high expression levels of Dlk1 in the kidney (P < 0.01). However, mRNA and protein levels presented an inconsistent correlation, possibly because of post-transcriptional regulation. RNA in situ hybridization indicated that Dlk1 mRNA was localized in the interlobular bile duct and alongside the hepatocyte nuclei, in the epithelial cells of proximal and distal convoluted tubules and in the connective region between the mesothelium and myocardium in the heart. The Dlk1 gene in goats produces alternatively spliced transcripts, with specific expression and cellular localization patterns. These findings would lay the foundation for further study. PMID:27108112

  15. Toward image phylogeny forests: automatically recovering semantically similar image relationships.

    Science.gov (United States)

    Dias, Zanoni; Goldenstein, Siome; Rocha, Anderson

    2013-09-10

    In the past few years, several near-duplicate detection methods appeared in the literature to identify the cohabiting versions of a given document online. Following this trend, there are some initial attempts to go beyond the detection task, and look into the structure of evolution within a set of related images overtime. In this paper, we aim at automatically identify the structure of relationships underlying the images, correctly reconstruct their past history and ancestry information, and group them in distinct trees of processing history. We introduce a new algorithm that automatically handles sets of images comprising different related images, and outputs the phylogeny trees (also known as a forest) associated with them. Image phylogeny algorithms have many applications such as finding the first image within a set posted online (useful for tracking copyright infringement perpetrators), hint at child pornography content creators, and narrowing down a list of suspects for online harassment using photographs. PMID:23890634

  16. Phase Transition in Distance-Based Phylogeny Reconstruction

    CERN Document Server

    Roch, Sebastien

    2011-01-01

    We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a logarithmic sequence-length requirement---improving significantly over previous polynomial bounds for distance-based methods and matching existing results for general methods. The technique is based on an averaging procedure that implicitly reconstructs ancestral sequences. In the same token, we extend previous results on phase transitions in phylogeny reconstruction to general time-reversible models. More precisely, we show that in the so-called Kesten-Stigum zone (roughly, a region of the parameter space where ancestral sequences are well approximated by "linear combinations" of the observed sequences) sequences of length $O(\\log n)$ suffice for reconstruction when branch lengths are discretized. Here $n$ is the number of extant species. Our results challenge, to some extent, the conventional wisdom that estimates of evolutionary distances alone carry significantly less infor...

  17. Phylogeny and biogeography of hogfishes and allies (Bodianus, Labridae).

    Science.gov (United States)

    Santini, Francesco; Sorenson, Laurie; Alfaro, Michael E

    2016-06-01

    Bodianus wrasses comprise one of the most diverse genera of labrids. Also known as hogfishes due to the presence of a large pig-like snout, Bodianus species are found in warm waters across the Pacific, Atlantic and Indian Oceans. To this date no densely sampled molecular phylogeny is available for this group, and a single morphological study did not include two genera (Clepticus and Semicossyphus) that have been shown to belong within hogfishes by molecular studies. Our study produced the first multi-locus molecular phylogeny of Bodianus species, and corroborated the non-monophyly of this group without the inclusion of the Creole wrasse (Clepticus) and the sheepheads (Semicossyphus). We further showed that hogfishes and allies started to radiate during the Early Miocene, ∼20Ma, and that while this group originated in the Indo-western and South-western Pacific, it experienced multiple episodes during which it successfully invaded different geographic regions and/or ocean basins. PMID:26944013

  18. Detection, phylogeny and population dynamics of syntrophic propionate-oxidizing bacteria in anaerobic granular sludge.

    OpenAIRE

    Harmsen, H. J. M.

    1996-01-01

    The research described this thesis concerns the diversity and phylogeny of syntrophic propionate-oxidizing bacteria and their ecology in granular sludge, from which they were obtained. 16S rRNA was used as a molecular marker to study both the phylogeny and the ecology of these bacteria. Sequence analysis of the 16S rRNA gave information on the phylogeny of the syntrophic bacteria, while specific oligonucleotide probes based on these sequences enabled quantification and detection of these bact...

  19. Phylogeny, diversity and toxin production related to cyanobacterial symbioses

    OpenAIRE

    Papaefthimiou, Dimitra

    2007-01-01

    Phylogeny and morphology were examined for the cyanobionts from the water fern Azolla and the cyanobacterial genus Nostoc originating from symbioses with different host plants (genera Gunnera, Cycas, Dioon, Encephalarthos, Macrozamia, and Anthoceros), the lichen genus Pannaria, and free-living Nostoc isolates from different habitats. Nostoc isolates of Pannaria formed a closely related group, but, in general, no monophyletic nature was attributed to the genus Nostoc, in contrast to the cyanob...

  20. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

    OpenAIRE

    Spielman, Stephanie J.; Wilke, Claus O

    2015-01-01

    We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexi...

  1. Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)

    OpenAIRE

    Guilhaumon Claire; Cenci Alberto; Scornavacca Céline; Escobar Juan S; Santoni Sylvain; Douzery Emmanuel JP; Ranwez Vincent; Glémin Sylvain; David Jacques

    2011-01-01

    Abstract Background Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a r...

  2. Revised phylogeny of whales suggested by mitochondrial ribosomal DNA sequences

    OpenAIRE

    Milinkovitch, M.C.; Orti, G.; Meyer, A.

    1993-01-01

    Living cetaceans are subdivided into two highly distinct suborders, Odontoceti (the echolocating toothed whales) and Mysticeti (the filter-feeding baleen whales), which are believed to have had a long independent history. Here we report the determination of DNA sequences from two mitochondrial ribosomal gene segments (930 base pairs per species) for 16 species of cetaceans, a perissodactyl and a sloth, and construct the first phylogeny for whales and dolphins based on explicit cladistic metho...

  3. Multigene phylogeny of the red algal subclass Nemaliophycidae.

    Science.gov (United States)

    Lam, Daryl W; Verbruggen, Heroen; Saunders, Gary W; Vis, Morgan L

    2016-01-01

    The red algae (Rhodophyta) are a lineage of primary endosymbionts whose ancestors represent some of the first photosynthetic eukaryotes on the planet. They primarily inhabit marine ecosystems, with only ∼5% of species found in freshwater systems. The subclass Nemaliophycidae is very diverse in ecological and life history features and therefore a useful model to study these traits, but the phylogenetic relationships among the orders are, for the most part, poorly resolved. To elucidate the phylogeny of the Nemaliophycidae, we constructed a nine-gene dataset comprised of nuclear, plastid, and mitochondrial markers for 67 red algal specimens. The resulting maximum likelihood (ML) phylogeny confirmed the monophyly of all orders. The sister relationship of the Acrochaetiales and Palmariales received high support and the relationship of the Balliales with Balbianiales and Entwisleiales with Colaconematales was moderately supported. The Nemaliales, Entwisleiales, Colaconematales, Palmariales and Acrochaetiales formed a highly supported clade. Unfortunately, all other relationships among the orders had low bootstrap support. Although the ML analysis did not resolve many of the relationships, further analyses suggested that a resolution is possible. A Phycas analysis supported a dichotomously branching tree and Bayesian analysis showed a similar topology with all relationships highly supported. Simulations extrapolating the number of nucleotide characters beyond the current size of the dataset suggested that most nodes in the phylogeny would be resolved if more data become available. Phylogenomic approaches will be necessary to provide a well-supported phylogeny of this subclass with all relationships resolved such that the evolution of freshwater species from marine ancestors as well as reproductive traits can be explored. PMID:26518739

  4. Incomplete Lineage Sorting: Consistent Phylogeny Estimation From Multiple Loci

    CERN Document Server

    Mossel, Elchanan

    2008-01-01

    We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our technique is statistically consistent under standard stochastic assumptions, that is, it returns the correct tree given sufficiently many unlinked loci. We also show that it can tolerate moderate estimation errors.

  5. Teleostean phylogeny based on osteological and myological characters

    OpenAIRE

    Diogo, R.; Doadrio, I.; Vandewalle, P

    2008-01-01

    Despite the progresses done in the field of teleostean phylogeny in the last decades, recent studies continue to raise questions concerning the higher-level relationships of this remarkably diverse group of fishes. The main aim of the present work is to help to clarify teleostean higher-level relationships. For that purpose, we undertook a cladistic analysis including 70 terminal taxa of 20 different orders and 271 morphological characters, concerning mainly osteological and myological struct...

  6. Congruence of morphologically-defined genera with molecular phylogenies

    OpenAIRE

    Jablonski, David; Finarelli, John A.

    2009-01-01

    Morphologically-defined mammalian and molluscan genera (herein “morphogenera”) are significantly more likely to be monophyletic relative to molecular phylogenies than random, under 3 different models of expected monophyly rates: ≈63% of 425 surveyed morphogenera are monophyletic and 19% are polyphyletic, although certain groups appear to be problematic (e.g., nonmarine, unionoid bivalves). Compiled nonmonophyly rates are probably extreme values, because molecular analyses have focused on “pro...

  7. Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives

    OpenAIRE

    Swalla, Billie J.; Smith, Andrew B.

    2008-01-01

    Deuterostomes are a monophyletic group of animals that include the vertebrates, invertebrate chordates, ambulacrarians and xenoturbellids. Fossil representatives from most major deuterostome groups, including some phylum-level crown groups, are found in the Lower Cambrian, suggesting that evolutionary divergence occurred in the Late Precambrian, in agreement with some molecular clock estimates. Molecular phylogenies, larval morphology and the adult heart/kidney complex all support echinoderms...

  8. Deep phylogeny and evolution of sponges (phylum Porifera).

    Science.gov (United States)

    Wörheide, G; Dohrmann, M; Erpenbeck, D; Larroux, C; Maldonado, M; Voigt, O; Borchiellini, C; Lavrov, D V

    2012-01-01

    Sponges (phylum Porifera) are a diverse taxon of benthic aquatic animals of great ecological, commercial, and biopharmaceutical importance. They are arguably the earliest-branching metazoan taxon, and therefore, they have great significance in the reconstruction of early metazoan evolution. Yet, the phylogeny and systematics of sponges are to some extent still unresolved, and there is an on-going debate about the exact branching pattern of their main clades and their relationships to the other non-bilaterian animals. Here, we review the current state of the deep phylogeny of sponges. Several studies have suggested that sponges are paraphyletic. However, based on recent phylogenomic analyses, we suggest that the phylum Porifera could well be monophyletic, in accordance with cladistic analyses based on morphology. This finding has many implications for the evolutionary interpretation of early animal traits and sponge development. We further review the contribution that mitochondrial genes and genomes have made to sponge phylogenetics and explore the current state of the molecular phylogenies of the four main sponge lineages (Classes), that is, Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha, in detail. While classical systematic systems are largely congruent with molecular phylogenies in the class Hexactinellida and in certain parts of Demospongiae and Homoscleromorpha, the high degree of incongruence in the class Calcarea still represents a challenge. We highlight future areas of research to fill existing gaps in our knowledge. By reviewing sponge development in an evolutionary and phylogenetic context, we support previous suggestions that sponge larvae share traits and complexity with eumetazoans and that the simple sedentary adult lifestyle of sponges probably reflects some degree of secondary simplification. In summary, while deep sponge phylogenetics has made many advances in the past years, considerable efforts are still required to achieve a

  9. Phylogeny and disjunct distribution: evolution of Saintpaulia (Gesneriaceae).

    OpenAIRE

    Möller, M; Cronk, Q C

    1997-01-01

    The molecular phylogeny of African violets (Saintpaulia H. Wendl.), based on ribosomal DNA internal transcribed spacer (ITS) sequences, follows the disjunct biogeography of the genus. Sequence analysis by parsimony of 19 accessions, representing 17 currently recognized Saintpaulia species, resulted in four trees of 182 steps. The first major division is between S. goetzeana, from the Uluguru Mts, Tanzania, and the rest of the genus. The basal position of S. goetzeana, and its putative primiti...

  10. The higher-level phylogeny of Archosauria (Tetrapoda:Diapsida)

    OpenAIRE

    Brusatte, S. L.; Benton, M. J.; Desojo, J.B.; Langer, M.C.

    2010-01-01

    Crown group Archosauria, which includes birds, dinosaurs, crocodylomorphs, and several extinct Mesozoic groups, is a primary division of the vertebrate tree of life. However, the higher-level phylogenetic relationships within Archosauria are poorly resolved and controversial, despite years of study. The phylogeny of crocodile-line archosaurs (Crurotarsi) is particularly contentious, and has been plagued by problematic taxon and character sampling. Recent discoveries and renewed focus on archo...

  11. Phylogeny of Rosellinia capetribulensis sp. nov. and its allies (Xylariaceae)

    OpenAIRE

    Bahl, J; Jeewon, R; Hyde, KD

    2005-01-01

    A new Rosellinia species, R. capetribulensis isolated from Calamus sp. in Australia is described. R. capetribulensis is characterized by perithecia immersed within a carbonaceous stroma surrounded by subiculum-like hyphae, asci with large, barrel-shaped amyloid apical apparatus and large dark brown spores. Morphologically, R. capetribulensis appears to be similar to R. bunodes, R. markhamiae and R. megalospora. To gain further insights into the phylogeny of this new taxon we analyzed the ITS-...

  12. Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification.

    OpenAIRE

    Gundersen, D E; Lee, I M; Rehner, S A; Davis, R. E.; Kingsbury, D T

    1994-01-01

    A global phylogenetic analysis using parsimony of 16S rRNA gene sequences from 46 mollicutes, 19 mycoplasmalike organisms (MLOs) (new trivial name, phytoplasmas), and several related bacteria placed the MLOs definitively among the members of the class Mollicutes and revealed that MLOs form a large discrete monophyletic clade, paraphyletic to the Acholeplasma species, within the Anaeroplasma clade. Within the MLO clade resolved in the global mollicutes phylogeny and a comprehensive MLO phyloge...

  13. Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification.

    Science.gov (United States)

    Gundersen, D E; Lee, I M; Rehner, S A; Davis, R E; Kingsbury, D T

    1994-09-01

    A global phylogenetic analysis using parsimony of 16S rRNA gene sequences from 46 mollicutes, 19 mycoplasmalike organisms (MLOs) (new trivial name, phytoplasmas), and several related bacteria placed the MLOs definitively among the members of the class Mollicutes and revealed that MLOs form a large discrete monophyletic clade, paraphyletic to the Acholeplasma species, within the Anaeroplasma clade. Within the MLO clade resolved in the global mollicutes phylogeny and a comprehensive MLO phylogeny derived by parsimony analyses of 16S rRNA gene sequences from 30 diverse MLOs representative of nearly all known distinct MLO groups, five major phylogenetic groups with a total of 11 distinct subclades (monophyletic groups or taxa) could be recognized. These MLO subclades (roman numerals) and designated type strains were as follows: i, Maryland aster yellows AY1; ii, apple proliferation AP-A; iii, peanut witches'-broom PnWB; iv, Canada peach X CX; v, rice yellow dwarf RYD; vi, pigeon pea witches'-broom PPWB; vii, palm lethal yellowing LY; viii, ash yellows AshY; ix, clover proliferation CP; x, elm yellows EY; and xi, loofah witches'-broom LfWB. The designations of subclades and their phylogenetic positions within the MLO clade were supported by a congruent phylogeny derived by parsimony analyses of ribosomal protein L22 gene sequences from most representative MLOs. On the basis of the phylogenies inferred in the present study, we propose that MLOs should be represented taxonomically at the minimal level of genus and that each phylogenetically distinct MLO subclade identified should represent at least a distinct species under this new genus. PMID:8071198

  14. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

    OpenAIRE

    Lartillot, Nicolas; Philippe, Hervé

    2008-01-01

    Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both gene...

  15. An Evaluation of State Energy Program Accomplishments: 2002 Program Year

    Energy Technology Data Exchange (ETDEWEB)

    Schweitzer, M.

    2005-07-13

    cost savings and emissions reductions associated with SEP activities performed by the states during the 2002 program year, based on primary data provided by the states themselves. This is the second systematic evaluation of SEP accomplishments performed by Oak Ridge National Laboratory (ORNL) for DOE. A report documenting the findings of the first study was published in January 2003 (Schweitzer et.al., 2003).

  16. FY2000 Hanford Technology Deployment Accomplishments Fact Sheets

    International Nuclear Information System (INIS)

    strategic needs of the future. This report contains descriptions of the benefits and features of the FY 2000 demonstrations and deployed technologies. We hope you find this information useful in understanding the contributions that new technologies are providing to help accomplish the Hanford cleanup mission

  17. Accomplishing Mars exploration goals by returning a simple "locality" sample

    Science.gov (United States)

    McKay, G.; Draper, D.; Bogard, D.; Agee, C.; Ming, D.; Jones, J.

    A major stumbling block to a Mars sample return (MSR) mission is cost. This problem is greatly exacerbated by using elaborate rovers, sophisticated on-board instruments, and complex sample selection techniques to maximize diversity. We argue that many key science goals of the Mars Exploration Program may be accomplished by returning a simple "locality" sample from a well-chosen landing site. Such a sample , collected by a simple scoop, would consist of local regolith containing soil, windblown fines, and lithic fragments (plus Martian atmosphere). Even the simplest sample return mission could revolutionize our understanding of Mars, without the need for expensive rovers or sophisticated on-board instruments. We expect that by the time a MSR mission could be flown, information from the Mars Odyssey, Mars Express, 2003 Mars Exploration Rovers, and 2005 Mars Reconnaissance Orbiter will be sufficient to choose a good landing site. Returned samples of Martian regolith have the potential to answer key questions of fundamental importance to the Mars Exploration Program: The search for life; the role and history of water and other volatiles; interpreting remotely-sensed spectral data; and understanding the planet as a system. A locality sample can further the search for life by identifying trace organics, biogenic elements and their isotopic compositions, evidence for water such as hydrous minerals or cements, the Martian soil oxidant, and trace biomarkers. Learning the nature and timing of atmosphere-soil-rock interactions will improve understanding of the role and history of water. An atmosphere sample will reveal fundamental information about current atmospheric processes. Information about the mineralogy and lithology of sample materials, the extent of impact gardening, and the nature of dust coatings and alteration rinds will provide much-needed ground truth for interpreting remotely-sensed data, including Mars Pathfinder. Basic planetology questions that might be

  18. Bovine Tuberculosis, A Zoonotic Disease

    OpenAIRE

    Tarmudji; Supar

    2008-01-01

    Bovine tuberculosis is caused by the infection of Mycobacterium tuberculosis var. bovis (M. bovis). This species is one of Mycobacterium tuberculosis complex, can infect wide range of hosts: cattle and other domesticated animals, wild mammals and humans (zoonotic). M. bovis bacterium from infected hosts can be transmitted to other susceptible animals and humans through respiratory excretes and secretion materials. Humans can be infected with M. bovis by ingested M. bovis contaminated animal p...

  19. Phylogeny, diet, and cranial integration in australodelphian marsupials.

    Directory of Open Access Journals (Sweden)

    Anjali Goswami

    Full Text Available Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials.

  20. Potential Anticarcinogenic Peptides from Bovine Milk

    OpenAIRE

    Giacomo Pepe; Gian Carlo Tenore; Raffaella Mastrocinque; Paola Stusio; Pietro Campiglia

    2013-01-01

    Bovine milk possesses a protein system constituted by two major families of proteins: caseins (insoluble) and whey proteins (soluble). Caseins ( α S1, α S2, β , and κ ) are the predominant phosphoproteins in the milk of ruminants, accounting for about 80% of total protein, while the whey proteins, representing approximately 20% of milk protein fraction, include β -lactoglobulin, α -lactalbumin, immunoglobulins, bovine serum albumin, bovine lactoferrin, and lactoperoxidase, together with other...

  1. Detection of a Novel Bovine Lymphotropic Herpesvirus

    OpenAIRE

    Rovnak, Joel; Quackenbush, Sandra L.; Reyes, Richard A.; Baines, Joel D.; Parrish, Colin R.; Casey, James W.

    1998-01-01

    Degenerate PCR primers which amplify a conserved region of the DNA polymerase genes of the herpesvirus family were used to provide sequence evidence for a new bovine herpesvirus in bovine B-lymphoma cells and peripheral blood mononuclear cells (PBMC). The sequence of the resultant amplicon was found to be distinct from those of known herpesvirus isolates. Alignment of amino acid sequences demonstrated 70% identity with ovine herpesvirus 2, 69% with alcelaphine herpesvirus 1, 65% with bovine h...

  2. Mycobacterium bovis (Bovine Tuberculosis) in Humans

    Science.gov (United States)

    Mycobacterium bovis (Bovine Tuberculosis) in Humans What is Mycobacterium bovis ? In the United States, the majority of tuberculosis (TB) cases in people are caused by Mycobacterium tuberculosis ( ...

  3. Clinical applications of bovine colostrum therapy

    DEFF Research Database (Denmark)

    Rathe, Mathias; Müller, Klaus; Sangild, Per Torp;

    2014-01-01

    Bovine colostrum, the first milk that cows produce after parturition, contains high levels of growth factors and immunomodulatory components. Some healthy and diseased individuals may gain health benefits by consuming bovine colostrum as a food supplement. This review provides a systematic...

  4. Scientific Opinion on bovine lactoferrin

    OpenAIRE

    EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA)

    2012-01-01

    Following a request from the European Commission, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) was asked to carry out the additional assessment for ‘lactoferrin’ as a food ingredient in the context of Regulation (EC) No 258/97 taking into account the comments and objections of a scientific nature raised by Member States. Bovine lactoferrin (bLF) is a protein that occurs naturally in cow’s milk. The applicant intends to market bLF that is isolated from cheese whe...

  5. A Simple Characterization of the Minimal Obstruction Sets for Three-State Perfect Phylogenies

    CERN Document Server

    Shutters, Brad

    2011-01-01

    Lam, Gusfield, and Sridhar (2009) showed that a set of three-state characters has a perfect phylogeny if and only if every subset of three characters has a perfect phylogeny. They also gave a complete characterization of the sets of three three-state characters that do not have a perfect phylogeny. However, it is not clear from their characterization how to find a subset of three characters that does not have a perfect phylogeny without testing all triples of characters. In this note, we build upon their result by giving a simple characterization of when a set of three-state characters does not have a perfect phylogeny that can be inferred from testing all pairs of characters.

  6. PhyloGrid: a development for a workflow in Phylogeny

    CERN Document Server

    Montes, Esther; Mayo, Rafael

    2010-01-01

    In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment of the sequences previously to the final result. To do this, no knowledge from his/her side about the computational procedure is required.

  7. Pollination, biogeography and phylogeny of oceanic island bellflowers (Campanulaceae)

    DEFF Research Database (Denmark)

    Olesen, Jens Mogens; Alarcón, M.; Ehlers, Bodil;

    2012-01-01

    the species, and at least C. jacobaea had both insect- and self-pollination. Several morphological traits were interpreted as adaptations to bird and lizard pollination, e.g. all had a robust flower morphology and, in addition, bird-pollinated species were scentless, whereas lizard-pollinated species...... of these species and their relatives were gathered from atpB, matK, rbcL and trnL-F regions, building the most complete phylogeny of Campanulaceae to date. Six of the island bellflower species were bird-pollinated and two (A. vidalii and M. aurea) were lizard-pollinated. Insects also visited some of...

  8. PhyloGrid: a development for a workflow in Phylogeny

    OpenAIRE

    Montes, Esther; Isea, Raul; Mayo, Rafael

    2010-01-01

    In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment of the sequences previously to the final result. To do t...

  9. Updating of the bovine neosporosis

    Directory of Open Access Journals (Sweden)

    Alexander Martínez Contreras

    2012-06-01

    Full Text Available In the fields of Medicine and bovine production, there is a wide variety of diseases affecting reproduction, in relation to the number of live births, the interval between births and open days, among others. Some of these diseases produce abortions and embryonic death, which explain the alteration of reproductive parameters. Many of these diseases have an infectious origin, such as parasites, bacteria, viruses and fungi, which are transmitted among animals. Besides, some of them have zoonotic features that generate problems to human health. Among these agents, the Neospora caninum, protozoan stands out. Its life cycle is fulfilled in several species of animals like the dog and the coyote. These two act as its definitive hosts and the cattle as its intermediary host. The Neospora caninum causes in the infected animals, reproductive disorders, clinical manifestations and decreased production which affects productivity of small, medium and large producers. Because of this, diagnostic techniques that allow understanding the epidemiological behavior of this disease have been developed. However in spite of being a major agent in the bovine reproductive health, few studies have been undertaken to determine the prevalence of this agent around the world. Therefore, the objective of this review was to collect updated information on the behavior of this parasite, targeting its epidemiology, its symptoms, its impact on production and the methods of its control and prevention.

  10. Adipogenesis of bovine perimuscular preadipocytes

    International Nuclear Information System (INIS)

    In this study, non-transformed progeny adipofibroblasts, derived from mature adipocyte dedifferentiation, was used as a novel in vitro model to study adipogenic gene expression in cattle. Adipofibroblasts from dedifferentiated mature perimuscular fat (PMF) tissue were cultured with differentiation stimulants until the cells exhibited morphological differentiation. Treated cells were harvested from day 2 to 16 for RNA extraction, whereas control cells were cultured without addition of stimulants. Results from time course gene expression assays by quantitative real-time PCR revealed that peroxisome proliferator-activated receptor gamma (PPAR-γ), sterol regulatory element binding protein 1 (SREBP-1) and their six down-stream genes were co-expressed at day 2 post-differentiation induction. When compared to other adipogenesis culture systems, the adipogenic gene expression of bovine PMF adipofibroblasts culture was different, especially to the rodent model. Collectively, these results demonstrated PPAR-γ and SREBP-1 cooperatively play a key role to regulate the re-differentiation of bovine adipofibroblasts, during early conversion stages in vitro

  11. 9 CFR 113.310 - Bovine Rhinotracheitis Vaccine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Rhinotracheitis Vaccine. 113... REQUIREMENTS Live Virus Vaccines § 113.310 Bovine Rhinotracheitis Vaccine. Bovine Rhinotracheitis Vaccine shall...-five infectious bovine rhinotracheitis susceptible calves shall be used as test animals (20...

  12. 21 CFR 184.1034 - Catalase (bovine liver).

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Catalase (bovine liver). 184.1034 Section 184.1034... Listing of Specific Substances Affirmed as GRAS § 184.1034 Catalase (bovine liver). (a) Catalase (bovine liver) (CAS Reg. No. 81457-95-6) is an enzyme preparation obtained from extracts of bovine liver. It...

  13. Benefit-analysis of accomplishments from the magnetic fusion energy (MFE) research program

    International Nuclear Information System (INIS)

    This report presents the results of a study commissioned by the US Department of Energy's (DOE) Office of Program Analysis to examine benefits from selected accomplishments of DOE's Magnetic Fusion Energy (MFE) Research Program. The study objectives are presented. The MFE-induced innovation and accomplishments which were studied are listed. Finally, the benefit estimation methodology used is described in detail. The next seven chapters document the results of benefit estimation for the MFE accomplishments studied

  14. Planning and accomplishment narrative : F.Y. 1973 : Merced National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Content includes refuge highlight statement, refuge accomplishments, environmental education, wildlifewildlands recreation, professional services, wildlife, and...

  15. Phylogeny and Evolution of Bracts and Bracteoles in Tacca (Dioscoreaceae)

    Institute of Scientific and Technical Information of China (English)

    Ling Zhang; Hong-Tao Li; Lian-Ming Gao; Jun-Bo Yang; De-Zhu Li; Charles H. Cannon; Jin Chen; Qing-Jun Li

    2011-01-01

    Most species in the genus Tacca (Dioscoreaceae) feature green to black purple,conspicuous inflorescence involucral bracts with variable shapes,motile filiform appendages (bracteoles),and diverse types of inflorescence morphology.To infer the evolution of these inflorescence traits,we reconstructed the molecular phylogeny of the genus,using DNA sequences from one nuclear,one mitochondrial,and three plastid loci (Internal Transcribed Spacer (ITS),atpA,rbcL,trnL-F,and trnH-psbA).Involucres and bracteoles characters were mapped onto the phylogeny to analyze the sequence of inflorescence trait evolution.In all analyses,species with showy involucres and bracteoles formed the most derived clade,while ancestral Tacca had small and plain involucres and short bracteoles,namely less conspicuous inflorescence structures.Two of the species with the most elaborate inflorescence morphologies (T.chantrieri in southeast China and T.integrifolia in Tibet),are predominantly self-pollinated,indicating that these conspicuous floral displays have other functions rather than pollinator attraction.We hypothesize that the motile bracteoles and involucres may facilitate selfing; display photosynthesis in the dim understory,and protect flowers from herbivory.

  16. Molecular Phylogeny of the Bamboo Sharks (Chiloscyllium spp.

    Directory of Open Access Journals (Sweden)

    Noor Haslina Masstor

    2014-01-01

    Full Text Available Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences’ lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate that can clearly be used to differentiate each species.

  17. Refining the Y chromosome phylogeny with southern African sequences.

    Science.gov (United States)

    Barbieri, Chiara; Hübner, Alexander; Macholdt, Enrico; Ni, Shengyu; Lippold, Sebastian; Schröder, Roland; Mpoloka, Sununguko Wata; Purps, Josephine; Roewer, Lutz; Stoneking, Mark; Pakendorf, Brigitte

    2016-05-01

    The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species. PMID:27043341

  18. Phylogeny and biogeography of the fruit doves (Aves: Columbidae).

    Science.gov (United States)

    Cibois, Alice; Thibault, Jean-Claude; Bonillo, Céline; Filardi, Christopher E; Watling, Dick; Pasquet, Eric

    2014-01-01

    We reconstruct the phylogeny of fruit doves (genus Ptilinopus) and allies with a dense sampling that includes almost all species, based on mitochondrial and nuclear sequence data. We evaluate the most likely biogeographic scenario for the evolution of this group that colonized many islands of the Pacific Ocean. We also investigate the evolution of one of the main plumage character of fruit doves (the color of the crown), and we propose several revisions of the group's systematics. All Ptilinopus taxa formed a monophyletic group that includes two morphologically distinct genera, Alectroenas and Drepanoptila, confirming a previous result found with less species and genes. The divergence time analysis suggests that the basal divergences within Ptilinopus dated to the Early Oligocene, and the biogeographic analysis indicates that fruit doves originated most probably from the proto New Guinea region. The earliest dispersals from the New Guinea region to Oceania occurred with the colonization of New Caledonia and Fiji. A large group of Polynesian species (Central and Eastern), as well as the three taxa found in Micronesia and four species from the Guinean-Moluccan region, form the "purpuratus" clade, the largest diversification of fruit doves within Oceania, which also has a New Guinean origin. However, the eastbound colonization of fruit doves was not associated with a significant increase of their diversification rate. Overall, the Melanesian region did not act as a cradle for fruit doves, in contrast to the New Guinea region which is found as the ancestral area for several nodes within the phylogeny. PMID:24012584

  19. Orally administered bovine lactoferrin inhibits bacterial translocation in mice fed bovine milk.

    OpenAIRE

    Teraguchi, S.; Shin, K.; Ogata, T; Kingaku, M; Kaino, A; Miyauchi, H; Fukuwatari, Y; Shimamura, S

    1995-01-01

    Feeding of bovine milk to mice induced a high incidence of bacterial translocation from the intestines to the mesenteric lymph nodes, and the bacteria involved were mainly members of the family Enterobacteriaceae. Supplementation of the milk diet with bovine lactoferrin or a pepsin-generated hydrolysate of bovine lactoferrin resulted in significant suppression of bacterial translocation. Our findings suggest that this ability of lactoferrin to inhibit bacterial translocation may be due to its...

  20. Search for the genome of bovine herpesvirus types 1, 4 and 5 in bovine semen

    OpenAIRE

    P.E. Morán; Favier, P.A.; Lomónaco, M.; Catena, M.C.; M.L. Chiapparrone; Odeón, A.C.; Verna, A.E.; S.E. Pérez

    2013-01-01

    Bovine herpesvirus type 1 (BoHV-1) causes respiratory and reproductive disorders in cattle. Recently, bovine herpesvirus type 5 (BoHV-5) and bovine herpesvirus type 4 (BoHV-4) have been identified to be associated with genital disease. In this study, the presence of the genome of BoHV-1, BoHV-4 and BoHV-5 in bovine semen of Argentinean and international origin was analyzed by PCR assays. The most important finding of this study is the detection of the genome of BoHV-1 and BoHV-4 in semen of b...

