WorldWideScience

Sample records for bovin phylogeny accomplishments

  1. Mutational and Evolutionary Analyses of Bovine Reprimo Gene ...

    African Journals Online (AJOL)

    It can therefore be concluded that bovine RPRM gene contained 4 transition mutations and 5 indels that can be used in marker assisted selection. Evolutionary findings also demonstrated the existence of a divergent evolution between bovine RPRM gene and RPRM gene of fishes and frog. Keywords: Identity, phylogeny ...

  2. Life Sciences Accomplishments 1994

    Science.gov (United States)

    Burnell, Mary Lou (Editor)

    1993-01-01

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

  3. The phylogeny of Arthrotardigrada

    DEFF Research Database (Denmark)

    Hansen, Jesper Guldberg

    2011-01-01

    The order Arthrotardigrada, or water bears, constitutes a small group of 160 species of marine, microscopical invertebrates, within the phylum Tardigrada. Although the position of tardigrades in the Animal Kingdom has received much attention focusing on the metazoan phylogeny, the phylogenetic...

  4. Fossils and decapod phylogeny

    NARCIS (Netherlands)

    Schram, Frederick R.; Dixon, Christopher

    2003-01-01

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

  5. Building a Twig Phylogeny

    Science.gov (United States)

    Flinn, Kathryn M.

    2015-01-01

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

  6. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

    Directory of Open Access Journals (Sweden)

    Beaulieu Jeremy M

    2009-02-01

    Full Text Available Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Results Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae with 13,533 species and 1,401 sites. Conclusion By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously

  7. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches.

    Science.gov (United States)

    Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

    2009-02-11

    Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylogenies for addressing conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare. Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses databased sequences as well as taxonomic hierarchies to make extremely large trees with denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites. By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations

  8. The virtual accomplishment of knitting

    DEFF Research Database (Denmark)

    Heinemann, T.; Möller, R. L.

    2016-01-01

    . This means, among other things, that learners need to detect, diagnose and correct their errors without assistance from an expert. In this paper we focus on how this is accomplished by individuals attempting to learn how to knit by following instructions from a video tutorial. We show that novice knitters...

  9. Advanced Fuels Campaign 2012 Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed

    2012-11-01

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

  10. Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing

    Science.gov (United States)

    Naushad, Sohail; Barkema, Herman W.; Luby, Christopher; Condas, Larissa A. Z.; Nobrega, Diego B.; Carson, Domonique A.; De Buck, Jeroen

    2016-01-01

    Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity. PMID:28066335

  11. Advanced Fuels Campaign 2016 Accomplishments

    International Nuclear Information System (INIS)

    Richardson, Kate M.

    2016-01-01

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

  12. Advanced Fuels Campaign 2016 Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-01

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

  13. GESAMP: Two decades of accomplishments

    International Nuclear Information System (INIS)

    Windom, H.L

    1991-01-01

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

  14. Advanced fuels campaign 2013 accomplishments

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Suchard Marc A

    2007-03-01

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

  16. NPAR program - Status and accomplishments

    International Nuclear Information System (INIS)

    Vora, J.P.

    1991-01-01

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

  17. Transmutation Fuels Campaign FY-09 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Lori Braase

    2009-09-01

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

  18. 77 FR 29914 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2012-05-21

    ... Spongiform Encephalopathy; Importation of Bovines and Bovine Products AGENCY: Animal and Plant Health... derived from bovines with regard to bovine spongiform encephalopathy. This action will allow interested... importation of live bovines and products derived from bovines with regard to bovine spongiform encephalopathy...

  19. The shape of mammalian phylogeny

    DEFF Research Database (Denmark)

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

    2011-01-01

    an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions...

  20. High-Performance Phylogeny Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Tiffani L. Williams

    2004-11-10

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

  1. Engineering Accomplishments in the Construction of NCSX

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  2. Overview of LAMPF and its accomplishments

    International Nuclear Information System (INIS)

    Rosen, L.

    1978-04-01

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

  3. Biomass Program 2007 Accomplishments - Full Report

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2009-10-27

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

  4. Biomass Program 2007 Accomplishments - Report Introduction

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2009-10-27

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

  5. Phylogeny and subgeneric taxonomy of Aspergillus

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  6. Accomplishments and challenges of surgical simulation.

    Science.gov (United States)

    Satava, R M

    2001-03-01

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

  7. Advanced Fuels Campaign FY 2011 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Not Listed

    2011-11-01

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

  8. Accomplish the Application Area in Cloud Computing

    OpenAIRE

    Bansal, Nidhi; Awasthi, Amit

    2012-01-01

    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 whe...

  9. NASA total quality management 1990 accomplishments report

    Science.gov (United States)

    1991-01-01

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

  10. Basic Energy Sciences: Summary of Accomplishments

    Science.gov (United States)

    1990-05-01

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

  11. The phylogeny of amphibian metamorphosis.

    Science.gov (United States)

    Reiss, John O

    2002-01-01

    Frogs have one of the most extreme metamorphoses among vertebrates. How did this metamorphosis evolve? By combining the methods previously proposed by Mabee and Humphries (1993) and Velhagen (1997), I develop a phylogenetic method suited for rigorous analysis of this question. In a preliminary analysis using 12 transformation sequence characters and 36 associated event sequence characters, all drawn from the osteology of the skull, the evolution of metamorphosis is traced on an assumed phylogeny. This phylogeny has lissamphibians (frogs, salamanders, and caecilians) monophyletic, with frogs the sister group of salamanders. Successive outgroups used are temnospondyls and discosauriscids, both of which are fossil groups for which ontogenetic data are available. In the reconstruction of character evolution, an unambiguous change (synapomorphy) along the branch leading to lissamphibians is a delay in the lengthening of the maxilla until metamorphosis, in accordance with my previous suggestion (Reiss, 1996). However, widening of the interpterygoid vacuity does not appear as a synapomophy of lissamphibians, due to variation in the character states in the outgroups. From a more theoretical perspective, the reconstructed evolution of amphibian metamorphosis involves examples of heterochrony, through the shift of ancestral premetamorphic events to the metamorphic period, caenogenesis, through the origin of new larval features, and terminal addition, through the origin of new adult features. Other changes don't readily fit these categories. This preliminary study provides evidence that metamorphic changes in frogs arose as further modifications of changes unique to lissamphibians, as well as a new method by which such questions can be examined.

  12. The discursive accomplishment of regimes of automobility

    DEFF Research Database (Denmark)

    Lindegaard, Laura Bang

    2016-01-01

    conceptualisation of mobility, I address impacts of thought schemes and structures on current social and political discourses of mobility as I discuss and demonstrate how rationalities of advanced liberalism co-constitute a car-dependent way of living. Drawing on both studies of governmentality and ethnomethodology...... case study in a decentralised Danish village that demonstrates how citizens accomplish the rationalities that co-constitute their car-dependent mobility in discursive interaction. During the time of the case study (2010-11), the village was engaged in an energy village project, and the study...

  13. Sandia technology engineering and science accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    1993-03-01

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

  14. Accomplishments and needs in safety research

    International Nuclear Information System (INIS)

    Beckjord, E.S.

    1988-01-01

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

  15. Advanced Fuels Campaign FY 2015 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-29

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

  16. Advanced Fuels Campaign FY 2010 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

    Lori Braase

    2010-12-01

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

  17. Molecular phylogeny of Ranunculaceae based on internal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... evidence regarding the systematic classification of Ranunculaceae plants, we used molecular ... Ranunculaceae is a family of flowering plants known as ... and in the analysis of the evolutionary rate for lower level phylogeny ...

  18. NASA total quality management 1989 accomplishments report

    Science.gov (United States)

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

    1990-01-01

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

  19. The space shuttle program technologies and accomplishments

    CERN Document Server

    Sivolella, Davide

    2017-01-01

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

  20. Health and environmental research. Summary of accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    1984-04-01

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

  1. Bovine Herpesvirus 4 infections and bovine mastitis

    NARCIS (Netherlands)

    Wellenberg, Gerardus Johannus

    2002-01-01

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

  2. Molecular phylogeny of Duvenhage virus

    Directory of Open Access Journals (Sweden)

    Louis H. Nel

    2011-11-01

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

  3. PREVALENCE OF BOVINE (1)

    African Journals Online (AJOL)

    408 heads of cattle to determine the prevalence of bovine tuberculosis and assess its public health implications. A comparative ..... (78.6%) of the respondents consume raw and poorly heat ... compromises related to certain stress factors.

  4. Light Water Reactor Sustainability Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-01

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

  5. Lunabotics Mining Competition: Inspiration Through Accomplishment

    Science.gov (United States)

    Mueller, Robert P.

    2011-01-01

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

  6. Some History and Accomplishments of the IUSS

    Science.gov (United States)

    Brevik, Eric C.; Hartemink, Alfred E.

    2013-04-01

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

  7. Advanced Fuels Campaign FY 2014 Accomplishments Report

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-01

    accident conditions than traditional fuel systems. AFC management and integration activities included continued support for international collaborations, primarily with France, Japan, the European Union, Republic of Korea, and China, as well as various working group and expert group activities in the Organization for Economic Cooperation and Development Nuclear Energy Agency (OECD-NEA) and the International Atomic Energy Agency (IAEA). Three industry-led Funding Opportunity Announcements (FOAs) and two university-led Integrated Research Projects (IRPs), funded in 2013, made significant progress in fuels and materials development. All are closely integrated with AFC and Accident Tolerant Fuels (ATF) research. Accomplishments made during fiscal year (FY) 2014 are highlighted in this report, which focuses on completed work and results. The process details leading up to the results are not included; however, the lead technical contact is provided for each section.

  8. Juvenile morphology in baleen whale phylogeny.

    Science.gov (United States)

    Tsai, Cheng-Hsiu; Fordyce, R Ewan

    2014-09-01

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

  9. Ribosomal RNA: a key to phylogeny

    Science.gov (United States)

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

    1993-01-01

    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.

  10. Molecular data and phylogeny of family

    International Nuclear Information System (INIS)

    Shinwari, Z.K.; Shinwari, S.

    2010-01-01

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

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

    DEFF Research Database (Denmark)

    Vilhelmsen, Lars

    2007-01-01

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

  12. Molecular phylogeny of Ranunculaceae based on internal ...

    African Journals Online (AJOL)

    The botanical family Ranunculaceae contains important medicinal plants. To obtain new evolutionary evidence regarding the systematic classification of Ranunculaceae plants, we used molecular phylogenies to test relationships based on the internal transcribed spacer region. The results of phylogenetic analysis of 92 ...

  13. Book review: Insect morphology and phylogeny

    Directory of Open Access Journals (Sweden)

    Susanne Randolf

    2014-05-01

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

  14. Plastome phylogeny and early diversification of Brassicaceae.

    Science.gov (United States)

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

    2017-02-16

    The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

  15. Bayesian inference of the metazoan phylogeny

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  16. Primate diversification inferred from phylogenies and fossils.

    Science.gov (United States)

    Herrera, James P

    2017-12-01

    Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  17. A molecular phylogeny of living primates.

    Science.gov (United States)

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

    2011-03-01

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

  18. A Molecular Phylogeny of Living Primates

    Science.gov (United States)

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

    2011-01-01

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

  19. A molecular phylogeny of living primates.

    Directory of Open Access Journals (Sweden)

    Polina Perelman

    2011-03-01

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

  20. Whole genome phylogenies for multiple Drosophila species

    Directory of Open Access Journals (Sweden)

    Seetharam Arun

    2012-12-01

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

  1. Camel and bovine chymosin

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  2. PREVALENCE OF BOVINE HERPESVIRUS-1,PARAINFLUENZA-3,BOVINE ROTAVIRUS, BOVINE VIRAL DIARRHEA, BOVINE ADENOVIRUS-7,BOVINE LEUKEMIA VIRUS AND BLUETONGUE VIRUS ANTIBODIES IN CATTLE IN MEXICO

    OpenAIRE

    SUZAN, Victor M.; ONUMA, Misao; AGUILAR, Romero E.; MURAKAMI, Yosuke

    1983-01-01

    Sera were collected from dairy and beef cattle in 19 different states of Mexico. These sera were tested for bovine herpesvirus-1 (BHV-1), parainfluenza-3 virus (PIV-3), bovine rotavirus (BRV), bovine leukemia virus (BLV), bovine adenovirus-7 (BAV-7), bluetongue virus (BTV) and bovine viral diarrhea virus (BVDV). Seropositive rates for each virus for dairy cattle tested were 158/277(57.0%) for BHV-1,217/286(75.0%) for PIV-3,541/1498(36.1%) for BLV, 134/144(93.1%) for BRV, 39/90(43.3%) for BTV,...

  3. Enhanced surveillance program FY97 accomplishments. Progress report

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-10-01

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

  4. Non-proliferation and nuclear cooperation - accomplishments and challenges

    International Nuclear Information System (INIS)

    Marshall, H.R. Jr.

    1983-01-01

    The purpose of this paper is to assess the accomplishments in non-proliferation and nuclear co-operation since the beginning of President Reagan's administration, and the challenges remaining to be met in those fields. (NEA) [fr

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

    Science.gov (United States)

    2012-03-01

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

  6. Accomplishments Report for the National Strategy for Electronics Stewardship

    Science.gov (United States)

    This page holds the NSES report, which charts the progress and accomplishments of the NSES in addressing sustainable management of electronics and highlights the benefits of continued leadership from the federal government.

  7. 5 CFR 3301.102 - Procedure for accomplishing disqualification.

    Science.gov (United States)

    2010-01-01

    ... ETHICAL CONDUCT FOR EMPLOYEES OF THE DEPARTMENT OF ENERGY § 3301.102 Procedure for accomplishing...) Disqualification from matter effecting prospective employers. A DOE employee who is required, in accordance with 5...

  8. Idaho National Laboratory Mission Accomplishments, Fiscal Year 2015

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-01

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

  9. Studies in Phylogeny. I. On the relation of Taxonomy, Phylogeny and Biogeography

    NARCIS (Netherlands)

    Lam, H.J.

    1938-01-01

    Taxonomy is static, its symbols are therefore two-dimensional, representing 1. differences or resemblances and 2. diversity (eventually are also area). Phylogeny is dynamic and its symbols are three-dimensional, representing 1. Time, 2. differences or resemblances and 3. diversity (eventually also

  10. Bovine Virus Diarrhea (BVD)

    OpenAIRE

    Hoar, Bruce R.

    2004-01-01

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

  11. Algorithms For Phylogeny Reconstruction In a New Mathematical Model

    NARCIS (Netherlands)

    Lenzini, Gabriele; Marianelli, Silvia

    1997-01-01

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

  12. Proteomic Analysis of Bovine Nucleolus

    Institute of Scientific and Technical Information of China (English)

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

    2010-01-01

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

  13. Chromosomal phylogeny of Lagothrix, Brachyteles, and Cacajao.

    Science.gov (United States)

    Viegas Péquignot, E; Koiffmann, C P; Dutrillaux, B

    1985-01-01

    Based on a comparison of the karyotypes of two Plathyrrhini species, Cacajao melanocephalus (Pitheciinae) and Brachyteles arachnoides (Atelinae), with those of two previously studied species, Lagothrix lagothrica (Atelinae) and C calvus rubicundus (Pitheciinae), it appears that the two Cacajao species have undergone the same number of chromosome rearrangements since they diverged from their common ancestor and that the karyotype of Brachyteles is ancestral to that of Lagothrix. The chromosomal phylogeny of these four species is proposed. A Y-autosome translocation is present in the karyotypes of the two Cacajao species.

  14. Explaining evolution via constrained persistent perfect phylogeny

    Science.gov (United States)

    2014-01-01

    Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to

  15. Mutational, Phylogeny and Evolution Analyses of Salvia Copalyl Diphosphate Synthase

    International Nuclear Information System (INIS)

    Hao, D. C.; Thimmappa, R. B.; Xiao, P. G.

    2016-01-01

    The cyclization of geranylgeranyl diphosphate (GGPP) is catalyzed by copalyl diphosphate synthase (CPS), a class II diterpene synthase (diTPS), to form copalyl diphosphate (CPP), which is an essential substrate of a variety of diterpenes in secondary metabolism of angiosperm including Salvia medicinal plants. The protein environment of the N-terminal class II active site stabilizes the carbocation intermediates and maintains the catalytic activity of angiosperm class II diTPS. The virtual modeling and mutagenesis of the class II diTPS of Salvia miltiorrhiza (SmCPS) were accomplished to illuminate the catalytic activity of SmCPS. Terminal truncations and point mutations established the role of the Beta-Gamma domain and Alpha domain, i.e., they facilitate the flexible conformational change of the class II active site after substrate binding. E203 and K238 in the N-ter Gamma domain of SmCPS1 are functional in the substrate binding and conformational transition and might be essential in catalysis. Similar to other CPSs, the ensuing protonation of the GGPP substrate and coordination of the diphosphate group are governed by highly conserved residues in the DxDD motif of SmCPS, e.g., D372 of CPS1. Moreover, F256 and Y505 stabilize the carbocation and control the enzymatic activity during CPP formation. The amino acids of the predicted active sites, despite under purifying selection, vary greatly, corresponding to the functional flexibility of angiosperm CPSs. Molecular phylogeny and evolution analyses suggest early and ongoing evolution of labdane-related diterpenoid metabolism in angiosperm. (author)

  16. The mitogenomic phylogeny of the Elasmobranchii (Chondrichthyes).

    Science.gov (United States)

    Amaral, Cesar R L; Pereira, Filipe; Silva, Dayse A; Amorim, António; de Carvalho, Elizeu F

    2017-09-20

    Here we present a mitogenomic perspective on the evolution of sharks and rays, being a first glance on the complete mitochondrial history of such an old and diversified group of vertebrates. The Elasmobranchii is a diverse subclass of Chondrichthyes, or cartilaginous fish, with about 1200 species of ocean- and freshwater-dwelling fishes spread all over the world's seas, including some of the ocean's largest fishes. The group dates back about 400 million years near the Devonian-Silurian boundary, being nowadays represented by several derivative lineages, mainly related to Mesozoic forms. Although considered of ecological, commercial and conservation importance, the phylogeny of this old group is poorly studied and still under debate. Here we apply a molecular systematic approach on 82 complete mitochondrial genomes to investigate the phylogeny of the Elasmobranchii. By using maximum likelihood (ML) and Bayesian analyses, we found a clear separation within the shark clade between the Galeomorphii and the Squalomorphii, as well as sister taxa relationships between the Carcharhiniformes and the Lamniformes. Moreover, we found that Pristoidei clusters within the Rhinobatoidei, having been recovered as the sister taxon of the Rhinobatos genus in a clade which also includes the basal Zapteryx. Our results also reject the Hypnosqualea hypothesis, which proposes that the Batoidea should be placed within the Selachii.

  17. Phylogeny and species traits predict bird detectability

    Science.gov (United States)

    Solymos, Peter; Matsuoka, Steven M.; Stralberg, Diana; Barker, Nicole K. S.; Bayne, Erin M.

