Sample records for bovin phylogeny accomplishments

  1. Molecular phylogeny of the filaria genus Onchocerca with special emphasis on Afrotropical human and bovine parasites. (United States)

    Krueger, A; Fischer, P; Morales-Hojas, R


    Filarial parasites of the genus Onchocerca are found in a broad spectrum of ungulate hosts. One species, O. volvulus, is a human parasite that can cause severe disease (onchocerciasis or 'river blindness'). The phylogenetic relationships and the bionomics of many of the nearly 30 known species remain dubious. Here, the phylogeny of 11 species representing most major lineages of the genus is investigated by analysing DNA sequences from three mitochondrial genes (ND5, 12S and 16S rRNA) and portions of the intergenic spacer of the nuclear 5s rRNA. Special emphasis is given to a clade containing a yet unassigned specimen from Uganda (O. sp. 'Siisa'), which appears to be intermediate between O. volvulus and O. ochengi. While the latter can be differentiated by the O-150 tandem repeat commonly used for molecular diagnostics, O. volvulus and O. sp.'Siisa' cannot be differentiated by this marker. In addition, a worm specimen from an African bushbuck appears to be closely related to the bovine O. dukei and represents the basal taxon of the human/bovine clade. At the base of the genus, our data suggest O. flexuosa (red deer), O. ramachandrini (warthog) and O. armillata (cow) to be the representatives of ancient lineages. The results provide better insight into the evolution and zoogeography of Onchocerca. They also have epidemiological and taxonomic implications by providing a framework for more accurate molecular diagnosis of filarial larvae in vectors.

  2. CDBG Accomplishment Data (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...

  3. Partners in Accomplished Teaching. (United States)

    National Board for Professional Teaching Standards, Arlington, VA.

    This report describes Partners in Accomplished Teaching, a project of the National Board for Professional Teaching Standards (NBPTS) designed to help increase the number of teachers achieving National Board Certification. It focuses on efforts in St. Paul, Minnesota; Mississippi; North Carolina; and San Antonio, Texas. The St. Paul program is a…

  4. EFRC CMSNF Major Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    D. Hurley; Todd R. Allen


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

  5. NASA space biology accomplishments, 1982 (United States)

    Halstead, T. W.; Pleasant, L. G.


    Summaries of NASA's Space Biology Program projects are provided. The goals, objectives, accomplishments, and future plans of each project are described in this publication as individual technical summaries.

  6. Advanced Fuels Campaign 2012 Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed


    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.

  7. The phylogeny of Arthrotardigrada

    DEFF Research Database (Denmark)

    Hansen, Jesper Guldberg


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

  8. Building a Twig Phylogeny (United States)

    Flinn, Kathryn M.


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


    Energy Technology Data Exchange (ETDEWEB)

    Not Listed


    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.

  10. Research on assessment system of accomplishment

    Institute of Scientific and Technical Information of China (English)

    Fu Zhimin; Li Hanling


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

  11. The shape of mammalian phylogeny

    DEFF Research Database (Denmark)

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


    Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'-points at which net diversification rate has changed-identifying 15...... significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of 'rules'. Third, we simulate...... six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within...

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

    Directory of Open Access Journals (Sweden)

    Suchard Marc A


    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.

  13. Transmutation Fuels Campaign FY-09 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Lori Braase


    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.

  14. Mapping Mutations on Phylogenies

    DEFF Research Database (Denmark)

    Nielsen, Rasmus


    This chapter provides a short review of recent methodologies developed for mapping mutations on phylogenies. Mapping of mutations, or character changes in general, using the maximum parsimony principle has been one of the most powerful tools in phylogenetics, and it has been used in a variety...... of different applications, for example, in the detection of correlated evolution and to identify selection acting on DNA sequences. However, many uses of parsimony mappings have been criticized because they focus on only one of many possible mappings and/or because they do not incorporate statistical...... 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....

  15. 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


    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

  16. Summary of Laurasiatheria (Mammalia) Phylogeny

    Institute of Scientific and Technical Information of China (English)

    Jingyang HU; Yaping ZHANG; Li YU


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

  17. Biomass Program 2007 Accomplishments - Full Report

    Energy Technology Data Exchange (ETDEWEB)



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

  18. Overview of LAMPF and its accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, L.


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

  19. Accomplished Teachers Implementation of Quality Teaching Practices (United States)

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


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

  20. 77 FR 29914 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products (United States)


    ... 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... with regard to bovine spongiform encephalopathy. Comments on the proposed rule were required to......

  1. 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 African...

  2. Advanced Fuels Campaign FY 2011 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed


    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).

  3. Photovoltaics: Electricity from sunlight, FY 1985 accomplishments (United States)


    This summary of FY 1985 accomplishments contains the technical highlights of SERI's program in photovoltaic research and development and a bibliography of technical publications. Also included are several management highlights. Selected accomplishments are categorized according to research tasks identified in the DOE National PV Program's Five-Year Research Plan. The DOE task areas appearing here are Single-Junction Thin Films, High-Efficiency Multijunction Concepts, Innovative Concepts, Flat-Plate Collectors, and System Experiments. Subcontract program categories include amorphous thin films, high-efficiency concepts, polycrystalline thin films, crystalline silicon, and innovative concepts, which are further subdivided into new ideas, the University Participation Program, and photoelectrochemical cells. SERI's internal PV task areas are PV Devices and Measurements, Solid State Research, Insolation Resource Assessment, Advanced PV Systems Research, and solar electric research activities. The bibliography is a compilation of the technical publications resulting from all of SERI's research during FY 1984 and FY 1985. The entries are listed alphabetically by author.

  4. Enhanced surveillance program FY1998 accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Kass, J


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

  5. NASA total quality management 1990 accomplishments report (United States)


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

  6. NASA total quality management 1989 accomplishments report (United States)


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

  7. Basic Energy Sciences: Summary of Accomplishments (United States)


    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.

  8. Sandia technology engineering and science accomplishments

    Energy Technology Data Exchange (ETDEWEB)


    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.

  9. 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)


    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.

  10. Advanced Fuels Campaign FY 2010 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Lori Braase


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

  11. Molecular phylogeny of Arthrotardigrada (Tardigrada). (United States)

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


    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.

  12. [The ACCOMPLISH trial: are results really unexpected?]. (United States)

    Waeber, Bernard; Feihl, François


    The ACCOMPLISH trial consists of a randomized morbidity-mortality study involving 11506 hypertensive patients at high cardiovascular risk, randomly allocated to a fixed dose combination containing an angiotensin converting enzyme inhibitor (B, benazepril) and either a calcium antagonist (A, amlodipine) or a diuretic (HCTZ, hydrochlorothiazide). The target blood pressure (< 140/90 mmHg) was achieved after a 6 month titration period in 75.4% of patients receiving B+A, versus 72.4% in those on B + HCTZ. Over a mean follow-up of 3 years, the B + A drug regimen was found to reduce significantly more effectively the relative risk cardiovascular mortality (-20%), fatal and non fatal myocardial infarction (-22%) and coronary revascularization (-14%), appearing therefore particularly effective to prevent complications due to myocardial ischemia.

  13. Measuring Asymmetry in Time-Stamped Phylogenies.

    Directory of Open Access Journals (Sweden)

    Bethany L Dearlove


    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.

  14. Phylogeny Constructed by Using Dsing Diversity Increment

    Institute of Scientific and Technical Information of China (English)

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


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

  15. Accomplish the Application Area in Cloud Computing

    CERN Document Server

    Bansal, Nidhi


    In the cloud computing application area of accomplish, we find the fact that cloud computing covers a lot of areas are its main asset. At a top level, it is an approach to IT where many users, some even from different companies get access to shared IT resources such as servers, routers and various file extensions, instead of each having their own dedicated servers. This offers many advantages like lower costs and higher efficiency. Unfortunately there have been some high profile incidents where some of the largest cloud providers have had outages and even lost data, and this underscores that it is important to have backup, security and disaster recovery capabilities. In education field, it gives better choice and flexibility to IT departments than others. The platform and applications you use can be on-premises, off-premises, or a combination of both, depending on your academic organization's needs. With cloud computing in education, you get powerful software and massive computing resources where and when you...

  16. Eumetazoan cryptochrome phylogeny and evolution. (United States)

    Haug, Marion F; Gesemann, Matthias; Lazović, Viktor; Neuhauss, Stephan C F


    Cryptochromes (Crys) are light sensing receptors that are present in all eukaryotes. They mainly absorb light in the UV/blue spectrum. The extant Crys consist of two subfamilies, which are descendants of photolyases but are now involved in the regulation of circadian rhythms. So far, knowledge about the evolution, phylogeny, and expression of cry genes is still scarce. The inclusion of cry sequences from a wide range of bilaterian species allowed us to analyze their phylogeny in detail, identifying six major Cry subgroups. Selective gene inactivations and stabilizations in multiple chordate as well as arthropod lineages suggest several sub- and/or neofunctionalization events. An expression study performed in zebrafish, the model organism harboring the largest amount of crys, showed indeed only partially overlapping expression of paralogous mRNA, supporting gene sub- and/or neofunctionalization. Moreover, the daily cry expression in the adult zebrafish retina indicated varying oscillation patterns in different cell types. Our extensive phylogenetic analysis provides for the first time an overview of cry evolutionary history. Although several, especially parasitic or blind species, have lost all cry genes, crustaceans have retained up to three crys, teleosts possess up to seven, and tetrapods up to four crys. The broad and cyclic expression pattern of all cry transcripts in zebrafish retinal layers implies an involvement in retinal circadian processes and supports the hypothesis of several autonomous circadian clocks present in the vertebrate retina.

  17. Planning and accomplishment narrative FY 1973 Modoc National Wildlife Refuge (United States)

    US Fish and Wildlife Service, Department of the Interior — This report provides short summaries of refuge highlights and various accomplishments for the 1973 fiscal year. Accomplishments described include Demonstrations,...

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

  19. Some History and Accomplishments of the IUSS (United States)

    Brevik, Eric C.; Hartemink, Alfred E.


    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.

  20. 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


    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.

  1. Light Water Reactor Sustainability Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

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


    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

  2. 77 FR 20319 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products (United States)


    ...; ] 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...

  3. 78 FR 73993 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products (United States)


    ... 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...

  4. Unlocking the bovine genome

    Directory of Open Access Journals (Sweden)

    Worley Kim C


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

  5. Camel and bovine chymosin

    DEFF Research Database (Denmark)

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


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

  6. Bovine Herpesvirus 4 infections and bovine mastitis

    NARCIS (Netherlands)

    Wellenberg, Gerardus Johannus


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

  7. Accomplishments in 2007 in the Management of Hepatobiliary Cancers (United States)

    Chan, Anthony T.C.; Kishi, Yoji; Chan, Stephen L.


    SUMMARY Hepatocellular CarcinomaOverview of the Disease IncidencePrognostic or Predictive FactorsCurrent Therapy Standards SurgeryLocoablative TreatmentSystemic TreatmentAccomplishments and Lack of Accomplishments TherapyMilan Criteria to Select Patients for Liver TransplantBiologic AgentsBiomarkersBasic ScienceWhat Needs To Be DoneFuture Directions Comments on ResearchObstacles to Progress Biliary Tract CancerOverview of the Disease IncidencePrognostic or Predictive FactorsCurrent Therapy StandardsAccomplishments and Lack of Accomplishments TherapyBiomarkersWhat Needs To Be DoneFuture Directions PMID:19352465

  8. Phylogeny and taxonomy of Chlorobiaceae. (United States)

    Imhoff, Johannes F; Thiel, Vera


    Based on phylogenetic relationships found according to gene sequences of the 16S rRNA and the FMO (Fenna-Matthews-Olson protein) genes, and supported by the G + C content of the DNA and sequence signatures, the strains and species of green sulfur bacteria have been grouped into a phylogenetic system. Since properties used previously for classification such as cell morphology, photosynthetic pigments and substrate utilization do not conform with their phylogeny, a reassignment of strains to species, and a rearrangement among the species were necessary. The comparison of the traditional classification system of these bacteria with their phylogenetic relationship yielded a confusing picture. As a consequence of this rearrangement, species of the green sulfur bacteria were classified into the genera Chlorobium, Chlorobaculum, Prosthecochloris, and Chloroherpeton. Strains were assigned to the species according to their phylogenetic similarity and a number of new combinations, and new species were defined. New isolates and also environmental gene sequences fit very well into the established groups or may form new species, some of which have been described and others are awaiting their description. New strains and available gene sequences are included into the phylogenetic system, and a taxonomic classification on the species level is proposed.

  9. Outcomes and Accomplishments of The Circles of Care Planing Efforts (United States)

    Duclos, Christine W.; Phillips, Mary; LeMaster, Pamela L.


    This paper presents outcomes and accomplishments of the first round of participating individuals, communities, and grantees of the Circles of Care program (CoC). While accomplishing all CoC program goals, the initiative supported grantees in developing individual service delivery system models and positioned each grantee advantageously for…

  10. Space directorate research and technology accomplishments for fiscal year 1987 (United States)

    Avery, Don E.


    The major accomplishments and test highlights of the Space Directorate of NASA Langley Research Center for FY87 are presented. Accomplishments and test highlights are listed by Division and Branch. This information should be useful in coordinating programs with government organizations, universities, and industry in areas of mutual interest.

  11. Perfect Phylogeny Problems with Missing Values. (United States)

    Kirkpatrick, Bonnie; Stevens, Kristian


    The perfect phylogeny problem is of central importance to both evolutionary biology and population genetics. Missing values are a common occurrence in both sequence and genotype data, but they make the problem of finding a perfect phylogeny NPhard even for binary characters. We introduce new and efficient perfect phylogeny algorithms for broad classes of binary and multistate data with missing values. Specifically, we address binary missing data consistent with the rich data hypothesis (RDH) introduced by Halperin and Karp and give an efficient algorithm for enumerating phylogenies. This algorithm is useful for computing the probability of data with missing values under the coalescent model. In addition, we use the partition intersection (PI) graph and chordal graph theory to generalize the RDH to multi-state characters with missing values. For a bounded number of states, we provide a fixed parameter tractable algorithm for the perfect phylogeny problem with missing data. Utilizing the PI graph, we are able to show that under multiple biologically motivated models for character data, our generalized RDH holds with high probability, and we evaluate our results with extensive empirical analysis.

  12. Juvenile morphology in baleen whale phylogeny. (United States)

    Tsai, Cheng-Hsiu; Fordyce, R Ewan


    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.

  13. Juvenile morphology in baleen whale phylogeny (United States)

    Tsai, Cheng-Hsiu; Fordyce, R. Ewan


    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.

  14. The phylogeny graphs of doubly partial orders

    CERN Document Server

    Park, Boram


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

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

    DEFF Research Database (Denmark)

    Vilhelmsen, Lars


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

  16. Ribosomal RNA: a key to phylogeny (United States)

    Olsen, G. J.; Woese, C. R.


    As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.

  17. Sexing Bovine Embryos Using PCR Amplification of Bovine SRY Sequence

    Institute of Scientific and Technical Information of China (English)

    曾溢滔; 张美兰; 陈美珏; 周霞娣; 黄英; 任兆瑞; 黄淑帧; 胡明信; 吴学清; 高建明; 张斌; 徐慧如


    This study analyses the bovine SRY DNA sequence by direct sequencing procedure, followed by the designation of the PCR primers specific for bovine SRY. Using PCR amplification of bovine SRY gene, the embryo sex was determined. The results of the embryo sex identification were confirmed after the embryo transfer and pregnancies.

  18. Planning and accomplishment narrative: FY - 1975: Mingo National Wildlife Refuge (United States)

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

  19. 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)


    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.

  20. Refuge Accomplishment Report Highlights: Canaan National Wildlife Refuge FY2012 (United States)

    US Fish and Wildlife Service, Department of the Interior — This annual narrative report for Canaan Valley National Wildlife Refuge highlights Refuge accomplishments during the 2012 fiscal year. The report begins with a...

  1. Waubay National Wildlife Refuge : Annual Summary of Accomplishments [1944 (United States)

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

  2. Waubay National Wildlife Refuge : Annual Summary of Accomplishments (United States)

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

  3. Process development accomplishments: Waste and hazard minimization, FY 1991

    Energy Technology Data Exchange (ETDEWEB)

    Homan, D.A.


    This report summarizes significant technical accomplishments of the Mound Waste and Hazard Minimization Program for FY 1991. The accomplishments are in one of eight major areas: environmentally responsive cleaning program; nonhalogenated solvent trials; substitutes for volatile organic compounds; hazardous material exposure minimization; nonhazardous plating development; explosive processing waste reduction; tritium capture without conversion to water; and robotic assembly. Program costs have been higher than planned.

  4. Estimating the duration of speciation from phylogenies. (United States)

    Etienne, Rampal S; Morlon, Hélène; Lambert, Amaury


    Speciation is not instantaneous but takes time. The protracted birth-death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.

  5. Bayesian inference of the metazoan phylogeny

    DEFF Research Database (Denmark)

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


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

  6. The Binary Perfect Phylogeny with Persistent characters

    CERN Document Server

    Braghin, Chiara; Trucco, Gabriella; Bonizzoni, Paola


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

  7. Enzootic bovine leukosis and Bovine leukemia virus


    Amauri Alcindo Alfieri; Alice Fernandes Alfieri; Luis Álvaro Leuzzi Junior


    All over de World the Enzootic Bovine Leukosis is a important viral infection in cattle herds. This revision points out topics relative to the etiological agent, clinical signals, diagnosis methods, control and prophylaxis of the infection.A Leucose Enzoótica Bovina é uma infecção viral amplamente disseminada em rebanhos bovinos de todo o mundo. Esta revisão tem por objetivo apresentar tópicos relacionados ao agente etiológico, à doença clínica e aos métodos de diagnóstico, controle e profila...

  8. Phylogeny and character behavior in the family Lemuridae. (United States)

    Wyner, Y; DeSalle, R; Absher, R


    A phylogenetic analysis of the family Lemuridae was accomplished using multiple gene partitions and morphological characters. The results of the study suggest that several nodes in the lemurid phylogeny can be robustly resolved; however, the relationships of the species within the genus Eulemur are problematically nonrobust. The genus Varecia is strongly supported as the basal genus in the family. Hapalemur and Lemur catta are strongly supported as sister taxa and together are the sister group to the genus Eulemur. E. mongoz is the most basal species in the genus Eulemur. E. fulvus subspecies form a monophyletic group with three distinct lineages. E. coronatus is strongly supported as the sister taxon to E. macaco. The relationships of E. rubriventer, E. fulvus, and the E. macaco-E. coronatus pair are unresolved. Our combined molecular and morphological analysis demonstrates the lack of influence that morphology has on the simultaneous analysis tree when these two kinds of data are given equal weight. The effects of several extreme weighting schemes (removal of transitions and of third positions in protein-coding regions) and maximum-likelihood analysis were also explored. We suggest that these other forms of inference add little to resolving the problematic relationships of the species in the genus Eulemur.

  9. Bovine milk glycome. (United States)

    Tao, N; DePeters, E J; Freeman, S; German, J B; Grimm, R; Lebrilla, C B


    Bovine milk oligosaccharides have several potentially important biological activities including the prevention of pathogen binding to the intestinal epithelial and as nutrients for beneficial bacteria. It has been suggested that milk oligosaccharides are an important source of complex carbohydrates as supplements for the food and the pharmaceutical industries. However, only a small number of structures of bovine milk oligosaccharides (bMO) are known. There have been no systematic studies on bMO. High-performance mass spectrometry and separation methods are used to evaluate bMO, and nearly 40 oligosaccharides are present in bovine milk. Bovine milk oligosaccharides are composed of shorter oligomeric chains than are those in human milk. They are significantly more anionic with nearly 70%, measured abundances, being sialylated. Additionally, bMO are built not only on the lactose core (as are nearly all human milk oligosaccharides), but also on lactose amines. Sialic acid residues include both N-acetyl and N-glycolylneuraminic acid, although the former is significantly more abundant.

  10. Bovine milk exosome proteome (United States)

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

  11. 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.


    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 sy

  12. Bovine Spongiform Encephalopathy (United States)

    Bovine spongiform encephalopathy (BSE) is caused by a novel contagion, known to as a prion. Prions are proteins capable of converting a normal cellular protein into a prion, thereby propagating an infection. BSE is the first known prion zoonotic. As such it has attracted broad scientific and, to a r...

  13. The 1989-1990 NASA space biology accomplishments (United States)

    Halstead, Thora W. (Editor)


    Individual technical summaries of research projects on NASA's Space Biology Program for research conducted during the period May 1989 to April 1990 are presented. This program is concerned with using the unique characteristics of the space environment, particularly microgravity, as a tool to advance the following: (1) knowledge in the biological sciences; (2) understanding of how gravity has shaped and affected life on the Earth; and (3) understanding of how the space environment affects both plants and animals. The summaries for each project include a description of the research, a list of accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

  14. The 1987-1988 NASA space/gravitational biology accomplishments (United States)

    Halstead, Thora W. (Editor)


    Individual technical summaries of research projects of the NASA Space/Gravitational Biology Program, for research conducted during the period January 1987 to April 1988 are presented. This Program is concerned with using the characteristics of the space environment, particularly microgravity, as a tool to advance knowledge in the biological sciences; understanding how gravity has shaped and affected life on earth; and understanding how the space environment affects both plant and animal species. The summaries for each project include a description of the research, a list of the accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

  15. The 1985-86 NASA space/gravitational biology accomplishments (United States)


    Individual Technical summaries of research projects of NASA's Space/Gravitational Biology Program are presented. This Program is concerned with using the unique characteristics of the space environment, particularly microgravity, as a tool to advance knowledge in the biological sciences; understanding how gravity has shaped and affected life on Earth; and understanding how the space environment affects both plant and animal species. The summaries for each project include a description of the research, a listing of the accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

  16. The 1986-87 NASA space/gravitational biology accomplishments (United States)

    Halstead, Thora W. (Editor)


    This report consists of individual technical summaries of research projects of NASA's Space/Gravitational Biology program, for research conducted during the period January 1986 to April 1987. This program utilizes the unique characteristics of the space environment, particularly microgravity, as a tool to advance knowledge in the biological sciences; understanding how gravity has shaped and affected life on Earth; and understanding how the space environment affects both plant and animal species. The summaries for each project include a description of the research, a list of accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

  17. The 1988-1989 NASA Space/Gravitational Biology Accomplishments (United States)

    Halstead, Thora W. (Editor)


    This report consists of individual technical summaries of research projects of NASA's space/gravitational biology program, for research conducted during the period May 1988 to April 1989. This program is concerned with using the unique characteristics of the space environment, particularly microgravity, as a tool to advance knowledge in the biological sciences; understanding how gravity has shaped and affected life on Earth; and understanding how the space environment affects both plant and animal species. The summaries for each project include a description of the research, a list of the accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

  18. Phylogeny and subgeneric taxonomy of Aspergillus

    DEFF Research Database (Denmark)

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


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

  19. Whole genome phylogenies for multiple Drosophila species

    Directory of Open Access Journals (Sweden)

    Seetharam Arun


    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. Primate jumping genes elucidate strepsirrhine phylogeny



    Transposable elements provide a highly informative marker system for analyzing evolutionary histories. To solve controversially discussed topics in strepsirrhine phylogeny, we characterized 61 loci containing short interspersed elements (SINEs) and determined the SINE presence–absence pattern at orthologous loci in a representative strepsirrhine panel. This SINE monolocus study was complemented by a Southern blot analysis tracing multiple loci of two different strepsirrhine specific SINEs. Th...

  1. Marine Corps Transition Team Program in Iraq: Mission Accomplished (United States)


    to Mission Accomplishment.. .................................................................... 21 Figures Figure 1. MATIS Score Improvement...CORPS ADVISOR TRAINING IMPACT SYSTEM ( MATIS ) The Interaction Research Institute (IRI), a private company, conducted a study that measured specifically focused on I Marine Expeditionary Force sourced transition teams who deployed to OIF from October 2007- September 2009. The : MATIS

  2. Business accomplishments, gender and entrepreneurial self-image

    NARCIS (Netherlands)

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


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

  3. Women in History--Abigail Adams: Life, Accomplishments, and Ideas (United States)

    Kenan, Sharon K.


    This article profiles the life, accomplishments, and ideas of Abigail Adams. Born in 1944, Adams lacked a formal education, but she more than made up for that shortcoming with her love of reading, especially literature, and her interests in politics and events surrounding the young colonies. Adams was supportive of the advancement of women. She…

  4. Phylogeny mandalas for illustrating the Tree of Life. (United States)

    Hasegawa, Masami


    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.

  5. Phylogeny and evolution of RNA structure. (United States)

    Gesell, Tanja; Schuster, Peter


    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.

  6. Mycotic bovine nasal granuloma. (United States)

    Conti Díaz, Ismael Alejandro; Vargas, Roberto; Apolo, Ada; Moraña, José Antonio; Pedrana, Graciela; Cardozo, Elena; Almeida, Edgardo


    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.

  7. Selenium in bovine spermatozoa. (United States)

    Niemi, S M; Kuzan, F B; Senger, P L


    This study investigated the association of selenium with ejaculated bovine spermatozoa. Over 75% of the radioactive spermatozoa. Over 75% of the radioactive selenium-75 was released after 30 min of incubation in 2 X 10(-3) dithiothreitol. Of the selenium-75 released by dithiothreitol, 85% was associated with spermatozoal protein. Protein containing selenium-75 was found predominantly in a single band after polyacrylamide gel electrophoresis. Molecular weight was approximately 21,500 daltons.

  8. Infectious bovine keratoconjunctivitis (pinkeye)


    Angelos, JA


    Copyright © 2015 Elsevier Inc. All rights reserved. As is the case for controlling other infectious livestock diseases, the most successful efforts to control infectious bovine keratoconjunctivitis (IBK) will include consideration of the host, the environment, herd management, and ongoing surveillance even after the immediate crisis has passed. Research over many years has led to the discovery of a variety of antibiotic treatments and antibiotic regimens that can be effective against IBK. The...

  9. Diagnostic imaging in bovine orthopedics. (United States)

    Kofler, Johann; Geissbühler, Urs; Steiner, Adrian


    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.

  10. Abstract and research accomplishments of University Coal Research Projects

    Energy Technology Data Exchange (ETDEWEB)



    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.

  11. The 1992-1993 NASA Space Biology Accomplishments (United States)

    Halstead, Thora W. (Editor)


    This report consists of individual technical summaries of research projects of NASA's Space Biology Program, for research conducted during the calendar years of 1992 and 1993. This program includes both plant and animal research, and is dedicated to understanding the role of gravity and the effects of microgravity on biological processes; determining the effects of the interaction of gravity and other environmental factors on biological systems; and using the microgravity of the space environment as a tool to advance fundamental scientific knowledge in the biological sciences to improve the quality of life on Earth and contribute to NASA's goal of manned exploration of space. The summaries for each project include a description of the research, a list of the accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

  12. The 1990-1991 NASA space biology accomplishments (United States)

    Halstead, Thora W. (Editor)


    This report consists of individual technical summaries of research projects of NASA's Space Biology Program, for research conducted during the period May 1990 through May 1991. This program includes both plant and animal research, and is dedicated to understanding the role of gravity and other environmental factors on biological systems and to using the microgravity of the space environment as a tool to advance fundamental scientific knowledge in the biological sciences to improve the quality of life on Earth and contribute to NASA's goal of manned exploration of space. The summaries for each project include a description of the research, a list of the accomplishments, an explanation of the significance of the accomplishments, and a list of publications.

