WorldWideScience

Sample records for bovin phylogeny accomplishments

  1. Phylogeny of bovine species based on AFLP fingerprinting.

    Science.gov (United States)

    Buntjer, J B; Otsen, M; Nijman, I J; Kuiper, M T R; Lenstra, J A

    2002-01-01

    The Bovini species comprise both domestic and wild cattle species. Published phylogenies of this tribe based on mitochondrial DNA contain anomalies, while nuclear sequences show only low variation. We have used amplified fragment length polymorphism (AFLP) fingerprinting in order to detect variation in loci distributed over the nuclear genome. Computer-assisted scoring of electrophoretic fingerprinting patterns yielded 361 markers, which provided sufficient redundancy to suppress stochastic effects of intraspecies polymorphisms and length homoplasies (comigration of non-homologous fragments). Tree reconstructions reveal three clusters: African buffalo with water buffalo, ox with zebu, and bison with wisent. Similarity values suggest a clustering of gaur and banteng, but bifurcating clustering algorithms did not assign consistent positions to these species and yak. We propose that because of shared polymorphisms and reticulations, tree topologies are only partially adequate to represent the phylogeny of the Bovini. Principal-coordinate analysis positions zebu between a gaur/banteng cluster and taurine cattle. This correlates with the region of origin of these species and suggests that genomic distances between the cattle species have been influenced by genetic exchange between neighbouring ancestral populations.

  2. bovine

    African Journals Online (AJOL)

    of various breeds under local conditions of management. (Hale, 1974b). AdditionaIly, this procedure has been used to assess the production of LH by the bovine anterior pituitary in vitro and to study the relationships between this production and the activity of the pineal- hypothalamic axis (Hayes, Knight & Symington, 1974;.

  3. 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...

  4. 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.

  5. The Joint Accomplishment of Identity

    Science.gov (United States)

    Hand, Victoria; Gresalfi, Melissa

    2015-01-01

    Identity has become a central concept in the analysis of learning from social perspectives. In this article, we draw on a situative perspective to conceptualize identity as a "joint accomplishment" between individuals and their interactions with norms, practices, cultural tools, relationships, and institutional and cultural contexts.…

  6. The virtual accomplishment of knitting

    DEFF Research Database (Denmark)

    Heinemann, T.; Möller, R. L.

    2016-01-01

    . This means, among other things, that learners need to detect, diagnose and correct their errors without assistance from an expert. In this paper we focus on how this is accomplished by individuals attempting to learn how to knit by following instructions from a video tutorial. We show that novice knitters...... the same error over and over again. We also demonstrate, however, that novice knitters eventually turn to the video tutorial as a kind of diagnostic tool; and that when they do so, they typically manage to diagnose and correct the initial error they made and succeed in the instructed task. © 2015 Elsevier...

  7. Advanced Fuels Campaign 2016 Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Richardson, Kate M. [Idaho National Lab., Idaho Falls, ID (United States)

    2016-11-01

    AFC management and integration activities in FY-16 included continued support for international collaborations, primarily with France, Japan, the European Union, Republic of Korea, and China, as well as various working group and expert group activities in the Organization for Economic Cooperation and Development Nuclear Energy Agency (OECD-NEA) and the International Atomic Energy Agency (IAEA). Three industry-led Funding Opportunity Announcements (FOAs) and two university-led Integrated Research Projects (IRPs) funded in 2013, made significant progress in fuels and materials development. All are closely integrated with AFC and accident-tolerant fuels (ATF) research. Accomplishments made during FY-16 are highlighted in this report, which focuses on completed work and results.

  8. 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...

  9. 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

  10. Advanced fuels campaign 2013 accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Braase, Lori [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hamelin, Doug [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    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.

  11. 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.

  12. 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...... uncertainty in the mapping. Recently developed probabilistic methods can incorporate statistical uncertainty in the character mappings. In these methods, focus is on a probability distribution of mutational mappings instead of a single estimate of the mutational mapping....

  13. 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.

  14. Assessing Accomplished Teaching: Good Strides, Great Challenges

    Science.gov (United States)

    Norman, Antony D.

    2010-01-01

    This article surveys efforts at the national and international level to define and assess accomplished teaching with particular attention devoted to how assessments of accomplished teaching connect to student learning. The author finds that most assessments are based on aspects of teaching that, presumably, come together as accomplished teaching.…

  15. 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.

  16. 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.

  17. 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... products to revise the conditions for the importation of live bovines and products derived from bovines...

  18. 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 Highlight...

  19. 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...

  20. 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.

  1. 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

  2. Phylogeny and Evolution of Lepidoptera.

    Science.gov (United States)

    Mitter, Charles; Davis, Donald R; Cummings, Michael P

    2017-01-31

    Until recently, deep-level phylogeny in Lepidoptera, the largest single radiation of plant-feeding insects, was very poorly understood. Over the past two decades, building on a preceding era of morphological cladistic studies, molecular data have yielded robust initial estimates of relationships both within and among the ∼43 superfamilies, with unsolved problems now yielding to much larger data sets from high-throughput sequencing. Here we summarize progress on lepidopteran phylogeny since 1975, emphasizing the superfamily level, and discuss some resulting advances in our understanding of lepidopteran evolution.

  3. 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.

  4. The Assessment of Student Accomplishment in College.

    Science.gov (United States)

    Richards, James M., Jr.; And Others

    To assess the non-academic accomplishments of college students more broadly than do grades, a questionnaire having 12 scales was designed and administered to 3147 freshmen, 5127 sophomores, and 1566 seniors in a variety of colleges. The scales measured achievement, as determined by the students themselves, in leadership, social participation, the…

  5. Overview of LAMPF and its accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, L.

    1978-04-01

    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.

  6. The shape of mammalian phylogeny

    DEFF Research Database (Denmark)

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

    2011-01-01

    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...

  7. 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).

  8. Accomplishments and challenges of surgical simulation.

    Science.gov (United States)

    Satava, R M

    2001-03-01

    For nearly a decade, advanced computer technologies have created extraordinary educational tools using three-dimensional (3D) visualization and virtual reality. Pioneering efforts in surgical simulation with these tools have resulted in a first generation of simulators for surgical technical skills. Accomplishments include simulations with 3D models of anatomy for practice of surgical tasks, initial assessment of student performance in technical skills, and awareness by professional societies of potential in surgical education and certification. However, enormous challenges remain, which include improvement of technical fidelity, standardization of accurate metrics for performance evaluation, integration of simulators into a robust educational curriculum, stringent evaluation of simulators for effectiveness and value added to surgical training, determination of simulation application to certification of surgical technical skills, and a business model to implement and disseminate simulation successfully throughout the medical education community. This review looks at the historical progress of surgical simulators, their accomplishments, and the challenges that remain.

  9. New accomplishments of Ambiente & Agua scientific journal

    OpenAIRE

    Getulio Teixeira Batista

    2009-01-01

    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 D...

  10. 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.

  11. 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.

  12. 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.

  13. PREVALENCE OF BOVINE (1)

    African Journals Online (AJOL)

    BACKGROUND: Tuberculosis is caused by a number of Mycobacterium species, of which Mycobacterium bovis, causing 'bovine tuberculosis' is ... KEY WORDS: Mycobacterium bovis, Zoonosis, Holeta, Ethiopia causing 'bovine tuberculosis ..... isolation of infected animals in which communal grazing and watering practiced.

  14. 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.

  15. 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.

  16. NASA's Big Earth Data Initiative Accomplishments

    Science.gov (United States)

    Klene, Stephan A.; Pauli, Elisheva; Pressley, Natalie N.; Cechini, Matthew F.; McInerney, Mark

    2017-01-01

    The goal of NASA's effort for BEDI is to improve the usability, discoverability, and accessibility of Earth Observation data in support of societal benefit areas. Accomplishments: In support of BEDI goals, datasets have been entered into Common Metadata Repository(CMR), made available via the Open-source Project for a Network Data Access Protocol (OPeNDAP), have a Digital Object Identifier (DOI) registered for the dataset, and to support fast visualization many layers have been added in to the Global Imagery Browse Services (GIBS).

  17. 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.

  18. Molecular phylogeny of Arthrotardigrada (Tardigrada).

    Science.gov (United States)

    Jørgensen, Aslak; Faurby, Søren; Hansen, Jesper G; Møbjerg, Nadja; Kristensen, Reinhardt M

    2010-03-01

    Tardigrades are microscopic ecdysozoans with a worldwide distribution covering marine, limnic and terrestrial habitats. They are regarded as a neglected phylum with regard to studies of their phylogeny. During the last decade molecular data have been included in the investigation of tardigrades. However, the marine arthrotardigrades are still poorly sampled due to their relative rarity, difficult identification and minute size even for tardigrades. In the present study, we have sampled various arthrotardigrades and sequenced the 18S and partial 28S ribosomal subunits. The phylogenetic analyses based on Bayesian inference and maximum parsimony inferred Heterotardigrada (Arthrotardigrada+Echiniscoidea) and Eutardigrada to be monophyletic. Arthrotardigrada was inferred to be paraphyletic as the monophyletic Echiniscoidea is included within the arthrotardigrades. The phylogenetic positions of Stygarctidae and Batillipedidae are poorly resolved with low branch support. The Halechiniscidae is inferred to be polyphyletic as the currently recognized Styraconyxinae is not part of the family. Archechiniscus is the sister-group to the Halechiniscidae and Orzeliscus is placed as one of the basal halechiniscids. The phylogeny of the included eutardigrade taxa resembles the current molecular phylogenies. The genetic diversity within Arthrotardigrada is much larger (18S 15.1-26.5%, 28S 7.2-20.7%) than within Eutardigrada (18S 1.0-12.6%, 28S 1.3-8.2%). This can be explained by higher substitution rates in the arthrotardigrades or by a much younger evolutionary age of the sampled eutardigrades. Copyright 2009 Elsevier Inc. All rights reserved.

  19. Health and Environmental Research. Summary of Accomplishments

    Science.gov (United States)

    1984-04-01

    This is a short account of a 40-year-old health and environmental research program performed in national laboratories, universities, and research institutes. Under the sponsorship of the federal agencies that were consecutively responsible for the national energy mission, this research program has contributed to the understanding of the human health and environmental effects of emergining energy technologies. In so doing, it has also evolved several nuclear techniques for the diagnosis and treatment of human ills. The form of this presentation is through examples of significant, tangible accomplishments in each of these areas at certain times to illustrate the role and impact of the research program. The narrative of this research program concludes with a perspective of its past and a prospectus on its future.

  20. 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.

  1. 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.

  2. The space shuttle program technologies and accomplishments

    CERN Document Server

    Sivolella, Davide

    2017-01-01

    This book tells the story of the Space Shuttle in its many different roles as orbital launch platform, orbital workshop, and science and technology laboratory. It focuses on the technology designed and developed to support the missions of the Space Shuttle program. Each mission is examined, from both the technical and managerial viewpoints. Although outwardly identical, the capabilities of the orbiters in the late years of the program were quite different from those in 1981. Sivolella traces the various improvements and modifications made to the shuttle over the years as part of each mission story. Technically accurate but with a pleasing narrative style and simple explanations of complex engineering concepts, the book provides details of many lesser known concepts, some developed but never flown, and commemorates the ingenuity of NASA and its partners in making each Space Shuttle mission push the boundaries of what we can accomplish in space. Using press kits, original papers, newspaper and magazine articles...

  3. Low Cost Methods to Accomplish Aeronomy Science

    Science.gov (United States)

    Swenson, G. R.

    2013-12-01

    Accomplishment of aeronomy science using low cost methods involves a number of innovative considerations. These methods will be discussed. They include making broad use of internet to control and operate distributed sensors. Sensor controls should be simple and most important reliable. Imagers are a common sensor for optical systems and include common computer interfaces and menu driven operations which often don't require special software or engineering development. Small, inexpensive but reliable satellite systems are evolving in the Cubesat community. Effective use of students is invaluable, giving them responsibility to operate instrumentation and to routinely archive the data. Management of students is especially important in the early phase of their training to insure quality performance. These ideas will be elaborated on, and most importantly, the science motive is the most important driver for what is done.

  4. The discursive accomplishment of regimes of automobility

    DEFF Research Database (Denmark)

    Lindegaard, Laura Bang

    2016-01-01

    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...... findings, ethnomethodologically informed discourse analysis acknowledges the importance of studies of how rationalities are continuously made observably relevant for all practical purposes. However, it is not the entire domain of ethnomethodological research that invites to be connected up with Foucauldian...

  5. Measuring Asymmetry in Time-Stamped Phylogenies.

    Directory of Open Access Journals (Sweden)

    Bethany L Dearlove

    2015-07-01

    Full Text Available 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 phylogeny are sampled at different times and (b only test for global asymmetry, and hence suffer from false negatives when asymmetry is localised to part of a phylogeny. We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate. We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry. In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models.

  6. 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 ...

  7. 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 on...

  8. 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 document...

  9. Diagnosis of bovine neosporosis.

    Science.gov (United States)

    Dubey, J P; Schares, G

    2006-08-31

    The protozoan parasite Neospora caninum is a major cause of abortion in cattle. The diagnosis of neosporosis-associated mortality and abortion in cattle is difficult. In the present paper we review histologic, serologic, immunohistochemical, and molecular methods for dignosis of bovine neosporosis. Although not a routine method of diagnosis, methods to isolate viable N. caninum from bovine tissues are also reviewed.

  10. 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....

  11. 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

  12. Advanced Fuels Campaign FY 2014 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Braase, Lori [Idaho National Lab. (INL), Idaho Falls, ID (United States). INL Systems Analyses; May, W. Edgar [Idaho National Lab. (INL), Idaho Falls, ID (United States). INL Systems Analyses

    2014-10-01

    accident conditions than traditional fuel systems. AFC management and integration activities included continued support for international collaborations, primarily with France, Japan, the European Union, Republic of Korea, and China, as well as various working group and expert group activities in the Organization for Economic Cooperation and Development Nuclear Energy Agency (OECD-NEA) and the International Atomic Energy Agency (IAEA). Three industry-led Funding Opportunity Announcements (FOAs) and two university-led Integrated Research Projects (IRPs), funded in 2013, made significant progress in fuels and materials development. All are closely integrated with AFC and Accident Tolerant Fuels (ATF) research. Accomplishments made during fiscal year (FY) 2014 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 lead technical contact is provided for each section.

  13. Some History and Accomplishments of the IUSS

    Science.gov (United States)

    Brevik, Eric C.; Hartemink, Alfred E.

    2013-04-01

    Urban Soils) and three standing committees (Committee on awards and prizes, Committee on budget and finances, and Committee on statutes and byelaws). Membership in ISSS/IUSS increased from around 550 after WWII to over 60,000 today. The IUSS also provides Honorary Membership to soil scientists who have significant accomplishments in the field; to date 87 soil scientists have been so recognized from all over the globe. The IUSS is the most important global link to the world's leading soil science and soil scientists.

  14. Ontogeny and phylogeny of language.

    Science.gov (United States)

    Yang, Charles

    2013-04-16

    How did language evolve? A popular approach points to the similarities between the ontogeny and phylogeny of language. Young children's language and nonhuman primates' signing both appear formulaic with limited syntactic combinations, thereby suggesting a degree of continuity in their cognitive abilities. To evaluate the validity of this approach, as well as to develop a quantitative benchmark to assess children's language development, I propose a formal analysis that characterizes the statistical profile of grammatical rules. I show that very young children's language is consistent with a productive grammar rather than memorization of specific word combinations from caregivers' speech. Furthermore, I provide a statistically rigorous demonstration that the sign use of Nim Chimpsky, the chimpanzee who was taught American Sign Language, does not show the expected productivity of a rule-based grammar. Implications for theories of language acquisition and evolution are discussed.

  15. 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

  16. Phylogeny Inference Based on Spectral Graph Clustering

    National Research Council Canada - National Science Library

    Zhang, Shu-Bo; Zhou, Song-Yu; He, Jian-Guo; Lai, Jian-Huang

    2011-01-01

    ...; this may enlarge the error gradually, and lead to an inaccurate tree topology. In this study, a splitting algorithm is proposed for phylogeny inference by using the spectral graph clustering (SGC) technique...

  17. Phylogeny of nematodes from birds of prey

    OpenAIRE

    Honisch, Michaela

    2010-01-01

    Birds of prey host a wide variety of endoparasites. The majority of these endoparasites are nematodes. They can be found mainly in the digestive and respiratory system. The current accepted phylogeny of nematodes found in birds of prey is based on morphological traits. In this study molecular data were used to assess phylogenetic relationships in this group of parasitic nematodes. The aim of the study was to evaluate a method for rapid species identification, to construct a phylogeny of paras...

  18. 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.

  19. Taxonomy and phylogeny of chytrids.

    Science.gov (United States)

    Barr, D J

    1978-04-01

    Thallus development, zoospore size, zoospore ultrastructural complexity and organization, and flagellum length are cited as important in phylogeny of the Chytridiales (chytrids) and should be the bases for this classification. Discharge of zoospores is also cited as important although emphasis is not placed on operculation. It is proposed that simple, eucarpic, monocentric chytrids which discharge zoospores following dissolution of the sporangium wall evolved into multipapilliate species of Rhizophydium and 2 lines of evolution from these species are documented with examples. In one line they evolved into single-pored species such as R. pollinis-pini, then to Chytridium and tendochytrium-like chytrids and to polycentric chytrids such as Nowakowskiella and Cladochytrium. The second line evolved from multipapilliate Rhizophydium species to Phlyctochytrium and Entophlyctis, and to the order Blastocladiales. Rhizophlyctis rosea and some olpidiaceous chytrids, because of a fibrillar rhizoplast in their zoospores do not appear close to Rhizophydium-related chytrids and may require separate subordinal rank in classification. It is proposed that zoospores of the advanced members of the class Chytridiomycetes have reached limits for further zoospore development because of size; however, the zoospore is no longer essential for them because they have developed a filamentous habit of growth.

  20. Phylogeny inference based on spectral graph clustering.

    Science.gov (United States)

    Zhang, Shu-Bo; Zhou, Song-Yu; He, Jian-Guo; Lai, Jian-Huang

    2011-04-01

    Phylogeny inference is an importance issue in computational biology. Some early approaches based on characteristics such as the maximum parsimony algorithm and the maximum likelihood algorithm will become intractable when the number of taxonomic units is large. Recent algorithms based on distance data which adopt an agglomerative scheme are widely used for phylogeny inference. However, they have to recursively merge the nearest pair of taxa and estimate a distance matrix; this may enlarge the error gradually, and lead to an inaccurate tree topology. In this study, a splitting algorithm is proposed for phylogeny inference by using the spectral graph clustering (SGC) technique. The SGC algorithm splits graphs by using the maximum cut criterion and circumvents optimization problems through solving a generalized eigenvalue system. The promising features of the proposed algorithm are the following: (i) using a heuristic strategy for constructing phylogenies from certain distance functions, which are not even additive; (ii) distance matrices do not have to be estimated recursively; (iii) inferring a more accurate tree topology than that of the Neighbor-joining (NJ) algorithm on simulated datasets; and (iv) strongly supporting hypotheses induced by other methods for Baculovirus genomes. Our numerical experiments confirm that the SGC algorithm is efficient for phylogeny inference. © Mary Ann Liebert, Inc.

  1. Conodont affinity and chordate phylogeny.

    Science.gov (United States)

    Donoghue, P C; Forey, P L; Aldridge, R J

    2000-05-01

    Current information on the conodonts Clydagnathus windsorensis (Globensky) and Promissum pulchrum Kovács-Endrödy, together with the latest interpretations of conodont hard tissues, are reviewed and it is concluded that sufficient evidence exists to justify interpretation of the conodonts on a chordate model. A new phylogenetic analysis is undertaken, consisting of 17 chordate taxa and 103 morphological, physiological and biochemical characters; conodonts are included as a primary taxon. Various experiments with character coding, taxon deletion and the use of constraint trees are carried out. We conclude that conodonts are cladistically more derived than either hagfishes or lampreys because they possess a mineralised dermal skeleton and that they are the most plesiomorphic member of the total group Gnathostomata. We discuss the evolution of the nervous and sensory systems and the skeleton in the context of our optimal phylogenetic tree. There appears to be no simple evolution of free to canal-enclosed neuromasts; organised neuromasts within canals appear to have arisen at least three times from free neuromasts or neuromasts arranged within grooves. The mineralised vertebrate skeleton first appeared as odontodes of dentine or dentine plus enamel in the paraconodont/euconodont feeding apparatus. Bone appeared later, co-ordinate with the development of a dermal skeleton, and it appears to have been primitively acellular. Atubular dentine is more primitive than tubular dentine. However, the subsequent distribution of the different types of dentine (e.g. mesodentine, orthodentine), suggests that these tissue types are homoplastic. The topology of relationships and known stratigraphic ranges of taxa in our phylogeny predict the existence of myxinoids and petromyzontids in the Cambrian.

  2. Enzootic bovine leucosis.

    Science.gov (United States)

    Tyler, L

    1978-09-02

    Enzootic bovine leucosis is associated with infection by bovine leucosis virus. The incubation period is measured in years and a minority of infected animals develop clinical signs. The disease is widespread in Europe and elsewhere and can cause significant economic loss. The epidemiology is incompletely understood and findings from one cattle production system may not be directly applicable to another. Major control programmes exist in Denmark and West Germany and control schemes are being developed elsewhere. Eradication of enzootic bovine leucosis has been established as a goal in the EEC and research is revealing the ways in which this goal may be attained. To be effective, control and epidemiological monitoring must be interactive. Recently introduced serological tests, of improved sensitivity, provide a valuable tool.

  3. 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.

  4. Intervet Symposium: bovine neosporosis

    NARCIS (Netherlands)

    Schetters, T.; Dubey, J.P.; Adrianarivo, A.; Frankena, K.; Romero, J.J.; Pérez, E.; Heuer, C.; Nicholson, C.; Russell, D.; Weston, J.

    2004-01-01

    This article summarises the most relevant data of presentations delivered at the 19th International Conference of the World Association for the Advancement of Veterinary Parasitology (WAAVP) held in New Orleans, LA, USA, from 10 to 14 August 2003) in a symposium session on bovine neosporosis. The

  5. 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 ...

  6. 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.

  7. 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.

  8. FTA fuel cell bus program : research accomplishments through 2011.

    Science.gov (United States)

    2012-03-01

    Prepared by the Federal Transit Administration (FTA) Office of Research, Demonstration, and Innovation (TRI), this report summarizes the accomplishments of fuel-cell-transit-bus-related research and demonstrations projects supported by FTA through 20...

  9. 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 p...

  10. Book review: Insect morphology and phylogeny

    Directory of Open Access Journals (Sweden)

    Susanne Randolf

    2014-05-01

    Full Text Available Beutel RG, Friedrich F, Ge S-Q, Yang X-K (2014 Insect Morphology and Phylogeny: A textbook for students of entomology. De Gruyter, Berlin/Boston, 516 pp., softcover. ISBN 978-3-11-026263-6.

  11. Bovine parainfluenza-3 virus.

    Science.gov (United States)

    Ellis, John A

    2010-11-01

    Bovine parainfluenza-3 virus (bPI(3)V) is a long-recognized, currently underappreciated, endemic infection in cattle populations. Clinical disease is most common in calves with poor passive transfer or decayed maternal antibodies. It is usually mild, consisting of fever, nasal discharge, and dry cough. Caused at least partly by local immunosuppressive effects, bPI(3)V infection is often complicated by coinfection with other respiratory viruses and bacteria, and is therefore an important component of enzootic pneumonia in calves and bovine respiratory disease complex in feedlot cattle. Active infection can be diagnosed by virus isolation from nasal swabs, or IF testing on smears made from nasal swabs. Timing of sampling is critical in obtaining definitive diagnostic test results. Parenteral and intranasal modified live vaccine combination vaccines are available. Priming early in calfhood with intranasal vaccine, followed by boosting with parenteral vaccine, may be the best immunoprophylactic approach. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. Camel and bovine chymosin

    DEFF Research Database (Denmark)

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

    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...... chymosin. Both enzymes possess local positively charged patches on their surface that can play a role in interactions with the overall negatively charged C-terminus of κ-casein. Camel chymosin contains two additional positive patches that favour interaction with the substrate. The improved electrostatic...... 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....

  13. Mycotic bovine nasal granuloma

    Directory of Open Access Journals (Sweden)

    Conti Díaz Ismael Alejandro

    2003-01-01

    Full Text Available A case of mycotic bovine nasal granuloma in a 10 year-old Jersey cow, produced by Drechslera halodes is presented. Histopathological sections showed abundant hyaline and pigmented extra and intracellular fungal structures together with a polymorphic cellular granuloma formed by neutrophils, lymphocytes, plasmocytes, histiocytes and giant cells of the Langhans type. It is the first case of mycotic bovine nasal granuloma recognized in Uruguay although this disease seems to be frequent according to the opinion of veterinarian specialists. Another similar clinical case also in a Jersey cow from the same dairy house with an intense cellular infiltrate rich in eosinophils without granulomatous image, together with extracellular hyaline and fuliginous fungal forms, is also referred for comparative purposes. Geotrichum sp. was isolated. The need of an early diagnosis and treatment of the disease is stressed.

  14. Viral infections and bovine mastitis: a review.

    Science.gov (United States)

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

    2002-08-02

    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 parainfluenza 3 virus-induced clinical mastitis, while an intramammary inoculation of foot-and-mouth disease virus resulted in necrosis of the mammary gland. Subclinical mastitis has been induced after a simultaneous intramammary and intranasal inoculation of lactating cows with bovine herpesvirus 4. Bovine leukaemia virus has been detected in mammary tissue of cows with subclinical mastitis, but whether this virus was able to induce bovine mastitis has not been reported. Bovine herpesvirus 2, vaccinia, cowpox, pseudocowpox, vesicular stomatitis, foot-and-mouth disease viruses, and bovine papillomaviruses can play an indirect role in the aetiology of bovine mastitis. These viruses can induce teat lesions, for instance in the ductus papillaris, which result in a reduction of the natural defence mechanisms of the udder and indirectly in bovine mastitis due to bacterial pathogens. Bovine herpesvirus 1, bovine viral diarrhoea virus, bovine immunodeficiency virus, and bovine leukaemia virus infections may play an indirect role in bovine mastitis, due to their immunosuppressive properties. But, more research is warranted to underline their indirect role in bovine mastitis. We conclude that viral infections can play a direct or indirect role in the aetiology of bovine mastitis; therefore, their importance in the aetiology of bovine mastitis and their economical impact needs further attention.

  15. Diagnostic imaging in bovine orthopedics.

    Science.gov (United States)

    Kofler, Johann; Geissbühler, Urs; Steiner, Adrian

    2014-03-01

    Although a radiographic unit is not standard equipment for bovine practitioners in hospital or field situations, ultrasound machines with 7.5-MHz linear transducers have been used in bovine reproduction for many years, and are eminently suitable for evaluation of orthopedic disorders. The goal of this article is to encourage veterinarians to use radiology and ultrasonography for the evaluation of bovine orthopedic disorders. These diagnostic imaging techniques improve the likelihood of a definitive diagnosis in every bovine patient but especially in highly valuable cattle, whose owners demand increasingly more diagnostic and surgical interventions that require high-level specialized techniques. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. A molecular phylogeny of living primates.

    Directory of Open Access Journals (Sweden)

    Polina Perelman

    2011-03-01

    Full Text Available Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb from 186 primates representing 61 (~90% of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

  17. A Molecular Phylogeny of Living Primates

    Science.gov (United States)

    Perelman, Polina; Johnson, Warren E.; Roos, Christian; Seuánez, Hector N.; Horvath, Julie E.; Moreira, Miguel A. M.; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C.; Silva, Artur; O'Brien, Stephen J.; Pecon-Slattery, Jill

    2011-01-01

    Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. PMID:21436896

  18. Plastome phylogeny and early diversification of Brassicaceae

    OpenAIRE

    Guo, Xinyi; Liu, Jianquan; Hao, Guoqian; Zhang, Lei; Mao, Kangshan; Wang, Xiaojuan; Zhang, Dan; Ma, Tao; Hu, Quanjun; Al-Shehbaz, Ihsan A.; Koch, Marcus A.

    2017-01-01

    Background The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Results Bayesian and maximum likelihood phylogenetic analyses using a partiti...

  19. 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

  20. Introduction. [accomplishments of Apollo 17 flight during lunar exploration

    Science.gov (United States)

    Calio, A. J.

    1973-01-01

    The accomplishments of the Apollo 17 flight are briefly described. The characteristics of the Taurus-Littrow region landing site are analyzed. The experiments conducted to analyze the composition of the lunar surface are reported. The extent to which the results of the Apollo 17 experiments confirmed theories concerning lunar seismology, thermal characteristics, presence of radioactive materials, and origin of the moon is developed.

  1. 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.

  2. The socio-educational context of literacy accomplishment in ...

    African Journals Online (AJOL)

    Literacy does not develop in a vacuum. Reading is taught and is learnt within a social context, and the school and teachers are a central part of this context. This context will affect the way learners acquire literacy as well as the consequences of their literacy accomplishments within the learning environment. This article ...

  3. Psychological Type and the Accomplishment of Student Development Tasks.

    Science.gov (United States)

    Anchors, W. Scott; Robinson, Daniel C.

    1992-01-01

    Examined relationship between Jung's concept of psychological type and accomplishment of developmental tasks among matriculating traditional-age college students (n=472) using Myers-Briggs Type Indicator-Form F and Student Development Task Inventory (2nd edition). Results supported notion that individual differences exist beyond traditional models…

  4. Breeding drought tolerant cowpea: constraints, accomplishments, and future prospects

    NARCIS (Netherlands)

    Agbicodo, A.C.M.E.; Fatokun, C.A.; Muranaka, S.; Visser, R.G.F.; Linden, van der C.G.

    2009-01-01

    This review presents an overview of accomplishments on different aspects of cowpea breeding for drought tolerance. Furthermore it provides options to enhance the genetic potential of the crop by minimizing yield loss due to drought stress. Recent efforts have focused on the genetic dissection of

  5. 2014 Science Accomplishments Report of the Pacific Northwest Research Station

    Science.gov (United States)

    Rhonda Mazza

    2015-01-01

    Communicating the scientific knowledge generated by the Pacific Northwest Research Station is integral to our mission. The 2014 Science Accomplishments reports highlights the breadth of the station’s research, the relevance of our science findings, and the application of these findings. The photographs throughout the report showcase the region where we work and how...

  6. 2013 Science Accomplishments Report of the Pacific Northwest Research Station

    Science.gov (United States)

    Rhonda Mazza

    2014-01-01

    Communicating the scientific knowledge generated by the Pacific Northwest Research Station is integral to our mission. The 2013 Science Accomplishments reports highlights the breadth of the station’s research, the relevance of our science findings, and the application of these findings. The photographs throughout the report showcase the region where we work and how...

  7. 2009 Science Accomplishments Report of the Pacific Northwest Research Station

    Science.gov (United States)

    Rhonda Mazza

    2010-01-01

    This report highlights significant research findings and accomplishments by scientists at the Pacific Northwest (PNW) Research Station during fiscal year 2009. The mission of the PNW Research Station is to generate and communicate scientific knowledge that helps people understand and make informed choices about people, natural resources...

  8. Towards a phylogeny of the Tenebrionoidea (Coleoptera).

    Science.gov (United States)

    Gunter, Nicole L; Levkaničová, Zuzana; Weir, Tom H; Ślipiński, Adam; Cameron, Stephen L; Bocak, Ladislav

    2014-10-01

    The phylogenetic relationships of the beetle superfamily Tenebrionoidea are investigated using the most comprehensive genetic data set compiled to date. With ∼34,000 described species in approximately 1250 genera and 28 families, Tenebrionoidea represent one of the most diverse and species-rich superfamilies of beetles. The interfamilial relationships of the Tenebrionoidea are poorly known; previous morphological and molecular phylogenies recovered few well-supported and often conflicting relationships between families. Here we present a molecular phylogeny of Tenebrionoidea based on genes commonly used to resolve family and superfamily-level phylogenies of beetles (18S, 28S, 16S, 12S, tRNA Val and COI). The alignment spanned over 6.5KB of DNA sequence and over 300 tenebrionoid genera from 24 of the 28 families were sampled. Maximum Likelihood and Bayesian analysis could not resolve deeper level divergences within the superfamily and very few relationships between families were supported. Increasing gene coverage in the alignment by removing taxa with missing data did not improve clade support but when rogue taxa were removed increased resolution was recovered. Investigation of signal strength suggested conflicting phylogenetic signal was present in the standard genes used for beetle phylogenetics, even when rogue taxa were removed. Our study of Tenebrionoidea highlights that even with relatively comprehensive taxon sampling within a lineage, this standard set of genes is unable to resolve relationships within this superfamily. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Phylogeny and evolution of RNA structure.

    Science.gov (United States)

    Gesell, Tanja; Schuster, Peter

    2014-01-01

    Darwin's conviction that all living beings on Earth are related and the graph of relatedness is tree-shaped has been essentially confirmed by phylogenetic reconstruction first from morphology and later from data obtained by molecular sequencing. Limitations of the phylogenetic tree concept were recognized as more and more sequence information became available. The other path-breaking idea of Darwin, natural selection of fitter variants in populations, is cast into simple mathematical form and extended to mutation-selection dynamics. In this form the theory is directly applicable to RNA evolution in vitro and to virus evolution. Phylogeny and population dynamics of RNA provide complementary insights into evolution and the interplay between the two concepts will be pursued throughout this chapter. The two strategies for understanding evolution are ultimately related through the central paradigm of structural biology: sequence ⇒ structure ⇒ function. We elaborate on the state of the art in modeling both phylogeny and evolution of RNA driven by reproduction and mutation. Thereby the focus will be laid on models for phylogenetic sequence evolution as well as evolution and design of RNA structures with selected examples and notes on simulation methods. In the perspectives an attempt is made to combine molecular structure, population dynamics, and phylogeny in modeling evolution.

  10. Phylogeny of Opiliones (Arachnida): An Assessment of the "Cyphopalpatores" Concept

    National Research Council Canada - National Science Library

    Jeffrey W. Shultz

    1998-01-01

    .... Because most genitalic characters within Opiliones are unique to that order, genitalic characters cannot be polarized and opilion phylogeny cannot be rooted using objective outgroup comparison...

  11. Material Recover and Waste Form Development--2016 Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Todd, Terry A. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Vienna, John [Idaho National Lab. (INL), Idaho Falls, ID (United States); Paviet, Patricia [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-12-01

    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). This MRWFD accomplishments report summarizes the results of the research and development (R&D) efforts performed within MRWFD in Fiscal Year (FY) 2016. Each section of the report contains an overview of the activities, results, technical point of contact, applicable references, and documents produced during the FY. This report briefly outlines campaign management and integration activities but primarily focuses on the many technical accomplishments of FY 2016. The campaign continued to use an engineering-driven, science-based approach to maintain relevance and focus.

  12. Pioneer unmanned air vehicle accomplishments during Operation Desert Storm

    Science.gov (United States)

    Christner, James H.

    1991-12-01

    This paper will describe the accomplishments and lessons learned of the Pioneer Unmanned Air Vehicle (UAV) during Operations Desert Shield and Desert Storm. The Pioneer UAV has been deployed with three branches of the U.S. military (USA, USN, and USMC) for the past four years. Although the system has compiled over 6,000 flight hours, the recent conflict in the Gulf is the first opportunity to demonstrate its true value in a combat scenario. In a relatively short time (42 days), 307 flights and 1,011 flight hours were completed on Operation Desert Storm. This, coupled with the accuracy of various weapons systems that Pioneer observed/cued for, resulted in timely target engagements. This paper will chronicle the Pioneer deployment and accomplishments on Operations Desert Shield and Desert Storm. Various employment methods, tactics, doctrine, and lessons learned will be presented.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Health and Environmental Research: Summary of Accomplishments. Volume 2

    Science.gov (United States)

    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. When Lightning Strikes Twice: Profoundly Gifted, Profoundly Accomplished.

    Science.gov (United States)

    Makel, Matthew C; Kell, Harrison J; Lubinski, David; Putallaz, Martha; Benbow, Camilla P

    2016-07-01

    The educational, occupational, and creative accomplishments of the profoundly gifted participants (IQs ⩾ 160) in the Study of Mathematically Precocious Youth (SMPY) are astounding, but are they representative of equally able 12-year-olds? Duke University's Talent Identification Program (TIP) identified 259 young adolescents who were equally gifted. By age 40, their life accomplishments also were extraordinary: Thirty-seven percent had earned doctorates, 7.5% had achieved academic tenure (4.3% at research-intensive universities), and 9% held patents; many were high-level leaders in major organizations. As was the case for the SMPY sample before them, differential ability strengths predicted their contrasting and eventual developmental trajectories-even though essentially all participants possessed both mathematical and verbal reasoning abilities far superior to those of typical Ph.D. recipients. Individuals, even profoundly gifted ones, primarily do what they are best at. Differences in ability patterns, like differences in interests, guide development along different paths, but ability level, coupled with commitment, determines whether and the extent to which noteworthy accomplishments are reached if opportunity presents itself. © The Author(s) 2016.

  2. Composition and similarity of bovine rumen microbiota across individual animals.

    Directory of Open Access Journals (Sweden)

    Elie Jami

    Full Text Available The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.