  1. The Role of "Accomplished Teachers" in Professional Learning Communities: Uncovering Practice and Enabling Leadership

    Science.gov (United States)

    Lieberman, Ann; Mace, Desiree H. Pointer

    2009-01-01

    This paper describes the signature role played by accomplished, experienced teachers in professional learning communities, and the importance that these practitioners make their teaching public and shared. In so doing, the authors describe how accomplished practices can be shared between classrooms and between practitioners with varying levels of…

  2. Working Memory and Short-Term Memory Abilities in Accomplished Multilinguals

    Science.gov (United States)

    Biedron, Adriana; Szczepaniak, Anna

    2012-01-01

    The role of short-term memory and working memory in accomplished multilinguals was investigated. Twenty-eight accomplished multilinguals were compared to 36 mainstream philology students. The following instruments were used in the study: three memory subtests of the Wechsler Intelligence Scale (Digit Span, Digit-Symbol Coding, and Arithmetic,…

  3. Program Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2011-10-01

    The U.S. Department of Energy's (DOE's) efforts have greatly advanced the state of the art of hydrogen and fuel cell technologies—making significant progress toward overcoming many of the key challenges to widespread commercialization. DOE has also made major advances by demonstrating and validating the technologies under real-world conditions, supporting early markets through Recovery Act deployments, and leveraging domestic and international partnerships to advance the pace of commercialization.

  4. Interfacial behaviour of bovine testis hyaluronidase

    OpenAIRE

    Belem-Gonçalves, Silvia; Tsan, Pascale; Lancelin, Jean-Marc; Alves, Tito L. M.; Salim, Vera M.; Besson, Françoise

    2006-01-01

    Abstract The interfacial properties of bovine testicular hyaluronidase were suggested by demonstrating the association of hyaluronidase activity with membranes prepared from bovine testis. Protein adsorption to the air/water interface was investigated using surface pressure-area isotherms. Whatever the way to obtain interfacial films (protein injection or deposition), the hyaluronidase exhibited a significant affinity for the air/water interface. The isotherm obtained 180 min after...

  5. Bovine viral diarrhea virus: biotypes and disease.

    OpenAIRE

    Deregt, D; Loewen, K G

    1995-01-01

    Bovine viral diarrhea virus continues to produce significant economic losses for the cattle industry and challenges investigators with the complexity of diseases it produces and the mechanisms by which it causes disease. This paper updates and attempts to clarify information regarding the roles of noncytopathic and cytopathic bovine viral diarrhea viruses in persistent infections and mucosal disease. It also covers, in brief, what is known of the new diseases: thrombocytopenia and hemorrhagic...

  6. Echinothurioid phylogeny and the phylogenetic significance of Kamptosoma (Echinoidea: Echinodermata)

    Science.gov (United States)

    Mooi, Rich; Constable, Heather; Lockhart, Susanne; Pearse, John

    2004-07-01

    The Echinothurioida is an unusual group of regular sea urchins that are characterized by soft, flexible tests and in some cases, hoof-shaped spines used for locomotion across soft, deep-sea sediments. As far as is known, all species are armed with venom-bearing spines that have been known to cause serious injury in humans. There are 50 species of echinothurioids arranged in 11 extant genera. Their fossil record is very poor, being limited to two additional fossil taxa (one of which is only tentatively considered an echinothurioid), two assigned to extant taxa, and three of more dubious affinity. With very few exceptions, only disjointed plates are preserved—and those very rarely. Today, echinothurioids are found around the globe from as far north as the Arctic Circle and as far south as Antarctica, with a bathymetric distribution ranging from inshore on coral reefs to depths of almost 5000 m. The majority of species are characteristic of the deep sea, and consequently little is known about these urchins. Many are known only from type and associated material. Their fragile tests, deep benthic habitat, and rarity make it difficult to develop a complete picture of their morphology, and as we demonstrate, breakage of the test can lead to misinterpretations of plate architecture in some taxa. The sole Antarctic species, Kamptosoma asterias, is usually considered an echinothurioid, but its unusual morphology has made its position difficult to ascertain. In addition, previous genus-level phylogenies do not test the monophyly of the genera, and some studies even suggest that the echinothurioids themselves do not constitute a monophyletic group. This study focuses on finding a species level phylogeny of the echinothurioids in order to perform these tests, and to place the enigmatic Kamptosoma in a phylogenetic context that determines whether it is indeed an echinothurioid, and if so, to which clade it is most closely related. The present analysis surveys ambulacral

  7. Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae

    Directory of Open Access Journals (Sweden)

    Guilhaumon Claire

    2011-06-01

    Full Text Available Abstract Background Introgressive events (e.g., hybridization, gene flow, horizontal gene transfer and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. Here, we obtain the most comprehensive molecular dataset to date in Triticeae, including one chloroplastic and 26 nuclear genes. We aim to test whether it is possible to infer phylogenetic relationships in the face of (potentially large-scale introgressive events and/or incomplete lineage sorting; to identify parts of the evolutionary history that have not evolved in a tree-like manner; and to decipher the biological causes of gene-tree conflicts in this tribe. Results We obtain resolved phylogenetic hypotheses using the supermatrix and Bayesian Concordance Factors (BCF approaches despite numerous incongruences among gene trees. These phylogenies suggest the existence of 4-5 major clades within Triticeae, with Psathyrostachys and Hordeum being the deepest genera. In addition, we construct a multigenic network that highlights parts of the Triticeae history that have not evolved in a tree-like manner. Dasypyrum, Heteranthelium and genera of clade V, grouping Secale, Taeniatherum, Triticum and Aegilops, have evolved in a reticulated manner. Their relationships are thus better represented by the multigenic network than by the supermatrix or BCF trees. Noteworthy, we demonstrate that gene-tree incongruences increase with genetic distance and are greater in telomeric than centromeric genes. Together, our results suggest that recombination is the main factor

  8. Activation of bovine neutrophils by Brucella spp.

    Science.gov (United States)

    Keleher, Lauren L; Skyberg, Jerod A

    2016-09-01

    Brucellosis is a globally important zoonotic infectious disease caused by gram negative bacteria of the genus Brucella. While many species of Brucella exist, Brucella melitensis, Brucella abortus, and Brucella suis are the most common pathogens of humans and livestock. The virulence of Brucella is largely influenced by its ability to evade host factors, including phagocytic killing mechanisms, which are critical for the host response to infection. The aim of this study was to characterize the bovine neutrophil response to virulent Brucella spp. Here, we found that virulent strains of smooth B. abortus, B. melitensis, B. suis, and virulent, rough, strains of Brucella canis possess similar abilities to resist killing by resting, or IFN-γ-activated, bovine neutrophils. Bovine neutrophils responded to infection with a time-dependent oxidative burst that varied little between Brucella spp. Inhibition of TAK1, or SYK kinase blunted the oxidative burst of neutrophils in response to Brucella infection. Interestingly, Brucella spp. did not induce robust death of bovine neutrophils. These results indicate that bovine neutrophils respond similarly to virulent Brucella spp. In addition, virulent Brucella spp., including naturally rough strains of B. canis, have a conserved ability to resist killing by bovine neutrophils. PMID:27436438

  9. Bovine endometrial stromal cells display osteogenic properties

    Directory of Open Access Journals (Sweden)

    Cavirani Sandro

    2008-12-01

    Full Text Available Abstract The endometrium is central to mammalian fertility. The endometrial stromal cells are very dynamic, growing and differentiating throughout the estrous cycle and pregnancy. In humans, stromal cells appear to have progenitor or stem cell capabilities and the cells can even differentiate into bone. It is not clear whether bovine endometrial stromal cells exhibit a similar phenotypic plasticity. So, the present study tested the hypothesis that bovine endometrial stromal cells could be differentiated along an osteogenic lineage. Pure populations of bovine stromal cells were isolated from the endometrium. The endometrial stromal cell phenotype was confirmed by morphology, prostaglandin secretion, and susceptibility to viral infection. However, cultivation of the cells in standard endometrial cell culture medium lead to a mesenchymal phenotype similar to that of bovine bone marrow cells. Furthermore, the endometrial stromal cells developed signs of osteogenesis, such as alizarin positive nodules. When the stromal cells were cultured in a specific osteogenic medium the cells rapidly developed the characteristics of mineralized bone. In conclusion, the present study has identified that stromal cells from the bovine endometrium show a capability for phenotype plasticity similar to mesenchymal progenitor cells. These observations pave the way for further investigation of the mechanisms of stroma cell differentiation in the bovine reproductive tract.

  10. Frequently Asked Questions on BSE (Bovine Spongiform Encephalopathy or Mad Cow Disease)

    Science.gov (United States)

    ... BSE / FAQ on BSE (Bovine Spongiform Encephalopathy or Mad Cow Disease) Programs Beginning Farmer and Rancher Development Farm Storage ... Asked Questions on BSE (Bovine Spongiform Encephalopathy or Mad Cow Disease) Q. What is Bovine Spongiform Encephalopathy? A. Bovine ...

  11. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

    Directory of Open Access Journals (Sweden)

    Stephanie J Spielman

    Full Text Available We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve.

  12. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

    Science.gov (United States)

    Spielman, Stephanie J; Wilke, Claus O

    2015-01-01

    We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve. PMID:26397960

  13. Linguistic phylogenies support back-migration from Beringia to Asia.

    Directory of Open Access Journals (Sweden)

    Mark A Sicoli

    Full Text Available Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America.

  14. Phylogeny and evolution of Perezia (Asteraceae: Mutisieae: Nassauviinae)

    Institute of Scientific and Technical Information of China (English)

    Beryl B. SIMPSON; Mary T. K. ARROYO; Sandra SIPE; Marta DIAS de MORAES; Joshua McDILL

    2009-01-01

    A molecular phylogenetic analysis of most of the species of Perezia reveals that, as traditionally defined, the genus is not monophyletic with two species more closely related to Nassauvia than to Perezia. In addition, our results show that Burkartia (Perezia) lanigera is related to Acourtia and is the only member of that clade in South America. The remaining species are monophyletic and show a pattern of an early split between a western temperate and an eastern subtropical clade of species. Within the western clade, the phylogeny indicates a pattern of diversification that proceeded from southern, comparatively low-elevation habitats to southern high-elevation habitats, and ultimately into more northern high-elevation habitats. The most derived clades are found in the high central Andes, where significant radiation has occurred.

  15. Future trypanosomatid phylogenies: refined homologies, supertrees and networks

    Directory of Open Access Journals (Sweden)

    Stothard JR

    2000-01-01

    Full Text Available There has been good progress in inferring the evolutionary relationships within trypanosomes from DNA data as until relatively recently, many relationships have remained rather speculative. Ongoing molecular studies have provided data that have adequately shown Trypanosoma to be monophyletic and, rather surprisingly, that there are sharply contrasting levels of genetic variation within and between the major trypanosomatid groups. There are still, however, areas of research that could benefit from further development and resolution that broadly fall upon three questions. Are the current statements of evolutionary homology within ribosomal small sub-unit genes in need of refinement? Can the published phylograms be expanded upon to form `supertrees' depicting further relationships? Does a bifurcating tree structure impose an untenable dogma upon trypanosomatid phylogeny where hybridisation or reticulate evolutionary steps have played a part? This article briefly addresses these three questions and, in so doing, hopes to stimulate further interest in the molecular evolution of the group.

  16. Phylogeny and comparative genome analysis of a Basidiomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert W.; Salamov, Asaf; Grigoriev, Igor; Hibbett, David

    2011-03-14

    Fungi of the phylum Basidiomycota, make up some 37percent of the described fungi, and are important from the perspectives of forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, plant pathogenic rusts and smuts, and some human pathogens. To better understand these important fungi, we have undertaken a comparative genomic analysis of the Basidiomycetes with available sequenced genomes. We report a phylogeny that sheds light on previously unclear evolutionary relationships among the Basidiomycetes. We also define a `core proteome? based on protein families conserved in all Basidiomycetes. We identify key expansions and contractions in protein families that may be responsible for the degradation of plant biomass such as cellulose, hemicellulose, and lignin. Finally, we speculate as to the genomic changes that drove such expansions and contractions.

  17. Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

    KAUST Repository

    Salari, Raheleh

    2013-01-01

    Next-generation sequencing technologies provide a powerful tool for studying genome evolution during progression of advanced diseases such as cancer. Although many recent studies have employed new sequencing technologies to detect mutations across multiple, genetically related tumors, current methods do not exploit available phylogenetic information to improve the accuracy of their variant calls. Here, we present a novel algorithm that uses somatic single nucleotide variations (SNVs) in multiple, related tissue samples as lineage markers for phylogenetic tree reconstruction. Our method then leverages the inferred phylogeny to improve the accuracy of SNV discovery. Experimental analyses demonstrate that our method achieves up to 32% improvement for somatic SNV calling of multiple related samples over the accuracy of GATK\\'s Unified Genotyper, the state of the art multisample SNV caller. © 2013 Springer-Verlag.

  18. The Contribution of Infections with Bovine Viral Diarrhea Viruses to Bovine Respiratory Disease

    Science.gov (United States)

    The contribution of bovine viral diarrhea viruses (BVDV) to the development of bovine respiratory disease is the sum of a number of different factors. These factors include the contribution of acute uncomplicated BVDV infections, the high incidence of respiratory disease in animals persistently inf...

  19. Design and Construction of Chimeric VP8-S2 Antigen for Bovine Rotavirus and Bovine Coronavirus

    OpenAIRE

    Nasiri, Khadijeh; Nassiri, Mohammadreza; Tahmoorespur, Mojtaba; Haghparast, Alireza; Zibaee, Saeed

    2016-01-01

    Purpose: Bovine Rotavirus and Bovine Coronavirus are the most important causes of diarrhea in newborn calves and in some other species such as pigs and sheep. Rotavirus VP8 subunit is the major determinant of the viral infectivity and neutralization. Spike glycoprotein of coronavirus is responsible for induction of neutralizing antibody response.

  20. Bovine viral diarrhea virus: involvement in bovine respiratory disease and diagnostic challenges

    Science.gov (United States)

    This paper reviews the contribution of bovine viral diarrhea viruses (BVDV) to the development of Bovine Respiratory Disease (BRD). Veterinarians and producers generally consider BRD as one of the most significant diseases affecting production in the cattle industry. BRD can affect the performance (...

  1. Complete Genome Sequence of a Bovine Viral Diarrhea Virus 2 from Commercial Fetal Bovine Serum

    OpenAIRE

    Liu, Hua; Li, Yan; Gao, Mingchun; Wen, Kai; Jia, Ying; Liu, Xiaomei; Zhang, Wenlong; Ma, Bo; Wang, Junwei

    2012-01-01

    We isolated a bovine viral diarrhea virus (BVDV) from commercial fetal bovine serum and designated it HLJ-10. The complete genome is 12,284 nucleotides (nt); the open reading frame is 11,694 nt, coding 3,898 amino acids. Phylogenetic analysis indicated that this strain belongs to BVDV group 2.

  2. Phylogeny and biogeography of the carnivorous plant family Sarraceniaceae.

    Science.gov (United States)

    Ellison, Aaron M; Butler, Elena D; Hicks, Emily Jean; Naczi, Robert F C; Calie, Patrick J; Bell, Charles D; Davis, Charles C

    2012-01-01

    The carnivorous plant family Sarraceniaceae comprises three genera of wetland-inhabiting pitcher plants: Darlingtonia in the northwestern United States, Sarracenia in eastern North America, and Heliamphora in northern South America. Hypotheses concerning the biogeographic history leading to this unusual disjunct distribution are controversial, in part because genus- and species-level phylogenies have not been clearly resolved. Here, we present a robust, species-rich phylogeny of Sarraceniaceae based on seven mitochondrial, nuclear, and plastid loci, which we use to illuminate this family's phylogenetic and biogeographic history. The family and genera are monophyletic: Darlingtonia is sister to a clade consisting of Heliamphora+Sarracenia. Within Sarracenia, two clades were strongly supported: one consisting of S. purpurea, its subspecies, and S. rosea; the other consisting of nine species endemic to the southeastern United States. Divergence time estimates revealed that stem group Sarraceniaceae likely originated in South America 44-53 million years ago (Mya) (highest posterior density [HPD] estimate = 47 Mya). By 25-44 (HPD = 35) Mya, crown-group Sarraceniaceae appears to have been widespread across North and South America, and Darlingtonia (western North America) had diverged from Heliamphora+Sarracenia (eastern North America+South America). This disjunction and apparent range contraction is consistent with late Eocene cooling and aridification, which may have severed the continuity of Sarraceniaceae across much of North America. Sarracenia and Heliamphora subsequently diverged in the late Oligocene, 14-32 (HPD = 23) Mya, perhaps when direct overland continuity between North and South America became reduced. Initial diversification of South American Heliamphora began at least 8 Mya, but diversification of Sarracenia was more recent (2-7, HPD = 4 Mya); the bulk of southeastern United States Sarracenia originated co-incident with Pleistocene glaciation, <3 Mya

  3. Phylogeny of Gobioidei and the origin of European gobies

    Directory of Open Access Journals (Sweden)

    Ainhoa Agorreta

    2015-11-01

    Full Text Available The percomorph order Gobioidei comprises over 2200 species worldwide distributed that occupy most freshwater, brackish and marine environments, and show a spectacular variety in morphology, ecology, and behaviour. However, phylogenetic relationships among many gobioid groups still remain poorly understood. Such is the case of Gobiidae, a rapidly radiating lineage that encompass an unusually high diversity of species (nearly 2000, including the largely endemic European species whose origin and ancestry remain uncertain. The resolution and accuracy of previous molecular phylogenetic studies has been limited due to the use of only a few (generally mitochondrial molecular markers and/or the absence of representatives of several key lineages. Our study (built on Agorreta et al. 2013 is the first to include multiple nuclear and mitochondrial genes for nearly 300 terminal taxa representing the vast diversity of gobioid lineages. We have used this information to reconstruct a robust phylogeny of Gobioidei, and we are now investigating the historical biogeography and diversification times of European gobies with a time-calibrated molecular phylogeny. Robustness of the inferred phylogenetic trees is significantly higher than that of previous studies, hence providing the most compelling molecular phylogenetic hypotheses for Gobioidei thus far. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae + Odontobutidae clade followed by the Butidae as the sister-group of the Gobiidae. Several monophyletic groups are identified within the two major Gobiidae subclades, the gobionelline-like and the gobiine-like gobiids. The European gobies cluster in three distinct lineages (Pomatoschistus-, Aphia-, and Gobius-lineages, each with different affinities with gobiids from the Indo-Pacific and perhaps the New World. Our ongoing more-detailed study on European gobies will reveal whether their origin is related to vicariant events linked to the

  4. Can phylogeny predict chemical diversity and potential medicinal activity of plants? A case study of Amaryllidaceae

    DEFF Research Database (Denmark)

    Rønsted, Nina; Symonds, Matthew RE; Birkholm, Trine;

    2012-01-01

    Background: During evolution, plants and other organisms have developed a diversity of chemical defences, leading to the evolution of various groups of specialized metabolites selected for their endogenous biological function. A correlation between phylogeny and biosynthetic pathways could offer ...

  5. Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction

    Czech Academy of Sciences Publication Activity Database

    Pečnerová, P.; Martínková, Natália

    2012-01-01

    Roč. 41, č. 3 (2012), s. 211-219. ISSN 0300-3256 Institutional research plan: CEZ:AV0Z60930519 Keywords : phylogeny * Sciurus * biogeography * colonisation Subject RIV: EG - Zoology Impact factor: 2.793, year: 2012

  6. An evaluation of ELISA using recombinant Brucella abortus bacterioferritin (Bfr) for bovine brucellosis.

    Science.gov (United States)

    Hop, Huynh Tan; Arayan, Lauren Togonon; Simborio, Hannah Leah; Reyes, Alisha Wehdnesday Bernardo; Min, WonGi; Lee, Hu Jang; Lee, Jin Ju; Chang, Hong Hee; Kim, Suk

    2016-04-01

    To date, detection of antibodies against the lipopolysaccharide portion is the backbone of most serodiagnostic methods for brucellosis screening. However this pose a risk for false positive reactions related to other pathogens especially that of Yersinia enterocolitica O:9 which has the most prominent cross reactivity with Brucella spp. In this study, cloning and expression of Brucella abortus bacterioferritin (Bfr) was accomplished by PCR amplification into an expression vector system, and purification of a recombinant B. abortus Bfr (rBfr). The immunogenicity of rBfr was confirmed by Western blot with Brucella-positive bovine serum. To determine whether rBfr has a potential benefit for use in the serodiagnosis of bovine brucellosis, rBfr-based ELISA was performed. Interestingly, rBfr was able to detect anti-Brucella antibodies in positive sera in a dependent manner of TAT values but did not show an immunoreaction with negative samples. Particularly, average OD492 values at the lowest, medium and highest TAT titer levels were 1.4, 2.2 and 2.6-fold increase compared with the cutoff value, respectively. The accuracy, specificity and sensitivity of rBfr showed 89.09%, 93.6% and 85.33%, respectively. These findings suggest that rBfr might be a good candidate for serological diagnosis development of bovine brucellosis. PMID:27012915

  7. Effect of the daily consumption of ostrich and bovine meat on the lipid metabolism in rats

    Directory of Open Access Journals (Sweden)

    Edvaldo Vasconcelos de Carvalho-Filho

    2011-03-01

    Full Text Available The objective of this study is to evaluate the effect of the daily consumption of ostrich meat (lliofemuralis internus and bovine meat (Psoas major on the lipid metabolism in adult mice. The analyses of the centesimal composition of the meats and preparation of the diets were accomplished following the recommendations of the American Institute of Nutrition-AIN-93. Three groups of 150 day-old animals: group I (diet I, with casein, group II (diet II, with ostrich meat, and group III (diet III with bovine meat were fed for 13 weeks with the respective diets and weight gain, food efficiency coefficient, total cholesterol, lipoprotein fractions, hepatic, transaminases and body fat percentage and hepatic fat content were evaluated. No difference (p < 0.05 it was found for weight gain and coefficients for feed efficiency among the groups. Total cholesterol, HDL-cholesterol, LDL-cholesterol, relationship of total cholesterol/HDL-cholesterol, VLDL, triglycerides and hepatic transaminases were also not different among the groups (p < 0.05. This research suggests that the consumption of ostrich meat or thin bovine meat on a daily basis does not raise concerns about weight gain, and an increase in the plasma concentrations of lipoprotein and levels of hepatic transaminase.

  8. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

    OpenAIRE

    Pyron, R. Alexander; Burbrink, Frank T.; Wiens, John J.

    2013-01-01

    Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species...

  9. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

    OpenAIRE

    Michelle Klein Sercundes; Samantha Yuri Oshiro Branco Valadas; Lara Borges Keid; Tricia Maria Ferreira Souza Oliveira; Helena Lage Ferreira; Ricardo Wagner Almeida Vitor; Fábio Gregori; Rodrigo Martins Soares

    2016-01-01

    Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula ...

  10. Bovine colostrum: an emerging nutraceutical.

    Science.gov (United States)

    Bagwe, Siddhi; Tharappel, Leo J P; Kaur, Ginpreet; Buttar, Harpal S

    2015-09-01

    Nutraceutical, a term combining the words "nutrition" and "pharmaceuticals", is a food or food product that provides health benefits as an adjuvant or alternative therapy, including the treatment and prevention of infectious diseases in children and adults. There is emerging evidence that bovine colostrum (BC) may be one of the promising nutraceuticals which can prevent or mitigate various diseases in newborns and adults. Immunity-related disorders are one of the leading causes of mortality in the world. BC is rich in immunity, growth and antimicrobial factors, which promote tissue growth and the maturation of digestive tract and immune function in neonatal animals and humans. The immunoglobulins and lactoferrin present in colostrum are known to build natural immunity in newborns which helps to reduce the mortality rate in this population. Also, the side-effect profile of colostrum proteins and possible lactose intolerance is relatively less in comparison with milk. In general, BC is considered safe and well tolerated. Since colostrum has several important nutritional constituents, well-designed, double-blind, placebo-controlled studies with colostrum products should be conducted to widen its therapeutic use. The objectives of this review are to create awareness about the nutraceutical properties of colostrum and to discuss the various ongoing alternative treatments of colostrum and its active ingredients as well as to address colostrum's future nutraceutical and therapeutic implications in humans. PMID:25781716

  11. Bovine reproduction in tropical environment

    International Nuclear Information System (INIS)

    In this document it has met relating data to the reproduction of bovine and their handling for the man that it can serve as norms to judge reproductive efficiency but always view in the aspect of the nutritious, climatic circumstances and of handling under which met. Under the previous description one can say that the fertility is the resultant of the interaction among the inheritance, the means and the handling, they vary in particular for each region and property. The fertility can be good, regulate or bad in the measure in that the factors that intervene. The environmental effect on the reproductive processes of the cow represents 80 percent of the variation factors and they include climate, effect of the light, effect of the temperature, effect of the nutritious contribution, effect of psychological factors: the loss of the tendency to the seasonal reproduction is in fact an answer from the animals to its association with the man. The influence of the environment and the feeding of the animals are more intense in the females than in the males, being evidenced that the reproduction control is under the influence hormonal joint with the nutrition. An appropriate nutrition is prerequisite for the beginning of the sexual maturation with an appropriate weight and corporal condition. It is also described the effect and the relationship of the energy contribution about the fertility, the restart of the ovarian activity, its cause of the continuation of the interval childbirth-conception, silent ovulation, organic ancestry and interval among childbirths

  12. Composite sampling a novel method to accomplish observational economy in environmental studies

    CERN Document Server

    Patil, Ganapati P; Taillie, Charles

    2010-01-01

    This monograph provides a comprehensive statistical account of composite sampling as an ingenious environmental sampling method to help accomplish observational economy in a variety of environmental and ecological studies.

  13. WISM - A Wideband Instrument for Snow Measurement: Past Accomplishments, Current Status, and Path Forward

    Science.gov (United States)

    Bonds, Quenton; Racette, Paul; Durham, Tim (Principal Investigator)

    2016-01-01

    Presented are the prior accomplishments, current status and path forward for GSFC's Wideband Instrument for Snow Measurement (WISM). This work is a high level overview of the project, presented via Webinar to the IEEE young professionals.

  14. A human genome-wide library of local phylogeny predictions for whole-genome inference problems

    Directory of Open Access Journals (Sweden)

    Schwartz Russell

    2008-08-01

    Full Text Available Abstract Background Many common inference problems in computational genetics depend on inferring aspects of the evolutionary history of a data set given a set of observed modern sequences. Detailed predictions of the full phylogenies are therefore of value in improving our ability to make further inferences about population history and sources of genetic variation. Making phylogenetic predictions on the scale needed for whole-genome analysis is, however, extremely computationally demanding. Results In order to facilitate phylogeny-based predictions on a genomic scale, we develop a library of maximum parsimony phylogenies within local regions spanning all autosomal human chromosomes based on Haplotype Map variation data. We demonstrate the utility of this library for population genetic inferences by examining a tree statistic we call 'imperfection,' which measures the reuse of variant sites within a phylogeny. This statistic is significantly predictive of recombination rate, shows additional regional and population-specific conservation, and allows us to identify outlier genes likely to have experienced unusual amounts of variation in recent human history. Conclusion Recent theoretical advances in algorithms for phylogenetic tree reconstruction have made it possible to perform large-scale inferences of local maximum parsimony phylogenies from single nucleotide polymorphism (SNP data. As results from the imperfection statistic demonstrate, phylogeny predictions encode substantial information useful for detecting genomic features and population history. This data set should serve as a platform for many kinds of inferences one may wish to make about human population history and genetic variation.

  15. Accomplishments in 2008 in the Management of Curable Metastatic Colorectal Cancer

    OpenAIRE

    Adam, René; Hoti, Emir; Folprecht, Gunnar; Benson, Al B.

    2009-01-01

    Overview of the Disease IncidencePrognosisCurrent Therapy Standards Colorectal Liver Metastases (CRLM) Resectable TumorsStrategies to Convert Nonresectable Liver Metastases to Resectable StatusSynchronous Colorectal Liver MetastasesPredictors of Survival After Resection of CRLMPeritoneal Carcinomatosis (PC) From Colorectal CancerColorectal Pulmonary Metastases (CRPM)Colorectal Liver Metastases With Extrahepatic DiseaseAccomplishments (or Lack of Accomplishments) During the Year Th...

  16. Is bovine dentine an appropriate substitute in abrasion studies

    OpenAIRE

    Wegehaupt, F J; Widmer, R.; Attin, T.

    2010-01-01

    The study aimed to compare the wear behaviour of human and bovine dentine due to toothbrushing with different relative dentin abrasivity (RDA) toothpastes. Forty human and 40 bovine dentine samples were prepared from bovine lower incisors or human premolars roots, and baseline surface profiles were recorded. The samples were distributed to four groups (each group n = 10 human and 10 bovine samples) and brushed with fluoridated experimental toothpastes with different RDAs (group A: RDA 10, B: ...

  17. The evolution of bovine viral diarrhea: a review

    OpenAIRE

    Goens, Denise

    2002-01-01

    The economic importance of bovine viral diarrhea is increasing with the emergence of seemingly more virulent viruses, as evidenced by outbreaks of hemorrhagic syndrome and severe acute bovine viral diarrhea beginning in the 1980s and 1990s. It appears that evolutionary changes in bovine viral diarrhea virus were responsible for these outbreaks. The genetic properties of the classical bovine viral diarrhea virus that contribute to the basis of current diagnostic tests, vaccines, and our unders...

  18. Production of cattle immunotolerant to bovine viral diarrhea virus.

    OpenAIRE

    McClurkin, A W.; Littledike, E T; Cutlip, R C; Frank, G H; Coria, M F; Bolin, S R

    1984-01-01

    Inoculation of bovine virus diarrhea virus into 58 to 125 day old fetuses of bovine virus diarrhea virus seropositive pregnant cows, or inoculation of bovine virus diarrhea virus into seronegative cows 42 to 114 days pregnant, may produce clinically normal calves which are persistently infected with the specific isolate of bovine virus diarrhea virus yet seronegative to the homologous and heterologous isolates. Reinoculation of these persistently infected cattle with their homologous isolate ...

  19. Understanding and evaluating bovine testes.

    Science.gov (United States)

    Kastelic, John P

    2014-01-01

    The objective is to briefly review bovine testes and how they are assessed, with an emphasis on articles from Theriogenology. Scrotal circumference (SC) is the most common method to assess testicular size; it varies among individual bulls and breeds and is highly heritable. In general, a large SC is associated with early puberty, more sperm, a higher percentage of morphologically normal sperm, and better reproductive performance in closely related females. Consequently, there are minimum requirements for SC for breeding soundness. In prepubertal bull calves, there is an early rise (10-20 weeks of age) in LH, which is critically related to onset of puberty and testicular development. Feeding bulls approximately 130% of maintenance requirements of energy and protein from approximately 8 to 30 weeks of age increased LH release during the early rise, hastened puberty (approximately 1 month), and increased mature testis size and sperm production (approximately 20%-30%). However, high-energy diets after weaning (>200 days) often reduced sperm production and semen quality. A bull's testes and scrotum have opposing (complementary) temperature gradients, which keep the testicular temperature 2 °C to 6 °C cooler than core body temperature for production of fertile sperm (increased testicular temperature reduces semen quality). Infrared thermography, a quick and noninvasive method of assessing scrotal surface temperature, may be beneficial for evaluations of breeding soundness. The primary clinical use of ultrasonography in assessment of reproductive function in the bull is characterization of grossly detectable lesions in the testes and scrotum. In conclusion, testis size and function are critical for bull fertility, affected by nutrition, and readily assessed clinically. PMID:24274406

  20. Arachidonate metabolism in bovine gallbladder muscle

    International Nuclear Information System (INIS)

    Incubation of (1-14C]arachidonic acid (AA) with homogenates of bovine gallbladder muscle generated a large amount of radioactive material having the chromatographic mobility of 6-keto-PGF1 alpha (stable product of PGI2) and smaller amounts of products that comigrated with PGF2 alpha PGE2. Formation of these products was inhibited by the cyclooxygenase inhibitor indomethacin. The major radioactive product identified by thin-layer chromatographic mobility and by gas chromatography - mass spectrometric analysis was found to be 6-keto-PGF1 alpha. The quantitative metabolic pattern of [1-14C]PGH2 was virtually identical to that of [1-14C]AA. Incubation of arachidonic acid with slices of bovine gallbladder muscle released labile anti-aggregatory material in the medium, which was inhibited by aspirin or 15-hydroperoxy-AA. These results indicate that bovine gallbladder muscle has a considerable enzymatic capacity to produce PGI2 from arachidonic acid

  1. 9 CFR 113.68 - Pasteurella Haemolytica Vaccine, Bovine.

    Science.gov (United States)

    2010-01-01

    ..., Bovine. 113.68 Section 113.68 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE... REQUIREMENTS Live Bacterial Vaccines § 113.68 Pasteurella Haemolytica Vaccine, Bovine. Pasteurella Haemolytica Vaccine, Bovine, shall be prepared as a desiccated live culture bacterial vaccine of an avirulent...