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

    Energy Technology Data Exchange (ETDEWEB)



    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. Knowledge translation in health care as a multimodal interactional accomplishment

    DEFF Research Database (Denmark)

    Kjær, Malene


    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...... knowledge gets translated through the use of rich multimodal embodied interactions, whereas the more abstract aspects of knowledge remain untranslated. Overall, the study contributes to the understanding of knowledge translation as a multimodal, locally situated accomplishment....

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

    Energy Technology Data Exchange (ETDEWEB)

    Charles V Park


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

  16. Accomplishments in 2008 in the Management of Gastrointestinal Stromal Tumors (United States)

    Renouf, Daniel; Blay, Jean-Yves; Blanke, Charles


    SUMMARY Overview of the Disease ProcessIncidencePrognosisPredictive MarkersCurrent General Therapy Standards in North America and EuropeLocalized or Potentially Resectable DiseaseUnresectable or Metastatic DiseaseAccomplishments During the YearTherapySurgical Issues and Perioperative TherapyImatinibSunitinibNew DrugsBiomarkersBasic and Other Translational ScienceWhat Needs to Be DoneFuture DirectionsComments on ResearchObstacles to Progress PMID:20011569

  17. The eighth NASA total quality management accomplishments report, 1990 (United States)


    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.

  18. Abstracts and research accomplishments of university coal research projects

    Energy Technology Data Exchange (ETDEWEB)


    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 (United States)


    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

    Energy Technology Data Exchange (ETDEWEB)


    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. Algorithms For Phylogeny Reconstruction In a New Mathematical Model

    NARCIS (Netherlands)

    Lenzini, Gabriele; Marianelli, Silvia


    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 regard

  2. Construction of random perfect phylogeny matrix

    Directory of Open Access Journals (Sweden)

    Mehdi Sadeghi


    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 perfect phylogeny, minimum allele frequency (MAF, tree, recursive algorithm 

  3. Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha). (United States)

    Blackwell, Meredith; Hibbett, David S; Taylor, John W; Spatafora, Joseph W


    Research in fungal phylogenetics and systematics progressed rapidly in the past decade due to advances in DNA sequencing technologies and analytical methods. A newfound wealth of sequence data acquired through community-wide initiatives has advanced the process of acquiring a stable phylogenetic classification of many fungal taxa. Financial support from the National Science Foundation Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha) for 5 y enabled more than 100 fungal systematists to assess the taxon sampling, molecular markers and analytical methods necessary to facilitate such a project. Later a second NSF program provided financial support for the Assembling the Fungal Tree of Life (AFTOL) project to accomplish much of the research. Deep Hypha may be viewed as an involved parent of AFTOL with a continuing role as coordinator of likeminded workers. Many questions posed at the beginning of the Deep Hypha project have been addressed, at least in part, although some details remain to be clarified. Many of the main branches of the fungal tree are stable and well supported, often as a result of multigene analyses that involved collaboration of many laboratories. More work is necessary, however, to resolve certain branching events near the base of the tree, as well as to reconstruct relationships in some terminal groups. The phylogenetic classification in this issue of Mycologia is a product of the AFTOL project and many other independent research initiatives, and it is an initial synthesis of a working classification designed to be used for all major publications that require a phylogenetic classification of fungi.

  4. Bayesian coestimation of phylogeny and sequence alignment

    Directory of Open Access Journals (Sweden)

    Jensen Jens


    Full Text Available Abstract Background Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to first build a multiple alignment of these sequences, followed by a phylogenetic reconstruction step based on this multiple alignment. However, alignment and phylogenetic inference are fundamentally interdependent, and ignoring this fact leads to biased and overconfident estimations. Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both. Results We developed a fully Bayesian Markov chain Monte Carlo method for coestimating phylogeny and sequence alignment, under the Thorne-Kishino-Felsenstein model of substitution and single nucleotide insertion-deletion (indel events. In our earlier work, we introduced a novel and efficient algorithm, termed the "indel peeling algorithm", which includes indels as phylogenetically informative evolutionary events, and resembles Felsenstein's peeling algorithm for substitutions on a phylogenetic tree. For a fixed alignment, our extension analytically integrates out both substitution and indel events within a proper statistical model, without the need for data augmentation at internal tree nodes, allowing for efficient sampling of tree topologies and edge lengths. To additionally sample multiple alignments, we here introduce an efficient partial Metropolized independence sampler for alignments, and combine these two algorithms into a fully Bayesian co-estimation procedure for the alignment and phylogeny problem. Our approach results in estimates for the posterior distribution of evolutionary rate parameters, for the maximum a-posteriori (MAP phylogenetic tree, and for the posterior decoding alignment. Estimates for the evolutionary tree and multiple alignment are augmented with confidence estimates for each node height and alignment column

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

    NARCIS (Netherlands)

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


    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 answe

  6. Significant effects due to rephrasing the Maslach Burnout Inventory's personal accomplishment items. (United States)

    Bouman, Anne Marthe; Te Brake, Hans; Hoogstraten, Johan


    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 answers given.

  7. Bovine coronavirus hemagglutinin protein. (United States)

    King, B; Potts, B J; Brian, D A


    Treatment of purified bovine coronavirus (Mebus strain) with pronase destroyed the integrity of virion surface glycoproteins gp140, gp120, gp100, reduced the amount of gp26 and destroyed the hemagglutinating activity of the virus. Bromelain, on the other hand, destroyed the integrity of gp120, gp100 and gp26 but failed to remove gp140 and failed to destroy viral hemagglutinating activity. These experiments suggest that gp140 is the virion hemagglutinin. Immunoblotting studies using monospecific antiserum demonstrate that gp140 is a disulfide-linked dimeric structure reducible to monomers of 65 kDa.

  8. Infectious bovine keratoconjunctivitis (pinkeye). (United States)

    Angelos, John A


    As is the case for controlling other infectious livestock diseases, the most successful efforts to control infectious bovine keratoconjunctivitis (IBK) will include consideration of the host, the environment, herd management, and ongoing surveillance even after the immediate crisis has passed. Research over many years has led to the discovery of a variety of antibiotic treatments and antibiotic regimens that can be effective against IBK. The discoveries of Mor bovoculi and reports of IBK associated with Mycoplasma spp without concurrent Mor bovis or Mor bovoculi have raised new questions into the roles that other organisms may play in IBK pathogenesis.

  9. Proteomic Analysis of Bovine Nucleolus

    Institute of Scientific and Technical Information of China (English)

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


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

  10. The United States Geological Survey in Alaska: Accomplishments during 1981 (United States)

    Coonrad, Warren L.; Elliot, Raymond L.


    This report of accomplishments of the U.S. Geological Survey in Alaska during 1981 contains summary and topical accounts of the results of studies on a wide range of topics of economic and scientific interest. In addition, many more detailed maps and reports are included in the lists of references cited for each article and in the appended compilations of 277 reports on Alaska published by the U.S. Geological Survey and of 103 reports, by U.S. Geological Survey authors in various other scientific publications.

  11. The United States Geological Survey in Alaska: Accomplishments during 1980 (United States)

    Coonrad, Warren L.


    This report of accomplishments of the U.S. Geological Survey in Alaska during 1980 contains summary and topical accounts of results of studies in a wide range of topics of economic and scientific interest. In addition, many more detailed maps and reports are included in the lists of references cited for each article and in the appended compilations of 297 reports on Alaska published by the U.S. Geological Survey and of 177 reports by U.S. Geological Survey authors in various other scientific publications.

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

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, M.D.


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

  13. Accomplishments of the Oak Ridge National Laboratory Seed Money program (United States)


    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)

  14. Personalized medicine: CCO's vision, accomplishments and future plans. (United States)

    Guo, Jennifer; Kamel-Reid, Suzanne; Rutherford, Michael; Hart, Jennifer; Melamed, Saul; Pollett, Aaron


    Personalized medicine is a rapidly expanding field, with the potential to improve patient care. Its benefits include increasing efficiency in cancer screening, diagnosis and treatment through early detection, targeted therapy and identifying individuals with an underlying genetic risk for cancer or adverse outcomes. Through the work of Cancer Care Ontario (CCO)'s Pathology and Laboratory Medicine Program, a number of initiatives have been undertaken to support developments in personalized medicine. In keeping with the momentum of recent accomplishments, CCO has led the formation of the Personalized Medicine Steering Committee to develop a comprehensive provincial genetics strategy for the future of cancer care.

  15. Towards a mitogenomic phylogeny of Lepidoptera. (United States)

    Timmermans, Martijn J T N; Lees, David C; Simonsen, Thomas J


    The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire mitochondrial genomes both practical and economically viable. Prior phylogenetic studies utilised just eight of 43 currently recognised lepidopteran superfamilies. Here, we add 23 full and six partial mitochondrial genomes (comprising 22 superfamilies of which 16 are newly represented) to those publically available for a total of 24 superfamilies and ask whether such a sample can resolve deeper lepidopteran phylogeny. Using recoded datasets we obtain topologies that are highly congruent with prior nuclear and/or morphological studies. Our study shows support for an expanded Obtectomera including Gelechioidea, Thyridoidea, plume moths (Alucitoidea and Pterophoroidea; possibly along with Epermenioidea), Papilionoidea, Pyraloidea, Mimallonoidea and Macroheterocera. Regarding other controversially positioned higher taxa, Doidae is supported within the new concept of Drepanoidea and Mimallonidae sister to (or part of) Macroheterocera, while among Nymphalidae butterflies, Danainae and not Libytheinae are sister to the remainder of the family. At the deepest level, we suggest that a tRNA rearrangement occurred at a node between Adeloidea and Ditrysia+Palaephatidae+Tischeriidae.

  16. Progress in nemertean biology: development and phylogeny. (United States)

    Turbeville, J M


    This paper reviews progress in developmental biology and phylogeny of the Nemertea, a common but poorly studied spiralian taxon of considerable ecological and evolutionary significance. Analyses of reproductive biology (including calcium dynamics during fertilization and oocyte maturation), larval morphology and development and developmental genetics have significantly extended our knowledge of spiralian developmental biology. Developmental genetics studies have in addition provided characters useful for reconstructing metazoan phylogeny. Reinvestigation of the cell lineage of Cerebratulus lacteus using fluorescent tracers revealed that endomesoderm forms from the 4d cell as in other spiralians and that ectomesoderm is derived from the 3a and 3b cells as in annelids, echiurans and molluscs. Studies examining blastomere specification show that cell fates are established precociously in direct developers and later in indirect developers. Morphological characters used to estimate the phylogenetic position of nemerteans are critically re-evaluated, and cladistic analyses of morphology reveal that conflicting hypotheses of nemertean relationships result because of different provisional homology statements. Analyses that include disputed homology statements (1, gliointerstitial cell system 2, coelomic circulatory system) suggest that nemerteans form the sister taxon to the coelomate spiralian taxa rather than the sister taxon to Platyhelminthes. Analyses of small subunit rRNA (18S rDNA) sequences alone or in combination with morphological characters support the inclusion of the nemerteans in a spiralian coelomate clade nested within a more inclusive lophotrochozoan clade. Ongoing evaluation of nemertean relationships with mitochondrial gene rearrangements and other molecular characters is discussed.

  17. A supertree approach to shorebird phylogeny

    Directory of Open Access Journals (Sweden)

    Thomas Gavin H


    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.

  18. Evolution, phylogeny, and molecular epidemiology of Chlamydia. (United States)

    Nunes, Alexandra; Gomes, João P


    The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia.

  19. SERI photovoltaics advanced research and development: FY 1983 accomplishments (United States)


    This report contains the technical highlights of SERI's program in photovoltaics research and development and a bibliography of resulting publications for FY 1983, SERI's participation in a Thin Film Research Task Force appointed by the U.S. Department of Energy led to the formation of technology offices having broad program and implementation responsibilities. This kind of an office was begun at SERI in the amorphous silicon area. A multiyear cost-sharing (federal-industry) initiative was also begun to spur industrial R and D in high-efficiency, single-junction and multijunction amorphous silicon thin film solar cells, and steps were taken to further develop measurement and device analysis capablities of solar cells. The FY 1983 accomplishments are categorized according to SERI's subcontract R and D areas: amorphous thin films, advanced high-efficiency concepts, polycrystalline thin flms, polycrystalline silicon, and photoelectrochemical cells. These accomplishments are also broken down according to SERI's internal PV tasks: PV devices and measurements, solid state research, insulation resource assessment, advanced PV systems research, and performance criteria/test methods development.

  20. 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)


    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.

  1. Viral infections and bovine mastitis: a review

    NARCIS (Netherlands)

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


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

  2. Emergence of new genotype and diversity of Theileria orientalis parasites from bovines in India. (United States)

    George, Neena; Bhandari, Vasundhra; Reddy, D Peddi; Sharma, Paresh


    Bovine theileriosis is a serious threat to livestock worldwide. Uncertainty around species prevalence, antigenic diversity and genotypes of strains make it difficult to assess the impact of this parasite and to provide necessary treatment. We aimed to characterize genotypic diversity, phylogeny and prevalence of Theileria orientalis parasites from the states of Telangana and Andhra Pradesh, India by collecting bovine blood samples from the major districts of the two states. Bioinformatic analysis identified antigenic diversity among the prevalent parasite strains using major piroplasm surface protein (MPSP) gene. Our study revealed a prevalence rate of 4.8% (n=41/862) of T. orientalis parasites in bovine animals and a new genotype of T. orientalis parasite which was not previously reported in India. The emergence of these new genotypes could be an explanation for the frequent outbreaks of bovine theileriosis. Further, whole genome sequencing of T. orientalis strains will help to elucidate the genetic factors relevant for transmissibility and virulence as well as vaccine and new drug development.

  3. International Research Results and Accomplishments From the International Space Station (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; Karabadzhak, Georgy; Sorokin, Igor V.; Cotronei, Vittorio; Sabbagh, Jean


    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 ( 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

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


    Gusfield, Dan


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

  5. Fiscal Year 2005 Solar Radiometry and Metrology Task Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Myers, D.; Andreas, A.; Reda, I.; Gotseff, P.; Wilcox, S.; Stoffel, T.; Anderberg, M.; Kay, B.; Bowen, A.


    The National Renewable Energy Laboratory (NREL) Solar Radiometry and Metrology task provides traceable optical radiometric calibrations and measurements to photovoltaic (PV) researchers and the PV industry. Traceability of NREL solar radiometer calibrations to the World Radiometric Reference (WRR) was accomplished during Pyrheliometer Comparison at NREL in October 2004. Ten spectral and more than 200 broadband radiometers for solar measurements were calibrated this year. We measured detailed spectral distributions of the NREL and PV industry Pulsed Solar Simulators and are analyzing the influence of environmental variables on radiometer uncertainty. New systems for indoor and outdoor solar radiometer calibrations and ultraviolet (UV) spectral measurements and UV radiometer calibrations were purchased and tested. Optical metrology functions support the NREL Measurement and Characterization Task effort for ISO 17025 accreditation of NREL Solar Reference Cell Calibrations and have been integrated into the NREL quality system and audited for ISO17025 compliance.

  6. Recent Accomplishments in Laser-Photovoltaic Wireless Power Transmission (United States)

    Fikes, John C.; Henley, Mark W.; Mankins, John C.; Howell, Joe T.; Fork, Richard L.; Cole, Spencer T.; Skinner, Mark


    Wireless power transmission can be accomplished over long distances using laser power sources and photovoltaic receivers. Recent research at AMOS has improved our understanding of the use of this technology for practical applications. Research by NASA, Boeing, the University of Alabama-Huntsville, the University of Colorado, Harvey Mudd College, and the Naval Postgraduate School has tested various commercial lasers and photovoltaic receiver configurations. Lasers used in testing have included gaseous argon and krypton, solid-state diodes, and fiber optic sources, at wavelengths ranging from the visible to the near infra-red. A variety of Silicon and Gallium Arsenide photovoltaic have been tested with these sources. Safe operating procedures have been established, and initial tests have been conducted in the open air at AMOS facilities. This research is progressing toward longer distance ground demonstrations of the technology and practical near-term space demonstrations.

  7. Bovine herpesvirus 1 infection and infectious bovine rhinotracheitis



    International audience; Bovine herpesvirus 1 (BoHV-1), classified as an alphaherpesvirus, is a major pathogen of cattle. Primary infection is accompanied by various clinical manifestations such as infectious bovine rhinotracheitis, abortion, infectious pustular vulvovaginitis, and systemic infection in neonates. When animals survive, a life-long latent infection is established in nervous sensory ganglia. Several reactivation stimuli can lead to viral re-excretion, which is responsible for the...

  8. 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


    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.

  9. Intervet symposium: bovine neosporosis. (United States)

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


    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 symposium was organised by Juan Muñoz-Bielsa,Wicher Holland, Enzo Foccoliand Theo Schetters (chairman). The focus was on the present state of knowledge of the biology, epidemiology(presented by J.P. Dubey) and immunology of Neospora infection (presented by A. Adrianarivo),with special emphasis on the prospects of vaccination of cattle against Neospora-induced abortion (presentations of K. Frankena (Costa Rican trial) and C. Heuer (New Zealand trial)).

  10. Coloration mechanisms and phylogeny of Morpho butterflies. (United States)

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


    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.

  11. Gene order phylogeny of the genus Prochlorococcus.

    Directory of Open Access Journals (Sweden)

    Haiwei Luo

    Full Text Available BACKGROUND: Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria. METHODOLOGY/PRINCIPAL FINDINGS: Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based trees. Also, a previously unresolved clade was resolved, that of MIT9211 and SS120. CONCLUSIONS/SIGNIFICANCE: This is the first study to use gene order data to resolve a bacterial phylogeny at the genus level. It suggests that the technique is useful in resolving the Tree of Life.

  12. Homology and phylogeny and their automated inference (United States)

    Fuellen, Georg


    The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this “historical” approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of ‘my closest relative looks and behaves like I do’, often referred to as ‘guilt by association’. To enable knowledge transfer on a large scale, several automated ‘phylogenomics pipelines’ have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.

  13. Phylogeny and forelimb disparity in waterbirds. (United States)

    Wang, Xia; Clarke, Julia A


    Previous work has shown that the relative proportions of wing components (i.e., humerus, ulna, carpometacarpus) in birds are related to function and ecology, but these have rarely been investigated in a phylogenetic context. Waterbirds including "Pelecaniformes," Ciconiiformes, Procellariiformes, Sphenisciformes, and Gaviiformes form a highly supported clade and developed a great diversity of wing forms and foraging ecologies. In this study, forelimb disparity in the waterbird clade was assessed in a phylogenetic context. Phylogenetic signal was assessed via Pagel's lambda, Blomberg's K, and permutation tests. We find that different waterbird clades are clearly separated based on forelimb component proportions, which are significantly correlated with phylogeny but not with flight style. Most of the traditional contents of "Pelecaniformes" (e.g., pelicans, cormorants, and boobies) cluster with Ciconiiformes (herons and storks) and occupy a reduced morphospace. These taxa are closely related phylogenetically but exhibit a wide range of ecologies and flight styles. Procellariiformes (e.g., petrels, albatross, and shearwaters) occupy a wide range of morphospace, characterized primarily by variation in the relative length of carpometacarpus and ulna. Gaviiformes (loons) surprisingly occupy a wing morphospace closest to diving petrels and penguins. Whether this result may reflect wing proportions plesiomorphic for the waterbird clade or a functional signal is unclear. A Bayesian approach detecting significant rate shifts across phylogeny recovered two such shifts. At the base of the two sister clades Sphenisciformes + Procellariiformes, a shift to an increase evolutionary rate of change is inferred for the ulna and carpometacarpus. Thus, changes in wing shape begin prior to the loss of flight in the wing-propelled diving clade. Several shifts to slower rate of change are recovered within stem penguins.

  14. Phylogeny and Species Diversity of Gulf of California Oysters (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...

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


    Gascuel, Olivier; Pardi, Fabio; Truszkowski, Jakub


    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 ...

  16. Phylogeny reconstruction based on protein phylogenetic profiles of organisms

    Institute of Scientific and Technical Information of China (English)


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

  17. EarthScope Education and Outreach: Accomplishments and Emerging Opportunities (United States)

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


    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

  18. Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida). (United States)

    Cornils, Astrid; Blanco-Bercial, Leocadio


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

  19. Bengt Liliequist: life and accomplishments of a true renaissance man. (United States)

    Connor, David E; Nanda, Anil


    In the 1970s, the membrane of Liliequist became the accepted name for a small band of arachnoid membrane separating the interpeduncular and chiasmatic cisterns, making it one of the most recent of the universally accepted medical eponyms. The story of its discovery, however, cannot be told without a thorough understanding of the man responsible and his contribution to the growth of a specialty. Bengt Liliequist lived during what many would consider the Golden Age of neuroradiology. With his colleagues at the Serafimer Hospital in Stockholm, he helped set the standard for appropriate imaging of the CNS and contributed to more accurate localization of intracerebral as well as spinal lesions. The pneumoencephalographic discovery of the membrane that was to bear his name serves merely as a starting point for a career that spanned five decades and included the defense of two separate doctoral theses, the last of which occurred after his 80th birthday. Although the recognition of neuroradiology as a subspecialty did not occur in his home country of Sweden until after his retirement, and technological progress saw the obsolescence of the procedure that he had mastered, Dr. Liliequist's accomplishments and his contributions to the current understanding of neuroanatomy merit our continued praise.

  20. National Climate Change and Wildlife Science Center project accomplishments: highlights (United States)

    Holl, Sally


    The National Climate Change and Wildlife Science Center (NCCWSC) has invested more than $20M since 2008 to put cutting-edge climate science research in the hands of resource managers across the Nation. With NCCWSC support, more than 25 cooperative research initiatives led by U.S. Geological Survey (USGS) researchers and technical staff are advancing our understanding of habitats and species to provide guidance to managers in the face of a changing climate. Projects focus on quantifying and predicting interactions between climate, habitats, species, and other natural resources such as water. Spatial scales of the projects range from the continent of North America, to a regional scale such as the Pacific Northwest United States, to a landscape scale such as the Florida Everglades. Time scales range from the outset of the 20th century to the end of the 21st century. Projects often lead to workshops, presentations, publications and the creation of new websites, computer models, and data visualization tools. Partnership-building is also a key focus of the NCCWSC-supported projects. New and on-going cooperative partnerships have been forged and strengthened with resource managers and scientists at Federal, tribal, state, local, academic, and non-governmental organizations. USGS scientists work closely with resource managers to produce timely and relevant results that can assist managers and policy makers in current resource management decisions. This fact sheet highlights accomplishments of five NCCWSC projects.

  1. Phylogeny of suckermouth catfishes (Mochokidae: Chiloglanis) from Kenya: the utility of Growth Hormone introns in species level phylogenies. (United States)

    Schmidt, Ray C; Bart, Henry L; Nyingi, Dorothy Wanja; Gichuki, Nathan Ndegwa


    African suckermouth catfishes (Mochokidae: Chiloglanis) occur in freshwater throughout tropical Africa. Specimens from all major drainages across Kenya were collected over three field seasons. Here we present a phylogeny inferred from both mitochondrial cytochrome b (cyt b) and introns of the nuclear Growth Hormone gene (GH). The phylogeny inferred from introns is largely congruent with the results from an analysis of cyt b. The length and variability of GH introns make them ideal species level nuclear markers without the problem of introgression commonly encountered with mitochondrial genes. This analysis confirmed the presence of two previously known undescribed Chiloglanis species and also suggests the presence of previously unknown diversity within the Athi River system. The resulting phylogeny also indicates the presence of two separate lineages within C. brevibarbis. The historical biogeography of Chiloglanis within Kenya is discussed. The utility of GH intron for species level phylogenies of Siluriformes is compared to that in other groups.

  2. Astrobiology at Arizona State University: An Overview of Accomplishments (United States)

    Farmer, Jack


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

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

    Directory of Open Access Journals (Sweden)

    Corander Jukka


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

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

  5. Higher classification and phylogeny of Euglenozoa. (United States)

    Cavalier-Smith, Thomas


    Discoveries of numerous new taxa and advances in ultrastructure and sequence phylogeny (including here the first site-heterogeneous 18S rDNA trees) require major improvements to euglenozoan higher-level taxonomy. I therefore divide Euglenozoa into three subphyla of substantially different body plans: Euglenoida with pellicular strips; anaerobic Postgaardia (class Postgaardea) dependent on surface bacteria and with uniquely modified feeding apparatuses; and new subphylum Glycomonada characterised by glycosomes (Kinetoplastea, Diplonemea). Euglenoida comprise two new infraphyla: Entosiphona with three feeding rods and Dipilida ancestrally with two. Dipilida comprise basal superclass Rigimonada with longitudinal rigid strips [i.e. new classes Stavomonadea (Petalomonadida, Decastavida and new order Heterostavida) and Ploeotarea (Ploeotiida) with contrasting oral cytoskeletons] and derived superclass Spirocuta with more numerous spirally arranged, often slideable, strips (clade Peranemea/Euglenophyceae) and a different, highly conserved microtubule pattern at strip joints. Peranemea comprise four orders: Peranemida (anterior gliding, protrusible rods), and three new, Anisonemida (posterior gliders), Natomonadida (swimmers including phagotrophic new suborder Metanemina and osmotrophic suborder Rhabdomonadina), and Acroglissida (anterior gliders with cytoproct). I establish orders Entosiphonida, Rapazida, Bihospitida; and seven new euglenoid families (Entosiphonidae, peranemean Neometanemidae, Rapazidae, two stavomonad, two ploeotiid) and three new postgaardian, and three kinetoplastid families (Neobodonidae, Rhynchomonadidae, Parabodonidae), plus new diplonemid family Hemistasiidae for Hemistasia.

  6. Multigene phylogeny resolves deep branching of Amoebozoa. (United States)

    Cavalier-Smith, Thomas; Fiore-Donno, Anna Maria; Chao, Ema; Kudryavtsev, Alexander; Berney, Cédric; Snell, Elizabeth A; Lewis, Rhodri


    Amoebozoa is a key phylum for eukaryote phylogeny and evolutionary history, but its phylogenetic validity has been questioned since included species are very diverse: amoebo-flagellate slime-moulds, naked and testate amoebae, and some flagellates. 18S rRNA gene trees have not firmly established its internal topology. To rectify this we sequenced cDNA libraries for seven diverse Amoebozoa and conducted phylogenetic analyses for 109 eukaryotes (17-18 Amoebozoa) using 60-188 genes. We conducted Bayesian inferences with the evolutionarily most realistic site-heterogeneous CAT-GTR-Γ model and maximum likelihood analyses. These unequivocally establish the monophyly of Amoebozoa, showing a primary dichotomy between the previously contested subphyla Lobosa and Conosa. Lobosa, the entirely non-flagellate lobose amoebae, are robustly partitioned into the monophyletic classes Tubulinea, with predominantly tube-shaped pseudopodia, and Discosea with flattened cells and different locomotion. Within Conosa 60/70-gene trees with very little missing data show a primary dichotomy between the aerobic infraphylum Semiconosia (Mycetozoa and Variosea) and secondarily anaerobic Archamoebae. These phylogenetic features are entirely congruent with the most recent major amoebozoan classification emphasising locomotion modes, pseudopodial morphology, and ultrastructure. However, 188-gene trees where proportionally more taxa have sparser gene-representation weakly place Archamoebae as sister to Macromycetozoa instead, possibly a tree reconstruction artefact of differentially missing data.