  3. 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

  4. Construction of random perfect phylogeny matrix

    Directory of Open Access Journals (Sweden)

    Mehdi Sadeghi

    2010-11-01

    Full Text Available Mehdi Sadeghi1,2, Hamid Pezeshk4, Changiz Eslahchi3,5, Sara Ahmadian6, Sepideh Mah Abadi61National Institute of Genetic Engineering and Biotechnology, Tehran, Iran; 2School of Computer Science, 3School of Mathematics, Institute for Research in Fundamental Sciences (IPM, Tehran, Iran; 4School of Mathematics, Statistics and Computer Sciences, Center of Excellence in Biomathematics, College of Science, University of Tehran, Tehran, Iran; 5Department of Mathematics, Shahid Beheshti University, G.C., Tehran, Iran; 6Department of Computer Engineering, Sharif University of Technology, Tehran, IranPurpose: Interest in developing methods appropriate for mapping increasing amounts of genome-wide molecular data are increasing rapidly. There is also an increasing need for methods that are able to efficiently simulate such data.Patients and methods: In this article, we provide a graph-theory approach to find the necessary and sufficient conditions for the existence of a phylogeny matrix with k nonidentical haplotypes, n single nucleotide polymorphisms (SNPs, and a population size of m for which the minimum allele frequency of each SNP is between two specific numbers a and b.Results: We introduce an O(max(n2, nm algorithm for the random construction of such a phylogeny matrix. The running time of any algorithm for solving this problem would be Ω (nm.Conclusion: We have developed software, RAPPER, based on this algorithm, which is available at http://bioinf.cs.ipm.ir/softwares/RAPPER.Keywords: perfect phylogeny, minimum allele frequency (MAF, tree, recursive algorithm 

  5. Phylogeny of Artemisia L. : Recent developments | Hayat | African ...

    African Journals Online (AJOL)

    The genus is divided into five large groups Absinthium DC., Artemisia L., Dracunculus Besser, Seriphidium Besser and Tridantatae (Rydb.) McArthur. Its phylogeny was based on the two hypothesized evolutionary trends, loss of fertility in the disc florets and loss of ray florets. Recently its molecular phylogeny based on ...

  6. Algorithms For Phylogeny Reconstruction In a New Mathematical Model

    NARCIS (Netherlands)

    Lenzini, Gabriele; Marianelli, Silvia

    1997-01-01

    The evolutionary history of a set of species is represented by a tree called phylogenetic tree or phylogeny. Its structure depends on precise biological assumptions about the evolution of species. Problems related to phylogeny reconstruction (i.e., finding a tree representation of information

  7. Significant effects due to rephrasing the Maslach Burnout Inventory's personal accomplishment items.

    NARCIS (Netherlands)

    Bouman, A.M.; Hoogstraten, J.; te Brake, H.

    2002-01-01

    Subjects, 292 Dutch psychology students answering negatively phrased Personal Accomplishment items, reported a more personally competent feeling than subjects answering positively phrased personal accomplishment items. The way of phrasing personal accomplishment items significantly affects the

  8. Pathogenesis of bovine neosporosis.

    Science.gov (United States)

    Dubey, J P; Buxton, D; Wouda, W

    2006-05-01

    The protozoan parasite Neospora caninum is a major pathogen of cattle and dogs, being a significant cause of abortion in cattle in many countries. It is one of the most efficiently transmitted parasites, with up to 90% of cattle infected in some herds. The pathogenesis of abortion due to Neospora is complex and only partially understood. Losses occur after a primary infection during pregnancy but more commonly as the result of recrudescence of a persistent infection during pregnancy. Parasitaemia is followed by invasion of the placenta and fetus. It is suggested that abortion occurs when primary parasite-induced placental damage jeopardises fetal survival directly or causes release of maternal prostaglandins that in turn cause luteolysis and abortion. Fetal damage may also occur due to primary tissue damage caused by the multiplication of N. caninum in the fetus or due to insufficient oxygen/nutrition, secondary to placental damage. In addition, maternal immune expulsion of the fetus may occur associated with maternal placental inflammation and the release of maternal pro-inflammatory cytokines in the placenta. Thus N. caninum is a primary pathogen capable of causing abortion either through maternal placental inflammation, maternal and fetal placental necrosis, fetal damage, or a combination of all three. The question of how N. caninum kills the fetus exposes the complex and finely balanced biological processes that have evolved to permit bovine and other mammalian pregnancies to occur. Defining these immunological mechanisms will shed light on potential methods of control of bovine neosporosis and enrich our understanding of the continuity of mammalian and protozoal survival.

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

    Energy Technology Data Exchange (ETDEWEB)

    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)

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

    DEFF Research Database (Denmark)

    Kjær, Malene

    2014-01-01

    In the theory of health care, knowledge translation is regarded as a crucial phenomenon that makes the whole health care system work in a desired manner. The present paper studies knowledge translation from the student nurses’ perspective and does that through a close analysis of the part...... 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...

  11. 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)

  12. Angiosperm phylogeny: 17 genes, 640 taxa.

    Science.gov (United States)

    Soltis, Douglas E; Smith, Stephen A; Cellinese, Nico; Wurdack, Kenneth J; Tank, David C; Brockington, Samuel F; Refulio-Rodriguez, Nancy F; Walker, Jay B; Moore, Michael J; Carlsward, Barbara S; Bell, Charles D; Latvis, Maribeth; Crawley, Sunny; Black, Chelsea; Diouf, Diaga; Xi, Zhenxiang; Rushworth, Catherine A; Gitzendanner, Matthew A; Sytsma, Kenneth J; Qiu, Yin-Long; Hilu, Khidir W; Davis, Charles C; Sanderson, Michael J; Beaman, Reed S; Olmstead, Richard G; Judd, Walter S; Donoghue, Michael J; Soltis, Pamela S

    2011-04-01

    Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

  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. Molecular phylogeny of the Siphonocladales (Chlorophyta: Cladophorophyceae).

    Science.gov (United States)

    Leliaert, Frederik; De Clerck, Olivier; Verbruggen, Heroen; Boedeker, Christian; Coppejans, Eric

    2007-09-01

    The Siphonocladales are tropical to warm-temperate, marine green macro-algae characterized by a wide variety of thallus morphologies, ranging from branched filaments to pseudo-parenchymatous plants. Phylogenetic analyses of partial large subunit (LSU) rDNA sequences sampled from 166 isolates revealed nine well-supported siphonocladalean clades. Analyses of a concatenated dataset of small subunit (SSU) and partial LSU rDNA sequences greatly clarified the phylogeny of the Siphonocladales. However, the position of the root of the Siphonocladales could not be determined unambiguously, as outgroup rooting and molecular clock rooting resulted in a different root placement. Different phylogenetic methods (likelihood, parsimony and distance) yielded similar tree topologies with comparable internal node resolution. Likewise, analyses under more realistic models of sequence evolution, taking into account differences in evolution between stem and loop regions of rRNA, did not differ markedly from analyses using standard four-state models. The molecular phylogeny revealed that all siphonocladalean architectures may be derived from a single Cladophora-like ancestor. Parallel and convergent evolution of various morphological characters (including those traditionally employed to circumscribe the families and genera) have occurred in the Siphonocladales. Consequently, incongruence with traditional classifications, including non-monophyly in all families and most genera, was shown.

  15. 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.

  16. 2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner.

    Science.gov (United States)

    Fogg, Christiana N; Kovats, Diane E; Berger, Bonnie

    2017-01-01

    The International Society for Computational Biology ( ISCB) recognizes an established scientist each year with the Accomplishment by a Senior Scientist Award for significant contributions he or she has made to the field. This award honors scientists who have contributed to the advancement of computational biology and bioinformatics through their research, service, and education work. Pavel Pevzner, PhD, Ronald R. Taylor Professor of Computer Science and Director of the NIH Center for Computational Mass Spectrometry at University of California, San Diego, has been selected as the winner of the 2017 Accomplishment by a Senior Scientist Award. The ISCB awards committee, chaired by Dr. Bonnie Berger of the Massachusetts Institute of Technology, selected Pevzner as the 2017 winner. Pevzner will receive his award and deliver a keynote address at the 2017 Intelligent Systems for Molecular Biology-European Conference on Computational Biology joint meeting ( ISMB/ECCB 2017) held in Prague, Czech Republic from July 21-July 25, 2017. ISMB/ECCB is a biennial joint meeting that brings together leading scientists in computational biology and bioinformatics from around the globe.

  17. Accomplishing Transformative Research in a Challenging Fiscal Environment

    Science.gov (United States)

    Mitchell, E. J.; Paxton, L. J.; Bust, G.

    2014-12-01

    The shift in funding is forcing scientists to promise transformative research for a pittance. To accomplish this, researchers need to transform their methodology to include societal buy-in, use of commercial off-the-shelf (COTS) technology, and cross-discipline platform usage. As the cutting edge of research expands to view the system on the global scale with extremely fine resolution, fiscally reasonable budgets present a challenge to be met. Consider how do we measure a specific variable over 45-degrees of latitude in an isolated and hostile region of Earth - the total electron count over the South Pole? This work examines this transformative research using hosted payloads on buoys, balloons, and unmanned aerial vehicles (UAVs). We will show cutting edge research occurring simultaneous with education and public outreach, offering societal buy-in through interactive websites and student-built hosted payloads. These interactions provide a vision to the public and a new database to the scientists. The use of COTS technology and cross-discipline (oceanography and space) platforms keep the cost low. We will discuss a general methodology for accomplishing transformative research in a challenging fiscal environment through integration of COTS technology, assimilative and first principle models, and observing systems simulation experiments (OSSEs).

  18. International Research Results and Accomplishments From the International Space Station

    Science.gov (United States)

    Ruttley, Tara M.; Robinson, Julie A.; Tate-Brown, Judy; Perkins, Nekisha; Cohen, Luchino; Marcil, Isabelle; Heppener, Marc; Hatton, Jason; Tasaki, Kazuyuki; Umemura, Sayaka; hide

    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. The International Space Station Research Accomplishments: An Analysis of Results From 2000-2011 is a collection of summaries 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/issscience) that tracks and communicates ISS research activities across the entire ISS partnership, and it is continuously updated. It captures ISS experiment summaries and results and includes citations to the journals, conference proceedings, and patents as they become available. 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 reflects 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 way that will impact humanity like no laboratory on Earth. The ISS Program Science Forum will continue to capture and report on these results in the form of journal publications, conference proceedings, and patents. We anticipate that successful ISS research will

  19. The roots of phylogeny: how did Haeckel build his trees?

    Science.gov (United States)

    Dayrat, Benoît

    2003-08-01

    Haeckel created much of our current vocabulary in evolutionary biology, such as the term phylogeny, which is currently used to designate trees. Assuming that Haeckel gave the same meaning to this term, one often reproduces Haeckel's trees as the first illustrations of phylogenetic trees. A detailed analysis of Haeckel's own evolutionary vocabulary and theory revealed that Haeckel's trees were genealogical trees and that Haeckel's phylogeny was a morphological concept. However, phylogeny was actually the core of Haeckel's tree reconstruction, and understanding the exact meaning Haeckel gave to phylogeny is crucial to understanding the information Haeckel wanted to convey in his famous trees. Haeckel's phylogeny was a linear series of main morphological stages along the line of descent of a given species. The phylogeny of a single species would provide a trunk around which lateral branches were added as mere ornament; the phylogeny selected for drawing a tree of a given group was considered the most complete line of progress from lower to higher forms of this group, such as the phylogeny of Man for the genealogical tree of Vertebrates. Haeckel's phylogeny was mainly inspired by the idea of the scala naturae, or scale of being. Therefore, Haeckel's genealogical trees, which were only branched on the surface, mainly represented the old idea of scale of being. Even though Haeckel decided to draw genealogical trees after reading On the Origin of Species and was called the German Darwin, he did not draw Darwinian branching diagrams. Although Haeckel always saw Lamarck, Goethe, and Darwin as the three fathers of the theory of evolution, he was mainly influenced by Lamarck and Goethe in his approach to tree reconstruction.

  20. Fort Collins Science Center - Fiscal Year 2008 Science Accomplishments

    Science.gov (United States)

    Wilson, Juliette T.

    2009-01-01

    Public land and natural resource managers in the United States are confronted with increasingly complex decisions that have important ramifications for both ecological and human systems. The scientists and technical professionals at the U.S. Geological Survey (USGS) Fort Collins Science Center (FORT) contribute a unique blend of ecological, socioeconomic, and technological expertise to investigating complicated ecological problems that address critical management questions. In Fiscal Year 2008 (FY08), FORT's scientific and technical professionals continued research vital to the science and management needs of U.S. Department of the Interior agencies and other entities. This annual report describes select FY08 accomplishments in research and technical assistance involving biological information management and delivery; aquatic, riparian, and managed-river ecosystems; invasive species; status and trends of biological resources (including human dimensions and social science); terrestrial ecosystems; and fish and wildlife resources.

  1. 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.

  2. Phylogeny mandalas for illustrating the Tree of Life.

    Science.gov (United States)

    Hasegawa, Masami

    2017-12-01

    A circular phylogeny with photos or drawings of species is named a phylogeny mandala. This is one of the ways for illustrating the Tree of Life, and is suitable to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. To demonstrate the recent progress of molecular phylogenetics, six phylogeny mandalas for various taxonomic groups of life were presented; i.e., (1) Eukaryota, (2) Metazoa, (3) Hexapoda, (4) Tetrapoda, (5) Eutheria, and (6) Primates. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Coloration mechanisms and phylogeny of Morpho butterflies.

    Science.gov (United States)

    Giraldo, M A; Yoshioka, S; Liu, C; Stavenga, D G

    2016-12-15

    Morpho butterflies are universally admired for their iridescent blue coloration, which is due to nanostructured wing scales. We performed a comparative study on the coloration of 16 Morpho species, investigating the morphological, spectral and spatial scattering properties of the differently organized wing scales. In numerous previous studies, the bright blue Morpho coloration has been fully attributed to the multi-layered ridges of the cover scales' upper laminae, but we found that the lower laminae of the cover and ground scales play an important additional role, by acting as optical thin film reflectors. We conclude that Morpho coloration is a subtle combination of overlapping pigmented and/or unpigmented scales, multilayer systems, optical thin films and sometimes undulated scale surfaces. Based on the scales' architecture and their organization, five main groups can be distinguished within the genus Morpho, largely agreeing with the accepted phylogeny. © 2016. Published by The Company of Biologists Ltd.

  4. Future of phylogeny in HIV prevention.

    Science.gov (United States)

    Brenner, Bluma G; Wainberg, Mark A

    2013-07-01

    The success of the HIV Prevention Trials Network 052 trial has led to revisions in HIV-1 treatment guidelines. Antiretroviral therapy may reduce the risk of HIV-1 transmissions at the population level. The design of successful treatment as prevention interventions will be predicated on a comprehensive understanding of the spatial, temporal, and biological dynamics of heterosexual men who have sex with men and intravenous drug user epidemics. Viral phylogenetics can capture the underlying structure of transmission networks based on the genetic interrelatedness of viral sequences and cluster networks that could not be otherwise identified. This article describes the phylogenetic expansion of the Montreal men who have sex with men epidemic over the last decade. High rates of coclustering of primary infections are associated with 1 infection leading to 13 onward transmissions. Phylogeny substantiates the role of primary and recent stage infection in transmission dynamics, underlying the importance of timely diagnosis and immediate antiretroviral therapy initiation to avert transmission cascades.

  5. Inferring phylogenies from RAD sequence data.

    Directory of Open Access Journals (Sweden)

    Benjamin E R Rubin

    Full Text Available Reduced-representation genome sequencing represents a new source of data for systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been explored. One approach that seems especially promising is the use of inexpensive short-read technologies (e.g., Illumina, SOLiD to sequence restriction-site associated DNA (RAD--the regions of the genome that flank the recognition sites of restriction enzymes. In this study, we simulated the collection of RAD sequences from sequenced genomes of different taxa (Drosophila, mammals, and yeasts and developed a proof-of-concept workflow to test whether informative data could be extracted and used to accurately reconstruct "known" phylogenies of species within each group. The workflow consists of three basic steps: first, sequences are clustered by similarity to estimate orthology; second, clusters are filtered by taxonomic coverage; and third, they are aligned and concatenated for "total evidence" phylogenetic analysis. We evaluated the performance of clustering and filtering parameters by comparing the resulting topologies with well-supported reference trees and we were able to identify conditions under which the reference tree was inferred with high support. For Drosophila, whole genome alignments allowed us to directly evaluate which parameters most consistently recovered orthologous sequences. For the parameter ranges explored, we recovered the best results at the low ends of sequence similarity and taxonomic representation of loci; these generated the largest supermatrices with the highest proportion of missing data. Applications of the method to mammals and yeasts were less successful, which we suggest may be due partly to their much deeper evolutionary divergence times compared to Drosophila (crown ages of approximately 100 and 300 versus 60 Mya, respectively. RAD sequences thus appear to hold promise for reconstructing phylogenetic relationships in younger clades in

  6. Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Vincent P Richards

    Full Text Available Escherichia coli is an important cause of bovine mastitis and can cause both severe inflammation with a short-term transient infection, as well as less severe, but more chronic inflammation and infection persistence. E. coli is a highly diverse organism that has been classified into a number of different pathotypes or pathovars, and mammary pathogenic E. coli (MPEC has been proposed as a new such pathotype. The purpose of this study was to use genome sequence data derived from both transient and persistent MPEC isolates (two isolates of each phenotype to construct a genome-based phylogeny that places MPEC in its phylogenetic context with other E. coli pathovars. A subsidiary goal was to conduct comparative genomic analyses of these MPEC isolates with other E. coli pathovars to provide a preliminary perspective on loci that might be correlated with the MPEC phenotype. Both concatenated and consensus tree phylogenies did not support MPEC monophyly or the monophyly of either transient or persistent phenotypes. Three of the MPEC isolates (ECA-727, ECC-Z, and ECA-O157 originated from within the predominately commensal clade of E. coli, referred to as phylogroup A. The fourth MPEC isolate, of the persistent phenotype (ECC-1470, was sister group to an isolate of ETEC, falling within the E. coli B1 clade. This suggests that the MPEC phenotype has arisen on numerous independent occasions and that this has often, although not invariably, occurred from commensal ancestry. Examination of the genes present in the MPEC strains relative to the commensal strains identified a consistent presence of the type VI secretion system (T6SS in the MPEC strains, with only occasional representation in commensal strains, suggesting that T6SS may be associated with MPEC pathogenesis and/or as an inter-bacterial competitive attribute and therefore could represent a useful target to explore for the development of MPEC specific inhibitors.

  7. A Preliminary Molecular Investigation of Aleocharine Phylogeny (Coleoptera: Staphylinidae)

    National Research Council Canada - National Science Library

    J. C. Thomas

    2009-01-01

    .... As a preliminary step toward building a tribal-level phylogeny for this lineage of beetles, a molecular investigation of partial sequences of 12s and 16s mitochondrial genes was undertaken for 21...

  8. 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...

  9. 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...

  10. 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

  11. Distance-Based Phylogeny Reconstruction: Safety and Edge Radius

    OpenAIRE

    Gascuel, Olivier; Pardi, Fabio; Truszkowski, Jakub

    2015-01-01

    International audience; A phylogeny is an evolutionary tree tracing the shared history, including common ancestors, of a set of extant species or “taxa”. Phylogenies are increasingly reconstructed on the basis of molecular data (DNA and protein sequences) using statistical techniques such as likelihood and Bayesian methods. Algorithmically, these techniques suffer from the discrete nature of tree topology space. Since the number of tree topologies increases exponentially as a function of the ...

  12. The NASA Space Life Sciences Training Program: Accomplishments Since 2013

    Science.gov (United States)

    Rask, Jon; Gibbs, Kristina; Ray, Hami; Bridges, Desireemoi; Bailey, Brad; Smith, Jeff; Sato, Kevin; Taylor, Elizabeth

    2017-01-01

    The NASA Space Life Sciences Training Program (SLSTP) provides undergraduate students entering their junior or senior years with professional experience in space life science disciplines. This challenging ten-week summer program is held at NASA Ames Research Center. The primary goal of the program is to train the next generation of scientists and engineers, enabling NASA to meet future research and development challenges in the space life sciences. Students work closely with NASA scientists and engineers on cutting-edge research and technology development. In addition to conducting hands-on research and presenting their findings, SLSTP students attend technical lectures given by experts on a wide range of topics, tour NASA research facilities, participate in leadership and team building exercises, and complete a group project. For this presentation, we will highlight program processes, accomplishments, goals, and feedback from alumni and mentors since 2013. To date, 49 students from 41 different academic institutions, 9 staffers, and 21 mentors have participated in the program. The SLSTP is funded by Space Biology, which is part of the Space Life and Physical Sciences Research and Application division of NASA's Human Exploration and Operations Mission Directorate. The SLSTP is managed by the Space Biology Project within the Science Directorate at Ames Research Center.

  13. Molecular phylogeny of thorny catfishes (Siluriformes: Doradidae).

    Science.gov (United States)

    Arce H, Mariangeles; Reis, Roberto E; Geneva, Anthony J; Sabaj Pérez, Mark H

    2013-06-01

    Doradidae is a monophyletic catfish family endemic to continental South America, and composed of 93 valid species here placed in 31 genera. Existing phylogenetic hypotheses for Doradidae are derived from comprehensive analyses of morphological data, and a single molecular-based study on a limited subset of taxa. To provide a robust molecular phylogeny commensurate with those based on morphology, we gathered original and published sequence data for 86 species-level taxa (at least 70 valid species plus 16 new or questionably nominal species) and all genera of Doradidae, as well as 10 species (nine genera) of Auchenipteridae and three species and genera of Aspredinidae as outgroups. 3011 base pairs were aligned for two mitochondrial genes (cytochrome c oxidase subunit 1, and 16S ribosomal RNA) and one nuclear gene (recombination activating gene 1), and analyzed for a total of 143 specimens (130 doradids, 10 auchenipterids and three aspredinids). Tree topologies generated by Maximum Parsimony, Maximum Likelihood, and Bayesian analyses were largely congruent, and are compared to existing phylogenies based on morphology and molecules. Although many of the relationships supported by our molecular analyses corroborated those based on morphology, others are newly hypothesized or remain in conflict. The monotypic Wertheimeria, Franciscodoras and Kalyptodoras, for example, form a newly proposed clade, and the subfamily Astrodoradinae is placed at the base of the doradid tree. The monotypic Doraops and Centrochir, endemic to Caribbean drainages north and west of the Andes, are sister to Pterodoras and Platydoras, respectively, two genera that are widely distributed in Atlantic drainages. Additional biogeographic implications are discussed for hypothesized relationships among doradids. Molecular evidence strongly supports synonymization of monotypic Merodoras with Amblydoras, and transfer of Amblydoras bolivarensis to genus Scorpiodoras. Furthermore, we consider Opsodoras

  14. Diprosopia em bovino Bovine diprosopus

    Directory of Open Access Journals (Sweden)

    I.T. Rotta

    2008-04-01

    Full Text Available This work describes a malformation in one newborn female bovine, with two faces and two skull fused, showing one single head. Duplications of the nasal and oral structures, tetraofthalmy, two brains, one single cerebellum, and pons were observed. The right thyroid was hypertrophic and the other organs had normal morphology. Every change observed in this case was compatibles with diprosopus.

  15. Bovine spongiform encephalopathy in sheep?

    NARCIS (Netherlands)

    Schreuder, B.E.C.; Somerville, R.A.

    2003-01-01

    Bovine spongiform encephalopathy (BSE) in sheep has not been identified under natural conditions at the time of writing and remains a hypothetical issue. However, rumours about the possible finding of a BSE-like isolate in sheep have led to great unrest within the sheep industry, among the general

  16. Infectious bovine rhinotracheitis in Scotland.

    Science.gov (United States)

    2017-10-14

    A cattle dashboard has recently been developed to share surveillance information gathered from submissions to the Great Britain veterinary diagnostic network. Data relating to Scotland come from the SAC C VS. This article, by Tim Geraghty, relates to cases of infectious bovine rhinotracheitis in Scotland, as summarised on the APHA Cattle Dashboard. British Veterinary Association.

  17. 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.

  18. 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.

  19. A transcriptome approach to ecdysozoan phylogeny.

    Science.gov (United States)

    Borner, Janus; Rehm, Peter; Schill, Ralph O; Ebersberger, Ingo; Burmester, Thorsten

    2014-11-01

    The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. A Framework for Studying Emotions Across Phylogeny

    Science.gov (United States)

    Anderson, David J.; Adolphs, Ralph

    2014-01-01

    Since the 19th century, there has been disagreement over the fundamental question of whether “emotions” are cause or consequence of their associated behaviors. This question of causation is most directly addressable in genetically tractable model organisms, including invertebrates such as Drosophila. Yet there is ongoing debate about whether such species even have “emotions,” since emotions are typically defined with reference to human behavior and neuroanatomy. Here we argue that emotional behaviors are a class of behaviors that express internal emotion states. These emotion states exhibit certain general functional and adaptive properties that apply across any specific human emotions like fear or anger, as well as across phylogeny. These general properties, which can be thought of as “emotion primitives”, can be modeled and studied in evolutionarily distant model organisms, allowing functional dissection of their mechanistic bases, and tests of their causal relationships to behavior. More generally, our approach aims not only at better integration of such studies in model organisms with studies of emotion in humans, but also suggests a revision of how emotion should be operationalized within psychology and psychiatry. PMID:24679535

  1. Dating phylogenies with hybrid local molecular clocks.

    Directory of Open Access Journals (Sweden)

    Stéphane Aris-Brosou

    Full Text Available BACKGROUND: Because rates of evolution and species divergence times cannot be estimated directly from molecular data, all current dating methods require that specific assumptions be made before inferring any divergence time. These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models or on both rates and times (penalized likelihood, Bayesian methods. However, most of these assumptions can affect estimated dates, oftentimes because they underestimate large amounts of rate change. PRINCIPAL FINDINGS: A significant modification to a recently proposed ad hoc rate-smoothing algorithm is described, in which local molecular clocks are automatically placed on a phylogeny. This modification makes use of hybrid approaches that borrow from recent theoretical developments in microarray data analysis. An ad hoc integration of phylogenetic uncertainty under these local clock models is also described. The performance and accuracy of the new methods are evaluated by reanalyzing three published data sets. CONCLUSIONS: It is shown that the new maximum likelihood hybrid methods can perform better than penalized likelihood and almost as well as uncorrelated Bayesian models. However, the new methods still tend to underestimate the actual amount of rate change. This work demonstrates the difficulty of estimating divergence times using local molecular clocks.

  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. A mitogenomic phylogeny of living primates.

    Science.gov (United States)

    Finstermeier, Knut; Zinner, Dietmar; Brameier, Markus; Meyer, Matthias; Kreuz, Eva; Hofreiter, Michael; Roos, Christian

    2013-01-01

    Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels.

  4. Identification of lactoferrin in bovine tears.

    Science.gov (United States)

    Brown, M H; Brightman, A H; Fenwick, B W; Rider, M A

    1996-09-01

    To determine whether bovine tear film contains the iron-binding glycoprotein, lactoferrin. 40 Adult Hereford, Angus, and Simmental cattle. Protein analysis: pooled bovine tears were used for protein analysis (size exclusion high-performance liquid chromatography [HPLC] fractionation). HPLC was used for tear analysis. A diode array detector was used (215 and 280 microns) for chromatogram analysis and comparisons. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE): protein electrophoresis was performed, using 7.5% running gels with 4% stacking gels. Molecular weight of proteins in the unknown samples was determined as recommended by the manufacturer of the standards. Protein sequencing: amino acid sequencing, using automated Edman degradation of HPLC purified protein, was performed. The sequence obtained was compared with the known protein sequence of bovine lactoferrin. HPLC analysis of whole bovine tears resulted in a consistent chromatogram. Peak collection was performed to recover a protein from the bovine tear film with chromatogram characteristics nearly identical to purified bovine lactoferrin. Silver-stained SDS-PAGE of this peak revealed a band with molecular mass consistent with bovine lactoferrin (estimated mass of 78 kd). The first 13 amino acid residues of this protein were identical to the amino acid sequence of bovine lactoferrin. Analysis of whole bovine tears, using size exclusion HPLC, SDS-PAGE, and amino acid sequencing, provided evidence that bovine tears contain lactoferrin. Lactoferrin probably exerts a bacteriostatic effect in bovine tear film. Locally produced lactoferrin may bathe the ocular surface and sequester iron from potential pathogens.

  5. 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).

  6. Bovine leukemia virus: current perspectives

    Directory of Open Access Journals (Sweden)

    Juliarena MA

    2017-08-01

    Full Text Available Marcela Alicia Juliarena,1 Clarisa Natalia Barrios,1 Claudia María Lützelschwab,1 Eduardo Néstor Esteban,2 Silvina Elena Gutiérrez1 1Department of Animal Health and Preventive Medicine, Veterinary Research Center of Tandil (CIVETAN, CIC-CONICET, Faculty of Veterinary Science, National University of the Center of Buenos Aires Province, Tandil, Argentina; 2BIOALPINA Program (GENIAL/COTANA, Colonia Alpina, Argentina Abstract: Enzootic bovine leukosis, caused by bovine leukemia virus (BLV, is the most common neoplasm of dairy cattle. Although beef and dairy cattle are susceptible to BLV infection and BLV-associated lymphosarcoma, the disease is more commonly detected in dairy herds, mostly because of the management practices in dairy farms. The pathogenicity of BLV in its natural host, the bovine, depends mainly on the resistance/susceptibility genetics of the animal. The majority of infected cattle are asymptomatic, promoting the extremely high dissemination rate of BLV in many bovine populations. The important productive losses caused by the BLV, added to the health risk of maintaining populations with a high prevalence of infection with a retrovirus, generates the need to implement control measures. Different strategies to control the virus have been attempted. The most effective approach is to identify and cull the totality of infected cattle in the herd. However, this approach is not suitable for herds with high prevalence of infection. At present, no treatment or vaccine has proven effective for the control of BLV. Thus far, the genetic selection of resistant animals emerges as a natural strategy for the containment of the BLV dissemination. In natural conditions, most of the infected, resistant cattle can control the infection, and therefore do not pass the virus to other animals, gradually decreasing the prevalence of the herd. Keywords: bovine leukemia virus, control, genetic resistance, BoLA-DRB3

  7. Phylogeny of ruminants secretory ribonuclease gene sequences of pronghorn (Antilocapra americana).

    Science.gov (United States)

    Beintema, Jaap J; Breukelman, Heleen J; Dubois, Jean-Yves F; Warmels, Hayo W

    2003-01-01

    Phylogenetic analyses based on primary structures of mammalian ribonucleases, indicated that three homologous enzymes (pancreatic, seminal and brain ribonucleases) present in the bovine species are the results of gene duplication events, which occurred in the ancestor of the ruminants after divergence from other artiodactyls. In this paper sequences are presented of genes encoding pancreatic and brain-type ribonuclease genes of pronghorn (Antilocapra americana). The seminal-type ribonuclease gene could not be detected in this species, neither by PCR amplification nor by Southern blot analyses, indicating that it may be deleted completely in this species. Previously we demonstrated of a study of amino acid sequences of pancreatic ribonucleases of a large number of ruminants the monophyly of bovids and cervids, and that pronghorn groups with giraffe. Here we present phylogenetic analyses of nucleotide sequences of ribonucleases and other molecules from ruminant species and compare these with published data. Chevrotain (Tragulus) always groups with the other ruminants as separate taxon from the pecora or true ruminants. Within the pecora the relationships between Bovidae, Cervidae, Giraffidae, and pronghorn (Antilocapra) cannot be decided with certainty, although in the majority of analyses Antilocapra diverges first, separately or joined with giraffe. Broad taxon sampling and investigation of specific sequence features may be as important for reliable conclusions in phylogeny as the lengths of analyzed sequences.

  8. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

    NARCIS (Netherlands)

    Etienne, Rampal S.; Haegeman, Bart; Stadler, Tanja; Aze, Tracy; Pearson, Paul N.; Purvis, Andy; Phillimore, Albert B.

    2012-01-01

    The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there

  9. 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

  10. THE RETICULATING PHYLOGENY OF ISLAND BIOGEOGRAPHY THEORY

    Science.gov (United States)

    Lomolino, Mark V.; Brown, James H.

    2010-01-01

    Biogeographers study all patterns in the geographic variation of life, from the spatial variation in genetic and physiological characteristics of cells and individuals, to the diversity and dynamics of biological communities among continental biotas or across oceanic archipelagoes. The field of island biogeography, in particular, has provided some genuinely transformative insights for the biological sciences, especially ecology and evolutionary biology. Our purpose here is to review the historical development of island biogeography theory during the 20th century by identifying the common threads that run through four sets of contributions made during this period, including those by Eugene Gordon Munroe (1948, 1953), Edward O. Wilson (1959, 1961), Frank W. Preston (1962a,b), and the seminal collaborations between Wilson and Robert H. MacArthur (1963, 1967), which revolutionized the field and served as its paradigm for nearly four decades. This epistemological account not only reviews the intriguing history of island theory, but it also includes fundamental lessons for advancing science through transformative integrations. Indeed, as is likely the case with many disciplines, island theory advanced not as a simple accumulation of facts and an orderly succession of theories and paradigms, but rather in fits and starts through a reticulating phylogeny of ideas and alternating periods of specialization and reintegration. We conclude this review with a summary of the salient features of this scientific revolution in the context of Kuhn’s structure, which strongly influenced theoretical advances during this period, and we then describe some of the fundamental assumptions and tenets of an emerging reintegration of island biogeography theory. PMID:20039528

  11. The reticulating phylogeny of island biogeography theory.

    Science.gov (United States)

    Lomolino, Mark V; Brown, James H

    2009-12-01

    Biogeographers study all patterns in the geographic variation of life, from the spatial variation in genetic and physiological characteristics of cells and individuals, to the diversity and dynamics of biological communities among continental biotas or across oceanic archipelagoes. The field of island biogeography, in particular, has provided some genuinely transformative insights for the biological sciences, especially ecology and evolutionary biology. Our purpose here is to review the historical development of island biogeography theory during the 20th century by identifying the common threads that run through four sets of contributions made during this period, including those by Eugene Gordon Munroe (1948, 1953), Edward O. Wilson (1959, 1961), Frank W. Preston (1962a,b), and the seminal collaborations between Wilson and Robert H. MacArthur (1963, 1967), which revolutionized the field and served as its paradigm for nearly four decades. This epistemological account not only reviews the intriguing history of island theory, but it also includes fundamental lessons for advancing science through transformative integrations. Indeed, as is likely the case with many disciplines, island theory advanced not as a simple accumulation of facts and an orderly succession of theories and paradigms, but rather in fits and starts through a reticulating phylogeny of ideas and alternating periods of specialization and reintegration. We conclude this review with a summary of the salient features of this scientific revolution in the contest of Kuhn's structure, which strongly influenced theoretical advances during this period, and we then describe some of the fundamental assumptions and tenets of an emerging reintegration of island biogeography theory.

  12. Bayesian phylogeny analysis via stochastic approximation Monte Carlo.

    Science.gov (United States)

    Cheon, Sooyoung; Liang, Faming

    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.

  13. 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.

  14. 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.

  15. [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.

  16. DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).

    Science.gov (United States)

    Huang, Zuhao; Tu, Feiyun

    2017-07-01

    The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

  17. Bovine cysticercosis situation in Brazil

    Directory of Open Access Journals (Sweden)

    Gabriel Augusto Marques Rossi

    2014-02-01

    Full Text Available The taeniasis-cysticercosis complex is a long known zoonotic parasitosis characteristic of underdeveloped countries. In addition to its public health significance, this parasitosis is cause of economic losses to the beef production chain, and synonymous of technical inadequacy in relation to the adoption of Good Agricultural Practices. The occurrences of both human teniasis and bovine cysticercosis could and should be controlled with basic sanitary measures. However, there is much variation in the occurrence of the disease in cattle, characterizing a low rate of technical development as well as problems related to the adoption of basic sanitation measures. This review describes, in details, the causative agent and its epidemiological chain, besides raising current information about the occurrence of bovine cysticercosis in different regions of Brazil, aiming at the adoption of prophylactic measures by different segments responsible.

  18. 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...

  19. Polymorphisms in the bovine hemoglobin-beta gene provide evidence for gene-flow between wild species of Bos (Bibos) and domestic cattle in Southeast Asia.

    Science.gov (United States)

    Tanaka, Kazuaki; Takizawa, Tatsuya; Dorji, Tashi; Amano, Takashi; Mannen, Hideyuki; Maeda, Yoshizane; Yamamoto, Yoshio; Namikawa, Takao

    2011-02-01

    The electrophoretic variation in bovine hemoglobin-beta (HBB) is one of the most investigated genetic markers. The presence of a unique HBB variant, HBB(X), in Southeast Asian cattle has been reputed as a sign of gene-flow from wild bovine species. In this study, we analyzed the DNA sequences of HBB genes in domestic and wild bovine species to verify this belief. Isoelectric focusing of HBB chain revealed that the HBB(X) in domestic cattle had dimorphism and was separated into HBB(X1) and HBB(X2). The HBB(X1) had the same DNA sequence of the common HBB variant in gayal (Bos gaurus frontalis), while some of the HBB(X2) were identical with that of Cambodian banteng (Bos javanicus birmanicus). As a result, we confirmed that the bovine HBB variants can be a good indicator of introgression between wild and domestic cattle. The HBB(X1) was always predominant to HBB(X2) in the continental populations, suggesting that the gaur had contributed to the gene pool of domestic cattle in this region much more than the banteng. On the other hand, the mitochondrial DNA analysis could not detect gene-flow from wild species. Autosomal markers that can trace the phylogeny between alleles are suitable for the assessment of bovine interspecific introgression. © 2010 The Authors. Journal compilation © 2010 Japanese Society of Animal Science.

  20. 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 ( ...

  1. Ethnobotany, Phylogeny, and 'Omics' for Human Health and Food Security.

    Science.gov (United States)

    Garnatje, Teresa; Peñuelas, Josep; Vallès, Joan

    2017-03-01

    Here, we propose a new term, 'ethnobotanical convergence', to refer to the similar uses for plants included in the same node of a phylogeny. This phylogenetic approach, together with the 'omics' revolution, shows how combining modern technologies with traditional ethnobotanical knowledge could be used to identify potential new applications of plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies.