  2. 21 CFR 522.1125 - Hemoglobin glutamer-200 (bovine).

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Hemoglobin glutamer-200 (bovine). 522.1125 Section... § 522.1125 Hemoglobin glutamer-200 (bovine). (a) Specifications. Each 125 milliliter bag contains 13 grams per deciliter of polymerized hemoglobin of bovine origin in modified Lactated Ringer's...

  3. 9 CFR 113.309 - Bovine Parainfluenza3 Vaccine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Parainfluenza3 Vaccine. 113.309... Virus Vaccines § 113.309 Bovine Parainfluenza3 Vaccine. Bovine Parainfluenza3 Vaccine shall be produced... virus dose from the lot of Master Seed Virus shall be established as follows: (1) Twenty-five...

  4. 78 FR 1718 - Approved Tests for Bovine Tuberculosis in Cervids

    Science.gov (United States)

    2013-01-09

    ... Animal and Plant Health Inspection Service 9 CFR Part 77 Approved Tests for Bovine Tuberculosis in... of antibodies to bovine tuberculosis in certain species of captive cervids. This action is necessary..., CO 80526-8117; (970) 494-7378. SUPPLEMENTARY INFORMATION: Background Bovine tuberculosis is...

  5. 9 CFR 113.69 - Pasteurella Multocida Vaccine, Bovine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Pasteurella Multocida Vaccine, Bovine... REQUIREMENTS Live Bacterial Vaccines § 113.69 Pasteurella Multocida Vaccine, Bovine. Pasteurella Multocida Vaccine, Bovine, shall be prepared as a desiccated live culture bacterial vaccine of an avirulent...

  6. 9 CFR 113.311 - Bovine Virus Diarrhea Vaccine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Virus Diarrhea Vaccine. 113.311... Virus Vaccines § 113.311 Bovine Virus Diarrhea Vaccine. Bovine Virus Diarrhea Vaccine shall be prepared... virus diarrhea susceptible calves shall be used as test animals (20 vaccinates and five controls)....

  7. Bovine HEXIM1 inhibits bovine immunodeficiency virus replication through regulating BTat-mediated transactivation

    OpenAIRE

    Guo, Hong-yan; Ma, Yong-gang; Gai, Yuan-ming; Liang, Zhi-bin; Ma, Jing; Su, Yang; Zhang, Qi-cheng; Chen, Qi-Min; Tan, Juan

    2013-01-01

    The bovine immunodeficiency virus (BIV) transactivator (BTat) recruits the bovine cyclin T1 (B-cyclin T1) to the LTR to facilitate the transcription of BIV. Here, we demonstrate that bovine hexamethylene bisacetamide (HMBA)-induced protein 1 (BHEXIM1) inhibits BTat-mediated BIV LTR transcription. The results of in vivo and in vitro assays show direct binding of BHEXIM1 to the B-cyclin T1. These results suggest that the repression arises from BHEXIM1-BTat competition for B-cyclin T1, which all...

  8. Preparation of prostaglandins from bovine lipid

    International Nuclear Information System (INIS)

    A fast reliable method was designed for extraction and purification of prostaglandins from the local lipid which is extracted from bovine milk. The purified extract was about 13.4 mg/gm lipid. The obtained results of high performance liquid chromatography (HPLC) indicated that, the extract consisted of more than one type of prostaglandins and the concentration of these types ranged between 250 and more than 263 mg/ml especially of PGF2 α. Although this study was performed using standards and purified extracts bovine lipid, it is highly promising for future application to biological fluids, milk and its derivatives. (authors). 21 refs., 2 figs

  9. Economics of bovine leukemia virus infection.

    Science.gov (United States)

    Pelzer, K D

    1997-03-01

    A herd infected with bovine leukemia virus suffers a direct economic loss due to clinical lymphosarcoma. A major indirect cost associated with infection is restriction of the sale of animals and germplasma to foreign markets. Reports on the economic effects of infection on production have been variable and are reviewed in this article. In order to develop cost-effective bovine leukemia virus control programs, costs associated with the disease, the cost of prevention, and expected economic returns from a program need to be considered. PMID:9071750

  10. Identification of bovine material in porcine spray-dried blood derivatives using the Polymerase Chain Reaction technique

    Directory of Open Access Journals (Sweden)

    Sánchez A.

    2004-01-01

    Full Text Available Due to the widely supported theory of bovine spongiform encephalopathy (BSE spread in cattle by contaminated animal feeds, screening of feed products has become essential. For many years, manufacturers have used blood and plasma proteins as high quality ingredients of foods for both pets and farm animals. However, in Europe, the Commission Regulation 1234/2003/EC temporally bans the use of processed animal proteins, including blood-derivative products, in feedstuffs for all farm animals which are fattened or bred for the production of food. This regulation has some exceptions, such as the use of non ruminant blood products into the feed of farm fish. Authorization of the re-introduction of these proteins into animal feed formulations, especially non ruminant proteins into the feed for non ruminant farm animals, is expected when adequate control methods to discriminate ruminant proteins exist. Currently, the number of validated methods to differentiate the species of origin for most of the animal by-products is limited. Here we report the development of a rapid and sensitive polymerase chain reaction (PCR-based assay, which allows detection of bovine or porcine specific mitochondrial DNAfrom spray-dried blood derivate products (plasma, whole blood and red cells, as a marker for bovine contamination in porcine products. Sample extracts, suitable for PCR, were easily and quickly obtained with the commercial PrepManTM Ultra reagent (Applied Biosystems. To confirm the porcine origin of the samples, primers targeting a specific region of 134 bp of the porcine cytochrome b coding sequence were designed (cytbporc1-F and cytbporc2-R. Previously published PCR primers (L8129 and H8357, specific for a 271 bp fragment of the bovine mitochondrial ATPase 8-ATPase 6 genes, were chosen to accomplish amplification of bovine DNA. The limit of detection (LOD of the bovine PCR assay was at least of 0.05% (v/v of bovine inclusion in spray-dried porcine plasma or red

  11. RISK ANALYSIS FOR SHIP CONVERTING PROJECT ACCOMPLISHMENT (Case study of KRI KP Converting Project

    Directory of Open Access Journals (Sweden)

    Dimas Endro W

    2013-10-01

    Full Text Available Ship converting has become as prospective activity in ship building area. Operational and economical aspect are the most dominant rationale. Baseon a new fuction of converted ship, a task list which contain several jobs that must be done is listed. This accomplishment schedule not only contain a task list, but also duration for certain job title. In practical apllication job duration is maintained based on experience of project manager.  Further more, total accomplish duration is setted as time accomplishment for the project. This setted time has become reference for the project bid. Occasionaly, if accomplishment time which offered is strict, than schedule slip become as potencial nightmare. For this situation, project manager has had a cristal clearconsideration to select a proper decision wheter he will take the tender offer or not. practically, project mananger has layed on his experience to handle previous project and face  penalty if the project delayed. This paper focussed on how to measure tender offer based on risk analysis, specially for converted ship tender which has a strike time accomplishment.A new application method to analysis proposed tender based on time and penalty parameter has become a topic of this paper.

  12. A mitogenomic phylogeny and genetic history of sable (Martes zibellina).

    Science.gov (United States)

    Malyarchuk, Boris; Derenko, Miroslava; Denisova, Galina

    2014-10-15

    We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200-300 thousandyears ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~50-140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~23-50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka. PMID:25110108

  13. Robust markers reflecting phylogeny and taxonomy of rhizobia.

    Directory of Open Access Journals (Sweden)

    Yan Ming Zhang

    Full Text Available Genomic ANI (Average Nucleotide Identity has been found to be able to replace DNA-DNA hybridization in prokaryote taxonomy. The ANI of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ANI. This allowed us to identify three housekeeping genes (SMc00019-truA-thrA whose ANI reflected the intraspecies and interspecies genomic ANI among rhizobial strains, revealing an ANI gap (≥2% between the inter- and intra-species comparisons. The intraspecies (96% and interspecies (94% ANI boundaries calculated from three genes (SMc00019-truA-thrA provided a criterion for bacterial species definition and confirmed 621/629 of known interspecies relationships within Bradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium. Some widely studied strains should be renamed. The SMc00019-truA-thrA ANI also correlates well with the genomic ANI of strains in Agrobacterium, Methylobacterium, Ralstonia, Rhodopseudomonas, Cupriavidus and Burkholderia, suggesting their wide applicability in other bacteria.

  14. Shedding light on vampires: the phylogeny of vampyrellid amoebae revisited.

    Directory of Open Access Journals (Sweden)

    Sebastian Hess

    Full Text Available With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the 'vampire amoebae' have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa Cavalier-Smith, 2002 (Cercozoa, grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella Cienkowski, 1865, the other containing the genus Leptophrys Hertwig & Lesser, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae Zopf, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida West, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed.

  15. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

    Science.gov (United States)

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay

    2016-05-01

    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development of methods for species tree inference under MSC, owing mainly to the accumulating evidence of incomplete lineage sorting in phylogenomic analyses. However, the evolutionary history of a set of genomes, or species, could be reticulate due to the occurrence of evolutionary processes such as hybridization or horizontal gene transfer. We report on a novel method for Bayesian inference of genome and species phylogenies under the multispecies network coalescent (MSNC). This framework models gene evolution within the branches of a phylogenetic network, thus incorporating reticulate evolutionary processes, such as hybridization, in addition to incomplete lineage sorting. As phylogenetic networks with different numbers of reticulation events correspond to points of different dimensions in the space of models, we devise a reversible-jump Markov chain Monte Carlo (RJMCMC) technique for sampling the posterior distribution of phylogenetic networks under MSNC. We implemented the methods in the publicly available, open-source software package PhyloNet and studied their performance on simulated and biological data. The work extends the reach of Bayesian inference to phylogenetic networks and enables new evolutionary analyses that account for reticulation. PMID:27144273

  16. Molecular phylogeny and ultrastructure of Aphelidium aff. melosirae (Aphelida, Opisthosporidia).

    Science.gov (United States)

    Karpov, Sergey A; Mamkaeva, Maria A; Benzerara, Karim; Moreira, David; López-García, Purificación

    2014-08-01

    Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position. Together with Cryptomycota and the highly derived Microsporidia, they have been recently re-classified as Opisthosporidia, being the sister group to fungi. Despite their huge diversity, as revealed by molecular environmental studies, and their phylogenetic interest, only three genera have been described (Aphelidium, Amoeboaphelidium, and Pseudaphelidium), from which 18S rRNA gene sequences exist only for Amoeboaphelidium species. Here, we describe the life cycle and ultrastructure of Aphelidium aff. melosirae, and provide the first 18S rRNA gene sequence obtained for this genus. Molecular phylogeny analysis indicates that Aphelidium is very distantly related to Amoebaphelidium, highlighting the wide genetic diversity of the aphelids. The parasitoid encysts and penetrates the host alga, Tribonema gayanum through an infection tube. Cyst germination leads to a young trophont that phagocytes the algal cell content and progressively develops a plasmodium, which becomes a zoospore-producing sporangium. Aphelidium aff. melosirae has amoeboflagellate zoospores, tubular/lamellar mitochondrial cristae, a metazoan type of centrosome, and closed orthomitosis with an intranuclear spindle. These features together with trophont phagocytosis distinguish Aphelidium from fungi and support the erection of the new superphylum Opisthosporidia as sister to fungi. PMID:24995586

  17. Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

    Science.gov (United States)

    Kozlov, Alexey M; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-06-20

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences ('mislabels') using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  18. Molecular phylogeny of the Drosophila melanogaster species subgroup.

    Science.gov (United States)

    Ko, Wen-Ya; David, Ryan M; Akashi, Hiroshi

    2003-11-01

    Although molecular and phenotypic evolution have been studied extensively in Drosophila melanogaster and its close relatives, phylogenetic relationships within the D. melanogaster species subgroup remain unresolved. In particular, recent molecular studies have not converged on the branching orders of the D. yakuba-D. teissieri and D. erecta-D. orena species pairs relative to the D. melanogaster-D. simulans-D. mauritiana-D. sechellia species complex. Here, we reconstruct the phylogeny of the melanogaster species subgroup using DNA sequence data from four nuclear genes. We have employed "vectorette PCR" to obtain sequence data for orthologous regions of the Alcohol dehydrogenase (Adh), Alcohol dehydrogenase related (Adhr), Glucose dehydrogenase (Gld), and rosy (ry) genes (totaling 7164 bp) from six melanogaster subgroup species (D. melanogaster, D. simulans, D. teissieri, D. yakuba, D. erecta, and D. orena) and three species from subgroups outside the melanogaster species subgroup [D. eugracilis (eugracilis subgroup), D. mimetica (suzukii subgroup), and D. lutescens (takahashii subgroup)]. Relationships within the D. simulans complex are not addressed. Phylogenetic analyses employing maximum parsimony, neighbor-joining, and maximum likelihood methods strongly support a D. yakuba-D. teissieri and D. erecta-D. orena clade within the melanogaster species subgroup. D. eugracilis is grouped closer to the melanogaster subgroup than a D. mimetica-D. lutescens clade. This tree topology is supported by reconstructions employing simple (single parameter) and more complex (nonreversible) substitution models. PMID:14738315

  19. Molecular phylogeny of the forensically important genus Cochliomyia (Diptera: Calliphoridae).

    Science.gov (United States)

    Yusseff-Vanegas, Sohath; Agnarsson, Ingi

    2016-01-01

    Cochliomyia Townsend includes several abundant and one of the most broadly distributed, blow flies in the Americas, and is of significant economic and forensic importance. For decades, Cochliomyia hominivorax (Coquerel) and Cochliomyia macellaria (Fabricius) have received attention as livestock parasites and primary indicator species in forensic entomology. However, Cochliomyia minima Shannon and Cochliomyia aldrichi Del Ponte have only been subject to basic taxonomy and faunistic studies. Here we present the first complete phylogeny of Cochliomyia including numerous specimens per species, collected from 13 localities in the Caribbean. Four genes, the mitochondrial COI and the nuclear EF-1α, 28S rRNA, and ITS2, were analyzed. While we found some differences among gene trees, a concatenated gene matrix recovered a robustly supported monophyletic Cochliomyia with Compsomyiops Townsend as its sister group and recovered the monophyly of Cochliomyia hominivorax, Cochliomyia macellaria and Cochliomyia minima. Our results support a close relationship between Cochliomyia minima and Cochliomyia aldrichi. However, we found Cochliomyia aldrichi containing Cochliomyia minima, indicating recent speciation, or issues with the taxonomy of the group. We provide basic information on habitat preference, distribution and feeding habits of Cochliomyia minima and Cochliomyia aldrichi that will be useful for future forensic studies in the Caribbean. PMID:27563274

  20. Genomes-based phylogeny of the genus Xanthomonas

    Directory of Open Access Journals (Sweden)

    Rodriguez-R Luis M

    2012-03-01

    Full Text Available Abstract Background The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. Results Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. Conclusions Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.

  1. The phylogeny and evolutionary history of tyrannosauroid dinosaurs

    Science.gov (United States)

    Brusatte, Stephen L.; Carr, Thomas D.

    2016-02-01

    Tyrannosauroids—the group of carnivores including Tyrannosaurs rex—are some of the most familiar dinosaurs of all. A surge of recent discoveries has helped clarify some aspects of their evolution, but competing phylogenetic hypotheses raise questions about their relationships, biogeography, and fossil record quality. We present a new phylogenetic dataset, which merges published datasets and incorporates recently discovered taxa. We analyze it with parsimony and, for the first time for a tyrannosauroid dataset, Bayesian techniques. The parsimony and Bayesian results are highly congruent, and provide a framework for interpreting the biogeography and evolutionary history of tyrannosauroids. Our phylogenies illustrate that the body plan of the colossal species evolved piecemeal, imply no clear division between northern and southern species in western North America as had been argued, and suggest that T. rex may have been an Asian migrant to North America. Over-reliance on cranial shape characters may explain why published parsimony studies have diverged and filling three major gaps in the fossil record holds the most promise for future work.

  2. Phylogeny and Classification of Prunus sensu lato (Rosaceae)

    Institute of Scientific and Technical Information of China (English)

    Shuo Shi; Jinlu Li; Jiahui Sun; Jing Yu; Shiliang Zhou

    2013-01-01

    The classification of the economically important genus Prunus L. sensu lato (s.l.) is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.l. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions (atpB-rbcL, matK, ndhF, psbA-trnH, rbcL, rpL16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycf1) and three nuclear genes (ITS, s6pdh and SbeI) to explore their infrageneric relationships. The results of these analyses were used to develop a new, phylogeny-based classification of Prunus s.l. Our phylogenetic reconstructions resolved three main clades of Prunus s.l. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades: subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae (T. T. Yü&L. T. Lu) S. L. Zhou and one new species name, Prunus tianshanica (Pojarkov) S. Shi, were proposed.

  3. A unified phylogeny-based nomenclature for histone variants

    Directory of Open Access Journals (Sweden)

    Talbert Paul B

    2012-06-01

    Full Text Available Abstract Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure.

  4. Phylogeny and disjunct distribution: evolution of Saintpaulia (Gesneriaceae).

    Science.gov (United States)

    Möller, M; Cronk, Q C

    1997-12-22

    The molecular phylogeny of African violets (Saintpaulia H. Wendl.), based on ribosomal DNA internal transcribed spacer (ITS) sequences, follows the disjunct biogeography of the genus. Sequence analysis by parsimony of 19 accessions, representing 17 currently recognized Saintpaulia species, resulted in four trees of 182 steps. The first major division is between S. goetzeana, from the Uluguru Mts, Tanzania, and the rest of the genus. The basal position of S. goetzeana, and its putative primitive characters, may indicate an Uluguru origin for Saintpaulia and subsequent colonization of the more northerly mountains. Of the remainder, S. teitensis, from the Teita Hills of Kenya, is sister taxon to the other species (which occur mainly in the Usambara Mts of north-east Tanzania). A group of nine Usambaran species that we call the 'ionantha complex' show minimal ITS genetic differentiation and are also taxonomically critical. Species diversity in the Usambara Mts appears to be the result of rapid, recent (possibly Pleistocene) radiation. This study reveals the limitations of ITS sequences for elucidating the radiation of poorly differentiated species (the ionantha complex). However, the molecular data strongly suggest that conservation of the Uluguru and Teita populations is essential for the protection of the full range of diversity within the genus. PMID:9447739

  5. Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2013-11-01

    Full Text Available Phylogeny is an evolutionary reconstruction of the past relationships of DNA or protein sequences and it can further be used as a tool to assess population structuring, genetic diversity and biogeographic patterns. In the microbial world, the concept that everything is everywhere is widely accepted. However, it is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. Biogeography can be defined as the science that documents the spatial and temporal distribution of a given taxa in the environment at local, regional and continental scales. Speciation, extinction and dispersal are proposed to explain the generation of biogeographic patterns. Cyanobacteria are a diverse group of microorganisms that inhabit a wide range of ecological niches and are well known for their toxic secondary metabolite production. Knowledge of the evolution and dispersal of these microorganisms is still limited, and further research to understand such topics is imperative. Here, we provide a compilation of the most relevant information regarding these issues to better understand the present state of the art as a platform for future studies, and we highlight examples of both phylogenetic and biogeographic studies in non-symbiotic cyanobacteria and cyanotoxins.

  6. Molecular phylogeny of the forensically important genus Cochliomyia (Diptera: Calliphoridae)

    Science.gov (United States)

    Yusseff-Vanegas, Sohath; Agnarsson, Ingi

    2016-01-01

    Abstract Cochliomyia Townsend includes several abundant and one of the most broadly distributed, blow flies in the Americas, and is of significant economic and forensic importance. For decades, Cochliomyia hominivorax (Coquerel) and Cochliomyia macellaria (Fabricius) have received attention as livestock parasites and primary indicator species in forensic entomology. However, Cochliomyia minima Shannon and Cochliomyia aldrichi Del Ponte have only been subject to basic taxonomy and faunistic studies. Here we present the first complete phylogeny of Cochliomyia including numerous specimens per species, collected from 13 localities in the Caribbean. Four genes, the mitochondrial COI and the nuclear EF-1α, 28S rRNA, and ITS2, were analyzed. While we found some differences among gene trees, a concatenated gene matrix recovered a robustly supported monophyletic Cochliomyia with Compsomyiops Townsend as its sister group and recovered the monophyly of Cochliomyia hominivorax, Cochliomyia macellaria and Cochliomyia minima. Our results support a close relationship between Cochliomyia minima and Cochliomyia aldrichi. However, we found Cochliomyia aldrichi containing Cochliomyia minima, indicating recent speciation, or issues with the taxonomy of the group. We provide basic information on habitat preference, distribution and feeding habits of Cochliomyia minima and Cochliomyia aldrichi that will be useful for future forensic studies in the Caribbean. PMID:27563274

  7. Multigene phylogeny reveals eusociality evolved twice in vespid wasps

    Science.gov (United States)

    Hines, Heather M.; Hunt, James H.; O'Connor, Timothy K.; Gillespie, Joseph J.; Cameron, Sydney A.

    2007-01-01

    Eusocial wasps of the family Vespidae are thought to have derived their social behavior from a common ancestor that had a rudimentary caste-containing social system. In support of this behavioral scenario, the leading phylogenetic hypothesis of Vespidae places the eusocial wasps (subfamilies Stenogastrinae, Polistinae, and Vespinae) as a derived monophyletic clade, thus implying a single origin of eusocial behavior. This perspective has shaped the investigation and interpretation of vespid social evolution for more than two decades. Here we report a phylogeny of Vespidae based on data from four nuclear gene fragments (18S and 28S ribosomal DNA, abdominal-A and RNA polymerase II) and representatives from all six extant subfamilies. In contrast to the current phylogenetic perspective, our results indicate two independent origins of vespid eusociality, once in the clade Polistinae+Vespinae and once in the Stenogastrinae. The stenogastrines appear as an early diverging clade distantly related to the vespines and polistines and thus evolved their distinctive form of social behavior from a different ancestor than that of Polistinae+Vespinae. These results support earlier views based on life history and behavior and have important implications for interpreting transitional stages in vespid social evolution. PMID:17360641

  8. The interaction between bovine herpesvirus type 1 and activated bovine T lymphocytes.

    Science.gov (United States)

    Griebel, P J; Ohmann, H B; Lawman, M J; Babiuk, L A

    1990-02-01

    The interaction between activated bovine T lymphocytes (BTLs) and bovine herpesvirus type 1 (BHV-1) was investigated. BHV-1 infection of BTLs reduced the amplitude of recombinant bovine interleukin 2-induced proliferative responses. This decreased proliferation was caused by a virus-induced lymphocytolysis which was dependent on viable virus and was not inhibited by recombinant bovine interferon-alpha I1. Furthermore, lymphocytolysis was not associated with virus replication or with the synthesis of detectable levels of viral proteins. Electron microscopic examination of virus-infected cells revealed that lymphocytolysis was characterized by early nuclear disintegration resembling apoptosis. These observations suggest that activated T cells, localized at the site of BHV-1 infection, may be susceptible to virus-induced cytolysis. PMID:2155290

  9. Molecular differentiation of bovine sarcocysts.

    Science.gov (United States)

    Akhlaghi, Majedeh; Razavi, Mostafa; Hosseini, Arsalan

    2016-07-01

    Cattle are common intermediate hosts of Sarcocystis, and the prevalence in adult bovine muscle is close to 100 % in most regions of the world. Three Sarcocystis spp. are known to infect cattle as intermediate hosts, namely, S. cruzi, S. hirsuta, and S. hominis. The aim of the present study was the molecular identification and differentiation of these three species, Neospora caninum and Besnoitia by PCR and RFLP methods. Tissue samples were obtained from diaphragmatic muscle of 101 cattle slaughtered in Shiraz, Fars Province, Iran, for both smear preparation and DNA extraction. The samples were digested by Pepsin, washed three times with PBS solution before taking smears, fixed in absolute methanol and stained with 10 % Giemsa. The slides were examined microscopically for Sarcocystis bradyzoites and DNA was extracted from 100 mg of Sarcocystis-infected meat samples. Since the primers also bind to 18S rRNA gene of some tissue cyst-forming coccidian protozoa, DNA was also extracted from 100 μl of tachyzoite-containing suspension of N. caninum and Besnoitia isolated from goat to compare RFLP pattern. Polymerase chain reaction (PCR) was performed on DNA of samples which were microscopically positive for Sarcocystis. Five restriction enzymes Dra1, EcoRV, RsaI, AvaI, and SspI were used for RFLP and DNA of one sample from protozoa was sequenced. Based on the RFLP results, 87 (98.9 %) DNA samples were cut with DraI, indicating infection by S. cruzi. One sample (1.1 %) of PCR products of infected samples was cut only with EcoRV which showed S. hominis infection. Forty-eight samples (53.3 %) of PCR products were cut with both DraI, EcoRV, or with DraI, EcoRV, and RsaI while none of them was cut with SspI, which shows the mixed infection of both S. cruzi and S. hominis and no infection with S. hirsuta. It seems by utilizing these restriction enzymes, RLFP could be a suitable method not only for identification of Sarcocystis species but also for differentiating them

  10. Scientific Opinion on bovine lactoferrin

    Directory of Open Access Journals (Sweden)

    EFSA Panel on Dietetic Products, Nutrition and Allergies

    2012-07-01

    Full Text Available

    Following a request from the European Commission, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA was asked to carry out the additional assessment for ‘lactoferrin’ as a food ingredient in the context of Regulation (EC No 258/97 taking into account the comments and objections of a scientific nature raised by Member States. Bovine lactoferrin (bLF is a protein that occurs naturally in cow’s milk. The applicant intends to market bLF that is isolated from cheese whey and skimmed milk, and purified. The applicant intends to add bLF to foods for particular nutritional uses, i.e. infant and follow-on formulae, dietary food for special medical purposes, dairy products, yoghurts and yoghurt drinks, and chewing gums. According to the applicant, the high intake estimate for infants would be 1.1 g bLF per day. For adults, the applicant’s calculation estimates a mean and 97.5th percentile intake of 0.6 and 2.1 mg/kg bodyweight per day, respectively, and a mean and 97.5th percentile daily intake of about 45 mg and 150 mg, respectively. The Panel notes that the safety of bLF as a novel food ingredient has already been assessed with a favourable outcome. That evaluation was to a significant extent based on safety data on bLF produced by Morinaga. The Panel also notes that the applicant intends maximum use levels of bLF in foods which are equivalent or lower than those intended by the applicant of the previous Opinion, and that the range of foods to which it is intended to add bLF is smaller. Consequently, the estimated intake levels described for the present application are comparable for infants and lower for all other population groups. The Panel concludes that the novel food ingredient, bLF, is safe under the proposed uses and use levels.

  11. Survey on vertical infection of bovine viral diarrhea virus from fetal bovine sera in the field

    OpenAIRE

    NAGAYAMA, Kumiko; OGUMA, Keisuke; SENTSUI, Hiroshi

    2015-01-01

    Bovine viral diarrhea virus (BVDV) isolation and antibody survey were performed using 2,758 fetal bovine sera (FBS) collected from slaughterhouses in New Zealand, Australia and the Dominican Republic, and then sent to Japan to manufacture commercial serum for cell culture use. FBS in the Dominican Republic were pooled for each several individuals, and those collected in other countries were separated according to each individual and subjected to the tests. BVDV was isolated from 25 (0.91%) FB...

  12. Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae).

    Science.gov (United States)

    Ritz, C M; Reiker, J; Charles, G; Hoxey, P; Hunt, D; Lowry, M; Stuppy, W; Taylor, N

    2012-11-01

    The cacti of tribe Tephrocacteae (Cactaceae-Opuntioideae) are adapted to diverse climatic conditions over a wide area of the southern Andes and adjacent lowlands. They exhibit a range of life forms from geophytes and cushion-plants to dwarf shrubs, shrubs or small trees. To confirm or challenge previous morphology-based classifications and molecular phylogenies, we sampled DNA sequences from the chloroplast trnK/matK region and the nuclear low copy gene phyC and compared the resulting phylogenies with previous data gathered from nuclear ribosomal DNA sequences. The here presented chloroplast and nuclear low copy gene phylogenies were mutually congruent and broadly coincident with the classification based on gross morphology and seed micro-morphology and anatomy. Reconstruction of hypothetical ancestral character states suggested that geophytes and cushion-forming species probably evolved several times from dwarf shrubby precursors. We also traced an increase of embryo size at the expense of the nucellus-derived storage tissue during the evolution of the Tephrocacteae, which is thought to be an evolutionary advantage because nutrients are then more rapidly accessible for the germinating embryo. In contrast to these highly concordant phylogenies, nuclear ribosomal DNA data sampled by a previous study yielded conflicting phylogenetic signals. Secondary structure predictions of ribosomal transcribed spacers suggested that this phylogeny is strongly influenced by the inclusion of paralogous sequence probably arisen by genome duplication during the evolution of this plant group. PMID:22877645

  13. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.

    Science.gov (United States)

    FitzJohn, Richard G; Maddison, Wayne P; Otto, Sarah P

    2009-12-01

    Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies. PMID:20525612

  14. Concomitant infection of Neospora caninum and Bovine Herpesvirus type 5 in spontaneous bovine abortions

    Directory of Open Access Journals (Sweden)

    Maia S. Marin

    2013-11-01

    Full Text Available Bovine Herpesvirus type 5 (BoHV-5 has not been conclusively demonstrated to cause bovine abortion. Brain lesions produced by Neospora caninum and Bovine Herpesvirus type 1 (BoHV-1 exhibit common features. Therefore, careful microscopic evaluation and additional diagnostic procedures are required to achieve an accurate final etiological diagnosis. The aim of the present work was to investigate the occurrence of infections due to BoHV-1, BoHV-5 and N. caninum in 68 cases of spontaneous bovine abortions which showed microscopic lesions in the fetal central nervous system. This study allowed the identification of 4 (5.9% fetuses with dual infection by BoHV-5 and N. caninum and 33 (48.5% cases in which N. caninum was the sole pathogen identified. All cases were negative to BoHV-1. The results of this study provide evidence that dual infection by BoHV-5 and N. caninum occur during pregnancy in cattle; however, the role of BoHV-5 as a primary cause of bovine abortion needs further research. Molecular diagnosis of BoHV-5 and N. caninum confirmed the importance of applying complementary assays to improve the sensitivity of diagnosing bovine abortion.

  15. Detection and identification of the atypical bovine pestiviruses in commercial foetal bovine serum batches.

    Directory of Open Access Journals (Sweden)

    Hongyan Xia

    Full Text Available The recently emerging atypical bovine pestiviruses have been detected in commercial foetal bovine serum (FBS of mainly South American origin so far. It is unclear how widely the viruses are presented in commercial FBS of different geographic origins. To further investigate the possible pestivirus contamination of commercially available FBS batches, 33 batches of FBS were obtained from ten suppliers and analysed in this study for the presence of both the recognised and the atypical bovine pestiviruses. All 33 batches of FBS were positive by real-time RT-PCR assays for at least one species of bovine pestiviruses. According to the certificate of analysis that the suppliers claimed for each batch of FBS, BVDV-1 was detected in all 11 countries and BVDV-2 was detected exclusively in the America Continent. The atypical pestiviruses were detected in 13 batches claimed to originate from five countries. Analysis of partial 5'UTR sequences showed a high similarity among these atypical bovine pestiviruses. This study has demonstrated, for the first time that commercial FBS batches of different geographic origins are contaminated not only with the recognised species BVDV-1 and BVDV-2, but also with the emerging atypical bovine pestiviruses.

  16. EVOLUTION AND RECOMBINATION OF BOVINE DNA REPEATS

    NARCIS (Netherlands)

    JOBSE, C; BUNTJER, JB; HAAGSMA, N; BREUKELMAN, HJ; BEINTEMA, JJ; LENSTRA, JA

    1995-01-01

    The history of the abundant repeat elements in the bovine genome has been studied by comparative hybridization and PCR. The Bov-A and Bov-B SINE elements both emerged just after the divergence of the Camelidae and the true ruminants. A 31-bp subrepeat motif in satellites of the Bovidae species cattl

  17. A physical map of the bovine genome

    Science.gov (United States)

    Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential geneti...