  7. Dobrava-Belgrade virus: phylogeny, epidemiology, disease. (United States)

    Papa, Anna


    Dobrava-Belgrade virus (DOBV) is an Old World hantavirus that causes hemorrhagic fever with renal syndrome in humans. With a case fatality rate up to 12%, DOBV infection is the most life-threatening hantavirus disease in Europe. The virus was initially identified in the Balkans, but the discovery of new endemic foci have expanded its recognized geographic range. The recent description of novel genetic variants with different degrees of pathogenicity have complicated its taxonomic analysis. The original rodent host of DOBV is Apodemus flavicollis, however additional Apodemus species, such Apodemus agrarius and Apodemus ponticus, have been found to serve as hosts of the various DOBV genotypes. The complex evolution and genetic diversity of the virus are still under investigation. The present review aims to provide an update on the phylogeny of DOBV and the epidemiology of infection in rodents and humans; to describe the clinical characteristics of the disease; to present current knowledge about laboratory diagnosis, treatment and prevention; discuss the current state of the art in antiviral drug and vaccine development.

  8. A transcriptome approach to ecdysozoan phylogeny. (United States)

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


    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.

  9. Phylogeny based discovery of regulatory elements

    Directory of Open Access Journals (Sweden)

    Cohen Barak A


    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.

  10. Bacterial phylogeny structures soil resistomes across habitats (United States)

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


    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.

  11. Planning and Accomplishment Narrative : Tewaukon Wetland Management District : January 1 - June 30, 1973 (United States)

    US Fish and Wildlife Service, Department of the Interior — This planning and accomplishment narrative for Tewaukon WMD outlines the District's highlights and accomplishments between January and July of 1973.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schweitzer, M.


    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, 2003).

  13. Phylogeny of Cirsium spp. in North America: Host Specificity Does Not Follow Phylogeny

    Directory of Open Access Journals (Sweden)

    Tracey A. Bodo Slotta


    Full Text Available Weedy invasive Cirsium spp. are widespread in temperate regions of North America and some of their biological control agents have attacked native Cirsium spp. A phylogenetic tree was developed from DNA sequences for the internal transcribed spacer and external transcribed spacer regions from native and non-native Great Plains Cirsium spp. and other thistles to determine if host specificity follows phylogeny. The monophyly of Cirsium spp. and Carduus within the tribe Cardinae was confirmed with native North American and European lineages of the Cirsium spp. examined. We did not detect interspecific hybridization between the introduced invasive and the native North American Cirsium spp. Selected host-biological control agent interactions were mapped onto the phylogenic tree derived by maximum likelihood analysis to examine the co-occurrence of known hosts with biological control agents. Within Cirsium-Cardueae, the insect biological control agents do not associate with host phylogenetic lines. Thus, more comprehensive testing of species in host-specificity trials, rather than relying on a single representative of a given clade may be necessary; because the assumption that host-specificity follows phylogeny does not necessarily hold. Since the assumption does not always hold, it will also be important to evaluate ecological factors to provide better cues for host specificity.

  14. When integration fails: Prokaryote phylogeny and the tree of life. (United States)

    O'Malley, Maureen A


    Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today's literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history (often called 'universal phylogeny'). Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a 'meta-heuristic' in the normative commitments guiding scientific practice.

  15. On simulated annealing phase transitions in phylogeny reconstruction. (United States)

    Strobl, Maximilian A R; Barker, Daniel


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

  16. Genetic diversity in a Brazilian bovine herd based on four microsatellite loci

    Directory of Open Access Journals (Sweden)

    Almeida Sabrina E. Matos


    Full Text Available Microsatellites or short tandem repeats (STRs, DNA markers relatively abundant in the genome, have a high degree of polymorphism and therefore great potential for characterizing populations. The present study estimates genetic variability in a set of four microsatellites (BMS3013, BMS3004, HEL10 and TGLA122 in a Brazilian hybrid bovine breed (5/8 Aberdeen Angus x 3/8 Nelore. The objectives were to determine the effect of crossbreeding and selection in these animals' genetic diversity as well as to discover the herd's genetic relationship with that of other breeds. Low diversity was verified in BMS3013 and high diversity was detected in BMS3004, HEL10 and TGLA122. Two alleles in TGLA122 are described here for the first time (TGLA122*155 and TGLA122*163. These genes are possibly characteristics of Zebu animals since they have not been found in other taurine samples so far investigated. Low interpopulational diversity was observed among taurine cattle populations, and clusters obtained on TGLA122 phylogenetic trees agreed with the bovine herd's geographic origin. Therefore, despite TGLA122's high polymorphism and high levels of intrapopulational diversity, the system engenders consistent bovine phylogenies. We detected an intriguingly high similarity between Brangus Ibagé and Red Angus since the former is a hybrid having 3/8 of Nelore genes. Either these animals' environment or genetic selective practices applied to the breed probably favor the Angus genotype.

  17. Material Properties of Inorganic Bovine Cancellous Bovine: Nukbone (United States)

    Piña, Cristina; Palma, Benito; Munguía, Nadia


    In this work, inorganic cancellous bovine bone implants prepared in the Instituto de Investigaciones en Materiales — UNAM were characterized. Elementary chemical analysis was made, toxic elements concentration were measured and the content of organic matter also. These implants fulfill all the requirements of the ASTM standards, and therefore it is possible their use in medical applications.

  18. Bayesian phylogeny analysis via stochastic approximation Monte Carlo

    KAUST Repository

    Cheon, Sooyoung


    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.

  19. Bayesian phylogeny analysis via stochastic approximation Monte Carlo. (United States)

    Cheon, Sooyoung; Liang, Faming


    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.

  20. pHMM-tree: phylogeny of profile hidden Markov models. (United States)

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


    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.

  1. Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea). (United States)

    Puillandre, N; Bouchet, P; Duda, T F; Kauferstein, S; Kohn, A J; Olivera, B M; Watkins, M; Meyer, C


    We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper.

  2. Bovine spongiform encephalopathy in sheep?

    NARCIS (Netherlands)

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


    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 p

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

    Institute of Scientific and Technical Information of China (English)


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

  4. Phylogeny, culturing, and metagenomics of the human gut microbiota. (United States)

    Walker, Alan W; Duncan, Sylvia H; Louis, Petra; Flint, Harry J


    The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.

  5. Bioactivity and phylogeny of the marine bacterial genus Pseudoalteromonas

    DEFF Research Database (Denmark)

    Vynne, Nikolaj Grønnegaard

    . luteoviolacea strains showed confirmed that production of antibiotics was related to phylogeny within this species, which indicates that the underlying biosynthetic pathways are maintained under selective pressure and hence are important traits for the organism. One strain stood out during work with the strain...... homologue system, and further work will resolve is this system has implications for antibiotic production. In summary, this Ph.D. work explored the phylogeny and chemical diversity of the genus Pseudoalteromonas. Novel compounds were discovered but they possessed no antibiotic activity. However, analysis...

  6. 77 FR 15847 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products (United States)


    ... been fed ruminant protein, other than milk protein, during their lifetime; The bovines from which the... from animals that are not known to have been fed ruminant protein, other than milk protein, during... community is that the agent is an abnormal form of a normal protein known as cellular prion protein. The...

  7. Ecological interaction and phylogeny, studying functionality on composed networks (United States)

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


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


    Directory of Open Access Journals (Sweden)

    Laura Buburuzan


    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.

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

    NARCIS (Netherlands)

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


    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

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

    DEFF Research Database (Denmark)

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


    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...

  11. Ontogeny and Phylogeny from an Epigenetic Point of View. (United States)

    Lovtrup, Soren


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

  12. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus (United States)

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

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

    DEFF Research Database (Denmark)

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


    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...

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

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


    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.

  15. Low frequency of paleoviral infiltration across the avian phylogeny

    DEFF Research Database (Denmark)

    Cui, Jie; Zhao, Wei; Huang, Zhiyong


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

  16. Phylogeny and adaptation shape the teeth of insular mice. (United States)

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


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

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

    DEFF Research Database (Denmark)

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


    of these species and their relatives were gathered from atpB, matK, rbcL and trnL-F regions, building the most complete phylogeny of Campanulaceae to date. Six of the island bellflower species were bird-pollinated and two (A. vidalii and M. aurea) were lizard-pollinated. Insects also visited some of the species...

  18. A multigene phylogeny of the Dothideomycetes using four nuclear loci

    NARCIS (Netherlands)

    Schoch, C.; Shoemaker, R.A.; Seifert, K.; Hambleton, S.; Spatafora, J.W.; Crous, P.W.


    We present an expanded multigene phylogeny of the Dothideomycetes. The final data matrix consisted of four loci (nuc SSU rDNA, nuc LSU rDNA, TEF1, RPB2) for 96 taxa, representing five of the seven orders in the current classification of Dothideomycetes and several outgroup taxa representative of the

  19. Advances and challenges in resolving the angiosperm phylogeny

    Directory of Open Access Journals (Sweden)

    Liping Zeng


    Full Text Available Angiosperm phylogenetics investigates the evolutionary history and relationships of angiosperms based on the construction of phylogenetic trees. Since the 1990s, nucleotide or amino acid sequences have been widely used for this and angiosperm phylogenetic analysis has advanced from using single or a combination of a few organellar genes to whole plastid genome sequences, resulting in the widely accepted modern molecular systematics of angiosperms. The current framework of the angiosperm phylogeny includes highly supported basal angiosperm relationships, five major clades (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales, orders grouped within these clades, and core groups in the monocots or eudicots. However, organellar genes have some limitations; these involve uniparental inheritance in most instances and a relatively low percentage of phylogenetic informative sites. Thus, they are unable to resolve some relationships even when whole plastid genome sequences are used. Therefore, the utility of biparentally inherited nuclear genes with more information about evolutionary history, has gradually received more attention. Nevertheless, there are still some plant groups that are difficult to place in the angiosperm phylogeny, such as those involving the relative positions of the five major groups as well as those of several orders of eudicots. In this review, we discuss the applications, advantages and disadvantages of marker genes, the deep relationships that have been resolved in angiosperm phylogeny, groups with uncertain positions, and the challenges that remain in resolving an accurate phylogeny for angiosperms.

  20. Planning and accomplishment narrative : F.Y. 1973 : Merced National Wildlife Refuge (United States)

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

  1. Bovine cysticercosis situation in Brazil

    Directory of Open Access Journals (Sweden)

    Gabriel Augusto Marques Rossi


    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.

  2. Angiosperm phylogeny inferred from sequences of four mitochondrial genes

    Institute of Scientific and Technical Information of China (English)

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


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

  3. Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: a case study with the lizard Anolis roosevelti. (United States)

    Revell, Liam J; Mahler, D Luke; Reynolds, R Graham; Slater, Graham J


    In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as subfossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established maximum likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a "crown-giant" ecomorph anole hypothesized to have once been found throughout the Spanish, United States, and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method.

  4. Infectious bovine keratoconjunctivitis: a review. (United States)

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


    The economic impact of infectious bovine keratoconjunctivitis (IBK) warrants continued investigation of the mechanisms by which Moraxella bovis survives on and colonizes the corneal surface. Virulent strains of M bovis produce hemolysin and exhibit different plasmid profiles than nonvirulent strains. Interactions among host, environment, vector, season, and concurrent infection influence the prevalence of IBK. Mycoplasma sp. or infectious bovine rhinotracheitis virus may enhance or hasten the disease process. The manifestations of IBK may range from mild conjunctivitis to severe ulceration, corneal perforation, and blindness. Treatment of IBK is dictated by economic considerations, intended animal use, and feasibility of administration. Antibiotic therapy is aimed at achieving drug concentrations in tears to meet or exceed the minimum inhibitory concentration for prolonged periods. At present, IBK is not a preventable disease. Affected animals must be separated from the herd and vector control vigorously instituted. Carrier animals must be identified and removed from the herd. Vaccination trials have been unsuccessful because of pili antigen cross-reactivity, variable strains, and uncontrolled environmental factors. Recent investigations have determined that M bovis may utilize host iron sources via iron-repressible outer membrane proteins and siderophores for growth. Elucidation of normal defense mechanisms of the bovine eye may lead to new strategies to enhance the immune response against M bovis.

  5. 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


    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...

  6. Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction. (United States)

    Soon, Villu; Saarma, Urmas


    The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute

  7. Summaries of 1984-85 NASA space-gravitational biology accomplishments (United States)

    Halstead, T. W. (Compiler); Dutcher, F. R. (Compiler); Pleasant, L. G. (Compiler)


    Individual technical summaries of research projects of NASA's Space/Gravitational Biology Program are presented. The summaries for each project include a description of the research, a listing of the accomplishments, and an explanation of the significance of the accomplishments. Bibliographies for each project are also included.

  8. Mission Accomplished

    Institute of Scientific and Technical Information of China (English)


    Australian Prime Minister John Howard arrived in south China's Guangdong Province on June 27 to launch a multi-billion-dollar liquefied natural gas (LNG) deal, a landmark project in the two nations' ever-deepening

  9. Delta-like 1 homolog in Capra hircus: molecular characteristics, expression pattern and phylogeny. (United States)

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


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

  10. Phylogenies support out-of-equilibrium models of biodiversity. (United States)

    Manceau, Marc; Lambert, Amaury; Morlon, Hélène


    There is a long tradition in ecology of studying models of biodiversity at equilibrium. These models, including the influential Neutral Theory of Biodiversity, have been successful at predicting major macroecological patterns, such as species abundance distributions. But they have failed to predict macroevolutionary patterns, such as those captured in phylogenetic trees. Here, we develop a model of biodiversity in which all individuals have identical demographic rates, metacommunity size is allowed to vary stochastically according to population dynamics, and speciation arises naturally from the accumulation of point mutations. We show that this model generates phylogenies matching those observed in nature if the metacommunity is out of equilibrium. We develop a likelihood inference framework that allows fitting our model to empirical phylogenies, and apply this framework to various mammalian families. Our results corroborate the hypothesis that biodiversity dynamics are out of equilibrium.

  11. Obscured phylogeny and possible recombinational dormancy in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Sawyer Stanley A


    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. Phase Transition in Distance-Based Phylogeny Reconstruction

    CERN Document Server

    Roch, Sebastien


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

  13. In vitro production of bovine embryos

    DEFF Research Database (Denmark)

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


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

  14. Ontogeny And Phylogeny. To The Problem Of The Relation Of Individual And Historical Development In Organisms

    Directory of Open Access Journals (Sweden)

    Kovtun M. F.


    Full Text Available The theory of filembriogenesis is only an introduction to the problem’s development of ontogeny’ and phylogeny’ relation (hereinafter — «relation». Discussions as to whether ontogeny creates phylogeny, or vice versa, are devoid of meaning. The opinion of O. Hertwig (Hertwig, 1906 that the ontogeny and phylogeny are two parallel and independent developmental processes is valid only in the first part; thesis about independence distorts the essence of «relation.» According to the authors, one of the essential characteristics of the «relation» is that ontogeny gives the material for phylogeny, and phylogeny renews ontogeny, leading away ontogeny from inbreeding; that ontogeny ensures the life continuity and phylogeny — its differentiation, that is, creates biodiversity; that ontogeny and phylogeny can exist and function only in conjunction or in parallel, changing places (in terms of priority in the life evolution.

  15. Deep phylogeny, ancestral groups and the four ages of life


    Thomas Cavalier-Smith


    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly op...

  16. Multigene phylogeny of the red algal subclass Nemaliophycidae. (United States)

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


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

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

    CERN Document Server

    Mossel, Elchanan


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

  18. The Aplacophora: History, Taxonomy, Phylogeny, Biogeography, and Ecology (United States)


    871-882. Field, K. G., G. J. Olsen, D. J. Lane, S. J. Giovannoni, M. T. Ghiselin, E. C. Raff, N. R. Pace and R. A. Raff. 1988. Molecular phylogeny of...Laboratory, Beaufort, North Carolina. 9. Harbor Branch Laboratory, FL Pierce, Florida. 10. Dives 492. 563, 752-754, 849, 1072. 11. Intituto de Biologia ...University (1965) Stns 351, 2361, 2732. and 3417 (14 specimens): and from the Inslituto de Biologia . Universidade Federal do Rio de Janeiro (9 specimens). 52

  19. Deep phylogeny and evolution of sponges (phylum Porifera). (United States)

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


    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

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

    DEFF Research Database (Denmark)

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


    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...... 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...

  1. Contribution of genosystematics to current concepts of phylogeny and classification of bryophytes. (United States)

    Troitsky, A V; Ignatov, M S; Bobrova, V K; Milyutina, I A


    This paper is a survey of the current state of molecular studies on bryophyte phylogeny. Molecular data have greatly contributed to developing a phylogeny and classification of bryophytes. The previous traditional systems of classification based on morphological data are being significantly revised. New data of the authors are presented on phylogeny of Hypnales pleurocarpous mosses inferred from nucleotide sequence data of the nuclear DNA internal transcribed spacers ITS1-2 and the trnL-F region of the chloroplast genome.

  2. 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.

  3. Phylogeny and evolution of apicoplasts and apicomplexan parasites. (United States)

    Arisue, Nobuko; Hashimoto, Tetsuo


    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.

  4. Phylogeny of metabolic networks: a spectral graph theoretical approach. (United States)

    Deyasi, Krishanu; Banerjee, Anirban; Deb, Bony


    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 79 fully sequenced organisms and compared their architectures. We used spectral density of normalized Laplacian matrix for comparing the structure of networks. The eigenvalues of this matrix reflect not only the global architecture of a network but also the local topologies that are produced by different graph evolutionary processes like motif duplication or joining. A divergence measure on spectral densities is used to quantify the distances between various metabolic networks, and a split network is constructed to analyse the phylogeny from these distances. In our analysis, we focused on the species that belong to different classes, but appear more related to each other in the phylogeny. We tried to explore whether they have evolved under similar environmental conditions or have similar life histories. With this focus, we have obtained interesting insights into the phylogenetic commonality between different organisms.

  5. Bovine milk antibodies for health. (United States)

    Korhonen, H; Marnila, P; Gill, H S


    The immunoglobulins of bovine colostrum provide the major antimicrobial protection against microbial infections and confer a passive immunity to the newborn calf until its own immune system matures. The concentration in colostrum of specific antibodies against pathogens can be raised by immunising cows with these pathogens or their antigens. Immune milk products are preparations made of such hyperimmune colostrum or antibodies enriched from it. These preparations can be used to give effective specific protection against different enteric diseases in calves and suckling pigs. Colostral immunoglobulin supplements designed for farm animals are commercially available in many countries. Also, some immune milk products containing specific antibodies against certain pathogens have been launched on the market. A number of clinical studies are currently in progress to evaluate the efficacy of immune milks in the prevention and treatment of various human infections, including those caused by antibiotic resistant bacteria. Bovine colostrum-based immune milk products have proven effective in prophylaxis against various infectious diseases in humans. Good results have been obtained with products targeted against rotavirus, Shigella flexneri, Escherichia coli, Clostridium difficile, Streptococcus mutans, Cryptosporidium parvum and Helicobacter pylori. Some successful attempts have been made to use immune milk in balancing gastrointestinal microbial flora. Immune milk products are promising examples of health-promoting functional foods, or nutraceuticals. This review summarises the recent progress in the development of these products and evaluates their potential as dietary supplements and in clinical nutrition.

  6. [Toxinology of bovine paraplegic syndrome]. (United States)

    Sevcik, C; Brito, J C; D'Suze, G; Mijares, A J; Domínguez, M G


    A clinical entity named "Bovine Paraplegic Syndrome" ("Síndrome Parapléjico de los Bovinos") has spread alarmingly, in the cattle growing areas of the central and eastern plains of Venezuela. Approximately four million cattle are bread in the area were the disease occurs. The mortality index due to the disease ranges 5 to 25% of the animals at risk, mostly cows, pregnant or lactating. The principal characteristic of the bovine paraplegic syndrome is decubitus, ventral or sternal, in animals that make vane efforts to stand when stimulated. The diagnosis is established ruling out, clinically and with laboratory findings, that the animals are suffering known diseases with similar symptoms such as paralytic rabies, botulism and blood parasites such Trypanosoma sp., Babesia sp., and Anaplasma sp.. Death occurs always, usually after few days, and to this date there is no known treatment able to save the sick cows. In this work, we describe results that suggest the presence of a toxin in the cattle suffering and prone to suffer the syndrome; it is a natural toxin produced by ruminal bacteria. In squid giant axons under voltage clamp conditions, this toxin is very specific to block sodium current during nerve electrical activity.

  7. Bovine somatic cell nuclear transfer. (United States)

    Ross, Pablo J; Cibelli, Jose B


    Somatic cell nuclear transfer (SCNT) is a technique by which the nucleus of a differentiated cell is introduced into an oocyte from which its genetic material has been removed by a process called enucleation. In mammals, the reconstructed embryo is artificially induced to initiate embryonic development (activation). The oocyte turns the somatic cell nucleus into an embryonic nucleus. This process is called nuclear reprogramming and involves an important change of cell fate, by which the somatic cell nucleus becomes capable of generating all the cell types required for the formation of a new individual, including extraembryonic tissues. Therefore, after transfer of a cloned embryo to a surrogate mother, an offspring genetically identical to the animal from which the somatic cells where isolated, is born. Cloning by nuclear transfer has potential applications in agriculture and biomedicine, but is limited by low efficiency. Cattle were the second mammalian species to be cloned after Dolly the sheep, and it is probably the most widely used species for SCNT experiments. This is, in part due to the high availability of bovine oocytes and the relatively higher efficiency levels usually obtained in cattle. Given the wide utilization of this species for cloning, several alternatives to this basic protocol can be found in the literature. Here we describe a basic protocol for bovine SCNT currently being used in our laboratory, which is amenable for the use of the nuclear transplantation technique for research or commercial purposes.

  8. Planning and Accomplishment Narrative : Sabine National Wildlife Refuge : Fiscal Year 1973 (United States)

    US Fish and Wildlife Service, Department of the Interior — This planning and accomplishment report for Sabine National Wildlife Refuge summarizes refuge activities for the 1973 fiscal year. An overview of weather conditions,...

  9. Benton Lake National Wildlife Refuge : Planning and Accomplishment Narrative : Fiscal Year 1974 (United States)

    US Fish and Wildlife Service, Department of the Interior — This annual narrative report for Benton Lake National Wildlife Refuge outlines Refuge accomplishments during the 1974 fiscal year. The report begins by summarizing...

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

    CERN Document Server

    Patil, Ganapati P; Taillie, Charles


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

  11. WISM - A Wideband Instrument for Snow Measurement: Past Accomplishments, Current Status, and Path Forward (United States)

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


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

  12. Eastern Neck National Wildlife Refuge: Annual narrative and accomplishment report: Fiscal year 2001 (United States)

    US Fish and Wildlife Service, Department of the Interior — This annual narrative report for Eastern Neck NWR outlines activities and accomplishments during the 2001 fiscal year. The report begins with an introduction to the...

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

  14. Planning and accomplishment narrative: Lake Andes Wetlands District: July 1, 1972 through June 30, 1973 (United States)

    US Fish and Wildlife Service, Department of the Interior — This annual narrative report for Lake Andes Wetlands District describes Refuge activities during the 1973 fiscal year. Highlights and accomplishments are described.

  15. 29 CFR 779.218 - Methods to accomplish “unified operation.” (United States)


    ... many instances where several establishments, persons, corporations, or other business organizations, join together to perform some or all of their activities as a unified business or business system. They may accomplish such unification through agreements, franchises, grants, leases, or other...

  16. Planning and Accomplishment Narrative for Back Bay National Wildlife Refuge Fiscal Year 1973 (United States)

    US Fish and Wildlife Service, Department of the Interior — This report is a series of figures showing refuge outputs and accomplishments for the fiscal year 1973. Some of the categories covered in this report show statistics...

  17. Planning and Accomplishment Narrative for Prime Hook National Wildlife Refuge Fiscal Year 1973 (United States)

    US Fish and Wildlife Service, Department of the Interior — This report is a series of figures showing refuge outputs and accomplishments for the fiscal year 1973. Some of the categories covered in this report show statistics...

  18. Planning and Accomplishment Narrative : Pea Island National Wildlife Refuge : FY-1973 (United States)

    US Fish and Wildlife Service, Department of the Interior — This narrative report for Pea Island National Wildlife Refuge summarizes Refuge highlights and accomplishments for the 1973 fiscal year. Wildlife-wildlands...

  19. 21 CFR 184.1034 - Catalase (bovine liver). (United States)


    ... 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...

  20. Clinical applications of bovine colostrum therapy

    DEFF Research Database (Denmark)

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


    to populations, outcomes, and methodological quality, as judged by the Jadad assessment tool. Many studies used surrogate markers to study the effects of bovine colostrum. Studies suggesting clinical benefits of colostrum supplementation were generally of poor methodological quality, and results could...... not be confirmed by other investigators. Bovine colostrum may provide gastrointestinal and immunological benefits, but further studies are required before recommendations can be made for clinical application. Animal models may help researchers to better understand the mechanisms of bovine colostrum supplementation......, the dosage regimens required to obtain clinical benefits, and the optimal methods for testing these effects in humans....

  1. Immunoprophylaxis of bovine respiratory syndrome

    Directory of Open Access Journals (Sweden)

    Rogan Dragan


    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.

  2. Bovine Mastitis: Frontiers in Immunogenetics

    Directory of Open Access Journals (Sweden)

    Kathleen eThompson-Crispi


    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

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

    NARCIS (Netherlands)

    Harmsen, H.J.M.


    The research described this thesis concerns the diversity and phylogeny of syntrophic propionate-oxidizing bacteria and their ecology in granular sludge, from which they were obtained. 16S rRNA was used as a molecular marker to study both the phylogeny and the ecology of these bacteria. Sequence ana

  4. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae). (United States)

    Weng, Mao-Lun; Ruhlman, Tracey A; Gibby, Mary; Jansen, Robert K


    The phylogeny of 58 Pelargonium species was estimated using five plastid markers (rbcL, matK, ndhF, rpoC1, trnL-F) and one mitochondrial gene (nad5). The results confirmed the monophyly of three major clades and four subclades within Pelargonium but also indicate the need to revise some sectional classifications. This phylogeny was used to examine karyotype evolution in the genus: plotting chromosome sizes, numbers and 2C-values indicates that genome size is significantly correlated with chromosome size but not number. Accelerated rates of nucleotide substitution have been previously detected in both plastid and mitochondrial genes in Pelargonium, but sparse taxon sampling did not enable identification of the phylogenetic distribution of these elevated rates. Using the multigene phylogeny as a constraint, we investigated lineage- and locus-specific heterogeneity of substitution rates in Pelargonium for an expanded number of taxa and demonstrated that both plastid and mitochondrial genes have had accelerated substitution rates but with markedly disparate patterns. In the plastid, the exons of rpoC1 have significantly accelerated substitution rates compared to its intron and the acceleration was mainly due to nonsynonymous substitutions. In contrast, the mitochondrial gene, nad5, experienced substantial acceleration of synonymous substitution rates in three internal branches of Pelargonium, but this acceleration ceased in all terminal branches. Several lineages also have dN/dS ratios significantly greater than one for rpoC1, indicating that positive selection is acting on this gene, whereas the accelerated synonymous substitutions in the mitochondrial gene are the result of elevated mutation rates.

  5. Phylogeny and evolution of glass sponges (porifera, hexactinellida). (United States)

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


    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.