    2018-01-01

    Avian acoustic communication has resulted from evolutionary pressures and ecological constraints. We therefore expect that auditory detectability in birds might be predictable by species traits and phylogenetic relatedness. We evaluated the relationship between phylogeny, species traits, and field‐based estimates of the two processes that determine species detectability (singing rate and detection distance) for 141 bird species breeding in boreal North America. We used phylogenetic mixed models and cross‐validation to compare the relative merits of using trait data only, phylogeny only, or the combination of both to predict detectability. We found a strong phylogenetic signal in both singing rates and detection distances; however the strength of phylogenetic effects was less than expected under Brownian motion evolution. The evolution of behavioural traits that determine singing rates was found to be more labile, leaving more room for species to evolve independently, whereas detection distance was mostly determined by anatomy (i.e. body size) and thus the laws of physics. Our findings can help in disentangling how complex ecological and evolutionary mechanisms have shaped different aspects of detectability in boreal birds. Such information can greatly inform single‐ and multi‐species models but more work is required to better understand how to best correct possible biases in phylogenetic diversity and other community metrics.

  18. A supertree approach to shorebird phylogeny

    Directory of Open Access Journals (Sweden)

    Thomas Gavin H

    2004-08-01

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

  19. Asian horses deepen the MSY phylogeny.

    Science.gov (United States)

    Felkel, S; Vogl, C; Rigler, D; Jagannathan, V; Leeb, T; Fries, R; Neuditschko, M; Rieder, S; Velie, B; Lindgren, G; Rubin, C-J; Schlötterer, C; Rattei, T; Brem, G; Wallner, B

    2018-02-01

    Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages. © 2018 Stichting International Foundation for Animal Genetics.

  20. Viral infections and bovine mastitis: a review

    NARCIS (Netherlands)

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

    2002-01-01

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

  1. Accomplishments and challenges of the severe accident research

    International Nuclear Information System (INIS)

    Sehga, B.R.

    1998-01-01

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

  2. Emergence of new genotype and diversity of Theileria orientalis parasites from bovines in India.

    Science.gov (United States)

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

    2015-12-01

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. China Accomplished Its First Space Rendezvous and Docking

    Institute of Scientific and Technical Information of China (English)

    Chen Xiaoli

    2011-01-01

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

  4. Research accomplishments in particle physics: Annual progress report

    International Nuclear Information System (INIS)

    1988-01-01

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

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

    Science.gov (United States)

    Rhonda Mazza

    2015-01-01

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

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

    Science.gov (United States)

    Rhonda Mazza

    2014-01-01

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

  7. 2008 Science Accomplishments Report of the Pacific Northwest Research Station

    Science.gov (United States)

    Rhonda Mazza

    2009-01-01

    This report highlights significant research findings and accomplishments by scientists at the Pacific Northwest (PNW) Research Station during fiscal year 2008. The mission of the PNW Research Station is to generate and communicate scientific knowledge that helps people understand and make informed choices about people, natural resources, and the environment. The work...

  8. Business accomplishments, gender and entrepreneurial self-image

    NARCIS (Netherlands)

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

    2003-01-01

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

  9. Phylogeny mandalas for illustrating the Tree of Life.

    Science.gov (United States)

    Hasegawa, Masami

    2017-12-01

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

  10. Coloration mechanisms and phylogeny of Morpho butterflies.

    Science.gov (United States)

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

    2016-12-15

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

  11. Haemoprotozoa: Making biological sense of molecular phylogenies

    Directory of Open Access Journals (Sweden)

    Peter O'Donoghue

    2017-12-01

    Full Text Available A range of protistan parasites occur in the blood of vertebrates and are transmitted by haematophagous invertebrate vectors. Some 48 genera are recognized in bood primarily on the basis of parasite morphology and host specificity; including extracellular kinetoplastids (trypanosomatids and intracellular apicomplexa (haemogregarines, haemococcidia, haemosporidia and piroplasms. Gene sequences are available for a growing number of species and molecular phylogenies often link parasite and host or vector evolution. This review endeavours to reconcile molecular clades with biological characters. Four major trypanosomatid clades have been associated with site of development in the vector: salivarian or stercorarian for Trypanosoma, and supra- or peri-pylorian for Leishmania. Four haemogregarine clades have been associated with acarine vectors (Hepatozoon A and B, Karyolysus, Hemolivia and another two with leeches (Dactylosoma, Haemogregarina sensu stricto. Two haemococcidian clades (Lankesterella, Schellackia using leeches and mosquitoes (as paratenic hosts! were paraphyletic with monoxenous enteric coccidia. Two major haemosporidian clades have been associated with mosquito vectors (Plasmodium from mammals, Plasmodium from birds and lizards, two with midges (Hepatocystis from bats, Parahaemoproteus from birds and two with louse-flies and black-flies (Haemoproteus and Leucocytozoon from birds. Three major piroplasm clades were recognized: one associated with transovarian transmission in ticks (Babesia sensu stricto; one with pre-erythrocytic schizogony in vertebrates (Theileria/Cytauxzoon; and one with neither (Babesia sensu lato. Broad comparative studies with allied groups suggest that trypanosomatids and haemogregarines evolved first in aquatic and then terrestrial environments, as evidenced by extant lineages in invertebrates and their radiation in vertebrates. In contrast, haemosporidia and haemococcidia are thought to have evolved first in

  12. Towards improving searches for optimal phylogenies.

    Science.gov (United States)

    Ford, Eric; St John, Katherine; Wheeler, Ward C

    2015-01-01

    Finding the optimal evolutionary history for a set of taxa is a challenging computational problem, even when restricting possible solutions to be "tree-like" and focusing on the maximum-parsimony optimality criterion. This has led to much work on using heuristic tree searches to find approximate solutions. We present an approach for finding exact optimal solutions that employs and complements the current heuristic methods for finding optimal trees. Given a set of taxa and a set of aligned sequences of characters, there may be subsets of characters that are compatible, and for each such subset there is an associated (possibly partially resolved) phylogeny with edges corresponding to each character state change. These perfect phylogenies serve as anchor trees for our constrained search space. We show that, for sequences with compatible sites, the parsimony score of any tree [Formula: see text] is at least the parsimony score of the anchor trees plus the number of inferred changes between [Formula: see text] and the anchor trees. As the maximum-parsimony optimality score is additive, the sum of the lower bounds on compatible character partitions provides a lower bound on the complete alignment of characters. This yields a region in the space of trees within which the best tree is guaranteed to be found; limiting the search for the optimal tree to this region can significantly reduce the number of trees that must be examined in a search of the space of trees. We analyze this method empirically using four different biological data sets as well as surveying 400 data sets from the TreeBASE repository, demonstrating the effectiveness of our technique in reducing the number of steps in exact heuristic searches for trees under the maximum-parsimony optimality criterion. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Molecular phylogeny of extant Holothuroidea (Echinodermata).

    Science.gov (United States)

    Miller, Allison K; Kerr, Alexander M; Paulay, Gustav; Reich, Mike; Wilson, Nerida G; Carvajal, Jose I; Rouse, Greg W

    2017-06-01

    Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown

  14. Archaebacterial phylogeny: perspectives on the urkingdoms

    Science.gov (United States)

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

    1986-01-01

    Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.

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

    DEFF Research Database (Denmark)

    Kjær, Malene

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

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

  17. Abstract and research accomplishments of University Coal Research Projects

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

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

  18. Accomplishments and challenges of the severe accident research

    International Nuclear Information System (INIS)

    Sehgal, B.R.

    2001-01-01

    This paper briefly describes the progress of the severe accident research since 1980, in terms of the accomplishments made so far and the challenges that remain. Much has been accomplished: many important safety issues have been resolved and consensus is near on some others. However, some of the previously identified safety issues remain as challenges, while some new ones have arisen due to the shift in focus from containment to vessel integrity. New reactor designs have also created some new challenges. In general, the regulatory demands for new reactor designs are stricter, thereby requiring much greater attention to the safety issues concerned with the containment design of the new large reactors, and to the accident management procedures for mitigating the consequences of a severe accident. We apologize for not providing references to many fine investigations that contributed to the great progress made so far in the severe accident research

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-12-01

    The Material Recovery and Waste Form Development (MRWFD) Campaign under the U.S. Department of Energy (DOE) Fuel Cycle Technologies (FCT) Program is responsible for developing advanced separation and waste form technologies to support the various fuel cycle options defined in the DOE Nuclear Energy Research and Development Roadmap, Report to Congress (April 2010). This MRWFD accomplishments report summarizes the results of the research and development (R&D) efforts performed within MRWFD in Fiscal Year (FY) 2016. Each section of the report contains an overview of the activities, results, technical point of contact, applicable references, and documents produced during the FY. This report briefly outlines campaign management and integration activities but primarily focuses on the many technical accomplishments of FY 2016. The campaign continued to use an engineering-driven, science-based approach to maintain relevance and focus.

  20. Phylogeny and taxonomy of the Inonotus linteus complex

    Czech Academy of Sciences Publication Activity Database

    Tian, X.-M.; Yu, H.-Y.; Zhou, L.-W.; Decock, C.; Vlasák, Josef; Dai, Y.C.

    2013-01-01

    Roč. 58, č. 1 (2013), s. 159-169 ISSN 1560-2745 Institutional support: RVO:60077344 Keywords : Hymenochaetaceae * Phellinus * Phylogeny * ITS Subject RIV: EF - Botanics Impact factor: 6.938, year: 2013

  1. Phylogeny and Species Diversity of Gulf of California Oysters

    Data.gov (United States)

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

  2. Gene structure, phylogeny and expression profile of the sucrose ...

    Indian Academy of Sciences (India)

    Gene structure, phylogeny and expression profile of the sucrose synthase gene family in .... 24, 701–713. Bate N. and Twell D. 1998 Functional architecture of a late pollen .... Manzara T. and Gruissem W. 1988 Organization and expression.

  3. Bayesian phylogeny analysis via stochastic approximation Monte Carlo

    KAUST Repository

    Cheon, Sooyoung; Liang, Faming

    2009-01-01

    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

  4. Abstracts and research accomplishments of university coal research projects

    International Nuclear Information System (INIS)

    1991-06-01

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

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

    Science.gov (United States)

    1990-01-01

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

  6. Abstracts and research accomplishments of university coal research projects

    Energy Technology Data Exchange (ETDEWEB)

    1991-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Charles V Park

    2011-01-01

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

  8. The History and Accomplishments of the LIVESTRONG Young Adult Alliance.

    Science.gov (United States)

    Mathews-Bradshaw, Beth; Johnson, Rebecca; Kaplan, Stuart; Craddock, Kelli; Hayes-Lattin, Brandon

    2011-03-01

    This article outlines the history, background, and accomplishments of the LIVESTRONG Young Adult Alliance. The LIVESTRONG Young Adult Alliance, a program of the Lance Armstrong Foundation, was developed as a vehicle for a strategic plan designed to implement the Adolescent and Young Adult Oncology Progress Review Group (AYAO PRG) recommendations. The AYAO PRG was co-sponsored by Lance Armstrong Foundation and the National Cancer Institute (NCI); both LIVESTRONG and NCI provide strategic oversight and guidance to the Alliance. Highlights and accomplishments: The Alliance accomplishments include the publication of disease-specific retrospective analyses, funding of an AYA cohort study and biorepository proposal, publication of two position statements on guidelines for care of AYAs with cancer and training for AYA oncology health professionals, promotion of an international charter of rights for AYA cancer patients, creation and distribution of a survey to college health professionals, creation and implementation of a Cancer Centers Working Group and Institutional Review Board Toolkit, and continued growth and collaboration through an annual meeting. The growth and success of the Alliance has coincided with the growth of AYA oncology as a field. The collaborative environment of the Alliance draws together a diverse group of individuals united in the effort to increase survival rates and improve the quality of life for adolescents and young adults diagnosed with cancer.

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

    International Nuclear Information System (INIS)

    1986-08-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    1986-08-01

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

  11. Molecular phylogeny and morphological change in the Psittacula parakeets

    OpenAIRE

    Groombridge, Jim J.; Jones, Carl G.; Nichols, Richard A.; Carlton, Mark; Bruford, Michael W.

    2004-01-01

    We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800 bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that ext...

  12. Bovine Tuberculosis, A Zoonotic Disease

    Directory of Open Access Journals (Sweden)

    Tarmudji

    2008-12-01

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

  13. Direct maximum parsimony phylogeny reconstruction from genotype data.

    Science.gov (United States)

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

    2007-12-05

    Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

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

    Science.gov (United States)

    Cornils, Astrid; Blanco-Bercial, Leocadio

    2013-12-01

    The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Bootstrapping phylogenies inferred from rearrangement data

    Directory of Open Access Journals (Sweden)

    Lin Yu

    2012-08-01

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

  16. Bootstrapping phylogenies inferred from rearrangement data.

    Science.gov (United States)

    Lin, Yu; Rajan, Vaibhav; Moret, Bernard Me

    2012-08-29

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

  17. Personalized medicine: CCO's vision, accomplishments and future plans.

    Science.gov (United States)

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

    2015-01-01

    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. Copyright © 2014 Longwoods Publishing.

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

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, M.D.

    1999-01-01

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

  19. Accomplishments in 2007 in the treatment of advanced colorectal cancer.

    Science.gov (United States)

    Goldberg, Richard M; Carrato, Alfredo

    2008-05-01

    Overview of the Disease IncidencePrognosis Prognostic or Predictive FactorsCurrent General Therapy Standards and Regional Variations STANDARDS IN THE US AND EUROPE: Combination Therapy Plus a Biologic FOCUS and CAIRO 1: Serial Single Agents vs. Combination TherapyStop-and-Go StrategyLimited Availability of Biologics in Some RegionsAccomplishments During the Year TherapyWhat Needs To Be Done Controversies and Disagreements BOND-2 and PACCE: Chemotherapy + Bevacizumab + Cetuximab or PanitumumabSpecial Populations (Elderly and Poor Performance Status)Future Directions Comments on ResearchObstacles to Progress.

  20. A Framework for Studying Emotions Across Phylogeny

    Science.gov (United States)

    Anderson, David J.; Adolphs, Ralph

    2014-01-01

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

  1. Phylogeny and evolutionary history of the silkworm.

    Science.gov (United States)

    Sun, Wei; Yu, Hongsong; Shen, Yihong; Banno, Yutaka; Xiang, Zhonghuai; Zhang, Ze

    2012-06-01

    The silkworm, Bombyx mori, played an important role in the old Silk Road that connected ancient Asia and Europe. However, to date, there have been few studies of the origins and domestication of this species using molecular methods. In this study, DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives. All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm. Domestication was estimated to have occurred about 4100 years ago (ya), and the radiation of the different geographic strains of B. mori about 2000 ya. The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya. These estimates are in good agreement with the fossil evidence and historical records. In addition, we show that the domesticated silkworm experienced a population expansion around 1000 ya. The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics, in the genetic analysis of domestic animals, and for understanding the spread of human civilizations.

  2. Bacterial phylogeny structures soil resistomes across habitats

    Science.gov (United States)

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

    2014-05-01

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

  3. A transcriptome approach to ecdysozoan phylogeny.

    Science.gov (United States)

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

    2014-11-01

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

  4. Phylogeny based discovery of regulatory elements

    Directory of Open Access Journals (Sweden)

    Cohen Barak A

    2006-05-01

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

  5. Fort Collins Science Center fiscal year 2010 science accomplishments

    Science.gov (United States)

    Wilson, Juliette T.

    2011-01-01

    The scientists and technical professionals at the U.S. Geological Survey (USGS), Fort Collins Science Center (FORT), apply their diverse ecological, socioeconomic, and technological expertise to investigate complicated ecological problems confronting managers of the Nation's biological resources. FORT works closely with U.S. Department of the Interior (DOI) agency scientists, the academic community, other USGS science centers, and many other partners to provide critical information needed to help answer complex natural-resource management questions. In Fiscal Year 2010 (FY10), FORT's scientific and technical professionals conducted ongoing, expanded, and new research vital to the science needs and management goals of DOI, other Federal and State agencies, and nongovernmental organizations in the areas of aquatic systems and fisheries, climate change, data and information integration and management, invasive species, science support, security and technology, status and trends of biological resources (including the socioeconomic aspects), terrestrial and freshwater ecosystems, and wildlife resources, including threatened and endangered species. This report presents selected FORT science accomplishments for FY10 by the specific USGS mission area or science program with which each task is most closely associated, though there is considerable overlap. The report also includes all FORT publications and other products published in FY10, as well as staff accomplishments, appointments, committee assignments, and invited presentations.

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

    International Nuclear Information System (INIS)

    1991-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Peixoto, Orpet J.M. [ABACC- Brazilian Argentine Agency for Accounting and Control of Nuclear Materials, Rio de Janeiro (Brazil)

    2012-06-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Tracey A. Bodo Slotta

    2012-10-01

    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.

  10. On simulated annealing phase transitions in phylogeny reconstruction.

    Science.gov (United States)

    Strobl, Maximilian A R; Barker, Daniel

    2016-08-01

    Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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

    International Nuclear Information System (INIS)

    Burns, H.; Langton, C.; Flach, G.; Kosson, D.

    2010-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

    In 2016, the International Space Station (ISS) partnership published the first-ever compilation of international ISS research publications resulting from research performed on the ISS through 2011. The International Space Station Research Accomplishments: An Analysis of Results From 2000-2011 is a collection of summaries of over 1,200 journal publications that describe ISS research in the areas of biology and biotechnology; Earth and space science; educational activities and outreach; human research; physical sciences; technology development and demonstration; and, results from ISS operations. This paper will summarize the ISS results publications obtained through 2011 on behalf of the ISS Program Science Forum that is made up of senior science representatives across the international partnership. NASA's ISS Program Science office maintains an online experiment database (www.nasa.gov/issscience) that tracks and communicates ISS research activities across the entire ISS partnership, and it is continuously updated. It captures ISS experiment summaries and results and includes citations to the journals, conference proceedings, and patents as they become available. The International Space Station Research Accomplishments: An Analysis of Results From 2000-2011 is a testament to the research that was underway even as the ISS laboratory was being built. It reflects the scientific knowledge gained from ISS research, and how it impact the fields of science in both space and traditional science disciplines on Earth. Now, during a time when utilization is at its busiest, and with extension of the ISS through at least 2024, the ISS partners work together to track the accomplishments and the new knowledge gained in a way that will impact humanity like no laboratory on Earth. The ISS Program Science Forum will continue to capture and report on these results in the form of journal publications, conference proceedings, and patents. We anticipate that successful ISS research will

  13. Diprosopia em bovino Bovine diprosopus

    Directory of Open Access Journals (Sweden)

    I.T. Rotta

    2008-04-01

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

  14. Diprosopia em bovino Bovine diprosopus

    OpenAIRE

    I.T. Rotta; M.B.A.M. Torres; R.G. Motta

    2008-01-01

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

  15. Phylogeny of culturable cyanobacteria from Brazilian mangroves.

    Science.gov (United States)

    Silva, Caroline Souza Pamplona; Genuário, Diego Bonaldo; Vaz, Marcelo Gomes Marçal Vieira; Fiore, Marli Fátima

    2014-03-01

    The cyanobacterial community from Brazilian mangrove ecosystems was examined using a culture-dependent method. Fifty cyanobacterial strains were isolated from soil, water and periphytic samples collected from Cardoso Island and Bertioga mangroves using specific cyanobacterial culture media. Unicellular, homocytous and heterocytous morphotypes were recovered, representing five orders, seven families and eight genera (Synechococcus, Cyanobium, Cyanobacterium, Chlorogloea, Leptolyngbya, Phormidium, Nostoc and Microchaete). All of these novel mangrove strains had their 16S rRNA gene sequenced and BLAST analysis revealed sequence identities ranging from 92.5 to 99.7% when they were compared with other strains available in GenBank. The results showed a high variability of the 16S rRNA gene sequences among the genotypes that was not associated with the morphologies observed. Phylogenetic analyses showed several branches formed exclusively by some of these novel 16S rRNA gene sequences. BLAST and phylogeny analyses allowed for the identification of Nodosilinea and Oxynema strains, genera already known to exhibit poor morphological diacritic traits. In addition, several Nostoc and Leptolyngbya morphotypes of the mangrove strains may represent new generic entities, as they were distantly affiliated with true genera clades. The presence of non-ribosomal peptide synthetase, polyketide synthase, microcystin and saxitoxin genes were detected in 20.5%, 100%, 37.5% and 33.3%, respectively, of the 44 tested isolates. A total of 134 organic extracts obtained from 44 strains were tested against microorganisms, and 26% of the extracts showed some antimicrobial activity. This is the first polyphasic study of cultured cyanobacteria from Brazilian mangrove ecosystems using morphological, genetic and biological approaches. Copyright © 2014 Elsevier GmbH. All rights reserved.