    Science.gov (United States)

    Min, Xiaoping; Zhang, Mouzhao; Yuan, Sisi; Ge, Shengxiang; Liu, Xiangrong; Zeng, Xiangxiang; Xia, Ningshao

    2017-12-26

    In recent years, to infer phylogenies, which are NP-hard problems, more and more research has focused on using metaheuristics. Maximum Parsimony and Maximum Likelihood are two effective ways to conduct inference. Based on these methods, which can also be considered as the optimal criteria for phylogenies, various kinds of multi-objective metaheuristics have been used to reconstruct phylogenies. However, combining these two time-consuming methods results in those multi-objective metaheuristics being slower than a single objective. Therefore, we propose a novel, multi-objective optimization algorithm, MOEA-RC, to accelerate the processes of rebuilding phylogenies using structural information of elites in current populations. We compare MOEA-RC with two representative multi-objective algorithms, MOEA/D and NAGA-II, and a non-consensus version of MOEA-RC on three real-world datasets. The result is, within a given number of iterations, MOEA-RC achieves better solutions than the other algorithms.

  3. Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies

    Directory of Open Access Journals (Sweden)

    Xiaoping Min

    2017-12-01

    Full Text Available In recent years, to infer phylogenies, which are NP-hard problems, more and more research has focused on using metaheuristics. Maximum Parsimony and Maximum Likelihood are two effective ways to conduct inference. Based on these methods, which can also be considered as the optimal criteria for phylogenies, various kinds of multi-objective metaheuristics have been used to reconstruct phylogenies. However, combining these two time-consuming methods results in those multi-objective metaheuristics being slower than a single objective. Therefore, we propose a novel, multi-objective optimization algorithm, MOEA-RC, to accelerate the processes of rebuilding phylogenies using structural information of elites in current populations. We compare MOEA-RC with two representative multi-objective algorithms, MOEA/D and NAGA-II, and a non-consensus version of MOEA-RC on three real-world datasets. The result is, within a given number of iterations, MOEA-RC achieves better solutions than the other algorithms.

  4. Molecular phylogeny of Eriocaulon (Eriocaulaceae)

    DEFF Research Database (Denmark)

    Ito, Yu; Tanaka, Norio; Barfod, Anders

    Eriocaulon is a genus of about 400 species of monocotyledonous flowering plants in the family Eriocaulaceae. The genus is widely distributed in the world, with the centers of diversity in tropical regions, such as tropical Asia and tropical Africa. A previous molecular phylogeny implied an Africa...

  5. TYPES OF DNA USED IN SPECIATION AND PHYLOGENY STUDIES

    Directory of Open Access Journals (Sweden)

    Laura Buburuzan

    2007-12-01

    Full Text Available The present paper represents a synthesis of the main types of molecular markers used in contemporary phylogeny and phylogeography studies. Our purpose is also to reveal the recent discovered role of nuclear DNA polymorphic loci in the studies of filiation.

  6. Phylogeny of metabolic networks: A spectral graph theoretical ...

    Indian Academy of Sciences (India)

    Many methods have been developed for finding the commonalities between different organisms in order to study their phylogeny. The structure of metabolic networks also reveals valuable insights into metabolic capacity of species as well as into the habitats where they have evolved. We constructed metabolic networks of ...

  7. Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

    Science.gov (United States)

    D. Jean Lodge; Mahajabeen Padamsee; P. Brandon Matheny; M. Catherine Aime; Sharon A. Cantrell; David Boertmann; Alexander Kovalenko; Alfredo Vizzini; Bryn T.M. Dentinger; Paul M. Kirk; A. Martin Ainsworth; Jean-Marc Moncalvo; Rytas Vilgalys; Ellen Larsson; Robert Lucking; Gareth W. Griffith; Matthew E. Smith; Lorilei L. Norvell; Dennis E. Desjardin; Scott A. Redhead; Clark L. Ovrebo; Edgar B. Lickey; Enrico Ercole; Karen W. Hughes; Regis Courtecuisse; Anthony Young; Manfred Binder; Andrew M. Minnis; Daniel L. Lindner; Beatriz Ortiz-Santana; John Haight; Thomas Laessoe; Timothy J. Baroni; Jozsef Geml; Tsutomu Hattori

    2013-01-01

    Molecular phylogenies using 1–4 gene regions and information on ecology, morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae. The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are: Acantholichen, Ampulloclitocybe, Arrhenia, Cantharellula, Cantharocybe,...

  8. Plankton composition, biomass, phylogeny and toxin genes in Lake ...

    African Journals Online (AJOL)

    Plankton composition, biomass, phylogeny and toxin genes in Lake Big Momela, Tanzania. ... cyanobacteria during the whole year. In general, our data illustrate the presence of rich planktonic communities, including some unique and potentially endemic cyanobacteria. Keywords: cyanotoxin, limnology, plankton diversity, ...

  9. PhyloPars: estimation of missing parameter values using phylogeny.

    NARCIS (Netherlands)

    Bruggeman, J.; Heringa, J.; Brandt, B.W.

    2009-01-01

    A wealth of information on metabolic parameters of a species can be inferred from observations on species that are phylogenetically related. Phylogeny-based information can complement direct empirical evidence, and is particularly valuable if experiments on the species of interest are not feasible.

  10. 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 ...... spirochetal biodiversity....

  11. Multiple Nuclear Ortholog (COSII) Phylogeny of Wild Potatoes and Tomatoes

    Science.gov (United States)

    Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined more than 80 c...

  12. Phylogeny and biogeography of midwife toads (Alytes, Discoglossidae): a reappraisal

    NARCIS (Netherlands)

    Altaba, Cristian R.

    1997-01-01

    The allozyme data base of Arntzen & García-París (1995) on midwife toads (Alytes, Discoglossidae) is reanalysed considering each locus as a discrete character. The phylogeny thus inferred differs from the one obtained with genetic distances in the position of A. dickhilleni from the Betic region –

  13. Phylogeny of basal descendants of cocoon-forming annelids (Clitellata)

    OpenAIRE

    Christoffersen,Martin Lindsey

    2012-01-01

    Molecular analyses have been unsuccessful in placing the clitellates among annelids. Available morphological characters are ordered into congruent transformation series according to Hennigian principles. Orbiniidae is chosen as the outgroup. I propose the following phylogeny [number of apomorphies within brackets]: (Clitellata sensu lato [6] (Questidae [6] + Apodadrilida, new [2] (Parergodrilidae [3] (Stygocapitella [3] + Parergodrilus [4]) + Oligochaeta [7] (Aphanoneura [2] (Aeolosomatidae [...

  14. A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides).

    Science.gov (United States)

    Jønsson, Knud Andreas; Fabre, Pierre-Henri; Kennedy, Jonathan D; Holt, Ben G; Borregaard, Michael K; Rahbek, Carsten; Fjeldså, Jon

    2016-01-01

    The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world's major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial relationships have been resolved, based on phylogenetic analyses using multiple nuclear loci. In the current study we analyse eight nuclear and four mitochondrial loci to generate a dated phylogeny for the majority of corvoid species. This phylogeny includes 667 out of 780 species (85.5%), 141 out of 143 genera (98.6%) and all 31 currently recognized families, thus providing a baseline for comprehensive macroecological, macroevolutionary and biogeographical analyses. Using this phylogeny we assess the temporal consistency of the current taxonomic classification of families and genera. By adopting an approach that enforces temporal consistency by causing the fewest possible taxonomic changes to currently recognized families and genera, we find the current familial classification to be largely temporally consistent, whereas that of genera is not. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Phylogeny Predicts Future Habitat Shifts Due to Climate Change

    Science.gov (United States)

    Kuntner, Matjaž; Năpăruş, Magdalena; Li, Daiqin; Coddington, Jonathan A.

    2014-01-01

    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. PMID:24892737

  16. 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

  17. 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

  18. Rapid and accurate simultaneous determination of abamectin and ivermectin in bovine milk by high performance liquid chromatography with fluorescence detection

    OpenAIRE

    Kolberg, D. I. S.; Presta, M.A.; Wickert, C.; Adaime,M. B.; R. Zanella

    2009-01-01

    An analytical method using high performance liquid chromatography with fluorescence detection for the simultaneous determination of abamectin and ivermectin in bovine milk was developed and validated. The best recovery results were achieved by using acetonitrile for extraction of the compounds followed by solid phase extraction in cartridges containing C18 for the purification of the extract. Pre-column derivatization was accomplished with N-methylimidazole and trifluoroacetic anhydride. The ...

  19. (Npro) protein of bovine viral d

    Indian Academy of Sciences (India)

    Prakash

    Bovine viral diarrhoea virus (BVDV) is an economically important pathogen of cattle and sheep, and causes significant respiratory and reproductive disease worldwide. Bovine viral diarrhoea virus type 1 (BVDV-1), BVDV-2 along with the border disease virus (BDV) and classical swine fever virus (CSFV) belong to the genus ...

  20. Bovine cysticercosis in the European Union

    DEFF Research Database (Denmark)

    Blagojevic, Bojan; Robertson, Lucy J.; Vieira-Pinto, Madalena

    2017-01-01

    Bovine cysticercosis is caused by the larval stage of Taenia saginata and has a global distribution. This zoonosis usually causes only mild disease in humans, but has an important economic impact on the meat sector as bovine carcasses that are found to be infected are either condemned or undergo ...

  1. Pellet-free isolation of human and bovine milk extracellular vesicles by size-exclusion chromatography

    DEFF Research Database (Denmark)

    Blans, Kristine Ingrid Marie; Hansen, Maria Stenum; Sørensen, Laila V.

    2017-01-01

    Studies have suggested that nanoscale extracellular vesicles (EV) in human and bovine milk carry immune modulatory properties which could provide beneficial health effects to infants. In order to assess the possible health effects of milk EV, it is essential to use isolates of high purity from...... other more abundant milk structures with well-documented bioactive properties. Furthermore, gentle isolation procedures are important for reducing the risk of generating vesicle artefacts, particularly when EV subpopulations are investigated. In this study, we present two isolation approaches...... accomplished in three steps based on size-exclusion chromatography (SEC) resulting in effective and reproducible EV isolation from raw milk. The approaches do not require any EV pelleting and can be applied to both human and bovine milk. We show that SEC effectively separates phospholipid membrane vesicles...

  2. Models of bovine babesiosis including juvenile cattle.

    Science.gov (United States)

    Saad-Roy, C M; Shuai, Zhisheng; van den Driessche, P

    2015-03-01

    Bovine Babesiosis in cattle is caused by the transmission of protozoa of Babesia spp. by ticks as vectors. Juvenile cattle (Bovine Babesiosis, rarely show symptoms, and acquire immunity upon recovery. Susceptibility to the disease varies between breeds of cattle. Models of the dynamics of Bovine Babesiosis transmitted by the cattle tick that include these factors are formulated as systems of ordinary differential equations. Basic reproduction numbers are calculated, and it is proved that if these numbers are below the threshold value of one, then Bovine Babesiosis dies out. However, above the threshold number of one, the disease may approach an endemic state. In this case, control measures are suggested by determining target reproduction numbers. The percentage of a particular population (for example, the adult bovine population) needed to be controlled to eradicate the disease is evaluated numerically using Columbia data from the literature.

  3. A Comparison of Content: Florida's Certification Examination and Florida's Educator Accomplished Practices.

    Science.gov (United States)

    Fields, Lynette J.; Gayle-Evans, Guda; Michael, Deanna; Lang, Steve; Hewitt, Margaret; Micklo, Stephen J.

    2003-01-01

    Examines relationship between content of the Florida Professional Education Test for teacher certification and an evaluation of teacher-accomplished practices, using an investigator-developed instrument. Finds that 73 percent of content of certification test either did not relate or related weakly to Florida teacher-accomplished practices. Draws…

  4. 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,…

  5. 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.

  6. Bovine papillomavirus isolation by ultracentrifugation.

    Science.gov (United States)

    Araldi, R P; Giovanni, D N S; Melo, T C; Diniz, N; Mazzuchelli-de-Souza, J; Sant'Ana, T A; Carvalho, R F; Beçak, W; Stocco, R C

    2014-11-01

    The bovine papillomavirus (BPV) is the etiological agent of bovine papillomatosis, which causes significant economic losses to livestock, characterized by the presence of papillomas that regress spontaneously or persist and progress to malignancy. Currently, there are 13 types of BPVs described in the literature as well as 32 putative new types. This study aimed to isolate viral particles of BPV from skin papillomas, using a novel viral isolation method. The virus types were previously identified with new primers designed. 77 cutaneous papilloma samples of 27 animals, Simmental breed, were surgically removed. The DNA was extracted and subjected to PCR using Delta-Epsilon and Xi primers. The bands were purified and sequenced. The sequences were analyzed using software and compared to the GenBank database, by BLAST tool. The viral typing showed a prevalence of BPV-2 in 81.81% of samples. It was also detected the presence of the putative new virus type BR/UEL2 in one sample. Virus isolation was performed by ultracentrifugation in a single density of cesium chloride. The method of virus isolation is less laborious than those previously described, allowing the isolation of complete virus particles of BPV-2. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association.

    Science.gov (United States)

    La Reau, Alex J; Meier-Kolthoff, Jan P; Suen, Garret

    2016-12-01

    It has become increasingly clear that the composition of mammalian gut microbial communities is substantially diet driven. These microbiota form intricate mutualisms with their hosts, which have profound implications on overall health. For example, many gut microbes are involved in the conversion of host-ingested dietary polysaccharides into host-usable nutrients. One group of important gut microbial symbionts are bacteria in the genus Ruminococcus. Originally isolated from the bovine rumen, ruminococci have been found in numerous mammalian hosts, including other ruminants, and non-ruminants such as horses, pigs and humans. All ruminococci require fermentable carbohydrates for growth, and their substrate preferences appear to be based on the diet of their particular host. Most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic non-ruminant-associated species, and even less is known about the environmental distribution of ruminococci as a whole. Here, we capitalized on the wealth of publicly available 16S rRNA gene sequences, genomes and large-scale microbiota studies to both resolve the phylogenetic placement of described species in the genus Ruminococcus, and further demonstrate that this genus has largely unexplored diversity and a staggering host distribution. We present evidence that ruminococci are predominantly associated with herbivores and omnivores, and our data supports the hypothesis that very few ruminococci are found consistently in non-host-associated environments. This study not only helps to resolve the phylogeny of this important genus, but also provides a framework for understanding its distribution in natural systems.

  8. 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 bovine...

  9. 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 is...

  10. Extrapolating demography with climate, proximity and phylogeny: approach with caution.

    Science.gov (United States)

    Coutts, Shaun R; Salguero-Gómez, Roberto; Csergő, Anna M; Buckley, Yvonne M

    2016-12-01

    Plant population responses are key to understanding the effects of threats such as climate change and invasions. However, we lack demographic data for most species, and the data we have are often geographically aggregated. We determined to what extent existing data can be extrapolated to predict population performance across larger sets of species and spatial areas. We used 550 matrix models, across 210 species, sourced from the COMPADRE Plant Matrix Database, to model how climate, geographic proximity and phylogeny predicted population performance. Models including only geographic proximity and phylogeny explained 5-40% of the variation in four key metrics of population performance. However, there was poor extrapolation between species and extrapolation was limited to geographic scales smaller than those at which landscape scale threats typically occur. Thus, demographic information should only be extrapolated with caution. Capturing demography at scales relevant to landscape level threats will require more geographically extensive sampling. © 2016 John Wiley & Sons Ltd/CNRS.

  11. Obscured phylogeny and possible recombinational dormancy in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Sawyer Stanley A

    2011-06-01

    Full Text Available Abstract Background Escherichia coli is one of the best studied organisms in all of biology, but its phylogenetic structure has been difficult to resolve with current data and analytical techniques. We analyzed single nucleotide polymorphisms in chromosomes of representative strains to reconstruct the topology of its emergence. Results The phylogeny of E. coli varies according to the segment of chromosome analyzed. Recombination between extant E. coli groups is largely limited to only three intergroup pairings. Conclusions Segment-dependent phylogenies most likely are legacies of a complex recombination history. However, E. coli are now in an epoch in which they no longer broadly share DNA. Using the definition of species as organisms that freely exchange genetic material, this recombinational dormancy could reflect either the end of E. coli as a species, or herald the coalescence of E. coli groups into new species.

  12. Generation by self re-fusion of bovine³ × murine² heterohybridomas secreting virus-neutralizing bovine monoclonal antibodies to bovine herpesvirus 1 glycoproteins gB, gC, and gD.

    Science.gov (United States)

    Levings, Randall L; Stoll, Ione R; Warg, Janet V; Patterson, Peggy A; Hobbs, Lea Ann; Kaeberle, Merlin L; Roth, James A

    2014-05-15

    Seventy-eight heterohybridomas (HH) stably secreting bovine monoclonal antibodies (BomAb) to Bovine herpesvirus 1 (BHV1) were produced by fusing lymph node cells from a BHV1 hyperimmunized calf with 3 types of non-secreting fusion partners. Seven were generated through fusion with the murine × murine (murine(2)) hybridoma SP2/0, 3 through fusion with bovine-murine(2) HH previously generated using cells from the same calf, and 68 through fusion with bovine(2)-murine(2) HH previously generated by sequential fusions using cells from the same calf. The chromosome number of example HH increased with increasing numbers of input fusions. A variety of indirect fluorescent antibody assay patterns was observed using the BomAb, suggesting diverse antigen specificity. Three bovine(3)-murine(2) HH secreted IgG1 BomAb neutralizing BHV1 without complement, and were chosen for further characterization. SDS-PAGE of detergent-solubilized BHV1 proteins bound to the 3 neutralizing BomAb demonstrated their individual specificities for BHV1 envelope glycoproteins gB, gC, and gD, the major neutralization targets for BHV1. The 3 HH stably secreted the BomAb in culture for over one year, and pilot-scale production of the BomAb was accomplished by in vivo and in vitro methods. A cocktail of the 3 BomAb was administered intravenously (i.v.) to a 6-month-old calf and its serum neutralization activity decreased with a half-life consistent with non-immune clearance, suggesting that BomAb may be useful for passive immune treatment of disease in cattle. Rabbits were passively protected by i.v. injection with each of the anti-gB and anti-gD BomAb when challenged i.v. with BHV1 24h later. Self re-fusion was shown to be advantageous for efficiently producing HH stably secreting host monoclonal antibodies. The BomAb described should prove useful in studies of the host immune response to BHV1, as reagents, and as sources of bovine immunoglobulin sequences. Published by Elsevier B.V.

  13. 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...

  14. Romanian cyprinids phylogeny based on 16S ARN mitochondrial genes

    OpenAIRE

    Luca C.; Kevorkian S.; Elvira M.; Dinischiotu A.; Costache M.

    2007-01-01

    The vertebrate mitochondrial genome has been an important model system for studying molecular evolution, organism phylogeny, and genome structure. Phylogenetic relatioships were inferred from analysis of 570 base pairs (bp) of mithocondrial DNA (mtDNA), representing a conserved region of 16S rRNA. We sequenced 13 cyprinids species and one putative outgroup (Misgurnus fossilis) from Romania. Based upon nucleotide sequence comparisons of cyprinid mitochondrial 16SRNA genes, we established the p...

  15. 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

  16. Immunoprophylaxis of bovine respiratory syndrome

    Directory of Open Access Journals (Sweden)

    Rogan Dragan

    2010-01-01

    Full Text Available Bovine Respiratory Syndrome (BRS is a multifactorial disease caused by the interaction of infective agents, the environment and the individual immunological response of animals in the herd. Despite five decades of research on BRS, no clear understanding of how environmental factors influence pathogenic outcomes of the disease has been defined. As such, the development of immunoprophylaxis and vaccine programmes to prevent outbreaks of BRS in cattle has not been successful. The current paper discusses vaccination programmes for all categories of cattle and presents a review of existing vaccines being used for immunoprophylaxis of respiratory syndrome in cattle and discusses the advantages and disadvantages of the currently used vaccines and vaccination programmes. Lastly, a discussion detailing the design of future perfect vaccines is presented.

  17. Lateral gene transfer in phylogeny of azoreductase enzyme.

    Science.gov (United States)

    Bafana, Amit; Chakrabarti, Tapan

    2008-06-01

    This paper attempts to reconstruct the phylogeny of azoreductase enzyme from different organisms and compare it with the small subunit rRNA-based phylogeny of the organisms. The two phylogenies were found to be incongruent, indicating several events of lateral transfer of azoreductase gene between phylogenetically diverse organisms. However, the phylogenetic analysis methods have several limitations and a single method may not give the true pattern. Hence, it is necessary to corroborate the results with other complementary analysis tools. We used several tools to test our hypothesis of lateral transfer and found that it was supported not only by the analysis of the whole sequences, but also by the conserved motifs detected in these sequences. There were ample evidences for lateral transfer of azoreductase gene among enteric bacteria. There were also indications that azoreductase probably evolved in prokaryotes and then it was laterally transferred to eukaryotes in multiple events, resulting in some sequence variation among eukaryotic azoreductases. Finally, profile HMMs and conserved motifs extracted from these azoreductase sequences were found to provide sensitive tools for identifying potential azoreductases from the database. The analysis techniques used in this study can be extended to other gene trees to verify their evolutionary histories.

  18. Mitogenomic perspectives on the origin and phylogeny of living amphibians.

    Science.gov (United States)

    Zhang, Peng; Zhou, Hui; Chen, Yue-Qin; Liu, Yi-Fei; Qu, Liang-Hu

    2005-06-01

    Establishing the relationships among modern amphibians (lissamphibians) and their ancient relatives is necessary for our understanding of early tetrapod evolution. However, the phylogeny is still intractable because of the highly specialized anatomy and poor fossil record of lissamphibians. Paleobiologists are still not sure whether lissamphibians are monophyletic or polyphyletic, and which ancient group (temnospondyls or lepospondyls) is most closely related to them. In an attempt to address these problems, eight mitochondrial genomes of living amphibians were determined and compared with previously published amphibian sequences. A comprehensive molecular phylogenetic analysis of nucleotide sequences yields a highly resolved tree congruent with the traditional hypotheses (Batrachia). By using a molecular clock-independent approach for inferring dating information from molecular phylogenies, we present here the first molecular timescale for lissamphibian evolution, which suggests that lissamphibians first emerged about 330 million years ago. By observing the fit between molecular and fossil times, we suggest that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses. Moreover, under this timescale, the potential geographic origins of the main living amphibian groups are discussed: (i) advanced frogs (neobatrachians) may possess an Africa-India origin; (ii) salamanders may have originated in east Asia; (iii) the tropic forest of the Triassic Pangaea may be the place of origin for the ancient caecilians. An accurate phylogeny with divergence times can be also helpful to direct the search for "missing" fossils, and can benefit comparative studies of amphibian evolution.

  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. PhyloPars: estimation of missing parameter values using phylogeny.

    Science.gov (United States)

    Bruggeman, Jorn; Heringa, Jaap; Brandt, Bernd W

    2009-07-01

    A wealth of information on metabolic parameters of a species can be inferred from observations on species that are phylogenetically related. Phylogeny-based information can complement direct empirical evidence, and is particularly valuable if experiments on the species of interest are not feasible. The PhyloPars web server provides a statistically consistent method that combines an incomplete set of empirical observations with the species phylogeny to produce a complete set of parameter estimates for all species. It builds upon a state-of-the-art evolutionary model, extended with the ability to handle missing data. The resulting approach makes optimal use of all available information to produce estimates that can be an order of magnitude more accurate than ad-hoc alternatives. Uploading a phylogeny and incomplete feature matrix suffices to obtain estimates of all missing values, along with a measure of certainty. Real-time cross-validation provides further insight in the accuracy and bias expected for estimated values. The server allows for easy, efficient estimation of metabolic parameters, which can benefit a wide range of fields including systems biology and ecology. PhyloPars is available at: http://www.ibi.vu.nl/programs/phylopars/.

  1. pHMM-tree: phylogeny of profile hidden Markov models.

    Science.gov (United States)

    Huo, Luyang; Zhang, Han; Huo, Xueting; Yang, Yasong; Li, Xueqiong; Yin, Yanbin

    2017-04-01

    Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families. This software is implemented in C/C ++ and is available at http://cys.bios.niu.edu/pHMM-Tree/source/. zhanghan@nankai.edu.cn or yyin@niu.edu. Supplementary data are available at Bioinformatics online.

  2. Phylogeny and evolution of apicoplasts and apicomplexan parasites.

    Science.gov (United States)

    Arisue, Nobuko; Hashimoto, Tetsuo

    2015-06-01

    The phylum Apicomplexa includes many parasitic genera of medical and veterinary importance including Plasmodium (causative agent of malaria), Toxoplasma (toxoplasmosis), and Babesia (babesiosis). Most of the apicomplexan parasites possess a unique, essential organelle, the apicoplast, which is a plastid without photosynthetic ability. Although the apicoplast is considered to have evolved through secondary endosymbiosis of a red alga into the common ancestral cell of apicomplexans, its evolutionary history has been under debate until recently. The apicoplast has a genome around 30-40 kb in length. Repertoire and arrangement of the apicoplast genome-encoded genes differ among apicomplexan genera, although within the genus Plasmodium these are almost conserved. Genes in the apicoplast genome may be useful markers for Plasmodium phylogeny, because these are single copy (except for the inverted repeat region) and may have more phylogenetic signal than the mitochondrial genome that have been most commonly used for Plasmodium phylogeny. This review describes recent studies concerning the evolutionary origin of the apicoplast, presents evolutionary comparison of the primary structures of apicoplast genomes from apicomplexan parasites, and summarizes recent findings of malaria phylogeny based on apicoplast genome-encoded genes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  3. Bovine Mastitis: Frontiers in Immunogenetics

    Directory of Open Access Journals (Sweden)

    Kathleen eThompson-Crispi

    2014-10-01

    Full Text Available Mastitis is one of the most prevalent and costly diseases in the dairy industry with losses attributable to reduced milk production, discarded milk, early culling, veterinary services, and labor costs. Typically, mastitis is an inflammation of the mammary gland most often, but not limited to, bacterial infection, and is characterized by the movement of leukocytes and serum proteins from the blood to the site of infection. It contributes to compromised milk quality and the potential spread of antimicrobial resistance if antibiotic treatment is not astutely applied. Despite the implementation of management practises and genetic selection approaches, bovine mastitis control continues to be inadequate. However, some novel genetic strategies have recently been demonstrated to reduce mastitis incidence by taking advantage of a cow’s natural ability to make appropriate immune responses against invading pathogens. Specifically, dairy cattle with enhanced and balanced immune responses have a lower occurrence of disease, including mastitis, and they can be identified and selected for using the High Immune Response (HIR technology. Enhanced immune responsiveness is also associated with improved response to vaccination, increased milk and colostrum quality. Since immunity is an important fitness trait, beneficial associations with longevity and reproduction are also often noted. This review highlights the genetic regulation of the bovine immune system and its vital contributions to disease resistance. Genetic selection approaches currently used in the dairy industry to reduce the incidence of disease are reviewed, including the HIR technology, genomics to improve disease resistance or immune response, as well as the Immunity+TM sire line. Improving the overall immune responsiveness of cattle is expected to provide superior disease resistance, increasing animal welfare and food quality while maintaining favourable production levels to feed a growing

  4. Bovine Mastitis: Frontiers in Immunogenetics

    Science.gov (United States)

    Thompson-Crispi, Kathleen; Atalla, Heba; Miglior, Filippo; Mallard, Bonnie A.

    2014-01-01

    Mastitis is one of the most prevalent and costly diseases in the dairy industry with losses attributable to reduced milk production, discarded milk, early culling, veterinary services, and labor costs. Typically, mastitis is an inflammation of the mammary gland most often, but not limited to, bacterial infection, and is characterized by the movement of leukocytes and serum proteins from the blood to the site of infection. It contributes to compromised milk quality and the potential spread of antimicrobial resistance if antibiotic treatment is not astutely applied. Despite the implementation of management practises and genetic selection approaches, bovine mastitis control continues to be inadequate. However, some novel genetic strategies have recently been demonstrated to reduce mastitis incidence by taking advantage of a cow’s natural ability to make appropriate immune responses against invading pathogens. Specifically, dairy cattle with enhanced and balanced immune responses have a lower occurrence of disease, including mastitis, and they can be identified and selected for using the high immune response (HIR) technology. Enhanced immune responsiveness is also associated with improved response to vaccination, increased milk, and colostrum quality. Since immunity is an important fitness trait, beneficial associations with longevity and reproduction are also often noted. This review highlights the genetic regulation of the bovine immune system and its vital contributions to disease resistance. Genetic selection approaches currently used in the dairy industry to reduce the incidence of disease are reviewed, including the HIR technology, genomics to improve disease resistance or immune response, as well as the Immunity+™ sire line. Improving the overall immune responsiveness of cattle is expected to provide superior disease resistance, increasing animal welfare and food quality while maintaining favorable production levels to feed a growing population. PMID

  5. Volpe Center Annual Accomplishments: Advancing Transportation Innovation for the Public Good - January 2018

    Science.gov (United States)

    2018-01-01

    The Volpe Centers Annual Accomplishments highlights our best work of 2017 and illustrates the sustained impact of the Volpe Center in supporting the U.S. DOTs top priorities and strategic goals: safety, infrastructure, innovation, and accountab...

  6. Planning and accomplishment narrative : January 1 - June 30, 1973 : Des Lacs National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This planning and accomplishment report for Des Lacs National Wildlife Refuge outlines Refuge activities from January 1st through June 30th, 1973. The report begins...

  7. The genetics of music accomplishment: evidence for gene-environment correlation and interaction.

    Science.gov (United States)

    Hambrick, David Z; Tucker-Drob, Elliot M

    2015-02-01

    Theories of skilled performance that emphasize training history, such as K. Anders Ericsson and colleagues' deliberate-practice theory, have received a great deal of recent attention in both the scientific literature and the popular press. Twin studies, however, have demonstrated evidence for moderate-to-strong genetic influences on skilled performance. Focusing on musical accomplishment in a sample of over 800 pairs of twins, we found evidence for gene-environment correlation, in the form of a genetic effect on music practice. However, only about one quarter of the genetic effect on music accomplishment was explained by this genetic effect on music practice, suggesting that genetically influenced factors other than practice contribute to individual differences in music accomplishment. We also found evidence for gene-environment interaction, such that genetic effects on music accomplishment were most pronounced among those engaging in music practice, suggesting that genetic potentials for skilled performance are most fully expressed and fostered by practice.

  8. Recombinant viral vaccines for enzootic bovine leucosis

    National Research Council Canada - National Science Library

    Daniel, R C; Gatei, M H; Good, M F; Boyle, D B; Lavin, M F

    1993-01-01

    ...) and part of gp30 of the bovine leukaemia virus (BLV) are described. It has been reported that vaccination of sheep with recombinant VV vaccines containing the complete env gene appears to protect sheep against challenge infection with BLV...

  9. Virome of US bovine calf serum.

    Science.gov (United States)

    Sadeghi, Mohammadreza; Kapusinszky, Beatrix; Yugo, Danielle M; Phan, Tung Gia; Deng, Xutao; Kanevsky, Isis; Opriessnig, Tanja; Woolums, Amelia R; Hurley, David J; Meng, Xiang-Jin; Delwart, Eric

    2017-03-01

    Using viral metagenomics we analyzed four bovine serum pools assembled from 715 calves in the United States. Two parvoviruses, bovine parvovirus 2 (BPV2) and a previously uncharacterized parvovirus designated as bosavirus (BosaV), were detected in 3 and 4 pools respectively and their complete coding sequences generated. Based on NS1 protein identity, bosavirus qualifies as a member of a new species in the copiparvovirus genus. Also detected were low number of reads matching ungulate tetraparvovirus 2, bovine hepacivirus, and several papillomaviruses. This study further characterizes the diversity of viruses in calf serum with the potential to infect fetuses and through fetal bovine serum contaminate cell cultures. Copyright © 2017 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  10. Structural dynamics division research and technology accomplishments for FY 1993 and plans for FY 1994

    Science.gov (United States)

    Wynne, Eleanor C.

    1994-01-01

    The purpose is to present the Structural Dynamics Division's research accomplishments for F.Y. 1993 and research plans for F.Y. 1994. The work under each Branch (technical area) is described in terms of highlights of accomplishments during the past year and highlights of plans for the current year as they relate to 5-year plans for each technical area. This information will be useful in program coordination with other government organizations and industry in areas of mutual interest.

  11. Metabolism and Calcification of Bovine Tooth Enamel

    OpenAIRE

    高木, 亨; 田上, 順次; 中村, 聡; Tohru, Takagi; Junji, TAGAMI; Satoshi, Nakamura; 東京医科歯科大学歯学部 生化学講座; 東京医科歯科大学歯学部 歯科保存学第1講座; 東京医科歯科大学歯学部 医用器材研究所; Department of Biochemistry, Faculty of Dentistry Tokyo Medical and Dental University; Department of Operative Dentistry, Faculty of Dentistry Tokyo Medical and Dental University; Institute of Medical and Dental Engineering, Faculty of Dentistry Tokyo Medical and Dental University

    1997-01-01

    The purpose of this study was to investigate the mineralization mechanism in developing enamel using pH staining. Unerupted bovine teeth were used for the expriment. The activity of a proteolytic enzyme was evaluated against enamel protein obtainedfrom bovine enamel. Crystals in developing enamel, which were classlfied into neutral zone 1 and 2, acid zone 1 and 2, were investigated using infrared spectroscopy, thermal analysis, and power X-ray diffractometry. Proteolytic enzyme showed the hig...

  12. Interactions between bovine cornea proteoglycans and collagen.

    OpenAIRE

    Speziale, P.; Bardoni, A; Balduini, C.

    1980-01-01

    Two types of proteoglycan subunits were obtained from bovine cornea, the first mainly composed of proteochondroitin sulphate and the second of proteokeratan sulphate. These two fractions can be obtained from the tissue as an aggregate, and are able to recombine each other after separation, to re-form the original structure. In order to investigate collagen-proteoglycan interactions, type-I collagen was isolated from bovine cornea by pepsin digestion followed by 3.5% (w/v) NaCl precipitation, ...

  13. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Bovine leukaemia virus genotypes 5 and 6 are circulating in cattle from the state of São Paulo, Brazil.

    Science.gov (United States)

    Gregory, Lilian; Carrillo Gaeta, Natália; Araújo, Jansen; Matsumiya Thomazelli, Luciano; Harakawa, Ricardo; Ikuno, Alice A; Hiromi Okuda, Liria; de Stefano, Eliana; Pituco, Edviges Maristela

    2017-12-01

    Enzootic bovine leucosis (EBL) is a silent disease caused by a retrovirus [bovine leukaemia virus (BLV)]. BLV is classified into almost 10 genotypes that are distributed in several countries. The present research aimed to describe two BLV gp51 env sequences of strains detected in the state of São Paulo, Brazil and perform a phylogenetic analysis to compare them to other BLV gp51 env sequences of strains around the world. Two bovines from different herds were admitted to the Bovine and Small Ruminant Hospital, School of Veterinary Medicine and Animal Science, University of São Paulo, Brazil. In both, lymphosarcoma was detected and the presence of BLV was confirmed by nested PCR. The neighbour-joining algorithm distance method was used to genotype the BLV sequences by phylogenetic reconstruction, and the maximum likelihood method was used for the phylogenetic reconstruction. The phylogeny estimates were calculated by performing 1000 bootstrap replicates. Analysis of the partial envelope glycoprotein (env) gene sequences from two isolates (25 and 31) revealed two different genotypes of BLV. Isolate 25 clustered with ten genotype 6 isolates from Brazil, Argentina, Thailand and Paraguay. On the other hand, isolate 31 clustered with two genotype 5 isolates (one was also from São Paulo and one was from Costa Rica). The detected genotypes corroborate the results of previous studies conducted in the state of São Paulo, Brazil. The prediction of amino acids showed substitutions, particularly between positions 136 and 150 in 11 out of 13 sequences analysed, including sequences from GenBank. BLV is still important in Brazil and this research should be continued.

  15. Anti-Bovine Programmed Death-1 Rat-Bovine Chimeric Antibody for Immunotherapy of Bovine Leukemia Virus Infection in Cattle.

    Science.gov (United States)

    Okagawa, Tomohiro; Konnai, Satoru; Nishimori, Asami; Maekawa, Naoya; Ikebuchi, Ryoyo; Goto, Shinya; Nakajima, Chie; Kohara, Junko; Ogasawara, Satoshi; Kato, Yukinari; Suzuki, Yasuhiko; Murata, Shiro; Ohashi, Kazuhiko

    2017-01-01

    Blockade of immunoinhibitory molecules, such as programmed death-1 (PD-1)/PD-ligand 1 (PD-L1), is a promising strategy for reinvigorating exhausted T cells and preventing disease progression in a variety of chronic infections. Application of this therapeutic strategy to cattle requires bovinized chimeric antibody targeting immunoinhibitory molecules. In this study, anti-bovine PD-1 rat-bovine chimeric monoclonal antibody 5D2 (Boch5D2) was constructed with mammalian expression systems, and its biochemical function and antiviral effect were characterized in vitro and in vivo using cattle infected with bovine leukemia virus (BLV). Purified Boch5D2 was capable of detecting bovine PD-1 molecules expressed on cell membranes in flow cytometric analysis. In particular, Biacore analysis determined that the binding affinity of Boch5D2 to bovine PD-1 protein was similar to that of the original anti-bovine PD-1 rat monoclonal antibody 5D2. Boch5D2 was also capable of blocking PD-1/PD-L1 binding at the same level as 5D2. The immunomodulatory and therapeutic effects of Boch5D2 were evaluated by in vivo administration of the antibody to a BLV-infected calf. Inoculated Boch5D2 was sustained in the serum for a longer period. Boch5D2 inoculation resulted in activation of the proliferation of BLV-specific CD4+ T cells and decrease in the proviral load of BLV in the peripheral blood. This study demonstrates that Boch5D2 retains an equivalent biochemical function to that of the original antibody 5D2 and is a candidate therapeutic agent for regulating antiviral immune response in vivo. Clinical efficacy of PD-1/PD-L1 blockade awaits further experimentation with a large number of animals.