  6. The contribution of the ACCOMPLISH trial to the treatment of stage 2 hypertension. (United States)

    Byrd, James Brian; Bakris, George; Jamerson, Kenneth


    The Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure (JNC 7) recommended a thiazide-like diuretic, alone or in combination with other antihypertensive drug classes, as initial therapy for hypertension. JNC 7, however, did not specify preferred combinations. The Avoiding Cardiovascular Events through Combination Therapy in Patients Living with Systolic Hypertension (ACCOMPLISH) trial was completed five years after the JNC 7 and demonstrated a 20 % advantage in cardiovascular risk reduction when blood pressure was lowered using the single-pill combination of benazepril-amlodipine compared to benazepril-hydrochlorothiazide (Jamerson et al. 359(23):2417-28 [1]). This new and significant finding provided compelling evidence that the long-standing preference for diuretics as initial therapy could be refuted, but it may also be relevant to the lower-than-expected reduction in coronary disease related events (compared to stroke) observed for decades prior to the ACCOMPLISH approach to therapy. The JNC 8 panel members recently published their recommendations, and while the group did not recommend benazepril-hydrochlorothiazide over other combinations, they did highlight the findings of ACCOMPLISH, rating the primary ACCOMPLISH paper as "good." The American Society of Hypertension position paper and the European Hypertension Society guidelines endorse such combinations as a first-line agent for patients with stage 2 hypertension. We review the current position of ACCOMPLISH in the guidelines regarding treatment of stage 2 hypertension.

  7. PhyloGrid: a development for a workflow in Phylogeny

    CERN Document Server

    Montes, Esther; Mayo, Rafael


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

  8. The phylogeny of invertebrates and the evolution of myelin. (United States)

    Roots, Betty I


    Current concepts of invertebrate phylogeny are reviewed. Annelida and Arthropoda, previously regarded as closely related, are now placed in separate clades. Myelin, a sheath of multiple layers of membranes around nerve axons, is found in members of the Annelida, Arthropoda and Chordata. The structure, composition and function of the sheaths in Annelida and Arthropoda are examined and evidence for the separate evolutionary origins of myelin in the three clades is presented. That myelin has arisen independently at least three times, namely in Annelids, Arthropodas and Chordates, provides a remarkable example of convergent evolution.

  9. Mitochondrial genome organization and phylogeny of two vespid wasps. (United States)

    Cameron, Stephen L; Dowton, Mark; Castro, Lyda R; Ruberu, Kalani; Whiting, Michael F; Austin, Andy D; Diement, Kieren; Stevens, Julia


    We sequenced the entire mitochondrial genome of Abispa ephippium (Hymenoptera: Vespoidea: Vespidae: Eumeninae) and most of the mitochondrial genome of Polistes humilis synoecus (Hymenoptera: Vespoidea: Vespidae: Polistinae). The arrangement of genes differed between the two genomes and also differed slightly from that inferred to be ancestral for the Hymenoptera. The genome organization for both vespids is different from that of all other mitochondrial genomes previously reported. A number of tRNA gene rearrangements were identified that represent potential synapomorphies for a subset of the Vespidae. Analysis of all available hymenopteran mitochondrial genome sequences recovered an uncontroversial phylogeny, one consistent with analyses of other types of data.

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

    CERN Document Server

    Shutters, Brad


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

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

    Meinel, Thomas; Krause, Antje


    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. Innovative Partnerships Program Accomplishments: 2009-2010 at NASA's Kennedy Space Center (United States)

    Makufka, David


    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

  13. 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


    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.

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

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


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

  15. First insights into fern matK phylogeny. (United States)

    Kuo, Li-Yaung; Li, Fay-Wei; Chiou, Wen-Liang; Wang, Chun-Neng


    MatK, the only maturase gene in the land plant plastid genome, is a very popular phylogenetic marker that has been extensively applied in reconstructing angiosperm phylogeny. However, the use of matK in fern phylogeny is largely unknown, due to difficulties with amplification: ferns have lost the flanking trnK exons, typically the region used for designing stable priming sites. We developed primers that are either universal or lineage-specific that successfully amplify matK across all fern families. To evaluate whether matK is as powerful a phylogenetic marker in ferns as in angiosperms, we compared its sequence characteristics and phylogenetic performance to those of rbcL and atpA. Among these three genes, matK has the highest variability and substitution evenness, yet shows the least homoplasy. Most importantly, applying matK in fern phylogenetics better resolved relationships among families, especially within eupolypods I and II. Here we demonstrate the power of matK for fern phylogenetic reconstruction, as well as provide primers and extensive sequence data that will greatly facilitate future evolutionary studies of ferns.

  16. Towards a practical O(nlogn phylogeny algorithm

    Directory of Open Access Journals (Sweden)

    Truszkowski Jakub


    Full Text Available Abstract Recently, we have identified a randomized quartet phylogeny algorithm that has O(nlogn runtime with high probability, which is asymptotically optimal. Our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(loglogn taxa that is correct with high probability. In practice, none of these assumptions is correct: quartet errors are positively correlated and occur with unknown probability, and the guide tree is often error prone. Here, we bring our work out of the purely theoretical setting. We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of Neighbour Joining , which requires Θ(n3 runtime in existing implementations. Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed improvements at minimal accuracy cost. An early prototype implementation of our software is available at

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

    Institute of Scientific and Technical Information of China (English)

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


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

  18. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. (United States)

    Bernt, Matthias; Bleidorn, Christoph; Braband, Anke; Dambach, Johannes; Donath, Alexander; Fritzsch, Guido; Golombek, Anja; Hadrys, Heike; Jühling, Frank; Meusemann, Karen; Middendorf, Martin; Misof, Bernhard; Perseke, Marleen; Podsiadlowski, Lars; von Reumont, Björn; Schierwater, Bernd; Schlegel, Martin; Schrödl, Michael; Simon, Sabrina; Stadler, Peter F; Stöger, Isabella; Struck, Torsten H


    About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.

  19. Phylogeny Explains Variation in The Root Chemistry of Eucalyptus Species. (United States)

    Senior, John K; Potts, Brad M; Davies, Noel W; Wooliver, Rachel C; Schweitzer, Jennifer A; Bailey, Joseph K; O'Reilly-Wapstra, Julianne M


    Plants are dependent on their root systems for survival, and thus are defended from belowground enemies by a range of strategies, including plant secondary metabolites (PSMs). These compounds vary among species, and an understanding of this variation may provide generality in predicting the susceptibility of forest trees to belowground enemies and the quality of their organic matter input to soil. Here, we investigated phylogenetic patterns in the root chemistry of species within the genus Eucalyptus. Given the known diversity of PSMs in eucalypt foliage, we hypothesized that (i) the range and concentrations of PSMs and carbohydrates in roots vary among Eucalyptus species, and (ii) that phylogenetic relationships explain a significant component of this variation. To test for interspecific variation in root chemistry and the influence of tree phylogeny, we grew 24 Eucalyptus species representing two subgenera (Eucalyptus and Symphyomyrtus) in a common garden for two years. Fine root samples were collected from each species and analyzed for total phenolics, condensed tannins, carbohydrates, terpenes, and formylated phloroglucinol compounds. Compounds displaying significant interspecific variation were mapped onto a molecular phylogeny and tested for phylogenetic signal. Although all targeted groups of compounds were present, we found that phenolics dominated root defenses and that all phenolic traits displayed significant interspecific variation. Further, these compounds displayed a significant phylogenetic signal. Overall, our results suggest that within these representatives of genus Eucalyptus, more closely related species have more similar root chemistry, which may influence their susceptibility to belowground enemies and soil organic matter accrual.

  20. Phylogeny and biogeography of the fruit doves (Aves: Columbidae). (United States)

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


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

  1. Phylogeny of the Gondwanan beetle family Ulodidae (Tenebrionoidea). (United States)

    Leschen, Richard A B; Escalona, Hermes E; Elgueta, Mario


    Ulodidae is a small family of saproxylic and fungus feeding beetles restricted to New Zealand, Australia, Chile and New Caledonia. The phylogeny of this family is presented for the first time, based on a cladistic analysis of 53 adult characters from 16 ulodid genera, rooted with Parahelops Waterhouse (Promecheilidae). The topology shows Arthopus Sharp at the base of the tree and confirms the placement of Meryx Latreille as a member of Ulodidae and closely related to the Chilean genus Trachyderas Philippi & Philippi. The extinct New Zealand genus Waitomophylax Leschen & Rhode was placed among a clade consisting of Brouniphylax Strand, Exohadrus Broun, and Pteroderes Germain. Two new genera and two new species are described: Ulobostrichus gen. n. (type species: Ulobostrichus monteithi sp. n.) and Ulocyphaleus gen. n. (type species: Cyphaleus valdivianus Philippi & Philippi, 1864, now U. valdivianus (Philippi & Philippi) n. comb.; U. laetus sp. n.). Dipsaconia pyritosa Pascoe is designated as the type species of Dipsaconia Pascoe and a lectotype was designated for C. valdivianus. A fully illustrated key to the genera and a checklist of the 16 genera and 42 species is included. Based on the phylogeny, the following characters are derived in the family: tuberculate body surface and the presence of scales and /or encrustations. The presence of pore-fields in the abdominal cuticle has evolved at least three times in Meryx Latreille (Australia), Syrphetodes Pascoe (New Zealand) and Trachyderastes Kaszab (New Caledonia).

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

    Directory of Open Access Journals (Sweden)

    Noor Haslina Masstor


    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. 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.

  4. Mixed integer linear programming for maximum-parsimony phylogeny inference. (United States)

    Sridhar, Srinath; Lam, Fumei; Blelloch, Guy E; Ravi, R; Schwartz, Russell


    Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new advances in phylogeny inference will be required if we are to be able to continue to make effective use of the rapidly growing stores of variation data now being gathered. In this paper, we present two integer linear programming (ILP) formulations to find the most parsimonious phylogenetic tree from a set of binary variation data. One method uses a flow-based formulation that can produce exponential numbers of variables and constraints in the worst case. The method has, however, proven extremely efficient in practice on datasets that are well beyond the reach of the available provably efficient methods, solving several large mtDNA and Y-chromosome instances within a few seconds and giving provably optimal results in times competitive with fast heuristics than cannot guarantee optimality. An alternative formulation establishes that the problem can be solved with a polynomial-sized ILP. We further present a web server developed based on the exponential-sized ILP that performs fast maximum parsimony inferences and serves as a front end to a database of precomputed phylogenies spanning the human genome.

  5. Pellet-free isolation of human and bovine milk extracellular vesicles by size-exclusion chromatography (United States)

    Blans, Kristine; Hansen, Maria S.; Sørensen, Laila V.; Hvam, Michael L.; Howard, Kenneth A.; Möller, Arne; Wiking, Lars; Larsen, Lotte B.; Rasmussen, Jan T.


    ABSTRACT 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 from the primary casein and whey protein components in two differently obtained casein reduced milk fractions, with one of the fractions obtained without the use of ultracentrifugation. Milk EV isolates were enriched in lactadherin, CD9, CD63 and CD81 compared to minimal levels of the EV-marker proteins in other relevant milk fractions such as milk fat globules. Nanoparticle tracking analysis and electron microscopy reveals the presence of heterogeneous sized vesicle structures in milk EV isolates. Lipid analysis by thin layer chromatography shows that EV isolates are devoid of triacylglycerides and presents a phospholipid profile differing from milk fat globules surrounded by epithelial cell plasma membrane. Moreover, the milk EV fractions are enriched in RNA with distinct and diverging profiles from milk fat globules. Collectively, our data supports that successful milk EV isolation can be accomplished in few steps without the use of ultracentrifugation, as the presented isolation approaches based on SEC effectively isolates EV in both human and bovine milk. PMID:28386391

  6. Longitudinal Pathways from Math Intrinsic Motivation and Achievement to Math Course Accomplishments and Educational Attainment (United States)

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


    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…

  7. Accomplishing Marginalization in Bilingual Interaction: Relational Work as a Resource for the Intersubjective Construction of Identity (United States)

    Cashman, Holly R.


    This paper examines the use of impoliteness by Spanish-English bilingual pre-adolescents as a resource for accomplishing identities in spontaneous conversational interactions in an elementary school setting. The theoretical approach employed integrates the concept of relational work (Locher 2004; Locher and Watts 2005), which is based on Goffman's…

  8. Choosing Communication Portfolios to Accomplish Tasks: The Effects of Individual Differences (United States)

    Lee, Chei Sian; Goh, Dion Hoe-Lian; Chua, Alton Y. K; Luyt, Brendan


    The myriad of information communication technologies (ICTs) available today has changed the way students choose and use them. Specifically, individuals are increasingly relying on a mix of ICTs for communication to accomplish tasks. Yet, past studies on ICT use has largely assumed that people use a single ICT per task. We attempt to address this…

  9. DOE-NREL Minority University Research Associates Program FY 2005 Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Eddy, F. P.


    The DOE-NREL Minority University Research Associates (MURA) Program encourages minority students to pursue careers in science and technology. In 2003, eight minority-serving institutions were awarded 3-year subcontracts that began in the summer/fall of FY 2004. This paper lists accomplishments made in the project's first phase.

  10. Psycho-Social Influences on the Accomplishments of Mexican-American Students. (United States)

    MacCorquodale, Patricia

    The accomplishments of Mexican American students have been limited by the level of education completed and by concentration in particular occupations. As part of a larger research project concerning this problem, 259 eighth grade students from Tucson were compared on the basis of sex and ethnicity, with a focus on attitudes toward science. No…

  11. Empowering Adult Learners. NIF Literacy Program Helps ABE Accomplish Human Development Mission. (United States)

    Hurley, Mary E.


    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)

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

    NARCIS (Netherlands)

    Dijkstra, A; Ten Wolde, G


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

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

    Institute of Scientific and Technical Information of China (English)

    Zhang Yongtao


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

  14. Discussion on the teachers' language accomplishment%试论教师的语言素养

    Institute of Scientific and Technical Information of China (English)

    侯会美; 孙建翠


    The article discusses the new features of teachers'speech accomplishment and the meth-ods of improving teachers speech accomplishment. Teachers' language has the new features: personaliza-tion, emotionality, communicability, generative, reflexivity. Teachers should love the career of education, should study with an open mind and should train their own language in teaching practice. This article analy-zes teachers' language accomplishment and put forwards the suggestion of reform by the cultural heritage method and the method of observation. Teachers' language accomplishment affects directly the development of students' intelligence and the quality of the training.%新时期的教师语言呈现出新的特点:人格化、情感性、沟通性、生成性、反思性.教师只有热爱教育事业、虚心学习,在教育教学实践中不断锤炼,才能提高自身的语言素养.本文主要采用13常观察和文献检索的方法,探讨了教师的语言素养问题,指出教师的语言素养在很大程度上决定着学生的学习效率和教育教学的效果.

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

    Energy Technology Data Exchange (ETDEWEB)



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

  16. Activities and Accomplishments in Various Domains: Relationships with Creative Personality and Creative Motivation in Adolescence (United States)

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


    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.…

  17. Bovine colostrum: an emerging nutraceutical. (United States)

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


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

  18. YeastIP: a database for identification and phylogeny of Saccharomycotina yeasts. (United States)

    Weiss, Stéphanie; Samson, Franck; Navarro, David; Casaregola, Serge


    With the advances in sequencing techniques, identification of ascomycetous yeasts to the species level and phylogeny reconstruction increasingly require curated and updated taxonomic information. A specific database with nucleotide sequences of the most common markers used for yeast taxonomy and phylogeny and a user-friendly interface allowing identification, taxonomy and phylogeny of yeasts species was developed. By 1 September 2012, the YeastIP database contained all the described Saccharomycotina species for which sequences used for taxonomy and phylogeny, such as D1/D2 rDNA and ITS, are available. The database interface was developed to provide a maximum of relevant information and data mining tools, including the following features: (1) the blast n program for the sequences of the YeastIP database; (2) easy retrieval of selected sequences; (3) display of the available markers for each selected group of species; and (4) a tool to concatenate marker sequences, including those provided by the user. The concatenation tool allows phylogeny reconstruction through a direct link to the platform. YeastIP is thus a unique database in that it provides taxonomic information and guides users in their taxonomic analyses. YeastIP facilitates multigenic analysis to encourage good practice in ascomycetous yeast phylogeny (URL:

  19. Recent Progress in Cryopreservation of Bovine Oocytes

    Directory of Open Access Journals (Sweden)

    In-Sul Hwang


    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.

  20. Phylogeny mandalas of birds using the lithographs of John Gould's folio bird books. (United States)

    Hasegawa, Masami; Kuroda, Sayako


    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.

  1. Echinothurioid phylogeny and the phylogenetic significance of Kamptosoma (Echinoidea: Echinodermata) (United States)

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


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

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

    Directory of Open Access Journals (Sweden)

    Guilhaumon Claire


    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

  3. The evolution of bovine viral diarrhea: a review


    Goens, Denise


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

  4. Neurological disorder in cattle associated with bovine herpesvirus 4



    A nested PCR assay was used to diagnose bovine encephalitis through herpesviruses including bovine herpesvirus 5 (BHV-5), bovine herpesvirus 1 (BHV-1), Aujeszky's disease virus (SHV-1), and ovine herpesvirus 2 (OHV-2) in 14 fragments of central nervous system (CNS) from cattle that died with neurological signs. In addition, as some samples of bovine herpesvirus type 4 (BHV-4) have been isolated from neural tissue, it was also tested by nested PCR. The cases of encephalitis occurred in isolati...

  5. Arachidonate metabolism in bovine gallbladder muscle

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

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

    Institute of Scientific and Technical Information of China (English)

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


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

  7. Bilateral absence of fibularis tertius: clinical implications and phylogeny

    Directory of Open Access Journals (Sweden)

    Iyer PB


    Full Text Available Fibularis tertius (FT muscle is found in the anterior compartment of the leg. It assists in dorsiflexion and eversion of foot. The FT muscle originates from the distal third of the medial surface of fibula, the adjoining interosseous membrane and the anterior intermuscular septum. It is inserted on the dorsal surface of the base of the fifth metatarsal. During routine dissection of an adult female cadaver, a bilateral absence of FT was observed. Cases of absence of FT may be asymptomatic; it may be accidentally detected during dissection or autopsies. FT when present, may act in swing phase of gait. Its tendon may be used in transplantation and treatment of ankle laxity. Stress fracture of the fifth metatarsal may be produced by the pull of FT. Surgeons planning tendon transplants might be perplexed by absence of FT. The clinical implications and phylogeny of the bilateral absence of FT are discussed.

  8. Pericentric satellite DNA and molecular phylogeny in Acomys (Rodentia). (United States)

    Kunze, B; Traut, W; Garagna, S; Weichenhan, D; Redi, C A; Winking, H


    Satellite DNAs (stDNAs) of four Acomys species (spiny-mice), A. cahirinus, A. cineraceus, A. dimidiatus and A. russatus, belong to closely related sequence families. Monomer sizes range from 338 to 364 bp. Between-species sequence identity was from 81.0% to 97.2%. The molecular phylogeny of the sequences helps to clarify the taxonomy of this 'difficult' group. The A. dimidiatus genome contains about 60000 repeats. According to the restriction patterns, repeats are arranged in tandem. The stDNA maps to the centromeric heterochromatin of most autosomes, both acrocentric and metacentric, but appears to be absent in the centromeric region of Y chromosomes. A well-conserved centromere protein B (CENP-B) box is present in the stDNA of A. russatus while it is degenerated in the other species.

  9. A differentiation-based phylogeny of cancer subtypes.

    Directory of Open Access Journals (Sweden)

    Markus Riester


    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.

  10. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies. (United States)

    Spielman, Stephanie J; Wilke, Claus O


    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

  11. 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.

  12. Phylogeny and comparative genome analysis of a Basidiomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  13. Re-evaluating the phylogeny of allopolyploid Gossypium L. (United States)

    Grover, Corrinne E; Gallagher, Joseph P; Jareczek, Josef J; Page, Justin T; Udall, Joshua A; Gore, Michael A; Wendel, Jonathan F


    The formation of allopolyploid cotton precipitated a rapid diversification and colonization of dry coastal American tropical and subtropical regions. Previous phylogenetic analyses, combined with molecular divergence analyses, have offered a temporal framework for this radiation, but provide only weak support for some of the resolved branches. Moreover, these earlier analyses did not include the recently recognized sixth polyploid species, G. ekmanianum Wittmack. Here we use targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses to reevaluate the phylogeny of allopolyploid cotton species. Although phylogenetic resolution afforded by individual genes is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here.

  14. Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

    KAUST Repository

    Salari, Raheleh


    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.

  15. A composite molecular phylogeny of living lemuroid primates. (United States)

    DelPero, Massimiliano; Pozzi, Luca; Masters, Judith C


    Lemuroid phylogeny is a source of lively debate among primatologists. Reconstructions based on morphological, physiological, behavioural and molecular data have yielded a diverse array of tree topologies with few nodes in common. In the last decade, molecular phylogenetic studies have grown in popularity, and a wide range of sequences has been brought to bear on the problem, but consensus has remained elusive. We present an analysis based on a composite molecular data set of approx. 6,400 bp assembled from the National Center for Biotechnology Information (NCBI) database, including both mitochondrial and nuclear genes, and diverse analytical methods. Our analysis consolidates some of the nodes that were insecure in previous reconstructions, but is still equivocal on the placement of some taxa. We conducted a similar analysis of a composite data set of approx. 3,600 bp to investigate the controversial relationships within the family Lemuridae. Here our analysis was more successful; only the position of Eulemur coronatus remained uncertain.

  16. 76 FR 26239 - Bovine Tuberculosis and Brucellosis; Public Meetings (United States)


    ...; ] 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...

  17. 76 FR 38602 - Bovine Tuberculosis and Brucellosis; Program Framework (United States)


    ... 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...

  18. 9 CFR 113.310 - Bovine Rhinotracheitis Vaccine. (United States)


    ... 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...

  19. 9 CFR 113.309 - Bovine Parainfluenza3 Vaccine. (United States)


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

  20. 9 CFR 113.311 - Bovine Virus Diarrhea Vaccine. (United States)


    ... 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....

  1. Cloning and sequencing of the bovine gastrin gene

    DEFF Research Database (Denmark)

    Lund, T; Rehfeld, J F; Olsen, Jørgen


    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...

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


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

  3. Phylogeny of Gobioidei and the origin of European gobies

    Directory of Open Access Journals (Sweden)

    Ainhoa Agorreta


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

  4. Molecular phylogeny of the burying beetles (Coleoptera: Silphidae: Nicrophorinae). (United States)

    Sikes, Derek S; Venables, Chandra


    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.

  5. Nuclear and mitochondrial genes for inferring Trichuris phylogeny. (United States)

    Callejón, Rocío; Cutillas, Cristina; Nadler, Steven A


    Nucleotide sequences of the triose phosphate isomerase (TPI) gene (624 bp) and mitochondrial cytochrome b (cob) gene (520 bp) were obtained by PCR and evaluated for utility in inferring the phylogenetic relationships among Trichuris species. Published sequences of one other nuclear gene (18S or SSU rRNA, 1816-1846 bp) and one additional mitochondrial (mtDNA) gene (cytochrome oxidase 1, cox1, 342 bp) were also analyzed. Maximum likelihood and Bayesian inference methods were used to infer phylogenies for each gene separately but also for the combined mitochondrial data (two genes), the combined nuclear data (two genes), and the total evidence (four gene) dataset. Few Trichuris clades were uniformly resolved across separate analyses of individual genes. For the mtDNA, the cob gene trees had greater phylogenetic resolution and tended to have higher support values than the cox1 analyses. For nuclear genes, the SSU gene trees had slightly greater resolution and support values than the TPI analyses, but TPI was the only gene with reliable support for the deepest nodes in the tree. Combined analyses of genes yielded strongly supported clades in most cases, with the exception of the relationship among Trichuris clades 1, 2, and 3, which showed conflicting results between nuclear and mitochondrial genes. Both the TPI and cob genes proved valuable for inferring Trichuris relationships, with greatest resolution and support values achieved through combined analysis of multiple genes. Based on the phylogeny of the combined analysis of nuclear and mitochondrial genes, parsimony mapping of definitive host utilization depicts artiodactyls as the ancestral hosts for these Trichuris, with host-shifts into primates, rodents, and Carnivora.

  6. An Alu-Based Phylogeny of Lemurs (Infraorder: Lemuriformes) (United States)

    McLain, Adam T.; Meyer, Thomas J.; Faulk, Christopher; Herke, Scott W.; Oldenburg, J. Michael; Bourgeois, Matthew G.; Abshire, Camille F.


    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 exclusion of

  7. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed


    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. 公民信息素养教育%On the Education of Citizen Information Accomplishment

    Institute of Scientific and Technical Information of China (English)



    This paper briefly introduces the definition of informa-tion accomplishment and its education, as well as the current sit-uation of information accomplishment education. And it focuses on the countermeasures for the education of citizen information accomplishment—school education and public library education.%  本文简述了信息素养与信息素养教育的概念,及信息素养教育的现状,重点论述了对公民进行信息素养教育的对策——学校教育和公共图书馆教育。

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

    Directory of Open Access Journals (Sweden)

    Sánchez A.


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

  11. Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada, Heterotardigrada)

    DEFF Research Database (Denmark)

    Guil, Noemi; Jorgensen, Aslak; Giribet, Gonzalo


    Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ...

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

    DEFF Research Database (Denmark)

    Fredslund, Jakob


    Background The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like......-processing the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create...... a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus...

  13. Scientific Opinion on bovine lactoferrin

    Directory of Open Access Journals (Sweden)

    EFSA Panel on Dietetic Products, Nutrition and Allergies


    Full Text Available

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

  14. Molecular differentiation of bovine sarcocysts. (United States)

    Akhlaghi, Majedeh; Razavi, Mostafa; Hosseini, Arsalan


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

  15. Timing and order of transmission events is not directly reflected in a pathogen phylogeny. (United States)

    Romero-Severson, Ethan; Skar, Helena; Bulla, Ingo; Albert, Jan; Leitner, Thomas


    Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of more than 1 host occur within hosts, not at the moment of transmission, predating the transmission events as described by the pretransmission interval. Second, the order in which nodes in a phylogeny occur may be reflective of the within-host dynamics rather than epidemiologic relationships. To investigate these phenomena, motivated by within-host diversity patterns, we developed a two-phase coalescent model that includes a transmission bottleneck followed by linear outgrowth to a maximum population size followed by either stabilization or decline of the population. The model predicts that the pretransmission interval shrinks compared with predictions based on constant population size or a simple transmission bottleneck. Because lineages coalesce faster in a small population, the probability of a pathogen phylogeny to resemble the transmission history depends on when after infection a donor transmits to a new host. We also show that the probability of inferring the incorrect order of multiple transmissions from the same host is high. Finally, we compare time of HIV-1 infection informed by genetic distances in phylogenies to independent biomarker data, and show that, indeed, the pretransmission interval biases phylogeny-based estimates of when transmissions occurred. We describe situations where caution is needed not to misinterpret which parts of a phylogeny that may indicate outbreaks and tight transmission clusters.

  16. Variation in the transfer of radionuclide to freshwater fish: phylogeny or feeding strategy?


    Yankovich, T.; Beresford, N. A.; Wood, M.; Willey, N.


    For both terrestrial vascular plants and marine organisms if has been demonstrated the differences in radionuclide transfer between species can be related to their evolutionary history or phylogeny. Relationships between phylogeny and radionuclide transfer offer a potential approach to help to derive best estimate values if data for a given species-radionuclide are not available. In this paper we describe the analyses of data for radionuclide transfer to freshwater fish from a data base re...

  17. Recombinant Bovine Growth Hormone Criticism Grows. (United States)

    Gaard, Greta


    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.…

  18. Abnormal fibrillin metabolism in bovine Marfan syndrome. (United States)

    Potter, K. A.; Hoffman, Y.; Sakai, L. Y.; Byers, P. H.; Besser, T. E.; Milewicz, D. M.