  16. The reticulating phylogeny of island biogeography theory.

    Science.gov (United States)

    Lomolino, Mark V; Brown, James H

    2009-12-01

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

  17. A Mitogenomic Phylogeny of Living Primates

    Science.gov (United States)

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

    2013-01-01

    Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels. PMID:23874967

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

    International Nuclear Information System (INIS)

    Endou, A.; Saiki, A.; Yoshikawa, S.; Okusa, K.; Suda, K.

    1994-01-01

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

  19. Recent Accomplishments in Laser-Photovoltaic Wireless Power Transmission

    Science.gov (United States)

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

    2003-01-01

    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.

  20. The Mixed Waste Focus Area: Status and accomplishments

    International Nuclear Information System (INIS)

    Conner, J.E.

    1997-01-01

    The Mixed Waste Focus Area began operations in February of 1995. Its mission is to provide acceptable technologies that enable implementation of mixed waste treatment systems developed in partnership with end-users, stakeholders, tribal governments, and regulators. The MWFA will develop, demonstrate, and deliver implementable technologies for treatment of mixed waste within the DOE complex. Treatment refers to all post waste-generation activities including sampling and analysis, characterization, storage, processing, packaging, transportation, and disposal. The MWFA's mission arises from the Resources Conservation and Recovery Act (RCRA) as amended by the Federal Facility Compliance Act. Each DOE site facility that generates or stores mixed waste prepared a plan, the Site Treatment Plan, for developing treatment capacities and treating that waste. Agreements for each site were concluded with state regulators, resulting in Consent Orders providing enforceable milestones for achieving treatment of the waste. The paper discusses the implementation of the program, its status, accomplishments and goals for FY1996, and plans for 1997

  1. New Accomplishments and Development of INIS in Croatia

    International Nuclear Information System (INIS)

    Novosel, N.; Pleslic Jovicic, S.

    1998-01-01

    International Nuclear Information System (INIS) is the leading information system on peaceful use of nuclear energy in the world. INIS is realized through co-operation of International Atomic Energy Agency (IAEA) and its member states. It contains information related to literature on nuclear science and technology in the form of a bibliographic record. The Republic of croatia became an INIS member at the end of 1994 and since then this database has been available in a written form as INIS Atomindex and on CD-ROM. Moreover, several representatives of expert organizations have been trained for searching the database and for formulating of input data for INIS. This article describes new accomplishments in the development of the INIS database and joining of Croatia into the international exchange of nuclear information through national contribution in the form of INIS input data. (author)

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

    International Nuclear Information System (INIS)

    2002-01-01

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

  3. Research accomplishments and future goals in particle physics

    International Nuclear Information System (INIS)

    1991-12-01

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

  4. Water Power Technologies Office 2017 Marine Energy Accomplishments

    Energy Technology Data Exchange (ETDEWEB)

    Water Power Technologies Office

    2018-04-01

    The U.S. Department of Energy's Water Power Technologies Office's marine and hydrokinetic portfolio has numerous projects that support industry advancement in wave, tidal, and ocean and river current technologies. In order to strengthen state-of-the-art technologies in these fields and bring them closer to commercialization, the Water Power Technologies Office funds industry, academia, and the national laboratories. A U.S. chapter on marine and hydrokinetic energy research and development was included in the Ocean Energy Systems' Technology Programme—an intergovernmental collaboration between countries, which operates under a framework established by the International Energy Agency. This brochure is an overview of the U.S. accomplishments and updates from that report.

  5. IMHEX fuel cell repeat component manufacturing continuous improvement accomplishments

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-12-31

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

  6. Inference of Large Phylogenies Using Neighbour-Joining

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  7. Bayesian phylogeny analysis via stochastic approximation Monte Carlo

    KAUST Repository

    Cheon, Sooyoung

    2009-11-01

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

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

    Science.gov (United States)

    Huang, Zuhao; Tu, Feiyun

    2017-07-01

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

  9. Direct maximum parsimony phylogeny reconstruction from genotype data

    Directory of Open Access Journals (Sweden)

    Ravi R

    2007-12-01

    Full Text Available Abstract Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

  10. The Global Geodetic Observing System: Recent Activities and Accomplishments

    Science.gov (United States)

    Gross, R. S.

    2017-12-01

    The Global Geodetic Observing System (GGOS) of the International Association of Geodesy (IAG) provides the basis on which future advances in geosciences can be built. By considering the Earth system as a whole (including the geosphere, hydrosphere, cryosphere, atmosphere and biosphere), monitoring Earth system components and their interactions by geodetic techniques and studying them from the geodetic point of view, the geodetic community provides the global geosciences community with a powerful tool consisting mainly of high-quality services, standards and references, and theoretical and observational innovations. The mission of GGOS is: (a) to provide the observations needed to monitor, map and understand changes in the Earth's shape, rotation and mass distribution; (b) to provide the global frame of reference that is the fundamental backbone for measuring and consistently interpreting key global change processes and for many other scientific and societal applications; and (c) to benefit science and society by providing the foundation upon which advances in Earth and planetary system science and applications are built. The goals of GGOS are: (1) to be the primary source for all global geodetic information and expertise serving society and Earth system science; (2) to actively promote, sustain, improve, and evolve the integrated global geodetic infrastructure needed to meet Earth science and societal requirements; (3) to coordinate with the international geodetic services that are the main source of key parameters and products needed to realize a stable global frame of reference and to observe and study changes in the dynamic Earth system; (4) to communicate and advocate the benefits of GGOS to user communities, policy makers, funding organizations, and society. In order to accomplish its mission and goals, GGOS depends on the IAG Services, Commissions, and Inter-Commission Committees. The Services provide the infrastructure and products on which all contributions

  11. EarthScope Education and Outreach: Accomplishments and Emerging Opportunities

    Science.gov (United States)

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

    2014-12-01

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

  12. Major accomplishments of America's nuclear rocket program (ROVER)

    International Nuclear Information System (INIS)

    Finseth, J.L.

    1991-01-01

    The United States embarked on a program to develop nuclear rocket engines in 1955. This program was known as project Rover. Initially nuclear rockets were considered as a potential backup for intercontinental ballistic missile propulsion but later proposed applications included both a lunar second stage as well as use in manned-Mars flights. Under the Rover program, 19 different reactors were built and tested during the period of 1959-1969. Additionally, several cold flow (non-fuelled) reactors were tested as well as a nuclear fuels test cell. The Rover program was terminated in 1973, due to budget constraints and an evolving political climate. The Rover program would have led to the development of a flight engine had the program continued through a logical continuation. The Rover program was responsible for a number of technological achievements. The successful operation of nuclear rocket engines on a system level represents the pinnacle of accomplishment. This paper will discuss the engine test program as well as several subsystems

  13. Research accomplishments and future goals in particle physics

    International Nuclear Information System (INIS)

    1987-01-01

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

  14. A tribute to the life and accomplishments of Birdwell Finlayson.

    Science.gov (United States)

    Yeung, Lawrence L; Vieweg, Johannes W; Khan, Saeed R; Newman, Robert C; Dahm, Philipp

    2008-03-01

    Birdwell Finlayson was a talented researcher and clinician whose pioneering work in the field of urolithiasis led him to worldwide prominence in urology. We researched his life and accomplishments to provide a historical account of his career. The archives of the Department of Urology and the University of Florida Health Science Center Library were searched for publications, photographs and other records relating to Doctor Finlayson. Additionally, we interviewed many of his friends and colleagues for more information. Birdwell Finlayson was born in Pocatello Bannock, Idaho. He completed a urology residency and obtained a Ph.D. in biophysics at the University of Chicago. In 1967 he joined the faculty at the University of Florida. His interest in understanding the fundamentals of stone formation led to the discovery that crystal retention at a site of nephron injury was essential for stone formation. This fixed particle hypothesis continues to serve to as the foundation for urolithiasis research today. His computer model EQUIL is the gold standard for calculating urinary supersaturation with respect to kidney stone formation. Finlayson was 1 of the 6 original coinvestigators for shock wave lithotripsy in the United States. He is also remembered for his wit and his love of aeronautics, as he was a flight instructor and stunt pilot. Finlayson died unexpectedly of idiopathic hypertrophic cardiomyopathy on July 22, 1988. Birdwell Finlayson was an internationally renowned surgeon and stone disease expert whose research continues to serve as the basis of urolithiasis research at the University of Florida and worldwide.

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

    Science.gov (United States)

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

    2017-01-01

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

  16. New ways of understanding and accomplishing leadership in academic medicine.

    Science.gov (United States)

    Souba, Wiley W

    2004-04-01

    Understanding leadership as being about a person in charge is not wrong, but it is no longer adequate. The challenges and problems confronting medicine today are so complex and unpredictable that it is practically impossible for one person to accomplish the work of leadership alone. More leadership requires more shared work, but as hospitals and medical centers begin to break down departmental barriers, people have to learn to work with individuals and groups who may have different work ethics, dissimilar styles of solving problems, or even contrasting values. Successful academic medical centers will make use of a broader repertoire of leadership strategies--besides developing leaders, they will develop leadership as a property of the system, as an organizational capacity. While leader development involves enhancing human (individual) capital, the emphasis in leadership development is on social capital and building more productive relationships that enhance networking, collaboration, and resource exchange. Leadership is created in and emerges from the relational space that connects people--accordingly, leadership development involves building high-quality connections between people. To make leadership happen more effectively, academic medical centers will have to identify and study the ingredients that catalyze and enhance human connectivity, augment social capital and activate leadership. Leadership is a uniquely human activity--studying it and how it works is core to the learning organization.

  17. Bovine cysticercosis situation in Brazil

    Directory of Open Access Journals (Sweden)

    Gabriel Augusto Marques Rossi

    2014-02-01

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

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

    Science.gov (United States)

    Lovtrup, Soren

    1984-01-01

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-12-26

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 8, MAR 18 2015 (2015), s. 164 ISSN 1756-3305 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Phylogeny * Monogenea * Dactylogyridae * Neotropical region * Diversity * Siluriformes * 28S rRNA Subject RIV: EG - Zoology Impact factor: 3.234, year: 2015

  2. A molecular phylogeny of selected species of genus Prunus L ...

    African Journals Online (AJOL)

    (Syn. Prunus amygdalus) and Prunus cornuta (Wall. ex. Royle) Steudel. These are indigenous to Pakistan. In the ITS strict consensus results for example, the clade consisting of Laurocerasus, Padus and Cerasus subgenera are sister to the rest of the clades in the phylogenetic tree. Key words: Phylogeny, Prunus, Pakistan, ...

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

    Czech Academy of Sciences Publication Activity Database

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

    2004-01-01

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorina...... Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes....

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

    NARCIS (Netherlands)

    Maroyi, A.

    2012-01-01

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

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

    Science.gov (United States)

    Garnatje, Teresa; Peñuelas, Josep; Vallès, Joan

    2017-03-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-02-10

    By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation. © 2016 The Author(s).

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

    Science.gov (United States)

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

    2013-01-01

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

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

    DEFF Research Database (Denmark)

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

    1996-01-01

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

  11. A molecular approach to arthrotardigrade phylogeny (Heterotardigrada, Tardigrada)

    DEFF Research Database (Denmark)

    Fujimoto, Shinta; Jørgensen, Aslak; Hansen, Jesper Guldberg

    2017-01-01

    The marine order Arthrotardigrada (class Heterotardigrada, phylum Tardigrada) is known for its conspicuously high morphological diversity and has been traditionally recognized as the most ancestral group within the phylum. Despite its potential importance in understanding the evolution of the phy...... of the inferred phylogeny....

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

    Science.gov (United States)

    Farmer, Jack

    2005-01-01

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

  13. FY2000 Hanford Technology Deployment Accomplishments Fact Sheets

    International Nuclear Information System (INIS)

    WIBLE, R.A.

    2001-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Schweitzer, M.

    2005-07-13

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

  15. Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae).

    Science.gov (United States)

    Leduc-Robert, Geneviève; Maddison, Wayne P

    2018-02-22

    Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson's D statistics and D FOIL . We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti

  16. Bovine cysticercosis in the European Union

    DEFF Research Database (Denmark)

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

    2017-01-01

    -only inspection of slaughtered cattle in order to reduce the potential for cross-contamination with bacteria that are of greatest public health risk, is expected in the European Union in the near future. With this system, the detection sensitivity for bovine cysticercosis that is already low with the current meat...... of bovine cysticercosis in the European Union....

  17. Bovine Necrotic Vulvovaginitis Associated with Porphyromonas levii

    Science.gov (United States)

    Friedgut, Orly; Alpert, Nir; Stram, Yehuda; Lahav, Dan; Tiomkin, Doron; Avramson, Miriam; Grinberg, Kalia; Bernstein, Michael

    2004-01-01

    An outbreak of bovine necrotic vulvovaginitis associated with Porphyromonas levii, an emerging animal and human pathogen, affected 32 cows on a dairy farm in the northeast of Israel. Five animals had to be culled. This report appears to be the first that associates P. levii with bovine necrotic vulvovagnitis. PMID:15109423

  18. Clinical applications of bovine colostrum therapy

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  19. Phylogenies support out-of-equilibrium models of biodiversity.

    Science.gov (United States)

    Manceau, Marc; Lambert, Amaury; Morlon, Hélène

    2015-04-01

    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. © 2015 John Wiley & Sons Ltd/CNRS.

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

    DEFF Research Database (Denmark)

    Mailund, Thomas; Besenbacher, Søren; Schierup, Mikkel Heide

    2006-01-01

    around each marker that is compatible with a single phylogenetic tree. This perfect phylogenetic tree is treated as a decision tree for determining disease status, and scored by its accuracy as a decision tree. The rationale for this is that the perfect phylogeny near a disease affecting mutation should...... a fast method for accurate localisation of disease causing variants in high density case-control association mapping experiments with large numbers of cases and controls. The method searches for significant clustering of case chromosomes in the "perfect" phylogenetic tree defined by the largest region...... provide more information about the affected/unaffected classification than random trees. If regions of compatibility contain few markers, due to e.g. large marker spacing, the algorithm can allow the inclusion of incompatibility markers in order to enlarge the regions prior to estimating their phylogeny...

  1. Live phylogeny with polytomies: Finding the most compact parsimonious trees.

    Science.gov (United States)

    Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

    2017-08-01

    Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Molecular phylogeny and morphological change in the Psittacula parakeets.

    Science.gov (United States)

    Groombridge, Jim J; Jones, Carl G; Nichols, Richard A; Carlton, Mark; Bruford, Michael W

    2004-04-01

    We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that extends from the chin to the cheek. We examine the extent of sexual dimorphism in tail length across the phylogeny and reveal large differences between closely related forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. An ancestral Psittacula form appears to have evolved during the late Miocene-early Pliocene (3.4-9.7MYA), a time when regional geological processes on the Asian continent may have promoted subsequent diversity at the species level, and many forms diverged relatively early on in the evolutionary history of Psittacula (between 2.5 and 7.7MYA). However, others, such as the derbyan and moustached parakeets, diverged as recently as 0.2MYA. Our phylogeny also suggests that the echo parakeet from Mauritius diverged from the Indian ringneck parakeet as opposed to the African ringneck, and may have done so relatively recently. The molecular results indicate support for a southwards radiation from India across the Indian Ocean to Mauritius, where the arrival-date of the echo parakeet appears consistent with the island's volcanic formation.

  3. Bovine somatic cell nuclear transfer.

    Science.gov (United States)

    Ross, Pablo J; Cibelli, Jose B

    2010-01-01

    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.

  4. Shortest triplet clustering: reconstructing large phylogenies using representative sets

    Directory of Open Access Journals (Sweden)

    Sy Vinh Le

    2005-04-01

    Full Text Available Abstract Background Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies for large data sets is still a challenging task in Bioinformatics. Results We propose a new distance-based clustering method, the shortest triplet clustering algorithm (STC, to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2 time for n sequences. Simulations show that STC gives better topological accuracy than other tested methods that also build a first starting tree. STC appears as a very good method to start the tree reconstruction. However, all tested methods give similar results if balanced nearest neighbor interchange (BNNI is applied as a post-processing step. BNNI leads to an improvement in all instances. The program is available at http://www.bi.uni-duesseldorf.de/software/stc/. Conclusion The results demonstrate that the new approach efficiently reconstructs phylogenies for large data sets. We found that BNNI boosts the topological accuracy of all methods including STC, therefore, one should use BNNI as a post-processing step to get better topological accuracy.

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

    Science.gov (United States)

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

    2005-06-01

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

  6. Host phylogeny determines viral persistence and replication in novel hosts.

    Directory of Open Access Journals (Sweden)

    Ben Longdon

    2011-09-01

    Full Text Available Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts.

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

    Directory of Open Access Journals (Sweden)

    Anjali Goswami

    2007-10-01

    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.

  8. Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

    Science.gov (United States)

    Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

    2004-06-01

    A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

  9. Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

    Science.gov (United States)

    Longdon, Ben; Hadfield, Jarrod D.; Webster, Claire L.

    2011-01-01

    Pathogens switching to new hosts can result in the emergence of new infectious diseases, and determining which species are likely to be sources of such host shifts is essential to understanding disease threats to both humans and wildlife. However, the factors that determine whether a pathogen can infect a novel host are poorly understood. We have examined the ability of three host-specific RNA-viruses (Drosophila sigma viruses from the family Rhabdoviridae) to persist and replicate in 51 different species of Drosophilidae. Using a novel analytical approach we found that the host phylogeny could explain most of the variation in viral replication and persistence between different host species. This effect is partly driven by viruses reaching a higher titre in those novel hosts most closely related to the original host. However, there is also a strong effect of host phylogeny that is independent of the distance from the original host, with viral titres being similar in groups of related hosts. Most of this effect could be explained by variation in general susceptibility to all three sigma viruses, as there is a strong phylogenetic correlation in the titres of the three viruses. These results suggest that the source of new emerging diseases may often be predictable from the host phylogeny, but that the effect may be more complex than simply causing most host shifts to occur between closely related hosts. PMID:21966271

  10. 21 CFR 184.1034 - Catalase (bovine liver).