  16. Anti-Bovine Programmed Death-1 Rat–Bovine Chimeric Antibody for Immunotherapy of Bovine Leukemia Virus Infection in Cattle

    Science.gov (United States)

    Okagawa, Tomohiro; Konnai, Satoru; Nishimori, Asami; Maekawa, Naoya; Ikebuchi, Ryoyo; Goto, Shinya; Nakajima, Chie; Kohara, Junko; Ogasawara, Satoshi; Kato, Yukinari; Suzuki, Yasuhiko; Murata, Shiro; Ohashi, Kazuhiko

    2017-01-01

    Blockade of immunoinhibitory molecules, such as programmed death-1 (PD-1)/PD-ligand 1 (PD-L1), is a promising strategy for reinvigorating exhausted T cells and preventing disease progression in a variety of chronic infections. Application of this therapeutic strategy to cattle requires bovinized chimeric antibody targeting immunoinhibitory molecules. In this study, anti-bovine PD-1 rat–bovine chimeric monoclonal antibody 5D2 (Boch5D2) was constructed with mammalian expression systems, and its biochemical function and antiviral effect were characterized in vitro and in vivo using cattle infected with bovine leukemia virus (BLV). Purified Boch5D2 was capable of detecting bovine PD-1 molecules expressed on cell membranes in flow cytometric analysis. In particular, Biacore analysis determined that the binding affinity of Boch5D2 to bovine PD-1 protein was similar to that of the original anti-bovine PD-1 rat monoclonal antibody 5D2. Boch5D2 was also capable of blocking PD-1/PD-L1 binding at the same level as 5D2. The immunomodulatory and therapeutic effects of Boch5D2 were evaluated by in vivo administration of the antibody to a BLV-infected calf. Inoculated Boch5D2 was sustained in the serum for a longer period. Boch5D2 inoculation resulted in activation of the proliferation of BLV-specific CD4+ T cells and decrease in the proviral load of BLV in the peripheral blood. This study demonstrates that Boch5D2 retains an equivalent biochemical function to that of the original antibody 5D2 and is a candidate therapeutic agent for regulating antiviral immune response in vivo. Clinical efficacy of PD-1/PD-L1 blockade awaits further experimentation with a large number of animals. PMID:28638381

  17. Anti-Bovine Programmed Death-1 Rat–Bovine Chimeric Antibody for Immunotherapy of Bovine Leukemia Virus Infection in Cattle

    Directory of Open Access Journals (Sweden)

    Tomohiro Okagawa

    2017-06-01

    Full Text Available Blockade of immunoinhibitory molecules, such as programmed death-1 (PD-1/PD-ligand 1 (PD-L1, is a promising strategy for reinvigorating exhausted T cells and preventing disease progression in a variety of chronic infections. Application of this therapeutic strategy to cattle requires bovinized chimeric antibody targeting immunoinhibitory molecules. In this study, anti-bovine PD-1 rat–bovine chimeric monoclonal antibody 5D2 (Boch5D2 was constructed with mammalian expression systems, and its biochemical function and antiviral effect were characterized in vitro and in vivo using cattle infected with bovine leukemia virus (BLV. Purified Boch5D2 was capable of detecting bovine PD-1 molecules expressed on cell membranes in flow cytometric analysis. In particular, Biacore analysis determined that the binding affinity of Boch5D2 to bovine PD-1 protein was similar to that of the original anti-bovine PD-1 rat monoclonal antibody 5D2. Boch5D2 was also capable of blocking PD-1/PD-L1 binding at the same level as 5D2. The immunomodulatory and therapeutic effects of Boch5D2 were evaluated by in vivo administration of the antibody to a BLV-infected calf. Inoculated Boch5D2 was sustained in the serum for a longer period. Boch5D2 inoculation resulted in activation of the proliferation of BLV-specific CD4+ T cells and decrease in the proviral load of BLV in the peripheral blood. This study demonstrates that Boch5D2 retains an equivalent biochemical function to that of the original antibody 5D2 and is a candidate therapeutic agent for regulating antiviral immune response in vivo. Clinical efficacy of PD-1/PD-L1 blockade awaits further experimentation with a large number of animals.

  18. Susceptibility of bovine umbilical cord endothelial cells to bovine herpesviruses and pseudocowpox virus.

    NARCIS (Netherlands)

    Wellenberg, G.J.; Verstraten, E.R.A.M.; Jongejan, F.; Oirschot, van J.T.

    2002-01-01

    The purpose of the study was to determine the susceptibility of bovine umbilical cord endothelial (BUE) cells to bovine herpesvirus (BHV) 1, BHV2, BHV4 and BHV5, and to pseudocowpox virus. the detection limits and growth curves of these viruses in BUE cells were compared with those in Vero,

  19. Antimicrobial activity of bovine NK-lysin-derived peptides on bovine respiratory pathogen Histophilus somni

    Science.gov (United States)

    Bovine NK-lysins, which are functionally and structurally similar to human granulysin and porcine NK-lysin, are predominantly found in the granules of cytotoxic T-lymphocytes and NK-cells. Although antimicrobial activity of bovine NK-lysin has been assessed for several bacterial pathogens, not all t...

  20. 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.

  1. 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.

  2. Recapitulating phylogenies using k-mers: from trees to networks

    Science.gov (United States)

    Bernard, Guillaume; Ragan, Mark A.; Chan, Cheong Xin

    2016-01-01

    Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k-mers (subsequences at fixed length k). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel’s idea of ontogeny, we argue that genome phylogenies can be inferred using k-mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner. PMID:28105314

  3. Recapitulating phylogenies usingk-mers: from trees to networks.

    Science.gov (United States)

    Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

    2016-01-01

    Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

  4. Phylogeny and evolution of glass sponges (porifera, hexactinellida).

    Science.gov (United States)

    Dohrmann, Martin; Janussen, Dorte; Reitner, Joachim; Collins, Allen G; Worheide, Gert

    2008-06-01

    Reconstructing the phylogeny of sponges (Porifera) is one of the remaining challenges to resolve the metazoan Tree of Life and is a prerequisite for understanding early animal evolution. Molecular phylogenetic analyses for two of the three extant classes of the phylum, Demospongiae and Calcarea, are largely incongruent with traditional classifications, most likely because of a paucity of informative morphological characters and high levels of homoplasy. For the third class, Hexactinellida (glass sponges)--predominantly deep-sea inhabitants with unusual morphology and biology--we present the first molecular phylogeny, along with a cladistic analysis of morphological characters. We collected 18S, 28S, and mitochondrial 16S ribosomal DNA sequences of 34 glass sponge species from 27 genera, 9 families, and 3 orders and conducted partitioned Bayesian analyses using RNA secondary structure-specific substitution models (paired-sites models) for stem regions. Bayes factor comparisons of different paired-sites models against each other and conventional (independent-sites) models revealed a significantly better fit of the former but, contrary to previous predictions, the least parameter-rich of the tested paired-sites models provided the best fit to our data. In contrast to Demospongiae and Calcarea, our rDNA phylogeny agrees well with the traditional classification and a previously proposed phylogenetic system, which we ascribe to a more informative morphology in Hexactinellida. We find high support for a close relationship of glass sponges and Demospongiae sensu stricto, though the latter may be paraphyletic with respect to Hexactinellida. Homoscleromorpha appears to be the sister group of Calcarea. Contrary to most previous findings from rDNA, we recover Porifera as monophyletic, although support for this clade is low under paired-sites models.

  5. Empirical assessment of RAD sequencing for interspecific phylogeny.

    Science.gov (United States)

    Cruaud, Astrid; Gautier, Mathieu; Galan, Maxime; Foucaud, Julien; Sauné, Laure; Genson, Gwenaëlle; Dubois, Emeric; Nidelet, Sabine; Deuve, Thierry; Rasplus, Jean-Yves

    2014-05-01

    Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current bioinformatic and phylogenetic tools produced 400× more sites than our Sanger approach (2,262,825 nt/species), fully resolving relationships between 18 species of ground beetles (divergences up to 17 My). This suggests that RAD-seq is promising to infer phylogeny of eukaryotic species, though potential biases need to be evaluated and new methodologies developed to take full advantage of such data.

  6. The ITS-based phylogeny of fungi associated with tarballs

    Digital Repository Service at National Institute of Oceanography (India)

    Sanyal, O.; Shinde, V.L.; Meena, R.M.; Damare, S.R.; Shenoy, B.D.

     Version:  Mar. Pollut. Bull., vol.113(1‐2); 2016; 277‐281    The ITS‐based phylogeny of fungi associated with tarballs  Olivia Sanyal1, 2, Varsha Laxman Shinde2, Ram Murti Meena2, Samir Damare2, Belle Damodara Shenoy2, 3, *  1Department of Food and Biotechnology, Jayoti Vidyapeeth Women...

  7. Serological responses in calves to vaccines against bovine respiratory syncytial, infectious bovine rhinotracheitis, bovine viral diarrhoea and parainfluenza-3 viruses.

    Science.gov (United States)

    Tollis, M; Di Trani, L; Cordioli, P; Vignolo, E; Di Pasquale, I

    1996-01-01

    The Istituto Superiore di Sanità (ISS), the National Veterinary Services Laboratory in Italy, is in charge of assessing the quality, safety and efficacy of veterinary vaccines before and after licensing. To evaluate the relative potency of several vaccines against bovine respiratory syncytial virus (BRSV), infectious bovine rhinotracheitis virus (IBRV), bovine viral diarrhoea virus (BVDV) and parainfluenza-3 virus (PI3V), the serological responses in vaccinated calves were studied. Vaccination with any of the vaccines under study induced specific antibody titres against the different viral antigens. The differences of the mean antibody titres within and among the test group vaccines were statistically significant. The results confirm and support those obtained by other authors in similar studies, suggesting that serological responses in vaccinated calves can be used as a helpful means of assessing the relative potency of vaccines against viral respiratory diseases of cattle. The criteria allowing such an evaluation are discussed.

  8. Recent Progress in Cryopreservation of Bovine Oocytes

    Directory of Open Access Journals (Sweden)

    In-Sul Hwang

    2014-01-01

    Full Text Available Principle of oocyte cryoinjury is first overviewed and then research history of cryopreservation using bovine oocytes is summarized for the last two decades with a few special references to recent progresses. Various types of cryodevices have been developed to accelerate the cooling rate and applied to the oocytes from large domestic species enriched with cytoplasmic lipid droplets. Two recent approaches include the qualitative improvement of IVM oocytes prior to the vitrification and the short-term recovery culture of vitrified-warmed oocytes prior to the subsequent IVF. Supplementation of L-carnitine to IVM medium of bovine oocytes has been reported to reduce the amount of cytoplasmic lipid droplets and improve the cryotolerance of the oocytes, but it is still controversial whether the positive effect of L-carnitine is reproducible. Incidence of multiple aster formation, a possible cause for low developmental potential of vitrified-warmed bovine oocytes, was inhibited by a short-term culture of the postwarm oocytes in the presence of Rho-associated coiled-coil kinase (ROCK inhibitor. Use of an antioxidant α-tocopherol, instead of the ROCK inhibitor, also supported the revivability of the postwarm bovine oocytes. Further improvements of the vitrification procedure, combined with pre- and postvitrification chemical treatment, would overcome the high sensitivity of bovine oocytes to cryopreservation.

  9. Innovative Partnerships Program Accomplishments: 2009-2010 at NASA's Kennedy Space Center

    Science.gov (United States)

    Makufka, David

    2010-01-01

    This document reports on the accomplishments of the Innovative Partnerships Program during the two years of 2009 and 2010. The mission of the Innovative Partnerships Program is to provide leveraged technology alternatives for mission directorates, programs, and projects through joint partnerships with industry, academia, government agencies, and national laboratories. As outlined in this accomplishments summary, the IPP at NASA's Kennedy Space Center achieves this mission via two interdependent goals: (1) Infusion: Bringing external technologies and expertise into Kennedy to benefit NASA missions, programs, and projects (2) Technology Transfer: Spinning out space program technologies to increase the benefits for the nation's economy and humanity

  10. Structural dynamics division research and technology accomplishments for FY 1992 and plans for FY 1993

    Science.gov (United States)

    Wynne, Eleanor C.

    1993-01-01

    The purpose of this paper is to present the Structural Dynamics Division's research accomplishments for F.Y. 1992 and research plans for F.Y. 1993. The work under each Branch (technical area) is described in terms of highlights of accomplishments during the past year and highlights of plans for the current year as they relate to 5-year plans for each technical area. This information will be useful in program coordination with other government organizations and industry in areas of mutual interest.

  11. Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.

    Science.gov (United States)

    Meinel, Thomas; Krause, Antje

    2012-01-01

    In the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the Tree of Life (ToL). Underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. Diversity in data models together with the use of different tree reconstruction techniques, disruptive biological effects and the steadily increasing number of genomes have led to a huge diversity in published phylogenies. Comparison of those and, moreover, identification of the impact of inference properties (underlying data model, inference technique) on particular reconstructions is almost impossible. In this work, we introduce tree topology profiling as a method to compare already published whole-genome phylogenies. This method requires visual determination of the particular topology in a drawn whole-genome phylogeny for a set of particular bacterial clans. For each clan, neighborhoods to other bacteria are collected into a catalogue of generalized alternative topologies. Particular topology alternatives found for an ordered list of bacterial clans reveal a topology profile that represents the analyzed phylogeny. To simulate the inhomogeneity of published gene content phylogenies we generate a set of seven phylogenies using different inference techniques and the SYSTERS-PhyloMatrix data model. After tree topology profiling on in total 54 selected published and newly inferred phylogenies, we separate artefactual from biologically meaningful phylogenies and associate particular inference results (phylogenies) with inference background (inference techniques as well as data models). Topological relationships of particular bacterial species groups are presented. With this work we introduce tree topology profiling into the scientific field of comparative phylogenomics.

  12. Use of bovine carotid artery for buttonhole technique hemodialysis.

    Science.gov (United States)

    Schuman, Earl; Alexander, Philip; Ronfeld, Amy

    2017-11-08

    Assess the feasibility of using a bovine carotid artery graft for buttonhole technique hemodialysis in patients who are not candidates for a native fistula. Case reports used to demonstrate selection criteria and results for this approach. Criteria include: knowledgeable patient with prior dialysis experience, stable graft in place for 3 months minimum, not a candidate for a native fistula, and able to maintain close follow-up. Both grafts were based on axillary vessels and have been in place for a total of 64 months. They have been used for dialysis via buttonhole for a total of 40 months. There have been three procedures on these patients, post-buttonhole use (.87/year). There have been no infections. These patients were carefully selected based on desire, support, knowledge/experience and ability. Their success suggests that buttonhole technique for hemodialysis on a synthetic semi-biologic graft can be accomplished with morbidity and longevity similar to any graft using non-buttonhole needle access.

  13. Bovine Eimeria species in Austria.

    Science.gov (United States)

    Koutny, H; Joachim, A; Tichy, A; Baumgartner, W

    2012-05-01

    Bovine eimeriosis is considered to be of considerable importance for the productivity and health of cattle worldwide. Despite the importance of cattle farming in Austria, little is known in this country about the abundance and distribution of bovine Eimeria spp. The objective of this study was to obtain detailed information about the occurrence of different Eimeria spp. on Austrian dairy farms. Fecal samples from individual calves (n = 868) from 296 farms all over Austria (82 districts) were collected. Additionally, each farmer was questioned about the occurrence of calf diarrhea, and about the knowledge on coccidiosis and possible control measures. On 97.97% of the investigated farms, calves excreted Eimeria oocysts, and 83.67% of the individual samples were positive. After sporulation of positive samples pooled from each farm, 11 Eimeria species were found, with E. bovis (in 65.54% of the samples and 27.74% of the farms), E.zuernii (63.85%/13.86%), E. auburnensis (56.76%/13.41%) and E. ellipsoidalis (54.05%/14.38%) being the most prevalent, followed by E. alabamensis (45.61%/11.56%), E. subspherica (35.14%/5.5.05%), E. cylindrica (33.11%/7.00%), and E. canadensis (31.08%/7.74%). E. wyomingensis, E. pellita and E. bukidnonensis were only found sporadically (3.04-4.73% of the samples and 0.16-0.59% of the farms). Mixed infections were present on all farms (2-9 Eimeria species/farm). Prevalences by state provinces were high throughout with 77.1-87.9% of the samples and 93.8-100% of the farms. Lower Austria had the highest percentage of positive farms, and Vorarlberg the lowest. Individual OPG (oocysts per gram of feces) values were generally low; 75% of the samples had an OPG of 1,000 or less. The highest detected OPG was 72,400. The mean OPG was 2,525 with above average numbers in Tirol, Carinthia, and Lower Austria. The mean OPG values were significantly positively correlated with the cattle density in the different districts. The majority of the samples were from

  14. Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease

    Science.gov (United States)

    ... Search Form Controls Cancel Submit Search the CDC Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease Note: ... gov . Recommend on Facebook Tweet Share Compartir BSE (bovine spongiform encephalopathy) is a progressive neurological disorder of ...

  15. Investigation of the prevalence of bovine tuberculosis and risk ...

    African Journals Online (AJOL)

    Investigation of the prevalence of bovine tuberculosis and risk factors for human infection with bovine tuberculosis among dairy and non-dairy farming neighbour households in Dagoretti Division, Nairobi, Kenya.

  16. A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

    Science.gov (United States)

    Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

    2012-01-01

    Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses.

  17. Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida).

    Science.gov (United States)

    Smirnov, Alexey; Nassonova, Elena; Geisen, Stefan; Bonkowski, Michael; Kudryavtsev, Alexander; Berney, Cedric; Glotova, Anna; Bondarenko, Natalya; Dyková, Iva; Mrva, Martin; Fahrni, Jose; Pawlowski, Jan

    2017-04-01

    We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other. Copyright © 2016 Elsevier GmbH. All rights reserved.

  18. A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

    Directory of Open Access Journals (Sweden)

    Nan Song

    Full Text Available Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha,Cicadomorpha,Heteroptera, and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes demonstrated that rapidly evolving and saturated sites should be removed from the analyses.

  19. Estimating species phylogenies using coalescence times among sequences.

    Science.gov (United States)

    Liu, Liang; Yu, Lili; Pearl, Dennis K; Edwards, Scott V

    2009-10-01

    The estimation of species trees (phylogenies) is one of the most important problems in evolutionary biology, and recently, there has been greater appreciation of the need to estimate species trees directly rather than using gene trees as a surrogate. A Bayesian method constructed under the multispecies coalescent model can consistently estimate species trees but involves intensive computation, which can hinder its application to the phylogenetic analysis of large-scale genomic data. Many summary statistics-based approaches, such as shallowest coalescences (SC) and Global LAteSt Split (GLASS), have been developed to infer species phylogenies for multilocus data sets. In this paper, we propose 2 methods, species tree estimation using average ranks of coalescences (STAR) and species tree estimation using average coalescence times (STEAC), based on the summary statistics of coalescence times. It can be shown that the 2 methods are statistically consistent under the multispecies coalescent model. STAR uses the ranks of coalescences and is thus resistant to variable substitution rates along the branches in gene trees. A simulation study suggests that STAR consistently outperforms STEAC, SC, and GLASS when the substitution rates among lineages are highly variable. Two real genomic data sets were analyzed by the 2 methods and produced species trees that are consistent with previous results.

  20. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes).

    Science.gov (United States)

    Castoe, Todd A; Parkinson, Christopher L

    2006-04-01

    The subfamily Crotalinae (pitvipers) contains over 190 species of venomous snakes distributed in both the Old and New World. We incorporated an extensive sampling of taxa (including 28 of 29 genera), and sequences of four mitochondrial gene fragments (2.3kb) per individual, to estimate the phylogeny of pitvipers based on maximum parsimony and Bayesian phylogenetic methods. Our Bayesian analyses incorporated complex mixed models of nucleotide evolution that allocated independent models to various partitions of the dataset within combined analyses. We compared results of unpartitioned versus partitioned Bayesian analyses to investigate how much unpartitioned (versus partitioned) models were forced to compromise estimates of model parameters, and whether complex models substantially alter phylogenetic conclusions to the extent that they appear to extract more phylogenetic signal than simple models. Our results indicate that complex models do extract more phylogenetic signal from the data. We also address how differences in phylogenetic results (e.g., bipartition posterior probabilities) obtained from simple versus complex models may be interpreted in terms of relative credibility. Our estimates of pitviper phylogeny suggest that nearly all recently proposed generic reallocations appear valid, although certain Old and New World genera (Ovophis, Trimeresurus, and Bothrops) remain poly- or paraphyletic and require further taxonomic revision. While a majority of nodes were resolved, we could not confidently estimate the basal relationships among New World genera and which lineage of Old World species is most closely related to this New World group.

  1. History, objectivity, and the construction of molecular phylogenies.

    Science.gov (United States)

    Suárez-Díaz, Edna; Anaya-Muñoz, Victor H

    2008-12-01

    Despite the promises made by molecular evolutionists since the early 1960s that phylogenies would be readily reconstructed using molecular data, the construction of molecular phylogenies has both retained many methodological problems of the past and brought up new ones of considerable epistemic relevance. The field is driven not only by changes in knowledge about the processes of molecular evolution, but also by an ever-present methodological anxiety manifested in the constant search for an increased objectivity-or in its converse, the avoidance of subjectivity. This paper offers an exhaustive account of the methodological and conceptual difficulties embedded in each of the steps required to elaborate molecular phytogenies. The authors adopt a historical perspective on the field in order to follow the development of practices that seek to increase the objectivity of their methods and representations. These include the adoption and development of explicit criteria for evaluation of evidence, and of procedures associated with methods of statistical inference, quantification and automation. All these are linked to an increasing use of computers in research since the mid 1960s. We will show that the practices of objectivity described are highly dependent on the problems and tools of molecular phylogenetics.

  2. 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.

  3. Automatic selection of representative proteins for bacterial phylogeny

    Directory of Open Access Journals (Sweden)

    Goldberg David

    2005-05-01

    Full Text Available Abstract Background Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence. Results We describe an algorithm that automatically picks "representative" protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alone, gives an organismal distance matrix in good agreement with a distance matrix computed from all sufficiently conserved proteins. We then use maximum-likelihood methods to compute phylogenetic trees from a concatenation of representative sequences. We validate the use of representative proteins on a number of small phylogenetic questions with accepted answers. We then use our methodology to compute a robust and well-resolved phylogenetic tree for a diverse set of sequenced bacteria. The tree agrees closely with a recently published tree computed using manually curated proteins, and supports two proposed high-level clades: one containing Actinobacteria, Deinococcus, and Cyanobacteria ("Terrabacteria", and another containing Planctomycetes and Chlamydiales. Conclusion Representative proteins provide an effective solution to the problem of selecting phylogenetic characters.

  4. Arachidonate metabolism in bovine gallbladder muscle

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, M.; Hidaka, T.; Ueta, T.; Ogura, R.

    1983-04-01

    Incubation of (1-/sup 14/C)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-/sup 14/C)PGH2 was virtually identical to that of (1-/sup 14/C)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.

  5. Protection against bovine leukosis virus infection in sheep with the BL 20 bovine lymphoblastoid cell line.

    Science.gov (United States)

    Roberts, D H; Lucas, M H; Sands, J; Wibberley, G

    1982-11-01

    The bovine lymphoblastoid BL 20 cell line derived from a case of sporadic bovine leukosis when inoculated into sheep did not induce an antibody response directed against bovine leukosis virus (BLV) structural proteins. Sheep were inoculated twice with the BL 20 cell line and then challenged with BLV infected lymphocytes. Three out of four sheep challenged four weeks after BL 20 inoculation did not develop BLV antibodies. Of the 12 sheep challenged later, three sheep did not develop BLV antibodies. BLV was isolated from all the seropositive animals and from none of the seronegative animals.

  6. 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 Solution...

  7. Sexing bovine pre-implantation embryos using the polymerase ...

    African Journals Online (AJOL)

    The paper aims to present a bovine model for human embryo sexing. Cows were super-ovulated, artificially inseminated and embryos were recovered 7 days later. Embryo biopsy was performed; DNA was extracted from blastomeres and amplified using bovine-specific and bovine-Y-chromosomespecific primers, followed ...

  8. 9 CFR 113.216 - Bovine Rhinotracheitis Vaccine, Killed Virus.

    Science.gov (United States)

    2010-01-01

    ... cultures for vaccine production. All serials of vaccine shall be prepared from the first through the fifth... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Rhinotracheitis Vaccine, Killed... REQUIREMENTS Killed Virus Vaccines § 113.216 Bovine Rhinotracheitis Vaccine, Killed Virus. Infectious Bovine...

  9. 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..., and immunogenic shall be used for preparing the production seed virus for vaccine production. All...

  10. 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... as pure, safe, and immunogenic shall be used for preparing the production seed virus for vaccine...

  11. 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 followed...

  12. Effect of melatonin on in vitro maturation of bovine oocytes ...

    African Journals Online (AJOL)

    ... Vs 17.67, 15.68, 16.53). In conclusion in this experiment, melatonin cannot improve cumulus cell expansion and nuclear maturation of bovine oocytes. When concentrations is high, melatonin may affect bovine oocytes meiotic maturation at metaphase-1 stage, but it is improbable melatonin be toxic for bovine oocytes.

  13. 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... bovine brucellosis in the United States. The notice stated that USDA would hold four public meetings...

  14. 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... tuberculosis (TB) and bovine brucellosis in the United States. In keeping with its commitment to partnering...

  15. Empowering Adult Learners. NIF Literacy Program Helps ABE Accomplish Human Development Mission.

    Science.gov (United States)

    Hurley, Mary E.

    1991-01-01

    The National Issues Forum's Literacy Program uses study circles and group discussion to promote empowerment and enhance adult literacy through civic education. The program has helped the Westonka (Minnesota) Adult Basic Education project accomplish its mission and has expanded the staff's view of adult learning. (SK)

  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. Investigating Essential Factors on Students' Perceived Accomplishment and Enjoyment and Intention to Learn in Web Development

    Science.gov (United States)

    Zhang, Yulei; Dang, Yan

    2015-01-01

    Web development is an important component in the curriculum of computer science and information systems areas. However, it is generally considered difficult to learn among students. In this study,we examined factors that could influence students' perceptions of accomplishment and enjoyment and their intention to learn in the web development…

  18. Dual Outcomes of Psychology Assignments: Perceived Learning and Feelings of Prideful Accomplishment

    Science.gov (United States)

    Pines, Harvey A.; Larkin, Judith E.; Murray, Molly P.

    2016-01-01

    Two studies explored properties of psychology assignments from an atypical perspective: students' own perceptions of what they learned and their emotional reactions to the assignments, specifically feelings of pride in their work. Study 1 showed that assignments vary in their likelihood of generating prideful accomplishment and identified three…

  19. 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.…

  20. 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.

  1. Assembling the "Accomplished" Teacher: The Performativity and Politics of Professional Teaching Standards

    Science.gov (United States)

    Mulcahy, Dianne

    2011-01-01

    Set within the socio-political context of standards-based education reform, this article explores the constitutive role of teaching standards in the production of the practice and identity of the "accomplished" teacher. It contrasts two idioms for thinking about and studying these standards, the representational and the performative. Utilising the…

  2. Bovine rotavirus pentavalent vaccine development in India.

    Science.gov (United States)

    Zade, Jagdish K; Kulkarni, Prasad S; Desai, Sajjad A; Sabale, Rajendra N; Naik, Sameer P; Dhere, Rajeev M

    2014-08-11

    A bovine rotavirus pentavalent vaccine (BRV-PV) containing rotavirus human-bovine (UK) reassortant strains of serotype G1, G2, G3, G4 and G9 has been developed by the Serum Institute of India Ltd, in collaboration with the National Institute of Allergy and Infectious Diseases (NIAID), USA. The vaccine underwent animal toxicity studies and Phase I and II studies in adults, toddlers and infants. It has been found safe and immunogenic and will undergo a large Phase III study to assess efficacy against severe rotavirus gastroenteritis. Copyright © 2014. Published by Elsevier Ltd.

  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......, critical evaluation of the current state of knowledge in this area. Fifty-one eligible studies were identified from the following databases: Medline, Embase, Global Health, the Cochrane Library, and the Cumulative Index to Nursing and Allied Health Literature. Studies were heterogeneous with regard...

  4. Heterogeneity of Bovine Peripheral Blood Monocytes

    Directory of Open Access Journals (Sweden)

    Jamal Hussen

    2017-12-01

    Full Text Available Peripheral blood monocytes of several species can be divided into different subpopulations with distinct phenotypic and functional properties. Herein, we aim at reviewing published work regarding the heterogeneity of the recently characterized bovine monocyte subsets. As the heterogeneity of human blood monocytes was widely studied and reviewed, this work focuses on comparing bovine monocyte subsets with their human counterparts regarding their phenotype, adhesion and migration properties, inflammatory and antimicrobial functions, and their ability to interact with neutrophilic granulocytes. In addition, the differentiation of monocyte subsets into functionally polarized macrophages is discussed. Regarding phenotype and distribution in blood, bovine monocyte subsets share similarities with their human counterparts. However, many functional differences exist between monocyte subsets from the two species. In contrast to their pro-inflammatory functions in human, bovine non-classical monocytes show the lowest phagocytosis and reactive oxygen species generation capacity, an absent ability to produce the pro-inflammatory cytokine IL-1β after inflammasome activation, and do not have a role in the early recruitment of neutrophils into inflamed tissues. Classical and intermediate monocytes of both species also differ in their response toward major monocyte-attracting chemokines (CCL2 and CCL5 and neutrophil degranulation products (DGP in vitro. Such differences between homologous monocyte subsets also extend to the development of monocyte-derived macrophages under the influence of chemokines like CCL5 and neutrophil DGP. Whereas the latter induce the differentiation of M1-polarized macrophages in human, bovine monocyte-derived macrophages develop a mixed M1/M2 macrophage phenotype. Although only a few bovine clinical trials analyzed the correlation between changes in monocyte composition and disease, they suggest that functional differences between

  5. 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

  6. Biological and ecological traits of Trichoptera: the influence of phylogeny on life history and behavioral traits

    Science.gov (United States)

    Mendez, P. K.; Resh, V. H.

    2005-05-01

    Biological and ecological traits of fauna have the potential to indicate changes in community structure that relate to function as an alternative to using traditional taxonomic descriptors. However, traits may be inherited, and consequently, not all species traits are independent of phylogeny. When used in analyses of community structure, results based on traits may be difficult to interpret; suites of traits may respond together even if only one trait is responding to changes in the habitat. To determine the relationship between traits and phylogeny, we examined life history and behavioral traits for the extant 45 families of Trichoptera. Traits such as larval size, respiratory strategies, case or net materials, locomotion, food and functional feeding group, voltanism, diapause, habitat, and reproduction were collected from published life histories. Traits were then coded and mapped onto the phylogeny of Trichoptera to determine the correlations between traits, as well as correlations directly influenced by the phylogeny. Traits such as functional feeding group, reproductive strategies, and building materials were correlated with phylogeny, while traits such as locomotion and habitat type were less influenced by phylogeny. Consideration of macroinvertebrate phylogenies when selecting biological and ecological traits may be essential for accurate interpretation of community function.

  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. Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae).

    Science.gov (United States)

    Chao, Yi-Shan; Rouhan, Germinal; Amoroso, Victor B; Chiou, Wen-Liang

    2014-07-01

    Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the

  9. Bovine papillomavirus type 2 in reproductive tract and gametes of slaughtered bovine females

    OpenAIRE

    Carvalho,Claudemir de; Freitas,Antonio Carlos de; Brunner,Olga; Góes,Luiz Gustavo Bentim; Cavalcante,Andréa Yaguiu; Beçak,Willy; Santos,Rita de Cassia Stocco dos

    2003-01-01

    Papillomaviruses are described selectively infecting epithelial tissues and are associated with many forms of cancer in different species. Considering the widespread dissemination of papillomatosis in livestock, interest is being centred on possible forms of viral transmission and respective mechanisms. In the present study, we report the detection of bovine papillomavirus (BPV) DNA sequences in female reproductive tract tissues, fluids and oocytes from slaughtered bovines not afflicted by cu...

  10. Prototheca zopfii isolated from bovine mastitis induced oxidative stress and apoptosis in bovine mammary epithelial cells

    OpenAIRE

    Shahid, Muhammad; Gao, Jian; Zhou, Yanan; Liu, Gang; Ali, Tariq; Deng, Youtian; Sabir, Naveed; Su, Jingliang; Han, Bo

    2017-01-01

    Bovine protothecal mastitis results in considerable economic losses worldwide. However, Prototheca zopfii induced morphological alterations and oxidative stress in bovine mammary epithelial cells (bMECs) is not comprehensively studied yet. Therefore, the aim of this current study was to investigate the P. zopfii induced pathomorphological changes, oxidative stress and apoptosis in bMECs. Oxidative stress was assessed by evaluating catalase (CAT), superoxide dismutase (SOD), glutathione peroxi...

  11. Molecular phylogeny and taxonomic review of Premnobiini Browne 1962 (Coleoptera: Curculionidae: Scolytinae

    Directory of Open Access Journals (Sweden)

    Anthony I Cognato

    2013-11-01

    Full Text Available The taxonomy of Premnobiini is reviewed in the context a molecular phylogeny including species of Ipini, Dryocoeotini, and Xyleborini. DNA data from COI, 16S, 28S, and CAD (~ 2640 characters were generated for 79 species and phylogenies were reconstructed using parsimony and Bayesian methods under different nucleotide sequence alignment parameters. The topologies of these phylogenies were in general agreement. Ipini was monophyletic along with all genera except Acathotomicus. Premnobiini was nested within Ipini and consisted of two clades, which associated with Premnobius and Premnophilus. These results justified taxonomic changes. Premnophilus was resurrected as a valid genus and Premnobiini was considered a sub-tribe of Ipini.

  12. Phylogeny mandalas of birds using the lithographs of John Gould's folio bird books.

    Science.gov (United States)

    Hasegawa, Masami; Kuroda, Sayako

    2017-12-01

    The phylogeny mandala, which is a circular phylogeny with photos or drawings of species, is a suitable way to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. In this article, in order to demonstrate the recent progress of avian molecular phylogenetics, six phylogeny mandalas of various taxonomic groups of birds are presented with the lithographs of John Gould's folio bird books; i.e., (1) whole Aves, (2) Passeriformes, (3) Paradisaeidae in Corvoidea (Passeriformes), (4) Meliphagoidea (Passeriformes), (5) Trochili in Apodiformes, and (6) Galliformes. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. 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.

  14. Developing a vaccine for eradicating contagious bovine ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    The challenge. Contagious bovine pleuropneumonia (CBPP) — also known as lung plague — is a highly contagious bacterial disease of cattle that has serious economic and trade consequences in sub-Saharan Africa. CBPP kills up to 50% of infected animals, when newly introduced into a population, and many cattle.

  15. Activities for leptin in bovine trophoblast cells.

    Science.gov (United States)

    Hughes, C K; Xie, M M; McCoski, S R; Ealy, A D

    2017-01-01

    Leptin is involved in various reproductive processes in humans and rodents, including placental development and function. The specific ways that leptin influences placental development and function in cattle are poorly understood. This work was completed to explore how leptin regulates hormone, cytokine and metalloprotease transcript abundance, and cell proliferation in cultured bovine trophoblast cells. In the first set of studies, cells were cultured in the presence of graded recombinant bovine leptin concentrations (0, 10, 50, 250 ng/mL) for 6 or 24 h. Transcript profiles were examined from extracted RNA. Leptin supplementation did not affect abundance of the maternal recognition of pregnancy factor, interferon-tau (IFNT), but leptin increased (P leptin. Transcript abundance of the remodeling factor, metalloprotease 2 (MMP2), was greater (P leptin-treated cells at 24 h but not at 6 h. The 24 h MMP2 response was greatest (P leptin treatment. In a separate set of studies, cell proliferation assays were completed. Leptin supplementation did not affect bovine trophoblast cell line proliferation at any dose tested. In conclusion, leptin supplementation did not affect bovine trophoblast cell proliferation or IFNT expression, but leptin increases CSH2 and MMP2 transcript abundance. Both of these factors are involved with peri-implantation and postimplantation placental development and function, and this implicates leptin as a potential mediator of early placental development and function in cattle. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Seroprevalence Study Of Bovine Brucellosis In Extensive ...

    African Journals Online (AJOL)

    The prevalence of bovine brucellosis was measured in cross sectional study in Jimma zone, Western Ethiopia using Rose Bengal Plate Test (RBT) and CFT from October 2003 to April 2004. The study animals consisted of 1305 local breed found in extensive system in five districts of in the zone. The overall individual animal ...

  17. Pathogenesis of bovine spongiform encephalopathy in sheep

    NARCIS (Netherlands)

    Keulen, van L.J.M.; Vromans, M.E.W.; Dolstra, C.H.; Bossers, A.; Zijderveld, van F.G.

    2008-01-01

    The pathogenesis of bovine spongiform encephalopathy (BSE) in sheep was studied by immunohistochemical detection of scrapie-associated prion protein (PrPSc) in the gastrointestinal, lymphoid and neural tissues following oral inoculation with BSE brain homogenate. First accumulation of PrPSc was

  18. Hydrophobic interactions of phenoxazine modulators with bovine ...

    Indian Academy of Sciences (India)

    The binding of phenothiazine drugs to bovine serum albumin (BSA) has been studied 1. Although most of the authors obtained total binding constants of the same order of magnitude, the number of binding sites varied considerably. It has been found 2 that the number of binding sites on BSA for promazine and ...

  19. Transmission of new bovine prion to mice

    NARCIS (Netherlands)

    Baron, T.G.M.; Biacabe, A.G.; Bencsik, A.; Langeveld, J.P.M.