    Bovine Marfan syndrome is a disorder that closely resembles human Marfan syndrome in its clinical signs and pathological lesions. The similarities between the human and bovine diseases suggest that similar metabolic defects could be responsible. Although indirect immunofluorescent assays for fibrillin in skin biopsies did not distinguish affected cattle from control animals, cultures of skin fibroblasts of affected animals were distinguished from normal, unrelated control animals and normal half-siblings on the basis of fibrillin staining. After 72 to 96 hours in culture, stained with anti-fibrillin monoclonal antibody 201, hyperconfluent fibroblast cultures of affected cattle had less immunoreactive fibrillin than control cultures, and the staining pattern was granular rather than fibrillar. Under similar culture conditions, normal bovine aortic smooth muscle cells produced large amounts of immunoreactive fibrillin, but smooth muscle cells from a single affected cow showed markedly less fibrillin staining. In pulse-chase metabolic labeling experiments with [35S]cysteine, dermal fibroblasts from 6 affected calves, incorporated far less fibrillin into the extracellular matrix than control cells. These findings are similar to those reported in human Marfan syndrome, and they suggest that the bovine Marfan syndrome, like the human disorder, is caused by a mutation in fibrillin, leading to defective microfibrillar synthesis. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:8456941

  19. Bovine viral diarrhea virus: biosecurity and control (United States)

    This paper discusses the recommended procedures involved in setting up biosecurity and control programs designed to limit bovine viral diarrhea virus infections in beef cattle operations. For the purpose of these discussions, a working definition of a biosecurity plan was considered to be an organiz...

  20. Characterization of the bovine ampkgamma1 gene. (United States)

    Benkel, Bernhard; Kollers, Sonja; Fries, Ruedi; Sazanov, Alexei; Yoshida, Erin; Valle, Edith; Davoren, Jon; Hickey, Donal


    AMP-activated protein kinase (AMPK) represents the mammalian form of the core component of a kinase cascade that is conserved between fungi, plants, and animals. AMPK plays a major role in protecting mammalian cells from metabolic stress by switching off biosynthetic pathways that require ATP and switching on ATP-regenerating pathways. In this report, we describe the isolation and characterization of the gene for the noncatalytic bovine gamma1 subunit of AMPK. The bovine ampkgamma1 (PRKAG1) gene spans in excess of 14 kb and is located at BTA 5q21-q22. It consists of 12 exons ranging in size from 38 b to 166 b, interspersed with 11 introns that range between 97 b and 6753 b in length. The coding region of the bovine gene shares 93% and 90% nucleotide sequence similarity with its human and rat counterparts, and the bovine AMPKgamma1 protein is 98% and 95% identical to its human and rat homologs, respectively, in amino acid sequence. SNP discovery using a cattle DNA panel revealed a number of polymorphisms that may be useful for the evaluation of ampkgamma1 as a candidate gene for energy metabolism-related production traits.

  1. Vaccination of cattle against bovine viral diarrhoea

    NARCIS (Netherlands)

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


    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 va

  2. An unusual presentation of enzootic bovine leukosis.


    Sparling, A M


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


    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...

  4. Epidemiology and control of bovine ephemeral fever. (United States)

    Walker, Peter J; Klement, Eyal


    Bovine ephemeral fever (or 3-day sickness) is an acute febrile illness of cattle and water buffaloes. Caused by an arthropod-borne rhabdovirus, bovine ephemeral fever virus (BEFV), the disease occurs seasonally over a vast expanse of the globe encompassing much of Africa, the Middle East, Asia and Australia. Although mortality rates are typically low, infection prevalence and morbidity rates during outbreaks are often very high, causing serious economic impacts through loss of milk production, poor cattle condition at sale and loss of traction power at harvest. There are also significant impacts on trade to regions in which the disease does not occur, including the Americas and most of Europe. In recent years, unusually severe outbreaks of bovine ephemeral fever have been reported from several regions in Asia and the Middle East, with mortality rates through disease or culling in excess of 10-20%. There are also concerns that, like other vector-borne diseases of livestock, the geographic distribution of bovine ephemeral fever could expand into regions that have historically been free of the disease. Here, we review current knowledge of the virus, including its molecular and antigenic structure, and the epidemiology of the disease across its entire geographic range. We also discuss the effectiveness of vaccination and other strategies to prevent or control infection.


    Directory of Open Access Journals (Sweden)

    I. V. Goraichuk


    Full Text Available Bovine viral diarrhea is a widespread infection of cattle that has a wide range of clinical symptoms in domestic and wild ruminants. It is a major problem in cattle and causes significant economic losses in the cattle industry. The virus infects bovines of all ages and causes both immunosuppression and reproductive, respiratory and digestive disorders. Persistently infected cattle are the main factor in transmission of the disease between and among herds. Comparative results of antibodies presence received by two methods of enzymoimmunoassay and virus neutralization test are given in the paper. During the work, 1010 samples of blood serum of cattle from three farms in the Kharkiv region were selected and analyzed. Bovine viral diarrhea virus concerning antibodies were found by enzymoimmunoassay in 704 samples (69.7% using commercial kit and in 690 samples (68.3% using in house method. After results clarification by virus neutralization test, bovine viral diarrhea antibodies were found in 712 samples (70.5%. Immunoenzyme analysis is recommended for mass screening of cattle for viral diarrhea occurrence. The results confirm that the sensitivity immunoenzyme analysis satisfies the requirements of the diagnostic methods. Using the neutralization reaction of viruses as the «gold standard» of serological methods, it is appropriate to clarify the results of immunoenzyme analysis. Since the results contain a signi ficant number of false positive results, it is necessary to carry out comprehensive studies using both serological and molecular genetics methods.

  6. Transmission of new bovine prion to mice

    NARCIS (Netherlands)

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


    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 mi

  7. Aortic reconstruction with bovine pericardial grafts

    Directory of Open Access Journals (Sweden)

    Silveira Lindemberg Mota


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

  8. Molecular biology of bovine viral diarrhea virus (United States)

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

  9. 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.


    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 dete

  10. Pasteurella multocida and bovine respiratory disease. (United States)

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


    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.

  11. Proficiency test for antibiotics in bovine muscle

    NARCIS (Netherlands)

    Elbers, I.J.W.; Berendsen, B.J.A.; Pikkemaat, M.G.; Stolker, A.A.M.


    The aim of this proficiency study was to give laboratories the possibility to evaluate or demonstrate their competence for the analysis of antibiotics in bovine muscle, including the screening analysis. This study also provided an evaluation of the methods applied for screening and quantitative conf

  12. Aggregation and fibrillation of bovine serum albumin

    DEFF Research Database (Denmark)

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


    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...


    NARCIS (Netherlands)



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

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

    Directory of Open Access Journals (Sweden)

    Maia S. Marin


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

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

    Directory of Open Access Journals (Sweden)

    Iulia Tutuianu


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Menicucci, D.F.


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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


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

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

    Ballard, Richard O.


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

  19. Bovine rhinitis viruses are common in U.S. cattle with bovine respiratory disease. (United States)

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


    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.

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

    Directory of Open Access Journals (Sweden)

    Ben M Hause

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

  1. Therapeutic anticoagulation can be safely accomplished in selected patients with traumatic intracranial hemorrhage

    Directory of Open Access Journals (Sweden)

    Byrnes Matthew C


    Full Text Available Abstract Introduction Therapeutic anticoagulation is an important treatment of thromboembolic complications, such as DVT, PE, and blunt cerebrovascular injury. Traumatic intracranial hemorrhage has traditionally been considered to be a contraindication to anticoagulation. Hypothesis Therapeutic anticoagulation can be safely accomplished in select patients with traumatic intracranial hemorrhage. Methods Patients who developed thromboembolic complications of DVT, PE, or blunt cerebrovascular injury were stratified according to mode of treatment. Patients who underwent therapeutic anticoagulation with a heparin infusion or enoxaparin (1 mg/kg BID were evaluated for neurologic deterioration or hemorrhage extension by CT scan. Results There were 42 patients with a traumatic intracranial hemorrhage that subsequently developed a thrombotic complication. Thirty-five patients developed a DVT or PE. Blunt cerebrovascular injury was diagnosed in four patients. 26 patients received therapeutic anticoagulation, which was initiated an average of 13 days after injury. 96% of patients had no extension of the hemorrhage after anticoagulation was started. The degree of hemorrhagic extension in the remaining patient was minimal and was not felt to affect the clinical course. Conclusion Therapeutic anticoagulation can be accomplished in select patients with intracranial hemorrhage, although close monitoring with serial CT scans is necessary to demonstrate stability of the hemorrhagic focus.

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

    Directory of Open Access Journals (Sweden)

    Yaobin Lu


    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.

  3. robust phylogenetic analysis for the non-specialist (United States)

    Dereeper, A.; Guignon, V.; Blanc, G.; Audic, S.; Buffet, S.; Chevenet, F.; Dufayard, J.-F.; Guindon, S.; Lefort, V.; Lescot, M.; Gascuel, O.


    Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. offers three main modes. The ‘One Click’ mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The ‘Advanced’ mode uses the same pipeline but allows the parameters of each program to be customized by users. The ‘A la Carte’ mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. is available at: PMID:18424797

  4. Phylogeny of the Botryosphaeriaceae reveals patterns of host association. (United States)

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


    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.

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

    Directory of Open Access Journals (Sweden)

    Sebastian Hess

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

  6. Feeding innovations in a nested phylogeny of Neotropical passerines (United States)

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


    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. PMID:26926278

  7. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. (United States)

    Lartillot, Nicolas; Philippe, Hervé


    Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both genes and species, combined with a probabilistic method (maximum likelihood or Bayesian) using sophisticated models of sequence evolution, should alleviate these two major limitations. We applied this approach to a dataset of 94 genes and 79 species using CAT, a previously developed model accounting for site-specific amino acid replacement patterns. The resulting tree is in good agreement with current knowledge: the monophyly of most major groups (e.g. Chordata, Arthropoda, Lophotrochozoa, Ecdysozoa, Protostomia) was recovered with high support. Two results are surprising and are discussed in an evo-devo framework: the sister-group relationship of Platyhelminthes and Annelida to the exclusion of Mollusca, contradicting the Neotrochozoa hypothesis, and, with a lower statistical support, the paraphyly of Deuterostomia. These results, in particular the status of deuterostomes, need further confirmation, both through increased taxonomic sampling, and future improvements of probabilistic models.

  8. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers. (United States)

    Pavan-Kumar, A; Gireesh-Babu, P; Babu, P P Suresh; Jaiswar, A K; Hari Krishna, V; Prasasd, K Pani; Chaudhari, Aparna; Raje, S G; Chakraborty, S K; Krishna, Gopal; Lakra, W S


    The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing worldwide, the elasmobranch stocks are being decimated at an alarming rate. Appropriate management measures are necessary for restoring depleted elasmobranch stocks. One approach for restoring stocks is implementation of conservation measures and these measures can be formulated effectively by knowing the evolutionary relationship among the elasmobranchs. In this study, a total of 30 species were chosen for molecular phylogeny studies using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA gene and nuclear Internal Transcribed Spacer 2. Among different genes, the combined dataset of COI and 12S rRNA resulted in a well resolved tree topology with significant bootstrap/posterior probabilities values. The results supported the reciprocal monophyly of sharks and batoids. Within Galeomorphii, Heterodontiformes (bullhead sharks) formed as a sister group to Lamniformes (mackerel sharks): Orectolobiformes (carpet sharks) and to Carcharhiniformes (ground sharks). Within batoids, the Myliobatiformes formed a monophyly group while Pristiformes (sawfishes) and Rhinobatiformes (guitar fishes) formed a sister group to all other batoids.

  9. Global phylogeny and biogeography of grammitid ferns (Polypodiaceae). (United States)

    Sundue, Michael A; Parris, Barbara S; Ranker, Tom A; Smith, Alan R; Fujimoto, Erin L; Zamora-Crosby, Delia; Morden, Clifford W; Chiou, Wen-Liang; Chen, Cheng-Wei; Rouhan, Germinal; Hirai, Regina Y; Prado, Jefferson


    We examined the global historical biogeography of grammitid ferns (Polypodiaceae) within a phylogenetic context. We inferred phylogenetic relationships of 190 species representing 31 of the 33 currently recognized genera of grammitid ferns by analyzing DNA sequence variation of five plastid DNA regions. We estimated the ages of cladogenetic events on an inferred phylogeny using secondary fossil calibration points. Historical biogeographical patterns were inferred via ancestral area reconstruction. Our results supported four large-scale phylogenetic and biogeographic patterns: (1) a monophyletic grammitid clade that arose among Neotropical polypod ancestors about 31.4 Ma; (2) a paraphyletic assemblage of clades distributed in the Neotropics and the Afro-Malagasy region; (3) a large clade distributed throughout the Asia-Malesia-Pacific region that originated about 23.4 Ma; and, (4) an Australian or New Zealand origin of the circumaustral genus Notogrammitis. Most genera were supported as monophyletic except for Grammitis, Oreogrammitis, Radiogrammitis, and Zygophlebia. Grammitid ferns are a well-supported monophyletic group with two biogeographically distinct lineages: a primarily Neotropical grade exhibiting several independent successful colonizations to the Afro-Malagasy region and a primarily Paleotropical clade exhibiting multiple independent dispersals to remote Pacific islands and temperate, austral regions.

  10. Deep phylogeny, ancestral groups and the four ages of life. (United States)

    Cavalier-Smith, Thomas


    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.

  11. A unified phylogeny-based nomenclature for histone variants

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    Talbert Paul B


    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.

  12. Complete, accurate, mammalian phylogenies aid conservation planning, but not much (United States)

    Rodrigues, Ana S. L.; Grenyer, Richard; Baillie, Jonathan E. M.; Bininda-Emonds, Olaf R. P.; Gittlemann, John L.; Hoffmann, Michael; Safi, Kamran; Schipper, Jan; Stuart, Simon N.; Brooks, Thomas


    In the face of unprecedented global biodiversity loss, conservation planning must balance between refining and deepening knowledge versus acting on current information to preserve species and communities. Phylogenetic diversity (PD), a biodiversity measure that takes into account the evolutionary relationships between species, is arguably a more meaningful measure of biodiversity than species diversity, but cannot yet be applied to conservation planning for the majority of taxa for which phylogenetic trees have not yet been developed. Here, we investigate how the quality of data on the taxonomy and/or phylogeny of species affects the results of spatial conservation planning in terms of the representation of overall mammalian PD. The results show that the better the quality of the biodiversity data the better they can serve as a basis for conservation planning. However, decisions based on incomplete data are remarkably robust across different levels of degrading quality concerning the description of new species and the availability of phylogenetic information. Thus, given the level of urgency and the need for action, conservation planning can safely make use of the best available systematic data, limited as these data may be. PMID:21844044

  13. Moss Phylogeny Reconstruction Using Nucleotide Pangenome of Complete Mitogenome Sequences. (United States)

    Goryunov, D V; Nagaev, B E; Nikolaev, M Yu; Alexeevski, A V; Troitsky, A V


    Stability of composition and sequence of genes was shown earlier in 13 mitochondrial genomes of mosses (Rensing, S. A., et al. (2008) Science, 319, 64-69). It is of interest to study the evolution of mitochondrial genomes not only at the gene level, but also on the level of nucleotide sequences. To do this, we have constructed a "nucleotide pangenome" for mitochondrial genomes of 24 moss species. The nucleotide pangenome is a set of aligned nucleotide sequences of orthologous genome fragments covering the totality of all genomes. The nucleotide pangenome was constructed using specially developed new software, NPG-explorer (NPGe). The stable part of the mitochondrial genome (232 stable blocks) is shown to be, on average, 45% of its length. In the joint alignment of stable blocks, 82% of positions are conserved. The phylogenetic tree constructed with the NPGe program is in good correlation with other phylogenetic reconstructions. With the NPGe program, 30 blocks have been identified with repeats no shorter than 50 bp. The maximal length of a block with repeats is 140 bp. Duplications in the mitochondrial genomes of mosses are rare. On average, the genome contains about 500 bp in large duplications. The total length of insertions and deletions was determined in each genome. The losses and gains of DNA regions are rather active in mitochondrial genomes of mosses, and such rearrangements presumably can be used as additional markers in the reconstruction of phylogeny.

  14. The rRNA evolution and procaryotic phylogeny (United States)

    Fox, G. E.


    Studies of ribosomal RNA primary structure allow reconstruction of phylogenetic trees for prokaryotic organisms. Such studies reveal major dichotomy among the bacteria that separates them into eubacteria and archaebacteria. Both groupings are further segmented into several major divisions. The results obtained from 5S rRNA sequences are essentially the same as those obtained with the 16S rRNA data. In the case of Gram negative bacteria the ribosomal RNA sequencing results can also be directly compared with hybridization studies and cytochrome c sequencing studies. There is again excellent agreement among the several methods. It seems likely then that the overall picture of microbial phylogeny that is emerging from the RNA sequence studies is a good approximation of the true history of these organisms. The RNA data allow examination of the evolutionary process in a semi-quantitative way. The secondary structures of these RNAs are largely established. As a result it is possible to recognize examples of local structural evolution. Evolutionary pathways accounting for these events can be proposed and their probability can be assessed.

  15. Phylogeny of marine Bacillus isolates from the Gulf of Mexico (United States)

    Siefert, J. L.; Larios-Sanz, M.; Nakamura, L. K.; Slepecky, R. A.; Paul, J. H.; Moore, E. R.; Fox, G. E.; Jurtshuk, P. Jr


    The phylogeny of 11 pigmented, aerobic, spore-forming isolates from marine sources was studied. Forty-two biochemical characteristics were examined, and a 16S rDNA sequence was obtained for each isolate. In a phylogenetic tree based on 16S sequencing, four isolates (NRRL B-14850, NRRL B-14904, NRRL B-14907, and NRRL B-14908) clustered with B. subtilis and related organisms; NRRL B-14907 was closely related to B. amyloliquefaciens. NRRL B-14907 and NRRL B-14908 were phenotypically similar to B. amyloliquefaciens and B. pumilus, respectively. Three strains (NRRL B-14906, NRRL B-14910, and NRRL B-14911) clustered in a clade that included B. firmus, B. lentus, and B. megaterium. NRRL B-14910 was closely related phenotypically and phylogenetically to B. megaterium. NRRL B-14905 clustered with the mesophilic round spore-producing species, B. fusiformis and B. sphaericus; the isolate was more closely related to B. fusiformis. NRRL B-14905 displayed characteristics typical of the B. sphaericus-like organisms. NRRL B-14909 and NRRL B-14912 clustered with the Paenibacillus species and displayed characteristics typical of the genus. Only NRRL B-14851, an unusually thin rod that forms very small spores, may represent a new Bacillus species.

  16. Genomes-based phylogeny of the genus Xanthomonas

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    Rodriguez-R Luis M


    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.

  17. The phylogeny and evolutionary history of tyrannosauroid dinosaurs (United States)

    Brusatte, Stephen L.; Carr, Thomas D.


    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.

  18. Arthropod phylogeny based on eight molecular loci and morphology (United States)

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


    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.

  19. Neotropical mutualism between Acacia and Pseudomyrmex: phylogeny and divergence times. (United States)

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


    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.

  20. Robust markers reflecting phylogeny and taxonomy of rhizobia.

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    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.

  1. Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

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    Agostinho Antunes


    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.

  2. Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. (United States)

    White, Merlin M; James, Timothy Y; O'Donnell, Kerry; Cafaro, Matías J; Tanabe, Yuuhiko; Sugiyama, Junta


    The Zygomycota is an ecologically heterogenous assemblage of nonzoosporic fungi comprising two classes, Zygomycetes and Trichomycetes. Phylogenetic analyses have suggested that the phylum is polyphyletic; two of four orders of Trichomycetes are related to the Mesomycetozoa (protists) that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S (SSU), 5.8S and 28S (LSU) genes. Tree reconstruction by Bayesian analyses suggests the Zygomycota is paraphyletic. Although 12 clades were identified only some of these correspond to the nine orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales and Zoopagales, grouping together many symbiotic fungi, also is identified in part by a unique septal structure. Although Harpellales and Kickxellales are not monophyletic, these lineages are distinct from the Mucorales, Endogonales and Mortierellales, which appear more closely related to the Ascomycota + Basidiomycota + Glomeromycota. The final major group, the insect-associated Entomophthorales, appears to be polyphyletic. In the present analyses Basidiobolus and Neozygites group within Zygomycota but not with the Entomophthorales. Clades are discussed with special reference to traditional classifications, mapping morphological characters and ecology, where possible, as a snapshot of our current phylogenetic perspective of the Zygomycota.

  3. Phylogeny of kangaroo apples (Solanum subg. Archaesolanum, Solanaceae). (United States)

    Poczai, Péter; Hyvönen, Jaakko; Symon, David E


    Kangaroo apples, subgenus Archaesolanum, are a unique and still poorly known group within the genus Solanum. Here we aimed to reveal phylogeny, historical biogeography and age of diversification of Archaesolanum. We sampled all recognized species of the group and sequenced three chloroplast regions, the trnT-trnL spacer, trnL intron and trnL-trnF spacer to calibrate a molecular clock to estimate the age of the group. Distributional data were combined with the results of phylogenetic analysis to track the historical processes responsible for the current range of the group. Our analysis supported the monophyly of the kangaroo apples and the biogeographical disjunction between the two subclades within the group. Based on the divergence time estimates the most recent common ancestor of kangaroo apples is from the late Miocene age (~9 MYA). Based on the age estimate the common ancestors of the kangaroo apples are presumed to have arrived in Australia by long-distance dispersal. The two distinct lineages within the group have separated during the aridification of the continent and further speciated in the brief resurgence of rainforests during the Pliocene.

  4. Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. (United States)

    Fernández, Rosa; Laumer, Christopher E; Vahtera, Varpu; Libro, Silvia; Kaluziak, Stefan; Sharma, Prashant P; Pérez-Porro, Alicia R; Edgecombe, Gregory D; Giribet, Gonzalo


    Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.

  5. A comprehensive molecular phylogeny for the hornbills (Aves: Bucerotidae). (United States)

    Gonzalez, Juan-Carlos T; Sheldon, Ben C; Collar, Nigel J; Tobias, Joseph A


    The hornbills comprise a group of morphologically and behaviorally distinct Palaeotropical bird species that feature prominently in studies of ecology and conservation biology. Although the monophyly of hornbills is well established, previous phylogenetic hypotheses were based solely on mtDNA and limited sampling of species diversity. We used parsimony, maximum likelihood and Bayesian methods to reconstruct relationships among all 61 extant hornbill species, based on nuclear and mtDNA gene sequences extracted largely from historical samples. The resulting phylogenetic trees closely match vocal variation across the family but conflict with current taxonomic treatments. In particular, they highlight a new arrangement for the six major clades of hornbills and reveal that three groups traditionally treated as genera (Tockus, Aceros, Penelopides) are non-monophyletic. In addition, two other genera (Anthracoceros, Ocyceros) were non-monophyletic in the mtDNA gene tree. Our findings resolve some longstanding problems in hornbill systematics, including the placement of 'Penelopides exharatus' (embedded in Aceros) and 'Tockus hartlaubi' (sister to Tropicranus albocristatus). We also confirm that an Asiatic lineage (Berenicornis) is sister to a trio of Afrotropical genera (Tropicranus [including 'Tockus hartlaubi'], Ceratogymna, Bycanistes). We present a summary phylogeny as a robust basis for further studies of hornbill ecology, evolution and historical biogeography.

  6. Ribosomal DNA evolution and phylogeny in Aloe (Asphodelaceae). (United States)

    Adams, S P; Leitch, I J; Bennett, M D; Chase, M W; Leitch, A R


    All Aloe taxa (∼400 species) share a conserved bimodal karyotype with a basic genome of four large and three small submetacentric/acrocentric chromosomes. We investigated the physical organization of 18S-5.8S-26S and 5S ribosomal DNA (rDNA) using fluorescent in situ hybridization (FISH) to 13 Aloe species. The organization was compared with a phylogenetic tree of 28 species (including the 13 used for FISH) constructed by sequence analysis of the internal transcribed spacer (ITS) of 18S-5.8S-26S rDNA. The phylogeny showed little divergence within Aloe, although distinct, well-supported clades were found. FISH analysis of 5S rDNA distribution showed a similar interstitial location on a large chromosome in all species examined. In contrast, the distribution of 18S-5.8S-26S rDNA was variable, with differences in number, location, and size of loci found between species. Nevertheless, within well-supported clades, all species had the same organizational patterns. Thus, despite the striking stability of karyotype structure and location of 5S rDNA, the distribution of 18S-5.8S-26S rDNA is not so constrained and has clearly changed during Aloe speciation.

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

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


    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

  8. International Research Results and Accomplishments From the International Space Station - A New Compilation (United States)

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


    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 ( 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

  9. Dental fluorosis in bovine temporary teeth

    Energy Technology Data Exchange (ETDEWEB)

    Suttie, J.W.; Clay, A.B.; Shearer, T.R.


    Deciduous incisors from calves born to dams fed an average of 40 mg of fluoride/kg of forage ration (40 ppm) were compared with incisors from calves born to dams fed a normal dairy ration. Skeletal fluoride concentration in the calves born to fluoride-fed dams was increased 5 to 8 fold, but enamel mottling and hypoplasia, typical of permanent bovine incisor dental fluorosis were not seen by gross, histologic, or radiologic examination. Decreases in the amount of enamel on the tooth or hardness of the enamel were not observed. These data do not support recent reports of widespread dental fluorosis of deciduous bovine teeth as a clinical sign of fluoride toxicity.

  10. Mycoplasmas associated with bovine conjunctivitis and keratoconjunctivitis. (United States)

    Naglić, T; Sanković, F; Madić, J; Hajsig, D; Seol, B; Busch, K


    In two separate herds of fattening calves a sudden-onset outbreak of ocular disease with profuse lacrimation occurred. The disease resembled the early stage of infectious bovine keratoconjunctivitis but after a few days the clinical signs of bronchopneumonia appeared. From conjunctival swabs Mycoplasma (M.) bovigenitalium, M. bovirhinis and infectious bovine rhinotracheitis (IBR) virus were isolated. Moraxella bovis infection was not established. In one of the herds M. bovigenitalium was also found in the pneumonic lungs of dead calves. In one herd M. bovoculi was isolated from a cow with chronic keratoconjunctivitis, housed together with affected calves. Mycoplasmas were not isolated from ocular swabs of six bulls originating from a Reproductive Centre with temporary occurrence of unilateral serous conjunctivitis resistant to antibiotic therapy.

  11. Study of the protein-bound fraction of calcium, iron, magnesium and zinc in bovine milk (United States)

    Silva, Fernando V.; Lopes, Gisele S.; Nóbrega, Joaquim A.; Souza, Gilberto B.; Nogueira, Ana Rita A.


    Two approaches were used to study the interaction of Ca, Fe, Mg and Zn with bovine milk proteins by inductively coupled plasma optical emission spectrometry (ICPOES). Selective separations in bovine milk samples were accomplished employing an acid protein precipitation using 100 g l -1 trichloroacetic acid (TCA), and an enzymatic protein hydrolysis using 50 g l -1 pepsin (PEP) solution, respectively. The results were compared with total mineral contents determined after microwave-assisted acid digestion. The results obtained by enzymatic and acid precipitation evidenced the different interaction forms of Ca, Fe, Mg and Zn in the system formed by milk components. Iron was not solubilized by the TCA treatment, but was recovered completely after the enzymatic treatment. Quantitative recoveries of Ca, Mg and Zn were obtained using both approaches, showing that these analytes were bound to milk compounds affected by either treatment. Calcium, Mg and Zn are mainly associated with colloidal calcium phosphate and Fe is bound to the backbone of the casein polypeptide chain, cleaved by pepsin enzyme. The proposed approaches could be used to assess the complexity of these chemical interactions.