    Science.gov (United States)

    2010-04-01

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

  11. 76 FR 38602 - Bovine Tuberculosis and Brucellosis; Program Framework

    Science.gov (United States)

    2011-07-01

    ...] Bovine Tuberculosis and Brucellosis; Program Framework AGENCY: Animal and Plant Health Inspection Service... framework being developed for the bovine tuberculosis and brucellosis programs in the United States. This... proposed revisions to its programs regarding bovine tuberculosis (TB) and bovine brucellosis in the United...

  12. bovine

    African Journals Online (AJOL)

    'n Radio-irnmunologiese bepalingsmetode vir luteihiserende hormoon (LH) in bloed van die bees is ontwikkel duer die gebruik van buisies bestryk met teeliggame. .... proportion (%) of labelled LH bound by unadsorb- ed antisera in a double ... the location of the "protein" (elution volume 10-20 rnI) and "free iodine" (elution ...

  13. Removal of Bound Triton X-100 from Purified Bovine Heart Cytochrome bc1

    OpenAIRE

    Varhač, Rastislav; Robinson, Neal C.; Musatov, Andrej

    2009-01-01

    Cytochrome bc1 isolated from Triton X-100 solubilized mitochondrial membranes contains up to 120 nmol of Triton X-100 bound per nmol of the enzyme. Purified cytochrome bc1 is fully active; however, protein bound Triton X-100 significantly interferes with structural studies of the enzyme. Removal of Triton X-100 bound to bovine cytochrome bc1 was accomplished by incubation with Bio-Beads SM-2 in presence of sodium cholate. Sodium cholate is critical since it does not interfere with the adsorpt...

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

    International Nuclear Information System (INIS)

    Lago, A.M.; Weinblatt, H.; Hamilton, E.E.

    1987-01-01

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

  15. Bovine bone for white ceramic

    International Nuclear Information System (INIS)

    Souza, J.L. de; Harima, E.; Leite, J.I.P.; Monteiro, F.M.; Bezerra, M.T.T.

    2011-01-01

    The porcelain is composed of feldspar, kaolin and about 50% for bovine bone ashes. This work aims to analyze the properties acquired by the substitution of kaolin by its waste. For characterization of raw materials chemical analyzes were made by X-Ray Fluorescence (XRF) and mineralogical analysis by X-Ray Diffraction (XRD). Four formulations were produced varying the percentage of waste materials of kaolin and bone ashes of 25 and 55% by weight. The samples were sintered at temperatures of 1150, 1200 and 1250 deg C. The technological tests realized were: water absorption (WA), apparent porosity (AP), apparent density (AD) and linear retraction (LR). Improvement in the physical-mechanical properties of the samples with increasing temperature were observed, and 1250 deg C obtained 0.69% of WA, 1.22% AP, 2.26 g / cm3 AD, and 0.52% LR

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

    Science.gov (United States)

    Soon, Villu; Saarma, Urmas

    2011-07-01

    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

  17. Bovine Mastitis: Frontiers in Immunogenetics

    Science.gov (United States)

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

    2014-01-01

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

  18. Bovine Mastitis: Frontiers in Immunogenetics

    Directory of Open Access Journals (Sweden)

    Kathleen eThompson-Crispi

    2014-10-01

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

  19. Spectroscopic study of gamma irradiated bovine hemoglobin

    International Nuclear Information System (INIS)

    Maghraby, Ahmed Mohamed; Ali, Maha Anwar

    2007-01-01

    In the present study, the effects of ionizing radiation of Cs-137 and Co-60 from 4.95 to 743.14 Gy and from 40 Gy to 300 kGy, respectively, on some bovine hemoglobin characteristics were studied. Such an effect was evaluated using electron paramagnetic resonance (EPR) spectroscopy, and infra-red (IR) spectroscopy. Bovine hemoglobin EPR spectra were recorded and analyzed before and after irradiation and changes were explained in detail. IR spectra of unirradiated and irradiated Bovine hemoglobin were recorded and analyzed also. It was found that ionizing radiation may lead to the increase of free radicals production, the decrease in α-helices contents, which reflects the degradation of hemoglobin molecular structure, or at least its incomplete performance. Results also show that the combined application of EPR and FTIR spectroscopy is a powerful tool for determining structural modification of bovine hemoglobin samples exposed to gamma irradiation

  20. PREVALENCE OF BOVINE FASCIOLOSIS AT THE IBADAN ...

    African Journals Online (AJOL)

    Ismail

    Bovine fasciolosis is a parasitic disease of cattle caused by trematodes usually. Fasciola gigantic ... and impaired fertility [6,7]. The value of the .... especially males with good body condition, are transported to these cities with higher population ...

  1. Activation of bovine neutrophils by Brucella spp.

    Science.gov (United States)

    Keleher, Lauren L; Skyberg, Jerod A

    2016-09-01

    Brucellosis is a globally important zoonotic infectious disease caused by gram negative bacteria of the genus Brucella. While many species of Brucella exist, Brucella melitensis, Brucella abortus, and Brucella suis are the most common pathogens of humans and livestock. The virulence of Brucella is largely influenced by its ability to evade host factors, including phagocytic killing mechanisms, which are critical for the host response to infection. The aim of this study was to characterize the bovine neutrophil response to virulent Brucella spp. Here, we found that virulent strains of smooth B. abortus, B. melitensis, B. suis, and virulent, rough, strains of Brucella canis possess similar abilities to resist killing by resting, or IFN-γ-activated, bovine neutrophils. Bovine neutrophils responded to infection with a time-dependent oxidative burst that varied little between Brucella spp. Inhibition of TAK1, or SYK kinase blunted the oxidative burst of neutrophils in response to Brucella infection. Interestingly, Brucella spp. did not induce robust death of bovine neutrophils. These results indicate that bovine neutrophils respond similarly to virulent Brucella spp. In addition, virulent Brucella spp., including naturally rough strains of B. canis, have a conserved ability to resist killing by bovine neutrophils. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Bovine TLR2 and TLR4 mediate Cryptosporidium parvum recognition in bovine intestinal epithelial cells.

    Science.gov (United States)

    Yang, Zhengtao; Fu, Yunhe; Gong, Pengtao; Zheng, Jingtong; Liu, Li; Yu, Yuqiang; Li, Jianhua; Li, He; Yang, Ju; Zhang, Xichen

    2015-08-01

    Cryptosporidium parvum (C. parvum) is an intestinal parasite that causes diarrhea in neonatal calves. It results in significant morbidity of neonatal calves and economic losses for producers worldwide. Innate resistance against C. parvum is thought to depend on engagement of pattern recognition receptors. However, the role of innate responses to C. parvum has not been elucidated in bovine. The aim of this study was to evaluate the role of TLRs in host-cell responses during C. parvum infection of cultured bovine intestinal epithelial cells. The expressions of TLRs in bovine intestinal epithelial cells were detected by qRT-PCR. To determine which, if any, TLRs may play a role in the response of bovine intestinal epithelial cells to C. parvum, the cells were stimulated with C. parvum and the expression of TLRs were tested by qRT-PCR. The expression of NF-κB was detected by western blotting. Further analyses were carried out in bovine TLRs transfected HEK293 cells and by TLRs-DN transfected bovine intestinal epithelial cells. The results showed that bovine intestinal epithelial cells expressed all known TLRs. The expression of TLR2 and TLR4 were up-regulated when bovine intestinal epithelial cells were treated with C. parvum. Meanwhile, C. parvum induced IL-8 production in TLR2 or TLR4/MD-2 transfected HEK293 cells. Moreover, C. parvum induced NF-κB activation and cytokine expression in bovine intestinal epithelial cells. The induction of NF-κB activation and cytokine expression by C. parvum were reduced in TLR2-DN and TLR4-DN transfected cells. The results showed that bovine intestinal epithelial cells expressed all known TLRs, and bovine intestinal epithelial cells recognized and responded to C. parvum via TLR2 and TLR4. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2012-09-01

    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. Published by Elsevier Inc.

  5. Phylogeny of Selaginellaceae: There is value in morphology after all!

    Science.gov (United States)

    Weststrand, Stina; Korall, Petra

    2016-12-01

    The cosmopolitan lycophyte family Selaginellaceae, dating back to the Late Devonian-Early Carboniferous, is notorious for its many species with a seemingly undifferentiated gross morphology. This morphological stasis has for a long time hampered our understanding of the evolutionary history of the single genus Selaginella. Here we present a large-scale phylogenetic analysis of Selaginella, and based on the resulting phylogeny, we discuss morphological evolution in the group. We sampled about one-third of the approximately 750 recognized Selaginella species. Evolutionary relationships were inferred from both chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using a Bayesian inference approach. The morphology of the group was studied and important features mapped onto the phylogeny. We present an overall well-supported phylogeny of Selaginella, and the phylogenetic positions of some previously problematic taxa (i.e., S. sinensis and allies) are now resolved with strong support. We show that even though the evolution of most morphological characters involves reversals and/or parallelisms, several characters are phylogenetically informative. Seven major clades are identified, which each can be uniquely diagnosed by a suite of morphological features. There is value in morphology after all! Our hypothesis of the evolutionary relationships of Selaginella is well founded based on DNA sequence data, as well as morphology, and is in line with previous findings. It will serve as a firm basis for further studies on Selaginella with respect to, e.g., the poorly known alpha taxonomy, as well as evolutionary questions such as historical biogeographic reconstructions. © 2016 Weststrand and Korall. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY 4.0).

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

    Science.gov (United States)

    Biedron, Adriana; Szczepaniak, Anna

    2012-01-01

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

  7. Predicting College Student Success: A Historical and Predictive Examination of High School Activities and Accomplishments

    Science.gov (United States)

    Davey, Carla Mae

    2010-01-01

    According to generational theorists, the interests and experiences of incoming students have fluctuated over time, with Millennial students being more engaged and accomplished than their predecessors. This project explored data from 1974-2007 to determine the actual trends in engagement and accomplishments for three generations of students. Over…

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

    Science.gov (United States)

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

    2017-01-01

    Purpose: Winning several national championships is an extraordinary feat that very few university coaches have accomplished. The objective of this study was to investigate how some of Canada's most accomplished university team-sport coaches created and sustained a culture of excellence in their programs. Method: Six university coaches who had won…

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

    NARCIS (Netherlands)

    Harmsen, H.J.M.

    1996-01-01


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

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

    Science.gov (United States)

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

    2017-12-01

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

  11. The co phylogeny reconstruction problem is NP-complete.

    Science.gov (United States)

    Ovadia, Y; Fielder, D; Conow, C; Libeskind-Hadas, R

    2011-01-01

    The co phylogeny reconstruction problem is that of finding minimum cost explanations of differences between historical associations. The problem arises in parasitology, molecular systematics, and biogeography. Existing software tools for this problem either have worst-case exponential time or use heuristics that do not guarantee optimal solutions. To date, no polynomial time optimal algorithms have been found for this problem. In this article, we prove that the problem is NP-complete, suggesting that future research on algorithms for this problem should seek better polynomial-time approximation algorithms and heuristics rather than optimal solutions.

  12. Molecular phylogeny of Chrysomya albiceps and C. rufifacies (Diptera: Calliphoridae).

    Science.gov (United States)

    Wells, J D; Sperling, F A

    1999-05-01

    Mitochondrial DNA was used to infer the phylogeny and genetic divergences of Chrysomya albiceps (Wiedemann) and C. rufifacies (Maquart) specimens from widely separated localities in the Old and New World. Analyses based on a 2.3-kb region including the genes for cytochrome oxidase subunits I and II indicated that the 2 species were separate monophyletic lineages that have been separated for > 1 million years. Analysis of DNA, in the form of either sequence or restriction fragment-length polymorphism (RFLP) data, will permit the identification of problematic specimens.

  13. Adipokinetic hormones provide inference for the phylogeny of Odonata

    Czech Academy of Sciences Publication Activity Database

    Gäde, G.; Šimek, Petr; Fescemyer, H. W.

    2011-01-01

    Roč. 57, č. 1 (2011), s. 174-178 ISSN 0022-1910 R&D Projects: GA ČR GA203/09/2014 Grant - others:University of Cape Town for a Block grant(ZA) IFR 2008071500048; National Research Foundation, Pretoria(ZA) FA 2007021300002; USDA, ARS Specific Cooperative Agreement(US) 58-6402-5-066; US National Science Foundation(US) EF-0412651 Institutional research plan: CEZ:AV0Z50070508 Keywords : phylogeny of Odonata * Libellulidae * Corduliidae Subject RIV: ED - Physiology Impact factor: 2.236, year: 2011

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

    Directory of Open Access Journals (Sweden)

    Tomohiro Okagawa

    2017-06-01

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

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

    Science.gov (United States)

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

  16. Bovine reproduction in tropical environment

    International Nuclear Information System (INIS)

    Jimenez Lopez, J.

    2001-01-01

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

  17. Bovine petechial fever (Ondiri disease).

    Science.gov (United States)

    Davies, G

    1993-02-01

    Bovine petechial fever is a Rickettsial disease of cattle, which has been diagnosed, only in Kenya, East Africa. Other countries in the region share some of the biotopes in which the disease occurs, and may well have the infection. The disease is characterised by widespread petechial and ecchymotic haemorrhages on the mucosal surfaces, and throughout the serosal and subserosal surfaces of the body organs and cavities. It may be fatal in up to 50% of untreated cases. The causal organism may be demonstrated most readily in the cytoplasm of polymorphonuclear granulocytes of the peripheral blood, as well as other leucocytes, and has been classified as Cytoecetes ondirii, a member of the tribe Ehrlichiae. Circumstantial and other evidence suggests that the disease is transmitted by an arthropod vector, which has yet to be identified. The blood of a naturally infected wild ruminant, the bushbuck, Tragelaphus scriptus has been shown to remain infective for at least 2 years, and other species such as the African buffalo, Syncercus caffer for at least 5 weeks. These and possibly other species, may serve as the amplifying and reservoir hosts.

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

    Science.gov (United States)

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

    2016-04-01

    To date, detection of antibodies against the lipopolysaccharide portion is the backbone of most serodiagnostic methods for brucellosis screening. However this pose a risk for false positive reactions related to other pathogens especially that of Yersinia enterocolitica O:9 which has the most prominent cross reactivity with Brucella spp. In this study, cloning and expression of Brucella abortus bacterioferritin (Bfr) was accomplished by PCR amplification into an expression vector system, and purification of a recombinant B. abortus Bfr (rBfr). The immunogenicity of rBfr was confirmed by Western blot with Brucella-positive bovine serum. To determine whether rBfr has a potential benefit for use in the serodiagnosis of bovine brucellosis, rBfr-based ELISA was performed. Interestingly, rBfr was able to detect anti-Brucella antibodies in positive sera in a dependent manner of TAT values but did not show an immunoreaction with negative samples. Particularly, average OD492 values at the lowest, medium and highest TAT titer levels were 1.4, 2.2 and 2.6-fold increase compared with the cutoff value, respectively. The accuracy, specificity and sensitivity of rBfr showed 89.09%, 93.6% and 85.33%, respectively. These findings suggest that rBfr might be a good candidate for serological diagnosis development of bovine brucellosis. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Edvaldo Vasconcelos de Carvalho-Filho

    2011-03-01

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

  20. Molecular phylogeny of Eriocaulon (Eriocaulaceae)

    DEFF Research Database (Denmark)

    Ito, Yu; Tanaka, Norio; Barfod, Anders

    Eriocaulon is a genus of about 400 species of monocotyledonous flowering plants in the family Eriocaulaceae. The genus is widely distributed in the world, with the centers of diversity in tropical regions, such as tropical Asia and tropical Africa. A previous molecular phylogeny implied an Africa...... the genus. In this talk, we provide preliminary results of our molecular phylogenetic analysis of the genus aiming to i) assess the biogeographic origin, ii) explore phylogenetic origins of submerged species, and iii) address the evolutionary role of polyploids.......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...... origin for Eriocaulon as a sister relationship between the genus and an African endemic one was recovered. The species of Eriocaulon primarily grow in wetlands while some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. Polyploidy is known from...

  1. A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

    Science.gov (United States)

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

    2012-01-01

    Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses. PMID:23144967

  2. Phylogeny of the Gondwanan beetle family Ulodidae (Tenebrionoidea).

    Science.gov (United States)

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

    2016-07-18

    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).

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Noor Haslina Masstor

    2014-01-01

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

  5. 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.

  6. Mixed integer linear programming for maximum-parsimony phylogeny inference.

    Science.gov (United States)

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

    2008-01-01

    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.

  7. A synthetic phylogeny of freshwater crayfish: insights for conservation

    Science.gov (United States)

    Owen, Christopher L.; Bracken-Grissom, Heather; Stern, David; Crandall, Keith A.

    2015-01-01

    Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts. PMID:25561670

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

    Science.gov (United States)

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

    2017-04-01

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

  9. Evolutionary history of contagious bovine pleuropneumonia using next generation sequencing of Mycoplasma mycoides Subsp. mycoides "Small Colony".

    Directory of Open Access Journals (Sweden)

    Virginie Dupuy

    Full Text Available Mycoplasma mycoides subsp. mycoides "Small Colony" (MmmSC is responsible for contagious bovine pleuropneumonia (CBPP in bovidae, a notifiable disease to the World Organization for Animal Health (OIE. Although its origin is not documented, the disease was known in Europe in 1773. It reached nearly world-wide distribution in the 19(th century through the cattle trade and was eradicated from most continents by stamping-out policies. During the 20(th century it persisted in Africa, and it reappeared sporadically in Southern Europe. Yet, classical epidemiology studies failed to explain the re-occurrence of the disease in Europe in the 1990s. The objectives of this study were to obtain a precise phylogeny of this pathogen, reconstruct its evolutionary history, estimate the date of its emergence, and determine the origin of the most recent European outbreaks. A large-scale genomic approach based on next-generation sequencing technologies was applied to construct a robust phylogeny of this extremely monomorphic pathogen by using 20 representative strains of various geographical origins. Sixty two polymorphic genes of the MmmSC core genome were selected, representing 83601 bp in total and resulting in 139 SNPs within the 20 strains. A robust phylogeny was obtained that identified a lineage specific to European strains; African strains were scattered in various branches. Bayesian analysis allowed dating the most recent common ancestor for MmmSC around 1700. The strains circulating in Sub-Saharan Africa today, however, were shown to descend from a strain that existed around 1810. MmmSC emerged recently, about 300 years ago, and was most probably exported from Europe to other continents, including Africa, during the 19(th century. Its diversity is now greater in Africa, where CBPP is enzootic, than in Europe, where outbreaks occurred sporadically until 1999 and where CBPP may now be considered eradicated unless MmmSC remains undetected.

  10. Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).