    2006-01-01

    We previously reported that cattle were affected by a prion disorder that differed from bovine spongiform encephalopathy (BSE) by showing distinct molecular features of disease-associated protease-resistant prion protein (PrPres). We show that intracerebral injection of such isolates into C57BL/6

  20. Pasteurella multocida and bovine respiratory disease.

    Science.gov (United States)

    Dabo, S M; Taylor, J D; Confer, A W

    2007-12-01

    Pasteurella multocida is a pathogenic Gram-negative bacterium that has been classified into three subspecies, five capsular serogroups and 16 serotypes. P. multocida serogroup A isolates are bovine nasopharyngeal commensals, bovine pathogens and common isolates from bovine respiratory disease (BRD), both enzootic calf pneumonia of young dairy calves and shipping fever of weaned, stressed beef cattle. P. multocida A:3 is the most common serotype isolated from BRD, and these isolates have limited heterogeneity based on outer membrane protein (OMP) profiles and ribotyping. Development of P. multocida-induced pneumonia is associated with environmental and stress factors such as shipping, co-mingling, and overcrowding as well as concurrent or predisposing viral or bacterial infections. Lung lesions consist of an acute to subacute bronchopneumonia that may or may not have an associated pleuritis. Numerous virulence or potential virulence factors have been described for bovine respiratory isolates including adherence and colonization factors, iron-regulated and acquisition proteins, extracellular enzymes such as neuraminidase, lipopolysaccharide, polysaccharide capsule and a variety of OMPs. Immunity of cattle against respiratory pasteurellosis is poorly understood; however, high serum antibodies to OMPs appear to be important for enhancing resistance to the bacterium. Currently available P. multocida vaccines for use in cattle are predominately traditional bacterins and a live streptomycin-dependent mutant. The field efficacy of these vaccines is not well documented in the literature.

  1. 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...

  2. 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 cha...

  3. 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.…

  4. Contagious Bovine Pleuropneumonia and lung condemnation in ...

    African Journals Online (AJOL)

    Password, Remember me, or Register. DOWNLOAD FULL TEXT Open Access DOWNLOAD FULL TEXT Subscription or Fee Access. Contagious Bovine Pleuropneumonia and lung condemnation in Sokoto Metropolitan Abattoir in Nigeria. JE Onu. Abstract. No Abstract. Bulletin of Animal Health and Production in Africa Vol.

  5. Vaccination of cattle against bovine viral diarrhoea

    NARCIS (Netherlands)

    Oirschot, van J.T.; Bruschke, C.J.M.; Rijn, van P.A.

    1999-01-01

    This brief review describes types and quality (efficacy and safety) of bovine viral diarrhoea virus (BVDV) vaccines that are in the market or under development. Both conventional live and killed vaccines are available. The primary aim of vaccination is to prevent congenital infection, but the few

  6. 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.

  7. 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.

  8. Linguistic Phylogenies Support Back-Migration from Beringia to Asia

    Science.gov (United States)

    Sicoli, Mark A.; Holton, Gary

    2014-01-01

    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. PMID:24621925

  9. Evolution of consciousness: phylogeny, ontogeny, and emergence from general anesthesia.

    Science.gov (United States)

    Mashour, George A; Alkire, Michael T

    2013-06-18

    Are animals conscious? If so, when did consciousness evolve? We address these long-standing and essential questions using a modern neuroscientific approach that draws on diverse fields such as consciousness studies, evolutionary neurobiology, animal psychology, and anesthesiology. We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution. Thus, in agreement with Darwin's insight and the recent "Cambridge Declaration on Consciousness in Non-Human Animals," a review of modern scientific data suggests that the differences between species in terms of the ability to experience the world is one of degree and not kind.

  10. 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.

  11. 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.

  12. Mitogenomic phylogeny, diversification, and biogeography of South American spiny rats

    DEFF Research Database (Denmark)

    Fabre, Pierre-Henri; Upham, Nathan S.; Emmons, Louise H.

    2017-01-01

    Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae......), and 5 genera of West Indian hutias (Capromyidae) relatives. Here we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining...... of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae...

  13. 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.

  14. 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.

  15. A differentiation-based phylogeny of cancer subtypes.

    Directory of Open Access Journals (Sweden)

    Markus Riester

    2010-05-01

    Full Text Available Histopathological classification of human tumors relies in part on the degree of differentiation of the tumor sample. To date, there is no objective systematic method to categorize tumor subtypes by maturation. In this paper, we introduce a novel computational algorithm to rank tumor subtypes according to the dissimilarity of their gene expression from that of stem cells and fully differentiated tissue, and thereby construct a phylogenetic tree of cancer. We validate our methodology with expression data of leukemia, breast cancer and liposarcoma subtypes and then apply it to a broader group of sarcomas. This ranking of tumor subtypes resulting from the application of our methodology allows the identification of genes correlated with differentiation and may help to identify novel therapeutic targets. Our algorithm represents the first phylogeny-based tool to analyze the differentiation status of human tumors.

  16. Phylogeny- and Parsimony-Based Haplotype Inference with Constraints

    Science.gov (United States)

    Elberfeld, Michael; Tantau, Till

    Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. In their CPM 2009 paper, Fellows et al. studied an extension of this approach that incorporates prior knowledge in the form of a set of candidate haplotypes from which the right haplotypes must be chosen. While this approach may help to increase the accuracy of haplotyping methods, it was conjectured that the resulting formal problem constrained perfect phylogeny haplotyping might be NP-complete. In the present paper we present a polynomial-time algorithm for it. Our algorithmic ideas also yield new fixed-parameter algorithms for related haplotyping problems based on the maximum parsimony assumption.

  17. Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

    Science.gov (United States)

    Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

    2017-04-01

    Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Phylogeny and classification of Dickeya based on multilocus sequence analysis.

    Science.gov (United States)

    Marrero, Glorimar; Schneider, Kevin L; Jenkins, Daniel M; Alvarez, Anne M

    2013-09-01

    Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.

  19. Molecular phylogeny of the burying beetles (Coleoptera: Silphidae: Nicrophorinae).

    Science.gov (United States)

    Sikes, Derek S; Venables, Chandra

    2013-12-01

    Burying beetles (Silphidae: Nicrophorus) are well-known for their monopolization of small vertebrate carcasses in subterranean crypts and complex biparental care behaviors. They have been the focus of intense behavioral, ecological, and conservation research since the 1980s yet no thorough phylogenetic estimate for the group exists. Herein, we infer relationships, test past hypotheses of relationships, and test biogeographic scenarios among 55 of the subfamily Nicrophorinae's currently valid and extant 72 species. Two mitochondrial genes, COI and COII, and two nuclear genes, the D2 region of 28S, and the protein coding gene CAD, provided 3,971 nucleotides for 58 nicrophorine and 5 outgroup specimens. Ten partitions, with each modeled by GTR+I+G, were used for a 100 M generation MrBayes analysis and maximum likelihood bootstrapping with Garli. The inferred Bayesian phylogeny was mostly well-resolved with only three weak branches of biogeographic relevance. The common ancestor of the subfamily and of the genus Nicrophorus was reconstructed as Old World with four separate transitions to the New World and four reverse colonizations of the Old World from the New. Divergence dating from analysis with BEAST indicate the genus Nicrophorus originated in the Cretaceous, 127-99 Ma. Most prior, pre-cladistic hypotheses of relationships were strongly rejected while most modern hypotheses were largely congruent with monophyletic groups in our estimated phylogeny. Our results reject a recent hypothesis that Nicrophorus morio Gebler, 1817 (NEW STATUS as valid species) is a subspecies of N. germanicus (L., 1758). Two subgenera of Nicrophorus are recognized: NecroxenusSemenov-Tian-Shanskij, 1933, and NicrophorusFabricius, 1775. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. The comprehensive phylogeny of the superfamily Elateroidea (Coleoptera: Elateriformia).

    Science.gov (United States)

    Kundrata, Robin; Bocakova, Milada; Bocak, Ladislav

    2014-07-01

    Elateriformia consists of Dascilloidea, Buprestoidea (jewel beetles), Byrrhoidea and Elateroidea (click beetles, fireflies and relatives). Numerous elateroid lineages contain taxa with modified metamorphosis resulting in sexual maturity while retaining larval characters. Additionally, they evolved unique defensive strategies including clicking mechanism, aposematic coloration and bioluminescence. To investigate the phylogenetic position of Elateroidea within Coleoptera, we merged 1048 newly produced 18S rRNA, 28S rRNA, rrnL mtDNA, and cox1 mtDNA sequences for ∼300 elateriform taxa with data from GenBank. The 975-taxa dataset aligned in BlastAlign was analyzed under maximum likelihood criterion. The results agreed in most aspects with the current morphology-based classification and results of molecular studies. Elateriformia were monophyletic and Elateroidea were sister to Byrrhoidea. Further, we analyzed all-data (513 elateriform taxa) and pruned matrix (417 elateriform taxa, all fragments present) using parsimony and maximum likelihood methods to reveal the phylogenetic relationships among elateroid lineages and examine the evolution of soft-bodiedness, neoteny and bioluminescence. We confirmed the monophyly of Elateroidea sensu lato and most of the families, with Telegeusidae inferred in most trees within paraphyletic Omethidae. The clade Artematopodidae+Telegeusidae+Omethidae was a sister to remaining elateroids. All topologies reject the relationships of hard-bodied Elateridae, Eucnemidae, Throscidae and Cerophytidae, formerly supposed to be a monophylum. Eucnemidae and Throscidae formed independent lineages and the position of Cerophytidae was variable - either a sister to Throscidae, or an independent lineage. The Lampyridae+Cantharidae clade was in most trees sister to Phengodidae+Rhagophthalmidae+Omalisidae+Elateridae. Molecular phylogeny of Elateroidea confirmed the multiple origins of soft-bodied, neotenic and light emiting lineages. On the basis of our

  1. The geological record and phylogeny of the Myriapoda.

    Science.gov (United States)

    Shear, William A; Edgecombe, Gregory D

    2010-01-01

    We review issues of myriapod phylogeny, from the position of the Myriapoda amongst arthropods to the relationships of the orders of the classes Chilopoda and Diplopoda. The fossil record of each myriapod class is reviewed, with an emphasis on developments since 1997. We accept as working hypotheses that Myriapoda is monophyletic and belongs in Mandibulata, that the classes of Myriapoda are monophyletic, and that they are related as (Chilopoda (Symphyla (Diplopoda+Pauropoda))). The most pressing challenges to these hypotheses are some molecular and developmental evidence for an alliance between myriapods and chelicerates, and the attraction of symphylans to pauropods in some molecular analyses. While the phylogeny of the orders of Chilopoda appears settled, the relationships within Diplopoda remain unclear at several levels. Chilopoda and Diplopoda have a relatively sparse representation as fossils, and Symphyla and Pauropoda fossils are known only from Tertiary ambers. Fossils are difficult to place in trees based on living forms because many morphological characters are not very likely to be preserved in the fossils; as a consequence, most diplopod fossils have been placed in extinct higher taxa. Nevertheless, important information from diplopod fossils includes the first documented occurrence of air-breathing, and the first evidence for the use of a chemical defense. Stem-group myriapods are unknown, but evidence suggests the group must have arisen in the Early Cambrian, with a major period of cladogenesis in the Late Ordovician and early Silurian. Large terrestrial myriapods were on land at least by mid-Silurian. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  2. Phylogeny, systematics, and trait evolution of Carex section Glareosae.

    Science.gov (United States)

    Maguilla, Enrique; Escudero, Marcial; Waterway, Marcia J; Hipp, Andrew L; Luceño, Modesto

    2015-07-01

    • The circumboreal Carex section Glareosae comprises 20-25 currently accepted species. High variability in geographic distribution, ecology, cytogenetics, and morphology has led to historical problems both in species delimitation and in circumscribing the limits of the section, which is one of the major tasks facing caricologists today.• We performed phylogenetic reconstructions based on ETS, ITS, G3PDH, and matK DNA sequences from 204 samples. Concatenation of gene regions in a supermatrix approach to phylogenetic reconstruction was compared to coalescent-based species-tree estimation. Ancestral state reconstructions were performed for eight morphological characters to evaluate correspondence between phylogeny and traits used in traditional classification within the section.• The results confirm the existence of a core Glareosae comprising 23-25 species. Most species constitute exclusive lineages, and relationships among species are highly resolved with both the supermatrix and coalescent-based species-tree approaches. We used ancestral state reconstruction to investigate sources of homoplasy underlying traditional taxonomy and species circumscription. We found that even species apparently not constituting exclusive lineages are morphologically homogeneous, raising the question of whether paraphyly of species is a phylogenetic artifact in our study or evidence of widespread homoplasy in characters used to define species.• This study demonstrates the monophyly of Carex section Glareosae and establishes a phylogenetic framework for the section. Homoplasy makes many of morphological characters difficult to apply for taxon delimitation. The strong concordance between supermatrix and species-tree approaches to phylogenetic reconstructions suggests that even in the face of incongruence among molecular markers, section-level or species-level phylogenies in Carex are tractable. © 2015 Botanical Society of America, Inc.

  3. COI barcodes and phylogeny of doves (Columbidae family).

    Science.gov (United States)

    Khan, Haseeb Ahmad; Arif, Ibrahim Abdulwahid

    2013-12-01

    Cytochrome oxidase subunit I (COI) gene has been recognized as an authentic tool for species identification. Besides its potential barcoding capacity, COI sequences have also been used for inferring the phylogeny. Phylogenetic relationships among genera of Columbidae (pigeons and doves family) have not been fully resolved because of scarce sampling of taxa and limited availability of sequence data. In this study, we have evaluated the efficiency of COI barcodes for species identification and phylogenetic analysis of various doves. We sequenced the 693 bp region of COI gene of three species of doves including Oena capensis, Streptopelia decaocto, and Streptopelia senegalensis. After retrieving the relevant sequences from the GenBank, the entire data-set of 85 sequences represented 25 dove species from 11 different genera of the family Columbidae. The COI sequences of four species including Chalcophaps indica (two specimens), Columbina inca (five specimens), Geopelia striata (three specimens), and Macropygia phasianella (three specimens) were identical. The mean intraspecific base differences ranged from 0 to 37 while the P-distances ranged between 0 and 0.058. For most of the species, the P-distances were ≤ 0.008. Phylogenetic analysis differentiated the taxa into three major clusters. One of the clusters grouped five genera including Claravis, Columbina, Gallicolumba, Geopelia, and Geotrygon. The remaining two clusters grouped three genera each including Chalcophaps, Oena, and Turtur in one cluster and Macropygia, Streptopelia, and Zenaida in another cluster. Further sub-clustering clearly separated all the genera into individual clusters except two discrepancies for the genera Streptopelia and Turtur. Species-level cladistics clearly separated all the species into distinctive clades. In conclusion, COI barcoding is a powerful tool for species identification with added information on phylogenetic inference. The finding of this study will help to understand the

  4. 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

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

    Directory of Open Access Journals (Sweden)

    Aaron M Ellison

    Full Text Available 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

  6. An alu-based phylogeny of lemurs (infraorder: Lemuriformes.

    Directory of Open Access Journals (Sweden)

    Adam T McLain

    Full Text Available LEMURS (INFRAORDER: Lemuriformes are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ∼55-60 million years ago (mya. Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs, to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the

  7. Creating and Sustaining a Culture of Excellence: Insights From Accomplished University Team-Sport Coaches.

    Science.gov (United States)

    Donoso-Morales, Daniela; Bloom, Gordon A; Caron, Jeffrey G

    2017-12-01

    Winning several national championships is an extraordinary feat that very few university coaches have accomplished. The objective of this study was to investigate how some of Canada's most accomplished university team-sport coaches created and sustained a culture of excellence in their programs. Six university coaches who had won more than 30 national titles participated in this study. Each coach participated in a semistructured interview, and the qualitative data were inductively analyzed using a thematic analysis. The coaches noted that hard work and daily attention to detail, effective emotional management of themselves and their athletes, and continuous self-assessment (self-reflection and seeking mentors) were crucial elements that led to sustained excellence in their programs. This study offers one of the first empirical accounts of how highly successful university coaches developed and maintained a culture of excellence and success in their high-performance sport setting.

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

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    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.

  9. THE BLENDED LEARNING ACCOMPLISHMENT OF COMPUTER AND NETWORK ENGINEERING EXPERTISE PROGRAM IN VOCATIONAL SCHOOLS

    OpenAIRE

    Aries Alfian Prasetyo; Setiadi Cahyono Putro; I Made Wirawan

    2016-01-01

    This study aims to (1) describe supporting and inhibiting factors in blended learning implementation for the students of computer and network engineering expertise program and (2) describe the accomplishment level of the implementation. This study is designed as a descriptive study with quantitative approach. The research object is the blended learning implementation in computer and network engineering expertise program in SMK N 1 Baureno Bojonegoro. The research subjects consist of teachers,...

  10. Academic Procrastination and Goal Accomplishment: A Combined Experimental and Individual Differences Investigation.

    Science.gov (United States)

    Gustavson, Daniel E; Miyake, Akira

    2017-02-01

    This study examined the relationship between academic procrastination and goal accomplishment in two novel ways. First, we experimentally tested whether undergraduate students ( N = 177) could reduce their academic procrastination over a course of three weeks after performing goal-related exercises to set so-called SMART goals and/or to prepare those students with specific strategies to resist their temptations (forming implementation intentions). Second, we conducted systematic regression analyses to examine whether academic procrastination at baseline uniquely predicts later goal-related outcomes, controlling for various correlated variables, including personality traits (e.g., impulsivity), motivational factors (e.g., motivation for the generated goals), and situational factors (e.g., memory for the goals). Results indicated that neither the SMART-goal nor implementation-intention intervention significantly reduced academic procrastination in the three-week interval, even when relevant moderating variables were examined. Initial levels of academic procrastination, however, were predictive of the success of accomplishing the goals generated during the initial exercises, above and beyond a wide range of other candidate correlates. These results provided new correlational evidence for the association between academic procrastination and goal accomplishment, but suggest a need for further research to understand what interventions are effective at reducing academic procrastination.

  11. The phylogeny of brown lacewings (Neuroptera: Hemerobiidae) reveals multiple reductions in wing venation

    National Research Council Canada - National Science Library

    Garzón-Orduña, Ivonne J; Menchaca-Armenta, Imelda; Contreras-Ramos, Atilano; Liu, Xingyue; Winterton, Shaun L

    2016-01-01

    ... years ago and based exclusively on morphology. Our study builds upon this morphological evidence by adding sequence data from three gene loci to provide a total evidence phylogeny of brown lacewings (Neuroptera: Hemerobiidae...

  12. Molecular systematics of social skinks: phylogeny and taxonomy of the Egernia group (Reptilia: Scincidae)

    National Research Council Canada - National Science Library

    GARDNER, MICHAEL G; HUGALL, ANDREW F; DONNELLAN, STEPHEN C; HUTCHINSON, MARK N; FOSTER, RALPH

    2008-01-01

    .... Lack of a sound phylogeny for the Egernia group has limited our ability to understand the evolution and patterns of variation in social behaviour within this group, and evidence for the monophyly...

  13. Taxonomy and phylogeny of the brown-rot fungi: Fomitopsis and its related genera

    Czech Academy of Sciences Publication Activity Database

    Han, M.L.; Chen, Y.-Y.; Shen, L.-L.; Song, J.; Vlasák, Josef; Dai, Y.-C.; Cui, B.-K.

    2016-01-01

    Roč. 80, č. 1 (2016), s. 343-373 ISSN 1560-2745 Institutional support: RVO:60077344 Keywords : Fomitopsidaceae * Multi-marker analysis * Phylogeny Subject RIV: EF - Botanics Impact factor: 13.465, year: 2016

  14. 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.

  15. Bovine oocytes in secondary follicles grow in medium containing bovine plasma after vitrification.

    Science.gov (United States)

    Taketsuru, Hiroaki; Takajo, Asuka; Bao, Rong-Mei; Hamawaki, Atsushi; Yoshikawa, Motoichi; Miyano, Takashi

    2011-02-01

    There has been no culture system that supports the growth of bovine oocytes for more than 2 weeks. In the present study, bovine secondary follicles were cultured for 4 weeks, and the effects of supplemented protein components and FSH in the culture medium on the growth of the oocytes were examined. The effect of vitrification of secondary follicles on the subsequent oocyte growth was also examined. Secondary follicles (150 to 200 µm in diameter) containing growing oocytes (approximately 60 µm in diameter) were dissected from ovaries and cultured in a medium supplemented with FSH (0, 25 or 50 ng/ml) and one of the following four kinds of protein components: bovine serum albumin (BSA), bovine plasma (BPL), fetal calf serum (FCS) and bovine follicular fluid (BFF). In BSA- and BPL-supplemented media with 0 or 25 ng/ml FSH, more than 50% of follicles showed no degenerative signs during culture, and oocytes significantly increased in size after 4 weeks (Pbovine secondary follicles for 4 weeks, even after vitrification and warming of the follicles.

  16. Bovine serum albumin: survival and osmolarity effect in bovine spermatozoa stored above freezing point.

    Science.gov (United States)

    Nang, C F; Osman, K; Budin, S B; Ismail, M I; Jaffar, F H F; Mohamad, S F S; Ibrahim, S F

    2012-05-01

    Liquid nitrogen preservation in remote farms is a limitation. The goal of this study was to determine optimum temperature above freezing point for bovine spermatozoa preservation using bovine serum albumin (BSA) as a supplementation. Pooled semen sample from three ejaculates was subjected to various BSA concentration (1, 4, 8 and 12 mg ml(-1)), before incubation in different above freezing point temperatures (4, 25 and 37 °C). Viability assessment was carried out against time from day 0 (fresh sample) until all spermatozoa become nonviable. Optimal condition for bovine spermatozoa storage was at 4 °C with 1 mg ml(-1) BSA for almost 7 days. BSA improved bovine spermatozoa viability declining rate to 44.28% at day 4 and 57.59% at day 7 compared to control, with 80.54% and 98.57% at day 4 and 7 respectively. Increase in BSA concentration did not improve sperm viability. Our results also confirmed that there was a strong negative correlation between media osmolarity and bovine spermatozoa survival rate with r = 0.885, P freezing point. © 2011 Blackwell Verlag GmbH.

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

    Science.gov (United States)

    Polineni, Pavana; Aragonda, Prathyusha; Xavier, Suresh R; Furuta, Richard; Adelson, David L

    2006-06-05

    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. 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. 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.

  18. 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.

  19. Papillomatosis of the bovine teat (mammary papilla).

    Science.gov (United States)

    Olson, R O; Olson, C; Easterday, B C

    1982-12-01

    A 4th of 667 cattle examined at a Wisconsin abattoir had teat papillomas. Excised teat papillomas were sorted by gross morphologic characteristics into 3 groups: (i) atypical filiform, (ii) atypical flat, and (iii) typical fibropapilloma. Bovine papilloma virus capsid antigen was detected in thin-section slides of the 3 groups of teat papillomas by peroxidase-antiperoxidase assay. The bovine papilloma virus involved with the atypical papillomas could not be characterized by molecular hybridization, because enough pure virus could not be harvested. Homogenates of the 3 groups of teat papillomas were inoculated on 2 ponies and 4 calves. Typical fibropapillomas were produced on the 4 calves, and fibromas, on the 2 ponies. Atypical papillomas were produced only in 2 heifers.

  20. Leadership of United States Academic Departments of Ophthalmology: Chairperson Characteristics, Accomplishments, and Personal Insights.

    Science.gov (United States)

    Dotan, Gad; Qureshi, Hanya M; Saraf, Steven S; Darnley-Fisch, Deborah A

    2018-02-01

    To report on the characteristics, accomplishments, and past experiences of current academic ophthalmology department chairs. Cross-sectional study. Setting: A confidential online survey. Total of 111 chairs of US academic ophthalmology departments. Chairs' general characteristics, training/former positions held, academic accomplishments, previous organization/committee involvement, motivation/insight, and overall work satisfaction. Fifty-five chair responses were received (96% male, mean age 57 years, mean term 7 years). The majority were American medical graduates (93%), full professors of ophthalmology (93%), and permanent chairs (96%). All completed their residency in the US and 96% completed a fellowship (25% vitreoretinal surgery, 22% cornea and external disease, and 20% glaucoma). On average, chairs authored 98 peer-reviewed articles, 2 books, and 11 book chapters. They were also significantly involved in peer-reviewed journal literature, serving as editors (20%), associate editors (18%), or editorial board members (60%). The majority of chairs indicated they decided to seek their position late in their career, having already become a full (33%) or associate professor (26%), primarily owing to a desire to build and promote an academic ophthalmology department (61%). Chairs regarded their experience as head of service as most important for their current performance as department heads. Their principal advice to aspiring ophthalmology chairs was to focus on developing skills as a clinician, researcher, and educator ("triple threat"). Overall, academic department chairs are accomplished leaders in ophthalmology and prolific authors with an established academic record. Chairs regarded their previous leadership roles within the department as invaluable to their effectiveness as chair. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Pan-genome and phylogeny of Bacillus cereus sensu lato.

    Science.gov (United States)

    Bazinet, Adam L

    2017-08-02

    produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering. All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.

  2. Binding of anandamide to bovine serum albumin

    DEFF Research Database (Denmark)

    Bojesen, I.N.; Hansen, Harald S.

    2003-01-01

    The endocannabinoid anandamide is of lipid nature and may thus bind to albumin in the vascular system, as do fatty acids. The knowledge of the free water-phase concentration of anandamide is essential for the investigations of its transfer from the binding protein to cellular membranes, because a...... in aqueous compartments. - Bojesen, I. N., and H. S. Hansen. Binding of anandamide to bovine serum albumin....

  3. Consideration about moral accomplishment: a necessity in today’s world

    Directory of Open Access Journals (Sweden)

    Iulia Tutuianu

    2015-12-01

    Full Text Available Unlike in the atheist existentialism, the Christian one finds the individual in palpable situations, seen as opportunities in the process of personal accomplishment. The existentialism is not a quietude philosophy, but it asks for permanent effort. The religious man has a meaning, a purpose, The Encounter with Absolute, his entire life being part of Propedeutica. He replaces the anguish with hope, with the joy of being closed to God which occurs in each moment when we are aware that we follow our destiny.

  4. David C. Drum, DC, FCCS(C): an accomplished, multi-faceted individual.

    Science.gov (United States)

    Brown, Douglas M

    2017-03-01

    Pablo Picasso (1881-1973) is quoted as saying, "The meaning of life is to find your gift. The purpose of life is to give it away." With these few words Picasso captures the essence of David Drum's existence. From his birth in Moncton, NB, through his formal education in Toronto, ON, to his so-called "retirement" in Crystal Beach, ON, this paper spans 72 years, unveiling the broad range of opportunities for growth David Drum has encountered in his life's journey and documenting his acceptance of the obligations for proud philanthropy that accompany them. Dr. Drum's many accomplishments, gifts, and contributions to the profession and world of art are discussed.

  5. 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.

  6. Rapid Profiling of Bovine and Human Milk Gangliosides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

    Science.gov (United States)

    Lee, Hyeyoung; An, Hyun Joo; Lerno, Larry A; German, J Bruce; Lebrilla, Carlito B

    2011-08-15

    Gangliosides are anionic glycosphingolipids widely distributed in vertebrate tissues and fluids. Their structural and quantitative expression patterns depend on phylogeny and are distinct down to the species level. In milk, gangliosides are exclusively associated with the milk fat globule membrane. They may participate in diverse biological processes but more specifically to host-pathogen interactions. However, due to the molecular complexities, the analysis needs extensive sample preparation, chromatographic separation, and even chemical reaction, which makes the process very complex and time-consuming. Here, we describe a rapid profiling method for bovine and human milk gangliosides employing matrix-assisted desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS). Prior to the analyses of biological samples, milk ganglioside standards GM3 and GD3 fractions were first analyzed in order to validate this method. High mass accuracy and high resolution obtained from MALDI FTICR MS allow for the confident assignment of chain length and degree of unsaturation of the ceramide. For the structural elucidation, tandem mass spectrometry (MS/MS), specifically as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) were employed. Complex ganglioside mixtures from bovine and human milk were further analyzed with this method. The samples were prepared by two consecutive chloroform/methanol extraction and solid phase extraction. We observed a number of differences between bovine milk and human milk. The common gangliosides in bovine and human milk are NeuAc-NeuAc-Hex-Hex-Cer (GD3) and NeuAc-Hex-Hex-Cer (GM3); whereas, the ion intensities of ganglioside species are different between two milk samples. Kendrick mass defect plot yields grouping of ganglioside peaks according to their structural similarities. Gangliosides were further probed by tandem MS to confirm the compositional and structural assignments

  7. 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.

  8. Mycoplasma bovis escapes bovine neutrophil extracellular traps.

    Science.gov (United States)

    Gondaira, Satoshi; Higuchi, Hidetoshi; Nishi, Koji; Iwano, Hidetomo; Nagahata, Hajime

    2017-02-01

    Mycoplasma bovis is a significant pathogen in bovine infections including mastitis, pneumonia, arthritis and otitis media, and is the cause of large economic losses in beef and dairy farms. During infection with M. bovis, recruited neutrophils are not sufficient to eradicate M. bovis from the infection site. The release of neutrophil extracellular traps (NETs) is one of the innate immune responses of neutrophils but the effect of M. bovis on NET formation by bovine neutrophils has not yet been clarified. The objective of our research was to examine the effect of M. bovis on NET formation and the killing activity of bovine neutrophils. We showed that NETs were not detected following stimulation of neutrophils by M. bovis alone or with Phorbol 12-myristate 13-acetat (PMA). Reactive oxygen species production is essential for NET formation but the levels in neutrophils stimulated with M. bovis at multiplicity of infections of 10, 100, and 1000 were similar to those of unstimulated cells. NET formation induced by PMA stimulated neutrophils disappeared following the addition of M. bovis but this phenomenon was not observed when ethylenediaminetetraacetic acid (EDTA) was added. M. bovis colony forming units were significantly decreased by the addition of EDTA in the presence of NETs. Our results suggested that M. bovis infection alone did not induce NETs and that M. bovis nucleases, as hypothesis-based, contributed to resistance against the killing activity of NETs. Copyright © 2016. Published by Elsevier B.V.

  9. 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.

  10. 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

    2010-01-01

    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......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......) is found to be important for stabilizing the binding pose. The catalytic site (including the catalytic water molecule) is stable in the starting conformation of the previously proposed general acid/base catalytic mechanism for 18 ns of molecular dynamics simulations...

  11. 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

    The present work reports the characterization of carbohydrate structures and the distribution of the newly identified mucin MUC15, a highly glycosylated protein associated with the bovine milk fat globule membrane (MFGM). Distribution of MUC15 was investigated in various fractions of bovine milk......-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......-linked glycans were shown to contain mainly hybrid-type N-glycans. In addition, the N-glycans were shown to be sialylated and contain terminal poly-lactosamine structures. The O-linked glycans were found to constitute some unsubstituted Core-1 structures and a substantial number of sialylated Core-1 O...

  12. Design of a high activity and selectivity alcohol catalyst. Final status report and summary of accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Foley, H.C.; Mills, G.A.

    1994-07-15

    This final DOE report for grant award number DE-FG22-90PC 90291 presents the results of our efforts to better understand the Rh-Mo/{gamma}-Al{sub 2}O3 catalytic system for the hydrogenation of carbon monoxide and carbon dioxide to selectively form oxygenated products. The content of this report is divided into three major sections and a fourth, concluding section which addresses our major research accomplishments, as well as documents the most significant publications and presentations associated with this grant. The three main sections which make up the body of this report are presented in the in form of manuscripts which, in turn, summarize our progress in three areas of this project. The three body sections are organized as follows: Section I--Evidence for site isolation in Rh-Mo bimetallic catalysts derived from organometallic clusters; Section II--Surface Chemistry of Rh-Mo/{gamma}-Al{sub 2}O{sub 3}: An analysis of surface acidity; and Section III--Comparative study of Rh/Al{sub 2}O{sub 3} and Rh-Mo/Al{sub 2}O{sub 3} Catalysts. Section IV summarizes major accomplishments. The content of this final report is meant to generally highlight our progress in both characterizing the nature of the Rh-Mo/Al{sub 2}O{sub 3} system and probing its reactivity for insight on the oxygenate synergy present in this class of catalysts.

  13. Overview and Accomplishments of Advanced Mirror Technology Development Phase 2 (AMTD-2) Project

    Science.gov (United States)

    Stahl, H. Philip

    2015-01-01

    The Advance Mirror Technology Development (AMTD) project is in Phase 2 of a multiyear effort, initiated in FY12, to mature by at least a half TRL step critical technologies required to enable 4 meter or larger UVOIR space telescope primary mirror assemblies for both general astrophysics and ultra-high contrast observations of exoplanets. AMTD Phase 1 completed all of its goals and accomplished all of its milestones. AMTD Phase 2 started in 2014. Key accomplishments include deriving primary mirror engineering specifications from science requirements; developing integrated modeling tools and using those tools to perform parametric design trades; and demonstrating new mirror technologies via sub-scale fabrication and test. AMTD-1 demonstrated the stacked core technique by making a 43-cm diameter 400 mm thick 'biscuit-cut' of a 4-m class mirror. AMTD-2 is demonstrating lateral scalability of the stacked core method by making a 1.5 meter 1/3rd scale model of a 4-m class mirror.

  14. THE BLENDED LEARNING ACCOMPLISHMENT OF COMPUTER AND NETWORK ENGINEERING EXPERTISE PROGRAM IN VOCATIONAL SCHOOLS

    Directory of Open Access Journals (Sweden)

    Aries Alfian Prasetyo

    2016-10-01

    Full Text Available This study aims to (1 describe supporting and inhibiting factors in blended learning implementation for the students of computer and network engineering expertise program and (2 describe the accomplishment level of the implementation. This study is designed as a descriptive study with quantitative approach. The research object is the blended learning implementation in computer and network engineering expertise program in SMK N 1 Baureno Bojonegoro. The research subjects consist of teachers, facilities, materials and applications and students in the blended learning implementation process. The data was collected using observation, surveys and interviews. It was analyzed using percentages and classification analysis. The results reveals that the blended learning has been appropriately implemented. It is proven by the analysis result of supporting and inhibiting factors including facilities, teachers’ skill, materials and applications and blended learning accomplishment. The result is also supported by the description about blended learning activity, the use of facilities, blended learning composition and the impact of implementing blended learning. The weaknesses in the implementation process are the low quantity and quality of personal computers and inadequate internet connection. Teachers and school boards are expected to work collaboratively to solve the problems thus the implementation of blended learning can be maximized.

  15. 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.

  16. Life paths and accomplishments of mathematically precocious males and females four decades later.

    Science.gov (United States)

    Lubinski, David; Benbow, Camilla P; Kell, Harrison J

    2014-12-01

    Two cohorts of intellectually talented 13-year-olds were identified in the 1970s (1972-1974 and 1976-1978) as being in the top 1% of mathematical reasoning ability (1,037 males, 613 females). About four decades later, data on their careers, accomplishments, psychological well-being, families, and life preferences and priorities were collected. Their accomplishments far exceeded base-rate expectations: Across the two cohorts, 4.1% had earned tenure at a major research university, 2.3% were top executives at "name brand" or Fortune 500 companies, and 2.4% were attorneys at major firms or organizations; participants had published 85 books and 7,572 refereed articles, secured 681 patents, and amassed $358 million in grants. For both males and females, mathematical precocity early in life predicts later creative contributions and leadership in critical occupational roles. On average, males had incomes much greater than their spouses', whereas females had incomes slightly lower than their spouses'. Salient sex differences that paralleled the differential career outcomes of the male and female participants were found in lifestyle preferences and priorities and in time allocation. © The Author(s) 2014.

  17. Microstructure and hardness of bovine enamel in roselle extract solution

    Science.gov (United States)

    Dame, M. T.; Noerdin, A.; Indrani, D. J.

    2017-08-01

    The aim of this study was to analyze the effect of roselle extract solution on the microstructure and hardness of bovine enamel. Ten bovine teeth and a 5% concentration of roselle extract solution were prepared. Immersions of each bovine tooth in roselle extract solution were conducted up to 60 minutes. The bovine enamel surface was characterized in hardness and microscopy. It was apparent that the initial hardness was 328 KHN, and after immersion in 15 and 60 min, the values decrease to 57.4 KHN and 11 KHN, respectively. Scanning electron microscopy (SEM) revealed changes in enamel rods after immersion in the roselle extract solution.

  18. Neurogenic vasodilatation in isolated bovine and canine penile arteries

    National Research Council Canada - National Science Library

    A Bowman; J S Gillespie

    1983-01-01

    Field stimulation of isolated, perfused bovine or canine penile arteries produced dilatation, after the adrenergic motor component of the response had been blocked with guanethidine and the vessels...

  19. Morphologic and mechanical characteristics of engineered bovine arteries

    National Research Council Canada - National Science Library

    Niklason, Laura E; Abbott, William; Gao, Jinming; Klagges, Brian; Hirschi, Karen K; Ulubayram, Kezban; Conroy, Nancy; Jones, Rosemary; Vasanawala, Ami; Sanzgiri, Seema; Langer, Robert

    2001-01-01

    .... Engineered vessels were cultured from bovine aortic smooth muscle cells (SMCs) and endothelial cells that were seeded onto biodegradable polymer scaffolds and cultured under physiologically pulsatile conditions...

  20. Effects of resin or charcoal treatment on fetal bovine serum and bovine calf serum.

    Science.gov (United States)

    Cao, Zhimin; West, Clint; Norton-Wenzel, Carol S; Rej, Robert; Davis, Faith B; Davis, Paul J; Rej, Robert

    2009-01-01

    Charcoal- or resin-stripping of fetal bovine serum (FBS) or bovine calf serum (BCS) intended for supplementation of cell culture media is widely practiced to remove a variety of endogenous compounds, including steroid, peptide, and thyroid hormones. The possibility that stripping removes other biologically relevant factors from serum may not be appreciated. In this report, standardized clinical laboratory testing methods were used to assess the effects of resin- and charcoal-stripping on content in FBS and BCS of more than 25 analytes in the sera. In addition to hormones, the serum constituents affected by stripping are certain vitamins, electrolytes, enzyme activities, and metabolites.