  12. 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.

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

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


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

  14. Mitochondrial phylogeny of the genus Echinococcus (Cestoda: Taeniidae) with emphasis on relationships among Echinococcus canadensis genotypes. (United States)

    Nakao, Minoru; Yanagida, Tetsuya; Konyaev, Sergey; Lavikainen, Antti; Odnokurtsev, Valeriy A; Zaikov, Vladimir A; Ito, Akira


    The mitochondrial genomes of the genus Echinococcus have already been sequenced for most species and genotypes to reconstruct their phylogeny. However, two important taxa, E. felidis and E. canadensis G10 genotype (Fennoscandian cervid strain), were lacking in the published phylogeny. In this study, the phylogeny based on mitochondrial genome sequences was completed with these taxa. The present phylogeny highly supports the previous one, with an additional topology showing sister relationships between E. felidis and E. granulosus sensu stricto and between E. canadensis G10 and E. canadensis G6/G7 (closely related genotypes referred to as camel and pig strains, respectively). The latter relationship has a crucial implication for the species status of E. canadensis. The cervid strain is composed of two genotypes (G8 and G10), but the present phylogeny clearly suggests that they are paraphyletic. The paraphyly was also demonstrated by analysing the complete nucleotide sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) of E. canadensis genotypes from various localities. A haplotype network analysis using the short cox1 sequences from worldwide isolates clearly showed a close relatedness of G10 to G6/G7. Domestic and sylvatic life cycles based on the host specificity of E. canadensis strains have been important for epidemiological considerations. However, the taxonomic treatment of the strains as separate species or subspecies is invalid from a molecular cladistic viewpoint.

  15. Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae). (United States)

    Wang, Fang; Ballesteros, Jesus A; Hormiga, Gustavo; Chesters, Douglas; Zhan, Yongjia; Sun, Ning; Zhu, Chaodong; Chen, Wei; Tu, Lihong


    For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, sometimes neither the current taxonomic system nor the established phylogeny can provide sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increasing taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.

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

    Directory of Open Access Journals (Sweden)

    Aziz Mithani

    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. Evidence for Parachlamydia in bovine abortions


    Ruhl, S; Casson, N.; Kaiser, C.; Thoma, R; Pospischil, A.; Greub, G; Borel, N.


    Bovine abortion of unknown infectious aetiology still remains a major economic problem. In this study, we focused on new possible abortigenic agents such as Parachlamydia acanthamoebae and Waddlia chondrophila. Retrospective samples (n = 235) taken from late-term abortions in cattle were investigated by real-time diagnostic PCR for Chlamydiaceae, rachlamydia spp. and Waddlia spp., respectively. Histological sections of cases positive by real-time PCR for any Chlamydia-related agent were furth...

  18. [Bovine viral diarrhea control in Russian Federation]. (United States)

    Guliukin, M I; Iurov, K P; Glotov, A G; Donchenko, N A


    Bovine viral diarrhea (BVD) is one of the greatest challenges for breeding and commercial livestock. It is characterized by lesions of the respiratory and gastrointestinal tract, abortion, infertility, immune deficiency, and persistence of the pathogen. In this work, a set of measures for the rehabilitation and prevention of BVD in cattle is described. It includes the data of the literature, guidance documents for the diagnosis and control of BVD adopted by OIE, EU countries, USA, as well as the results of this research.

  19. Experimental production of infectious bovine keratoconjunctivitis. (United States)

    Aikman, J G; Allan, E M; Selman, I E


    The left eyes of 10 conventional dairy cross calves were inoculated with a pathogenic strain of Moraxella bovis and lesions of infectious bovine keratoconjunctivitis developed in nine of these eyes. M bovis was isolated from all inoculated eyes and lesions developed in five out of 10 eyes which had become naturally infected. The clinical and microbiological findings were similar to those described in field cases.

  20. Photodynamically generated bovine serum albumin radicals

    DEFF Research Database (Denmark)

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


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

  1. Evidence for Parachlamydia in bovine abortion. (United States)

    Ruhl, Silke; Casson, Nicola; Kaiser, Carmen; Thoma, Ruedi; Pospischil, Andreas; Greub, Gilbert; Borel, Nicole


    Bovine abortion of unknown infectious aetiology still remains a major economic problem. In this study, we focused on a new possible abortigenic agent called Parachlamydia acanthamoebae. Retrospective samples (n=235) taken from late-term abortions in cattle were investigated by real-time diagnostic PCR for Chlamydiaceae and Parachlamydia spp., respectively. Histological sections of cases positive by real-time PCR for any Chlamydia-related agent were further examined by immunohistochemistry using specific antibodies. Chlamydophila abortus was detected only in three cases (1.3%) by real-time PCR and ArrayTube Microarray playing a less important role in bovine abortion compared to the situation in small ruminants in Switzerland. By real-time PCR as many as 43 of 235 (18.3%) cases turned out to be positive for Parachlamydia. The presence of Parachlamydia within placental lesions was confirmed in 35 cases (81.4%) by immunohistochemistry. The main histopathological feature in parachlamydial abortion was purulent to necrotizing placentitis (25/43). Parachlamydia should be considered as a new abortigenic agent in Swiss cattle. Since Parachlamydia may be involved in lower respiratory tract infections in humans, bovine abortion material should be handled with care given the possible zoonotic risk.

  2. Potential Anticarcinogenic Peptides from Bovine Milk

    Directory of Open Access Journals (Sweden)

    Giacomo Pepe


    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.

  3. Oxytocin binding sites in bovine mammary tissue

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xin.


    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.

  4. An accomplished teacher's use of scaffolding during a second-grade unit on designing games. (United States)

    Chen, Weiyun; Rovegno, Inez; Cone, Stephen L; Cone, Theresa P


    The purpose of this study was to describe how an accomplished teacher taught second-grade students to design games that integrated movement and mathematics content. The participants were one physical education teacher; a classroom teacher, and an intact class of 20 second-grade students. Qualitative data were gathered through videotaping of all lessons, descriptions of 20 children's responses to all lesson segments, and interviews with all participants. In keeping with constructivist principles, the teacher used a progression of tasks and multiple instructional techniques to scaffold the design process allowing children to design games that were meaningful to them. Contrary to descriptions of scaffolding fading across a unit, in this study the scaffolding was a function of the interaction between learners' needs and task content.

  5. Advanced Industrial Materials (AIM) program. Compilation of project summaries and significant accomplishments FY 1996

    Energy Technology Data Exchange (ETDEWEB)



    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.

  6. Accomplishing the Visions for Teacher Education Programs Advocated in the National Science Education Standards (United States)

    Akcay, Hakan; Yager, Robert


    The purpose of this study was to investigate the advantages of an approach to instruction using current problems and issues as curriculum organizers and illustrating how teaching must change to accomplish real learning. The study sample consisted of 41 preservice science teachers (13 males and 28 females) in a model science teacher education program. Both qualitative and quantitative research methods were used to determine success with science discipline-specific “Societal and Educational Applications” courses as one part of a total science teacher education program at a large Midwestern university. Students were involved with idea generation, consideration of multiple points of views, collaborative inquiries, and problem solving. All of these factors promoted grounded instruction using constructivist perspectives that situated science with actual experiences in the lives of students.

  7. Advanced Mirror Technology Development (AMTD) project: overview and year four accomplishments (United States)

    Stahl, H. Philip


    The Advanced Mirror Technology Development (AMTD) project is in Phase 2 of a multiyear effort initiated in Fiscal Year (FY) 2012, to mature toward the next Technology Readiness Level (TRL) critical technologies required to enable 4-m-or-larger monolithic or segmented ultraviolet, optical, and infrared (UVOIR) space telescope primary-mirror assemblies for general astrophysics and ultra-high-contrast observations of exoplanets. Key hardware accomplishments of 2015/16 are the successful low-temperature fusion of a 1.5-meter diameter ULE mirror that is a 1/3rd scale model of a 4-meter mirror and the initiation of polishing of a 1.2-meter Extreme-Lightweight Zerodur mirror. Critical to AMTD's success is an integrated team of scientists, systems engineers, and technologists; and a science-driven systems engineering approach.

  8. Advanced Mirror Technology Development (AMTD) Project: Overview and Year 4 Accomplishments (United States)

    Stahl, H. Philip


    The Advanced Mirror Technology Development (AMTD) project is in Phase 2 of a multiyear effort initiated in Fiscal Year (FY) 2012, to mature toward the next Technology Readiness Level (TRL) critical technologies required to enable 4-m-or-larger monolithic or segmented ultraviolet, optical, and infrared (UVOIR) space telescope primary-mirror assemblies for general astrophysics and ultra-high-contrast observations of exoplanets. Key hardware accomplishments of 2015/16 are the successful low-temperature fusion of a 1.5-meter diameter ULE mirror that is a 1/3rd scale model of a 4-meter mirror and the initiation of polishing of a 1.2-meter Extreme-Lightweight Zerodur mirror. Critical to AMTD's success is an integrated team of scientists, systems engineers, and technologists; and a science-driven systems engineering approach.

  9. A 2D chaotic path planning for mobile robots accomplishing boundary surveillance missions in adversarial conditions (United States)

    Curiac, Daniel-Ioan; Volosencu, Constantin


    The path-planning algorithm represents a crucial issue for every autonomous mobile robot. In normal circumstances a patrol robot will compute an optimal path to ensure its task accomplishment, but in adversarial conditions the problem is getting more complicated. Here, the robot’s trajectory needs to be altered into a misleading and unpredictable path to cope with potential opponents. Chaotic systems provide the needed framework for obtaining unpredictable motion in all of the three basic robot surveillance missions: area, points of interests and boundary monitoring. Proficient approaches have been provided for the first two surveillance tasks, but for boundary patrol missions no method has been reported yet. This paper addresses the mentioned research gap by proposing an efficient method, based on chaotic dynamic of the Hénon system, to ensure unpredictable boundary patrol on any shape of chosen closed contour.

  10. Affordability as a discursive accomplishment in a changing National Health Service. (United States)

    Russell, Jill; Greenhalgh, Trisha


    Health systems worldwide face the challenges of rationing. The English National Health Service (NHS) was founded on three core principles: universality, comprehensiveness, and free at the point of delivery. Yet patients are increasingly hearing that some treatments are unaffordable on the NHS. We considered affordability as a social accomplishment and sought to explore how those charged with allocating NHS resources achieved this in practice. We undertook a linguistic ethnography to examine the work practices of resource allocation committees in three Primary Care Trusts (PCTs) in England between 2005 and 2012, specifically deliberations over 'individual funding requests' (IFRs)--requests by patients and their doctors for the PCT to support a treatment not routinely funded. We collected and analysed a diverse dataset comprising policy documents, legal judgements, audio recordings, ethnographic field notes and emails from PCT committee meetings, interviews and a focus group with committee members. We found that the fundamental values of universality and comprehensiveness strongly influenced the culture of these NHS organisations, and that in this context, accomplishing affordability was not easy. Four discursive practices served to confer legitimacy on affordability as a guiding value of NHS health care: (1) categorising certain treatments as only eligible for NHS funding if patients could prove 'exceptional' circumstances; (2) representing resource allocation decisions as being not (primarily) about money; (3) indexical labelling of affordability as an ethical principle, and (4) recontextualising legal judgements supporting refusal of NHS treatment on affordability grounds as 'rational'. The overall effect of these discursive practices was that denying treatment to patients became reasonable and rational for an organisation even while it continued to espouse traditional NHS values. We conclude that deliberations about the funding of treatments at the margins of NHS

  11. Potential Synthetic Biolubricant as an Alternative to Bovine Serum


    Scholes, Susan C.; Colledge, Coral J.; Naylor, Andrew; Mahdi, Mohammed H.; Smith, Alan M.; Joyce, Thomas


    It is crucial that orthopaedic implant materials are tested in conditions that replicate the natural body’s environment as closely as possible. Bovine serum is currently recommended for use by the International Organisation for Standardisation (ISO) for the wear testing of these implant materials, however, the rheological properties of bovine serum do not match fully those of the body’s natural lubricant, synovial fluid. This study looks at a potential alternative to bovine serum for the test...

  12. 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


    -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......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...... by densitometric scanning of Western blots. In raw milk, MUC15 was shown to constitute 0.08% (wt) of the protein and approximately 1.5% (wt) of the MFGM-associated proteins. Surprisingly, this study showed that in addition to the fat-containing fractions, such as MFGM and buttermilk, MUC15 was present in nonfat...

  13. 76 FR 35185 - Notice of Request for Extension of Approval of an Information Collection; Bovine Spongiform... (United States)


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

  14. Lactic Acid Bacteria Isolated from Bovine Mammary Microbiota: Potential Allies against Bovine Mastitis.

    Directory of Open Access Journals (Sweden)

    Damien S Bouchard

    Full Text Available Bovine mastitis is a costly disease in dairy cattle worldwide. As of yet, the control of bovine mastitis is mostly based on prevention by thorough hygienic procedures during milking. Additional strategies include vaccination and utilization of antibiotics. Despite these measures, mastitis is not fully under control, thus prompting the need for alternative strategies. The goal of this study was to isolate autochthonous lactic acid bacteria (LAB from bovine mammary microbiota that exhibit beneficial properties that could be used for mastitis prevention and/or treatment. Sampling of the teat canal led to the isolation of 165 isolates, among which a selection of ten non-redundant LAB strains belonging to the genera Lactobacillus and Lactococcus were further characterized with regard to several properties: surface properties (hydrophobicity, autoaggregation; inhibition potential of three main mastitis pathogens, Staphylococcus aureus, Escherichia coli and Streptococcus uberis; colonization capacities of bovine mammary epithelial cells (bMEC; and immunomodulation properties. Three strains, Lactobacillus brevis 1595 and 1597 and Lactobacillus plantarum 1610, showed high colonization capacities and a medium surface hydrophobicity. These strains are good candidates to compete with pathogens for mammary gland colonization. Moreover, nine strains exhibited anti-inflammatory properties, as illustrated by the lower IL-8 secretion by E. coli-stimulated bMEC in the presence of these LAB. Full genome sequencing of five candidate strains allowed to check for undesirable genetic elements such as antibiotic resistance genes and to identify potential bacterial determinants involved in the beneficial properties. This large screening of beneficial properties while checking for undesirable genetic markers allowed the selection of promising candidate LAB strains from bovine mammary microbiota for the prevention and/or treatment of bovine mastitis.

  15. Do orthologous gene phylogenies really support tree-thinking?

    Directory of Open Access Journals (Sweden)

    Leigh J


    Full Text Available Abstract Background Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. Results Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial. We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. Conclusion Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

  16. Phylogeny and biogeography of Tynanthus Miers (Bignonieae, Bignoniaceae). (United States)

    M P de Medeiros, Maria Cláudia; Lohmann, Lúcia G


    The origin of Neotropical biodiversity represents a key question in evolutionary biology. Despite the attempts to decipher the role of ecological and historical factors to present-day distribution patterns, robust phylogenetic studies of Neotropical clades are still needed before a comprehensive picture of the origin of Neotropical biodiversity can be achieved. Tynanthus Miers (Bignonieae, Bignoniaceae) is a well-circumscribed genus of Neotropical lianas with species that are narrowly distributed, except from a few taxa. The genus is characterized by a clove odor, small bilabiate flowers with the two upper lobes almost fused, and fruits with raised margins, all of which represent morphological synapomorphies for this clade. Other distinctive characters are the thecae reflexed forward, the densely pubescent ovaries and the poorly-developed nectariferous disk. The circumscription of the genus has remained constant over the years, despite the problematic limits of most genera of tribe Bignonieae. In this study, we reconstruct the phylogeny of Tynanthus based on two plastid (ndhF and rpl32-trnL) and one nuclear (pepC) markers and use this phylogenetic framework to investigate the biogeographical history of the genus. Our phylogenetic hypothesis provides further support for the monophyly of Tynanthus, and strongly supports a series of infra-generic clades. Most species are reconstructed as monophyletic, while T. cognatus and T. polyanthus are paraphyletic. Biogeographic reconstructions suggest that Tynanthus originated between 9.4 and 21.5Mya, most likely at approximately 15.3Mya. The MRCA of the genus was likely broadly distributed through lowland Amazonia, Western South America and Central America and diversified in the Neotropics during the Miocene. Closely related species are generally distributed within the same biogeographic area, suggesting that niche conservatism has played an important role in the diversification history of the group.

  17. Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases. (United States)

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


    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.

  18. Forelimb-hindlimb developmental timing changes across tetrapod phylogeny

    Directory of Open Access Journals (Sweden)

    Selwood Lynne


    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

  19. 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 ( present important new springboards for understanding the global biodiversity and evolution of asteroids.

  20. A revised dated phylogeny of the arachnid order Opiliones. (United States)

    Sharma, Prashant P; Giribet, Gonzalo


    Dating the Opiliones tree of life has become an important enterprise for this group of arthropods, due to their ancient origins and important biogeographic implications. To incorporate both methodological innovations in molecular dating as well as new systematic discoveries of harvestman diversity, we conducted total evidence dating on a data set uniting morphological and/or molecular sequence data for 47 Opiliones species, including all four well-known Palaeozoic fossils, to test the placement of both fossils and newly discovered lineages in a single analysis. Furthermore, we investigated node dating with a phylogenomic data set of 24,202 amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached molecular dating of basal harvestman phylogeny using different data sets and approaches to assess congruence of divergence time estimates. In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations (e.g., Opiliones, Palpatores). By contrast, derived nodes that lack fossil calibrations (e.g., the suborders Cyphophthalmi, and Laniatores) have large uncertainty intervals in diversification times, particularly in the total evidence dating analysis, reflecting the dearth of calibration points and undersampling of derived lineages. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils. Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery-both paleontological and neontological-in evolutionary inference.

  1. Blastocystis phylogeny among various isolates from humans to insects. (United States)

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


    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.

  2. [Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang]. (United States)

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


    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.

  3. Multi-level human evolution: ecological patterns in hominin phylogeny. (United States)

    Parravicini, Andrea; Pievani, Telmo


    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.

  4. Molecular phylogeny and evolution of the genus Neoerysiphe (Erysiphaceae, Ascomycota). (United States)

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


    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.

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

    KAUST Repository

    Díaz-Arce, Natalia


    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.

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

    CERN Document Server

    Roch, Sebastien


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

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

    CERN Document Server

    Kiyomi, Masashi; Saitoh, Toshiki


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

  8. Diagnosis and Control of Viral Diseases of Reproductive Importance: Infectious Bovine Rhinotracheitis and Bovine Viral Diarrhea. (United States)

    Newcomer, Benjamin W; Givens, Daniel


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

  9. Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies. (United States)

    Edgcomb, V P; Roger, A J; Simpson, A G; Kysela, D T; Sogin, M L


    Jakobids are free-living, heterotrophic flagellates that might represent early-diverging mitochondrial protists. They share ultrastructural similarities with eukaryotes that occupy basal positions in molecular phylogenies, and their mitochondrial genome architecture is eubacterial-like, suggesting a close affinity with the ancestral alpha-proteobacterial symbiont that gave rise to mitochondria and hydrogenosomes. To elucidate relationships among jakobids and other early-diverging eukaryotic lineages, we characterized alpha- and beta-tubulin genes from four jakobids: Jakoba libera, Jakoba incarcerata, Reclinomonas americana (the "core jakobids"), and Malawimonas jakobiformis. These are the first reports of nuclear genes from these organisms. Phylogenies based on alpha-, beta-, and combined alpha- plus beta-tubulin protein data sets do not support the monophyly of the jakobids. While beta-tubulin and combined alpha- plus beta-tubulin phylogenies showed a sister group relationship between J. libera and R. americana, the two other jakobids, M. jakobiformis and J. incarcerata, had unclear affinities. In all three analyses, J. libera, R. americana, and M. jakobiformis emerged from within a well-supported large "plant-protist" clade that included plants, green algae, cryptophytes, stramenopiles, alveolates, Euglenozoa, Heterolobosea, and several other protist groups, but not animals, fungi, microsporidia, parabasalids, or diplomonads. A preferred branching order within the plant-protist clade was not identified, but there was a tendency for the J. libera-R. americana lineage to group with a clade made up of the heteroloboseid amoeboflagellates and euglenozoan protists. Jakoba incarcerata branched within the plant-protist clade in the beta- and the combined alpha- plus beta-tubulin phylogenies. In alpha- tubulin trees, J. incarcerata occupied an unresolved position, weakly grouping with the animal/fungal/microsporidian group or with amitochondriate parabasalid and

  10. Structural dynamics division research and technology accomplishments for fiscal year 1990 and plans for fiscal year 1991 (United States)

    Wynne, Eleanor C.


    The research accomplishments of the Structural Dynamics Division for F.Y. 1991 are presented. The work is discussed in terms of highlights of accomplishments during the past year and plans for the current year as they relate to 5-year plans and the objectives of each technical area. Included is research on unsteady aerodynamics, helicopter rotors, computational fluid dynamics, oscillations of leading edge flaps of a delta wing, and aircraft wing loads.

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

    Directory of Open Access Journals (Sweden)

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


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

  12. 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


    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

  13. A novel phylogeny and morphological reconstruction of the PIN genes and first phylogeny of the ACC-oxidases (ACOs). (United States)

    Clouse, Ronald M; Carraro, Nicola


    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 derived.

  14. 绑架罪既遂的认定%On Determination of Accomplished Offence of the Kidnapping Crime

    Institute of Scientific and Technical Information of China (English)



    绑架罪既遂标准的通说观点使得绑架罪的既遂过于提前,而要求绑架行为实际勒索到了财物或实现其他不法要求的观点,则使绑架罪的既遂过于推后,甚至取消和否定了绑架罪的既遂。绑架罪应以行为人实施绑架行为后向人质的关系人提出不法要求为既遂标准。%The viewpoint of the accomplished offence of kidnapping crime makes the accomplished offence crime too ahead of time and the viewpoint of requiring kidnapping behavior actual blackmail of property or implementation other illegal requirements makes the accomplished offence crime too push-back,even canceled and negated the accomplished offence of the kidnapping crime.The standard accomplished offence of the kidnapping crime should be lied in the tortfeasor's requirement to the hostages for illegal requirement after the accomplishing of the kidnapping behavior.

  15. Professional conceptualisation and accomplishment of patient safety in mental healthcare: an ethnographic approach

    Directory of Open Access Journals (Sweden)

    Braithwaite Jeffrey


    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

  16. Perspectives on the History of Bovine TB and the Role of Tuberculin in Bovine TB Eradication

    Directory of Open Access Journals (Sweden)

    Margaret Good


    Full Text Available Tuberculosis remains a significant disease of animals and humans worldwide. Bovine tuberculosis is caused by Mycobacteria with an extremely wide host range and serious, although currently probably underdiagnosed, zoonotic potential. Where bovine tuberculosis controls are effective, human zoonotic TB, due to Mycobacterium bovis or M. caprae, is uncommon and clinical cases are infrequent in cattle. Therefore, the control and ultimate eradication of bovine tuberculosis is desirable. Tuberculin tests are the primary screening tool used in bovine eradication. The choice of tuberculin test is dependent on the environment in which it is to be used. Tuberculin potency is critical to test performance, and the accurate determination of potency is therefore particularly important. The design of a control or eradication programme should take into consideration the fundamental scientific knowledge, the epidemiological profile of disease, the experience of other eradication programmes, and the presence, in the same ecosystem, of maintenance hosts, in which infection is self-sustaining and which are capable of transmitting infection. A control or eradication programme will necessarily require modification as it progresses and must be under constant review to identify the optimal desirable goals, the efficacy of policy, and constraints to progress.

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

    Institute of Scientific and Technical Information of China (English)


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

  18. 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.


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

  19. The ICES Working Group on Zooplankton Ecology: Accomplishments of the first 25 years (United States)

    Wiebe, Peter H.; Harris, Roger; Gislason, Astthor; Margonski, Piotr; Skjoldal, Hein Rune; Benfield, Mark; Hay, Steve; O'Brien, Todd; Valdés, Luis


    The ICES Study Group on Zooplankton Ecology was created in 1991 to address issues of current and future concern within the field of zooplankton ecology. Within three years it became the ICES Working Group on Zooplankton Ecology (ICES WGZE) and this unique group in the world's oceanographic community has now been active for 25 years. This article reviews and synthesizes the products, and major accomplishments of the group. Achievements of the group, including the Zooplankton Methodology Manual, the Zooplankton Status Reports, and the International Zooplankton Symposia, have had an important impact on the wider field. Among the future issues that remain to be addressed by the group are the assessment of exploratory fisheries on zooplankton and micronekton species; further development of the zooplankton time-series; compilation and integration of allometric relationships for zooplankton species, and evaluation of new methodologies for the study of zooplankton distribution, abundance, physiology, and genetics. Marine science is an increasingly global undertaking and groups such as the ICES WGZE will continue to be essential to the advancement of understanding of zooplankton community structure and population dynamics in the world's oceans.

  20. Research accomplishments and future goals in particle physics. Final technical report

    Energy Technology Data Exchange (ETDEWEB)


    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.

  1. Quality management at Argonne National Laboratory: Status, accomplishments, and lessons learned

    Energy Technology Data Exchange (ETDEWEB)



    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.

  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. Advances in development and evaluation of bovine herpesvirus 1 vaccines

    NARCIS (Netherlands)

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


    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 inf

  4. Prevalence, transmission and impact of bovine leukosis in Michigan dairies (United States)

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

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

    Directory of Open Access Journals (Sweden)

    Soveri T


    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.

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

    Directory of Open Access Journals (Sweden)

    Jefferson Luis Oshiro Tanaka


    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.

  7. Detection of lipomannan in cattle infected with bovine tuberculosis (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-...

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

    Directory of Open Access Journals (Sweden)

    Shackney Stanley E


    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.

  9. Birth-death prior on phylogeny and speed dating

    Directory of Open Access Journals (Sweden)

    Sennblad Bengt


    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

  10. Bovine dental fluorosis: histologic and physical characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Shearer, T.R.; Kolstad, D.L.; Suttie, J.W.


    Incisor teeth from 5- to 6-year-old Holstein-Friesian cattle maintained on a ration averaging 40 ppm F annually from 4 months of age were analyzed by a variety of histologic techniques. These techniques included photomicroscopy, microradiography, protein staining, and microhardness testing. The features of fluorotic enamel that were noted were: hypomineralized outer enamel, coronal cementum hyperplasia, disrupted subsurface pigment band, hypoplastic pits, puckered incremental lines, periodic radiolucent regions, positive protein staining, and decreased microhardness of the outer enamel. These results were similar to the lesions of dental fluorosis observed in other species, and explain the external appearance of fluorotic bovine teeth observed under field conditions.

  11. Bovine Spongiform Encephalopathy (BSE, Mad Cow Disease

    Directory of Open Access Journals (Sweden)

    G. K. Bruckner


    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.

  12. Creep Behavior of Passive Bovine Extraocular Muscle


    Lawrence Yoo; Hansang Kim; Andrew Shin; Vijay Gupta; Demer, Joseph L.


    This paper characterized bovine extraocular muscles (EOMs) using creep, which represents long-term stretching induced by a constant force. After preliminary optimization of testing conditions, 20 fresh EOM samples were subjected to four different loading rates of 1.67, 3.33, 8.33, and 16.67%/s, after which creep was observed for 1,500 s. A published quasilinear viscoelastic (QLV) relaxation function was transformed to a creep function that was compared with data. Repeatable creep was observed...