    Science.gov (United States)

    Near, Thomas J; Bossu, Christen M; Bradburd, Gideon S; Carlson, Rose L; Harrington, Richard C; Hollingsworth, Phillip R; Keck, Benjamin P; Etnier, David A

    2011-10-01

    Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of

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

    Science.gov (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

    2017-01-01

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

  12. Recent Progress in Cryopreservation of Bovine Oocytes

    Directory of Open Access Journals (Sweden)

    In-Sul Hwang

    2014-01-01

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

  13. Radioimmunoassay of bovine heart protein kinase

    International Nuclear Information System (INIS)

    Fleischer, N.; Rosen, O.M.; Reichlin, M.

    1976-01-01

    Immunization of guinea pigs with bovine cardiac cAMP-dependent protein kinase (ATP : protein phosphotransferase, EC 2.7.1.37) resulted in the development of precipitating antibodies to the cAMP-binding subunit of the enzyme. Both the phosphorylated and nonphosphorylated cAMP-binding protein of the protein kinase reacted with the antiserum. A radioimmunoassay was developed that detects 10 ng of holoenzyme and permits measurement of enzyme concentrations in bovine cardiac muscle. Bovine liver, kidney, brain, and skeletal muscle contain protein kinases which are immunologically identical to those found in bovine cardiac muscle. However, the proportion of immunoreactive enzyme activity differed for each tissue. All of the immunologically nonreactive enzyme in skeletal muscle and heart was separable from immunoreactive enzyme by chromatography on DEAE-cellulose. Rat tissues and pig heart contained protein kinase activity that cross reacted immunologically in a nonparallel fashion with bovine cardiac enzyme. These results indicate that cAMP-dependent protein kinases within and between species are immunologically heterogeneous

  14. Expression of infectious bovine rhinotracheitis virus glycoprotein D ...

    African Journals Online (AJOL)

    USER

    2010-06-14

    Jun 14, 2010 ... Bovine Herpesvirus 1 (BHV-1) belongs to the genus of ... through vaccination with recombinant vaccines of thymidine kinase, manufacturing and applying ..... Resistance to bovine respiratory syncytial virus (BRSV) induced in.

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

    Science.gov (United States)

    Hambrick, David Z; Tucker-Drob, Elliot M

    2015-02-01

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

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

    Science.gov (United States)

    2018-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  18. 20180312 - US EPA-Unilever Collaborative Partnership: Accomplishments and Next Steps (SOT)

    Science.gov (United States)

    Reiterating the goals of the partnership, this summarizes the accomplishments and progress made so far in the collaboration, and announces a two phase extension focused on further development of high-throughput transcriptomic platform

  19. Bovine besnoitiosis emerging in Central-Eastern Europe, Hungary

    OpenAIRE

    Hornok, Sándor; Fedák, András; Baska, Ferenc; Hofmann-Lehmann, Regina; Basso, Walter

    2014-01-01

    BACKGROUND: Besnoitia besnoiti, the cause of bovine besnoitiosis, is a cyst-forming coccidian parasite that has recently been shown to be spreading in several Western and Southern European countries. FINDINGS: Clinical cases of bovine besnoitiosis were confirmed for the first time in Hungary, by histological, serological and PCR analyses. CONCLUSIONS: This is the first report of autochthonous bovine besnoitiosis in Central-Eastern Europe. The emergence of bovine besnoitiosis in this region re...

  20. Eumalacostracan phylogeny and total evidence: limitations of the usual suspects

    Directory of Open Access Journals (Sweden)

    Ferla Matteo P

    2009-01-01

    Full Text Available Abstract Background The phylogeny of Eumalacostraca (Crustacea remains elusive, despite over a century of interest. Recent morphological and molecular phylogenies appear highly incongruent, but this has not been assessed quantitatively. Moreover, 18S rRNA trees show striking branch length differences between species, accompanied by a conspicuous clustering of taxa with similar branch lengths. Surprisingly, previous research found no rate heterogeneity. Hitherto, no phylogenetic analysis of all major eumalacostracan taxa (orders has either combined evidence from multiple loci, or combined molecular and morphological evidence. Results We combined evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I with a newly synthesized morphological dataset. We tested the homogeneity of data partitions, both in terms of character congruence and the topological congruence of inferred trees. We also performed Bayesian and parsimony analyses on separate and combined partitions, and tested the contribution of each partition. We tested for potential long-branch attraction (LBA using taxon deletion experiments, and with relative rate tests. Additionally we searched for molecular polytomies (spurious clades. Lastly, we investigated the phylogenetic stability of taxa, and assessed their impact on inferred relationships over the whole tree. We detected significant conflict between data partitions, especially between morphology and molecules. We found significant rate heterogeneity between species for both the 18S rRNA and combined datasets, introducing the possibility of LBA. As a test case, we showed that LBA probably affected the position of Spelaeogriphacea in the combined molecular evidence analysis. We also demonstrated that several clades, including the previously reported and surprising clade of Amphipoda plus Spelaeogriphacea, are 'supported' by zero length branches. Furthermore we showed

  1. Chromosome phylogenies of man, great apes, and Old World monkeys.

    Science.gov (United States)

    De Grouchy, J

    1987-08-31

    The karyotypes of man and of the closely related Pongidae--chimpanzee, gorilla, and orangutan--differ by a small number of well known rearrangements, mainly pericentric inversions and one fusion which reduced the chromosome number from 48 in the Pongidae to 46 in man. Dutrillaux et al. (1973, 1975, 1979) reconstructed the chromosomal phylogeny of the entire primate order. More and more distantly related species were compared thus moving backward in evolution to the common ancestors of the Pongidae, of the Cercopithecoidae, the Catarrhini, the Platyrrhini, the Prosimians, and finally the common ancestor of all primates. Descending the pyramid it becomes possible to assign the rearrangements that occurred in each phylum, and the one that led to man in particular. The main conclusions are that this phylogeny is compatible with the occurrence during evolution of simple chromosome rearrangements--inversions, fusions, reciprocal translocation, acquisition or loss of heterochromatin--and that it is entirely consistent with the known primate phylogeny based on physical morphology and molecular evolution. If heterochromatin is not taken into account, man has in common with the other primates practically all of his chromosomal material as determined by chromosome banding. However, it is arranged differently, according to species, on account of chromosome rearrangements. This interpretation has been confirmed by comparative gene mapping, which established that the same chromosome segments, identified by banding, carry the same genes (Finaz et al., 1973; Human Gene Mapping 8, 1985). A remarkable observation made by Dutrillaux is that different primate phyla seem to have adopted different chromosome rearrangements in the course of evolution: inversions for the Pongidae, Robertsonian fusions for the lemurs, etc. This observation may raise many questions, among which is that of an organized evolution. Also, the breakpoints of chromosomal rearrangements observed during evolution

  2. Molecular phylogeny and evolutionary history of Moricandia DC (Brassicaceae

    Directory of Open Access Journals (Sweden)

    Francisco Perfectti

    2017-10-01

    Full Text Available Background The phylogeny of tribe Brassiceae (Brassicaceae has not yet been resolved because of its complex evolutionary history. This tribe comprises economically relevant species, including the genus Moricandia DC. This genus is currently distributed in North Africa, Middle East, Central Asia and Southern Europe, where it is associated with arid and semi-arid environments. Although some species of Moricandia have been used in several phylogenetic studies, the phylogeny of this genus is not well established. Methods Here we present a phylogenetic analysis of the genus Moricandia using a nuclear (the internal transcribed spacers of the ribosomal DNA and two plastidial regions (parts of the NADH dehydrogenase subunit F gene and the trnT-trnF region. We also included in the analyses members of their sister genus Rytidocarpus and from the close genus Eruca. Results The phylogenetic analyses showed a clear and robust phylogeny of the genus Moricandia. The Bayesian inference tree was concordant with the maximum likelihood and timing trees, with the plastidial and nuclear trees showing only minor discrepancies. The genus Moricandia appears to be formed by two main lineages: the Iberian clade including three species, and the African clade including the four species inhabiting the Southern Mediterranean regions plus M. arvensis. Discussion We dated the main evolutionary events of this genus, showing that the origin of the Iberian clade probably occurred after a range expansion during the Messinian period, between 7.25 and 5.33 Ma. In that period, an extensive African-Iberian floral and faunal interchange occurred due to the existence of land bridges between Africa and Europa in what is, at present-days, the Strait of Gibraltar. We have demonstrated that a Spanish population previously ascribed to Rytidocarpus moricandioides is indeed a Moricandia species, and we propose to name it as M. rytidocarpoides sp. nov. In addition, in all the phylogenetic

  3. Importance of bovine mastitis in Africa.

    Science.gov (United States)

    Motaung, Thabiso E; Petrovski, Kiro R; Petzer, Inge-Marie; Thekisoe, Oriel; Tsilo, Toi J

    2017-06-01

    Bovine mastitis is an important animal production disease that affects the dairy industry globally. Studies have estimated the prevalence of this disease in approximately 30% of African countries, with the highest prevalence found in Ethiopia. This is despite the wide cattle distribution in Africa, and the largest number of dairy farms and herds in countries such as South Africa, Kenya and Uganda. Furthermore, the estimated financial losses due to direct and indirect impacts of bovine mastitis are lacking in this continent. Therefore, intensive research efforts will help determine the continent-wide economic impacts and advance careful monitoring of disease prevalence and epidemiology. Here, published cases supporting the occurrence and importance of bovine mastitis in certain regions of Africa are outlined.

  4. Bovine herpes virus infections in cattle.

    Science.gov (United States)

    Nandi, S; Kumar, Manoj; Manohar, M; Chauhan, R S

    2009-06-01

    Bovine herpes virus 1 (BHV-1) is primarily associated with clinical syndromes such as rhinotracheitis, pustular vulvovaginitis and balanoposthitis, abortion, infertility, conjunctivitis and encephalitis in bovine species. The main sources of infection are the nasal exudates and the respiratory droplets, genital secretions, semen, fetal fluids and tissues. The BHV-1 virus can become latent following a primary infection with a field isolate or vaccination with an attenuated strain. The viral genomic DNA has been demonstrated in the sensory ganglia of the trigeminal nerve in infectious bovine rhinotracheitis (IBR) and in sacral spinal ganglia in pustular vulvovaginitis and balanoposthitis cases. BHV-1 infections can be diagnosed by detection of virus or virus components and antibody by serological tests or by detection of genomic DNA by polymerase chain reaction (PCR), nucleic acid hybridization and sequencing. Inactivated vaccines and modified live virus vaccines are used for prevention of BHV-1 infections in cattle; subunit vaccines and marker vaccines are under investigation.

  5. Seroprevalence of bovine theileriosis in northern China

    Directory of Open Access Journals (Sweden)

    Yaqiong Li

    2016-11-01

    Full Text Available Abstract Background Bovine theileriosis is a common disease transmitted by ticks, and can cause loss of beef and dairy cattle worldwide. Here, an indirect enzyme-linked immunosorbent assay (iELISA based on Theileria luwenshuni surface protein (TlSP was developed and used to carry out a seroepidemiological survey of bovine theileriosis in northern China. Methods We used the BugBuster Ni-NTA His•Bind Purification Kit to purify recombinant TlSP (rTlSP, which was subsequently analyzed by Western Blotting to evaluate cross-reactivity with other pathogen-positive sera. The iELISA method based on rTlSP was successfully developed. Sera from 2005 blood samples were tested with the rTlSP-iELISA method, and blood smears from these samples were observed by microscopy. Results The specificity of iELISA was 98.9%, the sensitivity was 98.5%, and the cut-off was selected as 24.6%. Western Blot analysis of rTlSP confirmed that there were cross-reactions with Theileria luwenshuni, Theileria uilenbergi, Theileria ovis, Theileria annulata, Theileria orientalis and Theileria sinensis. The epidemiological survey showed that the highest positive rate of bovine theileriosis was 98.3%, the lowest rate was 84.1%, and the average positive rate was 95.4% by iELISA. With microscopy, the highest positive rate was 38.9%, the lowest rate was 5.1%, and the relative average positive rate was 13.7%. Conclusions An rTlSP-iELISA was developed to detect circulating antibodies against bovine Theileria in northern China. This is the first report on the seroprevalence of bovine theileriosis in northern China, and it also provides seroepidemiological data on bovine theileriosis in China.

  6. Cloning and sequencing of the bovine gastrin gene

    DEFF Research Database (Denmark)

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

    1989-01-01

    In order to deduce the primary structure of bovine preprogastrin we therefore sequenced a gastrin DNA clone isolated from a bovine liver cosmid library. Bovine preprogastrin comprises 104 amino acids and consists of a signal peptide, a 37 amino acid spacer-sequence, the gastrin-34 sequence followed...

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

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

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

    Science.gov (United States)

    2011-05-06

    ... Inspection Service [Docket No. APHIS-2011-0044] Bovine Tuberculosis and Brucellosis; Public Meetings AGENCY... bovine tuberculosis and brucellosis programs in the United States. The meetings are being organized by... tuberculosis (TB) and bovine brucellosis in the United States. In keeping with its commitment to partnering...

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

    Science.gov (United States)

    Hasegawa, Masami; Kuroda, Sayako

    2017-12-01

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

  11. Heterogeneity of Bovine Peripheral Blood Monocytes

    Directory of Open Access Journals (Sweden)

    Jamal Hussen

    2017-12-01

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

  12. Radiography of the bovine cranioventral abdomen

    International Nuclear Information System (INIS)

    Partington, B.P.; Biller, D.S.

    1991-01-01

    This study consists of a review of 115 consecutively accrued bovine cranial abdomial radiographs. The sensitivity and specificity of radiography in detecting traumatic reticuloperitonitis or pericarditis was 83% and 90%, respectively. Increased reticular size was associated with vagal indigestion. Increased reticulo-diaphragmatic separation did not correlate with a specific disease process, 25/35 (71%) cattle presented for radiographic examination with a 1 cm or longer metallic reticular foreign body unattached to a magnet had traumatic reticuloperitonitis. Standing lateral abdominal radiographs were determined to be a valuable tool in the diagnosis of cranial abdominal disorders in the bovine

  13. Mapping and polymorphism of bovine ghreline gene

    OpenAIRE

    Colinet, Frédéric; Eggen, André; Halleux, Caroline; Arnould, Valérie; Portetelle, Daniel; Renaville, Robert

    2006-01-01

    Bovine ghrelin, a 27-amino-acid peptide has been identified in bovine oxyntic glands of the abomasum. It is an endogenous growth hormone secretagogue. Total mRNA was extracted from abomasum and complete ghrelin mRNA was sequenced by rapid amplification of cDNA ends. The gene contains five exons and four introns with a short noncoding first exon of 17 bp similar to mouse and human ghrelin gene. Using a radiation hybrid panel, the gene was mapped to chromosome 22 near microsat...

  14. Bovine rotavirus pentavalent vaccine development in India.

    Science.gov (United States)

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

    2014-08-11

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

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

    Science.gov (United States)

    Sicoli, Mark A.; Holton, Gary

    2014-01-01

    Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America. PMID:24621925

  16. Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

    KAUST Repository

    Salari, Raheleh

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Stothard JR

    2000-01-01

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

  18. Phylogeny and comparative genome analysis of a Basidiomycete fungi

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-03-14

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

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

    Science.gov (United States)

    Spielman, Stephanie J; Wilke, Claus O

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Stephanie J Spielman

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

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

    Science.gov (United States)

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

    2017-04-01

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

  2. 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

  3. A reassessment of the phylogeny and circumscription of Zaluzianskya (Scrophulariaceae).

    Science.gov (United States)

    Archibald, Jenny K; Cook, Jacqueline; Anderson, Bruce; Johnson, Steven D; Mort, Mark E

    2017-07-01

    The genus Zaluzianskya (Scrophulariaceae s.s.) encompasses a diversity of floral and ecological traits. However, this diversity, as described by the current taxonomic circumscription of Zaluzianskya, is an underestimate. We present molecular data suggesting that this genus requires expansion via incorporation of species from other genera and recognition of unnamed cryptic species. This study advances prior molecular phylogenies of the southern African genus through the addition of DNA regions and 51 populations that had not previously been sampled in a published phylogeny. A total of 82 species of Zaluzianskya and related genera are included, adding 48 to those previously sampled. Results are presented from analyses of five DNA regions, including nuclear ITS and four rapidly evolving chloroplast regions (trnL-trnF, rpl16, rps16, and trnS-trnfM). Our primary finding is that the genus Phyllopodium is polyphyletic as currently circumscribed, with some species placed within Zaluzianskya and others grouping with Polycarena, indicating the need for further phylogenetic work on these genera. Preliminary support for the incorporation of Reyemia into Zaluzianskya is reinforced here by the first molecular analysis to include both species of Reyemia and a strong sampling of species across Zaluzianskya and major clades of tribe Limoselleae. The two disjunct, tropical African species of Zaluzianskya are also confirmed as members of this genus. Finally, a broad sampling of 21 populations of Z. microsiphon establishes their phylogenetic division into two to five separate lineages. Hybridization, coevolution, and cryptic speciation may each play a role in the evolution of Z. microsiphon. Further resolution within a clade comprising sections Nycterinia and Macrocalyx is needed to better understand their relationships. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Phylogeny of Gobioidei and the origin of European gobies

    Directory of Open Access Journals (Sweden)

    Ainhoa Agorreta

    2015-11-01

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

  5. Nuclear and original DNA application in Oryza taxonomy and phylogeny

    International Nuclear Information System (INIS)

    Romero, Gabriel O.

    1998-01-01

    Conventional taxonomy and phylogeny of germplasm are based on the tedious characterization of morphological variation. The ability to assay DNA variation that underlies morphological variation offers great promise as a convenient alternative for the genetic characterization of germplasm. Restriction fragment length polymorphism (RFLP) was used to survey DNA variation in 22 species of the genus Oryza. At the ribosomal DNA (rDNA) multigene family, 15 rDNA spacer length (sl) variants were identified using restriction enzyme Sst1 and wheatrDNA unit as probe. Particular sl variants predominated in certain isozyme groups of O. sativa, indicating a potential of sl ploymorphism in varietal classification. The distribution of sl variants supports the origin of O. sativa and O. nivara from O. rufipogon, and that O. spontanea arose from introgressions among O. sativa, O. nivara, and O. rufipogon. The distribution also suggests that the CCgenome, of all the genomes in the Officinalis complex, may be closest to the Sativa complex genomes, and it affirms the genetic position of the Officinalis complex intermediate between the Sativa and Ridleyi complexes. Variation at the Oryza organelle genomes was probed with a maize mitochondrial gene, atpA, a wheat chloroplast inverted repeat segment, p6. Results indicated that the complexes can be differentiated by their mitochondrial genome, but not their chloroplast genome when digested by Sst1 or BamH1. Therefore, the natural DNA variation in the nuclear and mitochondrial genomes has demonstrated great potential in complementing the conventional basis of taxa classification and phylogeny in the genus Oryza. (Author)

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

    Directory of Open Access Journals (Sweden)

    Sánchez A.