  1. Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales).

    Science.gov (United States)

    Song, Jie; Cui, Bao-Kai

    2017-04-20

    The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU). Results of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area. Four intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.

  2. Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

    Science.gov (United States)

    Moreira, Cristiana; Vasconcelos, Vitor; Antunes, Agostinho

    2013-01-01

    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. PMID:24189276

  3. 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.

  4. 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.

  5. A unified phylogeny-based nomenclature for histone variants.

    Science.gov (United States)

    Talbert, Paul B; Ahmad, Kami; Almouzni, Geneviève; Ausió, Juan; Berger, Frederic; Bhalla, Prem L; Bonner, William M; Cande, W Zacheus; Chadwick, Brian P; Chan, Simon W L; Cross, George A M; Cui, Liwang; Dimitrov, Stefan I; Doenecke, Detlef; Eirin-López, José M; Gorovsky, Martin A; Hake, Sandra B; Hamkalo, Barbara A; Holec, Sarah; Jacobsen, Steven E; Kamieniarz, Kinga; Khochbin, Saadi; Ladurner, Andreas G; Landsman, David; Latham, John A; Loppin, Benjamin; Malik, Harmit S; Marzluff, William F; Pehrson, John R; Postberg, Jan; Schneider, Robert; Singh, Mohan B; Smith, M Mitchell; Thompson, Eric; Torres-Padilla, Maria-Elena; Tremethick, David John; Turner, Bryan M; Waterborg, Jakob Harm; Wollmann, Heike; Yelagandula, Ramesh; Zhu, Bing; Henikoff, Steven

    2012-06-21

    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.

  6. Sperm morphology and phylogeny of lagriids (Coleoptera, Tenebrionidae).

    Science.gov (United States)

    Dias, Glenda; Oliveira, Claudia M; Lino-Neto, José

    2013-09-01

    The systematics of tenebrionids remain unclear, principally at the subfamily level, as is the case of the Lagriinae. Considering that sperm morphology has contributed to the various insect group phylogenies, in this work we describe the structure and ultrastructure of these cells in Lagria villosa. Sperm in this species exhibit a strong morphological similarity to those of Tenebrio molitor and Tribolium castaneum, the only two species of Tenebrionidae with previously described sperm. In tenebrionids, the flagellar components offer good diagnostic characters, e.g. the symmetry of mitochondrial derivatives in L. villosa differentiates sperm of this species from those of Te. molitor and Tr. castaneum. However, the lateral association of the nucleus with flagellar components, the form of accessory bodies, and the presence of material connecting the axoneme to the accessory bodies and mitochondrial derivatives indicate that the three species form a sister group. Therefore, the sperm morphology of L. villosa support lagriid beetles as a subfamily (Lagriinae) of Tenebrionidae. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Arthropod phylogeny based on eight molecular loci and morphology

    Science.gov (United States)

    Giribet, G.; Edgecombe, G. D.; Wheeler, W. C.

    2001-01-01

    The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

  8. Molecular and morphological evidence on the phylogeny of the Elephantidae.

    Science.gov (United States)

    Thomas, M G; Hagelberg, E; Jone, H B; Yang, Z; Lister, A M

    2000-12-22

    The African and Asian elephants and the mammoth diverged ca. 4-6 million years ago and their phylogenetic relationship has been controversial. Morphological studies have suggested a mammoth Asian elephant relationship, while molecular studies have produced conflicting results. We obtained cytochrome b sequences of up to 545 base pairs from five mammoths, 14 Asian and eight African elephants. A high degree of polymorphism is detected within species. With a dugong sequence used as the outgroup, parsimony and maximum-likelihood analyses support a mammoth African elephant clade. As the dugong is a very distant outgroup, we employ likelihood analysis to root the tree with a molecular clock, and use bootstrap and Bayesian analyses to quantify the relative support for different topologies. The analyses support the mammoth African elephant relationship, although other trees cannot be rejected. Ancestral polymorphisms may have resulted in gene trees differing from the species phylogeny Examination of morphological data, especially from primitive fossil members, indicates that some supposed synapomorphies between the mammoth and Asian elephant are variable, others convergent or autapomorphous. A mammoth African elephant relationship is not excluded. Our results highlight the need, in both morphological and molecular phylogenetics, for multiple markers and close attention to within-taxon variation and outgroup selection.

  9. Neotropical mutualism between Acacia and Pseudomyrmex: phylogeny and divergence times.

    Science.gov (United States)

    Gómez-Acevedo, Sandra; Rico-Arce, Lourdes; Delgado-Salinas, Alfonso; Magallón, Susana; Eguiarte, Luis E

    2010-07-01

    The interaction between Acacia and Pseudomyrmex is a textbook example of mutualism between ants and plants, nevertheless aspects of its evolutionary biology have not been formally explored. In this paper we analyze primarily the phylogenies of both New World Acacia and of their associated species of ants, and the geographic origin of this mutualism. Until now, there has been no molecular analysis of this relationship in terms of its origin and age. We analyzed three chloroplast markers (matK, psaB-rps14, and trnL-trnF) on a total of 70 taxa of legumes from the subfamily Mimosoideae, and two nuclear regions (long-wavelength rhodopsine and wingless) on a total of 43 taxa of ants from subfamily Pseudomyrmecinae. The monophyly of subgenus Acacia and within the New World lineages that of the myrmecophilous Acacia group was established. In addition, our results supported the monophyly of the genus Pseudomyrmex and of the associated acacia-ants P. ferrugineus group. Using Bayesian methods and calibration data, the estimated divergence times for the groups involved in the mutualism are: 5.44+/-1.93 My for the myrmecophilous acacias and 4.58+/-0.82 My for their associated ant species, implying that their relationship originated in Mesoamerica between the late Miocene to the middle Pliocene, with eventual diversification of both groups in Mexico. Copyright 2010 Elsevier Inc. All rights reserved.

  10. Mitochondrial genome sequences effectively reveal the phylogeny of Hylobates gibbons.

    Directory of Open Access Journals (Sweden)

    Yi-Chiao Chan

    Full Text Available BACKGROUND: Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. CONCLUSIONS/SIGNIFICANCE: Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species.

  11. Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

    Science.gov (United States)

    González, Josefa; Casals, Ferran; Ruiz, Alfredo

    2007-01-01

    A combination of cytogenetic and bioinformatic procedures was used to test the chromosomal phylogeny relating Drosophila buzzatii with D. repleta. Chromosomes X and 2, harboring most of the inversions fixed between these two species, were analyzed. First, chromosomal segments conserved during the divergence of the two species were identified by comparative in situ hybridization to the D. repleta chromosomes of 180 BAC clones from a BAC-based physical map of the D. buzzatii genome. These conserved segments were precisely delimited with the aid of clones containing inversion breakpoints. Then GRIMM software was used to estimate the minimum number of rearrangements necessary to transform one genome into the other and identify all possible rearrangement scenarios. Finally, the most plausible inversion trajectory was tested by hybridizing 12 breakpoint-bearing BAC clones to the chromosomes of seven other species in the repleta group. The results show that chromosomes X and 2 of D. buzzatii and D. repleta differ by 12 paracentric inversions. Nine of them are fixed in chromosome 2 and entail two breakpoint reuses. Our results also show that the cytological relationship between D. repleta and D. mercatorum is closer than that between D. repleta and D. peninsularis, and we propose that the phylogenetic relationships in this lineage of the repleta group be reconsidered. We also estimated the rate of rearrangement between D. repleta and D. buzzatii and conclude that rates within the genus Drosophila vary substantially between lineages, even within a single species group. PMID:17028333

  12. Phylogeny of ladybirds (Coleoptera: Coccinellidae): are the subfamilies monophyletic?

    Science.gov (United States)

    Magro, A; Lecompte, E; Magné, F; Hemptinne, J-L; Crouau-Roy, B

    2010-03-01

    The Coccinellidae (ladybirds) is a highly speciose family of the Coleoptera. Ladybirds are well known because of their use as biocontrol agents, and are the subject of many ecological studies. However, little is known about phylogenetic relationships of the Coccinellidae, and a precise evolutionary framework is needed for the family. This paper provides the first phylogenetic reconstruction of the relationships within the Coccinellidae based on analysis of five genes: the 18S and 28S rRNA nuclear genes and the mitochondrial 12S, 16S rRNA and cytochrome oxidase subunit I (COI) genes. The phylogenetic relationships of 67 terminal taxa, representative of all the subfamilies of the Coccinellidae (61 species, 37 genera), and relevant outgroups, were reconstructed using multiple approaches, including Bayesian inference with partitioning strategies. The recovered phylogenies are congruent and show that the Coccinellinae is monophyletic but the Coccidulinae, Epilachninae, Scymninae and Chilocorinae are paraphyletic. The tribe Chilocorini is identified as the sister-group of the Coccinellinae for the first time. Copyright 2009 Elsevier Inc. All rights reserved.

  13. Phylogeny of the caniform carnivora: evidence from multiple genes.

    Science.gov (United States)

    Yu, Li; Zhang, Ya-ping

    2006-05-01

    The monophyletic group Caniformia in the order Carnivora currently comprises seven families whose relationships remain contentious. The phylogenetic positions of the two panda species within the Caniformia have also been evolutionary puzzles over the past decades, especially for Ailurus fulgens (the red panda). Here, new nuclear sequences from two introns of the beta-fibrinogen gene (beta-fibrinogen introns 4 and 7) and a complete mitochondrial (mt) gene (ND2) from 17 caniform representatives were explored for their utilities in resolving higher-level relationships in the Caniformia. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Combined analyses of four nuclear and one mt genes (4417 bp) recover a branching order in which almost all nodes were strongly supported. The present analyses provide evidence in favor of Ailurus fulgens as the closest taxon to the procyonid-mustelid (i.e., Musteloidea sensu stricto) clade, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae (including Ailuropoda melanoleuca), and Canidae, the most basal lineage in the Caniformia. The potential utilities of different genes in the context of caniform phylogeny were also evaluated, with special attention to the previously unexplored beta-fibrinogen intron 4 and 7 genes.

  14. Molecular phylogeny of the red panda (Ailurus fulgens).

    Science.gov (United States)

    Slattery, J P; O'Brien, S J

    1995-01-01

    The phylogenetic placement of the red panda (Ailurus fulgens) and the giant panda (Ailuropoda melanoleuca) has been an evolutionary enigma since their original descriptions in the nineteenth century. A series of recent molecular analyses led to a consensus that the giant panda's ancestors were derived from early bears (Ursidae), but left unsettled the phylogenetic relationship of the red panda. Previous molecular and morphological phylogenies were inconclusive and varied among placement of the red panda within the raccoon family (Procyonidae), within the bear family (Ursidae), or in a separate family of carnivores equidistant between the two. To examine a relatively ancient (circa 20-30 million years before the present, MYBP) phylogenetic divergence, we used two slowly evolving genetic markers: mitochondrial 12S rRNA sequence and 592 fibroblast proteins resolved by two dimensional gel electrophoresis. Four different carnivore outgroup species, including dog (Canidae: Canis familiaris), cat (Felidae: Felis catus), fanaloka (Viverridae: Fossa fossa), and mongoose (Herpestidae: Galidia elegans), were selected to identify the root of the phylogenetic topologies. Phylogenetic reconstruction by distance-based methods, maximum parsimony, and maximum likelihood clearly indicate a distinct bifurcation forming the Ursidae and the Procyonidae. Further, our data consistently place the red panda as an early divergence within the Procyonidae radiation and confirm the inclusion of giant panda in the Ursidae lineage.

  15. 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.

  16. Mitochondrial DNA phylogeny of camel spiders (Arachnida: Solifugae) from Iran.

    Science.gov (United States)

    Maddahi, Hassan; Khazanehdari, Mahsa; Aliabadian, Mansour; Kami, Haji Gholi; Mirshamsi, Amin; Mirshamsi, Omid

    2017-11-01

    In the present study, the mitochondrial DNA phylogeny of five solifuge families of Iran is presented using phylogenetic analysis of mitochondrial cytochrome c oxidase, subunit 1 (COI) sequence data. Moreover, we included available representatives from seven families from GenBank to examine the genetic distance between Old and New World taxa and test the phylogenetic relationships among more solifuge families. Phylogenetic relationships were reconstructed based on the two most probabilistic methods, Maximum Likelihood (ML) and Bayesian inference (BI) approaches. Resulting topologies demonstrated the monophyly of the families Daesiidae, Eremobatidae, Galeodidae, Karschiidae and Rhagodidae, whereas the monophyly of the families Ammotrechidae and Gylippidae was not supported. Also, within the family Eremobatidae, the subfamilies Eremobatinae and Therobatinae and the genus Hemerotrecha were paraphyletic or polyphyletic. According to the resulted topologies, the taxonomic placements of Trichotoma michaelseni (Gylippidae) and Nothopuga sp. 1 (Ammotrechidae) are still remain under question and their revision might be appropriate. According to the results of this study, within the family Galeodidae, the validity of the genus Galeodopsis is supported, while the validity of the genus Paragaleodes still remains uncertain. Moreover, our results revealed that the species Galeodes bacillatus, and Rhagodes melanochaetus are junior synonyms of G. caspius, and R. eylandti, respectively.

  17. 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.

  18. Phylogeny of the Botryosphaeriaceae reveals patterns of host association.

    Science.gov (United States)

    De Wet, Juanita; Slippers, Bernard; Preisig, Oliver; Wingfield, Brenda D; Wingfield, Michael J

    2008-01-01

    Three anamorph genera of the Botryosphaeriaceae namely Diplodia, Lasiodiplodia and Dothiorella have typically dark, ovoid conidia with thick walls, and are consequently difficult to distinguish from each other. These genera are well-known pathogens of especially pine species. We generated a multiple gene genealogy to resolve the phylogenetic relationships of Botryosphaeriaceae with dark conidial anamorphs, and mapped host associations based on this phylogeny. The multiple gene genealogy separated Diplodia, Lasiodiplodia and Dothiorella and it revealed trends in the patterns of host association. The data set was expanded to include more lineages of the Botryosphaeriaceae, and included all isolates from different host species for which ITS sequence data are available. Results indicate that Diplodia species occur mainly on gymnosperms, with a few species on both gymnosperms and angiosperms. Lasiodiplodia species occur equally on both gymnosperms and angiosperms, Dothiorella species are restricted to angiosperms and Neofusicoccum species occur mainly on angiosperms with rare reports on Southern Hemisphere gymnosperms. Botryosphaeria species with Fusicoccum anamorphs occur mostly on angiosperms with rare reports on gymnosperms. Ancestral state reconstruction suggests that a putative ancestor of the Botryosphaeriaceae most likely evolved on the angiosperms. Another interesting observation was that both host generalist and specialist species were observed in all the lineages of the Botryosphaeriaceae, with little evidence of host associated co-evolution.

  19. Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny.

    Science.gov (United States)

    Egan, Ashley N; Vatanparast, Mohammad; Cagle, William

    2016-11-01

    Several taxonomic and phylogenetic studies have hypothesized polyphyly within Pueraria DC., a genus comprising 19 species (24 with varieties) including the highly invasive Pueraria montana var. lobata (Kudzu) introduced to the U.S.A. about 150years ago. Previous efforts to investigate monophyly of the genus have been hampered by limited taxon sampling or a lack of comprehensive evolutionary context that would enable definitive taxonomic associations. This work presents a comprehensive phylogenetic investigation of Pueraria within the context of tribe Phaseoleae (Leguminosae). Polyphyly was found to be more extensive than previously thought, with five distinct lineages spread across the tribe and spanning over 25mya of divergence strongly supported by two chloroplast and one nuclear marker, AS2, presented here as a phylogenetic marker for the first time. Our phylogenies support taxonomic revisions to rectify polyphyly within Pueraria, including the resurrection of Neustanthus, moving one species to Teyleria, and the creation of two new genera, Haymondia and Toxicopueraria (taxonomic revisions published elsewhere). Published by Elsevier Inc.

  20. 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.

  1. 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.

  2. The origin of the cancer cell: oncogeny reverses phylogeny.

    Science.gov (United States)

    Johnston, R N; Pai, S B; Pai, R B

    1992-01-01

    The formulation in 1874 of the biogenetic law by Ernst Haeckel as "ontogeny recapitulates phylogeny" emphasized the structural similarities detected in metazoans between their developmental and ancestral forms. More recently, many workers have independently commented on the similarities observed between the behaviours displayed by dedifferentiated cancer cells and their embryonic precursors. This review will explore a possible linkage between these disparate observations and will suggest that cancer cells behave in ways that are reminiscent of primitive eukaryotic cells. In particular, we suggest that the acquisition of a multicellular level of organization during early metazoan evolution required a critical and difficult change in growth strategy as germ line and somatic cells became distinct. Whereas unicellular free living eukaryotes follow a simple strategy of rapid division as long as conditions permit, the elaboration of powerful growth inhibitory pathways must have been necessary in primitive multicellular organisms to enable some but not all sister cells to stop dividing, even under conditions of nutrient abundance. This limitation on cellular growth would than have permitted the appearance of tissues and organs with differentiated characteristics, ultimately enabling the enhanced survival of the meiotic lineage. Cancer cells might therefore be considered to represent, with their loss of tumor suppressor inhibitory activity and elevation of oncogene stimulatory activity, a reversion to a more primitive evolutionary state capable of indeterminate growth at the expense of the host. By this analogy, the growth phenotypes displayed by cancer cells, embryonic cells, and free-living eukaryotes are fundamentally similar.

  3. Feeding innovations in a nested phylogeny of Neotropical passerines.

    Science.gov (United States)

    Lefebvre, Louis; Ducatez, Simon; Audet, Jean-Nicolas

    2016-03-19

    Several studies on cognition, molecular phylogenetics and taxonomic diversity independently suggest that Darwin's finches are part of a larger clade of speciose, flexible birds, the family Thraupidae, a member of the New World nine-primaried oscine superfamily Emberizoidea. Here, we first present a new, previously unpublished, dataset of feeding innovations covering the Neotropical region and compare the stem clades of Darwin's finches to other neotropical clades at the levels of the subfamily, family and superfamily/order. Both in terms of raw frequency as well as rates corrected for research effort and phylogeny, the family Thraupidae and superfamily Emberizoidea show high levels of innovation, supporting the idea that adaptive radiations are favoured when the ancestral stem species were flexible. Second, we discuss examples of innovation and problem-solving in two opportunistic and tame Emberizoid species, the Barbados bullfinch Loxigilla barbadensis and the Carib grackle Quiscalus lugubris fortirostris in Barbados. We review studies on these two species and argue that a comparison of L. barbadensis with its closest, but very shy and conservative local relative, the black-faced grassquit Tiaris bicolor, might provide key insights into the evolutionary divergence of cognition. © 2016 The Author(s).

  4. Molecular phylogeny of North American Branchiobdellida (Annelida: Clitellata).

    Science.gov (United States)

    Williams, Bronwyn W; Gelder, Stuart R; Proctor, Heather C; Coltman, David W

    2013-01-01

    Branchiobdellidans, or crayfish worms, are ectosymbiotic clitellate annelids associated primarily with freshwater crayfishes. The main objectives of our study were to infer a molecular phylogeny for the North American Branchiobdellida, examine its congruence with morphology-based hypotheses of relationships at the subfamily and genus level, and use our dataset to assess consistency of GenBank-archived branchiobdellidan sequences. We used nucleotide sequence data from two mtDNA genes (COI and 16S rDNA) and three nuclear genes (28S rDNA, 18S rDNA, and ITS1) to estimate phylogenetic relationships among 47 described and one undescribed species of Branchiobdellida. We recovered a monophyletic branchiobdellidan clade with generally short branch lengths, suggesting that a large portion of the taxon has likely undergone a recent and rapid radiation in North America. Results from our phylogenetic analyses indicate that current taxonomic groupings are largely unsupported by the molecular data. All four subfamilies are either paraphyletic or polyphyletic, and only three of seven sampled non-monotypic genera were monophyletic. We found a high rate (49%) of inconsistency in GenBank-archived sequences, over 70% of which can be attributed to field- or laboratory-based error. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. 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.

  6. Family level phylogenies reveal modes of macroevolution in RNA viruses.

    Science.gov (United States)

    Kitchen, Andrew; Shackelton, Laura A; Holmes, Edward C

    2011-01-04

    Despite advances in understanding the patterns and processes of microevolution in RNA viruses, little is known about the determinants of viral diversification at the macroevolutionary scale. In particular, the processes by which viral lineages assigned as different "species" are generated remain largely uncharacterized. To address this issue, we use a robust phylogenetic approach to analyze patterns of lineage diversification in five representative families of RNA viruses. We ask whether the process of lineage diversification primarily occurs when viruses infect new host species, either through cross-species transmission or codivergence, and which are defined here as analogous to allopatric speciation in animals, or by acquiring new niches within the same host species, analogous to sympatric speciation. By mapping probable primary host species onto family level viral phylogenies, we reveal a strong clustering among viral lineages that infect groups of closely related host species. Although this is consistent with lineage diversification within individual hosts, we argue that this pattern more likely represents strong biases in our knowledge of viral biodiversity, because we also find that better-sampled human viruses rarely cluster together. Hence, although closely related viruses tend to infect related host species, it is unlikely that they often infect the same host species, such that evolutionary constraints hinder lineage diversification within individual host species. We conclude that the colonization of new but related host species may represent the principle mode of macroevolution in RNA viruses.

  7. Genomes-based phylogeny of the genus Xanthomonas

    Science.gov (United States)

    2012-01-01

    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. PMID:22443110

  8. Seroprevalence of viral and bacterial diseases among the bovines in Himachal Pradesh, India

    OpenAIRE

    Shailja Katoch; Shweta Dohru; Mandeep Sharma; Vikram Vashist; Rajesh Chahota; Prasenjit Dhar; Aneesh Thakur; Subhash Verma

    2017-01-01

    Aim: The study was designed to measure the seroprevalence of viral and bacterial diseases: Infectious bovine rhinotracheitis, bovine viral diarrhea, bovine leukemia, bovine parainfluenza, bovine respiratory syncytial disease, brucellosis, and paratuberculosis among bovine of Himachal Pradesh during the year 2013-2015. Materials and Methods: The serum samples were collected from seven districts of state, namely, Bilaspur, Kangra, Kinnaur, Lahul and Spiti, Mandi, Sirmour, and Solan. The sam...

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

    DEFF Research Database (Denmark)

    Aaboe, Merete; Schou, S.; Hjørting-Hansen, E.

    2000-01-01

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

  10. 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; hide

    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

  11. 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.

  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. 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.

  14. How the dynamics and structure of sexual contact networks shape pathogen phylogenies.

    Directory of Open Access Journals (Sweden)

    Katy Robinson

    Full Text Available The characteristics of the host contact network over which a pathogen is transmitted affect both epidemic spread and the projected effectiveness of control strategies. Given the importance of understanding these contact networks, it is unfortunate that they are very difficult to measure directly. This challenge has led to an interest in methods to infer information about host contact networks from pathogen phylogenies, because in shaping a pathogen's opportunities for reproduction, contact networks also shape pathogen evolution. Host networks influence pathogen phylogenies both directly, through governing opportunities for evolution, and indirectly by changing the prevalence and incidence. Here, we aim to separate these two effects by comparing pathogen evolution on different host networks that share similar epidemic trajectories. This approach allows use to examine the direct effects of network structure on pathogen phylogenies, largely controlling for confounding differences arising from population dynamics. We find that networks with more heterogeneous degree distributions yield pathogen phylogenies with more variable cluster numbers, smaller mean cluster sizes, shorter mean branch lengths, and somewhat higher tree imbalance than networks with relatively homogeneous degree distributions. However, in particular for dynamic networks, we find that these direct effects are relatively modest. These findings suggest that the role of the epidemic trajectory, the dynamics of the network and the inherent variability of metrics such as cluster size must each be taken into account when trying to use pathogen phylogenies to understand characteristics about the underlying host contact network.

  15. A Bayesian approach to the evolution of metabolic networks on a phylogeny.

    Science.gov (United States)

    Mithani, Aziz; Preston, Gail M; Hein, Jotun

    2010-08-05

    The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.

  16. A Bayesian approach to the evolution of metabolic networks on a phylogeny.

    Directory of Open Access Journals (Sweden)

    Aziz Mithani

    2010-08-01

    Full Text Available The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions or complex (incorporating dependencies among reactions stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.

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

    Directory of Open Access Journals (Sweden)

    Rønsted Nina

    2012-09-01

    Full Text Available Abstract 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 a predictive approach enabling more efficient selection of plants for the development of traditional medicine and lead discovery. However, this relationship has rarely been rigorously tested and the potential predictive power is consequently unknown. Results We produced a phylogenetic hypothesis for the medicinally important plant subfamily Amaryllidoideae (Amaryllidaceae based on parsimony and Bayesian analysis of nuclear, plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloid diversity and activity in bioassays related to the central nervous system are significantly correlated with phylogeny and found evidence for a significant phylogenetic signal in these traits, although the effect is not strong. Conclusions Several genera are non-monophyletic emphasizing the importance of using phylogeny for interpretation of character distribution. Alkaloid diversity and in vitro inhibition of acetylcholinesterase (AChE and binding to the serotonin reuptake transporter (SERT are significantly correlated with phylogeny. This has implications for the use of phylogenies to interpret chemical evolution and biosynthetic pathways, to select candidate taxa for lead discovery, and to make recommendations for policies regarding traditional use and conservation priorities.

  18. Effect of newborn bovine serum on cryopreservation of adult bovine testicular tissue.

    Science.gov (United States)

    Wu, J Y; Sun, Y X; Wang, A B; Che, G Y; Hu, T J; Zhang, X M

    2014-04-01

    Bovine serum is widely used for cryopreservation of various cells and tissues. However, its cryoprotective effects on the cells and tissues are ambiguous and controversial. To test the effects of newborn calf serum (NCS) on cryopreservation of bovine testis tissue, NCS of 0%, 5%, 10% and 20% (v/v) was added into minimum essential medium + 10% dimethyl sulphoxide (DMSO)-based medium according to our previous report. Interestingly, the testicular cell viabilities and spermatogonia percentages from four groups were very close. The results indicated that an increase in the concentration of NCS in freezing medium to 20% has no significant effect on survival of both testicular cells and spermatogonia, and 10% DMSO-based freezing medium can maintain the testicular cell viability and spermatogonia percentage at a relatively high level (83.4 ± 0.7 and 56.5 ± 2.2 respectively). Taken together, NCS is dispensable for cryopreservation of adult bovine testis tissue. Our results provide an evidence for cutting down the costs in cryopreservation research of bovine testis tissue by reducing or giving up the use of serum. © 2013 Blackwell Verlag GmbH.

  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

  20. 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

  1. Student Accomplishments in the Rapid Response Radiotherapy Program: A 10-Year Review.

    Science.gov (United States)

    McDonald, Rachel; Lechner, Breanne; Pulenzas, Natalie; Bedard, Gillian; Wong, Erin; Holden, Lori; Tsao, May; Barnes, Elizabeth; Szumacher, Ewa; Fenton, Gonenc; Chow, Edward; Popovic, Marko; Danjoux, Cyril

    2015-12-01

    In 1996, the Toronto Sunnybrook Regional Cancer Centre developed the Rapid Response Radiotherapy Program (RRRP). The objective of this clinic is to consult, simulate, plan, and treat patients with palliative radiotherapy on the same day. In 2004, the RRRP initiated a program to provide clinical and research experience to undergraduate students interested in health sciences. The purpose of this study is to review the 10-year (2004-2013) experience of the RRRP and to examine whether the goals of the student program have been met. Students who worked in the RRRP from 2004 to 2013 were contacted to complete a short survey regarding their overall experience with the program and their current endeavors. Student accomplishments were collected from an internal database as well as PubMed. Descriptive statistics were used to analyze results. A total of 54 students from ten postsecondary institutions have worked in the RRRP; 29 were from the University of Waterloo undergraduate co-op program. In total, 214 articles with first authorship from students were published, 93 (43%) of which can be found on PubMed. Other accomplishments include 40 book chapters, 58 invited presentations, and 99 awards cumulatively. Qualitative data regarding student perspectives of their experience in the RRRP were also analyzed. Over the past 10 years, the RRRP has achieved its goal of providing quality medical and research experience to students interested in the health sciences. Using the responses of past and present students, we hope to continue to shape our program and provide unique opportunities to future students.

  2. Discovery of a bovine enterovirus in alpaca.

    Directory of Open Access Journals (Sweden)

    Shasta D McClenahan

    Full Text Available A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. Genomic sequence data of the alpaca isolate was obtained and compared with sequences of known viruses. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs, viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Because bovine enteroviruses have not been previously reported in U.S. alpaca, we suspect that this type of infection is fairly rare, and in this case appeared not to spread beyond the original outbreak. The capsid sequence of the detected virus had greatest homology to Enterovirus F type 1 (indicating that the virus should be considered a member of serotype 1, but the virus had greater homology in 2A protease sequence to type 3, suggesting that it may have been a recombinant. Identifying pathogens that infect a new host species for the first time can be challenging. As the disease in a new host species may be quite different from that in the original or natural host, the pathogen may not be suspected based on the clinical presentation, delaying diagnosis. Although this virus replicated in MDBK cells, existing standard culture and molecular methods could not identify it. In this case, a highly sensitive generic PCR-based pathogen-detection method was used to identify this pathogen.

  3. Discovery of a bovine enterovirus in alpaca.

    Science.gov (United States)

    McClenahan, Shasta D; Scherba, Gail; Borst, Luke; Fredrickson, Richard L; Krause, Philip R; Uhlenhaut, Christine

    2013-01-01

    A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. Genomic sequence data of the alpaca isolate was obtained and compared with sequences of known viruses. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Because bovine enteroviruses have not been previously reported in U.S. alpaca, we suspect that this type of infection is fairly rare, and in this case appeared not to spread beyond the original outbreak. The capsid sequence of the detected virus had greatest homology to Enterovirus F type 1 (indicating that the virus should be considered a member of serotype 1), but the virus had greater homology in 2A protease sequence to type 3, suggesting that it may have been a recombinant. Identifying pathogens that infect a new host species for the first time can be challenging. As the disease in a new host species may be quite different from that in the original or natural host, the pathogen may not be suspected based on the clinical presentation, delaying diagnosis. Although this virus replicated in MDBK cells, existing standard culture and molecular methods could not identify it. In this case, a highly sensitive generic PCR-based pathogen-detection method was used to identify this pathogen.

  4. 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...

  5. Bovine neosporosis: clinical and practical aspects.

    Science.gov (United States)

    Almería, S; López-Gatius, F

    2013-10-01

    Neospora caninum is a protozoan parasite with a wide host range but with a preference for cattle and dogs. Since the description of N. caninum as a new genus and species in 1988, bovine neosporosis has become a disease of international concern as it is among the main causes of abortion in cattle. At present there is no effective treatment or vaccine. This review focuses on the epidemiology of the disease and on prospects for its control in cattle. Finally, based on the implications of clinical findings reported to date, a set of recommendations is provided for veterinarians and cattle farmers. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Fatty acids in bovine milk fat

    OpenAIRE

    Lindmark Månsson, Helena

    2008-01-01

    Milk fat contains approximately 400 different fatty acid, which make it the most complex of all natural fats. The milk fatty acids are derived almost equally from two sources, the feed and the microbial activity in the rumen of the cow and the lipids in bovine milk are mainly present in globules as an oil-in-water emulsion. Almost 70% of the fat in Swedish milk is saturated of which around 11% comprises short-chain fatty acids, almost half of which is butyric acid. Approximately 25% of the fa...

  7. Bluetongue virus infection of bovine monocytes.

    Science.gov (United States)

    Whetter, L E; Maclachlan, N J; Gebhard, D H; Heidner, H W; Moore, P F

    1989-07-01

    Cultures of adherent and non-adherent bovine blood mononuclear cells were infected with bluetongue virus (BTV) serotype 10. Production of BTV proteins in mononuclear cell cultures was detected by immune precipitation of viral proteins from [35S]methionine-labelled extracts of these cells, by immunofluorescence staining of cells using monoclonal antibodies (MAbs) to BTV proteins VP7 and NS2, and by flow cytometry with MAbs to VP2, VP7, NS1 and NS2. BTV-infected cells were most numerous in cultures of adherent mononuclear cells; infected cells were initially identified as monocytes on the basis of their morphology, and size and scatter characteristics as determined by analysis with a fluorescence-activated cell sorter (FACS). The majority of adherent mononuclear cells with these scatter characteristics were confirmed to be monocytes by FACS analysis with a MAb specific for bovine monocytes. Identification of BTV-infected adherent mononuclear cells as monocytes was further established by double immunofluorescent labelling, as infected adherent cells reacted with the MAb specific for bovine monocytes, and with another MAb specific for class II antigen. Infection of adherent mononuclear cells was also confirmed by transmission electron microscopy, as BTV virions and tubules were present in lysates of cultures of BTV-infected adherent mononuclear cells and within the cytoplasm of adherent cells. In contrast, BTV proteins were detected in few cells identified as lymphocytes on the basis of their scatter characteristics, and mean fluorescence of such cells was considerably less than that of BTV-infected monocytes. Viraemia persisted until 35 days after inoculation of a colostrum-deprived calf inoculated with BTV. Virus was isolated from blood mononuclear cells at 1 week after infection of the calf, but not thereafter. BTV infection of blood mononuclear cells was demonstrated until 9 days after inoculation by indirect immunofluorescence staining of mononuclear cells. In

  8. 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.

  9. Isolation of new serotypes of bovine rotavirus. Brief report.

    Science.gov (United States)

    Ihara, T; Samejima, T; Kuwahara, H; Tajima, M

    1983-01-01

    Two cytopathogenic bovine rotavirus strains were isolated. The infectivity of both isolates was relatively stable at pH 3.0 and resistant to ether. Their replication was not affected by 5-iodo-2'-deoxyuridine. The new isolates shared immunofluorescent antigen with the Lincoln strain of bovine rotavirus. By neutralization test, however, these strains were clearly distinguished from one another.

  10. Prevalence and economic loss of bovine tuberculosis in a municipal ...

    African Journals Online (AJOL)

    A 12 month cross-sectional study was carried out at Lafenwa Abattoir Abeokuta, Southwestern Nigeria from July, 2011 to June, 2012. This was to determine the prevalence and economic loss of bovine tuberculosis in this abattoir. A total of 928 cases of bovine tuberculosis out of 52,273 cattle slaughtered during this period ...

  11. Prevalence of Enzootic Bovine Leukosis (EBL) in the Northern ...

    African Journals Online (AJOL)

    In the present study, a commercial immuno enzymatic assay (blocking- ELISA), were used to detect BLV antibodies in bovine serum using two monoclonal antibodies against the viral gp51 from bovines of two major districts namely, Waqoyi Galbed, and Togdheer of northern Somalia (Somaliland). Out of 468 tested cows ...

  12. Comparison of bovine lymphocyte antigen DRB3.2 allele ...

    African Journals Online (AJOL)

    The bovine lymphocyte antigen (BoLA-DRB3) gene encodes cell surface glycoproteins that initiate immune responses by presenting processed antigenic peptides to CD4 T helper cells. DRB3 is the most polymorphic bovine MHC class II gene which encodes the peptide-binding groove. Since different alleles favor the ...

  13. Molecular Epidemiology of Bovine Tuberculosis and most Common ...

    African Journals Online (AJOL)

    Even though tuberculosis is endemic in Nigeria, information on the epidemiology of the disease especially bovine tuberculosis is still very scanty. Variable Number of Tandem Repeat (VNTR) was carried out on 113 tissue samples to have an idea of not only the epidemiology of bovine tuberculosis but also the most common ...

  14. Anticancer activities of bovine and human lactoferricin-derived peptides

    NARCIS (Netherlands)

    Arias, M.; Hilchie, A.L.; Haney, E.F.; Bolscher, J.G.M.; Hyndman, M.E.; Hancock, R.E.W.; Vogel, H.J.

    2017-01-01

    Lactoferrin (LF) is a mammalian host defense glycoprotein with diverse biological activities. Peptides derived from the cationic region of LF possess cytotoxic activity against cancer cells in vitro and in vivo. Bovine lactoferricin (LFcinB), a peptide derived from bovine LF (bLF), exhibits

  15. Sucrose/bovine serum albumin mediated biomimetic crystallization ...

    Indian Academy of Sciences (India)

    To understand the role of the sucrose/bovine serum albumin system in the biomineralization process, we have tested the influence of different concentration of the sucrose/bovine serum albumin (BSA) on calcium carbonate (CaCO3) precipitation. The CaCO3 crystals were characterized by scanning electron microscope ...

  16. Study on Seroprevalence of Bovine Brucellosis and Abortion and ...

    African Journals Online (AJOL)

    A cross sectional study was carried on bovine brucellosis from November 2008 to March 2009 to determine the sero-prevalence and distribution of bovine brucel osis in selected sites of Jimma zone, Southwestern Ethiopia. A total of 950 animals (541 female and 409 male) were examined serologically by using RBPT as ...

  17. Viral and Bacterial Pathogens in Bovine Respiratory Disease in Finland

    Directory of Open Access Journals (Sweden)

    Soveri T

    2004-12-01

    Full Text Available Pathogens causing bovine respiratory tract disease in Finland were investigated. Eighteen cattle herds with bovine respiratory disease were included. Five diseased calves from each farm were chosen for closer examination and tracheobronchial lavage. Blood samples were taken from the calves at the time of the investigation and from 86 calves 3–4 weeks later. In addition, 6–10 blood samples from animals of different ages were collected from each herd, resulting in 169 samples. Serum samples were tested for antibodies to bovine parainfluenza virus-3 (PIV-3, bovine respiratory syncytial virus (BRSV, bovine coronavirus (BCV, bovine adenovirus-3 (BAV-3 and bovine adenovirus-7 (BAV-7. About one third of the samples were also tested for antibodies to bovine virus diarrhoea virus (BVDV with negative results. Bacteria were cultured from lavage fluid and in vitro susceptibility to selected antimicrobials was tested. According to serological findings, PIV-3, BAV-7, BAV-3, BCV and BRSV are common pathogens in Finnish cattle with respiratory problems. A titre rise especially for BAV-7 and BAV-3, the dual growth of Mycoplasma dispar and Pasteurella multocida, were typical findings in diseased calves. Pasteurella sp. strains showed no resistance to tested antimicrobials. Mycoplasma bovis and Mannheimia haemolytica were not found.