  18. Recombinant Bovine Growth Hormone Criticism Grows.

    Science.gov (United States)

    Gaard, Greta

    1995-01-01

    Discusses concerns related to the use of recombinant bovine growth hormone in the United States and other countries. Analyses the issue from the perspectives of animal rights, human health, world hunger, concerns of small and organic farmers, costs to the taxpayer, and environmental questions. A sidebar discusses Canadian review of the hormone.…

  19. NUTRIENTS AND EPIGENETICS IN BOVINE CELLS

    Science.gov (United States)

    This is a chapter for a book titled “Livestock Epigenetics” edited by Dr. Hasan Khatib and published by Wiley-Blackwell. This chapter is focused on the research development in our laboratory in the area of interaction of nutrients and genomic phonotype in bovine cells. Briefly, the Research on nutri...

  20. Control of bovine hepatic fatty acid oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Jesse, B.W.; Emery, R.S.; Thomas, J.W.

    1986-09-01

    Fatty acid oxidation by bovine liver slices and mitochondria was examined to determine potential regulatory sites of fatty acid oxidation. Conversion of 1-(/sup 14/C)palmitate to /sup 14/CO/sub 2/ and total (/sup 14/C)acid-soluble metabolites was used to measure fatty acid oxidation. Oxidation of palmitate (1 mM) was linear in both liver slice weight and incubation time. Carnitine stimulated palmitate oxidation; 2 mM dl-carnitine produced maximal stimulation of palmitate oxidation to both CO/sup 2/ and acid-soluble metabolites. Propionate (10 mM) inhibited palmitate oxidation by bovine liver slices. Propionate (.5 to 10 mM) had no effect on palmitate oxidation by mitochondria, but malonyl Coenzyme A, the first committed intermediate of fatty acid synthesis, inhibited mitochondrial palmitate oxidation (inhibition constant = .3 ..mu..M). Liver mitochonndrial carnitine palmitoyltransferase exhibited Michaelis constants for palmitoyl Coenzyme A and l-carnitine of 11.5 ..mu..M and .59 mM, respectively. Long-chain fatty acid oxidation in bovine liver is regulated by mechanisms similar to those in rats but adapted to the unique digestive physiology of the bovine.

  1. Control of bovine hepatic fatty acid oxidation

    International Nuclear Information System (INIS)

    Fatty acid oxidation by bovine liver slices and mitochondria was examined to determine potential regulatory sites of fatty acid oxidation. Conversion of 1-[14C]palmitate to 14CO2 and total [14C]acid-soluble metabolites was used to measure fatty acid oxidation. Oxidation of palmitate (1 mM) was linear in both liver slice weight and incubation time. Carnitine stimulated palmitate oxidation; 2 mM dl-carnitine produced maximal stimulation of palmitate oxidation to both CO2 and acid-soluble metabolites. Propionate (10 mM) inhibited palmitate oxidation by bovine liver slices. Propionate (.5 to 10 mM) had no effect on palmitate oxidation by mitochondria, but malonyl Coenzyme A, the first committed intermediate of fatty acid synthesis, inhibited mitochondrial palmitate oxidation (inhibition constant = .3 μM). Liver mitochonndrial carnitine palmitoyltransferase exhibited Michaelis constants for palmitoyl Coenzyme A and l-carnitine of 11.5 μM and .59 mM, respectively. Long-chain fatty acid oxidation in bovine liver is regulated by mechanisms similar to those in rats but adapted to the unique digestive physiology of the bovine

  2. Molecular biology of bovine viral diarrhea virus

    Science.gov (United States)

    Bovine viral diarrhea viruses (BVDV) are arguably the most important viral pathogen of ruminants worldwide and can cause severe economic loss. Clinical symptoms of the disease caused by BVDV range from subclinical to severe acute hemorrhagic syndrome, with the severity of disease being strain depend...

  3. An unusual presentation of enzootic bovine leukosis.

    OpenAIRE

    Sparling, A M

    2000-01-01

    A 6-year-old, Holstein x Simmental cow diagnosed with pyelonephritis had increasing difficulty rising and became recumbent, despite treatment with antibiotics. A serological test for the bovine leukemia virus was positive; at necropsy, the left kidney and ureter and the myocardium showed lesions of lymphosarcoma, confirmed by histology.

  4. Aortic reconstruction with bovine pericardial grafts

    Directory of Open Access Journals (Sweden)

    Silveira Lindemberg Mota

    2003-01-01

    Full Text Available INTRODUCTION: Glutaraldehyde-treated crimped bovine pericardial grafts are currently used in aortic graft surgery. These conduits have become good options for these operations, available in different sizes and shapes and at a low cost. OBJECTIVE:To evaluate the results obtained with bovine pericardial grafts for aortic reconstruction, specially concerning late complications. METHOD: Between January 1995 and January 2002, 57 patients underwent different types of aortic reconstruction operations using bovine pericardial grafts. A total of 29 (50.8% were operated on an urgent basis (mostly acute Stanford A dissection and 28 electively. Thoracotomy was performed in three patients for descending aortic replacement (two patients and aortoplasty with a patch in one. All remaining 54 underwent sternotomy, cardiopulmonary bypass and aortic resection. Deep hypothermia and total circulatory arrest was used in acute dissections and arch operations. RESULTS: Hospital mortality was 17.5%. Follow-up was 24.09 months (18.5 to 29.8 months confidence interval and complication-free actuarial survival curve was 92.3% (standard deviation ± 10.6. Two patients lately developed thoracoabdominal aneurysms following previous DeBakey II dissection and one died from endocarditis. One "patch" aortoplasty patient developed local descending aortic pseudoaneurysm 42 months after surgery. All other patients are asymptomatic and currently clinically evaluated with echocardiography and CT scans, showing no complications. CONCLUSION: Use of bovine pericardial grafts in aortic reconstruction surgery is adequate and safe, with few complications related to the conduits.

  5. Comparative serological response in calves to eight commercial vaccines against infectious bovine rhinotracheitis, parainfluenza-3, bovine respiratory syncytial, and bovine viral diarrhea viruses

    OpenAIRE

    Van Donkersgoed, Joyce; van den Hurk, Jan V.; McCartney, Duane; Harland, Richard J.

    1991-01-01

    A field trial was conducted to compare the serological responses in calves to eight commercial vaccines against infectious bovine rhinotracheitis virus (IBRV), parainfluenza-3 virus (PI3V), bovine respiratory syncytial virus (BRSV), and/or bovine viral diarrhea virus (BVDV). Calves given IBRV, P13V, BRSV, and BVDV vaccines had significantly higher antibodies to these viruses than unvaccinated controls; however, serological responses to killed BVDV vaccines were low. Calves with preexisting an...

  6. Synergistic effects of bovine respiratory syncytial virus and non-cytopathic bovine viral diarrhea virus infection on selected bovine alveolar macrophage functions.

    OpenAIRE

    Liu, L.; Lehmkuhl, H D; Kaeberle, M L

    1999-01-01

    The effect of bovine respiratory syncytial virus (BRSV) and non-cytopathic bovine viral diarrhea virus (ncpBVDV) infection on selected bovine alveolar macrophage (AM) functions was investigated. Alveolar macrophages were harvested from 2- to 6-month-old calves seronegative for BRSV and BVDV and inoculated with approximately 1 median cell culture infective dose of virus per AM. Control, BRSV infected, ncpBVDV-infected and BRSV-ncpBVDV coinfected AM cultures were evaluated for Fc receptor expre...

  7. The relationship between the occurrence of undifferentiated bovine respiratory disease and titer changes to bovine coronavirus and bovine viral diarrhea virus in 3 Ontario feedlots.

    OpenAIRE

    O'Connor, A; Martin, S W; Nagy, E.; Menzies, P; Harland, R

    2001-01-01

    Serological evidence of previous viral exposure (titer at arrival) and current viral exposure (titer increase) during a 28-day study period, was used to determine if bovine coronavirus (BCV) or bovine viral diarrhea virus (BVDV) was associated with the occurrence of undifferentiated bovine respiratory disease (UBRD) in feedlot calves. Neutralizing antibody titers to BCV and BVDV were determined for 852 animals from 3 Ontario feedlots. Calves at 2 of the 3 feedlots (n = 753) received a modifie...

  8. Investigation of Bovine Viral Diarrheae Virus, Bovine Herpesvirus 1, and Bovine Leukosis Virus infections in a dairy cattle herd with abortion problem

    OpenAIRE

    Avcı, Oğuzhan; Yavru, Sibel; Kale, Mehmet

    2014-01-01

    A survey was conducted to determine of Bovine Viral Diarrhea Virus, Bovine Herpesvirus 1 and Bovine Leukosis Virus infections in a dairy cattle herd with abortion problem in Çankırı. A total of 172 serum and 172 leukocytes samples were collected from unvaccinated Holstein cows for mentioned infections in 2010. All sampled animals were over 3 years. While the serum samples were analysed by commercially available indirect enzyme linked immunosorbent assays (ELISA), leukocyte samples...

  9. Linkage mapping bovine EST-based SNP

    Directory of Open Access Journals (Sweden)

    Bennett Gary L

    2005-05-01

    Full Text Available Abstract Background Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. Results Bovine expressed sequence tag (EST and bacterial artificial chromosome (BACsequence data were used to develop 918 single nucleotide polymorphism (SNP markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM . Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum of 216 (366 informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum of 55 (191 informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. Conclusion Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other

  10. Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new Lophotrochozoa phylogeny and supports a paraphyletic basal acoelomorpha.

    Science.gov (United States)

    Paps, Jordi; Baguñà, Jaume; Riutort, Marta

    2009-10-01

    During the past decade, great progress has been made in clarifying the relationships among bilaterian animals. Studies based on a limited number of markers established new hypotheses such as the existence of three superclades (Deuterostomia, Ecdysozoa, and Lophotrochozoa) but left major questions unresolved. The data sets used to the present either bear few characters for many taxa (i.e., the ribosomal genes) or present many characters but lack many phyla (such as recent phylogenomic approaches) failing to provide definitive answers for all the regions of the bilaterian tree. We performed phylogenetic analyses using a molecular matrix with a high number of characters and bilaterian phyla. This data set is built from 13 genes (8,880 bp) belonging to 90 taxa from 27 bilaterian phyla. Probabilistic analyses robustly support the three superclades, the monophyly of Chordata, a spiralian clade including Brachiozoa, the basal position of a paraphyletic Acoelomorpha, and point to an ecdysozoan affiliation for Chaetognatha. This new phylogeny not only agrees with most classical molecular results but also provides new insights into the relationships between lophotrochozoans and challenges the results obtained using high-throughput strategies, highlighting the problems associated with the current trend to increase gene number rather than taxa. PMID:19602542

  11. Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America.

    Science.gov (United States)

    Perez, Manolo F; Carstens, Bryan C; Rodrigues, Gustavo L; Moraes, Evandro M

    2016-03-01

    Supportive data related to the article "Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America" (Perez et al., 2016) [1]. Here, we present pyrosequencing results, primer sequences, a cpDNA phylogeny, and a species tree phylogeny. PMID:26900589

  12. Ongoing interpretations of accomplishments in smoking cessation : Positive and negative self-efficacy interpretations

    NARCIS (Netherlands)

    Dijkstra, A; Ten Wolde, G

    2005-01-01

    Smokers and ex-smokers are considered to make ongoing interpretations of their accomplishments in terms of their ability to refrain from smoking. We assessed positive self-efficacy interpretations (PSEint) and negative self-efficacy interpretations (NSEint) as the frequencies with which smokers and

  13. Service Efforts and Accomplishments (SEA) Reporting: A Challenge for School Financial Reporting.

    Science.gov (United States)

    Walter, Donald L.

    1991-01-01

    Discusses the Government Accounting Standards Board (GASB) research concerning the identification of indicators of service efforts and service accomplishments. The GASB has proposed that financial reports should not only be useful in assessing accountability, but they should also assist in making economic, social, and political decisions. (six…

  14. Activities and Accomplishments in Various Domains: Relationships with Creative Personality and Creative Motivation in Adolescence

    Science.gov (United States)

    Hong, Eunsook; Peng, Yun; O'Neil, Harold F., Jr.

    2014-01-01

    This study examined relationships between five personal traits and adolescents' creative activities and accomplishments in five domains--music, visual arts, creative writing, science, and technology. Participants were 439 tenth graders (220 males and 219 females) in China. The relationships were examined using confirmatory factor analysis.…

  15. Reshaping American Energy - A Look Back at BETO's Accomplishments in 2013

    Energy Technology Data Exchange (ETDEWEB)

    None

    2013-11-01

    For more than a decade, BETO has been shaping the bioenergy industry. BETO helps transform the nation's renewable biomass resources into high-performance biofuels, biopower, and bioproducts. This fact sheet outlines some of our biggest accomplishments in 2013.

  16. Longitudinal Pathways from Math Intrinsic Motivation and Achievement to Math Course Accomplishments and Educational Attainment

    Science.gov (United States)

    Gottfried, Adele Eskeles; Marcoulides, George A.; Gottfried, Allen W.; Oliver, Pamella H.

    2013-01-01

    Across 20 years, pathways from math intrinsic motivation and achievement (ages 9-17) to high school math course accomplishments and educational attainment (age 29) were analyzed. Academic intrinsic motivation was the theoretical foundation. To determine how initial status and change in motivation and achievement related to course accomplishments…

  17. NSFC Supported CERN LHC Accomplished Start-up in September,2008

    Institute of Scientific and Technical Information of China (English)

    Zhang Yongtao

    2008-01-01

    @@ After 15 years of construction,the Large Hadron Collider (LHC),the world's largest and highest-energy particle accelerator accomplished its start-up on September 10,2008.Scientists predict that this historical event will be a milestone on physics research.

  18. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas.

    Science.gov (United States)

    Díaz-Arce, Natalia; Arrizabalaga, Haritz; Murua, Hilario; Irigoien, Xabier; Rodríguez-Ezpeleta, Naiara

    2016-09-01

    Although species from the genus Thunnus include some of the most commercially important and most severely overexploited fishes, the phylogeny of this genus is still unresolved, hampering evolutionary and traceability studies that could help improve conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough phylogenetically informative markers. Here we infer the first genome-wide nuclear marker-based phylogeny of tunas using restriction site associated DNA sequencing (RAD-seq) data. Our results, derived from phylogenomic inferences obtained from 128 nucleotide matrices constructed using alternative data assembly procedures, support a single Thunnus evolutionary history that challenges previous assumptions based on morphological and molecular data. PMID:27286653

  19. Efficient Enumeration of the Directed Binary Perfect Phylogenies from Incomplete Data

    CERN Document Server

    Kiyomi, Masashi; Saitoh, Toshiki

    2012-01-01

    We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some species the states of some characters are missing. Our main object is to give an efficient algorithm to enumerate (or list) all perfect phylogenies that can be obtained when the missing entries are completed. While a simple branch-and-bound algorithm (B&B) shows a theoretically good performance, we propose another approach based on a zero-suppressed binary decision diagram (ZDD). Experimental results on randomly generated data exhibit that the ZDD approach outperforms B&B. We also prove that counting the number of phylogenetic trees consistent with a given data is #P-complete, thus providing an evidence that an efficient random sampling seems hard.

  20. Sequence-Length Requirement of Distance-Based Phylogeny Reconstruction: Breaking the Polynomial Barrier

    CERN Document Server

    Roch, Sebastien

    2009-01-01

    We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a polylogarithmic sequence-length requirement -- improving significantly over previous polynomial bounds for distance-based methods. The technique is based on an averaging procedure that implicitly reconstructs ancestral sequences. In the same token, we extend previous results on phase transitions in phylogeny reconstruction to general time-reversible models. More precisely, we show that in the so-called Kesten-Stigum zone (roughly, a region of the parameter space where ancestral sequences are well approximated by ``linear combinations'' of the observed sequences) sequences of length $\\poly(\\log n)$ suffice for reconstruction when branch lengths are discretized. Here $n$ is the number of extant species. Our results challenge, to some extent, the conventional wisdom that estimates of evolutionary distances alone carry significantly less information about phylogenies than full sequ...

  1. Genome-based phylogeny of dsDNA viruses by a novel alignment-free method.

    Science.gov (United States)

    Gao, Yang; Luo, Liaofu

    2012-01-15

    Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification. PMID:22100880

  2. RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

    KAUST Repository

    Díaz-Arce, Natalia

    2016-06-07

    Although species from the genus Thunnus include some of the most commercially important and most severely overexploited fishes, the phylogeny of this genus is still unresolved, hampering evolutionary and traceability studies that could help improve conservation and management strategies for these species. Previous attempts based on mitochondrial and nuclear markers were unsuccessful in inferring a congruent and reliable phylogeny, probably due to mitochondrial introgression events and lack of enough phylogenetically informative markers. Here we infer the first genome-wide nuclear marker-based phylogeny of tunas using restriction site associated DNA sequencing (RAD-seq) data. Our results, derived from phylogenomic inferences obtained from 128 nucleotide matrices constructed using alternative data assembly procedures, support a single Thunnus evolutionary history that challenges previous assumptions based on morphological and molecular data.

  3. Whole genome association mapping by incompatibilities and local perfect phylogenies

    Directory of Open Access Journals (Sweden)

    Besenbacher Søren

    2006-10-01

    Full Text Available Abstract Background With current technology, vast amounts of data can be cheaply and efficiently produced in association studies, and to prevent data analysis to become the bottleneck of studies, fast and efficient analysis methods that scale to such data set sizes must be developed. Results We present a fast method for accurate localisation of disease causing variants in high density case-control association mapping experiments with large numbers of cases and controls. The method searches for significant clustering of case chromosomes in the "perfect" phylogenetic tree defined by the largest region around each marker that is compatible with a single phylogenetic tree. This perfect phylogenetic tree is treated as a decision tree for determining disease status, and scored by its accuracy as a decision tree. The rationale for this is that the perfect phylogeny near a disease affecting mutation should provide more information about the affected/unaffected classification than random trees. If regions of compatibility contain few markers, due to e.g. large marker spacing, the algorithm can allow the inclusion of incompatibility markers in order to enlarge the regions prior to estimating their phylogeny. Haplotype data and phased genotype data can be analysed. The power and efficiency of the method is investigated on 1 simulated genotype data under different models of disease determination 2 artificial data sets created from the HapMap ressource, and 3 data sets used for testing of other methods in order to compare with these. Our method has the same accuracy as single marker association (SMA in the simplest case of a single disease causing mutation and a constant recombination rate. However, when it comes to more complex scenarios of mutation heterogeneity and more complex haplotype structure such as found in the HapMap data our method outperforms SMA as well as other fast, data mining approaches such as HapMiner and Haplotype Pattern Mining (HPM

  4. Global diversity and phylogeny of the Asteroidea (Echinodermata.

    Directory of Open Access Journals (Sweden)

    Christopher L Mah

    Full Text Available Members of the Asteroidea (phylum Echinodermata, popularly known as starfish or sea stars, are ecologically important and diverse members of marine ecosystems in all of the world's oceans. We present a comprehensive overview of diversity and phylogeny as they have figured into the evolution of the Asteroidea from Paleozoic to the living fauna. Living post-Paleozoic asteroids, the Neoasteroidea, are morphologically separate from those in the Paleozoic. Early Paleozoic asteroid faunas were diverse and displayed morphology that foreshadowed later living taxa. Preservation presents significant difficulties, but fossil occurrence and current accounts suggests a diverse Paleozoic fauna, which underwent extinction around the Permian-Triassic interval was followed by re-diversification of at least one surviving lineage. Ongoing phylogenetic classification debates include the status of the Paxillosida and the Concentricycloidea. Fossil and molecular evidence has been and continues to be part of the ongoing evolution of asteroid phylogenetic research. The modern lineages of asteroids include the Valvatacea, the Forcipulatacea, the Spinlosida, and the Velatida. We present an overview of diversity in these taxa, as well as brief notes on broader significance, ecology, and functional morphology of each. Although much asteroid taxonomy is stable, many new taxa remain to be discovered with many new species currently awaiting description. The Goniasteridae is currently one of the most diverse families within the Asteroidea. New data from molecular phylogenetics and the advent of global biodiversity databases, such as the World Asteroidea Database (http://www.marinespecies.org/Asteroidea/ present important new springboards for understanding the global biodiversity and evolution of asteroids.

  5. A multilocus molecular phylogeny of Fasciolariidae (Neogastropoda: Buccinoidea).

    Science.gov (United States)

    Couto, Diogo R; Bouchet, Philippe; Kantor, Yuri I; Simone, Luiz R L; Giribet, Gonzalo

    2016-06-01

    The neogastropod family Fasciolariidae Gray, 1853 - tulips, horse-conchs, spindles, etc., comprises important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae Gray, 1853, Fusininae Wrigley, 1927 and Peristerniinae Tryon, 1880. Fasciolariids have had a rather complicated taxonomical history, with several genus names for a long time used as waste baskets to group many unrelated species; based on shell characters, recent taxonomic revisions have, however, began to set some order in its taxonomy. The present work is the first molecular approach to the phylogeny of Fasciolariidae based on a multigene dataset, which provides support for fasciolariids, an old group with a fossil record dating back to the Cretaceous. Molecular markers used were the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I, and the nuclear genes 18S rRNA, 28S rRNA and histone H3, sequenced for up to 116 ingroup taxa and 17 outgroups. Phylogenetic analyses revealed monophyly of Dolicholatirus Bellardi, 1884 and Teralatirus Coomans, 1965, however it was not possible to discern if the group is the sister clade to the remaining fasciolariids; the latter, on the other hand, proved monophyletic and contained highly supported groups. A first split grouped fusinines and Pseudolatirus Bellardi, 1884; a second split grouped the peristerniine genera Peristernia Mörch, 1852 and Fusolatirus Kuroda and Habe, 1971, while the last group comprised fasciolariines and the remaining peristerniines. None of these clades correspond to the present-day accepted circumscription of the three recognized subfamilies. PMID:27033950

  6. Forelimb-hindlimb developmental timing changes across tetrapod phylogeny

    Directory of Open Access Journals (Sweden)

    Selwood Lynne

    2007-10-01

    Full Text Available Abstract Background Tetrapods exhibit great diversity in limb structures among species and also between forelimbs and hindlimbs within species, diversity which frequently correlates with locomotor modes and life history. We aim to examine the potential relation of changes in developmental timing (heterochrony to the origin of limb morphological diversity in an explicit comparative and quantitative framework. In particular, we studied the relative time sequence of development of the forelimbs versus the hindlimbs in 138 embryos of 14 tetrapod species spanning a diverse taxonomic, ecomorphological and life-history breadth. Whole-mounts and histological sections were used to code the appearance of 10 developmental events comprising landmarks of development from the early bud stage to late chondrogenesis in the forelimb and the corresponding serial homologues in the hindlimb. Results An overall pattern of change across tetrapods can be discerned and appears to be relatively clade-specific. In the primitive condition, as seen in Chondrichthyes and Osteichthyes, the forelimb/pectoral fin develops earlier than the hindlimb/pelvic fin. This pattern is either retained or re-evolved in eulipotyphlan insectivores (= shrews, moles, hedgehogs, and solenodons and taken to its extreme in marsupials. Although exceptions are known, the two anurans we examined reversed the pattern and displayed a significant advance in hindlimb development. All other species examined, including a bat with its greatly enlarged forelimbs modified as wings in the adult, showed near synchrony in the development of the fore and hindlimbs. Conclusion Major heterochronic changes in early limb development and chondrogenesis were absent within major clades except Lissamphibia, and their presence across vertebrate phylogeny are not easily correlated with adaptive phenomena related to morphological differences in the adult fore- and hindlimbs. The apparently conservative nature of this

  7. Bovine rhinitis viruses are common in U.S. cattle with bovine respiratory disease.

    Science.gov (United States)

    Hause, Ben M; Collin, Emily A; Anderson, Joe; Hesse, Richard A; Anderson, Gary

    2015-01-01

    Bovine rhinitis viruses (BRV) are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1) has been identified while bovine rhinitis A virus 2 (BRAV2) and bovine rhinitis B virus (BRBV) were previously only identified in England and Japan, respectively. Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD) diagnostic submission from Kansas identified contigs with approximately 90% nucleotide similarity to BRAV2 and BRBV. A combination of de novo and templated assemblies using reference genomes yielded near complete BRAV2 and BRBV genomes. The near complete genome of bovine rhinitis A virus 1 (BRAV1) was also determined from a historical isolate to enable further molecular epidemiological studies. A 5'-nuclease reverse transcription PCR assay targeting the 3D polymerase gene was designed and used to screen 204 archived BRD clinical specimens. Thirteen (6.4%) were positive. Metagenomic sequencing of six positive samples identified mixed BRAV1/BRAV2, BRAV1/BRBV and BRAV2/BRBV infections for five samples. One sample showed infection only with BRAV1. Seroprevalence studies using a cell culture adapted BRBV found immunofluorescence assay-reactive antibodies were common in the herds analyzed. Altogether, these results demonstrate that BRV infections are common in cattle with respiratory disease and that BRAV1, BRAV2 and BRBV co-circulate in U.S. cattle and have high similarity to viruses isolated more than 30 years ago from diverse locations. PMID:25789939

  8. Bovine rhinitis viruses are common in U.S. cattle with bovine respiratory disease.

    Directory of Open Access Journals (Sweden)

    Ben M Hause

    Full Text Available Bovine rhinitis viruses (BRV are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1 has been identified while bovine rhinitis A virus 2 (BRAV2 and bovine rhinitis B virus (BRBV were previously only identified in England and Japan, respectively. Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD diagnostic submission from Kansas identified contigs with approximately 90% nucleotide similarity to BRAV2 and BRBV. A combination of de novo and templated assemblies using reference genomes yielded near complete BRAV2 and BRBV genomes. The near complete genome of bovine rhinitis A virus 1 (BRAV1 was also determined from a historical isolate to enable further molecular epidemiological studies. A 5'-nuclease reverse transcription PCR assay targeting the 3D polymerase gene was designed and used to screen 204 archived BRD clinical specimens. Thirteen (6.4% were positive. Metagenomic sequencing of six positive samples identified mixed BRAV1/BRAV2, BRAV1/BRBV and BRAV2/BRBV infections for five samples. One sample showed infection only with BRAV1. Seroprevalence studies using a cell culture adapted BRBV found immunofluorescence assay-reactive antibodies were common in the herds analyzed. Altogether, these results demonstrate that BRV infections are common in cattle with respiratory disease and that BRAV1, BRAV2 and BRBV co-circulate in U.S. cattle and have high similarity to viruses isolated more than 30 years ago from diverse locations.

  9. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

    Directory of Open Access Journals (Sweden)

    Xavier Suresh R

    2006-06-01

    Full Text Available Abstract Background Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface. Description The QTL (Quantitative Trait Locus data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position. Conclusion We present a web accessible, integrated database of bovine (dairy and beef cattle QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

  10. Separations and Waste Forms Research and Development FY 2013 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed

    2013-12-01

    The Separations and Waste Form Campaign (SWFC) under the U.S. Department of Energy (DOE) Fuel Cycle Research and Development Program (FCRD) is responsible for developing advanced separation and waste form technologies to support the various fuel cycle options defined in the DOE Nuclear Energy Research and Development Roadmap, Report to Congress, April 2010. The fiscal year (FY) 2013 accomplishments report provides a highlight of the results of the research and development (R&D) efforts performed within SWFC in FY 2013. Each section contains a high-level overview of the activities, results, technical point of contact, applicable references, and documents produced during the fiscal year. This report briefly outlines campaign management and integration activities, but the intent of the report is to highlight the many technical accomplishments made during FY 2013.

  11. Accomplishments in 2008 in the Management of Curable Metastatic Colorectal Cancer

    Science.gov (United States)

    Adam, René; Hoti, Emir; Folprecht, Gunnar; Benson, Al B.

    2009-01-01

    SUMMARY Overview of the Disease IncidencePrognosisCurrent Therapy Standards Colorectal Liver Metastases (CRLM) Resectable TumorsStrategies to Convert Nonresectable Liver Metastases to Resectable StatusSynchronous Colorectal Liver MetastasesPredictors of Survival After Resection of CRLMPeritoneal Carcinomatosis (PC) From Colorectal CancerColorectal Pulmonary Metastases (CRPM)Colorectal Liver Metastases With Extrahepatic DiseaseAccomplishments (or Lack of Accomplishments) During the Year Therapy New Staging SystemSystemic Chemotherapy in Resectable Liver MetastasesSystemic Chemotherapy in Nonresectable Liver MetastasesSelective Internal Radiation Therapy (SIRT)Selection of Patients for Liver ResectionRadiofrequency AblationBiomarkersWhat Needs To Be Done? Optimizing Patient CareFuture Directions Comments on ResearchObstacles to Overcome PMID:20011559

  12. Bovine Mastitis Associated with Prototheca blaschkeae▿

    OpenAIRE

    Marques, Sara; Silva, Eliane; Kraft, Christine; Carvalheira, Júlio; Videira, Arnaldo; Huss, Volker A. R.; Thompson, Gertrude

    2008-01-01

    Bovine mastitis is an important and complex disease responsible for economic losses in the dairy industry. Biotype II strains of the green alga Prototheca zopfii can be involved, most often resulting in chronic mastitis of difficult treatment associated with reduced milk production. This type of infection is rare, but the number of reported cases is increasing worldwide. In order to determine the kind of species involved in mastitis by Prototheca in northwest Portugal, 41 Prototheca isolates ...

  13. CONSUMER PERCEPTIONS AND ATTITUDES TOWARDS BOVINE SOMATOTROPIN

    OpenAIRE

    Kaiser, Harry M.; Scherer, Clifford W.; Barbano, David M.

    1992-01-01

    This article investigates the possible negative effects of bovine somatotropin (bST) and antibiotic use in cows on fluid-milk consumption in New York State. Based on data from a consumer survey, the potential change in milk consumption due to bST and antibiotic use is estimated. In addition, the current perceptions of consumers about bST and antibiotics are measured, and the significant socioeconomic, demographic, and attitudinal characteristics of consumers that are related to their milk-con...

  14. Dynamics of perinatal bovine leukemia virus infection

    OpenAIRE

    Gutiérrez, Gerónimo; Alvarez, Irene; Merlini, Ramiro; Rondelli, Flavia; Trono, Karina

    2014-01-01

    Background Bovine leukemia virus (BLV) is highly endemic in many countries, including Argentina. As prevention of the spread from infected animals is of primary importance in breaking the cycle of BLV transmission, it is important to know the pathophysiology of BLV infection in young animals, as they are the main source of animal movement. In this work, we determined the proviral load and antibody titers of infected newborn calves from birth to first parturition (36 months). Results All calve...

  15. Photodynamically generated bovine serum albumin radicals

    DEFF Research Database (Denmark)

    Silvester, J A; Timmins, G S; Davies, Michael Jonathan

    1998-01-01

    Porphyrin-sensitized photoxidation of bovine serum albumin (BSA) results in oxidation of the protein at (at least) two different, specific sites: the Cys-34 residue giving rise to a thiyl radical (RS.); and one or both of the tryptophan residues (Trp-134 and Trp-214) resulting in the formation of...... by a range of proteases. The generation of protein-derived radicals also results in an enhancement of photobleaching of the porphyrin, suggesting that protein radical generation is linked to porphyrin photooxidation....

  16. Parameters for natural resistance in bovine milk

    OpenAIRE

    Ploegaert, T.C.W.

    2010-01-01

    Parameters for natural resistance in bovine milk Mastitis or udder inflammation is one of the most important health problems of dairy cattle. Resistance against mastitis and many other diseases is partly based on the naturally present disease resistance capacity: innate immunity. This research therefore aimed to identify adequate immune parameters and determine their relation with the susceptibility of the individual animal for mastitis and possibly also other health problems. Natural antibod...

  17. Antihelmintic Resistance For Gastrointestinal Bovine Nematodes

    OpenAIRE

    Patricia Torres Vásquez; Germán Alonso Prada Sanmiguel; Dildo Márquez Lara

    2007-01-01

    The gastrointestinal nematodes (GIN), in domestic animals, especially in bovines are a very important factor that affects their productivity, because cattle production systems have intervened in the relationship between gastrointestinal parasites (PGI) and the host, breaking therefore the ecological balance between them. In many opportunities the development of parasitic populations have been favored or a parasitic population have been led to extinction, it has made that these populations exp...

  18. Radioimmunoassay of bovine leukosis virus antibodies

    International Nuclear Information System (INIS)

    A RIA method was developed for identifying the presence of serum antibodies to the bovine leukosis virus. The chosen procedure uses the ability of the virus antigen to bind to the solid phase of a polystyrene carrier. The method was compared with the ELISA method and with the pseudoneutralization and immunodiffusion tests. A high level of agreement was achieved between the RIA and the ELISA methods (95%). By its accuracy the RIA method proves superior to the immunodiffusion test. (author)

  19. Bovine Enteroviruses as Indicators of Fecal Contamination

    OpenAIRE

    Ley, Victoria; Higgins, James; Fayer, Ronald

    2002-01-01

    Surface waters frequently have been contaminated with human enteric viruses, and it is likely that animal enteric viruses have contaminated surface waters also. Bovine enteroviruses (BEV), found in cattle worldwide, usually cause asymptomatic infections and are excreted in the feces of infected animals in large numbers. In this study, the prevalence and genotype of BEV in a closed herd of cattle were evaluated and compared with BEV found in animals in the immediate environment and in environm...