    2004-01-01

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

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

    KAUST Repository

    Dí az-Arce, Natalia; Arrizabalaga, Haritz; Murua, Hilario; Irigoien, Xabier; Rodrí guez-Ezpeleta, Naiara

    2016-01-01

    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

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

    Czech Academy of Sciences Publication Activity Database

    Pečnerová, P.; Martínková, Natália

    2012-01-01

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

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

    DEFF Research Database (Denmark)

    Guil, Noemi; Jørgensen, Aslak; Giribet, Gonzalo

    2013-01-01

    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 ...

  10. Antifungal susceptibility and phylogeny of opportunistic members of the order mucorales.

    NARCIS (Netherlands)

    Vitale, R.G.; Hoog, G.S. de; Schwarz, P.; Dannaoui, E.; Deng, S.; Machouart, M.; Voigt, K.; Sande, W.W. van de; Dolatabadi, S.; Meis, J.F.G.M.; Walther, G.

    2012-01-01

    The in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the nuclear

  11. Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales

    NARCIS (Netherlands)

    R.G. Vitale (Roxana); G.S. de Hoog; P. Schwarz (Peter); E. Dannaoui (Eric); S. Deng (Shuwen); M. Machouart (Marie); K. Voigt (Kerstin); W.W.J. van de Sande (Wendy); S. Dolatabadi (Somayeh); J.F. Meis; G. Walther

    2012-01-01

    textabstractThe in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the

  12. Antifungal Susceptibility and Phylogeny of Opportunistic Members of the Order Mucorales

    NARCIS (Netherlands)

    Vitale, R.G.; de Hoog, G.S.; Schwarz, P.; Dannaoui, E.; Deng, S.; Machouart, M.; Voigt, K.; de Sande, W.W.J.v.; Dolatabadi, S.; Meis, J.F.; Walther, G.

    2012-01-01

    The in vitro susceptibilities of 66 molecularly identified strains of the Mucorales to eight antifungals (amphotericin B, terbinafine, itraconazole, posaconazole, voriconazole, caspofungin, micafungin, and 5-fluorocytosine) were tested. Molecular phylogeny was reconstructed based on the nuclear

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

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

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

  14. Effects of methodology and analysis strategy on robustness of pestivirus phylogeny.

    Science.gov (United States)

    Liu, Lihong; Xia, Hongyan; Baule, Claudia; Belák, Sándor; Wahlberg, Niklas

    2010-01-01

    Phylogenetic analysis of pestiviruses is a useful tool for classifying novel pestiviruses and for revealing their phylogenetic relationships. In this study, robustness of pestivirus phylogenies has been compared by analyses of the 5'UTR, and complete N(pro) and E2 gene regions separately and combined, performed by four methods: neighbour-joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI). The strategy of analysing the combined sequence dataset by BI, ML, and MP methods resulted in a single, well-supported tree topology, indicating a reliable and robust pestivirus phylogeny. By contrast, the single-gene analysis strategy resulted in 12 trees of different topologies, revealing different relationships among pestiviruses. These results indicate that the strategies and methodologies are two vital aspects affecting the robustness of the pestivirus phylogeny. The strategy and methodologies outlined in this paper may have a broader application in inferring phylogeny of other RNA viruses.

  15. Control of bovine hepatic fatty acid oxidation

    International Nuclear Information System (INIS)

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

    1986-01-01

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

  16. Vaccination of cattle against bovine viral diarrhoea

    NARCIS (Netherlands)

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

    1999-01-01

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

  17. Pathogenesis of bovine spongiform encephalopathy in sheep

    NARCIS (Netherlands)

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

    2008-01-01

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

  18. NUTRIENTS AND EPIGENETICS IN BOVINE CELLS

    Science.gov (United States)

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

  19. diagnosis of bovine cysticercosis in Kenyan cattle

    African Journals Online (AJOL)

    A total of 55 cattle divided into two groups of experimentally (n =30) and naturally ... sensitive than meat inspection in the diagnosis of bovine cysticercosis, detecting .... The second group of 15 calves was ... ined for the presence of C. bovis. .... variable and pour ' ..... appropriate intermediate host is dependent on:- the state.

  20. Aortic reconstruction with bovine pericardial grafts

    Directory of Open Access Journals (Sweden)

    Silveira Lindemberg Mota

    2003-01-01

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

  1. Aggregation and fibrillation of bovine serum albumin

    DEFF Research Database (Denmark)

    Holm, NK; Jespersen, SK; Thomassen, LV

    2007-01-01

    The all-alpha helix multi-domain protein bovine serum albumin (BSA) aggregates at elevated temperatures. Here we show that these thermal aggregates have amyloid properties. They bind the fibril-specific dyes Thioflavin T and Congo Red, show elongated although somewhat worm-like morphology...

  2. Chemotherapy of experimental bovine petechial fever.

    Science.gov (United States)

    Snodgrass, D R

    1976-01-01

    A dithiosemicarbazone was compared with two tetracycline formulations in the treatment of bovine petechial fever (BPF) in experimentally infected sheep, and was then used to treat the disease in experimental cattle. The dithiosemicarbazone was found to be more efficacious than either of the other two drugs in treating ovine BPF, and also to be effective against BPF in cattle.

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

    Directory of Open Access Journals (Sweden)

    Maia S. Marin

    2013-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Hongyan Xia

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

  5. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

    Science.gov (United States)

    Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

    2014-01-01

    Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

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

    Directory of Open Access Journals (Sweden)

    Dimas Endro W

    2013-10-01

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

  7. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

    Directory of Open Access Journals (Sweden)

    David Lee Erickson

    2014-11-01

    Full Text Available Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1,347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK and psbA-trnH and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance metrics that are commonly used to infer assembly processes were estimated for each plot (Phylogenetic Distance [PD], Mean Phylogenetic Distance [MPD], and Mean Nearest Taxon Distance [MNTD]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for

  8. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

    OpenAIRE

    Smith, Stephen A; Beaulieu, Jeremy M; Donoghue, Michael J

    2009-01-01

    Abstract Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals as well as the patterns of seed evolution. In addition to these broad evolutionary questions there is increasing awareness of the importance of large phylog...

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

    Directory of Open Access Journals (Sweden)

    Schwartz Russell

    2008-08-01

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

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

    Science.gov (United States)

    Makufka, David

    2010-01-01

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

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

    Science.gov (United States)

    Bazinet, Adam L

    2017-08-02

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

  12. Phylogeny of the Acanthocephala based on morphological characters.

    Science.gov (United States)

    Monks, S

    2001-02-01

    Only four previous studies of relationships among acanthocephalans have included cladistic analyses, and knowledge of the phylogeny of the group has not kept pace with that of other taxa. The purpose of this study is to provide a more comprehensive analysis of the phylogenetic relationships among members of the phylum Acanthocephala using morphological characters. The most appropriate outgroups are those that share a common early cell-cleavage pattern (polar placement of centrioles), such as the Rotifera, rather than the Priapulida (meridional placement of centrioles) to provide character polarity based on common ancestry rather than a general similarity likely due to convergence of body shapes. The phylogeny of 22 species of the Acanthocephala was evaluated based on 138 binary and multistate characters derived from comparative morphological and ontogenetic studies. Three assumptions of cement gland structure were tested: (i) the plesiomorphic type of cement glands in the Rotifera, as the sister group, is undetermined; (ii) non-syncytial cement glands are plesiomorphic; and (iii) syncytial cement glands are plesiomorphic. The results were used to test an early move of Tegorhynchus pectinarius to Koronacantha and to evaluate the relationship between Tegorhynchus and Illiosentis. Analysis of the data-set for each of these assumptions of cement gland structure produced the same single most parsimonious tree topology. Using Assumptions i and ii for the cement glands, the trees were the same length (length = 404 steps, CI = 0.545, CIX = 0.517, HI = 0.455, HIX = 0.483, RI = 0.670, RC = 0.365). Using Assumption iii, the tree was three steps longer (length = 408 steps, CI = 0.539, CIX = 0.512, HI = 0.461, HIX = 0.488, RI = 0.665, RC = 0.359). The tree indicates that the Palaeacanthocephala and Eoacanthocephala both are monophyletic and are sister taxa. The members of the Archiacanthocephala are basal to the other two clades, but do not themselves form a clade. The results

  13. National Fire Plan Research and Development 2004-2005 accomplishment report

    Science.gov (United States)

    Michael W. Hilbruner; Paul Keller

    2007-01-01

    This report highlights accomplishments achieved by USDA Forest Service National Fire Plan Research and Development projects from 2004 through 2005 in four key areas: firefighting, rehabilitation and restoration, hazardous fuels reduction, and community assistance. These highlights illustrate the broad range of knowledge and tools introduced and generated by the...

  14. 29 CFR 779.218 - Methods to accomplish “unified operation.”

    Science.gov (United States)

    2010-07-01

    ..., 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 arrangements... others so that they constitute a single business or unified business system. Whether in any particular...

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

    Energy Technology Data Exchange (ETDEWEB)

    None

    2013-11-01

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

  16. Skylab experiments. Volume 6: Mechanics. [Skylab program accomplishments for high school level education

    Science.gov (United States)

    1973-01-01

    Skylab program activities are presented in a form adapted to instruction of high school students. The overall goals of the program are discussed. The specific accomplishments of the mechanics investigations are described. The subjects involved are as follows: (1) evaluation of mobility aids, (2) mass measurement devices, and (3) space guidance crew/vehicle disturbances.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

    Hurley, Mary E.

    1991-01-01

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

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

    Science.gov (United States)

    Zhang, Yulei; Dang, Yan

    2015-01-01

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

  20. The current status of the New World monkey phylogeny

    Directory of Open Access Journals (Sweden)

    SCHNEIDER HORACIO

    2000-01-01

    Full Text Available Four DNA datasets were combined in tandem (6700 bp and Maximum parsimony and Neighbor-Joining analyses were performed. The results suggest three groups emerging almost at the same time: Atelidae, Pitheciidae and Cebidae. The total analysis strongly supports the monophyly of the Cebidae family, grouping Aotus, Cebus and Saimiri with the small callitrichines. In the callitrichines, the data link Cebuela to Callithrix, place Callimico as a sister group of Callithrix/Cebuella, and show Saguinus to be the earliest offshoot of the callitrichines. In the family Pithecidae, Callicebus is the basal genus. Finally, combined molecular data showed congruent branching in the atelid clade, setting up Alouatta as the basal lineage and Brachyteles-Lagothrix as a sister group and the most derived branch. Two major points remain to be clarified in the platyrrhine phylogeny: (i what is the exact branching pattern of Aotus, Cebus, Saimiri and the small callitrichines, and (ii, which two of these three lineages, pitheciines, atelines or cebids, are more closely related?

  1. The phylogeny and evolutionary history of tyrannosauroid dinosaurs

    Science.gov (United States)

    Brusatte, Stephen L.; Carr, Thomas D.

    2016-02-01

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

  2. Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2013-11-01

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

  3. Phylogeny and Biogeography of Cyanobacteria and Their Produced Toxins

    Science.gov (United States)

    Moreira, Cristiana; Vasconcelos, Vitor; Antunes, Agostinho

    2013-01-01

    Phylogeny is an evolutionary reconstruction of the past relationships of DNA or protein sequences and it can further be used as a tool to assess population structuring, genetic diversity and biogeographic patterns. In the microbial world, the concept that everything is everywhere is widely accepted. However, it is much debated whether microbes are easily dispersed globally or whether they, like many macro-organisms, have historical biogeographies. Biogeography can be defined as the science that documents the spatial and temporal distribution of a given taxa in the environment at local, regional and continental scales. Speciation, extinction and dispersal are proposed to explain the generation of biogeographic patterns. Cyanobacteria are a diverse group of microorganisms that inhabit a wide range of ecological niches and are well known for their toxic secondary metabolite production. Knowledge of the evolution and dispersal of these microorganisms is still limited, and further research to understand such topics is imperative. Here, we provide a compilation of the most relevant information regarding these issues to better understand the present state of the art as a platform for future studies, and we highlight examples of both phylogenetic and biogeographic studies in non-symbiotic cyanobacteria and cyanotoxins. PMID:24189276

  4. A comprehensive molecular phylogeny for the hornbills (Aves: Bucerotidae).

    Science.gov (United States)

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

    2013-05-01

    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. Copyright © 2013. Published by Elsevier Inc.

  5. Genomes-based phylogeny of the genus Xanthomonas

    Directory of Open Access Journals (Sweden)

    Rodriguez-R Luis M

    2012-03-01

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

  6. The phylogeny and evolutionary history of tyrannosauroid dinosaurs.

    Science.gov (United States)

    Brusatte, Stephen L; Carr, Thomas D

    2016-02-02

    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.

  7. Phylogeny and photosynthetic pathway distribution in Anticharis Endl. (Scrophulariaceae).

    Science.gov (United States)

    Khoshravesh, Roxana; Hossein, Akhani; Sage, Tammy L; Nordenstam, Bertil; Sage, Rowan F

    2012-09-01

    C(4) photosynthesis independently evolved >62 times, with the majority of origins within 16 dicot families. One origin occurs in the poorly studied genus Anticharis Endl. (Scrophulariaceae), which consists of ~10 species from arid regions of Africa and southwest Asia. Here, the photosynthetic pathway of 10 Anticharis species and one species from each of the sister genera Aptosimum and Peliostomum was identified using carbon isotope ratios (δ(13)C). The photosynthetic pathway was then mapped onto an internal transcribed spacer (ITS) phylogeny of Anticharis and its sister genera. Leaf anatomy was examined for nine Anticharis species and plants from Aptosimum and Peliostomum. Leaf ultrastructure, gas exchange, and enzyme distributions were assessed in Anticharis glandulosa collected in SE Iran. The results demonstrate that C(3) photosynthesis is the ancestral condition, with C(4) photosynthesis occurring in one clade containing four species. C(4) Anticharis species exhibit the atriplicoid type of C(4) leaf anatomy and the NAD-malic enzyme biochemical subtype. Six Anticharis species had C(3) or C(3)-C(4) δ(13)C values and branched at phylogenetic nodes that were sister to the C(4) clade. The rest of Anticharis species had enlarged bundle sheath cells, close vein spacing, and clusters of chloroplasts along the centripetal (inner) bundle sheath walls. These traits indicate that basal-branching Anticharis species are evolutionary intermediates between the C(3) and C(4) conditions. Anticharis appears to be an important new group in which to study the dynamics of C(4) evolution.

  8. Genome rearrangements and phylogeny reconstruction in Yersinia pestis.

    Science.gov (United States)

    Bochkareva, Olga O; Dranenko, Natalia O; Ocheredko, Elena S; Kanevsky, German M; Lozinsky, Yaroslav N; Khalaycheva, Vera A; Artamonova, Irena I; Gelfand, Mikhail S

    2018-01-01

    Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis . Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.

  9. Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae).

    Science.gov (United States)

    Poliseno, Angelo; Feregrino, Christian; Sartoretto, Stéphane; Aurelle, Didier; Wörheide, Gert; McFadden, Catherine S; Vargas, Sergio

    2017-10-01

    Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Ectocranial suture fusion in primates: pattern and phylogeny.

    Science.gov (United States)

    Cray, James; Cooper, Gregory M; Mooney, Mark P; Siegel, Michael I

    2014-03-01

    Patterns of ectocranial suture fusion among Primates are subject to species-specific variation. In this study, we used Guttman Scaling to compare modal progression of ectocranial suture fusion among Hominidae (Homo, Pan, Gorilla, and Pongo), Hylobates, and Cercopithecidae (Macaca and Papio) groups. Our hypothesis is that suture fusion patterns should reflect their evolutionary relationship. For the lateral-anterior suture sites there appear to be three major patterns of fusion, one shared by Homo-Pan-Gorilla, anterior to posterior; one shared by Pongo and Hylobates, superior to inferior; and one shared by Cercopithecidae, posterior to anterior. For the vault suture pattern, the Hominidae groups reflect the known phylogeny. The data for Hylobates and Cercopithecidae groups is less clear. The vault suture site termination pattern of Papio is similar to that reported for Gorilla and Pongo. Thus, it may be that some suture sites are under larger genetic influence for patterns of fusion, while others are influenced by environmental/biomechanic influences. Copyright © 2013 Wiley Periodicals, Inc.

  11. Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets.

    Directory of Open Access Journals (Sweden)

    Aitor Blanco-Míguez

    2016-12-01

    Full Text Available Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.

  12. Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets.

    Science.gov (United States)

    Blanco-Míguez, Aitor; Meier-Kolthoff, Jan P; Gutiérrez-Jácome, Alberto; Göker, Markus; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, Anália

    2016-12-01

    Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.

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

    Science.gov (United States)

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

    2017-11-01

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

  14. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers.

    Science.gov (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

    2014-01-01

    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.

  15. Arthropod phylogeny based on eight molecular loci and morphology

    Science.gov (United States)

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

    2001-01-01

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

  16. The rRNA evolution and procaryotic phylogeny

    Science.gov (United States)

    Fox, G. E.

    1986-01-01

    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.

  17. Phylogeny of marine Bacillus isolates from the Gulf of Mexico

    Science.gov (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

    2000-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Xavier Suresh R

    2006-06-01

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

  19. Random laser action in bovine semen

    Science.gov (United States)

    Smuk, Andrei; Lazaro, Edgar; Olson, Leif P.; Lawandy, N. M.

    2011-03-01

    Experiments using bovine semen reveal that the addition of a high-gain water soluble dye results in random laser action when excited by a Q-switched, frequency doubled, Nd:Yag laser. The data shows that the linewidth collapse of the emission is correlated to the sperm count of the individual samples, potentially making this a rapid, low sample volume approach to count determination.

  20. Radioimmunoassay of bovine leukosis virus antibodies

    International Nuclear Information System (INIS)

    Franz, J.; Hampl, J.; Svoboda, I.; Granatova, M.; Hofirek, B.; Skrobak, F.

    1986-01-01

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

  1. Radioimmunoassay of bovine leukosis virus antibodies

    Energy Technology Data Exchange (ETDEWEB)

    Franz, J; Hampl, J; Svoboda, I; Granatova, M; Hofirek, B; Skrobak, F

    1986-08-01

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    -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...... 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...

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    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......The present work reports the characterization of carbohydrate structures and the distribution of the newly identified mucin MUC15, a highly glycosylated protein associated with the bovine milk fat globule membrane (MFGM). Distribution of MUC15 was investigated in various fractions of bovine milk......-containing fractions as well, such as skim milk and whey. Compositional and structural studies of the carbohydrates of bovine milk MUC15 showed that the glycans are composed of fucose, galactose, mannose, N-acetylgalactosamine, N-acetylglycosamine, and sialic acid. The carbohydrate was shown to constitute 65...

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

    Science.gov (United States)

    Bouchard, Damien S; Seridan, Bianca; Saraoui, Taous; Rault, Lucie; Germon, Pierre; Gonzalez-Moreno, Candelaria; Nader-Macias, Fatima M E; Baud, Damien; François, Patrice; Chuat, Victoria; Chain, Florian; Langella, Philippe; Nicoli, Jacques; Le Loir, Yves; Even, Sergine

    2015-01-01

    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.

  5. 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.