  18. Preliminary study on the impact of Bovine Tuberculosis on the ...

    African Journals Online (AJOL)

    A retrospective study was conducted on 100 (50 bovine TB positive and 50 negative) dairy cows to determine the effect of bovine tuberculosis (TB) on reproductive efficiency and productivity of Holstein dairy cows. In order to achieve this, five year records of reproductive/ productive variables including age at puberty, age at ...

  19. Detection of lipomannan in cattle infected with bovine tuberculosis

    Science.gov (United States)

    Early and rapid detection of bovine tuberculosis (bTB) is critical to controlling the spread of this disease in cattle and other animals. In this study, we demonstrate the development of an immunoassay for the direct detection of the bovine bTB biomarker, lipomannan (LM) in serum using a waveguide-...

  20. Research Article: Food Animal Practice Bovine Papillomatosis and ...

    African Journals Online (AJOL)

    Six cases of bovine papillomatosis were reported to the University of Nairobi veterinary clinic. Diagnosis was based on presented clinical signs and histopathology of affected skin lesions. The histological samples of the warts confirmed the diagnosis of papillomatosis. An autogenous formalin killed bovine specific wart ...

  1. Traitement De La Peripneumonie Contagieuse Bovine Par L ...

    African Journals Online (AJOL)

    oxytétracycline LA) dans le traitement des bovins atteints de péripneumonie contagieuse bovine (PPCB) et de déterminer le risque de transmission de la maladie à partir d'animaux traités. Une transmission expérimentale a été conduite par la mise ...

  2. Modulation of human immune responses by bovine interleukin-10.

    Directory of Open Access Journals (Sweden)

    Gerco den Hartog

    Full Text Available Cytokines can be functionally active across species barriers. Bovine IL-10 has an amino acid sequence identity with human IL-10 of 76.8%. Therefore, the aim of this study was to evaluate whether bovine IL-10 has immunomodulatory activities on human monocytes and dendritic cells. Peripheral blood monocytes were isolated from healthy donors, and used directly or allowed to differentiate to dendritic cells under the influence of IL-4 and GM-CSF. Recombinant bovine IL-10 inhibited TLR induced activation of monocytes, and dose-dependently inhibited LPS-induced activation of monocyte-derived DCs comparable to human IL-10. By using blocking antibodies to either bovine IL-10 or the human IL-10 receptor it was demonstrated that inhibition of monocyte activation by bovine IL-10 was dependent on binding of bovine IL-10 to the human IL-10R. These data demonstrate that bovine IL-10 potently inhibits the activation of human myeloid cells in response to TLR activation. Bovine IL-10 present in dairy products may thus potentially contribute to the prevention of necrotizing enterocolitis and allergy, enhance mucosal tolerance induction and decrease intestinal inflammation and may therefore be applicable in infant foods and in immunomodulatory diets.

  3. Seroprevalence and risk factors associated with bovine herpesvirus ...

    African Journals Online (AJOL)

    Bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus (BVDV) are well known etiological agents of cattle that produce important economic losses due to reproductive failures and calf mortality, as well as enteric and respiratory disease. Tamaulipas is located northeast of Mexico, an important cattle production and ...

  4. Computational identification of fertility functions of bovine Reprimo ...

    African Journals Online (AJOL)

    The domain structure of bovine RPRM protein was predicted using simple modular architecture research tool (SMART). Protein tertiary structures (3D structures) of bovine RPRM gene and other cattle fertility genes were predicted with Phyre2 software. To have structural and functional similarity, it has been found that protein ...

  5. Comparative analysis of human and bovine teeth: radiographic density

    Directory of Open Access Journals (Sweden)

    Jefferson Luis Oshiro Tanaka

    2008-12-01

    Full Text Available Since bovine teeth have been used as substitutes for human teeth in in vitro dental studies, the aim of this study was to compare the radiographic density of bovine teeth with that of human teeth to evaluate their usability for radiographic studies. Thirty bovine and twenty human teeth were cut transversally in 1 millimeter-thick slices. The slices were X-rayed using a digital radiographic system and an intraoral X-ray machine at 65 kVp and 7 mA. The exposure time (0.08 s and the target-sensor distance (40 cm were standardized for all the radiographs. The radiographic densities of the enamel, coronal dentin and radicular dentin of each slice were obtained separately using the "histogram" tool of Adobe Photoshop 7.0 software. The mean radiographic densities of the enamel, coronal dentin and radicular dentin were calculated by the arithmetic mean of the slices of each tooth. One-way ANOVA demonstrated statistically significant differences for the densities of bovine and human enamel (p 0.05. Based on the results, the authors concluded that: a the radiographic density of bovine enamel is significantly higher than that of human enamel; b the radiodensity of bovine coronal dentin is statistically lower than the radiodensity of human coronal dentin; bovine radicular dentin is also less radiodense than human radicular dentin, although this difference was not statistically significant; c bovine teeth should be used with care in radiographic in vitro studies.

  6. Diagnosis of enzootic bovine leucosis in single and pooled samples.

    Science.gov (United States)

    Hoff-Jørgensen, R

    1990-12-01

    Diagnosis of enzootic bovine leucosis is based on detection of antibodies against bovine leukemia virus, BLV. Some ELISA modifications have proved sensitive enough for use in the examination of pooled blood samples from slaughterhouses, milk and pooled milk samples. Suggestions for the standardisation of different ELISA modifications using a common reference serum are presented.

  7. The vaccines for Bovine Herpesvirus Type 1: A review | Zhao ...

    African Journals Online (AJOL)

    Bovine herpesvirus type 1 (BoHV-1) is the pathogen of Infectious Bovine Rhinothracheitis (IBR) disease, causing great economic losses in the livestock industry. Vaccine is a powerful means to control the virus. Here, the review described the currently available knowledge regarding to the advance in the field of BoHV-1 ...

  8. Advances in development and evaluation of bovine herpesvirus 1 vaccines

    NARCIS (Netherlands)

    Oirschot, van J.T.; Kaashoek, M.J.; Rijsewijk, F.A.M.

    1996-01-01

    This review deals with conventional and modern bovine herpesvirus 1 (BHV1) vaccines. Conventional vaccines are widely used to prevent clinical signs of infectious bovine rhinotracheitis. The use of conventional vaccines, however, does not appear to have resulted in reduction of the prevalence of

  9. Modulation of human immune responses by bovine interleukin-10

    NARCIS (Netherlands)

    Hartog, den C.G.; Savelkoul, H.F.J.; Schoemaker, R.; Tijhaar, E.; Westphal, A.H.; Ruiter, de T.; Weg-Schrijver, van de Elise; Neerven, van R.J.J.

    2011-01-01

    Cytokines can be functionally active across species barriers. Bovine IL-10 has an amino acid sequence identity with human IL-10 of 76.8%. Therefore, the aim of this study was to evaluate whether bovine IL-10 has immunomodulatory activities on human monocytes and dendritic cells. Peripheral blood

  10. 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

  11. 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.

  12. Mitogenomic phylogeny of cone snails endemic to Senegal.

    Science.gov (United States)

    Abalde, Samuel; Tenorio, Manuel J; Afonso, Carlos M L; Zardoya, Rafael

    2017-07-01

    Cone snails attain in Senegal one of their highest peaks of species diversity throughout the continental coast of Western Africa. A total of 15 endemic species have been described, all placed in the genus Lautoconus. While there is ample data regarding the morphology of the shell and the radular tooth of these species, virtually nothing is known regarding the genetic diversity and phylogenetic relationships of one of the most endangered groups of cones. In this work, we determined the complete or near-complete (only lacking the control region) mitochondrial (mt) genomes of 17 specimens representing 11 endemic species (Lautoconus belairensis, Lautoconus bruguieresi, Lautoconus cacao, Lautoconus cloveri, Lautoconus cf. echinophilus, Lautoconus guinaicus, Lautoconus hybridus, Lautoconus senegalensis, Lautoconus mercator, Lautoconus taslei, and Lautoconus unifasciatus). We also sequenced the complete mt genome of Lautoconus guanche from the Canary Islands, which has been related to the cones endemic to Senegal. All mt genomes share the same gene arrangement, which conforms to the consensus reported for Conidae, Neogastropoda and Caenogastropoda. Phylogenetic analyses using probabilistic methods recovered three major lineages, whose divergence coincided in time with sea level and ocean current changes as well as temperature fluctuations during the Messinian salinity crisis and the Plio-Pleistocene transition. Furthermore, the three lineages corresponded to distinct types of radular tooth (robust, small, and elongated), suggesting that dietary specialization could be an additional evolutionary driver in the diversification of the cones endemic to Senegal. The reconstructed phylogeny showed several cases of phenotypic convergence (cryptic species) and questions the validity of some species (ecotypes or phenotypic plasticity), both results having important taxonomic and conservation consequences. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Phylogenies reveal new interpretation of speciation and the Red Queen.

    Science.gov (United States)

    Venditti, Chris; Meade, Andrew; Pagel, Mark

    2010-01-21

    The Red Queen describes a view of nature in which species continually evolve but do not become better adapted. It is one of the more distinctive metaphors of evolutionary biology, but no test of its claim that speciation occurs at a constant rate has ever been made against competing models that can predict virtually identical outcomes, nor has any mechanism been proposed that could cause the constant-rate phenomenon. Here we use 101 phylogenies of animal, plant and fungal taxa to test the constant-rate claim against four competing models. Phylogenetic branch lengths record the amount of time or evolutionary change between successive events of speciation. The models predict the distribution of these lengths by specifying how factors combine to bring about speciation, or by describing how rates of speciation vary throughout a tree. We find that the hypotheses that speciation follows the accumulation of many small events that act either multiplicatively or additively found support in 8% and none of the trees, respectively. A further 8% of trees hinted that the probability of speciation changes according to the amount of divergence from the ancestral species, and 6% suggested speciation rates vary among taxa. By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation. This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events that cause reproductive isolation. Attempts to understand species-radiations or why some groups have more or fewer species should look to the size of the catalogue of potential causes of speciation shared by a group of closely related organisms rather than to how those causes combine.

  14. 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

  15. The discovery of Halictivirus resolves the Sinaivirus phylogeny.

    Science.gov (United States)

    Bigot, Diane; Dalmon, Anne; Roy, Bronwen; Hou, Chunsheng; Germain, Michèle; Romary, Manon; Deng, Shuai; Diao, Qingyun; Weinert, Lucy A; Cook, James M; Herniou, Elisabeth A; Gayral, Philippe

    2017-11-01

    By providing pollination services, bees are among the most important insects, both in ecological and economical terms. Combined next-generation and classical sequencing approaches were applied to discover and study new insect viruses potentially harmful to bees. A bioinformatics virus discovery pipeline was used on individual Illumina transcriptomes of 13 wild bees from three species from the genus Halictus and 30 ants from six species of the genera Messor and Aphaenogaster. This allowed the discovery and description of three sequences of a new virus termed Halictus scabiosae Adlikon virus (HsAV). Phylogenetic analyses of ORF1, RNA-dependent RNA-polymerase (RdRp) and capsid genes showed that HsAV is closely related to (+)ssRNA viruses of the unassigned Sinaivirus genus but distant enough to belong to a different new genus we called Halictivirus. In addition, our study of ant transcriptomes revealed the first four sinaivirus sequences from ants (Messor barbarus, M. capitatus and M. concolor). Maximum likelihood phylogenetic analyses were performed on a 594 nt fragment of the ORF1/RdRp region from 84 sinaivirus sequences, including 31 new Lake Sinai viruses (LSVs) from honey bees collected in five countries across the globe and the four ant viral sequences. The phylogeny revealed four main clades potentially representing different viral species infecting honey bees. Moreover, the ant viruses belonged to the LSV4 clade, suggesting a possible cross-species transmission between bees and ants. Lastly, wide honey bee screening showed that all four LSV clades have worldwide distributions with no obvious geographical segregation.

  16. Multi-level human evolution: ecological patterns in hominin phylogeny.

    Science.gov (United States)

    Parravicini, Andrea; Pievani, Telmo

    2016-06-20

    Evolution is a process that occurs at many different levels, from genes to ecosystems. Genetic variations and ecological pressures are hence two sides of the same coin; but due both to fragmentary evidence and to the influence of a gene-centered and gradualistic approach to evolutionary phenomena, the field of paleoanthropology has been slow to take the role of macro-evolutionary patterns (i.e. ecological and biogeographical at large scale) seriously. However, several very recent findings in paleoanthropology stress both climate instability and ecological disturbance as key factors affecting the highly branching hominin phylogeny, from the earliest hominins to the appearance of cognitively modern humans. Allopatric speciation due to geographic displacement, turnover-pulses of species, adaptive radiation, mosaic evolution of traits in several coeval species, bursts of behavioral innovation, serial dispersals out of Africa, are just some of the macro-evolutionary patterns emerging from the field. The multilevel approach to evolution proposed by paleontologist Niles Eldredge is adopted here as interpretative tool, and has yielded a larger picture of human evolution that integrates different levels of evolutionary change, from local adaptations in limited ecological niches to dispersal phenotypes able to colonize an unprecedented range of ecosystems. Changes in global climate and Earth's surface most greatly affected human evolution. Precisely because it is cognitively hard for us to appreciate the long-term common destiny we share with the whole biosphere, it is particularly valuable to highlight the accumulating evidence that human evolution has been deeply affected by global ecological changes that transformed our African continent of origin.

  17. Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases.

    Science.gov (United States)

    Adesioye, Fiyinfoluwa A; Makhalanyane, Thulani P; Biely, Peter; Cowan, Don A

    2016-11-01

    Acetyl xylan esterases (AcXEs), also termed xylan deacetylases, are broad specificity Carbohydrate-Active Enzymes (CAZymes) that hydrolyse ester bonds to liberate acetic acid from acetylated hemicellulose (typically polymeric xylan and xylooligosaccharides). They belong to eight families within the Carbohydrate Esterase (CE) class of the CAZy database. AcXE classification is largely based on sequence-dependent phylogenetic relationships, supported in some instances with substrate specificity data. However, some sequence-based predictions of AcXE-encoding gene identity have proved to be functionally incorrect. Such ambiguities can lead to mis-assignment of genes and enzymes during sequence data-mining, reinforcing the necessity for the experimental confirmation of the functional properties of putative AcXE-encoding gene products. Although one-third of all characterized CEs within CAZy families 1-7 and 16 are AcXEs, there is a need to expand the sequence database in order to strengthen the link between AcXE gene sequence and specificity. Currently, most AcXEs are derived from a limited range of (mostly microbial) sources and have been identified via culture-based bioprospecting methods, restricting current knowledge of AcXEs to data from relatively few microbial species. More recently, the successful identification of AcXEs via genome and metagenome mining has emphasised the huge potential of culture-independent bioprospecting strategies. We note, however, that the functional metagenomics approach is still hampered by screening bottlenecks. The most relevant recent reviews of AcXEs have focused primarily on the biochemical and functional properties of these enzymes. In this review, we focus on AcXE phylogeny, classification and the future of metagenomic bioprospecting for novel AcXEs. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. [Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

    Science.gov (United States)

    Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

    2014-10-01

    Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax.

  19. Blastocystis phylogeny among various isolates from humans to insects.

    Science.gov (United States)

    Yoshikawa, Hisao; Koyama, Yukiko; Tsuchiya, Erika; Takami, Kazutoshi

    2016-12-01

    Blastocystis is a common unicellular eukaryotic parasite found not only in humans, but also in various kinds of animal species worldwide. Since Blastocystis isolates are morphologically indistinguishable, many molecular biological approaches have been applied to classify these isolates. The complete or partial sequences of the small subunit rRNA gene (SSU rDNA) are mainly used for comparisons and phylogenetic analyses among Blastocystis isolates. However, various lengths of the partial SSU rDNA sequence have been used for phylogenetic inference among genetically different isolates. Based on the complete SSU rDNA sequences, consensus terminology of nine subtypes (STs) of Blastocystis sp. that were supported by phylogenetically monophyletic nine clades was proposed in 2007. Thereafter, eight additional kinds of STs comprising non-human mammalian Blastocystis isolates have been reported based on the phylogeny of SSU rDNA sequences, while STs 11 and 12 were only proposed on the base of partial sequences. Although many sequence data from mammalian and avian Blastocystis are registered in GenBank, only limited data on SSU rDNA are available for poikilotherm-derived Blastocystis isolates. Therefore, the phylogenetic positions of the reptilian/amphibian Blastocystis clades are unstable. The phylogenetic inference of various STs comprising mammalian and/or avian Blastocystis isolates was verified herein based on comparisons between partial and complete SSU rDNA sequences, and the phylogenetic positions of reptilian and amphibian Blastocystis isolates were also investigated using 14 new Blastocystis isolates from reptiles with all known isolates from other reptilians, amphibians, and insects registered in GenBank. Copyright © 2016. Published by Elsevier Ireland Ltd.

  20. A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes).

    Science.gov (United States)

    Kappas, Ilias; Vittas, Spiros; Pantzartzi, Chrysoula N; Drosopoulou, Elena; Scouras, Zacharias G

    2016-01-01

    A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae

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

    Science.gov (United States)

    Paster, B J; Dewhirst, F E; Cooke, S M; Fussing, V; Poulsen, L K; Breznak, J A

    1996-02-01

    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 products were cloned into Escherichia coli. Clones were screened with a spirochete-specific DNA probe. Analysis of 1,410 base positions of the 16S rDNA insert from one spirochete clone, designated NL1, supported its assignment to the genus Treponema, with average interspecies similarities of ca. 85%. The sequence of NL1 was most closely related (ca. 87 to 88% similarity) to sequences of Spirochaeta stenostrepta and Spirochaeta caldaria and to a previously published sequence (ca. 87% similarity) of spirochetal clone MDS1 from the Australian lower termite, Mastotermes darwiniensis (Froggatt). On the basis of 16S rRNA sequence comparisons and individual base signatures, clones NL1 and MDS1 clearly represent two novel species of Treponema, although specific epithets have not yet been proposed. The gross morphology of NL1 was determined from in situ hybridization experiments with an NL1-specific, fluorescently labeled oligonucleotide probe. Cells were approximately 0.3 to 0.4 by 30 microns in size, with a wavelength and amplitude of about 10 microns and 0.8 to 1.6 micron, respectively. Moreover, electron microscopy of various undulate cells present in gut contents confirmed that they possessed ultrastructural features typical of spirochetes, i.e., a wavy protoplasmic cylinder, periplasmic flagella, and an outer sheath. The sequence data suggest that termite gut spirochetes may represent a separate line of descent from other treponemes and that they constitute a significant reservoir of previously unrecognized spirochetal biodiversity.

  2. Molecular phylogeny and evolution of the genus Neoerysiphe (Erysiphaceae, Ascomycota).

    Science.gov (United States)

    Takamatsu, Susumu; Havrylenko, Maria; Wolcan, Silvia M; Matsuda, Sanae; Niinomi, Seiko

    2008-06-01

    The genus Neoerysiphe belongs to the tribe Golovinomyceteae of the Erysiphaceae together with the genera Arthrocladiella and Golovinomyces. This is a relatively small genus, comprising only six species, and having ca 300 species from six plant families as hosts. To investigate the molecular phylogeny and evolution of the genus, we determined the nucleotide sequences of the rDNA ITS regions and the divergent domains D1 and D2 of the 28S rDNA. The 30 ITS sequences from Neoerysiphe are divided into three monophyletic groups that are represented by their host families. Groups 1 and 3 consist of N. galeopsidis from Lamiaceae and N. galii from Rubiaceae, respectively, and the genetic diversity within each group is extremely low. Group 2 is represented by N. cumminsiana from Asteraceae. This group also includes Oidium baccharidis, O. maquii, and Oidium spp. from Galinsoga (Asteraceae) and Aloysia (Verbenaceae), and is further divided into four subgroups. N. galeopsidis is distributed worldwide, but is especially common in western Eurasia from Central Asia to Europe. N. galii is also common in western Eurasia. In contrast, the specimens of group 2 were all collected in the New World, except for one specimen that was collected in Japan; this may indicate a close relationship of group 2 with the New World. Molecular clock calibration demonstrated that Neoerysiphe split from other genera of the Erysiphaceae ca 35-45M years ago (Mya), and that the three groups of Neoerysiphe diverged between 10 and 15Mya, in the Miocene. Aloysia citriodora is a new host for the Erysiphaceae and the fungus on this plant is described as O. aloysiae sp. nov.

  3. Forelimb-hindlimb developmental timing changes across tetrapod phylogeny.

    Science.gov (United States)

    Bininda-Emonds, Olaf R P; Jeffery, Jonathan E; Sánchez-Villagra, Marcelo R; Hanken, James; Colbert, Matthew; Pieau, Claude; Selwood, Lynne; Ten Cate, Carel; Raynaud, Albert; Osabutey, Casmile K; Richardson, Michael K

    2007-10-01

    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. 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. 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 trait means that changes in chondrogenetic patterns may serve

  4. Tree thinking for all biology: the problem with reading phylogenies as ladders of progress.

    Science.gov (United States)

    Omland, Kevin E; Cook, Lyn G; Crisp, Michael D

    2008-09-01

    Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved "tree thinking" is crucial. The most-serious problem comes from reading trees as ladders from "left to right"--many biologists assume that species-poor lineages that appear "early branching" or "basal" are ancestral--we call this the "primitive lineage fallacy". This mistake causes misleading inferences about changes in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21(st) century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19(th) century notions about the ladder of progress driving evolution.

  5. Nuclear ribosomal DNA phylogeny and its implications for evolutionary trends in Mexican Bursera (Burseraceae).

    Science.gov (United States)

    Becerra, J X; Venable, D L

    1999-07-01

    The genus Bursera (Burseraceae) is one of the most diversified and abundant groups of plants of the tropical dry forests of Mexico. In order to provide a basis for better understanding of its evolutionary biology, we reconstructed a phylogeny of 57 species and varieties using the nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of 18S-26S and the 5.8S coding region of nuclear ribosomal DNA. We used four species of the allied genera Commiphora and Boswellia and one species of Spondias (Anacardiaceae) as outgroups. Our results support the views that Bursera is monophyletic and more closely related to Commiphora than to Boswellia. The division of Bursera into sections Bullockia and Bursera is also strongly supported by our phylogeny. Several other subclades also had high bootstrap values, especially within section Bursera. We use the phylogeny as a basis for discussing evolutionary tendencies in bark, leaves, breeding systems, and fruits.

  6. Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances

    Directory of Open Access Journals (Sweden)

    Jose L. Horreo

    2017-09-01

    Full Text Available The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.

  7. Molecular phylogeny of the benthic shallow-water octopuses (Cephalopoda: Octopodinae).

    Science.gov (United States)

    Guzik, Michelle T; Norman, Mark D; Crozier, Ross H

    2005-10-01

    Octopus has been regarded as a "catch all" genus, yet its monophyly is questionable and has been untested. We inferred a broad-scale phylogeny of the benthic shallow-water octopuses (subfamily Octopodinae) using amino acid sequences of two mitochondrial DNA genes: Cytochrome oxidase subunit III and Cytochrome b apoenzyme, and the nuclear DNA gene Elongation Factor-1alpha. Sequence data were obtained from 26 Octopus species and from four related genera. Maximum likelihood and Bayesian approaches were implemented to estimate the phylogeny, and non-parametric bootstrapping was used to verify confidence for Bayesian topologies. Phylogenetic relationships between closely related species were generally well resolved, and groups delineated, but the genes did not resolve deep divergences well. The phylogenies indicated strongly that Octopus is not monophyletic, but several monophyletic groups were identified within the genus. It is therefore clear that octopodid systematics requires major revision.

  8. 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.

  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. Lack of Virus-Specific Bacterial Adherence to Bovine Embryonic Lung Cells Infected with Bovine Parainfluenza Virus Type 3 †

    OpenAIRE

    Toth, Thomas E.; Gates, Connie

    1983-01-01

    Infection of bovine embryonic lung cells with bovine parainfluenza virus type 3 did not induce in vitro, virus-specific, hemadsorption-related adherence of Corynebacterium pyogenes, Haemophilus somnus, Staphylococcus aureus, Streptococcus zooepidemicus, Pasteurella haemolytica, Listeria monocytogenes, Escherichia coli, Pasteurella multocida, Brucella sp., or Salmonella typhimurium.

  11. Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species.

    Science.gov (United States)

    Govindarajulu, Rajanikanth; Parks, Matthew; Tennessen, Jacob A; Liston, Aaron; Ashman, Tia-Lynn

    2015-04-01

    Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries. Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests. The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins. This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria. © 2015 Botanical Society of America, Inc.

  12. Ultrasonographic anatomy of the bovine eye.

    Science.gov (United States)

    Potter, Timothy J; Hallowell, Gayle D; Bowen, I Mark

    2008-01-01

    The purposes of the study were to describe the ultrasonographic appearance and measurements of the normal bovine eye, to compare the measurements to those reported previously for cadaveric eyes and to describe differences between ocular dimensions of Holstein Friesian and Jersey cattle. Sixty transpalpebral ocular ultrasonographic examinations were performed on 30 adult Holstein Friesian cows, and 16 examinations were performed on 8 adult Jersey cows. Transpalpebral ultrasonographic images were obtained with a 10 MHz linear transducer in both horizontal and vertical imaging planes. The ultrasonographic appearance of structures within the bovine eye is similar to that in other species, although the ciliary artery was frequently identified, appearing as a 0.33 +/- 0.04 cm diameter hypoechoic area. The axial length of the globe was significantly greater in Holstein Friesian cattle (3.46 +/- 0.09 cm) compared with Jersey cattle (3.27 +/- 0.19 cm; P = 0.001), although the vitreous depth was smaller in Holstein Friesian cattle (1.46 +/- 0.09 cm) (P = 0.0009). The anterioposterior depth of the lens was significantly greater in Jersey cattle (1.92 +/- 0.11 cm) and the cornea was thinner in Jersey cattle (0.17 +/- 0.02 cm). The appearance and ocular distances for live animals were similar to those reported previously for cadaveric specimens. The knowledge of normal ocular dimensions facilitates the use of ultrasonography in the evaluation of ocular disease in cattle.

  13. Looseness in bovine leather: microstructural characterization.

    Science.gov (United States)

    Wells, Hannah C; Holmes, Geoff; Haverkamp, Richard G

    2016-06-01

    A substantial proportion of bovine leather production may be of poor quality, with the leather suffering from a characteristic known as looseness. This defect results in a poor visual appearance and greatly reduced value. The structural mechanism of looseness is not well understood. Samples of loose and tight bovine leather are characterized using small-angle X-ray scattering, ultrasonic imaging, and electron microscopy. The density of fibre packing and orientation of the fibrils are analysed. Tensile strength is also measured. Loose leather is characterized by more highly aligned collagen fibrils. This results in a weaker connection between the layers. There is a looser packing of the fibres in loose leather than in tight leather, with more gaps between fibre bundles, particularly in a region in the lower grain. This region is visible with in situ ultrasonic imaging. Loose leather has a higher tensile strength than tight leather. While a high degree of collagen fibril alignment is normally associated with strong leather, it has been shown that too much alignment results in loose leather. Understanding the physical basis of looseness is the first step in identifying looseness in hides and learning how to prevent looseness from developing during leather manufacture. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  14. 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.

  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. The collagens of the developing bovine cornea.

    Science.gov (United States)

    Lee, R E; Davison, P F

    1984-11-01

    The morphology of the developing bovine eye has been examined and the collagens in fetal bovine eyes from three months' gestation to maturity have been solubilized by pepsin treatment and analyzed to determine the ratios of the predominant types of collagen. The type I collagen decreased, while the type V collagen increased with age. Type III collagen comprised less than 1% of all the corneas, except for the three-month fetal calf. The anterior to posterior thickness of the paraffin-embedded fetal calf cornea increased from the third to the seventh month, decreased from the seventh month to birth, and then increased after birth. Descemet's membrane increased in thickness with age. Analysis of dissected regions of the calf cornea showed a uniform distribution of the collagen populations from the center to the limbus (89% type I, 10% type V and less than 1% type III collagen) and uniformity through the depth of the stroma, except that type III was concentrated around Bowman's layer, and type IV in Descement's membrane. The localization of the different collagens was consistent with the immunofluorescent staining studies with anticollagen antibodies, but the ratios of the intensities of the fluorescence did not correspond to the quantitative analyses. These results are concordant with other studies that have shown that antibody binding may be masked or diminished in certain tissues and therefore immunofluorescence cannot be used reliably for quantitative measurements.

  17. A novel phylogeny and morphological reconstruction of the PIN genes and first phylogeny of the ACC-oxidases (ACOs

    Directory of Open Access Journals (Sweden)

    Ronald Matthew Clouse

    2014-06-01

    Full Text Available The PIN and ACO gene families present interesting questions about the evolution of plant physiology, including testing hypotheses about the ecological drivers of their diversification and whether unrelated genes have been recruited for similar functions. The PIN-formed proteins contribute to the polar transport of auxin, a hormone which regulates plant growth and development. PIN loci are categorized into groups according to their protein length and structure, as well as subcellular localization. An interesting question with PIN genes is the nature of the ancestral form and location. ACOs are members of a superfamily of oxygenases and oxidases that catalyze the last step of ethylene synthesis, which regulates many aspects of the plant life cycle. We used publicly available PIN and ACO sequences to conduct phylogenetic analyses. Third codon positions of these genes in monocots have a high GC content, which could be historical but is more likely due to a mutational bias. Thus we developed methods to extract phylogenetic information from nucleotide sequences while avoiding this convergent feature. One method consisted in using only A-T transformations, and another used only the first and second codon positions for serine, which can only take A or T and G or C, respectively. We also conducted tree-searches for both gene families using unaligned amino acid sequences and dynamic homology. PIN genes appear to have diversified earlier than ACOs, with monocot and dicot copies more mixed in the phylogeny. However, gymnosperm PINs appear to be derived and not closely related to those from primitive plants. We find strong support for a long PIN gene ancestor with short forms subsequently evolving one or more times. ACO genes appear to have diversified mostly since the dicot-monocot split, as most genes cluster into a small number of monocot and dicot clades when the tree is rooted by genes from mosses. Gymnosperm ACOs were recovered as closely related and

  18. Geographical and Temporal Body Size Variation in a Reptile: Roles of Sex, Ecology, Phylogeny and Ecology Structured in Phylogeny

    Science.gov (United States)

    Aragón, Pedro; Fitze, Patrick S.

    2014-01-01

    Geographical body size variation has long interested evolutionary biologists, and a range of mechanisms have been proposed to explain the observed patterns. It is considered to be more puzzling in ectotherms than in endotherms, and integrative approaches are necessary for testing non-exclusive alternative mechanisms. Using lacertid lizards as a model, we adopted an integrative approach, testing different hypotheses for both sexes while incorporating temporal, spatial, and phylogenetic autocorrelation at the individual level. We used data on the Spanish Sand Racer species group from a field survey to disentangle different sources of body size variation through environmental and individual genetic data, while accounting for temporal and spatial autocorrelation. A variation partitioning method was applied to separate independent and shared components of ecology and phylogeny, and estimated their significance. Then, we fed-back our models by controlling for relevant independent components. The pattern was consistent with the geographical Bergmann's cline and the experimental temperature-size rule: adults were larger at lower temperatures (and/or higher elevations). This result was confirmed with additional multi-year independent data-set derived from the literature. Variation partitioning showed no sex differences in phylogenetic inertia but showed sex differences in the independent component of ecology; primarily due to growth differences. Interestingly, only after controlling for independent components did primary productivity also emerge as an important predictor explaining size variation in both sexes. This study highlights the importance of integrating individual-based genetic information, relevant ecological parameters, and temporal and spatial autocorrelation in sex-specific models to detect potentially important hidden effects. Our individual-based approach devoted to extract and control for independent components was useful to reveal hidden effects linked with

  19. 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

  20. Molecular phylogeny and systematic revision of the pleurocarpous moss genus Plagiothecium

    DEFF Research Database (Denmark)

    Wynns, Justin Thomas

    A systematic investigation of the pleurocarpous moss genus Plagiothecium Bruch & Schimp. was performed as a part of the author’s PhD study at the University of Copenhagen. Plagiothecium is mostly a well-defined genus, but the species limits and the interspecific relationships are poorly understood......K-psbA and rpl16 intron, and nuclear ribosomal ITS. Parsimony analyses of DNA sequence data from all three regions were performed to generate phylogenies for 110 specimens of Plagiothecium and similar mosses. Some sequence data were obtained for an additional 76 collections, yielding an rpl16 phylogeny for 147...

  1. Taxonomy, DNA barcoding and phylogeny of three new species of Pythium from Canada.

    Science.gov (United States)

    Bala, K; Robideau, G P; Désaulniers, N; de Cock, A W A M; Lévesque, C A

    2010-12-01

    Three new species of Pythium, namely, P. oopapillum, P. emineosum and P. camurandrum are presented in this paper based on morphological descriptions and molecular phylogenetic characterisation. These new species were isolated from various ecological regions in Canada. They have unique morphological features in the genus Pythium, and form distinct clades in maximum parsimony analyses, which are also supported by maximum likelihood phylogeny using general time reversible model (GTR), and Bayesian inference (BI) phylogeny using Markov Chain Monte Carlo (MCMC) analysis methods. A comparative study of the new species with closely related taxa, their clade positions, and morphological features are described in this paper.

  2. Accomplishing professional jurisdiction in intensive care: An ethnographic study of three units.

    Science.gov (United States)

    Xyrichis, Andreas; Lowton, Karen; Rafferty, Anne Marie

    2017-05-01

    This paper reports an ethnographic study examining health professional jurisdictions within three intensive care units (ICUs) in order to draw out the social processes through which ICU clinicians organised and delivered life-saving care to critically ill patients. Data collection consisted of 240 h observation of actual practice and 27 interviews with health professionals. The research was conducted against a backdrop of international political and public pressure for national healthcare systems to deliver safe, quality and efficient healthcare. As in many Western health systems, for the English Department of Health the key to containing these challenges was a reconfiguration of responsibilities for clinicians in order to break down professional boundaries and encourage greater interprofessional working under the guise of workforce modernisation. In this paper, through the analysis of health professional interaction, we examine the properties and conditions under which professional jurisdiction was negotiated and accomplished in day-to-day ICU practice. We discuss how staff seniority influenced the nature of professional interaction and how jurisdictional boundaries were reproduced and reconfigured under conditions of routine and urgent work. Consequently, we question theorisation that treats individual professions as homogenous groups and overlooks fluctuation in the flow and intensity of work; and conclude that in ICU, urgency and seniority have a part to play in shaping jurisdictional boundaries at the level of day-to-day practice. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. 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.

  4. 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.

  5. Accounting for abortion: Accomplishing transnational reproductive governance through post-abortion care in Senegal.

    Science.gov (United States)

    Suh, Siri

    2017-03-13

    Reproductive governance operates through calculating demographic statistics that offer selective truths about reproductive practices, bodies, and subjectivities. Post-abortion care, a global reproductive health intervention, represents a transnational reproductive regime that establishes motherhood as women's primary legitimate reproductive status. Drawing on ethnographic fieldwork conducted in Senegal between 2010 and 2011, I illustrate how post-abortion care accomplishes reproductive governance in a context where abortion is prohibited altogether and the US is the primary bilateral donor of population aid. Reproductive governance unfolds in hospital gynecological wards and the national health information system through the mobilization and interpretation of post-abortion care data. Although health workers search women's bodies and behavior for signs of illegal abortion, they minimize police intervention in the hospital by classifying most post-abortion care cases as miscarriage. Health authorities deploy this account of post-abortion care to align the intervention with national and global maternal health policies that valorize motherhood. Although post-abortion care offers life-saving care to women with complications of illegal abortion, it institutionalizes abortion stigma by scrutinizing women's bodies and masking induced abortion within and beyond the hospital. Post-abortion care reinforces reproductive inequities by withholding safe, affordable obstetric care from women until after they have resorted to unsafe abortion.

  6. Program accomplishments and future prospects for low-temperature geothermal resource assessment in New Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Icerman, L.; Ruscetta, C.A. (ed.)

    1982-07-01

    An important component of the State-coupled program has been basic studies in specific regions of New Mexico, including areas adjacent to the cities of Albuquerque, Las Cruces, Socorro, and Truth or Consequences. Considerable geological, hydrological, electrical resistivity, gravity, magnetic, seismic, water analysis, and subsurface temperature data have been compiled and analyzed for these locations. During the four-year research program, a total of 25 tasks have been undertaken. Eleven of these tasks were focused toward collecting and compiling statewide data, six were regional studies covering more than one county, and eight were research projects directed primarily toward data collection near specific cities or known resource areas. Two of these latter studies contributed significantly to the confirmation of the Las Alturas geothermal anomaly east of Las Cruces. A brief summary of the program accomplishments by task is presented. The resource assessment programs in New Mexico have been very successful in (1) delineating low-temperature geothermal resources throughout New Mexico on statewide, regional, and area-specific scales; (2) developing a strong community of in-state geothermal energy research and development professionals and practitioners; and (3) elevating the level of awareness of geothermal energy potential among commerce, industry, and the general public. Future prospects for the state are presented.