  20. Accomplishment of 10-year research in NUCEF and future development. Process safety and development research

    International Nuclear Information System (INIS)

    Researches on process safety of reprocessing, development of an advanced reprocessing and partitioning of high-level liquid waste(HLLW) have been conducted in NUCEF - BECKY (Back-end Fuel Cycle Key Elements Research Facility), which has α-γ concrete cells and many glove-boxes. This paper present 10 year accomplishment of the above researches and future activities to be conducted in the field of separation process development. (author)

  1. Mission (Largely) Accomplished: What's Next for Consumer BDT-JDM Researchers?

    OpenAIRE

    Simonson, Itamar

    2014-01-01

    A main objective of Behavioral Decision Theory (BDT) research--demonstrating that economic theory often fails as a description of decision making as well as gaining insights into systematic influences on judgment and choice--has been largely accomplished. This research program, published in psychology, decision making, marketing, and other fields, has had unique characteristics that combined criteria employed in economics and psychology. Now that the prominent portion of the BDT agenda has be...

  2. Accomplishment of the economics of sustainable development as an opportunity to build a competitive advantage

    OpenAIRE

    Sabina Zaremba-Warnke

    2015-01-01

    Currently creating economics of sustainable development is an alternative concept in relation to neoclassical economics. The aim of economics of sustainable development is sustainable management, which means to guarantee high economic, ecological and socio-cultural standards for present and future generations within the limits of environment’s natural resistance. The accomplishment of sustainable development concept requires the activeness of all socio-economic subjects, particulary the ones ...

  3. Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies.

    Directory of Open Access Journals (Sweden)

    Orion Penner

    Full Text Available BACKGROUND: Existing sequence alignment algorithms use heuristic scoring schemes based on biological expertise, which cannot be used as objective distance metrics. As a result one relies on crude measures, like the p- or log-det distances, or makes explicit, and often too simplistic, a priori assumptions about sequence evolution. Information theory provides an alternative, in the form of mutual information (MI. MI is, in principle, an objective and model independent similarity measure, but it is not widely used in this context and no algorithm for extracting MI from a given alignment (without assuming an evolutionary model is known. MI can be estimated without alignments, by concatenating and zipping sequences, but so far this has only produced estimates with uncontrolled errors, despite the fact that the normalized compression distance based on it has shown promising results. RESULTS: We describe a simple approach to get robust estimates of MI from global pairwise alignments. Our main result uses algorithmic (Kolmogorov information theory, but we show that similar results can also be obtained from Shannon theory. For animal mitochondrial DNA our approach uses the alignments made by popular global alignment algorithms to produce MI estimates that are strikingly close to estimates obtained from the alignment free methods mentioned above. We point out that, due to the fact that it is not additive, normalized compression distance is not an optimal metric for phylogenetics but we propose a simple modification that overcomes the issue of additivity. We test several versions of our MI based distance measures on a large number of randomly chosen quartets and demonstrate that they all perform better than traditional measures like the Kimura or log-det (resp. paralinear distances. CONCLUSIONS: Several versions of MI based distances outperform conventional distances in distance-based phylogeny. Even a simplified version based on single letter Shannon

  4. Potential Anticarcinogenic Peptides from Bovine Milk

    Directory of Open Access Journals (Sweden)

    Giacomo Pepe

    2013-01-01

    Full Text Available Bovine milk possesses a protein system constituted by two major families of proteins: caseins (insoluble and whey proteins (soluble. Caseins (αS1, αS2, β, and κ are the predominant phosphoproteins in the milk of ruminants, accounting for about 80% of total protein, while the whey proteins, representing approximately 20% of milk protein fraction, include β-lactoglobulin, α-lactalbumin, immunoglobulins, bovine serum albumin, bovine lactoferrin, and lactoperoxidase, together with other minor components. Different bioactivities have been associated with these proteins. In many cases, caseins and whey proteins act as precursors of bioactive peptides that are released, in the body, by enzymatic proteolysis during gastrointestinal digestion or during food processing. The biologically active peptides are of particular interest in food science and nutrition because they have been shown to play physiological roles, including opioid-like features, as well as immunomodulant, antihypertensive, antimicrobial, antiviral, and antioxidant activities. In recent years, research has focused its attention on the ability of these molecules to provide a prevention against the development of cancer. This paper presents an overview of antitumor activity of caseins and whey proteins and derived peptides.

  5. Potential anticarcinogenic peptides from bovine milk.

    Science.gov (United States)

    Pepe, Giacomo; Tenore, Gian Carlo; Mastrocinque, Raffaella; Stusio, Paola; Campiglia, Pietro

    2013-01-01

    BOVINE MILK POSSESSES A PROTEIN SYSTEM CONSTITUTED BY TWO MAJOR FAMILIES OF PROTEINS: caseins (insoluble) and whey proteins (soluble). Caseins ( α S1, α S2, β , and κ ) are the predominant phosphoproteins in the milk of ruminants, accounting for about 80% of total protein, while the whey proteins, representing approximately 20% of milk protein fraction, include β -lactoglobulin, α -lactalbumin, immunoglobulins, bovine serum albumin, bovine lactoferrin, and lactoperoxidase, together with other minor components. Different bioactivities have been associated with these proteins. In many cases, caseins and whey proteins act as precursors of bioactive peptides that are released, in the body, by enzymatic proteolysis during gastrointestinal digestion or during food processing. The biologically active peptides are of particular interest in food science and nutrition because they have been shown to play physiological roles, including opioid-like features, as well as immunomodulant, antihypertensive, antimicrobial, antiviral, and antioxidant activities. In recent years, research has focused its attention on the ability of these molecules to provide a prevention against the development of cancer. This paper presents an overview of antitumor activity of caseins and whey proteins and derived peptides. PMID:23533710

  6. Oxytocin binding sites in bovine mammary tissue

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xin.

    1989-01-01

    Oxytocin binding sites were identified and characterized in bovine mammary tissue. ({sup 3}H)-oxytocin binding reached equilibrium by 50 min at 20{degree}C and by 8 hr at 4{degree}C. The half-time of displacement at 20{degree}C was approximately 1 hr. Thyrotropin releasing hormone, adrenocorticotropin, angiotensin I, angiotensin II, pentagastrin, bradykinin, xenopsin and L-valyl-histidyl-L-leucyl-L-threonyl-L-prolyl-L-valyl-L-glutamyl-L-lysine were not competitive. In the presence of 10 nM LiCl, addition of oxytocin to dispersed bovine mammary cells, in which phosphatidylinositol was pre-labelled, caused a time and dose-dependent increase in radioactive inositiol monophosphate incorporation. The possibility that there are distinct vasopressin receptors in bovine mammary tissue was investigated. ({sup 3}H)-vasopressin binding reached equilibrium by 40 min at 20{degree}. The half-time of displacement at 20{degree}C was approximately 1 hr. The ability of the peptides to inhibit ({sup 3}H)-vasopressin binding was: (Thr{sup 4},Gly{sup 7})-oxytocin > Arg{sup 8}-vasopressin > (lys{sup 8})-vasopressin > (Deamino{sup 1},D-arg{sup 8})-vasopressin > oxytocin > d (CH{sub 2}){sub 5}Tyr(Me)AVP.

  7. A clinical comparison of purified bovine and purified porcine insulins.

    OpenAIRE

    Olczak, S A; Greenwood, R H

    1985-01-01

    Twenty four patients with established insulin dependent diabetes treated with twice daily soluble and isophane bovine insulins were changed to equivalent doses of either purified bovine Neusulin and Neuphane (Wellcome) or purified porcine Actrapid and Monotard (Novo) insulins. After 6 months treatment the porcine group showed a 35% fall in insulin binding antibodies and a 14% reduction in insulin dosage. The group changed to purified bovine insulins showed no significant change in insulin bin...

  8. 76 FR 35185 - Notice of Request for Extension of Approval of an Information Collection; Bovine Spongiform...

    Science.gov (United States)

    2011-06-16

    ... Collection; Bovine Spongiform Encephalopathy; Importation of Animals and Animal Products AGENCY: Animal and... byproducts to protect against the introduction of bovine spongiform encephalopathy into the United States... animal products and byproducts to prevent the introduction of bovine spongiform encephalopathy into...

  9. Bovine Chymosin: A Computational Study of Recognition and Binding of Bovine κ-Casein

    DEFF Research Database (Denmark)

    Palmer, David S.; Christensen, Anders Uhrenholt; Sørensen, Jesper; Celik, Leyla; Qvist, Karsten Bruun; Schiøtt, Hanne Birgit

    2010-01-01

    Bovine chymosin is an aspartic protease that selectively cleaves the milk protein κ-casein. The enzyme is widely used to promote milk clotting in cheese manufacturing. We have developed models of residues 97-112 of bovine κ-casein complexed with bovine chymosin, using ligand docking, conformational...... search algorithms, and molecular dynamics simulations. In agreement with limited experimental evidence, the model suggests that the substrate binds in an extended conformation with charged residues on either side of the scissile bond playing an important role in stabilizing the binding pose. Lys111 and...... Lys112 are observed to bind to the N-terminal domain of chymosin displacing a conserved water molecule. A cluster of histidine and proline residues (His98-Pro99-His100-Pro101-His102) in κ-casein binds to the C-terminal domain of the protein, where a neighboring conserved arginine residue (Arg97) is...

  10. Phylogeny and relationship of some isoetalean spores from the Devonian to the present

    Czech Academy of Sciences Publication Activity Database

    Bek, Jiří; Drábková, J.; Dašková, Jiřina; Chitaley, S.

    Prague : National Museum, 2006. s. 13-13. ISBN 80-7036-198-0. [European Palaeobotany- Palynology Conference /7./. 06.09.2006-11.09.2006, Prague] R&D Projects: GA AV ČR IAA3013902 Institutional research plan: CEZ:AV0Z30130516 Keywords : Isoetes * Polysporia * phylogeny * in situ spores * Palaeozoic Subject RIV: EF - Botanics

  11. Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed

    Czech Academy of Sciences Publication Activity Database

    Maslov, D. A.; Votýpka, Jan; Yurchenko, V.; Lukeš, Julius

    2013-01-01

    Roč. 29, č. 1 (2013), s. 43-52. ISSN 1471-4922 R&D Projects: GA ČR GA204/09/1667 Institutional support: RVO:60077344 Keywords : biodiversity * Kinetoplastea * insect trypanosomatids * monoxenous parasites * phylogeny * taxonomy * Trypanosomatidae Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.217, year: 2013

  12. Phylogeny of some vespertilionid bats from Western Africa, Senegal - comparison of molecular and cytogenetic approach

    Czech Academy of Sciences Publication Activity Database

    Koubínová, D.; Irwin, N.; Hulva, P.; Zima, Jan

    Vilnius: Gamtos tyrimu centras, 2011 - (Hutson, A.; Lina, P.). s. 73-74 ISBN 978-9986-443-55-1. [European Bat Research Symposium /12./. 22.08.2011-26.08.2011, Vilnius] Institutional research plan: CEZ:AV0Z60930519 Keywords : bats * phylogeny * Senegal Subject RIV: EG - Zoology

  13. Phantoms of Gondwana?-phylogeny of the spider subfamily Mynogleninae (Araneae: Linyphiidae)

    DEFF Research Database (Denmark)

    Frick, Holger; Scharff, Nikolaj

    2014-01-01

    This is the first genus-level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiin...

  14. Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola

    Czech Academy of Sciences Publication Activity Database

    Nováková, Eva; Hypša, Václav; Klein, J.; Foottit, R. G.; von Dohlen, C.D.; Moran, N. A.

    2013-01-01

    Roč. 68, č. 1 (2013), s. 42-54. ISSN 1055-7903 R&D Projects: GA ČR GD206/09/H026 Institutional support: RVO:60077344 Keywords : Aphid * Evolution * Buchnera * Phylogeny * Informative markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.018, year: 2013

  15. Site specific rates of mitochondrial genomes and the phylogeny of eutheria

    Directory of Open Access Journals (Sweden)

    Honeycutt Rodney L

    2007-01-01

    Full Text Available Abstract Background Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3rd codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand. We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs. Results Mitochondrial genomic data for 78 eutherian mammals, 8 metatherians, and 3 monotremes were analyzed with a Bayesian analysis and our site specific rate model. The resultant phylogeny revealed strong support for most nodes and was highly congruent with more recent phylogenies based on nuclear DNA sequences. In addition, many of the conflicting relationships observed by earlier mitochondrial-based analyses were resolved without need for the exclusion of large subsets of the data. Conclusion Rather than exclusion of data to minimize presumed noise associated with non-protein encoding genes in the mitochondrial genome, our results indicate that selection of an appropriate model that accommodates rate heterogeneity across data partitions and proper treatment of RNA genes can result in a mitochondrial genome-based phylogeny of eutherian mammals that is reasonably congruent with recent phylogenies derived from nuclear genes.

  16. Molecular phylogeny of anoplocephalid tapeworms (Cestoda: Anoplocephalidae) infecting humans and non-human primates

    Czech Academy of Sciences Publication Activity Database

    Doležalová, J.; Vallo, Peter; Petrželková, Klára Judita; Foitová, I.; Nurcahyo, W.; Mudakikwa, A.; Hashimoto, C.; Jirků, M.; Lukeš, J.; Scholz, T.; Modrý, D.

    2015-01-01

    Roč. 142, č. 10 (2015), s. 1278-1289. ISSN 0031-1820 R&D Projects: GA ČR GA524/06/0264; GA ČR GA206/09/0927 Institutional support: RVO:68081766 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: EG - Zoology Impact factor: 2.560, year: 2014

  17. Advances Achieved on Studies of East Asian mtDNA Phylogeny

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Agroup of geneticists at the CAS Kunming Institute of Zoology (KIZ)succeeded in advancing out knowledge on the East Asian phylogeny of human mitochondrial DNA (mtDNA). Their work, which was finished by Dr. Kong Qingpeng under the guidance of ZHANG Yaping, was published by the journal Human Molecular Genetics.

  18. Relationship of Individual and Group Change: Ontogeny and Phylogeny in Biology.

    Science.gov (United States)

    Gould, Steven Jay

    1984-01-01

    Considers the issue of parallels between ontogeny and phylogeny from an historical perspective. Discusses such parallels in relationship to two ontogenetic principles concerning recapitulation and sequence of stages. Differentiates between Piaget's use of the idea of recapitulation and Haeckel's biogenetic law. (Author/RH)

  19. A phylogeny-based revision of the family Luciferidae (Crustacea: Decapoda)

    DEFF Research Database (Denmark)

    Vereshchaka, Alexander L.; Olesen, Jørgen; Lunina, Anastasia A.

    2016-01-01

    Luciferidae is a family of peculiar and widely distributed shrimps with an unclear systematic position and uncertain internal phylogeny. We undertook a phylogenetic analysis of Luciferidae based on 169 morphological characters (147 binary, 22 multistate). Several characters were based on scanning...

  20. Improving the Analysis of Dinoflagellate Phylogeny based on rDNA

    DEFF Research Database (Denmark)

    Murray, Shauna; Jørgensen, Mårten Flø; Ho, Simon Y.W.;

    2005-01-01

    may not closely fit the data. We constructed and examined alignments of SSU and partial LSU rRNA along with a concatenated alignment of the two molecules. The alignments showed several characteristics that may confound phylogeny reconstruction: paired helix (stem) regions that contain non...

  1. A multi gene sequence-based phylogeny of the Musaceae (banana) family

    Czech Academy of Sciences Publication Activity Database

    Christelová, Pavla; Valárik, Miroslav; Hřibová, Eva; De Langhe, E.; Doležel, Jaroslav

    2011-01-01

    Roč. 11, č. 103 (2011), s. 1-13. ISSN 1471-2148 R&D Projects: GA AV ČR IAA600380703 Institutional research plan: CEZ:AV0Z50380511 Keywords : MOLECULAR PHYLOGENY * FLOWERING PLANTS * RIBOSOMAL DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.521, year: 2011

  2. Punctuated Equilibrium Behavior and Zipf's Law in the Stochastic Branching Process Model of Phylogeny

    Science.gov (United States)

    Matsumoto, T.; Aizawa, Y.

    1999-11-01

    A stochastic branching process model of phylogeny with niche space and interactions among species is considered. For an intermediate interaction range, the time series of diversity has long periods of stasis divided by periods of rapid increase. The concept of monophyletic size is introduced, and it is shown that the size distribution obeys Zipf's law.

  3. A molecular phylogeny of the Lecanora varia group, including a new species from western North America

    Czech Academy of Sciences Publication Activity Database

    Pérez-Ortega, J.; Spribille, T.; Palice, Zdeněk; Elix, J. A.; Printzen, C.

    2010-01-01

    Roč. 9, č. 4 (2010), s. 523-535. ISSN 1617-416X R&D Projects: GA AV ČR(CZ) KJB600050635 Institutional research plan: CEZ:AV0Z60050516 Keywords : ITS * phylogeny * Lecanoraceae Subject RIV: EF - Botanics Impact factor: 1.266, year: 2010

  4. Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data

    Czech Academy of Sciences Publication Activity Database

    Ogden, T. H.; Gattolliat, J. L.; Sartori, M.; Staniczek, A. H.; Soldán, Tomáš; Whiting, M. F.

    2009-01-01

    Roč. 34, č. 4 (2009), s. 616-634. ISSN 0307-6970 R&D Projects: GA AV ČR 1QS500070505 Institutional research plan: CEZ:AV0Z50070508 Keywords : Ephemeroptera * phylogeny * morfological a molecular data Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.467, year: 2009

  5. Some Histories of Molecular Evolution: Amniote Phylogeny, Vertebrate Eye Lens Evolution, and the Prion Gene

    NARCIS (Netherlands)

    Rheede, T. van

    2004-01-01

    In this thesis, the principles of molecular evolution and phylogeny are introduced in Chapter 1, while the subsequent chapters deal with the three topics mentioned in the title. Part I: Birds, reptiles and mammals are Amniota, organisms that have an amnion during their embryonal development. Even th

  6. Does phylogeny explain the host choice behaviour of potential biological control agents for Brassicaceae weeds?

    Science.gov (United States)

    Four invasive Brassicaceae are currently being studied for biological control at the CABI Centre in Switzerland. A phylogenetic approach to host testing has so far been hampered by the fact that the evolutionary relationships of taxa within the Brassicaceae were unclear. Recently, a new phylogeny of...

  7. Phylogeny of the ascomycetous yeasts and the renaming of Pichia anomala to Wickerhamomyces anomalus

    Science.gov (United States)

    Pichia anomala was reclassified as Wickerhamomyces anomalus following multigene phylogenetic analysis. In this review, the phylogeny of the ascomycetous yeasts is discussed, with emphasis on the genus Pichia. The genus, as defined from phenotype, had nearly 100 assigned species, but the number of ...

  8. Phylogeny, Morphology, and Metabolic and Invasive Capabilities of Epicellular Fish Coccidium Goussia janae

    Czech Academy of Sciences Publication Activity Database

    Dogga, S.K.; Bartošová-Sojková, Pavla; Lukeš, Julius; Soldati-Favre, D.

    2015-01-01

    Roč. 166, č. 6 (2015), s. 659-676. ISSN 1434-4610 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Apicomplexa * Coccidia * Goussia janae * phylogeny * ultrastructure * invasion * central carbon metabolism. Subject RIV: EG - Zoology Impact factor: 3.045, year: 2014

  9. A Well-Resolved Phylogeny of the Trees of Puerto Rico Based on DNA Barcode Sequence Data

    Science.gov (United States)

    Muscarella, Robert; Uriarte, María; Erickson, David L.; Swenson, Nathan G.; Zimmerman, Jess K.; Kress, W. John

    2014-01-01

    Background The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. Methodology/principal findings We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and

  10. A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

    Directory of Open Access Journals (Sweden)

    Robert Muscarella

    Full Text Available The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i low terminal phylogenetic resolution and (ii arbitrarily defined species pools.We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%. We used a maximum likelihood (ML approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%. We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types changed some of our results depending on which phylogeny (ML vs. Phylomatic was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny.With the DNA barcode phylogeny presented here (based on an island-wide species pool, we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii provide insight into

  11. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

    Directory of Open Access Journals (Sweden)

    Stajich Jason E

    2006-11-01

    Full Text Available Abstract Background To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available. Results A dataset of 345,829 genes was extracted from 42 publicly available fungal genomes. Supertree methods were employed to derive phylogenies from 4,805 single gene families. We found that the average consensus supertree method may suffer from long-branch attraction artifacts, while matrix representation with parsimony (MRP appears to be immune from these. A genome phylogeny was also reconstructed from a concatenated alignment of 153 universally distributed orthologs. Our MRP supertree and concatenated phylogeny are highly congruent. Within the Ascomycota, the sub-phyla Pezizomycotina and Saccharomycotina were resolved. Both phylogenies infer that the Leotiomycetes are the closest sister group to the Sordariomycetes. There is some ambiguity regarding the placement of Stagonospora nodurum, the sole member of the class Dothideomycetes present in the dataset. Within the Saccharomycotina, a monophyletic clade containing organisms that translate CTG as serine instead of leucine is evident. There is also strong support for two groups within the CTG clade, one containing the fully sexual species Candida lusitaniae, Candida guilliermondii and Debaryomyces hansenii, and the second group containing Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis and Lodderomyces elongisporus. The second major clade within the Saccharomycotina contains species whose genomes have undergone a whole genome duplication (WGD, and their close

  12. Detection of Infectious Bovine Rhinotracheitis and Bovine Viral Diarrhea Viruses in the Nasal Epithelial Cells by the Direct Immunofluorescence Technique

    OpenAIRE

    Silim, A.; Elazhary, M. A. S. Y.

    1983-01-01

    Nasal epithelial cells were collected by cotton swabs for the diagnosis in experimental and field cases of infectious bovine rhinotracheitis and field cases of bovine viral diarrhea in calves. A portion of the cells was washed twice in phosphate buffered saline and a 25 µL drop was placed on microscope slides. The cells were dried, fixed and stained according to the direct fluorescent antibody technique. Another portion of the same specimen was inoculated onto primary bovine skin cell culture...

  13. Diagnosis and Control of Viral Diseases of Reproductive Importance: Infectious Bovine Rhinotracheitis and Bovine Viral Diarrhea.

    Science.gov (United States)

    Newcomer, Benjamin W; Givens, Daniel

    2016-07-01

    Both bovine viral diarrhea virus and bovine herpesvirus 1 can have significant negative reproductive impacts on cattle health. Vaccination is the primary control method for the viral pathogens in US cattle herds. Polyvalent, modified-live vaccines are recommended to provide optimal protection against various viral field strains. Of particular importance to bovine viral diarrhea control is the limitation of contact of pregnant cattle with potential viral reservoirs during the critical first 125 days of gestation. PMID:27140298

  14. Osseointegration of subperiosteal implants using bovine bone substitute and various membranes

    DEFF Research Database (Denmark)

    Aaboe, Merete; Schou, S.; Hjørting-Hansen, E.; Helbo, M.; Vikjær, D.

    Osseointegration, subperiosteal implant, bone substitute, bovine bone, guided bone, regeneration, histology, rabbits......Osseointegration, subperiosteal implant, bone substitute, bovine bone, guided bone, regeneration, histology, rabbits...

  15. In vitro protective effect of bacteria-derived bovine alpha interferon I1 against selected bovine viruses.

    OpenAIRE

    Gillespie, J H; Robson, D. S.; Scott, F. W.; Schiff, E I

    1985-01-01

    We used bacteria-derived bovine alpha-interferon I1 (Bo IFN-alpha I1) to study its antiviral effect in a bovine turbinate cell line on bovine diarrhea virus, infectious bovine rhinotracheitis virus, parainfluenza 3 virus, and pseudorabies virus. We based our study upon replicate tests for each strain by using a block titration system with various concentrations of Bo IFN-alpha I1 against various concentrations of virus. The data were compiled in two-axis tables (replicate X concentration) and...

  16. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees.

    Science.gov (United States)

    Kenah, Eben; Britton, Tom; Halloran, M Elizabeth; Longini, Ira M

    2016-04-01

    Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

  17. Seroprevalence of Bovine Herpes Virus-1, Bovine Herpes Virus-4 and Bovine Viral Diarrhea Virus in Dairy Cattle in Sudan

    Directory of Open Access Journals (Sweden)

    Amira M. Elhassan*, M.A Fadol and A.M. El-Hussein

    2011-10-01

    Full Text Available A survey was conducted to determine prevalence of antibodies against Bovine herpes virus-1 (BoHv-1, Bovine herpes virus-4 (BoHv-4 and Bovine viral diarrhea (BVD in dairy cattle in farms with reproductive problems in two areas in Sudan. Sera samples were collected from Khartoum state and central Sudan during 2005-2008 and analyzed using direct ELISA. The prevalence of antibodies was discussed with respect to age, season, sex, breed and locality BoHv-1 and BVD antibodies were highly prevalent in Khartoum state (51.7 and 50.4%, respectively while in central Sudan BoHv-1 (32.7% antibodies were the most prevalent followed by, BVD (25.7% and BoHv-4 (19.3%. The highest prevalence of antibodies against the three viruses in both areas was found during the rainy season (July to October. The prevalence of antibodies to viruses studied was significantly associated with female sex except for BoHv-1. Prevalence of antibodies to BoHv-4 was significantly associated with breed while those of BoHv-1 and BVD were not. The present results indicated that older cattle were more likely to be seropositive in case of BoHv-4 but to BoHv-1 or BVD viruses. Furthermore, it was found that BoHv-1 and BVD antibodies were highly prevalent in aborted dams. While, infertility problems were highly associated with BoHv-1 antibodies. BVD antibodies showed the highest prevalence in case of death after birth. The results of this study provide better understanding of viral epidemics of reproductive disorders and represent the first report of BoHv-4 antibodies in cattle in Sudan.

  18. Establishment of bovine prion peptide-based monoclonal antibodies for identifying bovine prion

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    To obtain high titer monoclonal antibodies(McAbs) which can react with mammalian prion protein(PrP),Balb/C mice were immunized with bovine(Bo) PrP peptide(BoPrP 209-228 aa) coupled to keyhole limpet hemocyanin(KLH).The hybridoma cell lines secreting monoclonal antibodies against the peptide were established by cell fusion and cloning.The obtained McAbs were applied to detect recombinant human,bovine and hamster PrP,cellular prion protein(PrPc) in normal bovine brain and pathogenic scrapie prion protein(PrPSc) accumulated in the medulla oblongata of bovine spongiform encephalopathy(BSE)specimen with Western blot and immunohistochemical detection,respectively.The current procedure might offer a simple,feasible method to raise high titer antibodies for studying biological features of PrP in mammals,as well as detection of transmissible spongiform encephalopathy(TSE) and diagnosis of BSE,in particular.

  19. The major bovine mastitis pathogens have different cell tropisms in cultures of bovine mammary gland cells

    NARCIS (Netherlands)

    Lammers, A.; Vorstenbosch, van C.J.; Erkens, J.H.F.; Smith, H.E.

    2001-01-01

    We previously showed that Staphylococcus aureus cells adhered mainly to an elongated cell type, present in cultures of bovine mammary gland cells. Moreover. we showed that this adhesion was mediated by binding to fibronectin. The same in vitro model was used here, to study adhesion of other importan

  20. Characterization of carbohydrate structures of bovine MUC15 and distribution of the mucin in bovine milk

    DEFF Research Database (Denmark)

    Pallesen, Lone Tjener; Pedersen, Lise Refstrup Linnebjerg; Petersen, Torben Ellebæk;

    2007-01-01

    -containing fractions as well, such as skim milk and whey. Compositional and structural studies of the carbohydrates of bovine milk MUC15 showed that the glycans are composed of fucose, galactose, mannose, N-acetylgalactosamine, N-acetylglycosamine, and sialic acid. The carbohydrate was shown to constitute 65% of the...

  1. Prevalence of antibodies to infectious bovine rhinotracheitis, parainfluenza 3, bovine respiratory syncytial, and bovine viral diarrhea viruses in cattle in Saskatchewan and Alberta

    OpenAIRE

    Durham, Peter J.K.; Hassard, Lori E.

    1990-01-01

    A total of 1745 healthy cattle from 295 farms in Saskatchewan and Alberta was tested by ELISA for antibodies to four viruses. Antibodies to infectious bovine rhinotracheitis (IBR) virus were found in 37.8% of sera (59.5% of properties), to parainfluenza 3 (PI3) virus in 93.9% of sera (99.7% of properties), to bovine respiratory syncytial (BRS) virus in 78.5% of sera (86.6% of properties), and to bovine viral diarrhea (BVD) virus in 40.6% of sera (66.7% of properties)

  2. The Solar Thermal Design Assistance Center report of its activities and accomplishments in Fiscal Year 1993

    Energy Technology Data Exchange (ETDEWEB)

    Menicucci, D.F.

    1994-03-01

    The Solar Thermal Design Assistance Center (STDAC) at Sandia National Laboratories is a resource provided by the US Department of Energy`s Solar Thermal Program. Its major objectives are to accelerate the use of solar thermal systems through (a) direct technical assistance to users, (b) cooperative test, evaluation, and development efforts with private industry, and (c) educational outreach activities. This report outlines the major activities and accomplishments of the STDAC in Fiscal Year 1993. The report also contains a comprehensive list of persons who contacted the STDAC by telephone for information or technical consulting.

  3. Recent Accomplishments in the Irradiation Testing of Engineering-Scale Monolithic Fuel Specimens

    Energy Technology Data Exchange (ETDEWEB)

    N.E. Woolstenhulme; D.M. Wachs; M.K. Meyer; H.W. Glunz; R.B. Nielson

    2012-10-01

    The US fuel development team is focused on qualification and demonstration of the uranium-molybdenum monolithic fuel including irradiation testing of engineering-scale specimens. The team has recently accomplished the successful irradiation of the first monolithic multi-plate fuel element assembly within the AFIP-7 campaign. The AFIP-6 MKII campaign, while somewhat truncated by hardware challenges, exhibited successful irradiation of a large-scale monolithic specimen under extreme irradiation conditions. The channel gap and ultrasonic data are presented for AFIP-7 and AFIP-6 MKII, respectively. Finally, design concepts are summarized for future irradiations such as the base fuel demonstration and design demonstration experiment campaigns.

  4. Monitoring quality in Medicaid managed care: Accomplishments and challenges at the year 2000

    OpenAIRE

    Felt-Lisk, Suzanne

    2000-01-01

    This paper reviews the major developments during the late 1990s in quality monitoring for Medicaid managed care and offers an assessment of major challenges faced at the year 2000. We highlight the dramatic increase in activities to ensure and improve quality in Medicaid managed care. Prior to these developments, little was known about the actual level of quality of care. Thus, a major accomplishment of the late 1990s is that we now know more about quality, through some key indicators, and th...

  5. Overview and Recent Accomplishments of Advanced Mirror Technology Development Phase 2 (AMTD-2)

    Science.gov (United States)

    Stahl, H. Philip

    2015-01-01

    AMTD uses a science-driven systems engineering approach to define & execute a long-term strategy to mature technologies necessary to enable future large aperture space telescopes. Because we cannot predict the future, we are pursuing multiple technology paths including monolithic & segmented mirrors. Assembled outstanding team from academia, industry & government; experts in science & space telescope engineering. Derived engineering specifications from science measurement needs & implementation constraints. Maturing 6 critical technologies required to enable 4 to 8 meter UVOIR space telescope mirror assemblies for both general astrophysics & ultra-high contrast exoplanet imaging. AMTD achieving all its goals & accomplishing all its milestones.

  6. Nuclear Thermal Propulsion (NTP) Development Activities at the NASA Marshall Space Flight Center - 2006 Accomplishments

    Science.gov (United States)

    Ballard, Richard O.