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Rønsted Nina

    2012-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Aziz Mithani

    2010-08-01

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

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

    Science.gov (United States)

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

    2012-11-01

    The cacti of tribe Tephrocacteae (Cactaceae-Opuntioideae) are adapted to diverse climatic conditions over a wide area of the southern Andes and adjacent lowlands. They exhibit a range of life forms from geophytes and cushion-plants to dwarf shrubs, shrubs or small trees. To confirm or challenge previous morphology-based classifications and molecular phylogenies, we sampled DNA sequences from the chloroplast trnK/matK region and the nuclear low copy gene phyC and compared the resulting phylogenies with previous data gathered from nuclear ribosomal DNA sequences. The here presented chloroplast and nuclear low copy gene phylogenies were mutually congruent and broadly coincident with the classification based on gross morphology and seed micro-morphology and anatomy. Reconstruction of hypothetical ancestral character states suggested that geophytes and cushion-forming species probably evolved several times from dwarf shrubby precursors. We also traced an increase of embryo size at the expense of the nucellus-derived storage tissue during the evolution of the Tephrocacteae, which is thought to be an evolutionary advantage because nutrients are then more rapidly accessible for the germinating embryo. In contrast to these highly concordant phylogenies, nuclear ribosomal DNA data sampled by a previous study yielded conflicting phylogenetic signals. Secondary structure predictions of ribosomal transcribed spacers suggested that this phylogeny is strongly influenced by the inclusion of paralogous sequence probably arisen by genome duplication during the evolution of this plant group. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence.

    Science.gov (United States)

    Kropáčková, Lucie; Těšický, Martin; Albrecht, Tomáš; Kubovčiak, Jan; Čížková, Dagmar; Tomášek, Oldřich; Martin, Jean-François; Bobek, Lukáš; Králová, Tereza; Procházka, Petr; Kreisinger, Jakub

    2017-10-01

    Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intraspecific GM variation in wild populations are still poorly known. We analysed data on faecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region). Despite pronounced interindividual variation, GM composition exhibited significant differences at the interspecific level, accounting for approximately 20%-30% of total GM variation. We also observed a significant correlation between GM composition divergence and host's phylogenetic divergence, with strength of correlation higher than that of GM vs. ecological or life history traits and geographic variation. The effect of host's phylogeny on GM composition was significant, even after statistical control for these confounding factors. Hence, our data do not support codiversification of GM and passerine phylogeny solely as a by-product of their ecological divergence. Furthermore, our findings do not support that GM vs. host's phylogeny codiversification is driven primarily through trans-generational GM transfer as the GM vs. phylogeny correlation does not increase with higher sequence similarity used when delimiting operational taxonomic units. Instead, we hypothesize that the GM vs. phylogeny correlation may arise as a consequence of interspecific divergence of genes that directly or indirectly modulate composition of GM. © 2017 John Wiley & Sons Ltd.

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

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2013-12-01

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

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

    Science.gov (United States)

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

    2016-12-01

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

  13. Skipper genome sheds light on unique phenotypic traits and phylogeny.

    Science.gov (United States)

    Cong, Qian; Borek, Dominika; Otwinowski, Zbyszek; Grishin, Nick V

    2015-08-27

    Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the family Papilionidae (swallowtails) may be the sister to other butterflies including skippers. The moth-like features and the controversial position of skippers in Lepidoptera phylogeny make them valuable targets for comparative genomics. We obtained the 310 Mb draft genome of the Clouded Skipper (Lerema accius) from a wild-caught specimen using a cost-effective strategy that overcomes the high (1.6 %) heterozygosity problem. Comparative analysis of Lerema accius and the highly heterozygous genome of Papilio glaucus revealed differences in patterns of SNP distribution, but similarities in functions of genes that are enriched in non-synonymous SNPs. Comparison of Lepidoptera genomes revealed possible molecular bases for unique traits of skippers: a duplication of electron transport chain components could result in efficient energy supply for their rapid flight; a diversified family of predicted cellulases might allow them to feed on cellulose-enriched grasses; an expansion of pheromone-binding proteins and enzymes for pheromone synthesis implies a more efficient mate-recognition system, which compensates for the lack of clear visual cues due to the similarities in wing colors and patterns of many species of skippers. Phylogenetic analysis of several Lepidoptera genomes suggested that the position of Hesperiidae remains uncertain as the tree topology varied depending on the evolutionary model. Completion of the first genome from the family Hesperiidae allowed comparative analyses with other Lepidoptera that revealed potential genetic bases for the unique phenotypic traits of skippers. This work lays the foundation for future experimental studies of skippers and

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

    Directory of Open Access Journals (Sweden)

    Leigh J

    2005-05-01

    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.

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

    Science.gov (United States)

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

    2014-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Christopher L Mah

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

  17. Mitogenomic phylogeny of cone snails endemic to Senegal.

    Science.gov (United States)

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

    2017-07-01

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

  18. The discovery of Halictivirus resolves the Sinaivirus phylogeny.

    Science.gov (United States)

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

    2017-11-01

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

  19. Forelimb-hindlimb developmental timing changes across tetrapod phylogeny

    Directory of Open Access Journals (Sweden)

    Selwood Lynne

    2007-10-01

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

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

    Science.gov (United States)

    Gustavson, Daniel E; Miyake, Akira

    2017-02-01

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

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

    DEFF Research Database (Denmark)

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

    2000-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jose L. Horreo

    2017-09-01

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

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

    KAUST Repository

    Díaz-Arce, Natalia

    2016-06-07

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

  4. National Low-Level Waste Management Program final summary report of key activities and accomplishments for fiscal year 1995

    International Nuclear Information System (INIS)

    Forman, S.

    1995-12-01

    To assist the Department of Energy (DOE) in fulfilling its responsibilities under the Low-Level Radioactive Waste Policy Amendments Act of 1985, the National Low-Level Waste Management Program (NLLWMP) outlines the key activities that the NLLWMP will accomplish in the following fiscal year. Additional activities are added during the fiscal year as necessary to accomplish programmatic goals. This report summarizes the activities and accomplishments of the NLLWMP during fiscal year 1995

  5. National Low-Level Waste Management Program final summary report of key activities and accomplishments for fiscal year 1996

    International Nuclear Information System (INIS)

    Garcia, R.S.

    1996-12-01

    To assist the Department of Energy (DOE) in fulfilling its responsibilities under the Low-Level Radioactive Waste Policy Amendments Act of 1985, the National Low-Level Waste Management Program (NLLWMP) outlines the key activities tat the NLLWMP will accomplish in the following fiscal year. Additional activities are added during the fiscal year as necessary to accomplish programmatic goals. This report summarizes the activities and accomplishments of the NLLWMP during Fiscal Year 1996

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

    NARCIS (Netherlands)

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

    2001-01-01

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

  7. Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity

    OpenAIRE

    Marx, Felix G.; Fordyce, R. Ewan

    2015-01-01

    A new, fully dated total-evidence phylogeny of baleen whales (Mysticeti) shows that evolutionary phases correlate strongly with Caenozoic modernization of the oceans and climates, implying a major role for bottom-up physical drivers. The phylogeny of 90 modern and dated fossil species suggests three major phases in baleen whale history: an early adaptive radiation (36?30?Ma), a shift towards bulk filter-feeding (30?23?Ma) and a climate-driven diversity loss around 3?Ma. Evolutionary rates and...

  8. Quality control of commercial bovine lactoferrin.

    Science.gov (United States)

    Wakabayashi, Hiroyuki; Yamauchi, Koji; Abe, Fumiaki

    2018-06-01

    Herein we review commercial bovine lactoferrin quality issues by describing an example of industrial production, the current status of global quality standardization, and quality-activity concerns for further discussion. Morinaga Milk Industry has been industrially producing bovine lactoferrin in Milei GmbH, Germany, since 1989. We delineate its production and quality as an example of safe and high-quality manufacturing. Currently, global standardization in the quality of bovine lactoferrin is progressing through Novel Food and GRAS in the EU and USA, respectively. Novel Food was applied or notified to seven lactoferrin manufacturers and GRAS was notified to three manufacturers, two of which are for infant use and one is for adult use, by the end of 2017. The specifications of these regulations are relatively high, including more than 95% lactoferrin purity in protein, which means that such companies can supply relatively high-grade lactoferrin. There appear to be several concerns regarding lactoferrin quality affecting activities, including contamination of lipopolysaccharide (LPS) and angiogenin, purity, and degradation of lactoferrin sample. Although LPS is immunologically toxic when invading the body, it is distributed normally in foods and the gut. However, an industrial lactoferrin sample may contain LPS at a maximum LPS/lactoferrin molecule ratio = 1/1724, which means 99.9% of the lactoferrin molecule is LPS-free. It is difficult to speculate that LPS contained in a lactoferrin sample affects its activities. Finally in order to achieve good and reproducible results, we make proposals to researchers a use of high-grade lactoferrin, careful storage, and indication the manufacturers' names and specifications in the paper.

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

    African Journals Online (AJOL)

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

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

    NARCIS (Netherlands)

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

    2017-01-01

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

  11. 9 CFR 113.216 - Bovine Rhinotracheitis Vaccine, Killed Virus.

    Science.gov (United States)

    2010-01-01

    ... Virus. 113.216 Section 113.216 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS STANDARD REQUIREMENTS Killed Virus Vaccines § 113.216 Bovine Rhinotracheitis Vaccine, Killed Virus. Infectious Bovine...

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

    African Journals Online (AJOL)

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

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

    Directory of Open Access Journals (Sweden)

    Jefferson Luis Oshiro Tanaka

    2008-12-01

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

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

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

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

    NARCIS (Netherlands)

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

    1996-01-01

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

  17. Characterisation of bovine epiblast-derived outgrowth colonies

    DEFF Research Database (Denmark)

    Østrup, Esben; Gjørret, Jakob; Schauser, Kirsten Hallundbæk

    2010-01-01

    The aim of the present study was to characterise bovine epiblast-derived outgrowth colonies (OCs) with respect to the embryonic origin of their cellular components. Epiblasts were isolated mechanically from bovine Day 12 embryos. Epiblasts were cultured on feeder layers of SNL cells (neomycin...

  18. Production of biological nanoparticles from bovine serum albumin ...

    African Journals Online (AJOL)

    Production of biological nanoparticles from bovine serum albumin for drug delivery. ... Bovine serum albumin (BSA) was used for generation of nanoparticles in a drug delivery system. ... The impact of protein concentration and additional rate of organic solvent (i.e. ethanol) upon the particle ... AJOL African Journals Online.

  19. Detection of lipomannan in cattle infected with bovine tuberculosis

    Science.gov (United States)

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

  20. Sucrose/bovine serum albumin mediated biomimetic crystallization

    Indian Academy of Sciences (India)

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

  1. 21 CFR 522.1125 - Hemoglobin glutamer-200 (bovine).

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Hemoglobin glutamer-200 (bovine). 522.1125 Section... (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS IMPLANTATION OR INJECTABLE DOSAGE FORM NEW ANIMAL DRUGS § 522.1125 Hemoglobin glutamer-200 (bovine). (a) Specifications. Each 125 milliliter bag contains 13...

  2. Bovine Spongiform Encephalopathy (BSE, Mad Cow Disease

    Directory of Open Access Journals (Sweden)

    G. K. Bruckner

    1997-07-01

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

  3. Bovine aortic arch with supravalvular aortic stenosis.

    Science.gov (United States)

    Idhrees, Mohammed; Cherian, Vijay Thomas; Menon, Sabarinath; Mathew, Thomas; Dharan, Baiju S; Jayakumar, K

    2016-09-01

    A 5-year-old boy was diagnosed to have supravalvular aortic stenosis (SVAS). On evaluation of CT angiogram, there was associated bovine aortic arch (BAA). Association of BAA with SVAS has not been previously reported in literature, and to best of our knowledge, this is the first case report of SVAS with BAA. Recent studies show BAA as a marker for aortopathy. SVAS is also an arteriopathy. In light of this, SVAS can also possibly be a manifestation of aortopathy associated with BAA. Copyright © 2015 Cardiological Society of India. Published by Elsevier B.V. All rights reserved.

  4. Bovine aortic arch with supravalvular aortic stenosis

    Directory of Open Access Journals (Sweden)

    Mohammed Idhrees

    2016-09-01

    Full Text Available A 5-year-old boy was diagnosed to have supravalvular aortic stenosis (SVAS. On evaluation of CT angiogram, there was associated bovine aortic arch (BAA. Association of BAA with SVAS has not been previously reported in literature, and to best of our knowledge, this is the first case report of SVAS with BAA. Recent studies show BAA as a marker for aortopathy. SVAS is also an arteriopathy. In light of this, SVAS can also possibly be a manifestation of aortopathy associated with BAA.

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

    DEFF Research Database (Denmark)

    Larsen, Lars Erik

    2000-01-01

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

  6. BIOLOGICAL CLONING OF A BOVINE CORONAVIRUS ISOLATE

    OpenAIRE

    Betancourt, A; Rodríguez, Edisleidy; Relova, Damarys; Barrera, Maritza

    2008-01-01

    Con el objetivo de obtener un aislado de Coronavirus bovino clonado biológicamente se adaptó el aislado VB73/04 a la multiplicación en la línea celular MDBK. Este aislado indujo la formación de placas, las cuales resultaron homogéneas después del clonaje biológico. La población viral obtenida fue identificada como Coronavirus bovino por RT-PCR y Seroneutralización. In order to obtain a biologically cloned bovine coronavirus isolate, the isolate VB73/04 was adapted to multiplication in MDBK...

  7. A bovine aortic arch in humans

    Directory of Open Access Journals (Sweden)

    María Elena Arnáiz-García

    2014-05-01

    Full Text Available We describe a curious congenital variation of human aortic arch (AA branching pattern termed the “bovine aortic arch”. Rather than arising directly from the AA as a separate branch as occurs in the most common AA branching pattern, the left common carotid artery moves to the right and merges from the brachiocephalic trunk. It is the normal AA branching pattern presented in a number of animals (canines, felines or Macaque monkeys but it has nothing to do with anatomy of AA in ruminant animals, including cattle and buffalo. That is why it is one of the most widely misnomers used in medical literature whose origin is nowadays unknown.

  8. Phylogeny, biogeography and ecological diversification of Sarcocornia (Salicornioideae, Amaranthaceae)

    Science.gov (United States)

    Steffen, Simone; Ball, Peter; Mucina, Ladislav; Kadereit, Gudrun

    2015-01-01

    Background and Aims Sarcocornia comprises about 28 species of perennial succulent halophytes distributed worldwide, mainly in saline environments of warm-temperate and subtropical regions. The genus is characterized by strongly reduced leaves and flowers, which cause taxonomic difficulties; however, species in the genus show high diversity in growth form, with a mat-forming habit found in coastal salt marshes of all continents. Sarcocornia forms a monophyletic lineage with Salicornia whose species are all annual, yet the relationship between the two genera is poorly understood. This study is aimed at clarifying the phylogenetic relationship between Sarcocornia and Salicornia, interpreting biogeographical and ecological patterns in Sarcocornia, and gaining insights into putative parallel evolution of habit as an adaptation to environmental factors. Methods A comprehensively sampled and dated phylogeny of Sarcocornia is presented based on nuclear ribosomal DNA (external transcribed spacer) and chloroplast DNA (atpB-rbcL, rpl32-trnL) sequences; representative samples of Salicornia were also included in the analyses. To infer biogeographical patterns, an ancestral area reconstruction was conducted. Key Results The Sarcocornia/Salicornia lineage arose during the Mid-Miocene from Eurasian ancestors and diversified into four subclades: the Salicornia clade, the American Sarcocornia clade, the Eurasian Sarcocornia clade and the South African/Australian Sarcocornia clade. Sarcocornia is supported as paraphyletic, with Salicornia nested within Sarcocornia being sister to the American/Eurasian Sarcocornia clade. The American and the South African/Australian Sarcocornia clade as well as the Salicornia clade were reconstructed to be of Eurasian origin. The prostrate, mat-forming habit arose multiple times in Sarcocornia. Conclusions Sarcocornia diversified in salt-laden environments worldwide, repeatedly evolving superficially similar prostrate, mat-forming habits that seem

  9. Birth-death prior on phylogeny and speed dating

    Directory of Open Access Journals (Sweden)

    Sennblad Bengt

    2008-03-01

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

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

    NARCIS (Netherlands)

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

    2001-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Iulia Tutuianu

    2015-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Menicucci, D.F.

    1994-03-01

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

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

    Science.gov (United States)

    Ballard, Richard O.

    2007-01-01

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

  14. Human exposure to bovine polyomavirus: a zoonosis

    Energy Technology Data Exchange (ETDEWEB)

    Parry, J V; Gardner, S D

    1986-01-01

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

  15. Retinol improves bovine embryonic development in vitro

    Directory of Open Access Journals (Sweden)

    Edwards J Lannett

    2004-12-01

    Full Text Available Abstract Retinoids are recognized as important regulators of vertebrate development, cell differentiation, and tissue function. Previous studies, performed both in vivo and in vitro, indicate that retinoids influence several reproductive events, including follicular development, oocyte maturation and early embryonic development. The present study evaluated in vitro effects of retinol addition to media containing maturing bovine oocytes and developing embryos in both a low oxygen atmosphere (7% and under atmospheric oxygen conditions (20%. In the first experiment, abbatoir collected bovine oocytes were matured in the presence or absence of varying concentrations of retinol. After a 22–24 hour maturation period the oocytes were fertilized, denuded 18 hours later and cultured in a modified synthetic oviductal fluid (mSOF in a humidified atmosphere at 38.5 degrees C, 5% CO2, 7% O2 and 88% N2. Cleavage rates did not differ among control and retinol-treated oocytes in all three experiments. Addition of 5 micromolar retinol to the maturation medium (IVM tended (p

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

    Directory of Open Access Journals (Sweden)

    Yaobin Lu

    2014-12-01

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

  17. Message from the ISCB: 2015 ISCB Accomplishment by a Senior Scientist Award: Cyrus Chothia.

    Science.gov (United States)

    Fogg, Christiana N; Kovats, Diane E

    2015-07-01

    The International Society for Computational Biology (ISCB; http://www.iscb.org) honors a senior scientist annually for his or her outstanding achievements with the ISCB Accomplishment by a Senior Scientist Award. This award recognizes a leader in the field of computational biology for his or her significant contributions to the community through research, service and education. Cyrus Chothia, an emeritus scientist at the Medical Research Council Laboratory of Molecular Biology and emeritus fellow of Wolfson College at Cambridge University, England, is the 2015 ISCB Accomplishment by a Senior Scientist Award winner.Chothia was selected by the Awards Committee, which is chaired by Dr Bonnie Berger of the Massachusetts Institute of Technology. He will receive his award and deliver a keynote presentation at 2015 Intelligent Systems for Molecular Biology/European Conference on Computational Biology in Dublin, Ireland, in July 2015. dkovats@iscb.org. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. A Strategy for Accomplishing Human-Performance Monitoring of Constructing NPPs

    Energy Technology Data Exchange (ETDEWEB)

    Sung, Chanho; Jung, Yeonsub [KHNP Central Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    The main purpose of HPM(Human performance monitoring) is that no significant safety degradation occurs due to changes in design, procedures, training, or staffing during the plant operation. Accordingly, the strategy for accomplishing HPM should be to maintain the acceptable level of human performance for safety operation. This paper presents a strategy to fulfill HPM effectively for constructing NPPs in Korea. Activities for HPM in constructing plants need to be divided into two large parts on the basis of the fuel loading, which could be a good strategy to accomplish HPM effectively. That is, the activities such as making HPM plan and developing its indexes are performed before the fuel loading, while the activities of maintaining acceptable HP levels are conducted after the fuel loading. This HPM strategy includes not only maintaining the criteria of human performance established during ISV, but also improving human performance through existing activities during the plant operation. Constructing plants will also make actively use of the existing programs for enhancing human performance.