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

    DEFF Research Database (Denmark)

    Larsen, Lars Erik


    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...

  14. Interaction of Nicotine and Bovine Serum Albumin

    Institute of Scientific and Technical Information of China (English)


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

  15. Ultrasonography of bovine urinary tract disorders. (United States)

    Floeck, Martina


    Ultrasonography is a helpful diagnostic tool in cattle with urinary tract disorders. It can be used to diagnose pyelonephritis, urolithiasis, hydronephrosis, renal cysts, renal tumors, amyloidosis, cystitis, bladder paralysis, bladder rupture, bladder neoplasms, and, occasionally, nephrosis, glomerulonephritis, and embolic nephritis. This article describes the anatomy, scanning technique, indications, limitations, normal and pathologic sonographic appearance of the bovine urinary tract. References from horses and humans are included, especially when the sonographic findings in these species may complement the understanding of similar diseases reported in cattle.

  16. 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.


    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

  17. Relationships of Reproductive Traits With the Phylogeny of the African Noctuid Stem Borers. (United States)

    Calatayud, Paul-André; Dupas, Stéphane; Frérot, Brigitte; Genestier, Gilles; Ahuya, Peter; Capdevielle-Dulac, Claire; Le Ru, Bruno


    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.

  18. Detecting shifts in diversity limits from molecular phylogenies: what can we know? (United States)

    McInnes, Lynsey; Orme, C David L; Purvis, A


    Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a--probably untenable--model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification 'rules' and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.

  19. Molecular Phylogeny and Systematic Revision of the Pleurocarpus Moss Genus Plagiothecium

    DEFF Research Database (Denmark)

    Wynns, Justin Thomas

    . The relationships between Plagiothecium and other similar pleurocarps are also speculative. In this study, DNA sequence data were used for reconstructing the phylogeny of the genus. Based on the results of a preliminary survey of 16 DNA regions, three regions were chosen for genetic markers: plastid trn...

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

    DEFF Research Database (Denmark)

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


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

  1. How reliably can we infer diversity-dependent diversification from phylogenies?

    NARCIS (Netherlands)

    Etienne, Rampal S.; Pigot, Alex L.; Phillimore, Albert B.


    Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking. Here, we sim

  2. Molecular phylogeny of the Oriental butterfly genus Arhopala (Lycaenidae, Theclinae) inferred from mitochondrial and nuclear genes

    NARCIS (Netherlands)

    Megens, H.J.W.C.; Nes, Van W.J.; Moorsel, van C.H.M.; Pierce, N.E.; Jong, de R.


    We present a phylogeny for a selection of species of the butterfly genus Arhopala Boisduval, 1832 based on molecular characters. We sequenced 1778 bases of the mitochondrial genes Cytochrome Oxidase 1 and 2 including tRNALeu, and a 393-bp fragment of the nuclear wingless gene for a total of 42 speci

  3. Phylogeny of Anophelinae (Diptera: Culicidae) Based on Nuclear Ribosomal and Mitochondrial DNA Sequences (United States)


    combining data from nuclear protein-encoding enes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera ). Systematic Biology, 49, 202 224. Nixon... Systematic Entomology (2002) 27, 361 382 Phylogeny of Anophelinae (Diptera: Culicidae) based on nuclear ribosomal and mitochondrial DNA sequences...Entomologia M•dica, Departamento de Epidemiologia, Faculdade de Safide Pfiblica, Universidade de S•o Paulo, Brazil, -• Department of Systematic

  4. Phylogeny of Miliusa (Magnoliales: Annonaceae: Malmeoideae: Miliuseae), with descriptions of two new species from Malesia

    NARCIS (Netherlands)

    Chaowasku, T.; Kessler, P.J.A.; Chatrou, L.W.


    The molecular phylogeny of Miliusa (Annonaceae) is reconstructed, with 27 (of ca. 50) species included, using a combination of seven plastid markers (rbcL exon, trnL intron, trnL-F spacer, matK exon, ndhF exon, psbA-trnH spacer, and ycf1 exon) constituting ca. 7 kb. In addition, two new species of M

  5. Using Pseudozoids to Teach Classification and Phylogeny to Middle School Students (United States)

    Freidenberg, Rolfe Jr.; Kelly, Martin G.


    This research compared the outcomes of teaching middle school students two different methods of classification and phylogeny. Two classes were randomly selected and taught using traditional methods of instruction. Three classes were taught using the "Pseudozoid" approach, where students learned to classify, develop and read dichotomous keys, and…

  6. Advances Achieved on Studies of East Asian mtDNA Phylogeny

    Institute of Scientific and Technical Information of China (English)


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

  7. A novel molecular marker for the study of Neotropical cichlid phylogeny. (United States)

    Fabrin, T M C; Gasques, L S; Prioli, S M A P; Prioli, A J


    The use of molecular markers has contributed to phylogeny and to the reconstruction of species' evolutionary history. Each region of the genome has different evolution rates, which may or may not identify phylogenetic signal at different levels. Therefore, it is important to assess new molecular markers that can be used for phylogenetic reconstruction. Regions that may be associated with species characteristics and are subject to selective pressure, such as opsin genes, which encode proteins related to the visual system and are widely expressed by Cichlidae family members, are interesting. Our aim was to identify a new nuclear molecular marker that could establish the phylogeny of Neotropical cichlids and is potentially correlated with the visual system. We used Bayesian inference and maximum likelihood analysis to support the use of the nuclear opsin LWS gene in the phylogeny of eight Neotropical cichlid species. Their use concatenated to the mitochondrial gene COI was also tested. The LWS gene fragment comprised the exon 2-4 region, including the introns. The LWS gene provided good support for both analyses up to the genus level, distinguishing the studied species, and when concatenated to the COI gene, there was a good support up to the species level. Another benefit of utilizing this region, is that some polymorphisms are associated with changes in spectral properties of the LWS opsin protein, which constitutes the visual pigment that absorbs red light. Thus, utilization of this gene as a molecular marker to study the phylogeny of Neotropical cichlids is promising.

  8. Evidence for selective sweeps by Wolbachia infections: phylogeny of Altica leaf beetles and their reproductive parasites. (United States)

    Jäckel, Regina; Mora, Diana; Dobler, Susanne


    Infections with maternally inherited Wolbachia bacteria may have dramatic influences on reproductive traits and speciation patterns of their hosts. We here show that in the beetle genus Altica, infection has influenced phylogenetic patterns of the host's mtDNA and different strains led to repeated selective sweeps. By comparing a COI/II-based phylogeny of the hosts with a phylogeny of the bacteria based on ftsZ, we show that cospeciation is rare and restricted to few recently diverged species. While in general each species apparently harbours a single Wolbachia strain, Altica lythri presents a strikingly different pattern: in the polyphyletic species, three highly divergent mtDNA haplotypes (2.1-4.6% p-distance) are coupled with three different Wolbachia strains (wLytA1, wLytA2 and wLytB). These haplotypes and Wolbachia strains are widely distributed and mostly found in sympatry. A phylogeny based on microsatellite data supports the monophyly of A. lythri. The discrepancy between mtDNA and nuclear phylogeny may best be explained by interspecific hybridization that led to introgression of mtDNA coupled with a different Wolbachia strain. Selective sweeps apparently drove the introgressed haplotypes to widespread distribution. As for effects of Wolbachia on reproduction, infection with wLytA1 appears to be correlated with a substantial sex ratio distortion, which was most prominent in A. lythri.

  9. A molecular phylogeny of Asian barbets: speciation and extinction in the tropics. (United States)

    den Tex, Robert-Jan; Leonard, Jennifer A


    We reconstruct the phylogeny of all recognized species of the tropical forest associated Asian barbets based on mitochondrial and nuclear sequence data and test for the monophyly of species and genera. Tropical regions are well known for their extraordinarily high levels of biodiversity, but we still have a poor understanding of how this richness was generated and maintained through evolutionary time. Multiple theoretical frameworks have been developed to explain this diversity, including the Pleistocene pump hypothesis and the museum hypothesis. We use our phylogeny of the Asian barbets to test these hypotheses. Our data do not find an increase in speciation in the Pleistocene as predicted by the Pleistocene pump hypothesis. We do find evidence of extinctions, which apparently contradicts the museum hypothesis. However, the extinctions are only in a part of the phylogeny that is distributed mainly across Sundaland (the Malay peninsula and the islands off southeast Asia). The theory of island biogeography predicts a higher rate of extinction on islands than on mainland areas. The data from the part of the phylogeny primarily distributed on the mainland best fit a pure birth model of speciation, and thus supports the museum hypothesis.

  10. Improving the Analysis of Dinoflagellate Phylogeny based on rDNA

    DEFF Research Database (Denmark)

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


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

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

    NARCIS (Netherlands)

    Rheede, T. van


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

  12. Resolution of ray-finned fish phylogeny and timing of diversification. (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


    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."

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

    NARCIS (Netherlands)

    Bokma, Folmer


    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, paramet

  14. Relationships of Reproductive Traits With the Phylogeny of the African Noctuid Stem Borers (United States)

    Calatayud, Paul-André; Dupas, Stéphane; Frérot, Brigitte; Genestier, Gilles; Ahuya, Peter; Capdevielle-Dulac, Claire; Le Ru, Bruno


    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. PMID:27867304

  15. 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;


    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...

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

    DEFF Research Database (Denmark)

    Frick, Holger; Scharff, Nikolaj


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

  17. The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions

    Directory of Open Access Journals (Sweden)

    Ó'Fágáin Ciarán


    Full Text Available Abstract Background The mammalian heme peroxidases (MHPs are a medically important group of enzymes. Included in this group are myeloperoxidase, eosinophil peroxidase, lactoperoxidase, and thyroid peroxidase. These enzymes are associated with such diverse diseases as asthma, Alzheimer's disease and inflammatory vascular disease. Despite much effort to elucidate a clearer understanding of the function of the 4 major groups of this multigene family, we still do not have a clear understanding of their relationships to each other. Results Sufficient signal exists for the resolution of the evolutionary relationships of this family of enzymes. We demonstrate, using a root mean squared deviation statistic, how the removal of the fastest evolving sites aids in the minimisation of the effect of long branch attraction and the generation of a highly supported phylogeny. Based on this phylogeny we have pinpointed the amino acid positions that have most likely contributed to the diverse functions of these enzymes. Many of these residues are in close proximity to sites implicated in protein misfolding, loss of function or disease. Conclusion Our analysis of all available genomic sequence data for the MHPs from all available completed mammalian genomes, involved sophisticated methods of phylogeny reconstruction and data treatment. Our study has (i fully resolved the phylogeny of the MHPs and the subsequent pattern of gene duplication, and (ii, we have detected amino acids under positive selection that have most likely contributed to the observed functional shifts in each type of MHP.

  18. A Review: Passive System Reliability Analysis – Accomplishments and Unresolved Issues

    Directory of Open Access Journals (Sweden)



    Full Text Available Reliability assessment of passive safety systems is one of the important issues, since safety of advanced nuclear reactors rely on several passive features. In this context, a few methodologies such as Reliability Evaluation of Passive Safety System (REPAS, Reliability Methods for Passive Safety Functions (RMPS and Analysis of Passive Systems ReliAbility (APSRA have been developed in the past. These methodologies have been used to assess reliability of various passive safety systems. While these methodologies have certain features in common, but they differ in considering certain issues; for example, treatment of model uncertainties, deviation of geometric and process parameters from their nominal values, etc. This paper presents the state of the art on passive system reliability assessment methodologies, the accomplishments and remaining issues. In this review three critical issues pertaining to passive systems performance and reliability have been identified. The first issue is, applicability of best estimate codes and model uncertainty. The best estimate codes based phenomenological simulations of natural convection passive systems could have significant amount of uncertainties, these uncertainties must be incorporated in appropriate manner in the performance and reliability analysis of such systems. The second issue is the treatment of dynamic failure characteristics of components of passive systems. REPAS, RMPS and APSRA methodologies do not consider dynamic failures of components or process, which may have strong influence on the failure of passive systems. The influence of dynamic failure characteristics of components on system failure probability is presented with the help of a dynamic reliability methodology based on Monte Carlo simulation. The analysis of a benchmark problem of Hold-up tank shows the error in failure probability estimation by not considering the dynamism of components. It is thus suggested that dynamic reliability

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

    Directory of Open Access Journals (Sweden)

    Stajich Jason E


    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

  20. Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability

    Directory of Open Access Journals (Sweden)

    Wu Gang


    Full Text Available Abstract Background In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is measured by simulations on synthetic datasets with known "true" phylogenies, while little theoretical analysis has been done. In this paper, we present a new model-based approach to measuring the accuracy of a quartet-based phylogeny reconstruction method. Under this model, we propose three efficient algorithms to reconstruct the "true" phylogeny with a high success probability. Results The first algorithm can reconstruct the "true" phylogeny from the input quartet topology set without quartet errors in O(n2 time by querying at most (n - 4 log(n - 1 quartet topologies, where n is the number of the taxa. When the input quartet topology set contains errors, the second algorithm can reconstruct the "true" phylogeny with a probability approximately 1 - p in O(n4 log n time, where p is the probability for a quartet topology being an error. This probability is improved by the third algorithm to approximately 11+q2+12q4+116q5 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqaIXaqmaeaacqaIXaqmcqGHRaWkcqWGXbqCdaahaaqabeaacqaIYaGmaaGaey4kaSYaaSaaaeaacqaIXaqmaeaacqaIYaGmaaGaemyCae3aaWbaaeqabaGaeGinaqdaaiabgUcaRmaalaaabaGaeGymaedabaGaeGymaeJaeGOnaydaaiabdghaXnaaCaaabeqaaiabiwda1aaaaaaaaa@3D5A@, where q=p1−p MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaemyCaeNaeyypa0tcfa4aaSaaaeaacqWGWbaCaeaacqaIXaqmcqGHsislcqWGWbaCaaaaaa@3391@, with

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

    Directory of Open Access Journals (Sweden)

    Robert Muscarella

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

  2. Identification of Prototheca Zopfii from Bovine Mastitis

    Directory of Open Access Journals (Sweden)

    F Zaini


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

  3. Human exposure to bovine polyomavirus: a zoonosis

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  4. Toxicology of a bovine paraplegic syndrome. (United States)

    Sevcik, C; Brito, J C; D'Suze, G; Domínguez-Bello, M G; Lovera, M; Mijares, A J; Bónoli, S


    A clinical entity named 'bovine paraplegic syndrome' ('síndrome parapléjico de los bovinos') has spread alarmingly in the cattle-growing areas of the central and eastern plains of Venezuela. It is estimated that four million cattle are bred in the area where the disease occurs. The mortality ranges from 5 to 25% of the animals at risk, mostly pregnant or lactating cows. The principal characteristic of the bovine paraplegic syndrome is ventral or sternal decubitus, in animals that make vain efforts to stand when stimulated. The diagnosis is established when all other possible causes (e.g. paralytic rabies, botulism and blood parasites such as Anaplasma marginal, Babesia bovis, B. bigemina, and Trypanosoma vivax) have been ruled out clinically and by laboratory tests. Death always occurs, usually after a few days, and there is no known treatment. In this work, we describe results that show the presence of a toxin in the cattle suffering from, or liable to suffer from the syndrome. The toxin is produced by ruminal bacteria. In squid giant axons under voltage clamp conditions, the toxin blocks the sodium current. We detected the toxin analytically by absorbance measurements at 340 nm after reacting with picrylsulfonic acid. We obtained a good separation of the toxin with isocratic high pressure liquid chromatography, using 40% methanol in water on phenylborasil columns.

  5. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees. (United States)

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


    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.

  6. Rooting for the root of elongation factor-like protein phylogeny. (United States)

    Kamikawa, Ryoma; Sakaguchi, Miako; Matsumoto, Takuya; Hashimoto, Tetsuo; Inagaki, Yuji


    Lateral gene transfer (LGT) may play a pivotal role in the evolution of elongation factor-like (EFL) genes in eukaryotes. To date, numbers of putative cases for lateral transfer of EFL genes have been postulated based on unrooted EFL phylogenies. Nevertheless, the root position in EFL phylogeny is important to validate lateral EFL gene transfer: for instance, a clade of two EFL homologs from distantly related organisms in an unrooted EFL tree does not necessarily confirm the LGT, since the possibility that the root may locate in this clade cannot be excluded. Cocquyt et al. (2009, p. 39) recently demonstrated that a putative case of lateral EFL gene transfer, which was originally proposed based on an unrooted phylogeny, could not be endorsed by the corresponding rooted analysis. Although rooting EFL phylogeny is indispensable to elucidate various aspects in EFL gene evolution, we suspected that the outgroup clade comprised of EF-1alpha and eukaryote-specific EF-1alpha paralogs erroneously attached to long EFL branches in Cocquyt et al. (2009) - a typical long branch attraction (LBA) artifact. Here, we systematically assessed the putative LBA artifact between the branch leading to the outgroup clade and long ingroup branches by analyzing the original dataset used in Cocquyt et al. (2009) with and without modifying ingroup-sequence sampling. A series of the rooted EFL analyses indicated that the root inference was highly susceptible to presence and absence of long-branched ingroup-sequences, suggesting that the rooted EFL phylogenies cannot be free from severe LBA artifact. We also discussed a new aspect in EFL gene evolution in stramenopiles identified in the course of the EFL analyses described above. Finally, the relative timing of the first emergence of EFL gene in eukaryotes was contemplated based on the current EF-1alpha/EFL distribution.

  7. Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes). (United States)

    Vélez-Zuazo, Ximena; Agnarsson, Ingi


    Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively

  8. 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)


    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......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...... purposes; and (2) a diagnostic kit for detecting the presence or absence in a bovine subject of two or more genetic marker alleles comprising a detection member....

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


    Chia-Rong Tsao


    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 interpre...

  10. Gabor Weber Local Descriptor for Bovine Iris Recognition

    Directory of Open Access Journals (Sweden)

    Shengnan Sun


    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.

  11. [Bovine heterologous bone graft in orbital surgery]. (United States)

    Morax, S; Hurbli, T; Smida, R


    Lubboc (T650) is a bovine heterologous bone implant obtained by specific preparation of trabecular of bone. In vitro and in vivo biocompatibility studies have revealed the absence of any cytotoxicity or systemic toxicity. Lubboc has many fields of application, including all bone graft surgical indications. We report our first results concerning the use of this product in orbital surgery either as a filling or contention material or as an apposition material. On all 20 operated patients we did not encounter any intolerance, inflammation or infection. The follow-up is still too short to appreciate the long term integration of this material which has the advantage of being a substitute for autologous bone, avoiding bone graft harvesting.

  12. Human bovine tuberculosis - remains in the differential.

    LENUS (Irish Health Repository)

    Bilal, Shaukat


    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.

  13. Studies on bovine demodecosis in northern Nigeria. (United States)

    Slingenbergh, J; Mohammed, A N; Bida, S A


    Summary The study reported in the present paper discusses the clinical and histological picture of bovine demodecosis and the morphology of Demodex mites as seen in four cows suffering from generalized demodecosis. There were no clinical signs of other skin affections. Changes in both the number and the appearance of visible skin lesions were seen and related to the level of nutrition and the exposure to sunshine of the cattle. Histological sections of some skin nodules showed the presence of mite colonies in the hair follicles. Only adults were seen in the sebaceous glands. Microscopical study of the morphology of the mites revealed the presence of two types of demodicids in the skin lesions and three types from epilated eyelashes. Morphological criteria are presented to aid in identification of species and of life stages.

  14. Tear and decohesion of bovine pericardial tissue. (United States)

    Tobaruela, Almudena; Elices, Manuel; Bourges, Jean Yves; Rojo, Francisco Javier; Atienza, José Miguel; Guinea, Gustavo


    The aim of this study was to evaluate quantitatively the fracture-by tear and delamination-of bovine pericardium tissues which are usually employed for the manufacture of bioprosthetic valves. A large number of samples (77) were tested in root-to-apex and circumferential directions, according to a standardised tear test (ASTM D 1938). Before performing the tear test, some samples were subjected to 1000 cycles of fatigue to a maximum stress of 3MPa. Fracture toughness of tearing and delamination were computed by following a simple fracture model. The study showed significantly lower values of delamination toughness compared with tear delamination. Moreover, tear forces were different in each test direction, revealing a clear orthotropic behaviour. All these results, as well as the testing procedure, could be of value for future research in the physiological function of pericardium tissues and clinical applications.

  15. Electron probe microananlysis of fluorotic bovine teeth

    Energy Technology Data Exchange (ETDEWEB)

    Shearer, T.R.; Kolstad, D.L.; Suttie, J.W.


    Incisor teeth were obtained from adult cattle which since 4 months of age to 5 or 6 years were maintained on rations containing a yearly average of 40 ppM F in the forage. Microchemical analyses were performed on the fluorotic bovine incisors. The microdistribution of fluoride varied markedly at different sites within the same tooth. Fluoride concentrations varied with depth from the tooth surface and were influenced by the concentrations of fluoride present in the forage during amelogenesis, and the presence of hypoplastic pits and hyperplastic coronal cementum in enamel. The cementum in these lesions contained remarkably high concentrations of fluoride, and it was less calcified and more porous than adjacent enamel. 5 figures.

  16. Copy number variation in the bovine genome

    DEFF Research Database (Denmark)

    Fadista, João; Thomsen, Bo; Holm, Lars-Erik;


    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...

  17. Sigma Team for Advanced Actinide Recycle FY2015 Accomplishments and Directions

    Energy Technology Data Exchange (ETDEWEB)

    Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)


    The Sigma Team for Minor Actinide Recycle (STAAR) has made notable progress in FY 2015 toward the overarching goal to develop more efficient separation methods for actinides in support of the United States Department of Energy (USDOE) objective of sustainable fuel cycles. Research in STAAR has been emphasizing the separation of americium and other minor actinides (MAs) to enable closed nuclear fuel recycle options, mainly within the paradigm of aqueous reprocessing of used oxide nuclear fuel dissolved in nitric acid. Its major scientific challenge concerns achieving selectivity for trivalent actinides vs lanthanides. Not only is this challenge yielding to research advances, but technology concepts such as ALSEP (Actinide Lanthanide Separation) are maturing toward demonstration readiness. Efforts are organized in five task areas: 1) combining bifunctional neutral extractants with an acidic extractant to form a single process solvent, developing a process flowsheet, and demonstrating it at bench scale; 2) oxidation of Am(III) to Am(VI) and subsequent separation with other multivalent actinides; 3) developing an effective soft-donor solvent system for An(III) selective extraction using mixed N,O-donor or all-N donor extractants such as triazinyl pyridine compounds; 4) testing of inorganic and hybrid-type ion exchange materials for MA separations; and 5) computer-aided molecular design to identify altogether new extractants and complexants and theory-based experimental data interpretation. Within these tasks, two strategies are employed, one involving oxidation of americium to its pentavalent or hexavalent state and one that seeks to selectively complex trivalent americium either in the aqueous phase or the solvent phase. Solvent extraction represents the primary separation method employed, though ion exchange and crystallization play an important role. Highlights of accomplishments include: Confirmation of the first-ever electrolytic oxidation of Am(III) in a

  18. Tylosin susceptibility of Staphylococci from bovine mastitis. (United States)

    Entorf, Monika; Feßler, Andrea T; Kadlec, Kristina; Kaspar, Heike; Mankertz, Joachim; Peters, Thomas; Schwarz, Stefan


    Although the 16-membered macrolide tylosin is commonly used for the treatment of bovine mastitis, little information is currently available about the susceptibility of mastitis pathogens to tylosin. In the present study, 112 Staphylococcus aureus and 110 coagulase-negative Staphylococcus (CoNS) spp. isolates from cases of bovine mastitis were tested by broth microdilution and agar disk diffusion with 30 μg tylosin disks. Susceptibility to erythromycin was tested by broth microdilution and disk diffusion using 15 μg disks. Both test populations showed bimodal distributions of minimal inhibitory concentrations (MICs) and zone diameters with eleven S. aureus and eight CoNS isolates showing tylosin MICs of ≥ 256 μg/ml and no zones of growth inhibition around the tylosin 30 μg disks. All 19 isolates with tylosin MICs of ≥ 256 μg/ml were also resistant to erythromycin. For six additional erythromycin-resistant isolates, tylosin MICs of 1-8 μg/ml were observed. One S. aureus and two CoNS isolates showed inducible macrolide resistance. PCR analysis of the 25 erythromycin-resistant staphylococcal isolates identified the resistance genes erm(A), erm(B), erm(C), erm(T), mph(C) and msr(A) alone or in different combinations. An excellent correlation between the results of the different tylosin susceptibility tests (broth microdilution versus disk diffusion) was seen for S. aureus and CoNS isolates. Since tylosin does not induce the expression of the aforementioned erm genes, isolates with an inducible resistance phenotype may - if only tylosin is tested - be falsely classified as tylosin-susceptible. Thus, erythromycin should be tested in parallel and tylosin should only be used for the treatment of infections caused by erythromycin-susceptible staphylococci.

  19. Florida's Adult Education Programs: Challenges and Accomplishments. A Report for Fiscal Year 1991 [and] Fiscal Year 1992. (United States)

    Gardner, Daniel L.

    These two reports outline accomplishments and challenges faced by Florida's AE program in FY91 and FY92 in the following areas: adult literacy, social participation, career development, special needs of the AE program's diverse identified target groups, high school completion, General Educational Development, workplace literacy, networking,…

  20. 41 CFR 102-74.255 - How must occupant evacuation or relocation be accomplished when there is immediate danger to... (United States)


    ... evacuation or relocation be accomplished when there is immediate danger to persons or property, such as fire... danger to persons or property, such as fire, explosion or the discovery of an explosive device (not... immediate danger to persons or property, such as fire, explosion or the discovery of an explosive...

  1. What do younger and older workers want to accomplish? Age-related differences in content and characteristics of occupational goals

    NARCIS (Netherlands)

    Zacher, Hannes; Degner, Manuela; Seevaldt, Robert; Frese, Michael; Luedde, Joerg


    Demographic changes necessitate that companies commit younger workers and motivate older workers through work design. Age-related differences in occupational goals should be taken into account when accomplishing these challenges. In this study, we investigated goal contents and goal characteristics

  2. Quasi-Experimental Study: Head Start Preschoolers' Cognitive Development as Assessed by the Learning Accomplishment Profile--Diagnostic (United States)

    Hines, Jeanne M.


    Abstract Preschoolers' cognitive abilities were assessed each year as part of the Head Start Program requirements. The Head Start PK-4 Center evaluated preschoolers' cognition by administering the Learning Accomplishment Profile-Diagnostic (LAP-D), as a pretest and posttest measure. The LAP-D study used archival data collected from the 2009-2010…

  3. Phylogeny, Seed Trait, and Ecological Correlates of Seed Germination at the Community Level in a Degraded Sandy Grassland


    Wang, Zhengning; Wang, Lixin; Liu, Zhimin; Li, Yanjuan; Liu, Qingqing; Liu, Bo


    Seed germination strongly affects plant population growth and persistence, and it can be dramatically influenced by phylogeny, seed traits, and ecological factors. In this study, we examined the relationships among seed mass, seed shape, and germination percentage (GP), and assessed the extent to which phylogeny, seed traits (seed mass, shape, and color) and ecological factors (ecotype, life form, adult longevity, dispersal type, and onset of flowering) influence GP at the community level. Al...