    2007-01-01

    In 2005-06, the Prometheus program funded a number of tasks at the NASA-Marshall Space Flight Center (MSFC) to support development of a Nuclear Thermal Propulsion (NTP) system for future manned exploration missions. These tasks include the following: 1. NTP Design Develop Test & Evaluate (DDT&E) Planning 2. NTP Mission & Systems Analysis / Stage Concepts & Engine Requirements 3. NTP Engine System Trade Space Analysis and Studies 4. NTP Engine Ground Test Facility Assessment 5. Non-Nuclear Environmental Simulator (NTREES) 6. Non-Nuclear Materials Fabrication & Evaluation 7. Multi-Physics TCA Modeling. This presentation is a overview of these tasks and their accomplishments

  7. Comparative molecular analysis of ovine and bovine Streptococcus uberis isolates.

    Science.gov (United States)

    Gilchrist, T L; Smith, D G E; Fitzpatrick, J L; Zadoks, R N; Fontaine, M C

    2013-02-01

    Streptococcus uberis causes clinical and subclinical mastitis in cattle and sheep, but it is unknown whether the composition of Strep. uberis populations differs between host species. To address this, we characterized a collection of bovine and ovine Strep. uberis isolates with shared geographical and temporal origins by means of an expanded multilocus sequence typing scheme. Among 14 ovine and 35 bovine isolates, 35 allelic profiles were detected. Each allelic profile was associated with a single host species and all but one were new to the multilocus sequence typing database. The median number of new alleles per isolate was higher for ovine isolates than for bovine isolates. None of the ovine isolates belonged to the global clonal complexes 5 or 143, which are commonly associated with bovine mastitis and which have a wide geographical distribution. Ovine isolates also differed from bovine isolates in carriage of plasminogen activator genes, with significantly higher prevalence of pauB in ovine isolates. Isolates that were negative for yqiL, one of the targets of multilocus sequence typing, were found among ovine and bovine isolates and were not associated with a specific sequence type or global clonal complex. One bovine isolate carried a gapC allele that was probably acquired through lateral gene transfer, most likely from Streptococcus salivarius. We conclude that ovine isolates are distinct from bovine isolates of Strep. uberis, and that recombination between isolates from different host species or bacterial species could contribute to changes in virulence gene profiles with relevance for vaccine development. PMID:23200465

  8. 76 FR 38602 - Bovine Tuberculosis and Brucellosis; Program Framework

    Science.gov (United States)

    2011-07-01

    ... Animal and Plant Health Inspection Service Bovine Tuberculosis and Brucellosis; Program Framework AGENCY... extending the comment period on a new framework being developed for the bovine tuberculosis and brucellosis...-5256. SUPPLEMENTARY INFORMATION: On May 6, 2011, we published in the Federal Register (76 FR...

  9. 76 FR 26239 - Bovine Tuberculosis and Brucellosis; Public Meetings

    Science.gov (United States)

    2011-05-06

    ...; ] DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service Bovine Tuberculosis and Brucellosis... framework being developed for the bovine tuberculosis and brucellosis programs in the United States. The.... Department of Agriculture (USDA) is currently developing proposed revisions to its programs regarding...

  10. Structure and Function of Bovine and Camel Chymosin

    DEFF Research Database (Denmark)

    Jensen, Jesper Langholm

    complexes of bovine chymosin, human pepsin, and endothiapepsin with the inhibitor pepstatin were examined to explain pepstatin’s lower affinity towards bovine chymosin. Human pepsin has a loop insert and a more hydrophobic binding cleft leading to a larger interaction surface with the hydrophobic pepstatin...

  11. In vitro production of bovine embryos

    DEFF Research Database (Denmark)

    Stroebech, L.; Mazzoni, Gianluca; Pedersen, Hanne Skovsgaard;

    2015-01-01

    In vitro production (IVP) of bovine embryos has become a widespread technology implemented in cattle breeding and production. The implementation of genomic selection and systems biology adds great dimensions to the impact of bovine IVP. The physical procedures included in the IVP process can still...

  12. Prevalence, transmission and impact of bovine leukosis in Michigan dairies

    Science.gov (United States)

    Bovine leukosis, caused by infection with the retrovirus bovine leukemia virus (BLV), has been characterized as a contagious, but practically benign disease of the immune system. National Animal Health Monitoring Surveys in 1996 and 2007 indicate complacency has resulted in high prevalence of infect...

  13. Bovine viral diarrhea virus modulations of monocyte derived macrophages

    Science.gov (United States)

    Bovine viral diarrhea virus (BVDV) is a single stranded, positive sense RNA virus and is the causative agent of bovine viral diarrhea (BVD). Disease can range from persistently infected (PI) animals displaying no clinical symptoms of disease to an acute, severe disease. Presently, limited studies ha...

  14. Comparison of levels and duration of detection of antibodies to bovine viral diarrhea virus 1, bovine viral diarrhea virus 2, bovine respiratory syncytial virus, bovine herpesvirus 1, and bovine parainfluenza virus 3 in calves fed maternal colostrum or a colostrum-replacement product

    OpenAIRE

    Chamorro, Manuel F; Walz, Paul H.; Haines, Deborah M.; Passler, Thomas; Earleywine, Thomas; Palomares, Roberto A.; Riddell, Kay P; Galik, Patricia; Zhang, Yijing; Givens, M. Daniel

    2014-01-01

    Colostrum-replacement products are an alternative to provide passive immunity to neonatal calves; however, their ability to provide adequate levels of antibodies recognizing respiratory viruses has not been described. The objective of this study was to compare the serum levels of IgG at 2 d of age and the duration of detection of antibodies to bovine viral diarrhea virus 1 (BVDV-1), bovine viral diarrhea virus 2 (BVDV-2), bovine respiratory syncytial virus (BRSV), bovine herpesvirus 1 (BHV-1)...

  15. Phylogeny of species and cytotypes of mole rats (Spalacidae) in Turkey inferred from mitochondrial cytochrome b gene sequencees

    Czech Academy of Sciences Publication Activity Database

    Kandemir, I.; Sozen, M.; Matur, F.; Kankilic, T.; Martínková, Natália; Colak, F.; Ozkurt, S. O.; Colak, E.

    2012-01-01

    Roč. 61, č. 1 (2012), s. 25-33. ISSN 0139-7893 Institutional support: RVO:68081766 Keywords : Nannospalax * molecular phylogeny * chromosomal form * Anatolia * Thrace Subject RIV: EG - Zoology Impact factor: 0.494, year: 2012

  16. Transcriptional organization of bovine papillomavirus type 1.

    Science.gov (United States)

    Engel, L W; Heilman, C A; Howley, P M

    1983-09-01

    Multiple bovine papillomavirus type 1 (BPV-1)-specific polyadenylated RNA species in a BPV-1-infected bovine fibropapilloma were identified and mapped. All of the RNA species were transcribed from the same DNA strand of the BPV-1 genome. Five RNA species previously identified in BPV-1-transformed mouse cells were also present in the bovine fibropapilloma. These five species measured 1,050, 1,150, 1,700, 3,800, and 4,050 bases, mapped within the 69% transforming segment of the BPV-1 genome, and shared a 3' coterminus at 0.53 map units (m.u.). The 5' ends of the bodies of these distinct transcripts were located at ca. 0.03, 0.09, 0.34, 0.39, and 0.41 m.u. Additional polyadenylated RNA species not present in BPV-1-transformed mouse cells were specific for the BPV-1-infected bovine fibropapilloma and measured 1,700, 3,700, 3,800, 6,700, and 8,000 bases. These wart-specific species shared a 3' coterminus at 0.90 m.u. The 5' termini of the bodies of the 1,700- and 3,800-base species mapped at 0.71 and 0.42 m.u., respectively. Exonuclease VII analysis failed to reveal any internal splicing in these two species; however, the presence of small remote 5' leader sequences could not be ruled out. The 3,700-base species hybridized to DNA fragments from the 69% transforming segment as well as from the 31% nontransforming segment of the BPV-1 genome; however, this species was not precisely mapped. The 5' termini of the two largest RNA species (6,700 and 8,000 bases in size) were located at ca. 0.01 and 0.90 m.u., respectively. Since the 5' ends of these mapped adjacent to a TATAAA sequence which could possibly serve as an element of a transcriptional promoter, it is possible that one or both of these species represent nonspliced precursor RNA molecules. PMID:6137574

  17. Aggregation and fibrillation of bovine serum albumin

    DEFF Research Database (Denmark)

    Holm, NK; Jespersen, SK; Thomassen, LV;

    2007-01-01

    The all-alpha helix multi-domain protein bovine serum albumin (BSA) aggregates at elevated temperatures. Here we show that these thermal aggregates have amyloid properties. They bind the fibril-specific dyes Thioflavin T and Congo Red, show elongated although somewhat worm-like morphology and...... characteristic amyloid X-ray fiber diffraction peaks. Fibrillation occurs over minutes to hours without a lag phase, is independent of seeding and shows only moderate concentration dependence, suggesting intramolecular aggregation nuclei. Nevertheless, multi-exponential increases in dye-binding signal and...

  18. Bovine Spongiform Encephalopathy (BSE, Mad Cow Disease

    Directory of Open Access Journals (Sweden)

    G. K. Bruckner

    1997-07-01

    Full Text Available Mad Cow Disease or BSE (Bovine Spongiform Encephalopathy became a household name internationally and also in South Africa. International hysteria resulted following reports of a possible link between a disease diagnosed in cattle in Britain and a variant of the disease diagnosed in humans after the presumed ingestion or contact with meat from infected cattle. The European Union instituted a ban on the importation of beef from the United Kingdom during March 1996 that had a severe effect on the beef industry in the UK and also resulted in a world wide consumer resistance against beef consumption.

  19. Characterization of bovine viral diarrhea virus proteins.

    OpenAIRE

    Purchio, A F; Larson, R.; Collett, M S

    1984-01-01

    Virus-specific proteins were examined in cultured cells infected with bovine viral diarrhea virus. By using antisera obtained from virus-infected animals, three major virus-specific polypeptides with molecular weights of 115,000 (115K), 80K, and 55K were observed. Minor proteins of 45,000 and 38,000 daltons were also noted. Tryptic peptide mapping indicated that the 115K and the 80K polypeptides were structurally related. The 55K protein was glycosylated and appeared not to be related to the ...

  20. Extrachromosomal nucleic acids in bovine babesia

    Directory of Open Access Journals (Sweden)

    Isidro Hotzel

    1992-01-01

    Full Text Available Two kinds of small extrachromosomal nucleic acid elements were found in the bovine babesias, Babesia bovis and B. bigemina. One element with an apparent size of 5.5 kilobase pairs (kbp is a double stranded RNA related to virus like particles. Another molecule is a double stranded DNA with a molecular size of about 6.2 kbp. Southern blot comparison of restriction DNA fragments of the latter molecule, which is present in both B. bovis and B. bigemina is described.

  1. Bovine respiratory syncytial virus (BRSV): A review

    DEFF Research Database (Denmark)

    Larsen, Lars Erik

    2000-01-01

    Bovine respiratory syncytial virus (BRSV) infection is the major cause of respiratory disease in calves during the first year of life. The study of the virus has been difficult because of its lability and very poor growth in cell culture. However, during the last decade, the introduction of new...... complex and unpredictable which makes the diagnosis and subsequent therapy very difficult. BRSV is closely related to human respiratory syncytial virus (HRSV) which is an important cause of respiratory disease in young children. In contrast to BRSV, the recent knowledge of HRSV is regularly extensively...

  2. Interaction of Nicotine and Bovine Serum Albumin

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The binding of nicotine to bovine serum albumin (BSA) was studied by UV absorption, fluorescence, and 1H NMR methods. With the addition of nicotine, the absorption band of BSA at about 210 nm decreased gradually, moved to longer wavelengths, and narrowed. BSA fluorescence of tryptophan residue was quenched by nicotine. The 1H NMR peaks of nicotine moved to downfield by the addition of BSA. The experimental results showed that nicotine was capable of binding with BSA to form a 1:1 complex. BSA's high selectivity for nicotine binding suggests a unique role for this protein in the detoxification and/or transport of nicotine.

  3. When Bioelectrochemical Systems Meet Forward Osmosis: Accomplishing Wastewater Treatment and Reuse through Synergy

    Directory of Open Access Journals (Sweden)

    Yaobin Lu

    2014-12-01

    Full Text Available Bioelectrochemical systems (BES and forward osmosis (FO are two emerging technologies with great potential for energy-efficient water/wastewater treatment. BES takes advantage of microbial interaction with a solid electron acceptor/donor to accomplish bioenergy recovery from organic compounds, and FO can extract high-quality water driven by an osmotic pressure. The strong synergy between those two technologies may complement each other and collaboratively address water-energy nexus. FO can assist BES with achieving water recovery (for future reuse, enhancing electricity generation, and supplying energy for accomplishing the cathode reactions; while BES may help FO with degrading organic contaminants, providing sustainable draw solute, and stabilizing water flux. This work has reviewed the recent development that focuses on the synergy between BES and FO, analyzed the advantages of each combination, and provided perspectives for future research. The findings encourage further investigation and development for efficient coordination between BES and FO towards an integrated system for wastewater treatment and reuse.

  4. Characterization of Prototheca zopfii Genotypes Isolated from Cases of Bovine Mastitis and Cow Barns in China.

    Science.gov (United States)

    Shahid, Muhammad; Ali, Tariq; Zhang, Limei; Hou, Rongguang; Zhang, Shiyao; Ding, Laidi; Han, Dandan; Deng, Zhaoju; Rahman, Abdur; Han, Bo

    2016-04-01

    Protothecal mastitis, caused mostly by Prototheca zopfii (P. zopfii), is increasing in dairy herds and is being reported globally. The present study was aimed at studying the epidemiology of mastitis and at molecular characterization of P. zopfii isolates from dairy herds and their surroundings in three provinces of China using microbiological, biochemical and molecular methods, and antibiotic susceptibility tests. Samples from milk (n = 620) of mastitic cows and their barns sources (n = 410) including feces, feed, bedding materials and drinking water were analyzed. Among other pathogens recovered from mastitic milk, 84 (13.5 %) of the isolates were identified as P. zopfii. All of the P. zopfii isolates recovered from milk were recognized as genotype 2, whereas 58 (73.4 %) and 21 (26.6 %) isolates from environmental sources were found to be P. zopfii genotypes 1 and 2, respectively. The isolates were susceptible to some antibiotics and antifungal agents, including amikacin (78.1 %), streptomycin (58.5 %), gentamicin (17.8 %), amphotericin B (68.6 %) and nystatin (64.4 %). Additionally, the two genotypes displayed versatile patterns of susceptibility to different antimicrobials agents. Phylogeny of the genotypes on the basis of 18S SSU rDNA and 28S SSU rDNA was also investigated. The isolates of the two genotypes separated into different clades, and no interrelationship was observed among these as shown by phylogenetic analysis. The genotype 1 isolates from cow barn sources were non-pathogenic and may not present any risk of mastitis. We conclude that P. zopfii genotype 2 might play an important role in bovine mastitis in China. PMID:26450620

  5. Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution

    Directory of Open Access Journals (Sweden)

    Sommer Ralf J

    2009-08-01

    Full Text Available Abstract Background Nematodes are putatively the most species-rich animal phylum. They have various life styles and occur in a variety of habitats, ranging from free-living nematodes in aquatic or terrestrial environments to parasites of animals and plants. The rhabditid nematode Caenorhabditis elegans is one of the most important model organisms in modern biology. Pristionchus pacificus of the family of the Diplogastridae has been developed as a satellite model for comparison to C. elegans. The Diplogastridae, a monophyletic clade within the rhabditid nematodes, are frequently associated with beetles. How this beetle-association evolved and whether beetle-nematode coevolution occurred is still elusive. As a prerequisite to answering this question a robust phylogeny of beetle-associated Diplogastridae is needed. Results Sequences for the nuclear small subunit ribosomal RNA and for 12 ribosomal protein encoding nucleotide sequences were collected for 14 diplogastrid taxa yielding a dataset of 5996 bp of concatenated aligned sequences. A molecular phylogeny of beetle-associated diplogastrid nematodes was established by various algorithms. Robust subclades could be demonstrated embedded in a phylogenetic tree topology with short internal branches, indicating rapid ancestral divergences. Comparison of the diplogastrid phylogeny to a comprehensive beetle phylogeny revealed no major congruence and thus no evidence for a long-term coevolution. Conclusion Reconstruction of the phylogenetic history of beetle-associated Diplogastridae yields four distinct subclades, whose deep phylogenetic divergence, as indicated by short internal branch lengths, shows evidence for evolution by successions of ancient rapid radiation events. The stem species of the Diplogastridae existed at the same time period when the major radiations of the beetles occurred. Comparison of nematode and beetle phylogenies provides, however, no evidence for long-term coevolution of

  6. Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences.

    OpenAIRE

    Black, W C; Piesman, J

    1994-01-01

    Ticks are parasitiform mites that are obligate hematophagous ectoparasites of amphibians, reptiles, birds, and mammals. A phylogeny for tick families, subfamilies, and genera has been described based on morphological characters, life histories, and host associations. To test the existing phylogeny, we sequenced approximately 460 bp from the 3' end of the mitochondrial 16S rRNA gene (rDNA) in 36 hard- and soft-tick species; a mesostigmatid mite, Dermanyssus gallinae, was used as an outgroup. P...

  7. Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa

    OpenAIRE

    Jang Kuem; Hwang Ui

    2009-01-01

    Abstract Background The phylogenetic position of Bryozoa is one of the most controversial issues in metazoan phylogeny. In an attempt to address this issue, the first bryozoan mitochondrial genome from Flustrellidra hispida (Gymnolaemata, Ctenostomata) was recently sequenced and characterized. Unfortunately, it has extensive gene translocation and extremely reduced size. In addition, the phylogenies obtained from the result were conflicting, so they failed to assign a reliable phylogenetic po...

  8. Studies in phylogeny and biosystematics of bees: The bee genus Andrena (Andrenidae) and the tribe Anthophorini (Apidae) (Insecta: Hymenoptera: Apoidea)

    OpenAIRE

    Dubitzky, Andreas

    2006-01-01

    Zusammenfassung In der vorliegenden Arbeit wurde die Phylogenie der kurzzungigen Bienengattung Andrena, sowie die der langzungigen Bienentribus Anthophorini unter besonderer Berücksichtigung der Gattung Habropoda untersucht. Mit ca. 1500 gültig beschriebenen Arten weltweit stellt die holarktische Bienengattung Andrena (Sandbienen) die größte Bienengattung überhaupt dar. Die Phylogenie dieser Gattung ist bislang nur unzureichend erforscht worden. So beschränkten sich frühere Untersuchun...

  9. Detection of bovine herpesvirus 4 glycoprotein B and thymidine kinase DNA by PCR assays in bovine milk

    NARCIS (Netherlands)

    Wellenberg, G.J.; Verstraten, E.; Belak, S.; Verschuren, S.B.E.; Rijsewijk, F.A.M.; Peshev, R.; Oirschot, van J.T.

    2001-01-01

    A polymerase chain reaction (PCR) assay was developed to detect bovine herpesvirus 4 (BHV4) glycoprotein B (gB) DNA, and a nested-PCR assay was modified for the detection of BHV4 thymidine kinase (TK) DNA in bovine milk samples. To identify false-negative PCR results, internal control templates were

  10. Copy number variation in the bovine genome

    Directory of Open Access Journals (Sweden)

    Bendixen Christian

    2010-05-01

    Full Text Available Abstract Background Copy number variations (CNVs, which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease. Notwithstanding, little is known about the extent to which CNV contributes to genetic variation in cattle. Results We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb. About 20% of the CNVs co-localized with segmental duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences. Conclusions Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.

  11. Affinity purification of aprotinin from bovine lung.

    Science.gov (United States)

    Xin, Yu; Liu, Lanhua; Chen, Beizhan; Zhang, Ling; Tong, Yanjun

    2015-05-01

    An affinity protocol for the purification of aprotinin from bovine lung was developed. To simulate the structure of sucrose octasulfate, a natural specific probe for aprotinin, the affinity ligand was composed of an acidic head and a hydrophobic stick, and was then linked with Sepharose. The sorbent was then subjected to adsorption analysis with pure aprotinin. The purification process consisted of one step of affinity chromatography and another step of ultrafiltration. Then purified aprotinin was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, trypsin inhibitor activity, gel-filtration, and thin-layer chromatography analysis. As calculated, the theoretical maximum adsorption (Qmax ) of the affinity sorbent was 25,476.0 ± 184.8 kallikrein inactivator unit/g wet gel; the dissociation constant of the complex "immobilized ligand-aprotinin" (Kd ) was 4.6 ± 0.1 kallikrein inactivator unit/mL. After the affinity separation of bovine lung aprotinin, reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis and gel-filtration chromatography revealed that the protein was a single polypeptide, and the purities were ∼ 97 and 100%, respectively; the purified peptide was also confirmed with aprotinin standard by gel-filtration chromatography and thin-layer chromatography. After the whole purification process, protein, and bioactivity recoveries were 2.2 and 92.6%, respectively; and the specific activity was up to 15,907.1 ± 10.2 kallikrein inactivator unit/mg. PMID:25677462

  12. Antitumor action of bovine seminal ribonuclease

    International Nuclear Information System (INIS)

    Unlike the bovine pancreatic ribonuclease (RNase A), bovine seminal ribonuclease (BS RNase) displays various biological activities; including antitumor activity, immunosuppressivity, spermatogenicity and embryo-toxicity. To learn more about its antitumor effect we tested BS RNase on the growth of 16 cell lines derived from patients with various hematological malignancies. The cells of lymphoid origin were generally more susceptible to BS RNase, administered in the range of concentrations from 2 to 100 μg/ml, than the myeloid ones. RNase A used at the same concentrations did not exert any inhibitory effect. The inhibitory effect of BS RNase persisted in cultured cells three times wash in complete medium and cell re-cultivation in fresh medium free of BS RNase. Four cell lines were very little sensitive (KG-1 and U-937) or resistant (JOK and NAMALWA) to BS RNase regardless of their origin. The in vivo antitumor effect of BS RNase was tested on human prostate carcinoma transplanted to athymic nude mice. The daily dose of BS RNase (0.25 mg/20 g) was administered for three weeks except weekends (15 doses) by three different ways (intraperitoneally - i.p., subcutaneously - s.c. and intratumorally - i.t.). Whereas i.p. administration was ineffective, s.c. administration significantly reduced size of the tumors and i.t. administration abolished half of the tumors in treated mice. The average of treated mice decreased during the experiment by 10-15%. (author)

  13. Human exposure to bovine polyomavirus: a zoonosis

    Energy Technology Data Exchange (ETDEWEB)

    Parry, J.V.; Gardner, S.D.

    1986-01-01

    A competitive-type solid phase radioimmunoassay (RIA) was developed for the detection of antibody to bovine polyomavirus. Comparison of RIA and counter-immunoelectrophoresis (CIE) results on 273 cattle sera indicated that both techniques were detecting antibody of like specificity. Human sera from 256 blood donors, 219 people recently vaccinated against polio, rubella or rabies, 50 immunosuppressed patients and 472 people with various occupational exposure to cattle were tested for antibody to bovine polyomavirus, the foetal rhesus monkey kidney strain, (anti-FRKV) by RIA. Apart from one blood donor and one of 108 rabies vaccinees only those in close contact with cattle possessed anti-FRKV. Compared with 62 per cent seropositive in the natural hosts, cattle, 71 per cent of veterinary surgeons, 50 per cent of cattle farmers, 40 per cent of abattoir workers, 16 per cent of veterinary institute technical staff and 10 per cent of veterinary students were anti-FRKV positive. Our findings indicate that the theoretical hazard of FRKV infection from undetected contamination of current tissue culture derived vaccines may, in practice, be remote. Proposed wider use of primate kidney cells as substrates for new vaccines may increase this risk.

  14. Tensile strength of bovine trabecular bone.

    Science.gov (United States)

    Kaplan, S J; Hayes, W C; Stone, J L; Beaupré, G S

    1985-01-01

    Data on the tensile and compressive properties of trabecular bone are needed to define input parameters and failure criteria for modeling total joint replacements. To help resolve differences in reports comparing tensile and compressive properties of trabecular bone, we have developed new methods, based on porous foam technology, for tensile testing of fresh/frozen trabecular bone specimens. Using bovine trabecular bone from an isotropic region from the proximal humerus as a model material, we measured ultimate strengths in tension and compression for two groups of 24 specimens each. The average ultimate strength in tension was 7.6 +/- 2.2 (95% C.I.) MPa and in compression was 12.4 +/- 3.2 MPa. This difference was statistically significant (p = 0.013) and was not related to density differences between the test groups (p = 0.28). Strength was related by a power-law function of the local apparent density, but, even accounting for density influences, isotropic bovine trabecular bone exhibits significantly lower strengths in tension than in compression. PMID:4077868

  15. Antihelmintic Resistance For Gastrointestinal Bovine Nematodes

    Directory of Open Access Journals (Sweden)

    Patricia Torres Vásquez

    2007-06-01

    Full Text Available The gastrointestinal nematodes (GIN, in domestic animals, especially in bovines are a very important factor that affects their productivity, because cattle production systems have intervened in the relationship between gastrointestinal parasites (PGI and the host, breaking therefore the ecological balance between them. In many opportunities the development of parasitic populations have been favored or a parasitic population have been led to extinction, it has made that these populations express genes that would not express under normal conditions, favoring thus, resistance to medications that were made to their destruction. NGI are highly important in all cattle exploitations, but their inappropriate handling, mainly in the pharmacological aspect, has created vermifuge resistance by some parasitic populations. This article will determine the importance of the vermifuge resistance in cattle exploitations, as a factor of risk for the control of parasitic populations. The most important antihelmintic groups used in bovine are Benzimidazoles, Levamisol and Ivermectine and with these products resistance has been reported by parasitic populations such as in Haemochus contortus, Trichostrongylus. colubriformis, Ostertagia circumcicta, Ostertagia ostertagi. Different risk factors were classified in extrinsic (which don’t depend on the gastrointestinal parasite and intrinsic (which depend directly on gastrointestinal parasites related with genetics which occupy a great importance in the development of the vermifuge resistance.

  16. [Serological study of bovine leptospirosis in Mexico].

    Science.gov (United States)

    Moles Cervantes, Luis Pedro; Cisneros Puebla, Miguel Angel; Rosas, Dolores Gavaldón; Serranía, Nora Rojas; Torres Barranca, Jorge Isaac

    2002-01-01

    The results of 4 043 bovine sera samples from various Mexican regions, which were sent to a diagnosis lab, were analyzed. The method was the agglutination technique, taking the dilution rate 1:1000 or higher as positive. The analysis revealed 31,1% of seroprevalence and the most frequent serovarietes were hardjo (strain H 89 isolated in Mexico), wolffi and tarassovi. There is coincidence with early data obtained in Mexico on a 34% of prevalence found in a similar study performed in 1994, and with the scientific literature from other countries. The former study also indicated that tarassovi and wolffi were the most common leptospira, so there is coincidence with the figures in the reviewed literature. It was concluded that there was no significant variation in the prevalence rate between the 1994 study and the present one; therefore, it is recommended that this study be promoted so as to increase the bovine vaccination and achieve a reduction in leptospirosis in Mexico. PMID:15846936

  17. Identification of Prototheca Zopfii from Bovine Mastitis

    Directory of Open Access Journals (Sweden)

    F Zaini

    2012-08-01

    Full Text Available Background: The aim of this study was identification of the epidemiology of Prototheca zopfii species from the milk samples of dairy cattle in Isfahan, central Iran.Methods: Milk samples were obtained from 230 dairy cattle, 130 with and 100 without mastitis, in Isfahan. The samples were cultured in Prototheca Isolation Medium (PIM and Sabouraud's dextrose agar. All P. zopfii isolates were identified by morphological and biochemical methods. Then, as a confirmatory test they were examined by genotype-specific PCR.Results: Four P. zopfii strains (3.07% were isolated from the 130 samples of dairy cattle with clinical mastitis and there was no isolation from totally 100 samples of healthy bovines without mastitis. Specific PCR product (about 946 bp was detected in four isolates.Conclusion: It seems that P. zopfii genotype II plays a key role in affecting bovine mastitis that confirmed other previous studies. Our study was the first, which identified the Prototheca species by traditional and molecular methods in Iran and Middle East as well.

  18. International Research Results and Accomplishments From the International Space Station - A New Compilation

    Science.gov (United States)

    Ruttley, Tara; Robinson, Julie A.; Tate-Brown, Judy; Perkins, Nekisha; Cohen, Luchino; Marcil, Isabelle; Heppener, Marc; Hatton, Jason; Tasaki, Kazuyuki; Umemura, Sayaka; Karabadzhak, Georgy; Sorokin, Igor V.; Cotronei, Vittorio; Jean, Sabbagh

    2016-01-01

    In 2016, the International Space Station (ISS) partnership published the first-ever compilation of international ISS research publications resulting from research performed on the ISS through 2011 (Expeditions 0 through 30). International Space Station Research Accomplishments: An Analysis of Results. From 2000-2011 is a collection of over 1,200 journal publications that describe ISS research in the areas of biology and biotechnology; Earth and space science; educational activities and outreach; human research; physical sciences; technology development and demonstration; and, results from ISS operations. This paper will summarize the ISS results publications obtained through 2011 on behalf of the ISS Program Science Forum that is made up of senior science representatives across the international partnership. NASA's ISS Program Science office maintains an online experiment database (www.nasa.gov/iss- science) that tracks and communicates ISS research activities across the entire ISS partnership, and it is continuously updated by cooperation and linking with the results tracking activities of each partner. It captures ISS experiment summaries and results and includes citations to the journals, conference proceedings, and patents as they become available. This content is obtained through extensive and regular journal and patent database searches, and input provided by the ISS international partners ISS scientists themselves. The International Space Station Research Accomplishments: An Analysis of Results From 2000-2011 is a testament to the research that was underway even as the ISS laboratory was being built. It rejects the scientific knowledge gained from ISS research, and how it impact the fields of science in both space and traditional science disciplines on Earth. Now, during a time when utilization is at its busiest, and with extension of the ISS through at least 2024, the ISS partners work together to track the accomplishments and the new knowledge gained in a

  19. 9 CFR 113.215 - Bovine Virus Diarrhea Vaccine, Killed Virus.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Virus Diarrhea Vaccine, Killed... REQUIREMENTS Killed Virus Vaccines § 113.215 Bovine Virus Diarrhea Vaccine, Killed Virus. Bovine Virus Diarrhea... paragraph. (i) Eight bovine virus diarrhea susceptible calves (five vaccinates and three controls) shall...

  20. Phylogeny and resistance profiles of HIV-1 POL sequences from rectal biopsies and blood

    DEFF Research Database (Denmark)

    Katzenstein, Terese Lea; Petersen, A B; Storgaard, M;

    2010-01-01

    The phylogeny and resistance profiles of human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) sequences were compared among six patients with HIV-1 who had received numerous treatments. RNA and DNA fractions were obtained from concurrent blood and rectal biopsy...... acquired during earlier treatment regimens were detected in the sequences obtained from the rectal samples and in the PBMCs in several of the patients. Also, differences in the resistance profiles were observed between anatomical sites and between RNA and DNA fractions. Thus, a single sample probably will...... not be representative of the HIV-1 archived in different sites. Both the resistance profile and phylogeny of HIV-1 often differed in sequences obtained from RNA and DNA from the same site. These findings suggest that additional information regarding the antiviral resistance profile of the patient...

  1. Molecular phylogeny and evidence for an adaptive radiation of geophagine cichlids from South America (Perciformes: Labroidei).

    Science.gov (United States)

    López-Fernández, Hernán; Honeycutt, Rodney L; Winemiller, Kirk O

    2005-01-01

    Nucleotide sequences from the mitochondrial ND4 gene and the nuclear RAG2 gene were used to derive the most extensive molecular phylogeny to date for the Neotropical cichlid subfamily Geophaginae. Previous hypotheses of relationships were tested in light of these new data and a synthesis of all existing molecular information was provided. Novel phylogenetic findings included support for : (1) a 'Big Clade' containing the genera Geophagus sensu lato, Gymnogeophagus, Mikrogeophagus, Biotodoma, Crenicara, and Dicrossus; (2) a clade including the genera Satanoperca, Apistogramma, Apistogrammoides, and Taeniacara; and (3) corroboration for Kullander's clade Acarichthyini. ND4 demonstrated saturation effects at the third code position and lineage-specific rate heterogeneity, both of which influenced phylogeny reconstruction when only equal weighted parsimony was employed. Both branch lengths and internal branch tests revealed extremely short basal nodes that add support to the idea that geophagine cichlids have experienced an adaptive radiation sensu Schluter that involved ecomorphological specializations and life history diversification. PMID:15579395

  2. Molecular biological analysis of genotyping and phylogeny of severe acute respiratory syndrome associated coronavirus

    Institute of Scientific and Technical Information of China (English)

    王志刚; 李兰娟; 罗芸; 张俊彦; 王敏雅; 程苏云; 张严峻; 王晓萌; 卢亦愚; 吴南屏; 梅玲玲; 王赞信

    2004-01-01

    Background SARS-CoV is the causative agent of severe acute respiratory syndrome (SARS) which has been associated with outbreaks of SARS in Guangdong, Hong Kong and Beijing of China, and other regions worldwide. SARS-CoV from human has shown some variations but its origin is still unknown. The genotyping and phylogeny of SARS-CoV were analyzed and reported in this paper. Methods Full or partial genomes of 44 SARS-CoV strains were collected from GenBank. The genotype, single nucleotide polymorphism and phylogeny of these SARS-CoV strains were analyzed by molecular biological, bioinformatic and epidemiological methods. Conclusion The results mentioned above suggest that SARS-CoV is responding to host immunological pressures and experiencing variation which provide clues, information and evidence of molecular biology for the clinical pathology, vaccine developing and epidemic investigation.