  7. Seroprevalence of viral and bacterial diseases among the bovines in Himachal Pradesh, India

    Directory of Open Access Journals (Sweden)

    Shailja Katoch

    2017-12-01

    Full Text Available Aim: The study was designed to measure the seroprevalence of viral and bacterial diseases: Infectious bovine rhinotracheitis, bovine viral diarrhea, bovine leukemia, bovine parainfluenza, bovine respiratory syncytial disease, brucellosis, and paratuberculosis among bovine of Himachal Pradesh during the year 2013-2015. Materials and Methods: The serum samples were collected from seven districts of state, namely, Bilaspur, Kangra, Kinnaur, Lahul and Spiti, Mandi, Sirmour, and Solan. The samples were screened using indirect ELISA kits to measure the seroprevalence of viral and bacterial diseases. Results: The overall seroprevalence of infectious bovine rhinotracheitis was 24.24%, bovine viral diarrhea 1.52%, bovine leukemia 9.09%, bovine parainfluenza 57.58%, bovine respiratory syncytial disease 50%, brucellosis 19.69%, and paratuberculosis 9.09% in Himachal Pradesh. The seroprevalence of bovine rhinotracheitis, bovine leukemia, bovine parainfluenza, bovine respiratory syncytial disease, and paratuberculosis in the state varied significantly (p0.01. Multiple seropositivity has been observed in this study. Bovine parainfluenza virus 3 was observed commonly in mixed infection with almost all viruses and bacteria under study. Conclusion: The viral and bacterial diseases are prevalent in the seven districts of Himachal Pradesh investigated in the study. Therefore, appropriate management practices and routine vaccination programs should be adopted to reduce the prevalence of these diseases.

  8. Birth-death prior on phylogeny and speed dating

    Directory of Open Access Journals (Sweden)

    Sennblad Bengt

    2008-03-01

    Full Text Available Abstract Background In recent years there has been a trend of leaving the strict molecular clock in order to infer dating of speciations and other evolutionary events. Explicit modeling of substitution rates and divergence times makes formulation of informative prior distributions for branch lengths possible. Models with birth-death priors on tree branching and auto-correlated or iid substitution rates among lineages have been proposed, enabling simultaneous inference of substitution rates and divergence times. This problem has, however, mainly been analysed in the Markov chain Monte Carlo (MCMC framework, an approach requiring computation times of hours or days when applied to large phylogenies. Results We demonstrate that a hill-climbing maximum a posteriori (MAP adaptation of the MCMC scheme results in considerable gain in computational efficiency. We demonstrate also that a novel dynamic programming (DP algorithm for branch length factorization, useful both in the hill-climbing and in the MCMC setting, further reduces computation time. For the problem of inferring rates and times parameters on a fixed tree, we perform simulations, comparisons between hill-climbing and MCMC on a plant rbcL gene dataset, and dating analysis on an animal mtDNA dataset, showing that our methodology enables efficient, highly accurate analysis of very large trees. Datasets requiring a computation time of several days with MCMC can with our MAP algorithm be accurately analysed in less than a minute. From the results of our example analyses, we conclude that our methodology generally avoids getting trapped early in local optima. For the cases where this nevertheless can be a problem, for instance when we in addition to the parameters also infer the tree topology, we show that the problem can be evaded by using a simulated-annealing like (SAL method in which we favour tree swaps early in the inference while biasing our focus towards rate and time parameter changes

  9. Applying unmixing to gene expression data for tumor phylogeny inference

    Directory of Open Access Journals (Sweden)

    Shackney Stanley E

    2010-01-01

    methods provide a way to make use of both intra-tumor heterogeneity and large probe sets for tumor phylogeny inference, establishing a new avenue towards the construction of detailed, accurate portraits of common tumor sub-types and the mechanisms by which they develop. These reconstructions are likely to have future value in discovering and diagnosing novel cancer sub-types and in identifying targets for therapeutic development.

  10. Phylogeny of Myzostomida (Annelida) and their relationships with echinoderm hosts.

    Science.gov (United States)

    Summers, Mindi M; Rouse, Greg W

    2014-08-28

    Myzostomids are marine annelids, nearly all of which live symbiotically on or inside echinoderms, chiefly crinoids, and to a lesser extent asteroids and ophiuroids. These symbionts possess a variety of adult body plans and lifestyles. Most described species live freely on the exterior of their hosts as adults (though starting life on the host inside cysts), while other taxa permanently reside in galls, cysts, or within the host's mouth, digestive system, coelom, or gonads. Myzostomid lifestyles range from stealing incoming food from the host's food grooves to consuming the host's tissue directly. Previous molecular studies of myzostomids have had limited sampling with respect to assessing the evolutionary relationships within the group; therefore molecular data from 75 myzostomid taxa were analyzed using maximum likelihood and maximum parsimony methods. To compare relationships of myzostomids with their hosts, a phylogeny was inferred for 53 hosts and a tanglegram constructed with 88 associations. Gall- and some cyst-dwellers were recovered as a clade, while cyst-to-free-living forms were found as a grade including two clades of internal host-eaters (one infecting crinoids and the other asteroids and ophiuroids), mouth/digestive system inhabitants, and other cyst-dwellers. Clades of myzostomids were recovered that associated with asteroids, ophiuroids, and stalked or feather star crinoids. Co-phylogenetic analyses rejected a null-hypothesis of random associations at the global level, but not for individual associations. Event-based analyses relied most upon host-switching and duplication events to reconcile the association history. Hypotheses were revised concerning the systematics and evolution of Myzostomida, as well their relationships to their hosts. We found two or three transitions between food-stealing and host-eating. Taxa that dwell within the mouth or digestive system and some cyst forms are arguably derived from cyst-to-free-living ancestors

  11. Bovine-associated mucoprotein: de novo synthesis by nonmammary tissues.

    Science.gov (United States)

    Pringnitz, D J; Butler, J E

    1985-08-01

    Bovine tissues were cultured in vitro in the presence of carbon-14 amino acids and tritiated hexosamine to examine the de novo synthesis of the milk fat globule glycoprotein bovine-associated mucoprotein, by selected tissues. Among tissues examined, the relative synthesis of bovine-associated mucoprotein was highest in mammary tissue. The de novo synthesized bovine-associated mucoprotein in mammary and lacrimal gland cultures when examined for incorporation of carbon-14, had similar sedimentation profiles in sucrose density gradients and incorporated the same relative amount of carbohydrate. The bovine-associated mucoprotein synthesized by lung and spleen cultures sedimented in similar fashion to mammary gland bovine-associated mucoprotein when incorporation of carbon-14 was used as the marker, but it displayed greater heterogeneity when evaluated for tritium incorporation. Bovine-associated mucoprotein in the lung and spleen incorporated relatively less carbohydrate than that synthesized by mammary tissue. These findings support the concept of intertissue heterogeneity, which had been suggested by previous studies.

  12. Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of genetic marker alleles associated with a trait indicative of fertility of the bovine subject and/or off-spring

    DEFF Research Database (Denmark)

    2009-01-01

    NOVELTY - Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of two or more genetic marker alleles that are associated with a trait indicative of fertility of the bovine subject and/or off-spring. USE - The methods are useful...... for determining fertility in a bovine subject; and selecting bovine subjects for breeding purposes (all claimed). DETAILED DESCRIPTION - Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of two or more genetic marker alleles...... that are associated with a trait indicative of fertility of the bovine subject and/or off-spring, where the two or more genetic marker alleles are single nucleotide polymorphisms selected from Hapmap60827-rs29019866, ARS-BFGL-NGS-40979, Hapmap47854-BTA-119090, ARS-BFGL-NGS-114679, Hapmap43841-BTA-34601, Hapmap43407...

  13. 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.

  14. Determining bovine viral diarrhea and infectious bovine rhinotracheitis infections in dairy cattle using precolostral blood.

    Science.gov (United States)

    Baillargeon, Paul; Arango-Sabogal, Juan C; Wellemans, Vincent; Fecteau, Gilles

    2017-04-01

    The objective of this study was to determine if precolostral blood samples are useful to detect apparent fetal infections with bovine viral diarrhea (BVD) and infectious bovine rhinotracheitis (IBR) viruses. A convenience sample of 317 sera from 50 Canadian herds was used in the study. Antibody level was measured using 2 commercial IBR and BVD ELISA kits. Precolostral status of sera was confirmed on 304 samples using serum gamma-glutamyl transferase activity. Postcolostral serum samples yielded a higher proportion of positive results to IBR (OR = 86; 95% CI: 17.8 to 415.7) and BVD (OR = 199.3; 95% CI: 41.7 to 952.3) than did precolostral samples. All positive precolostral serum samples (n = 7 of 304) originated from calves born to vaccinated cows. Postcolostral positive serum samples (n = 11 of 13) originated mostly (60%) from calves born to non-vaccinated cows. Precolostral serum sampling can detect apparent fetal infections in a herd.

  15. [In vitro study of the interactions between bovine herpesvirus 4 and the bovine host cells].

    Science.gov (United States)

    Vanderplasschen, A

    1999-01-01

    This work was devoted to the study of the interactions between bovine herpesvirus 4 (BHV-4) and bovine cells in vitro. It led to the discovery of two interesting properties of BVH-4 replication cycle: first, the cellular receptor heparan sulfate was proven to mediate BVH-4 binding to target cells. This is the first description of the implication of heparan sulfate in the binding process of a gammaherpesvirus. Second, using synchronised cells, the replication of BVH-4 DNA was proven to be dependent on the S phase of the cell cycle. This dependence could explain some properties of BVH-4 infection in vitro and could play an important role in the biology of the infection in vivo. Finally, in order to produce monoclonal antibodies against BVH-4 IE1 and IE2 proteins, the genes coding for these proteins were cloned and expressed in prokaryotic cells.

  16. Prototheca zopfii isolated from bovine mastitis induced oxidative stress and apoptosis in bovine mammary epithelial cells.

    Science.gov (United States)

    Shahid, Muhammad; Gao, Jian; Zhou, Yanan; Liu, Gang; Ali, Tariq; Deng, Youtian; Sabir, Naveed; Su, Jingliang; Han, Bo

    2017-05-09

    Bovine protothecal mastitis results in considerable economic losses worldwide. However, Prototheca zopfii induced morphological alterations and oxidative stress in bovine mammary epithelial cells (bMECs) is not comprehensively studied yet. Therefore, the aim of this current study was to investigate the P. zopfii induced pathomorphological changes, oxidative stress and apoptosis in bMECs. Oxidative stress was assessed by evaluating catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), malondialdehyde (MDA) contents and lactate dehydrogenase (LDH) activity, while ROS generation and apoptosis was measured by confocal laser scanning microscopy. The results revealed that infection of P. zopfii genotype II (GTII) significantly changed bMECs morphology, increased apoptotic rate and MDA contents at 12 h (p effects in bMECs, and the findings of this study concluded that GTII induced apoptosis and oxidative stress in bMECs via the imbalance of oxidant and antioxidant defenses as well as the production of intracellular ROS.

  17. 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

  18. Detection of bovine herpesvirus type 4 antibodies and bovine lymphotropic herpesvirus in New Zealand dairy cows.

    Science.gov (United States)

    de Boer, M W; Zheng, T; Buddle, B M; McDougall, S

    2014-11-01

    To detect the presence of bovine herpesvirus (BoHV) type 4 in New Zealand dairy cows with clinical metritis. Serum samples taken from 92 dairy cows with clinical metritis, each from a different farm, were tested for the presence of antibodies against BoHV-4 using a commercially available, indirect ELISA. Peripheral blood mononuclear cells (PBMC) were collected from 10 BoHV-4 seropositive cows, and PBMC were examined by a pan-herpesvirus nested PCR to detect herpesvirus. PCR products were sequenced directly and a proportion of the PCR products were cloned and sequenced to identify the virus present. Antibodies to BoHV-4 were detected in 23/92 (25%) serum samples. The pan-herpesvirus PCR was positive in 8/10 PBMC samples. Cloning and sequencing identified that all of the eight PCR-positive PBMC contained bovine lymphotropic herpesvirus (BLHV); no BoHV-4 DNA was detected. This study reports the finding of the presence of apparent antibodies to BoHV-4, and BLHV DNA in New Zealand dairy cows affected by metritis. Bovine herpesvirus type 4 and BLHV are reported to have the potential to cause reproduction failure in cows. This is the first report of apparent BoHV-4 antibodies, and BLHV in New Zealand. The importance and epidemiology of these viruses in cattle in New Zealand requires further investigation.

  19. Bovine papillomavirus DNA in milk, blood, urine, semen, and spermatozoa of bovine papillomavirus-infected animals.

    Science.gov (United States)

    Lindsey, C L; Almeida, M E; Vicari, C F; Carvalho, C; Yaguiu, A; Freitas, A C; Beçak, W; Stocco, R C

    2009-01-01

    Papillomavirus infection in bovines is associated with cutaneous papillomatosis on the hide, udders and other epithelial tissues, as well as in oral respiratory, alimentary and urinary tract mucosa. Bovine papillomavirus (BPV) is also considered the etiological agent of esophageal tumors and the malignant bladder tumors that characterize the clinical condition associated with chronic enzootic hematuria. After infective viral DNA was found in cattle blood and BPV1, 2 and 4 DNA in cattle reproductive and embryonic tissues, we looked for and found BPV DNA in blood, milk, urine, seminal fluid, and spermatozoa of BPV-infected animals. Peripheral blood lymphocyte cultures from BPV-infected animals had high rates of chromosome aberrations, including radial rearrangements that signal oncogenic potential and viral interaction with telomeric regions. The finding of BPV DNA in body fluids and tissues other than the epithelium demonstrates co-infection of other tissues or cell types by papillomavirus and shows the potential role of lymphocytes, seminal fluid and spermatozoa in BPV transmission. Our findings reinforce a peremptory need for prophylactic and therapeutic instruments to curtail this disease in bovine livestock.

  20. Combining multiple autosomal introns for studying shallow phylogeny and taxonomy of Laurasiatherian mammals: Application to the tribe Bovini (Cetartiodactyla, Bovidae).

    Science.gov (United States)

    Hassanin, Alexandre; An, Junghwa; Ropiquet, Anne; Nguyen, Trung Thanh; Couloux, Arnaud

    2013-03-01

    Mitochondrial sequences are widely used for species identification and for studying phylogenetic relationships among closely related species or populations of the same species. However, many studies of mammals have shown that the maternal history of the mitochondrial genome can be discordant with the true evolutionary history of the taxa. In such cases, the analyses of multiple nuclear genes can be more powerful for deciphering interspecific relationships. Here, we designed primers for amplifying 13 new exon-primed intron-crossing (EPIC) autosomal loci for studying shallow phylogeny and taxonomy of Laurasiatherian mammals. Three criteria were used for the selection of the markers: gene orthology, a PCR product length between 600 and 1200 nucleotides, and different chromosomal locations in the bovine genome. Positive PCRs were obtained from different species representing the orders Carnivora, Cetartiodactyla, Chiroptera, Perissodactyla and Pholidota. The newly developed markers were analyzed in a phylogenetic study of the tribe Bovini (the group containing domestic and wild cattle, bison, yak, African buffalo, Asian buffalo, and saola) based on 17 taxa and 18 nuclear genes, representing a total alignment of 13,095 nucleotides. The phylogenetic results were compared to those obtained from analyses of the complete mitochondrial genome and Y chromosomal genes. Our analyses support a basal divergence of the saola (Pseudoryx) and a sister-group relationship between yak and bison. These results contrast with recent molecular studies but are in better agreement with morphology. The comparison of pairwise nucleotide distances shows that our nuDNA dataset provides a good signal for identifying taxonomic levels, such as species, genera, subtribes, tribes and subfamilies, whereas the mtDNA genome fails because of mtDNA introgression and higher levels of homoplasy. Accordingly, we conclude that the genus Bison should be regarded as a synonym of Bos, with the European bison

  1. 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.

  2. U.S. Spacesuit Knowledge Capture Accomplishments in Fiscal Years 2012 and 2013

    Science.gov (United States)

    Chullen, Cinda; Oliva, Vladenka R.

    2014-01-01

    The NASA U.S. Spacesuit Knowledge Capture (KC) program has existed since the beginning of 2008. The program was designed to augment engineers and other technical team members with historical spacesuit information to add to their understanding of the spacesuit, its evolution, its limitations, and its capabilities. Over 40 seminars have captured spacesuit history and knowledge over the last six years of the program's existence. Subject matter experts have provided lectures and some were interviewed to help bring the spacesuit to life so that lessons learned will never be lost. As well, the program concentrated in reaching out to the public and industry by making the recorded events part of the public domain through the NASA technical library through YouTube media. The U.S. Spacesuit KC topics have included lessons learned from some of the most prominent spacesuit experts and spacesuit users including current and former astronauts. The events have enriched the spacesuit legacy knowledge from Gemini, Apollo, Skylab, Space Shuttle and International Space Station Programs. As well, expert engineers and scientists have shared their challenges and successes to be remembered. Based on evidence by the thousands of people who have viewed the recordings online, the last few years have been some of the most successful years of the KC program's life with numerous digital recordings and public releases. This paper reviews the events accomplished and archived over Fiscal Years 2012 and 2013 and highlights a few of the most memorable ones. This paper also communicates ways to access the events that are available internally on the NASA domain as well as those released on the public domain.

  3. NASA's In-Situ Resource Utilization Project: Current Accomplishments and Exciting Future Plans

    Science.gov (United States)

    Larson, William E.; Sanders, Gerald B.; Sacksteder, Kurt R.

    2010-01-01

    The utilization of Space resources has been identified in publications for over 40 years for its potential as a "game changing" technology for the human exploration of Space. It is called "game changing" because of the mass leverage possible when local resources at the exploration destination arc used to reduce or even eliminate resources that are brought from the Earth. NASA, under the Exploration Technology Development Program has made significant investments in the development of Space resource utilization technologies as a part of the In-Situ Resource Utilization (ISRU) project. Over the last four years, the ISRU project has taken what was essentially an academic topic with lots of experimentation but little engineering and produced near-full-scale systems that have been demonstrated. In 2008 & again in early 2010, systems that could produce oxygen from lunar soils (or their terrestrial analogs) were tested at a lunar analog site on a volcano in Hawaii. These demonstrations included collaborations with International Partners that made significant contributions to the tests. The proposed federal budget for Fiscal Year 2011 encourages the continued development and demonstration of ISRU. However it goes beyond what the project is currently doing and directs that the scope of the project be expanded to cover destinations throughout the inner solar system with the potential for night demonstrations. This paper will briefly cover the past accomplishments of the ISRU project then move to a di scussion of the plans for the project's future as NASA moves to explore a new paradigm for Space Exploration that includes orbital fuel depots and even refueling on other planetary bodies in the solar system.

  4. 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 changes in morphology suggest the existence of different aggregate species. Although beta-sheet content increases from 0 to ca. 40% upon aggregation, the aggregates retain significant amounts of alpha-helix structure, and lack a protease-resistant core. Thus BSA is able to form well-ordered beta...

  5. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. 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...

  7. 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.

  8. Paternally inherited markers in bovine hybrid populations.

    Science.gov (United States)

    Verkaar, E L C; Vervaecke, H; Roden, C; Romero Mendoza, L; Barwegen, M W; Susilawati, T; Nijman, I J; Lenstra, J A

    2003-12-01

    The genetic integrity of crossfertile bovine- or cattle-like species may be endangered by species hybridization. Previously, amplified fragment length polymorphism, satellite fragment length polymorphism and microsatellite assays have been used to analyze the species composition of nuclear DNA in taurine cattle, zebu, banteng and bison populations, while mitochondrial DNA reveals the origin of the maternal lineages. Here, we describe species-specific markers of the paternally transmitted Y-chromosome for the direct detection of male-mediated introgression. Convenient PCR-restriction fragment length polymorphism and competitive PCR assays are shown to differentiate the Y-chromosomes of taurine cattle, American bison and European bison, and to detect the banteng origin of Indonesian Madura and Bali cattle bulls.

  9. Field Surgical Intervention of Bovine Actinomycosis

    Directory of Open Access Journals (Sweden)

    U. Farooq*, A. Qayyum, H. A. Samad, H. R. Chaudhry and N. Ahmad1

    2010-10-01

    Full Text Available Actinomycosis, or lumpy jaw, is an important cause of economic losses in livestock because of its widespread occurrence and poor response to the routine clinical treatment. The present study describes a typical case of bovine actinomycosis in a seven-month pregnant Sahiwal heifer with a hard swelling on the middle of the maxilla bone at the level of the central molar teeth. Tentative diagnosis was made through clinical signs. After maturation of the swelling, the area was incised under local anesthesia and debridement of the wound was achieved by sharp surgical debridement and mechanical debridement. Pus, having the appearance of sulphur granules, was completely removed from the excised cavity, which was closed by applying mattress sutures. Adjunct therapy of broad-spectrum antibiotic was administered intramuscularly for five days as a post-operative measure. Catamnesis revealed that the healing was complete in 15 days with no recurrence and untoward consequences.

  10. Spider mite (Acari : Tetranychidae) mitochondrial COI phylogeny reviewed: host plant relationships, phylogeography, reproductive parasites and barcoding

    NARCIS (Netherlands)

    Ros, V.I.D.; Breeuwer, J.A.J.

    2007-01-01

    The past 15 years have witnessed a number of molecular studies that aimed to resolve issues of species delineation and phylogeny of mites in the family Tetranychidae. The central part of the mitochondrial COI region has frequently been used for investigating intra- and interspecific variation. All

  11. Spider mite (Acari: Tetranychidae) mitochondrial COI phylogeny reviewed: host plant relationships, phylogeography, reproductive parasites and barcoding

    NARCIS (Netherlands)

    Ros, V.I.D.; Breeuwer, J.A.J.

    2007-01-01

    The past 15 years have witnessed a number of molecular studies that aimed to resolve issues of species delineation and phylogeny of mites in the family Tetranychidae. The central part of the mitochondrial COI region has frequently been used for investigating intra- and interspecific variation. All

  12. Phylogeny and Biogeography of Bees of the Tribe Osmiini (Hymenoptera: Megachilidae)

    Science.gov (United States)

    The Osmiini (Megachilidae) constitute a taxonomically and biologically diverse tribe of bees. To resolve their generic and suprageneric relationships, we inferred a phylogeny based on three nuclear genes (Elongation factor 1-alpha, LW-rhodopsin and CAD) applying both parsimony and Bayesian methods. ...

  13. Phylogeny and biogeography of North-American wild rice (Zizania L.Poaceae)

    Science.gov (United States)

    The wild-rice genus Zizania includes four species disjunctly distributed in eastern Asia and North America, with three species (Z. aquatica, Z. palustris, and Z. texana) in North America and one (Z. latifolia) in eastern Asia. The phylogeny and biogeography of Zizania were explored using sequences o...

  14. 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)

  15. Diversity and phylogeny of Baltic Sea picocyanobacteria inferred from their ITS and phycobiliprotein operons

    NARCIS (Netherlands)

    Haverkamp, T.H.A.; Acinas, S.G.; Doeleman, M.W.; Stomp, M.; Huisman, J.; Stal, L.J.

    2008-01-01

    Picocyanobacteria of the genus Synechococcus span a range of different colours, from red strains rich in phycoerythrin (PE) to green strains rich in phycocyanin (PC). Here, we show that coexistence of red and green picocyanobacteria in the Baltic Sea is widespread. The diversity and phylogeny of red

  16. Resolution of ray-finned fish phylogeny and timing of diversification.

    Science.gov (United States)

    Near, Thomas J; Eytan, Ron I; Dornburg, Alex; Kuhn, Kristen L; Moore, Jon A; Davis, Matthew P; Wainwright, Peter C; Friedman, Matt; Smith, W Leo

    2012-08-21

    Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

  17. Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis)

    Czech Academy of Sciences Publication Activity Database

    Phalen, D. N.; Hall, J.; Ganesh, G.; Hartigan, Ashlie; Smith, C.; De Jong, C.; Field, H.; Rose, K.

    2017-01-01

    Roč. 98, č. 2 (2017), s. 428-437 ISSN 0022-2372 Institutional support: RVO:60077344 Keywords : diversity * flying fox * mitochondrial DNA * phylogeny * Pteropus melanotus natalis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.630, year: 2016

  18. High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses

    NARCIS (Netherlands)

    Barry, A.F.; Durães-Carvalho, R.; Oliveira-Filho, Edmilson F.; Alfieri, A.; Poel, Van der W.H.M.

    2017-01-01

    The evolution, epidemiology and zoonotic aspects of Sapoviruses (SaV) are still not well explored. In this study, we applied high-resolution phylogeny to investigate the epidemiological and zoonotic origins as well as taxonomic classification of animal and human SaV. Bayesian framework analyses

  19. Incongruence between nuclear and chloroplast DNA phylogenies in pedicularis section Cyathophora (Orobanchaceae.

    Directory of Open Access Journals (Sweden)

    Wen-Bin Yu

    Full Text Available Pedicularis section Cyathophora is a monophyletic group characterized by perfoliate leaf and/or bract bases at each node. This section comprises four series, corresponding to four general corolla types of Pedicularis, i.e. toothless, toothed, beaked and long-tubed corollas. In this study, we aim to reconstruct a comprehensive phylogeny of section Cyathophora, and compare phylogenetic incongruence between nuclear and chloroplast datasets. Sixty-seven accessions belonging to section Cyathophora and 9 species for other Pedicularis were sampled, and one nuclear gene (nrITS and four chloroplast genes (matK, rbcL, trnH-psbA and trnL-F were sequenced. Phylogenetic analyses show that the topologies and networks inferred from nrITS and the concatenated chloroplast datasets were incongruent, and the nrITS phylogenies and network agreed with the morphology-based taxonomy to some degree. The chloroplast genome of two Sichuan samples of P. cyathophylloides (E4 and E5 may show introgression from an ancestor of P. cyathophylla. Neither the nrITS dataset nor the concatenated chloroplast dataset were able to adequately resolve relationships among species in the series Reges; this is most likely due to incomplete lineage sorting and/or introgression/hybridization. The nrITS phylogeny indicates the beakless (toothed and toothless and beaked galeas may have evolved independently within section Cyathophora, and the chloroplast phylogeny reveals that the long corolla tube with beaked galea is derived from the short one.

  20. Morphology, phylogeny and evolution of the superfamily Plectoidea Örley, 1880 (Nematoda: Plectida

    NARCIS (Netherlands)

    Holovachov, O.V.

    2004-01-01

    The phylogeny and classification of the superfamily Plectoidea Örley, 1880 is revised on the basis of published and updated morphological data for 35 ingroup and 2 outgroup species. The following features are here considered to support the monophyletic origin of the superfamily: 1) stegostom

  1. Relationships of Reproductive Traits with the Phylogeny of the African Noctuid Stem Borers

    Directory of Open Access Journals (Sweden)

    Paul-André Calatayud

    2016-01-01

    Full Text Available The display of the reproductive behavior in most noctuid Lepidoptera follows a diel periodicity and is limited to a precise period of either the day or the night. These behavioral traits and the sex pheromone chemistry can be species specific and thus might be linked to the phylogeny. The objective of this study was to test the relationship of these reproductive traits with phylogeny. The study was undertaken using eight closely related species of noctuid stem borers, which are easy to rear under artificial conditions, namely, Busseola fusca, B. nairobica, B . sp. nr. segeta, Manga melanodonta, M . sp. nr. nubifera, Pirateolea piscator, Sesamia calamistis , and S. nonagrioides . For each species, the adult emergence period, the mating time, and the oviposition period were estimated, referred as biological traits. The components of the sex pheromones emitted by the females of each species were also analyzed by gas chromatography–mass spectrometry. Among the biological traits measured, only those linked to the oviposition pattern (timing and egg loads per night were significantly correlated with the phylogeny of these species. For the sex pheromone components, among the 13 components identified in all species, only four, namely, Z9-tetradecenyl acetate (Z9-TDA, Z11-TDA, E11-TDA, and Z11-hexadecenyl acetate (Z11-HDA, showed the highest significant correlations with the phylogeny. These results suggest that among the different reproductive traits evaluated, only few are phylogenetically constrained. Their involvement in the reinforcement of ecological speciation in noctuid stem borers is discussed.

  2. Revisiting the phylogeny of Ocellularieae, the second largest tribe within Graphidaceae (lichenized Ascomycota: Ostropales)

    Science.gov (United States)

    Ekaphan Kraichak; Sittiporn Parnmen; Robert Lücking; Eimy Rivas Plata; Andre Aptroot; Marcela E.S. Caceres; Damien Ertz; Armin Mangold; Joel A. Mercado-Diaz; Khwanruan Papong; Dries Van der Broeck; Gothamie Weerakoon; H. Thorsten. Lumbsch; NO-VALUE

    2014-01-01

    We present an updated 3-locus molecular phylogeny of tribe Ocellularieae, the second largest tribe within subfamily Graphidoideae in the Graphidaceae. Adding 165 newly generated sequences from the mitochondrial small subunit rDNA (mtSSU), the nuclear large subunit rDNA (nuLSU), and the second largest subunit of the DNA-directed RNA polymerase II (RPB2), we currently...

  3. Heterochrony, generic distinction and phylogeny in the family Hydractiniidae (Hydrozoa: Cnidaria)

    NARCIS (Netherlands)

    Boero, F.; Bouillon, J.; Piraino, S.

    1998-01-01

    The taxonomy of Hydractinia, Stylactaria and Podocoryna is discussed and the three genera are merged into Hydractinia since their diagnostic characters are liable to lead to polyphyly and paraphyly, due to repeated episodes of medusa reduction via heterochrony (paedomorphosis). The phylogeny of the

  4. Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

    Science.gov (United States)

    Swain, Timothy D

    2018-01-01

    The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Optics and phylogeny: is there an insight? The evolution of superposition eyes in the Decapoda (Crustacea)

    NARCIS (Netherlands)

    Gaten, Edward

    1998-01-01

    This paper addresses the use of eye structure and optics in the construction of crustacean phylogenies and presents an hypothesis for the evolution of superposition eyes in the Decapoda, based on the distribution of eye types in extant decapod families. It is suggested that reflecting superposition

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

    DEFF Research Database (Denmark)

    Katzenstein, T L; 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...

  7. PHY∙FI: fast and easy online creation and manipulation of phylogeny color figures

    DEFF Research Database (Denmark)

    Fredslund, Jakob

    2006-01-01

    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...

  8. Artificial neural networks can learn to estimate extinction rates from molecular phylogenies

    NARCIS (Netherlands)

    Bokma, Folmer

    2006-01-01

    Molecular phylogenies typically consist of only extant species, yet they allow inference of past rates of extinction, because. recently originated species are less likely to be extinct than ancient species. Despite the simple structure of the assumed underlying speciation-extinction process,

  9. Molecular evolution and phylogeny of the Drosophila saltans species group inferred from the Xdh gene.

    Science.gov (United States)

    Rodríguez-Trelles, F; Tarrío, R; Ayala, F J

    1999-10-01

    The Drosophila saltans group of the subgenus Sophophora consists of five species subgroups whose phylogenetic relationships are poorly known. We have analyzed 2085 coding nucleotides from the xanthine dehydrogenase (Xdh) gene in six species, at least one from each subgroup. We follow a model-based maximum likelihood framework. We first model the substitution process using a tree topology that is approximately accurate. Then we evaluate several candidate tree topologies using a working model of nucleotide substitution. We found that a minimally realistic description of the substitution process along the Xdh region should allow two transition and four transversion rate parameters and different fixed rates for codon positions, which are distributed statistically according to different gamma distributions. The phylogeny obtained using this description differs in significant respects from a phylogeny based on anatomical criteria. We have also analyzed data from five additional (three nuclear and two mitochondrial) gene regions. In our analysis, these relatively short DNA sequences, either separately or jointly, fail to discriminate statistically among alternative phylogenies. When the data for these five gene regions are combined with the Xdh sequences, the strong phylogenetic signal emerging from Xdh becomes somewhat diluted rather than reinforced. The phylogeny of the species and biogeographical considerations suggest that the D. saltans group originated in the tropics of the New World, similarly as the closely related D. willistoni group. Copyright 1999 Academic Press.

  10. 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

  11. Nonenzymatic glycosylation of bovine myelin basic protein

    Energy Technology Data Exchange (ETDEWEB)

    Hitz, J.B.

    1987-01-01

    In the CNS myelin sheath the nonenzymatic glycosylation reaction (at the early stage of the Amadori product) occurs only with the myelin basic protein and not with the other myelin proteins. This was observed in isolated bovine myelin by in vitro incubation with (/sup 14/C)-galactose and (/sup 14/C)-glucose. The respective in-vitro incorporation rates for purified bovine myelin basic protein with D-galactose, D-glucose and D-mannose were 7.2, 2.4 and 2.4 mmoles/mole myelin basic protein per day at 37/sup 0/C. A more rapid, HPLC method was devised and characterized to specifically analyze for the Amadori product. The HPLC method was correlated to the (/sup 14/C)-sugar incorporation method for myelin basic protein under a set of standard reaction conditions using (/sup 14/C)-glucose and (/sup 14/C)-mannose with HPLC values at 1/6 and 1/5 of the (/sup 14/C)-sugar incorporation method. A novel myelin basic protein purification step has been developed that yields a relativity proteolytic free preparation that is easy to work with, being totally soluble at a neutral pH. Nine new spots appear for a trypsinized glycosylated MBP in the paper peptide map of which eight correspond to positions of the (/sup 3/H)-labeled Amadori product in affinity isolated peptides. These studies provide a general characterization of and a structural basis for investigations on nonenzymatically glycosylated MBP as well as identifying MBP as the only nonenzymatically glycosylated protein in the CNS myelin sheath which may accumulate during aging, diabetes, and demyelinating diseases in general.

  12. 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

  13. The proteomic advantage: label-free quantification of proteins expressed in bovine milk during experimentally induced coliform mastitis.

    Science.gov (United States)

    Boehmer, Jamie L; DeGrasse, Jeffrey A; McFarland, Melinda A; Tall, Elizabeth A; Shefcheck, Kevin J; Ward, Jeffrey L; Bannerman, Douglas D

    2010-12-15

    Coliform mastitis remains a primary focus of dairy cattle disease research due in part to the lack of efficacious treatment options for the deleterious side effects of exposure to LPS, including profound intra-mammary inflammation. To facilitate new veterinary drug approvals, reliable biomarkers are needed to evaluate the efficacy of adjunctive therapies for the treatment of inflammation associated with coliform mastitis. Most attempts to characterize the host response to LPS, however, have been accomplished using ELISAs. Because a relatively limited number of bovine-specific antibodies are commercially available, reliance on antibodies can be very limiting for biomarker discovery. Conversely, proteomic approaches boast the capability to analyze an unlimited number of protein targets in a single experiment, independent of antibody availability. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), a widely used proteomic strategy for the identification of proteins in complex mixtures, has gained popularity as a means to characterize proteins in various bovine milk fractions, both under normal physiological conditions as well as during clinical mastitis. The biological complexity of bovine milk has, however, precluded the complete annotation of the bovine milk proteome. Conventional approaches to reducing sample complexity, including fractionation and the removal of high abundance proteins, has improved proteome coverage, but the dynamic range of proteins present, and abundance of a relatively small number of proteins, continues to hinder comparative proteomic analyses of bovine milk. Nonetheless, advances in both liquid chromatography and mass spectrometry instrumentation, including nano-flow liquid chromatography (nano-LC), nano-spray ionization, and faster scanning speeds and ionization efficiency of mass spectrometers, have improved analyses of complex samples. In the current paper, we review the proteomic approaches used to conduct comparative

  14. 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.

  15. 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.

    2016-01-01

    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

  16. The Ongoing Accomplishment of the Mobile Telecommunication: An Ethnomethodological Study of “Talking on a Mobile Phone”

    Directory of Open Access Journals (Sweden)

    Chia-Rong Tsao

    2015-07-01

    Full Text Available This paper attempts to explore the practices of “talking on a mobile phone” through the ethnomethodological approach. Instead of paying attention to the influences of the prevalence of mobile phones, this paper focuses on the ongoing accomplishment of the practices of cellphone-using. This paper contends that the mobile phone users accomplish the practices of “talking on a mobile phone” continuously by methods such as “reading hermeneutically”, “embodying”, “the documentary method of interpretation”, and “accounting reasonably”, etc. Users not only take these methods for granted, but also see but unnoticed what they really do by these cellphone-using practices. The practices identify and reproduce reflexively the structural influences brought by the prevalence of mobile phones while accomplishing the process of “talking on a mobile phone”.

  17. Characterization of angiogenin receptors on bovine brain capillary endothelial cells.

    Science.gov (United States)

    Chamoux, M; Dehouck, M P; Fruchart, J C; Spik, G; Montreuil, J; Cecchelli, R

    1991-04-30

    The mitogenic effect of bovine milk angiogenin was studied on bovine brain capillary and aortic endothelial cells, smooth muscle cells and fibroblasts. The proliferation of only bovine brain capillary endothelial cells was detected at concentrations ranging from 10 to 1,000 ng/ml, with a maximum effect at 100 ng/ml. This mitogenic activity may be correlated with a specific binding of angiogenin which was demonstrated only to bovine brain capillary endothelial cells. [125I]-labeled angiogenin binding was time and concentration dependent and saturable. Scatchard analyses of binding data showed evidence of a single class of binding sites with an apparent dissociation constant of 5.10(-10)M. The molecular mass of the angiogenin receptor (49 kDa) was determined by ligand blotting.

  18. Fraction V of bovine albumin improves the adherence and survival ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-02-04

    2,3. , Y. Yong ... Key words: Adult, neocortex, primary culture, fraction V of bovine albumin. INTRODUCTION. Alzheimer's disease ... models to study development, aging and death (Lesuisse et al., 2002; Akasofu et al., 2006).

  19. 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

  20. Short communication Prevalence and risk factors of bovine mastitis ...

    African Journals Online (AJOL)

    were selected from all volunteer dairy farms in Ambo town of West Shewa Zone of ... economic implication of bovine mastitis derives from the high costs of treat- ... wot et al., 2013) and 95% statistical confidence level at 5% absolute precision.