  4. Detection and characterization of viruses as field and vaccine strains in feedlot cattle with bovine respiratory disease (United States)

    This study investigated viruses in bovine respiratory disease (BRD) cases in feedlots, including bovine herpesvirus-1 (BoHV-1), bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine coronaviruses (BoCV) and parainfluenza-3 virus (PI3V). Nasal swabs were collected fro...

  5. Prevalence and economics and bovine leukosis in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, D.K.; Beal, V.C. Jr.


    This paper reviews the prevalence of bovine leukosis in the US and discusses the economic significance of the disease. The term leukosis is used except when reporting the Meat Inspection Department data which used the term malignant lymphoma instead. (PCS)

  6. Proteomic analysis of bovine blastocoel fluid and blastocyst cells

    DEFF Research Database (Denmark)

    Jensen, Pernille Linnert; Grøndahl, Marie Louise; Beck, Hans Christian


    development, little information is available about the protein complement of early embryos. Modern, sensitive proteomic technology (nano HPLC tandem mass spectrometry) allowed us to describe the proteome of the scarce blastocoel fluid and cell material of expanded bovine blastocysts isolated...

  7. Cartilage (Bovine and Shark) (PDQ®)—Health Professional Version (United States)

    Expert-reviewed information summary about the use of bovine and shark cartilage as a treatment for people with cancer. Note: The information in this summary is no longer being updated and is provided for reference purposes only.

  8. X chromosome regulation of autosomal gene expression in bovine blastocysts


    Itoh, Yuichiro; Arnold, Arthur P.


    Although X chromosome inactivation in female mammals evolved to balance the expression of X chromosome and autosomal genes in the two sexes, female embryos pass through developmental stages in which both X chromosomes are active in somatic cells. Bovine blastocysts show higher expression of many X genes in XX than XY embryos, suggesting that X inactivation is not complete. Here we reanalyzed bovine blastocyst microarray expression data from a network perspective with a focus on interactions b...

  9. Occupational asthma caused by inhalation of bovine serum albumin powder


    Choi, Gil-Soon; Kim, Joo-Hee; Lee, Haet-Nim; Sung, Jun-Mo; Lee, Jin-Woo; Park, Hae-Sim


    Bovine serum albumin (BSA), which is present in bovine plasma, is one of the major allergens affecting patients with food allergies induced by milk and meat. It is also commonly used in research laboratories. Although some reports have documented food allergies associated with BSA, BSA-induced occupational asthma has not been reported. We report a case of occupational asthma and rhinitis in a laboratory worker caused by the inhalation of BSA powder, in which an IgE-mediated response was sugge...

  10. Phylogeny of Miliusa (Magnoliales: Annonaceae: Malmeoideae: Miliuseae, with descriptions of two new species from Malesia

    Directory of Open Access Journals (Sweden)

    Tanawat Chaowasku


    Full Text Available The molecular phylogeny of Miliusa (Annonaceae is reconstructed, with 27 (of ca. 50 species included, using a combination of seven plastid markers (rbcL exon, trnL intron, trnL-F spacer, matK exon, ndhF exon, psbA-trnH spacer, and ycf1 exon constituting ca. 7 kb. In addition, two new species of Miliusa are described from the Malesian area: M. butonensis sp. nov. from Buton Island, Indonesia and M. viridiflora sp. nov. from Papua New Guinea. The former is included in the molecular phylogenetic analysis. The reconstructed phylogeny corresponds well to the informal morphological grouping proposed earlier. A revised key to 13 Austro-Malesian species of Miliusa is provided.

  11. Phylogeny of the family Characidae (Teleostei: Characiformes: from characters to taxonomy

    Directory of Open Access Journals (Sweden)

    Juan Marcos Mirande

    Full Text Available The family Characidae is the most diverse among Neotropical fishes. Systematics of this family are mainly based on pre-cladistic papers, and only recently a phylogenetic hypothesis for Characidae was proposed by the author. That phylogeny was based on 360 morphological characters studied for 160 species, including representatives of families related to Characidae. This paper is based on that phylogenetic analysis, with the analyzed characters described herein and documented, accompanied by comparisons of their definition and coding in previous papers. Synapomorphies of each node of the proposed phylogeny are listed, comparisons with previous classifications provided, and autapomorphies of the analyzed species listed. Taxonomic implications of the proposed classification and the position of the incertae sedis genera within Characidae are discussed. A discussion of the phylogenetic information of the characters used in the classical systematics of the Characidae is provided.

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

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


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

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

    Institute of Scientific and Technical Information of China (English)

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


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

  14. A multilocus phylogeny of a major New World avian radiation: the Vireonidae. (United States)

    Slager, David L; Battey, C J; Bryson, Robert W; Voelker, Gary; Klicka, John


    The family Vireonidae represents one of the most widespread and well-known New World avian radiations, but a robust species-level phylogeny of the group is lacking. Here, we infer a phylogeny of Vireonidae using multilocus data obtained from 221 individuals from 46 of 52 vireonid species (representing all four genera) and five "core Corvoidea" outgroups. Our results show Vireonidae to be monophyletic, consistent with a single colonization of the New World by an Asian ancestor. Cyclarhis and Vireolanius are monophyletic genera that diverged early from the rest of Vireonidae. Hylophilus is polyphyletic, represented by three distinct clades concordant with differences in morphology, habitat, and voice. The poorly known South American species Hylophilus sclateri is embedded within the genus Vireo. Vireo, in turn, consists of several well-supported intrageneric clades. Overall, tropical vireonid species show much higher levels of intraspecific genetic structure than temperate species and several currently recognized species are probably comprised of multiple cryptic species.

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

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


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

  16. Phylogeny of the Glomerales and Diversisporales (fungi: Glomeromycota) from actin and elongation factor 1-alpha sequences. (United States)

    Helgason, Thorunn; Watson, Irene J; Young, J Peter W


    The arbuscular mycorrhizal (AM) fungi have been elevated to the phylum Glomeromycota based on a ribosomal gene phylogeny. In order to test this phylogeny, we amplified and sequenced small subunit ribosomal RNA (SSUrRNA), actin and elongation factor 1 (EF1)-alpha gene fragments from single spores of Acaulospora laevis, Glomus caledonium, Gigaspora margarita, and Scutellospora dipurpurescens. Sequence variation within and among spores of an isolate was low except for SSUrRNA in S. dipurpurescens, and the actin amino acid sequence was more conserved than that of EF1-alpha. The AM fungal sequences were more similar to one another than to any other fungal group. Joint phylogenetic analysis of the actin and EF1-alpha sequences suggested that the sister group to the AM fungi was a Zygomycete order, the Mortierellales.

  17. Homologous recombination in bovine pestiviruses. Phylogenetic and statistic evidence. (United States)

    Jones, Leandro Roberto; Weber, E Laura


    Bovine pestiviruses (Bovine Viral Diarrea Virus 1 (BVDV 1) and Bovine Viral Diarrea Virus 2 (BVDV 2)) belong to the genus Pestivirus (Flaviviridae), which is composed of positive stranded RNA viruses causing significant economic losses world-wide. We used phylogenetic and bootstrap analyses to systematically scan alignments of previously sequenced genomes in order to explore further the evolutionary mechanisms responsible for variation in the virus. Previously published data suggested that homologous crossover might be one of the mechanisms responsible for the genomic rearrangements observed in cytopathic (cp) strains of bovine pestiviruses. Nevertheless, homologous recombination involves not just homologous crossovers, but also replacement of a homologous region of the acceptor RNA. Furthermore, cytopathic strains represent dead paths in evolution, since they are isolated exclusively from the fatal cases of mucosal disease. Herein, we report evidence of homologous inter-genotype recombination in the genome of a non-cytopathic (ncp) strain of Bovine Viral Diarrea Virus 1, the type species of the genus Pestivirus. We also show that intra-genotype homologous recombination might be a common phenomenon in both species of Pestivirus. This evidence demonstrates that homologous recombination contribute to the diversification of bovine pestiviruses in nature. Implications for virus evolution, taxonomy and phylogenetics are discussed.

  18. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.

    Directory of Open Access Journals (Sweden)

    Emmanuelle Lerat


    Full Text Available The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205 of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.

  19. The Ecology, Life History, and Phylogeny of the Marine Thecate Heterotrophic Dinoflagellates Protoperidinium and Diplopsalidaceae (Dinophyceae) (United States)


    shape. LSU rDNA gene sequences are frequently used to infer the phylogeny of organisms. The many copies of the LSU rDNA found in the genome are thought... cyanobacteria . Large, thecate dinoflagellates were absent and small gymnodinoid dinoflagellates were present in this deeper chlorophyll layer. Kjaeret et al...the difference between the offshore and onshore Protoperidinium species seen in this study. Cyanobacteria and picoeukaryotes, while important for the

  20. Phylogeny and evolution of ontogeny of the family Oxytomidae Ichikawa, 1958 (Mollusca: Bivalvia) (United States)

    Lutikov, O. A.; Temkin, I. E.; Shurygin, B. N.


    We described ontogenies and reconstructed morphogeneses of hinges in some supraspecific taxa of the bivalve family Oxytomidae Ichikawa, 1958 from the Mesozoic of Russia. The phylogeny of the family is reconstructed using evolutionary and cladistic methods. The appearance of the endemic genus Arctotis Bodylevsky, 1960 in the epicontinental seas of Siberia can be explained in terms of gradual transformations of the ligament and byssal apparatus in the Northern Siberian members of Praemeleagrinella Lutikov et Shurygin, 2009 and Praearctotis Lutikov et Shurygin, 2009.

  1. What do we know about the phylogeny of the Semi-Aquatic Bugs (Hemiptera: Heteroptera: Gerromorpha)?

    DEFF Research Database (Denmark)

    Damgaard, Jakob


    The present study summarizes knowledge about phylogenetic relationships of the heteropteran infraorder Gerromorpha. A phylogeny for all families and subfamilies, and for all genera but those assigned to the two most diverse families, Veliidae and Gerridae, is compiled from the many studies by the...... by the late Dr. Nils Moller Andersen. Comparisons with recently published studies, including DNA sequence data show that the superfamilies Hydrometroidea and Gerroidea, the family Veliidae, the subfamily Mesoveliinae, and the genera Mesovelia and Microvelia are probably not monophyletic...

  2. PHY·FI: fast and easy online creation and manipulation of phylogeny color figures

    Directory of Open Access Journals (Sweden)

    Fredslund Jakob


    Full Text Available Abstract Background The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. Results This paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates". The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY·FI is free for all and is available from this web address:

  3. Bovine coronavirus antibody titers at weaning negatively correlate with incidence of bovine respiratory disease in the feed yard (United States)

    Bovine respiratory disease complex (BRDC) is a multifactorial disease caused by complex interactions among viral and bacterial pathogens, stressful management practices and host genetic variability. Although vaccines and antibiotic treatments are readily available to prevent and treat infection caus...

  4. Bovine lymphocytic leukemia: studies of etiology, pathogenesis and mode of transmission. Progress report, November 1, 1979-October 31, 1980

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, D.K.


    The primary project objectives are to elucidate the cause(s) and early pathogenesis of the adult form of lymphosarcoma in cattle. This goal is to be accomplished through experimental transmission of the disease. For these studies large quantities of bovine leukemia virus (BLV) were propagated in short-term, mitogen stimulated, lymphocyte cultures. Cultures containing abundant BLV particles were pooled (33 liters total) and further processed by continuous flow, density gradient, ultracentrifugation. This higly concentrated, cell free, BLV preparation was then used as inoculum for 12 late stage bovine fetuses (inoculated in utero) and two newborn calves. Extensive monitoring studies have been carrid out on these inoculated animals to detect precancerous changes and to obtain a detailed description of the events preceding the development of lymphosarcoma. These extensive records on lymphosarcoma associated blood parameters have established that all of the inoculated animals became persistently BLV infected. However, after more than five years of incubation, no cases of lymphosarcoma developed. Consequently, during the past seven months, five of these well characterized animals have been subjected to frequent BLV re-exposure in order to study BLV-host interactions in previously infected adults and to potentially accelerate tumor formation in these animals.

  5. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. (United States)

    Wiens, John J; Hutter, Carl R; Mulcahy, Daniel G; Noonan, Brice P; Townsend, Ted M; Sites, Jack W; Reeder, Tod W


    Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.

  6. [Comparison of phylogeny analysis methods for rhizobia asolated from Albizia spp., Acacia spp. and Leucaena leucocephala]. (United States)

    Wang, Fengqin; Zhang, Yongfa; Liu, Jie; Song, Andong; Liu, Quanjun; Chen, Wenxin


    Multilocus house-keeping gene sequence analysis is a hotspot of taxonomy and phylogeny of prokaryotes. In this research, we used atpD and gln II gene sequences to analyze the phylogeny of nine rhizobia strains of Albizia spp., Acacia spp. and Leucaena leucocephala and compared the results to that of 16S rDNA. The phylogenetic relationships based on the sequence analysis of these three genes were congruent at the genera level. CCBAU43060 and CCBAU 61139 were located in the branch of Rhizobium-Agrobacterium. CCBAU51471, CCBAU35220, CCBAU51276 and CCBAU61158 belonged to the genera of Mesorhizobium. CCBAU35234, CCBAU61178 and CCBAU35085 were assigned to Bradyrhizobium. Differences were found for some strains, for example CCBAU 61158, CCBAU43060, CCBAU61178, at the species level. Insertion fragment and mosaic gene were also found in some isolates. These results indicated that there was recombination between species in the same genera. It is reliable to determine the taxonomy status at genera levels based on the sequence analysis of 16S rDNA. If the relationships between strains belonging to the same genera were studied using the phylogeny methods, researches should be carried out with more than one house-keeping genes.

  7. Phylogeny of economically important insect pests that infesting several crops species in Malaysia (United States)

    Ghazali, Siti Zafirah; Zain, Badrul Munir Md.; Yaakop, Salmah


    This paper reported molecular data on insect pests of commercial crops in Peninsular Malaysia. Fifteen insect pests (Metisa plana, Calliteara horsefeldii, Cotesia vestalis, Bactrocera papayae, Bactrocera carambolae, Bactrocera latifrons, Conopomorpha cramella, Sesamia inferens, Chilo polychrysa, Rhynchophorus vulneratus, and Rhynchophorus ferrugineus) of nine crops were sampled (oil palm, coconut, paddy, cocoa, starfruit, angled loofah, guava, chili and mustard) and also four species that belong to the fern's pest (Herpetogramma platycapna) and storage and rice pests (Tribolium castaneum, Oryzaephilus surinamensis and Cadra cautella). The presented phylogeny summarized the initial phylogenetic hypothesis, which concerning by implementation of the economically important insect pests. In this paper, phylogenetic relationships among 39 individuals of 15 species that belonging to three orders under 12 genera were inferred from DNA sequences of mitochondrial marker, cytochrome oxidase subunit I (COI) and nuclear marker, ribosomal DNA 28S D2 region. The phylogenies resulted from the phylogenetic analyses of both genes are relatively similar, but differ in the sequence of evolution. Interestingly, this most recent molecular data of COI sequences data by using Bayesian Inference analysis resulted a more-resolved phylogeny that corroborated with traditional hypotheses of holometabolan relationships based on traditional hypotheses of holometabolan relationships and most of recently molecular study compared to 28S sequences. This finding provides the information on relationships of pests species, which infested several crops in Malaysia and also estimation on Holometabola's order relationships. The identification of the larval stages of insect pests could be done accurately, without waiting the emergence of adults and supported by the phylogenetic tree.

  8. Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy. (United States)

    Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang


    The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera.

  9. Genera of euophryine jumping spiders (Araneae: Salticidae), with a combined molecular-morphological phylogeny. (United States)

    Zhang, Junxia; Maddison, Wayne P


    Morphological traits of euophryine jumping spiders were studied to clarify generic limits in the Euophryinae and to permit phylogenetic classification of genera lacking molecular data. One hundred and eight genera are recognized within the subfamily. Euophryine generic groups and the delimitation of some genera are reviewed in detail. In order to explore the effect of adding formal morphological data to previous molecular phylogenetic studies, and to find morphological synapomorphies, eighty-two morphological characters were scored for 203 euophryine species and seven outgroup species. The morphological dataset does not perform as well as the molecular dataset (genes 28S, Actin 5C; 16S-ND1, COI) in resolving the phylogeny of Euophryinae, probably because of frequent convergence and reversal. The formal morphological data were mapped on the phylogeny in order to seek synapomorphies, in hopes of extending the phylogeny to include taxa for which molecular data are not available. Because of homoplasy, few globally-applicable morphological synapomorphies for euophryine clades were found. However, synapomorphies that are unique locally in subclades still help to delimit euophryine generic groups and genera. The following synonyms of euophryine genera are proposed: Maeotella with Anasaitis; Dinattus with Corythalia; Paradecta with Compsodecta; Cobanus, Chloridusa and Wallaba with Sidusa; Tariona with Mopiopia; Nebridia with Amphidraus; Asaphobelis and Siloca with Coryphasia; Ocnotelus with Semnolius; Palpelius with Pristobaeus; Junxattus with Laufeia; Donoessus with Colyttus; Nicylla, Pselcis and Thianitara with Thiania. The new genus Saphrys is erected for misplaced species from southern South America.

  10. Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. (United States)

    van Oven, Mannis; Van Geystelen, Anneleen; Kayser, Manfred; Decorte, Ronny; Larmuseau, Maarten H D


    During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y-chromosome single-nucleotide polymorphisms (Y-SNPs), has led to the construction of a well-established Y-chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y-SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of information included in the "complete" Y-chromosome phylogeny, which now already includes many thousands of identified Y-SNPs, can be overwhelming and complicates its understanding as well as the task of selecting suitable markers for genotyping purposes in evolutionary, demographic, anthropological, genealogical, medical, and forensic studies. As a solution, we introduce a concise reference phylogeny whereby we do not aim to provide an exhaustive tree that includes all known Y-SNPs but, rather, a quite stable reference tree aiming for optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. Furthermore, with this reference tree, we wish to propose a common standard for Y-marker as well as Y-haplogroup nomenclature. The current version of our tree is based on a core set of 417 branch-defining Y-SNPs and is available online at

  11. Phylogeny, paleontology, and primates: do incomplete fossils bias the tree of life? (United States)

    Pattinson, David J; Thompson, Richard S; Piotrowski, Aleks K; Asher, Robert J


    Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here, we apply a heuristic means to assess how a fossil's incompleteness detracts from inferring its phylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon's molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence. Real fossil templates sampled for 36 or more of the 360 available morphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based on the Eocene primate Darwinius masillae performs better than most other templates with a similar number of sampled characters, likely due to preservation of data across multiple partitions. Our results support the interpretation that Darwinius is strepsirhine, not haplorhine, and suggest that paleontological datasets are reliable in primate phylogeny reconstruction.

  12. Phylogeny to function: PE/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity. (United States)

    Fishbein, S; van Wyk, N; Warren, R M; Sampson, S L


    The pe/ppe genes represent one of the most intriguing aspects of the Mycobacterium tuberculosis genome. These genes are especially abundant in pathogenic mycobacteria, with more than 160 members in M. tuberculosis. Despite being discovered over 15 years ago, their function remains unclear, although various lines of evidence implicate selected family members in mycobacterial virulence. In this review, we use PE/PPE phylogeny as a framework within which we examine the diversity and putative functions of these proteins. We report on the evolution and diversity of the respective gene families, as well as the implications thereof for function and host immune recognition. We summarize recent findings on pe/ppe gene regulation, also placing this in the context of PE/PPE phylogeny. We collate data from several large proteomics datasets, providing an overview of PE/PPE localization, and discuss the implications this may have for host responses. Assessment of the current knowledge of PE/PPE diversity suggests that these proteins are not variable antigens as has been so widely speculated; however, they do clearly play important roles in virulence. Viewing the growing body of pe/ppe literature through the lens of phylogeny reveals trends in features and function that may be associated with the evolution of mycobacterial pathogenicity.

  13. Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China. (United States)

    Wang, Xuewei; Liu, Xingzhong; Groenewald, Johannes Z


    The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.

  14. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. (United States)

    Hinchliff, Cody E; Smith, Stephen A; Allman, James F; Burleigh, J Gordon; Chaudhary, Ruchi; Coghill, Lyndon M; Crandall, Keith A; Deng, Jiabin; Drew, Bryan T; Gazis, Romina; Gude, Karl; Hibbett, David S; Katz, Laura A; Laughinghouse, H Dail; McTavish, Emily Jane; Midford, Peter E; Owen, Christopher L; Ree, Richard H; Rees, Jonathan A; Soltis, Douglas E; Williams, Tiffani; Cranston, Karen A


    Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

  15. Molecular phylogeny and evolution of Scomber (Teleostei: Scombridae) based on mitochondrial and nuclear DNA sequences

    Institute of Scientific and Technical Information of China (English)

    CHENG Jiao; GAO Tianxiang; MIAO Zhenqing; YANAGIMOTO Takashi


    A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial (COI, Cyt b and control region) and nuclear (5S rDNA) DNA sequence data in multigene perspective. A variety of phylogenetic analytic methods were used to clarify the current taxonomic classification and to assess phylogenetic relationships and the evolutionary history of this genus. The present study produced a well-resolved phylogeny that strongly supported the monophyly of Scomber. We confirmed that S. japonicus and S. colias were genetically distinct. Although morphologically and ecologically similar to S. colias, the molecular data showed that S. japonicus has a greater molecular affinity with S. australasicus, which conflicts with the traditional taxonomy. This phyiogenetic pattern was corroborated by the mtDNA data, but incompletely by the nuclear DNA data. Phylogenetic concordance between the mitochondrial and nuclear DNA regions for the basal nodes supports an Atlantic origin for Scomber. The present-day geographic ranges of the species were compared with the resultant molecular phylogeny derived from partition Bayesian analyses of the combined data sets to evaluate possible dispersal routes of the genus. The present-day geographic distribution of Scomber species might be best ascribed to multiple dispersal events. In addition, our results suggest that phylogenies derived from multiple genes and long sequences exhibited improved phylogenetic resolution, from which we conclude that the phylogenetic reconstruction is a reliable representation of the evolutionary history of Scomber.

  16. The role of host phylogeny varies in shaping microbial diversity in the hindguts of lower termites. (United States)

    Tai, Vera; James, Erick R; Nalepa, Christine A; Scheffrahn, Rudolf H; Perlman, Steve J; Keeling, Patrick J


    The hindguts of lower termites and Cryptocercus cockroaches are home to a distinct community of archaea, bacteria, and protists (primarily parabasalids and some oxymonads). Within a host species, the composition of these hindgut communities appears relatively stable, but the evolutionary and ecological factors structuring community composition and stability are poorly understood, as are differential impacts of these factors on protists, bacteria, and archaea. We analyzed the microbial composition of parabasalids and bacteria in the hindguts of Cryptocercus punctulatus and 23 species spanning 4 families of lower termites by pyrosequencing variable regions of the small-subunit rRNA gene. Especially for the parabasalids, these data revealed undiscovered taxa and provided a phylogenetic basis for a more accurate understanding of diversity, diversification, and community composition. The composition of the parabasalid communities was found to be strongly structured by the phylogeny of their hosts, indicating the importance of historical effects, although exceptions were also identified. Particularly, spirotrichonymphids and trichonymphids likely were transferred between host lineages. In contrast, host phylogeny was not sufficient to explain the majority of bacterial community composition, but the compositions of the Bacteroidetes, Elusimicrobia, Tenericutes, Spirochaetes, and Synergistes were structured by host phylogeny perhaps due to their symbiotic associations with protists. All together, historical effects probably resulting from vertical inheritance have had a prominent role in structuring the hindgut communities, especially of the parabasalids, but dispersal and environmental acquisition have played a larger role in community composition than previously expected.

  17. Phylogeny of the glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. (United States)

    Redecker, Dirk; Raab, Philipp


    The fungal symbionts of arbuscular mycorrhiza form a monophyletic group in the true Fungi, the phylum Glomeromycota. Fewer than 200 described species currently are included in this group. The only member of this clade known to form a different type of symbiosis is Geosiphon pyriformis, which associates with cyanobacteria. Because none of these fungi has been cultivated without their plant hosts or cyanobacterial partners, progress in obtaining multigene phylogenies has been slow and the nuclear-encoded ribosomal RNA genes have remained the only widely accessible molecular markers. rDNA phylogenies have revealed considerable polyphyly of some glomeromycotan genera that has been used to reassess taxonomic concepts. Environmental studies using phylogenetic methods for molecular identification have recovered an amazing diversity of unknown phylotypes, suggesting considerable cryptic species diversity. Protein gene sequences that have become available recently have challenged the rDNA-supported sister group relationship of the Glomeromycota with Asco/Basidiomycota. However the number of taxa analyzed with these new markers is still too small to provide a comprehensive picture of intraphylum relationships. We use nuclear-encoded rDNA and rpb1 protein gene sequences to reassess the phylogeny of the Glomeromycota and discuss possible implications.

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

    Directory of Open Access Journals (Sweden)

    Michelle Klein Sercundes


    Full Text Available Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC and beta subunit of RNA polymerase (rpoB, and mitochondrial gene coding for cytochrome B (cytB were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG, Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

  19. The phylogeny and taxonomy of austral monodontine topshells (Mollusca: Gastropoda: Trochidae), inferred from DNA sequences. (United States)

    Donald, Kirsten M; Kennedy, Martyn; Spencer, Hamish G


    The systematics of topshells (family Trochidae) is currently unresolved: at present even the generic boundaries within this group are poorly defined. In this study, we used sequence data of two mitochondrial genes (16S and cytochrome oxidase 1, COI) and one nuclear gene (actin) to resolve the phylogeny of a closely related subgroup of the Trochidae, 30 species of largely Southern Hemisphere monodontine topshells. The phylogenies constructed revealed five well-supported generic clades: a South African clade (genus Oxystele Philippi, 1847), which lay basally to four internal Pacific clades (genera Chlorodiloma Pilsbry, 1889; Monodonta Lamarck, 1799; Austrocochlea Fischer, 1885; and Diloma Philippi, 1845). The molecular phylogenies constructed in this study shed light on previously unresolved relationships between different groups of topshells, allowing for the first time assignation (based on DNA sequence) of clearly defined, well-supported taxonomic and nomenclatural classification of monodontine topshells species. Austrocochlea crinita (Philippi, 1849), A. odontis (Wood, 1828), A. adelaidae (Philippi, 1849), and A. millelineata (Bonnet, 1864) are placed in the genus Chlorodiloma, which we resurrect from synonymy with Austrocochlea. The Japanese M. confusa Tapparone-Canefri, 1874 is treated as a separate species from M. labio (Linné, 1758). Melagraphia Gray, 1847 is synonymised with Diloma and its sole member, M. aethiops (Gmelin, 1791), along with A. concamerata (Wood, 1828), is transferred to that genus. The Juan Fernandez endemic D. crusoeana (Pilsbry, 1889) is synonymised with D. nigerrima (Gmelin, 1791). We find that morphologically cryptic species are not necessarily close genetically.

  20. Bovine PrP expression levels in transgenic mice influence transmission characteristics of atypical bovine spongiform encephalopathy



    Until recently, transmissible spongiform encephalopathy (TSE) disease in cattle was thought to be caused by a single agent strain, bovine spongiform encephalopathy (BSE) (classical BSE or BSE-C). However, due to the initiation of a large-scale surveillance programme throughout Europe, two atypical BSE strains, bovine amyloidotic spongiform encephalopathy (BASE, also named BSE-L) and BSE-H have since been discovered. These atypical BSE isolates have been previously transmitted to a range of tr...