  3. Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

    Science.gov (United States)

    Dumbacher, J.P.; Pratt, T.K.; Fleischer, R.C.

    2003-01-01

    The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper. ?? 2003 Elsevier Science (USA). All rights reserved.

  4. Phylogeny of cooperatively breeding cuckoos (Cuculidae, Crotophaginae) based on mitochondrial gene sequences

    Science.gov (United States)

    Hughes, Janice M.

    2003-05-01

    The Crotophaginae is a subfamily of New World cuckoos comprising the monotypic genus Guira and three ani species ( Crotophaga). All exhibit a rare form of cooperative breeding known as plural female joint-nesting, whereby two or more females lay eggs in a single nest. I reconstructed the phylogeny of Crotophaginae using the mitochondrial genes cytochrome oxidase I, II, and III, ATPase 6 and 8, and cytochrome b. The subfamily was monophyletic, implying a single origin of cooperative breeding in New World cuckoos. Crotophaga was also monophyletic with Guira as its sister taxon. Within Crotophaga, the smooth-billed ( C. ani) and groove-billed ( C. sulcirostris) anis formed the internal clade with the greater ani ( C. major) basal to this pair. This phylogeny is consistent with differences in reproductive patterns and social organization exhibited by crotophagine cuckoos, and will serve as a framework for future study of the evolution of cooperative breeding in this subfamily.

  5. Thuniopsis: A New Orchid Genus and Phylogeny of the Tribe Arethuseae (Orchidaceae.

    Directory of Open Access Journals (Sweden)

    Lin Li

    Full Text Available An investigation of a questionable orchid led to the discovery of a new genus and species Thuniopsis cleistogama, endemic to Yunnan province, China. It is characterized by having a subglobose corm, a spike-like (racemose inflorescence, half opened and spurless flowers, a collar-shaped stigma and subglobose capsules. Based on DNA sequence data from three gene regions (nuclear ribosomal ITS, chloroplast matK and trnL, we investigated its phylogenetic position within the tribe Arethuseae. Phylogenies using maximum likelihood and Bayesian inference support the recognition of Thuniopsis as a distinct genus, and suggest its close relationship to the genera Bletilla, Dilochia, and Thunia. The new genus is circumscribed and a description and illustrations of the new species are provided. The phylogenetic relationships among the genera in Arethuseae are accessed. Moreover, our phylogeny also shed light on the phylogenetic positions of several genera which, to date, remain uncertain.

  6. Tracing phylogeny through proteins of the layers of the eye lens nucleus.

    Science.gov (United States)

    Smith, A C

    1982-01-01

    1. In accordance with the concept that ontogeny recapitulates phylogeny, it was hypothesized that the proteins in the eye lens nucleus increase in antiquity with depth of layer and so can be used to reconstruct the phylogenetic past. 2. This hypothesis was tested by analyzing electrophoretic patterns of proteins from solubilized nuclear lens layers of three tuna species with well-studied phylogenies. The tuna species are the albacore, Thunnus alalunga; yellowfin, T. albacares; and skipjack, Katsuwonus pelamis. 3. The electrophoretic patterns fitted a scheme that is in agreement with major phylogenetic beliefs about these species. Additionally, the patterns seemed to indicate that (a) the skipjack diverged later (although to a lesser degree) from a common ancestor than did the other two tuna species, and (b) the albacore is more closely related to the skipjack than is the yellowfin. 4. It is concluded that electrophoretic analysis of proteins from nuclear lens layers is a promising new tool for tracing phylogenetic relationships. PMID:7083823

  7. A molecular phylogeny of Hypnales (Bryophyta inferred from ITS2 sequence-structure data

    Directory of Open Access Journals (Sweden)

    Wolf Matthias

    2010-11-01

    Full Text Available Abstract Background Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2 sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously. Findings We built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs. Conclusions Profile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes.

  8. Advanced Mirror Technology Development (AMTD) Project: Overview and Year 4 Accomplishments

    Science.gov (United States)

    Stahl, H. Philip

    2016-01-01

    The Advanced Mirror Technology Development (AMTD) project is in Phase 2 of a multiyear effort initiated in Fiscal Year (FY) 2012, to mature toward the next Technology Readiness Level (TRL) critical technologies required to enable 4-m-or-larger monolithic or segmented ultraviolet, optical, and infrared (UVOIR) space telescope primary-mirror assemblies for general astrophysics and ultra-high-contrast observations of exoplanets. Key hardware accomplishments of 2015/16 are the successful low-temperature fusion of a 1.5-meter diameter ULE mirror that is a 1/3rd scale model of a 4-meter mirror and the initiation of polishing of a 1.2-meter Extreme-Lightweight Zerodur mirror. Critical to AMTD's success is an integrated team of scientists, systems engineers, and technologists; and a science-driven systems engineering approach.

  9. Space Shuttle Program Primary Avionics Software System (PASS) Success Legacy -Major Accomplishments and Lessons Learned

    Science.gov (United States)

    Orr, James K.

    2010-01-01

    This presentation has shown the accomplishments of the PASS project over three decades and highlighted the lessons learned. Over the entire time, our goal has been to continuously improve our process, implement automation for both quality and increased productivity, and identify and remove all defects due to prior execution of a flawed process in addition to improving our processes following identification of significant process escapes. Morale and workforce instability have been issues, most significantly during 1993 to 1998 (period of consolidation in aerospace industry). The PASS project has also consulted with others, including the Software Engineering Institute, so as to be an early evaluator, adopter, and adapter of state-of-the-art software engineering innovations.

  10. The Legacy of the Space Shuttle Program: Scientific and Engineering Accomplishments

    Science.gov (United States)

    Torrez, Jonathan

    2009-01-01

    The goal of this project was to assist in the creation of the appendix for the book being written about the Space Shuttle that is titled The Legacy of the Space Shuttle Program: Scientific and Engineering Accomplishments. The specific responsibility of the intern was the creation of the human health and performance (life sciences) and space biology sections of the appendix. This included examining and finalizing the list of flights with life sciences and space biology experiments flown aboard them, researching the experiments performed, synopsizing each experiment into two sentences, and placing the synopses into an appendix template. Overall, approximately 70 flights had their experiments synopsized and a good method for researching and construction of the template was established this summer.

  11. Advanced Industrial Materials (AIM) program. Compilation of project summaries and significant accomplishments FY 1996

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-04-01

    In many ways, the Advanced Industrial Materials (AIM) Program underwent a major transformation in Fiscal Year 1995 and these changes have continued to the present. When the Program was established in 1990 as the Advanced Industrial Concepts (AIC) Materials Program, the mission was to conduct applied research and development to bring materials and processing technologies from the knowledge derived from basic research to the maturity required for the end use sectors for commercialization. In 1995, the Office of Industrial Technologies (OIT) made radical changes in structure and procedures. All technology development was directed toward the seven {open_quotes}Vision Industries{close_quotes} that use about 80% of industrial energy and generated about 90% of industrial wastes. These are: (1) Aluminum; (2) Chemical; (3) Forest Products; (4) Glass; (5) Metal Casting; (6) Refineries; and (7) Steel. This report is a compilation of project summaries and significant accomplishments on materials.

  12. Recent Accomplishments and Future Directions in US Fusion Safety & Environmental Program

    Energy Technology Data Exchange (ETDEWEB)

    David A. Petti; Brad J. Merrill; Phillip Sharpe; L. C. Cadwallader; L. El-Guebaly; S. Reyes

    2006-07-01

    The US fusion program has long recognized that the safety and environmental (S&E) potential of fusion can be attained by prudent materials selection, judicious design choices, and integration of safety requirements into the design of the facility. To achieve this goal, S&E research is focused on understanding the behavior of the largest sources of radioactive and hazardous materials in a fusion facility, understanding how energy sources in a fusion facility could mobilize those materials, developing integrated state of the art S&E computer codes and risk tools for safety assessment, and evaluating S&E issues associated with current fusion designs. In this paper, recent accomplishments are reviewed and future directions outlined.

  13. Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing

    OpenAIRE

    El-Kebir, Mohammed; Satas, Gryte; Oesper, Layla; Raphael, Benjamin J

    2016-01-01

    The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to reconstruct a perfect phylogeny tree from samples that contain mixtures of two-state characters, where each character/locus is either mutated or not. However, most cancers contain more complex mutations, such as copy-number aberrations, that exhibit more t...

  14. Cladistic analysis of ribosomal RNAs--the phylogeny of eukaryotes with respect to the endosymbiotic theory.

    Science.gov (United States)

    Wolters, J; Erdmann, V A

    1988-01-01

    A strict cladistic analysis of 5S and 16S rRNA secondary and primary structure confirms particular hypotheses concerning the phylogeny of eukaryotes: plastids of Euglena, green algae and land plants, and the cyanelle of Cyanophora share a specific character and are closely related to cyanobacteria of the Synechococcus-type. Angiosperm mitochondria share specific signatures with the alpha subdivision of rhodobacteria. Cyanophora is a member of the Euglenozoa, the Oomycetes are derived from a group of heterokont algae. PMID:3395680

  15. Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes, Cobitidae)

    Czech Academy of Sciences Publication Activity Database

    Bohlen, Jörg; Šlechtová, Vendula; Tan, H. H.; Britz, R.

    2011-01-01

    Roč. 61, č. 3 (2011), s. 854-865. ISSN 1055-7903 R&D Projects: GA ČR GA206/05/2556; GA ČR GA206/08/0637; GA AV ČR IAA600450508; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : pangio * eel loaches * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.609, year: 2011

  16. Phylogeny and sequence variability of the Sarcocystis singaporensis Zaman and Colley, (1975) 1976 ssrDNA

    Czech Academy of Sciences Publication Activity Database

    Šlapeta, Jan Roger; Kyselová, Iveta; Richardson, A. O.; Modrý, David; Lukeš, Julius

    2002-01-01

    Roč. 88, č. 9 (2002), s. 810-815. ISSN 0932-0113 R&D Projects: GA ČR GA524/00/P015; GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6022909 Keywords : Sarcocystis * phylogeny * ssrDNA Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.046, year: 2002

  17. “What’s in a Name?” The Taxonomy & Phylogeny of Early Homo

    OpenAIRE

    Galway-Witham, Julia Katrina Reitz

    2016-01-01

    Hominin systematics, encompassing both taxonomy and phylogeny (Strait, 2013), has significant implications for how the evolution of species and traits are understood and communicated. Following a recent influx of fossils (e.g., Brown et al., 2004; Lordkipanidze et al., 2013; Villmoare et al., 2015a; Berger et al., 2015) the amount of diversity in fossil morphology has increased correspondingly. As researchers do not yet approach diversity in a uniform manner, the literature has been flooded w...

  18. Molecular phylogeny of anoplocephalid tapeworms (Cestoda: Anoplocephalidae) infecting humans and non-human primates

    Czech Academy of Sciences Publication Activity Database

    Doležalová, J.; Vallo, P.; Petrželková, Klára Judita; Foitová, I.; Nurcahyo, W.; Mudakikwa, A.; Hashimoto, C.; Jirků, Milan; Lukeš, Julius; Scholz, Tomáš; Modrý, David

    2015-01-01

    Roč. 142, č. 10 (2015), s. 1278-1289. ISSN 0031-1820 R&D Projects: GA MŠk(CZ) EE2.3.30.0032; GA ČR GA206/09/0927 Institutional support: RVO:60077344 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.560, year: 2014

  19. A Tale That Morphology Fails to Tell: A Molecular Phylogeny of Aeolidiidae (Aeolidida, Nudibranchia, Gastropoda)

    OpenAIRE

    Carmona, Leila; Pola, Marta; Gosliner, Terrence M.; Cervera, Juan Lucas

    2013-01-01

    Aeolidida is one of the largest clades of nudibranchs with at least 560 known species. However, its systematics has not been studied in a comprehensive manner. Phylogenetic analyses of larger clades such as Nudibranchia or Cladobranchia have usually included a poor sample of aeolids. Furthermore, phylogenetic studies at the family or generic level in Aeolidida are a few and far between. The first molecular phylogeny of the aeolid family Aeolidiidae is presented here. This study, the most comp...

  20. Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

    Czech Academy of Sciences Publication Activity Database

    Musilová, Zuzana; Říčan, Oldřich; Janko, Karel; Novák, J.

    2008-01-01

    Roč. 46, - (2008), s. 659-672. ISSN 1055-7903 R&D Projects: GA MŠk LC06073 Grant ostatní: GA UK(CZ) 182/2004/B-BIO; GA UK(CZ) 139407 Institutional research plan: CEZ:AV0Z50450515 Keywords : molecular phylogeny * Cichlids * south America Subject RIV: EG - Zoology Impact factor: 3.871, year: 2008

  1. The evolutionary history of Mimosa (Leguminosae): toward a phylogeny of the sensitive plants

    OpenAIRE

    Simon, M. F.; Grether, R.; L.P. de Queiroz; Särkinen, T E; Dutra, V F; HUGHES, C E

    2011-01-01

    Premise of the study: Large genera provide remarkable opportunities to investigate patterns of morphological evolution and historical biogeography in plants. A molecular phylogeny of the species-rich and morphologically and ecologically diverse genus Mimosa was generated to evaluate its infrageneric classification, reconstruct the evolution of a set of morphological characters, and establish the relationships of Old World species to the rest of the genus. • Methods: We used trnD-trnT plastid ...

  2. Evidence of host specificity and congruence between phylogenies of bitterling and freshwater mussels

    Czech Academy of Sciences Publication Activity Database

    Liu, H.-Z.; Zhu, Y.-R.; Smith, C.; Reichard, Martin

    2006-01-01

    Roč. 45, č. 3 (2006), s. 428-434. ISSN 1021-5506 Grant ostatní: NSFC(CN) 30470237; NSFC(CN) 40432003; Innovation Program of the Chinese Academy of Sciences(CN) KZCX3-SW-126 Institutional research plan: CEZ:AV0Z60930519 Keywords : bitterling * host specificity * coevolution * phylogeny Subject RIV: EG - Zoology Impact factor: 0.943, year: 2006 http://zoolstud.sinica.edu.tw/Journals/45.3/428.pdf

  3. Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes

    OpenAIRE

    Milinkovitch, M C; Meyer., A; Powell, J R

    1994-01-01

    Traditionally, living cetaceans (order Cetacea) are classified into two highly distinct suborders: the echolocating toothed whales, Odontoceti, and the filter-feeding baleen whales, Mysticeti. A molecular phylogeny based on 1,352 base pairs of two mitochondrial ribosomal gene segments and the mitochondrial cytochrome b gene for all major groups of cetaceans contradicts this long-accepted taxonomic subdivision. One group of toothed whales, the sperm whales, is more closely related to the morph...

  4. Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales

    OpenAIRE

    Zhou Kaiya; Xu Shixia; Brandley Matthew C; Xiong Ye; Yang Guang

    2009-01-01

    Abstract Background The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitocho...

  5. Actinobase: Database on molecular diversity, phylogeny and biocatalytic potential of salt tolerant alkaliphilic actinomycetes

    OpenAIRE

    Sharma, Amit K; Gohel, Sangeeta; Singh, Satya P.

    2012-01-01

    Actinobase is a relational database of molecular diversity, phylogeny and biocatalytic potential of haloalkaliphilic actinomycetes. The main objective of this data base is to provide easy access to range of information, data storage, comparison and analysis apart from reduced data redundancy, data entry, storage, retrieval costs and improve data security. Information related to habitat, cell morphology, Gram reaction, biochemical characterization and molecular features would allow researchers...

  6. Maternal Phylogeny of a Newly-Found Yak Population in China

    OpenAIRE

    Deqiang Zou; Lei Zhang; Lu Li; Yi Ai; Hongwen Zhao; Changxiu Fu; Shanrong Li; Yongli Wen; Tserang Donko Mipam

    2012-01-01

    The Jinchuan yak is a new yak population identified in Sichuan, China. This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds. The genetic structure of this population is unknown. In the present study, we investigated the maternal phylogeny of this special yak population using the mitochondrial DNA variation. A total of 23 Jinchuan yaks were sequenced for a 823-bp fragment of D-loop control region and three individuals were sequenced...

  7. Phylogeny and evolution of ontogeny of the family Oxytomidae Ichikawa, 1958 (Mollusca: Bivalvia)

    Science.gov (United States)

    Lutikov, O. A.; Temkin, I. E.; Shurygin, B. N.

    2010-08-01

    We described ontogenies and reconstructed morphogeneses of hinges in some supraspecific taxa of the bivalve family Oxytomidae Ichikawa, 1958 from the Mesozoic of Russia. The phylogeny of the family is reconstructed using evolutionary and cladistic methods. The appearance of the endemic genus Arctotis Bodylevsky, 1960 in the epicontinental seas of Siberia can be explained in terms of gradual transformations of the ligament and byssal apparatus in the Northern Siberian members of Praemeleagrinella Lutikov et Shurygin, 2009 and Praearctotis Lutikov et Shurygin, 2009.

  8. PHY·FI: fast and easy online creation and manipulation of phylogeny color figures

    Directory of Open Access Journals (Sweden)

    Fredslund Jakob

    2006-06-01

    Full Text Available Abstract Background The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. Results This paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates". The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY·FI is free for all and is available from this web address: http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go

  9. Intraspecific Phylogeny of the Korean Water Deer, Hydropotes inermis argyropus (Artiodactyla, Cervidae)

    OpenAIRE

    Kim, Hye Ri; Kim, Eui Kyung; Jeon, Mi Gyung; Park, Yung Chul

    2015-01-01

    The water deer, Hydropotes inermis (Cervidae), is native to China and Korea and has two subspecies of the Chinese water deer (Hydropotes inermis inermis) and Korean water deer (Hydropotes inermis argyropus). To date, only the Korean water deer has been reported in South Korea. In this study, however, an intraspecific phylogeny and haplotype analysis based on mitochondrial cytochrome oxidase I indicated that both Korean and Chinese water deer are found in South Korea. The populations of the tw...

  10. Affordability as a discursive accomplishment in a changing National Health Service.

    Science.gov (United States)

    Russell, Jill; Greenhalgh, Trisha

    2012-12-01

    Health systems worldwide face the challenges of rationing. The English National Health Service (NHS) was founded on three core principles: universality, comprehensiveness, and free at the point of delivery. Yet patients are increasingly hearing that some treatments are unaffordable on the NHS. We considered affordability as a social accomplishment and sought to explore how those charged with allocating NHS resources achieved this in practice. We undertook a linguistic ethnography to examine the work practices of resource allocation committees in three Primary Care Trusts (PCTs) in England between 2005 and 2012, specifically deliberations over 'individual funding requests' (IFRs)--requests by patients and their doctors for the PCT to support a treatment not routinely funded. We collected and analysed a diverse dataset comprising policy documents, legal judgements, audio recordings, ethnographic field notes and emails from PCT committee meetings, interviews and a focus group with committee members. We found that the fundamental values of universality and comprehensiveness strongly influenced the culture of these NHS organisations, and that in this context, accomplishing affordability was not easy. Four discursive practices served to confer legitimacy on affordability as a guiding value of NHS health care: (1) categorising certain treatments as only eligible for NHS funding if patients could prove 'exceptional' circumstances; (2) representing resource allocation decisions as being not (primarily) about money; (3) indexical labelling of affordability as an ethical principle, and (4) recontextualising legal judgements supporting refusal of NHS treatment on affordability grounds as 'rational'. The overall effect of these discursive practices was that denying treatment to patients became reasonable and rational for an organisation even while it continued to espouse traditional NHS values. We conclude that deliberations about the funding of treatments at the margins of NHS

  11. A robust phylogeny among major lineages of the East African cichlids.

    Science.gov (United States)

    Takahashi, Tetsumi; Sota, Teiji

    2016-07-01

    The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR. PMID:27068840

  12. Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria).

    Science.gov (United States)

    Campanella, Daniela; Hughes, Lily C; Unmack, Peter J; Bloom, Devin D; Piller, Kyle R; Ortí, Guillermo

    2015-05-01

    Phylogenetic relationships among families within the order Atheriniformes have been difficult to resolve on the basis of morphological evidence. Molecular studies so far have been fragmentary and based on a small number taxa and loci. In this study, we provide a new phylogenetic hypothesis based on sequence data collected for eight molecular markers for a representative sample of 103 atheriniform species, covering 2/3 of the genera in this order. The phylogeny is calibrated with six carefully chosen fossil taxa to provide an explicit timeframe for the diversification of this group. Our results support the subdivision of Atheriniformes into two suborders (Atherinopsoidei and Atherinoidei), the nesting of Notocheirinae within Atherinopsidae, and the monophyly of tribe Menidiini, among others. We propose taxonomic changes for Atherinopsoidei, but a few weakly supported nodes in our phylogeny suggests that further study is necessary to support a revised taxonomy of Atherinoidei. The time-calibrated phylogeny was used to infer ancestral habitat reconstructions to explain the current distribution of marine and freshwater taxa. Based on these results, the current distribution of Atheriniformes is likely due to widespread marine dispersal along the margins of continents, infrequent trans-oceanic dispersal, and repeated invasion of freshwater habitats. This conclusion is supported by post-Gondwanan divergence times among families within the order, and a high probability of a marine ancestral habitat. PMID:25769409

  13. Does a tree-like phylogeny only exist at the tips in the prokaryotes?

    Science.gov (United States)

    Creevey, Christopher J; Fitzpatrick, David A; Philip, Gayle K; Kinsella, Rhoda J; O'Connell, Mary J; Pentony, Melissa M; Travers, Simon A; Wilkinson, Mark; McInerney, James O

    2004-12-22

    The extent to which prokaryotic evolution has been influenced by horizontal gene transfer (HGT) and therefore might be more of a network than a tree is unclear. Here we use supertree methods to ask whether a definitive prokaryotic phylogenetic tree exists and whether it can be confidently inferred using orthologous genes. We analysed an 11-taxon dataset spanning the deepest divisions of prokaryotic relationships, a 10-taxon dataset spanning the relatively recent gamma-proteobacteria and a 61-taxon dataset spanning both, using species for which complete genomes are available. Congruence among gene trees spanning deep relationships is not better than random. By contrast, a strong, almost perfect phylogenetic signal exists in gamma-proteobacterial genes. Deep-level prokaryotic relationships are difficult to infer because of signal erosion, systematic bias, hidden paralogy and/or HGT. Our results do not preclude levels of HGT that would be inconsistent with the notion of a prokaryotic phylogeny. This approach will help decide the extent to which we can say that there is a prokaryotic phylogeny and where in the phylogeny a cohesive genomic signal exists. PMID:15615680

  14. Reconciling molecular phylogeny, morphological divergence and classification of Madagascan narrow-mouthed frogs (Amphibia: Microhylidae).

    Science.gov (United States)

    Scherz, Mark D; Vences, Miguel; Rakotoarison, Andolalao; Andreone, Franco; Köhler, Jörn; Glaw, Frank; Crottini, Angelica

    2016-07-01

    A recent study clarified several aspects of microhylid phylogeny by combining DNA sequences from Sanger sequencing and anchored phylogenomics, although numerous aspects of tree topology proved highly susceptible to data partition and chosen model. Although the phylogenetic results of the study were in conflict with previous publications, the authors made several changes to the taxonomy of Madagascar's cophyline microhylids. We re-analyzed part of their data together with our own molecular and morphological data. Based on a supermatrix of 11 loci, we propose a new phylogeny of the Cophylinae, and discuss it in the context of a newly generated osteological dataset. We found several sample misidentifications, partially explaining their deviant results, and propose to resurrect the genera Platypelis and Stumpffia from the synonymy of Cophyla and Rhombophryne, respectively. We provide support for the previous genus-level taxonomy of this subfamily, and erect a new genus, Anilany gen. nov., in order to eliminate paraphyly of Stumpffia and to account for the osteological differences observed among these groups. Deep nodes in our phylogeny remain poorly supported, and future works will certainly refine our classification, but we are confident that these will not produce large-scale rearrangements. PMID:27085671

  15. Phylogeny of economically important insect pests that infesting several crops species in Malaysia

    Science.gov (United States)

    Ghazali, Siti Zafirah; Zain, Badrul Munir Md.; Yaakop, Salmah

    2014-09-01

    This paper reported molecular data on insect pests of commercial crops in Peninsular Malaysia. Fifteen insect pests (Metisa plana, Calliteara horsefeldii, Cotesia vestalis, Bactrocera papayae, Bactrocera carambolae, Bactrocera latifrons, Conopomorpha cramella, Sesamia inferens, Chilo polychrysa, Rhynchophorus vulneratus, and Rhynchophorus ferrugineus) of nine crops were sampled (oil palm, coconut, paddy, cocoa, starfruit, angled loofah, guava, chili and mustard) and also four species that belong to the fern's pest (Herpetogramma platycapna) and storage and rice pests (Tribolium castaneum, Oryzaephilus surinamensis and Cadra cautella). The presented phylogeny summarized the initial phylogenetic hypothesis, which concerning by implementation of the economically important insect pests. In this paper, phylogenetic relationships among 39 individuals of 15 species that belonging to three orders under 12 genera were inferred from DNA sequences of mitochondrial marker, cytochrome oxidase subunit I (COI) and nuclear marker, ribosomal DNA 28S D2 region. The phylogenies resulted from the phylogenetic analyses of both genes are relatively similar, but differ in the sequence of evolution. Interestingly, this most recent molecular data of COI sequences data by using Bayesian Inference analysis resulted a more-resolved phylogeny that corroborated with traditional hypotheses of holometabolan relationships based on traditional hypotheses of holometabolan relationships and most of recently molecular study compared to 28S sequences. This finding provides the information on relationships of pests species, which infested several crops in Malaysia and also estimation on Holometabola's order relationships. The identification of the larval stages of insect pests could be done accurately, without waiting the emergence of adults and supported by the phylogenetic tree.

  16. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

    Directory of Open Access Journals (Sweden)

    Michelle Klein Sercundes

    2016-03-01

    Full Text Available Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC and beta subunit of RNA polymerase (rpoB, and mitochondrial gene coding for cytochrome B (cytB were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG, Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

  17. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences.

    Science.gov (United States)

    Sercundes, Michelle Klein; Valadas, Samantha Yuri Oshiro Branco; Keid, Lara Borges; Oliveira, Tricia Maria Ferreira Souza; Ferreira, Helena Lage; Vitor, Ricardo Wagner de Almeida; Gregori, Fábio; Soares, Rodrigo Martins

    2016-01-01

    Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genus Hammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well. PMID:27007245

  18. Molecular phylogeny and evolution of Scomber (Teleostei: Scombridae) based on mitochondrial and nuclear DNA sequences

    Institute of Scientific and Technical Information of China (English)

    CHENG Jiao; GAO Tianxiang; MIAO Zhenqing; YANAGIMOTO Takashi

    2011-01-01

    A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial (COI, Cyt b and control region) and nuclear (5S rDNA) DNA sequence data in multigene perspective. A variety of phylogenetic analytic methods were used to clarify the current taxonomic classification and to assess phylogenetic relationships and the evolutionary history of this genus. The present study produced a well-resolved phylogeny that strongly supported the monophyly of Scomber. We confirmed that S. japonicus and S. colias were genetically distinct. Although morphologically and ecologically similar to S. colias, the molecular data showed that S. japonicus has a greater molecular affinity with S. australasicus, which conflicts with the traditional taxonomy. This phyiogenetic pattern was corroborated by the mtDNA data, but incompletely by the nuclear DNA data. Phylogenetic concordance between the mitochondrial and nuclear DNA regions for the basal nodes supports an Atlantic origin for Scomber. The present-day geographic ranges of the species were compared with the resultant molecular phylogeny derived from partition Bayesian analyses of the combined data sets to evaluate possible dispersal routes of the genus. The present-day geographic distribution of Scomber species might be best ascribed to multiple dispersal events. In addition, our results suggest that phylogenies derived from multiple genes and long sequences exhibited improved phylogenetic resolution, from which we conclude that the phylogenetic reconstruction is a reliable representation of the evolutionary history of Scomber.

  19. Epidemiology, pathology, immunology and diagnosis of bovine farcy: a review.

    Science.gov (United States)

    Hamid, Mohamed E

    2012-06-01

    Bovine farcy (which is caused by Mycobacterium farcinogenes and Mycobacterium senegalense) is a chronic suppurative granulomatous inflammation of the skin and lymphatics of cattle and is seen mostly in sub-Saharan Africa. It is not yet certain whether Nocardia farcinica causes cutaneous nocardiosis (farcy) in animals that mimics bovine farcy. Epidemiological data have steadily reported finding bovine farcy in adult cattle of the transhumance pastoralist tribes of the Sahel and the Sudanian savannah zones. M. farcinogenes and or M. senegalense do not affect other domestic or non-domestic animals; it is not known whether these bacteria are zoonotic. The disease--once widespread in many regions--has disappeared from some countries historically known to have it. Reports of bovine farcy prevalence seem to be linked to the existence of survey initiatives by governments and diagnostic capabilities in each country. Farcy causes economic loss due to damaged hides and also is a public-health burden (because the lymphadenitis due to farcy resembles the lesions of bovine tuberculosis in carcasses and the meat is considered inappropriate for human consumption). The current literature is deficient in establishing definitely the prevalence, transmission patterns, and risk factors of bovine farcy. Ixodid ticks transmit other skin diseases (such as dermatophilosis) and might play a role in bovine farcy (given the similarity in the bio-physiology and geographic distribution of the disease). In addition, the tick-resistance of cattle breeds such as the N'Dama, Fulani or the Nilotic might explain their resistance to bovine farcy. Apart from the judicious use of conventional smear-and-culture methods, few diagnostic tests have been developed; the molecular and serological tests have not been evaluated for reproducibility and accuracy. This review points out aspects of bovine farcy that need further research and updates available data on the prevalence, distribution, risk factors

  20. Three viruses of the bovine respiratory disease complex apply different strategies to initiate infection

    OpenAIRE

    Kirchhoff, Jana; Uhlenbruck, Sabine; Goris, Katherina; Keil, Günther M.; Herrler, Georg

    2014-01-01

    Bovine respiratory disease complex (BRDC) is the major cause of serious respiratory tract infections in calves. The disease is multifactorial, with either stress or reduced immunity allowing several pathogens to emerge. We investigated the susceptibility of bovine airway epithelial cells (BAEC) to infection by the three major viruses associated with the BRDC: bovine respiratory syncytial virus (BRSV), bovine herpesvirus type 1 (BHV-1) and bovine parainfluenza virus type 3 (BPIV3). For this pu...

  1. Single Pathogen Challenge with Agents of the Bovine Respiratory Disease Complex

    OpenAIRE

    Gershwin, LJ; Van Eenennaam, AL; Anderson, ML; McEligot, HA; Shao, MX; Toaff-Rosenstein, R; Taylor, JF; Neibergs, HL; Womack, J.; Complex, BRD

    2015-01-01

    Bovine respiratory disease complex (BRDC) is an important cause of mortality and morbidity in cattle; costing the dairy and beef industries millions of dollars annually, despite the use of vaccines and antibiotics. BRDC is caused by one or more of several viruses (bovine respiratory syncytial virus, bovine herpes type 1 also known as infectious bovine rhinotracheitis, and bovine viral diarrhea virus), which predispose animals to infection with one or more bacteria. These include: Pasteurella ...

  2. Guidance for Removal of Fetal Bovine Serum from Cryopreserved Heart Valve Processing

    OpenAIRE

    Brockbank, Kelvin G.M.; Heacox, Albert E.; Schenke-Layland, Katja

    2010-01-01

    Bovine serum is commonly used in cryopreservation of allogeneic heart valves; however, bovine serum carries a risk of product adulteration by contamination with bovine-derived infectious agents. In this study, we compared fresh and cryopreserved porcine valves that were processed by 1 of 4 cryopreservation formulations, 3 of which were serum-free and 1 that utilized bovine serum with 1.4 M dimethylsulfoxide. In the first serum-free group, bovine serum was simply removed from the cryopreservat...

  3. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

    OpenAIRE

    Xavier Suresh R; Aragonda Prathyusha; Polineni Pavana; Furuta Richard; Adelson David L

    2006-01-01

    Abstract Background Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these ...

  4. Gabor Weber Local Descriptor for Bovine Iris Recognition

    Directory of Open Access Journals (Sweden)

    Shengnan Sun

    2013-01-01

    Full Text Available Iris recognition is a robust biometric technology. This paper proposes a novel local descriptor for bovine iris recognition, named Gabor Weber local descriptor (GWLD. We first compute the Gabor magnitude maps for the input bovine iris image, and then calculate the differential excitation and orientation for each pixel over each Gabor magnitude map. After that, we use these differential excitations and orientations to construct the GWLD histogram representation. Finally, histogram intersection is adopted to measure the similarity between different GWLD histograms. The experimental results on the SEU bovine iris database verify the representation power of our proposed local descriptor.

  5. Cloning and sequencing of the bovine gastrin gene

    DEFF Research Database (Denmark)

    Lund, T; Rehfeld, J F; Olsen, Jørgen

    1989-01-01

    In order to deduce the primary structure of bovine preprogastrin we therefore sequenced a gastrin DNA clone isolated from a bovine liver cosmid library. Bovine preprogastrin comprises 104 amino acids and consists of a signal peptide, a 37 amino acid spacer-sequence, the gastrin-34 sequence follow...... by an amidation-site (Gly-Arg-Arg), and a C-terminal nonapeptide. Comparison with human, porcine, and rat cDNA sequences revealed extensive homology in the coding region as well as in short noncoding structures....

  6. Genomic analysis of the major bovine milk protein genes.

    OpenAIRE

    Threadgill, D.W.; Womack, J E

    1990-01-01

    The genomic arrangement of the major bovine milk protein genes has been determined using a combination of physical mapping techniques. The major milk proteins consist of the four caseins, alpha s1 (CASAS1), alpha s2 (CASAS2), beta (CASB), and kappa (CASK), as well as the two major whey proteins, alpha-lactalbumin (LALBA) and beta-lactoglobulin (LGB). A panel of bovine X hamster hybrid somatic cells analyzed for the presence or absence of bovine specific restriction fragments revealed the gene...

  7. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

    Directory of Open Access Journals (Sweden)

    Holland Barbara R

    2006-07-01

    Full Text Available Abstract Background Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. Results Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. δ values are found to be a reliable predictor of phylogenetic accuracy. Conclusion Using the most treelike distance matrices, as

  8. Clenbuterol Residues in Bovine Feed and Meat

    Directory of Open Access Journals (Sweden)

    2008-01-01

    Full Text Available The aim of this study was to measure the β-agonist, clenbuterol in bovine feeds and meat in North and South of Mexico. Clenbuterol is used illegally as growth promoter in animal feeding in farms animals due to muscle hypertrophy and lipolisis effect. In Mexico, there is a suspected in their unlicensed use in certain commercial feedlots. Total 16 food samples and 90 samples of meat were analyzed by 2 commercially clenbuterol enzyme immunoassays kits. The samples were collected during 2006. Approximately, 75% of the animal feed samples and 16.6 % of meat analyzed were found positives in levels ranged 2525-53787 ppt and 0.1-2.3 μg kg-1. These information indicate that the abuse of clenbuterol during the last 5 years is not declining in some farms of Mexico with a health human risk.

  9. Human bovine tuberculosis - remains in the differential.

    LENUS (Irish Health Repository)

    Bilal, Shaukat

    2010-11-01

    Mycobacterium bovis is a pathogen of cattle. The unpasteurized milk of affected cattle is a source of infection in humans. Despite the screening of cattle and the pasteurization of milk, M bovis has not been eradicated. A high index of clinical suspicion is needed in symptomatic patients with a history of possible exposure. At risk groups include animal workers, farmers, meat packers, vets and zoo keepers. Humans are usually infected by the aerosol route. We present two cases of human bovine tuberculosis. One was a presumptive case and the second was a confirmed case. Both responded well to antituberculous therapy. In the confirmed case, there was evidence of transmission to the partner living in the same house. Rifampicin prophylaxis was given to the exposed case. The M. bovis from the confirmed case was isoniazid resistant, in addition to having the well known resistance to pyrazinamide. Isoniazid resistance has been described before in those who are immunocompromised. We describe it in an immunocompetent patient.

  10. Diagnosis and Control of Bovine Neosporosis.

    Science.gov (United States)

    McAllister, Milton M

    2016-07-01

    Neosporosis is one of the most common and widespread causes of bovine abortion. The causative parasite is transmitted in at least two ways, horizontally from canids, and by endogenous transmission within maternal lines of infected cattle. The prevalence of neosporosis is higher in the dairy industry than in the beef industry because of risk factors associated with intensive feeding. There are no vaccines, but logical management options are discussed that can lower the risk of abortion outbreaks and gradually reduce the prevalence of infection within herds. Steps should be taken to prevent total mixed rations from becoming contaminated by canine feces. If a herd has a high rate of infection that is associated with abortions in heifers, then the rate of reduction of infection prevalence can be speeded by only selecting seronegative replacement heifers to enter the breeding herd. Elimination of all infected cattle is not a recommended goal. PMID:27161392

  11. Radioimmunoassay for progesterone in bovine milk

    International Nuclear Information System (INIS)

    A system for the measurement of progesterone in bovine milk by radioimmunoassay has been developed and validated. This assay includes an iodine tracer purified by HPLC, the standard prepared in fat-free milk and an antibody anti-progesterone combined with second antibody. The detection limit of the assay is at 0.2 nmol/L calculated from the maximum binding menus two standard deviations and the precision is satisfactory. In the recovery assay was used 4 milk different samples and the result was 98% of recuperation. The progesterone was determinate in milk samples from post-partum animals taking samples three times per week for 40 days. The assay is simple, rapid and possibility the progesterone measurement without sample dilution, distinguish the cyclic changes of this hormone that reflect the ovarian activity in the animals. (author)

  12. Copy number variation in the bovine genome

    DEFF Research Database (Denmark)

    Fadista, João; Thomsen, Bo; Holm, Lars-Erik;

    2010-01-01

    to genetic variation in cattle. Results We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation...... in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental...

  13. The Freedom SOLO bovine pericardial stentless valve

    Directory of Open Access Journals (Sweden)

    Stanger O

    2014-12-01

    Full Text Available Olaf Stanger, Hendrik Tevaearai, Thierry Carrel Clinic for Cardiovascular Surgery, University Hospital Berne, Switzerland Abstract: The third-generation bovine pericardium Freedom SOLO (FS stentless valve emerged in 2004 as a modified version of the Pericarbon Freedom stentless valve and as a very attractive alternative to stented bioprostheses. The design, choice of tissue, and anticalcification treatment fulfill most, if not all, requirements for an ideal valve substitute. The FS combines the single-suture, subcoronary implantation technique with the latest-generation bovine pericardial tissue and novel anticalcification treatment. The design allows imitation of the native healthy valve through unrestricted adaption to the patient's anatomy, reproducing a normal valve/root complex. However, despite hemodynamic performance superior to stented valves, we are approaching a critical observation period as superior durability, freedom from structural valve deterioration, and nonstructural failure has not been proven as expected. However, optimal performance and freedom from structural valve deterioration depend on correct sizing and perfect symmetric implantation, to ensure low leaflet stress. Any malpositioning can lead to tissue fatigue over time. Furthermore, the potential for better outcomes depends on optimal patient selection and observance of the limitations for the use of stentless valves, particularly for the FS. Clearly, stentless valve implantation techniques are less reproducible and standardized, and require surgeon-dependent experience and skill. Regardless of whether or not stentless valve durability surpasses third-generation stented bioprostheses, they will continue to play a role in the surgical repertoire. This review intends to help practitioners avoid pitfalls, observe limitations, and improve patient selection for optimal long-term outcome with the attractive FS stentless valve. Keywords: aortic valve, bioprosthesis, cardiac

  14. Pathological studies on bovine viral diarrhea

    International Nuclear Information System (INIS)

    Bovine viral diarrhea virus (BVDV) is classified as an RNA virus in the family flavin viride and is a member of the genus pest virus (Collet et al 1989). BVDV has a worldwide distribution and infections in cattle populations (Kahrs et al 1970). It was recognized since 50 years ago, the initial description of an acute enteric disease of cattle in North America, which was characterized by outbreaks of diarrhea and erosive of digestive tract (Olafsonp et al 1946). The disease and causative agent were named bovine viral diarrhea (B V D ) and (B V DV), respectively. This virus was subsequently associated with a sporadically occurring and highly fatal enteric disease that was termed mucosal disease (M D), (Ramsey and Chivers 1953). The initial isolate of BVDV did not produce cytopathic effect in cell culture, whereas an isolate from MD did produce cytopathic effects (Lee et al 1957). In vitro characteristic of non cytopathic or sytopathic effects of BVDV is referred to as the biotype of the virus. It has now been established that MD occurs only when xattle that are born immuno tolerant to and persistently infected with a noncyropathic BVDV become super infected with a cytopathic BVDV. The knowledge of the molecular biology. Pathogenesis and epidemiology of BVDV has greatly evolved in the past 10-15 years and has provided a better understanding of this complex infectious agent. Infection with BVDV can result in a wide spectrum of diseases ranging from subclinical infection s to a highly fatal from known as mucosal disease (ND). The clinical response to infection depends on multiple interactive factors. Host factors that influence the clinical outcome of BVDV infection include whether the host is immunocompetent or immuno tolerant to BVDV, pregnancy status, gestational age of the fetus, immune status (passively derived or actively derived from previous infection or vaccination) and concurrent level of environmental stress

  15. Lipidome signatures in early bovine embryo development.

    Science.gov (United States)

    Sudano, Mateus J; Rascado, Tatiana D S; Tata, Alessandra; Belaz, Katia R A; Santos, Vanessa G; Valente, Roniele S; Mesquita, Fernando S; Ferreira, Christina R; Araújo, João P; Eberlin, Marcos N; Landim-Alvarenga, Fernanda D C

    2016-07-15

    Mammalian preimplantation embryonic development is a complex, conserved, and well-orchestrated process involving dynamic molecular and structural changes. Understanding membrane lipid profile fluctuation during this crucial period is fundamental to address mechanisms governing embryogenesis. Therefore, the aim of the present work was to perform a comprehensive assessment of stage-specific lipid profiles during early bovine embryonic development and associate with the mRNA abundance of lipid metabolism-related genes (ACSL3, ELOVL5, and ELOVL6) and with the amount of cytoplasmic lipid droplets. Immature oocytes were recovered from slaughterhouse-derived ovaries, two-cell embryos, and eight- to 16-cell embryos, morula, and blastocysts that were in vitro produced under different environmental conditions. Lipid droplets content and mRNA transcript levels for ACSL3, ELOVL5, and ELOVL6, monitored by lipid staining and quantitative polymerase chain reaction, respectively, increased at morula followed by a decrease at blastocyst stage. Relative mRNA abundance changes of ACSL3 were closely related to cytoplasmic lipid droplet accumulation. Characteristic dynamic changes of phospholipid profiles were observed during early embryo development and related to unsaturation level, acyl chain length, and class composition. ELOVL5 and ELOVL6 mRNA levels were suggestive of overexpression of membrane phospholipids containing elongated fatty acids with 16, 18, and 20 carbons. In addition, putative biomarkers of key events of embryogenesis, embryo lipid accumulation, and elongation were identified. This study provides a comprehensive description of stage-specific lipidome signatures and proposes a mechanism to explain its potential relationship with the fluctuation of both cytoplasmic lipid droplets content and mRNA levels of lipid metabolism-related genes during early bovine embryo development. PMID:27107972

  16. Genetic diversity in a Brazilian bovine herd based on four microsatellite loci

    Directory of Open Access Journals (Sweden)

    Sabrina E. Matos Almeida

    2000-06-01

    Full Text Available Microsatellites or short tandem repeats (STRs, DNA markers relatively abundant in the genome, have a high degree of polymorphism and therefore great potential for characterizing populations. The present study estimates genetic variability in a set of four microsatellites (BMS3013, BMS3004, HEL10 and TGLA122 in a Brazilian hybrid bovine breed (5/8 Aberdeen Angus x 3/8 Nelore. The objectives were to determine the effect of crossbreeding and selection in these animals' genetic diversity as well as to discover the herd's genetic relationship with that of other breeds. Low diversity was verified in BMS3013 and high diversity was detected in BMS3004, HEL10 and TGLA122. Two alleles in TGLA122 are described here for the first time (TGLA122*155 and TGLA122*163. These genes are possibly characteristics of Zebu animals since they have not been found in other taurine samples so far investigated. Low interpopulational diversity was observed among taurine cattle populations, and clusters obtained on TGLA122 phylogenetic trees agreed with the bovine herd's geographic origin. Therefore, despite TGLA122's high polymorphism and high levels of intrapopulational diversity, the system engenders consistent bovine phylogenies. We detected an intriguingly high similarity between Brangus Ibagé and Red Angus since the former is a hybrid having 3/8 of Nelore genes. Either these animals' environment or genetic selective practices applied to the breed probably favor the Angus genotype.Microssatélites ou repetições curtas em tandem (STRs são marcadores moleculares de relativa abundância no genoma e apresentam alto grau de polimorfismo, constituindo-se numa excelente ferramenta para a caracterização das populações. Este trabalho estimou a variabilidade genética de quatro microssatélites (BMS3013, BMS3004, HEL10 e TGLA122 em um rebanho híbrido de bovinos brasileiros (5/8 Aberdeen Angus x 3/8 Nelore, com os objetivos de verificar o efeito do cruzamento e das pr

  17. Professional conceptualisation and accomplishment of patient safety in mental healthcare: an ethnographic approach

    Directory of Open Access Journals (Sweden)

    Braithwaite Jeffrey

    2011-05-01

    Full Text Available Abstract Background This study seeks to broaden current understandings of what patient safety means in mental healthcare and how it is accomplished. We propose a qualitative observational study of how safety is produced or not produced in the complex context of everyday professional mental health practice. Such an approach intentionally contrasts with much patient safety research which assumes that safety is achieved and improved through top-down policy directives. We seek instead to understand and articulate the connections and dynamic interactions between people, materials, and organisational, legal, moral, professional and historical safety imperatives as they come together at particular times and places to perform safe or unsafe practice. As such we advocate an understanding of patient safety 'from the ground up'. Methods/Design The proposed project employs a six-phase data collection framework in two mental health settings: an inpatient unit and a community team. The first four phases comprise multiple modes of focussed, unobtrusive observation of professionals at work, to enable us to trace the conceptualisation and enactment of safety as revealed in dialogue and narrative, use of artefacts and space, bodily activity and patterns of movement, and in the accomplishment of specific work tasks. An interview phase and a social network analysis phase will subsequently be conducted to offer comparative perspectives on the observational data. This multi-modal and holistic approach to studying patient safety will complement existing research, which is dominated by instrumentalist approaches to discovering factors contributing to error, or developing interventions to prevent or manage adverse events. Discussion This ethnographic research framework, informed by the principles of practice theories and in particular actor-network ideas, provides a tool to aid the understanding of patient safety in mental healthcare. The approach is novel in that it

  18. Grimsel test site - Phase VI: review of accomplishments and next steps

    International Nuclear Information System (INIS)

    The Grimsel Test Site owned and operated by Nagra is located in the Swiss Alps (www.grimsel.com). The sixth Phase of investigations was started in 2003 with a ten-year planning horizon. With the investigations and projects of Phase VI the focus is shifted more towards projects assessing perturbation effects of repository implementation and projects evaluating and demonstrating engineering and operational aspects of the repository system. More than 17 international partners participate in the various projects, which form the basic organisational 'elements' of Phase VI, each one further structured in field-testing, laboratory studies, design and modelling tasks, as appropriate. Each project phase is planned with a duration of 3 to 5 years, to facilitate all practical and administrative aspects, ensuring flexibility for updating the overall plan with the recent findings. Scientific and engineering interaction among the different projects is ensured via the annual international meeting and ad-hoc meetings, as appropriate. As Phase VI approaches its mid-term point, a review of the accomplishments to date is performed to provide a sound basis for the detailed planning of the next steps. The accomplishments to date are described and assessed below; the opportunities with the on-going projects as well as new projects - currently under discussion - are also presented and discussed. The on-going projects include: studies of the long-term diffusion with emphasis on the processes in the rock matrix (LTD); colloid studies under in-situ generation conditions and migration velocities closer to velocities expected in an actual repository site (CFM); studies of the long-term cement interactions with natural systems (LCS); evaluation of full-scale engineered systems under simulated heat production and long-term natural saturation (NF-Pro/FEBEX); gas migration through engineered barrier systems (GMT); emplacement of shot-crete low-pH plug (ESDRED/Module IV); test and evaluation of

  19. ADAPTABILITY, PERFORMANCE AND PRODUCTIVE LONGEVITY TO THE ELITE NUCLEUS OF BROWN BREED FROM RESEARCH AND DEVELOPMENT STATION FOR BOVINE RAISING ARAD

    Directory of Open Access Journals (Sweden)

    ANUłA MAGDIN

    2013-12-01

    Full Text Available Adaptability of Brown breed on the plain area it is possible in conditions that provide housing and nutrition technologies concordant with morpho-physiological necessity. Advance of productive level, over 7000 kg per lactation, in accomplish condition of six lactations average per productive period, is one definitive element regarding adaptation capacity. Accomplishment of some morphological and productive parameters in economic conditions comparable with Frisian breed is still one element authentic zoo-approbatory. The aim of this study was to evaluate the efficiency of adaptability and productive longevity of one nucleus of Brown breed from the Research and Development Station for Bovine Raising – Arad along of ten years on the plain area.

  20. Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease

    Science.gov (United States)

    ... Search The CDC Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease Note: Javascript is disabled or is not supported ... damages the central nervous system of cattle. More Mad Cow Disease is a neurological disorder of cattle. About BSE ...

  1. Prevalence and economics and bovine leukosis in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, D.K.; Beal, V.C. Jr.

    1979-01-01

    This paper reviews the prevalence of bovine leukosis in the US and discusses the economic significance of the disease. The term leukosis is used except when reporting the Meat Inspection Department data which used the term malignant lymphoma instead. (PCS)

  2. Cartilage (Bovine and Shark) (PDQ®)—Health Professional Version

    Science.gov (United States)

    Expert-reviewed information summary about the use of bovine and shark cartilage as a treatment for people with cancer. Note: The information in this summary is no longer being updated and is provided for reference purposes only.

  3. Guidelines for taking and interpreting radiographs of the bovine foot

    International Nuclear Information System (INIS)

    This step-by-step guide to radiographing the bovine foot tells you how to 1) obtain the radiograph you need, 2) allow for normal variations when assessing the findings, and 3) interpret abnormalities accurately by following a systematic approach

  4. Recognizing the radiographic features of some common bovine foot problems

    International Nuclear Information System (INIS)

    Radiographs of an injured or infected bovine foot can be tricky to interpret - the anatomy is complex, and the signs may be subtle. This guide leads you through the classic radiographic features of several common foot conditions

  5. Horosho li Iraku i Rossii vmeste? / Aleksandr Bovin

    Index Scriptorium Estoniae

    Bovin, Aleksandr

    2003-01-01

    Venemaa erakorraline ja täievoliline suursaadik Iisraelis Aleksandr Bovin arvab, et Venemaa ei tohiks võtta jäika positsiooni Iraagi kaitseks USA vastu, vaid ootama kõrvalseisjana konflikti lahendust

  6. Molecular and biological aspects of the bovine immunodeficiency virus.

    Science.gov (United States)

    Corredor, Andrea G; St-Louis, Marie-Claude; Archambault, Denis

    2010-01-01

    The bovine immunodeficiency virus (BIV) was isolated in 1969 from a cow, R-29, with a wasting syndrome suggesting bovine leucosis. The virus, first designated bovine visna-like virus, remained unstudied until HIV was discovered in 1983. Then, it was demonstrated in 1987 that the bovine R-29 isolate was a lentivirus with striking similarity to the human immunodeficiency virus (HIV). Moreover, BIV has the most complex genomic structure among all identified lentiviruses shown by several regulatory/accessory genes encoding proteins, some of which are involved in the regulation of virus gene expression. This manuscript aims to review biological and molecular aspects of BIV, with emphasis on regulatory/accessory viral genes/proteins which are involved in virus expression. PMID:20210777

  7. The ICES Working Group on Zooplankton Ecology: Accomplishments of the first 25 years

    Science.gov (United States)

    Wiebe, Peter H.; Harris, Roger; Gislason, Astthor; Margonski, Piotr; Skjoldal, Hein Rune; Benfield, Mark; Hay, Steve; O'Brien, Todd; Valdés, Luis

    2016-02-01

    The ICES Study Group on Zooplankton Ecology was created in 1991 to address issues of current and future concern within the field of zooplankton ecology. Within three years it became the ICES Working Group on Zooplankton Ecology (ICES WGZE) and this unique group in the world's oceanographic community has now been active for 25 years. This article reviews and synthesizes the products, and major accomplishments of the group. Achievements of the group, including the Zooplankton Methodology Manual, the Zooplankton Status Reports, and the International Zooplankton Symposia, have had an important impact on the wider field. Among the future issues that remain to be addressed by the group are the assessment of exploratory fisheries on zooplankton and micronekton species; further development of the zooplankton time-series; compilation and integration of allometric relationships for zooplankton species, and evaluation of new methodologies for the study of zooplankton distribution, abundance, physiology, and genetics. Marine science is an increasingly global undertaking and groups such as the ICES WGZE will continue to be essential to the advancement of understanding of zooplankton community structure and population dynamics in the world's oceans.

  8. Quality management at Argonne National Laboratory: Status, accomplishments, and lessons learned

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    In April 1992, Argonne National Laboratory (ANL) launched the implementation of quality management (QM) as an initiative of the Laboratory Director. The goal of the program is to seek ways of improving Laboratory performance and effectiveness by drawing from the realm of experiences in the global total quality management movement. The Argonne QM initiative began with fact finding and formulating a strategy for implementation; the emphasis is that the underlying principles of QM should be an integral part of how the Laboratory is managed and operated. A primary theme that has guided the Argonne QM initiative is to consider only those practices that offer the potential for real improvement, make sense, fit the culture, and would be credible to the broad population. In October 1993, the Laboratory began to pilot a targeted set of QM activities selected to produce outcomes important to the Laboratory--strengthening the customer focus, improving work processes, enhancing employee involvement and satisfaction, and institutionalizing QM. This report describes the results of the just-concluded QM development and demonstration phase in terms of detailed strategies, accomplishments, and lessons learned. These results are offered as evidence to support the conclusion that the Argonne QM initiative has achieved value-added results and credibility and is well positioned to support future deployment across the entire Laboratory as an integrated management initiative. Recommendations for follow-on actions to implement future deployment are provided separately.

  9. Research accomplishments and future goals in particle physics. Final technical report

    International Nuclear Information System (INIS)

    This proposal presents the research accomplishments and ongoing activities of Boston University researchers in high energy physics. Some changes have been made in the structure of the program from the previous arrangement of tasks. Task B, Accelerator Design Physics, is being submitted as a separate proposal for an independent grant; this will be consistent with the nature of the research and the source of funding. Boston University is active in seven principal areas: (1) Task A: Colliding Beams -- physics of e+e- and anti pp collisions; (2) Task C: MACRO Experiment -- search for magnetic monopoles and study of cosmic rays; (3) Task D: Proton Decay -- search for nucleon instability and study of neutrino interactions; (4) Tasks E, J, and N: Particle Theory -- theoretical high energy particle physics, including two Outstanding Junior Investigator awards; (5) Task F: Muon G-2 -- measurement of the anomalous magnetic moment of the muon; (6) Task K: SSCintcal -- calorimetry for the GEM Experiment; (7) Task L: Muon Detectors for the GEM Experiment. The body of the proposal is devoted to detailed discussions of each of the tasks. The total budget request for the program appears in a summary chapter that includes a general budget discussion and individual budget requests and explanations for each of the tasks

  10. International Space Station Research for the Next Decade: International Coordination and Research Accomplishments

    Science.gov (United States)

    Thumm, Tracy L.; Robinson, Julie A.; Johnson-Green, Perry; Buckley, Nicole; Karabadzhak, George; Nakamura, Tai; Sorokin, Igor V.; Zell, Martin; Sabbagh, Jean

    2011-01-01

    During 2011, the International Space Station reached an important milestone in the completion of assembly and the shift to the focus on a full and continuous utilization mission in space. The ISS partnership itself has also met a milestone in the coordination and cooperation of utilization activities including research, technology development and education. We plan and track all ISS utilization activities jointly and have structures in place to cooperate on common goals by sharing ISS assets and resources, and extend the impacts and efficiency of utilization activities. The basic utilization areas on the ISS include research, technology development and testing, and education/outreach. Research can be categorized as applied research for future exploration, basic research taking advantage of the microgravity and open space environment, and Industrial R&D / commercial research focused at industrial product development and improvement. Technology development activities range from testing of new spacecraft systems and materials to the use of ISS as an analogue for future exploration missions to destinations beyond Earth orbit. This presentation, made jointly by all ISS international partners, will highlight the ways that international cooperation in all of these areas is achieved, and the overall accomplishments that have come as well as future perspectives from the cooperation. Recently, the partnership has made special efforts to increase the coordination and impact of ISS utilization that has humanitarian benefits. In this context the paper will highlight tentative ISS utilization developments in the areas of Earth remote sensing, medical technology transfer, and education/outreach.

  11. Task III: UCSD/DIII-D/Textor FY-97-98 Accomplishments

    International Nuclear Information System (INIS)

    OAK (B204) Task III: UCSD/DIII-D/Textor FY-97-98 Accomplishments. A comprehensive report on the physics of pump limiters and particularly, the characterization of ALT-II, was published in Nuclear Fusion, bringing the project to a closure. The performance of the toroidal pump limiter was characterized under full auxiliary heating of 7 MW of NBI and ICRH and full pumping, as stated in the project milestones. Relevant highlights are: (1) Pumping with ALT-II allows for density control. (2) The achieved exhaust efficiency is 4% during NBI operation and near 2% during OH or ICRH operation. (3) We have shown that an exhaust efficiency of 2% is sufficient to satisfy the ash removal requirements of fusion reactors. (4) The plasma particle efflux and the pumped flux both increase with density and heating power. (5) The particle confinement time is less than the energy confinement time by a factor of 4. In summary, pumped belt limiters could provide the density control and ash exhaust requirements of fusion reactors

  12. Accomplishments of the Abrupt Wing Stall (AWS) Program and Future Research Requirements

    Science.gov (United States)

    Hall, Robert M.; Woodson, Shawn H.; Chambers, Joseph R.

    2003-01-01

    The Abrupt Wing Stall (AWS) Program has addressed the problem of uncommanded lateral motions, such as wing drop and wing rock, at transonic speeds. The genesis of this Program was the experience of the F/A-18E/F Program in the late 199O's, when wing drop was discovered in the heart of the maneuver envelope for the pre-production aircraft. While the F/A-18E/F problem was subsequently corrected by a leading-edge flap scheduling change and the addition of a porous door to the wing fold fairing, the AWS Program was initiated as a national response to the lack of technology readiness available at the time of the F/A-18E/F Development Program. The AWS Program objectives were to define causal factors for the F/A-18E/F experience, to gain insights into the flow physics associated with wing drop, and to develop methods and analytical tools so that future programs could identify this type of problem before going to flight test. The paper reviews, for the major goals of the AWS Program, the status of the technology before the program began, the program objectives, accomplishments, and impacts. Lessons learned are presented for the benefit of future programs that must assess whether a vehicle will have uncommanded lateral motions before going to flight test. Finally, recommended future research needs are presented in light of the AWS Program experience.

  13. Research accomplishments and future goals in particle physics. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    This proposal presents the research accomplishments and ongoing activities of Boston University researchers in high energy physics. Some changes have been made in the structure of the program from the previous arrangement of tasks. Task B, Accelerator Design Physics, is being submitted as a separate proposal for an independent grant; this will be consistent with the nature of the research and the source of funding. Boston University is active in seven principal areas: (1) Task A: Colliding Beams -- physics of e{sup +}e{sup {minus}} and {anti p}p collisions; (2) Task C: MACRO Experiment -- search for magnetic monopoles and study of cosmic rays; (3) Task D: Proton Decay -- search for nucleon instability and study of neutrino interactions; (4) Tasks E, J, and N: Particle Theory -- theoretical high energy particle physics, including two Outstanding Junior Investigator awards; (5) Task F: Muon G-2 -- measurement of the anomalous magnetic moment of the muon; (6) Task K: SSCintcal -- calorimetry for the GEM Experiment; (7) Task L: Muon Detectors for the GEM Experiment. The body of the proposal is devoted to detailed discussions of each of the tasks. The total budget request for the program appears in a summary chapter that includes a general budget discussion and individual budget requests and explanations for each of the tasks.

  14. BTA2 and BTA26 are linked with bovine respiratory disease and associated with persistent infection of bovine viral diarrhea virus

    Science.gov (United States)

    Bovine viral diarrhea virus is a pathogen associated with bovine respiratory disease (BRD). BRD causes 28% of all cattle deaths and an annual U.S. loss over $692 million. The objective of this study was to refine the linkage of BRD and association of bovine viral diarrhea-persistent infection (BVD-P...

  15. Local IL2 and IL12 treatment of Bovine Ocular Squamous Cell Carcinoma (BOSCC) and Bovine Vulval Papilloma and Carcinoma Complex (BVPCC) in Cattle in Zimbabwe

    NARCIS (Netherlands)

    Stewart, R.J.E.

    2007-01-01

    Effect of local IL-2 application on bovine cancer In tropical countries there is an increased prevalence of two important cancers in cattle: Bovine Ocular Squamous Cell Carcinoma (BOSCC) and Bovine Vulval Papilloma Carcinoma Complex (BVPCC). Both cancers are associated with increased annual hours of

  16. Gabor Weber Local Descriptor for Bovine Iris Recognition

    OpenAIRE

    Shicai Yang; Shengnan Sun; Lindu Zhao

    2013-01-01

    Iris recognition is a robust biometric technology. This paper proposes a novel local descriptor for bovine iris recognition, named Gabor Weber local descriptor (GWLD). We first compute the Gabor magnitude maps for the input bovine iris image, and then calculate the differential excitation and orientation for each pixel over each Gabor magnitude map. After that, we use these differential excitations and orientations to construct the GWLD histogram representation. Finally, histogram intersectio...

  17. Expression of pluripotency markers in the bovine uterus with adenomyosis

    OpenAIRE

    Łupicka, Martyna; Socha, Barbara; Szczepańska, Agata; Korzekwa, Anna

    2015-01-01

    Background Adenomyosis is a proliferative uterine dysfunction with unknown aetiology. One possible mechanism of its development involves disturbances in stem cell differentiation in uterine tissue. Previously, we identified pluripotent/multipotent cells in the bovine uterus, therefore our present study focused on determining expression of pluripotency markers, NANOG, OCT4 and SOX2, in bovine adenomyotic tissues and cells. Findings Immunolocalisation revealed protein expression of NANOG, OCT4 ...

  18. Bovine Papillomavirus Clastogenic Effect Analyzed in Comet Assay

    OpenAIRE

    Araldi, R. P.; Melo, T. C.; N. Diniz; J. Mazzuchelli-de-Souza; R.F. Carvalho; Beçak, W.; Stocco, R. C.

    2013-01-01

    Bovine papillomavirus (BPV) is an oncogenic virus related to serious livestock diseases. Oncoproteins encoded by BPV are involved in several steps of cellular transformation and have been reported as presenting clastogenic effects in peripheral lymphocytes and primary culture cells. The aim of this study was to evaluate the clastogenic potential of BPV types 1, 2, and 4 by comet assay. Peripheral blood was collected from 37 bovines, 32 infected with different levels of papillomatosis (12 anim...

  19. Application of Functional Genomics for Bovine Respiratory Disease Diagnostics

    OpenAIRE

    Rai, Aswathy N.; William B. Epperson; Bindu Nanduri

    2015-01-01

    Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional ge...

  20. Bovine Viral Diarrhea in Cattle in Indonesia and its Problems

    OpenAIRE

    Sudarisman

    2011-01-01

    Bovine Viral Diarrhea (BVD) is a disease caused by the bovine viral diarrhea virus (BVDV), an ubiquitous, easily transmitted virus with worldwide distribution. The majority of postnatal infections with BVDV are nonclinical, with biphasic temperature elevation and leucopenia followed by a spesific immune response measurable by serum neutralisation test. The infection can be diagnosed serologically or virologically and the disease is recognized by clinical signs and pathological lesions. Diseas...