  19. Capacity of small groups of muscles to accomplish precision grasping tasks.

    Science.gov (United States)

    Towles, Joseph D; Valero-Cuevas, Francisco J; Hentz, Vincent R

    2013-01-01

    An understanding of the capacity or ability of various muscle groups to generate endpoint forces that enable grasping tasks could provide a stronger biomechanical basis for the design of reconstructive surgery or rehabilitation for the treatment of the paralyzed or paretic hand. We quantified two-dimensional endpoint force distributions for every combination of the muscles of the index finger, in cadaveric specimens, to understand the capability of muscle groups to produce endpoint forces that accomplish three common types of grasps-tripod, tip and lateral pinch-characterized by a representative level of Coulomb friction. We found that muscle groups of 4 or fewer muscles were capable of generating endpoint forces that enabled performance of each of the grasping tasks examined. We also found that flexor muscles were crucial to accomplish tripod pinch; intrinsic muscles, tip pinch; and the dorsal interosseus muscle, lateral pinch. The results of this study provide a basis for decision making in the design of reconstructive surgeries and rehabilitation approaches that attempt to restore the ability to perform grasping tasks with small groups of muscles.

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

    Science.gov (United States)

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

    2014-12-01

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

  1. Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom.

    Science.gov (United States)

    Bourlat, Sarah J; Nielsen, Claus; Economou, Andrew D; Telford, Maximilian J

    2008-10-01

    The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.

  2. Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

    Science.gov (United States)

    Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

    2018-01-01

    Abstract Background Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. PMID:29186447

  3. Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

    Science.gov (United States)

    Shen, Hui; Jin, Dongmei; Shu, Jiang-Ping; Zhou, Xi-Le; Lei, Ming; Wei, Ran; Shang, Hui; Wei, Hong-Jin; Zhang, Rui; Liu, Li; Gu, Yu-Feng; Zhang, Xian-Chun; Yan, Yue-Hong

    2018-02-01

    Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants. © The Authors 2017. Published by Oxford University Press.

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

    NARCIS (Netherlands)

    Bokma, Folmer

    2006-01-01

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

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

    Science.gov (United States)

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

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

    Science.gov (United States)

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

    2012-08-21

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

  7. A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotylenons

    DEFF Research Database (Denmark)

    Scarcelli, Nora; Bernaud, Adeline; Eiserhardt, Wolf L.

    2011-01-01

    Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we...... anticipate that it will also be useful for phylogeny and bar-coding studies....

  8. What do we know about the phylogeny of the semi-aquatic bugs (Hemiptera: Heteroptera: Gerromorpha)?

    DEFF Research Database (Denmark)

    Damgaard, Jakob

    2012-01-01

    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...

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

    Czech Academy of Sciences Publication Activity Database

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

    2011-01-01

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

  10. New insights in Russula subsect. Rubrinae: phylogeny and the quest for synapomorphic characters

    Czech Academy of Sciences Publication Activity Database

    Caboň, M.; Eberhardt, U.; Looney, B.; Hampe, F.; Kolařík, Miroslav; Jančovičová, S.; Verbeken, A.; Adamčík, S.

    2017-01-01

    Roč. 16, č. 9 (2017), s. 877-892 ISSN 1617-416X Grant - others:AV ČR(CZ) SAV-16-06 Program:Bilaterální spolupráce Institutional support: RVO:61388971 Keywords : Sulphovanillin * Incrustations * Multi-locus phylogeny Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 1.616, year: 2016

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

    Directory of Open Access Journals (Sweden)

    Ó'Fágáin Ciarán

    2008-03-01

    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.

  12. Molecular phylogeny and systematics of the Echinostomatoidea Looss, 1899 (Platyhelminthes: Digenea)

    Czech Academy of Sciences Publication Activity Database

    Tkach, V.V.; Kudlai, Olena; Kostadinova, Aneta

    2016-01-01

    Roč. 46, č. 3 (2016), s. 171-185 ISSN 0020-7519 R&D Projects: GA ČR(CZ) GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Echinostomatoidea * Molecular phylogeny * Systematics * Echinostomatidae (sensu stricto) * Caballerotrematidae n. fam. * Himasthlidae * Echinochasmidae * Host associations Subject RIV: EG - Zoology Impact factor: 3.730, year: 2016

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

    NARCIS (Netherlands)

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

    2007-01-01

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

  14. Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae)

    Czech Academy of Sciences Publication Activity Database

    Fehrer, Judith; Gemeinholzer, B.; Chrtek, Jindřich; Bräutigam, S.

    2007-01-01

    Roč. 42, - (2007), s. 347-361 ISSN 1055-7903 R&D Projects: GA MŽP SE/610/3/00 Institutional research plan: CEZ:AV0Z60050516 Keywords : molecular phylogeny * Hieracium * chloroplast capture Subject RIV: EF - Botanics Impact factor: 3.994, year: 2007

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 166, č. 6 (2015), s. 659-676 ISSN 1434-4610 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Apicomplexa * Coccidia * Goussia janae * phylogeny * ultrastructure * invasion * central carbon metabolism. Subject RIV: EG - Zoology Impact factor: 2.898, year: 2015

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

    Czech Academy of Sciences Publication Activity Database

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

    2009-01-01

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

  17. A mitochondrial DNA phylogeny of the endangered vipers of the Vipera ursinii complex

    Czech Academy of Sciences Publication Activity Database

    Gvoždík, Václav; Jandzik, D.; Cordos, B.; Řehák, I.; Kotlík, Petr

    2012-01-01

    Roč. 62, č. 3 (2012), s. 1019-1024 ISSN 1055-7903 R&D Projects: GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : Conservation * Meadow viper * Phylogeny * Steppe viper * Systematics * Vipera ursinii complex Subject RIV: EH - Ecology, Behaviour Impact factor: 4.066, year: 2012

  18. 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.

    2004-01-01

    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

  19. Phylogeny of European bat Lyssavirus 1 in Eptesicus isabellinus bats, Spain.

    Science.gov (United States)

    Vázquez-Moron, Sonia; Juste, Javier; Ibáñez, Carlos; Berciano, José M; Echevarria, Juan E

    2011-03-01

    To better understand the epidemiology of European bat lyssavirus 1 (EBLV-1) in Europe, we phylogenetically characterized Lyssavirus from Eptesicus isabellinus bats in Spain. An independent cluster of EBLV-1 possibly resulted from geographic isolation and association with a different reservoir from other European strains. EBLV-1 phylogeny is complex and probably associated with host evolutionary history.

  20. Phylogeny of European Bat Lyssavirus 1 in Eptesicus isabellinus Bats, Spain

    OpenAIRE

    Vázquez-Morón, Sonia; Juste, Javier; Ibáñez, Carlos; Berciano, José M.; Echevarría, Juan E.

    2011-01-01

    To better understand the epidemiology of European bat lyssavirus 1 (EBLV-1) in Europe, we phylogenetically characterized Lyssavirus from Eptesicus isabellinus bats in Spain. An independent cluster of EBLV-1 possibly resulted from geographic isolation and association with a different reservoir from other European strains. EBLV-1 phylogeny is complex and probably associated with host evolutionary history.

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

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Paul-André Calatayud

    2016-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2017-01-01

    Roč. 98, č. 2 (2017), s. 428-437 ISSN 0022-2372 Institutional support: RVO:60077344 Keywords : diversity * flying fox * mitochondrial DNA * phylogeny * Pteropus melanotus natalis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.630, year: 2016

  4. Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

    Czech Academy of Sciences Publication Activity Database

    Haddad, S.; Shin, S.; Lemmon, A. R.; Lemmon, E. M.; Švácha, Petr; Farrell, B.; Ślipiński, A.; Windsor, D.; McKenna, D. D.

    2018-01-01

    Roč. 43, č. 1 (2018), s. 68-89 ISSN 0307-6970 Institutional support: RVO:60077344 Keywords : Chrysomeloidea * Cerambycidae * molecular phylogeny Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 4.474, year: 2016 http://onlinelibrary.wiley.com/doi/10.1111/syen.12257/abstract

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

    NARCIS (Netherlands)

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

    2017-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2015-01-01

    Roč. 142, č. 10 (2015), s. 1278-1289 ISSN 0031-1820 R&D Projects: GA ČR GA524/06/0264; GA ČR GA206/09/0927 Institutional support: RVO:68081766 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.031, year: 2015

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    The phylogeny and resistance profiles of human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) sequences were compared among six patients with HIV-1 who had received numerous treatments. RNA and DNA fractions were obtained from concurrent blood and rectal biopsy...

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

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

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

  9. A six-gene phylogeny provides new insights into choanoflagellate evolution.

    Science.gov (United States)

    Carr, Martin; Richter, Daniel J; Fozouni, Parinaz; Smith, Timothy J; Jeuck, Alexandra; Leadbeater, Barry S C; Nitsche, Frank

    2017-02-01

    Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the choanoflagellates. We examine the distribution within choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the choanoflagellates. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Swain, Timothy D

    2018-01-01

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

  11. Molecular phylogeny of Acerentomidae (Protura), with description of Acerentuloides bernardi sp. nov. from North America

    Czech Academy of Sciences Publication Activity Database

    Shrubovych, J.; Starý, Josef; D'Haese, C.A.

    2017-01-01

    Roč. 100, č. 2 (2017), s. 433-443 ISSN 0015-4040 R&D Projects: GA MŠk ME08019 Institutional support: RVO:60077344 Keywords : Acerentulus * DNA barcoding * Indiana * phylogeny * Podolinella * USA Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 0.964, year: 2016

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

    Science.gov (United States)

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

    2014-01-01

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

  13. A novel molecular marker for the study of Neotropical cichlid phylogeny.

    Science.gov (United States)

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

    2015-12-22

    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.

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

    DEFF Research Database (Denmark)

    Frick, Holger; Scharff, Nikolaj

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Shailja Katoch

    2017-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Stajich Jason E

    2006-11-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    DEFF Research Database (Denmark)

    2009-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

    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 Caribbean

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

    Science.gov (United States)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    -containing fractions as well, such as skim milk and whey. Compositional and structural studies of the carbohydrates of bovine milk MUC15 showed that the glycans are composed of fucose, galactose, mannose, N-acetylgalactosamine, N-acetylglycosamine, and sialic acid. The carbohydrate was shown to constitute 65......% of the total molecular weight, and the molar ratios of the individual sugars to protein of the O-linked glycans were determined. The glycan structures of MUC15 were further studied by enzymatic deglycosylation experiments using different endo- and exoglycosidases as well as a panel of lectins. The N......-linked glycans. By comparing the results of peanut agglutinin lectin binding, enzymatic deglycosylation, and monosaccharide composition analysis, we concluded that bovine MUC15 also contains more complex O-glycans containing high amounts N-acetylglucosamine residues. Furthermore, a small subset of the O...

  2. [Antiviral activity of different drugs in vitro against viruses of bovine infectious rhinotracheitis and bovine diarrhea].

    Science.gov (United States)

    Glotov, A G; Glotova, T I; Sergeev, A A; Belkina, T V; Sergeev, A N

    2004-01-01

    In vitro experiments studied the antiviral activity of 11 different drugs against viruses of bovine infective rhinotracheitis (BIRT) and bovine viral diarrhea (BVD). The 50% inhibiting concentrations of the test agents were determined in the monolayers of MDBK and KCT cell cultures. Only did phosprenyl show a virucidal activity against BIRT virus. All the tested drugs significantly inhibited the reproduction of BIRT virus in the sensitive MDBK cell cultures. Thus, bromuridin, acyclovir, ribavirin and methisazonum inhibited the virus by > or = 100,000 times; liposomal ribavirin, gossypolum, anandinum, polyprenolum, phosprenyl, by 1000-10,000 times; eracond and argovit, by 100 times. In experiments on BVD virus, the cultured KCT cells displayed the antiviral activity of bromuridin, phosprenil, polyprenolum, methisazonum, acyclovir, gossypolum, argovit, and ribavirin (in two variants), which caused a statistically significant (100-10,000-fold) decrease in the productive activity of this virus. Eracond and anandid proved to be ineffective.

  3. Genome analysis of an atypical bovine pestivirus from fetal bovine serum.

    Science.gov (United States)

    Gao, Shandian; Du, Junzheng; Tian, Zhancheng; Xing, Shanshan; Chang, Huiyun; Liu, Guangyuan; Luo, Jianxun; Yin, Hong

    2016-08-01

    We report the complete genome sequence of a bovine pestivirus LVRI/cont-1 originated from a commercial batch of fetal bovine serum. Its complete genome consists of 12,282 nucleotides (nt), which contain an open reading frame (ORF) of 11,700 bp flanked by 5' and 3' untranslated regions (383 and 199 bp). The size of the 5'UTR and the individual protein coding region of LVRI/cont-1 are identical to those of the reference virus Th/04_KhonKaen, but it has a deletion of the first 56 nt in the 3'UTR. Alignment of the complete nucleotide sequence and phylogenetic analysis indicate that this viral isolate belongs to atypical pestiviruses.

  4. Bovine Mastitis Resistance: Novel Quantitative Trait Loci and the Role of Bovine Mammary Epithelial Cells

    OpenAIRE

    Kurz, Jacqueline P.

    2018-01-01

    Bovine mastitis, or inflammation of the mammary gland, has substantial economic and animal welfare implications. A genetic basis for mastitis resistance traits is recognized and can be used to guide selective breeding programs. The discovery of regions of the genome associated with mastitis resistance, and knowledge of the underlying molecular mechanisms responsible, can facilitate development of efficient mastitis control and therapeutic strategies. The objectives of this dissertation resear...

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

    Science.gov (United States)

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

    2016-01-01

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

  6. Seroprevalence of bovine immunodeficiency virus and bovine leukemia virus in draught animals in Cambodia.

    Science.gov (United States)

    Meas, S; Ohashi, K; Tum, S; Chhin, M; Te, K; Miura, K; Sugimoto, C; Onuma, M

    2000-07-01

    Since bovine immunodeficiency virus (BIV), known as bovine lentivirus, has been detected in dairy and beef cattle in various countries around the world, a prevalence study of antibodies to BIV and bovine leukemia virus (BLV) was conducted in draught animals in five provinces in Cambodia, where protozoan parasite infections were suspected in some animals. To clarify the status of draught animals including Haryana, Brahman, mixed-breed, local breed cattle and muscle water buffaloes, a total of 544 cattle and 42 buffaloes were tested, and 26.3 and 16.7%, respectively, were found positive for anti-BIV p26 antibodies determined by Western blotting. There were 5.3% positive for anti-BLV antibodies detected by immunodiffusion test among the cattle, but no reactors among buffaloes and no dual infection for both BIV and BLV was determined in this study. Peripheral blood mononuclear cells from BIV-seropositive cattle were found to have BIV-provirus DNA, as detected by polymerase chain reaction and subsequent Southern blot hybridization. This is the first evidence for the presence of BIV and BLV infections in draught animals in tropical countries such as Cambodia. This wide distribution of BIV suggests its association with problems in animal health as reported worldwide, and that a primary BIV infection can predispose death of affected animals by other aggressive pathogens or stresses.

  7. Heterologous expression of bovine lactoferricin in Pichia methanolica.

    Science.gov (United States)

    Wang, Haikuan; Zhao, Xinhuai; Lu, Fuping

    2007-06-01

    According to the bias of codon utilization of Pichia methanolica, a fragment encoding bovine lactoferricin has been cloned and expressed in the P. methanolica under the control of the alcohol oxidase promoter, which was followed by the Saccharomyces cerevisiae alpha-factor signal peptide. The alpha-factor signal peptide efficiently directed the secretion of bovine lactoferricin from the recombinant yeast cell. The recombinant bovine lactoferricin appears to be successfully expressed, as it displays antibacterial activity (antibacterial assay). Moreover, the identity of the recombinant product was estimated by Tricine-SDS-PAGE.

  8. Photochemistry of modified proteins benzophenone-containing bovine serum albumin

    International Nuclear Information System (INIS)

    Mariano, P.S.; Glover, G.I.; Wilkinson, T.J.

    1976-01-01

    The results of exploratory and mechanistic studies of the photochemistry of poly-p-benzoyl-acetimido-bovine serum albumin, a modified protein containing photoreactive and photosensitizing groups, are reported. Specifically described are recent findings concerning (1) the synthesis and characterization of a modified bovine serum albumin that contains benzophenone-like moieties, (2) the photochemistry of this modified protein which appeared to involve photoreductive coupling of the benzophenone chromophores to the protein backbone, and (3) triplet energy transfer from modified bovine serum albumin to small molecule acceptors resulting in quenching of the photoreaction. (author)

  9. Gabor Weber Local Descriptor for Bovine Iris Recognition

    Directory of Open Access Journals (Sweden)

    Shengnan Sun

    2013-01-01

    Full Text Available Iris recognition is a robust biometric technology. This paper proposes a novel local descriptor for bovine iris recognition, named Gabor Weber local descriptor (GWLD. We first compute the Gabor magnitude maps for the input bovine iris image, and then calculate the differential excitation and orientation for each pixel over each Gabor magnitude map. After that, we use these differential excitations and orientations to construct the GWLD histogram representation. Finally, histogram intersection is adopted to measure the similarity between different GWLD histograms. The experimental results on the SEU bovine iris database verify the representation power of our proposed local descriptor.

  10. LukMF′ is the major secreted leukocidin of bovine Staphylococcus aureus and is produced in vivo during bovine mastitis

    Science.gov (United States)

    Vrieling, Manouk; Boerhout, Eveline M.; van Wigcheren, Glenn F.; Koymans, Kirsten J.; Mols-Vorstermans, Tanja G.; de Haas, Carla J. C.; Aerts, Piet C.; Daemen, Ineke J. J. M.; van Kessel, Kok P. M.; Koets, Ad P.; Rutten, Victor P. M. G.; Nuijten, Piet J.M.; van Strijp, Jos A. G.; Benedictus, Lindert

    2016-01-01

    Staphylococcus aureus is a major human and animal pathogen and a common cause of mastitis in cattle. S. aureus secretes several leukocidins that target bovine neutrophils, crucial effector cells in the defence against bacterial pathogens. In this study, we investigated the role of staphylococcal leukocidins in the pathogenesis of bovine S. aureus disease. We show that LukAB, in contrast to the γ-hemolysins, LukED, and LukMF′, was unable to kill bovine neutrophils, and identified CXCR2 as a bovine receptor for HlgAB and LukED. Furthermore, we assessed functional leukocidin secretion by bovine mastitis isolates and observed that, although leukocidin production was strain dependent, LukMF′ was most abundantly secreted and the major toxin killing bovine neutrophils. To determine the role of LukMF′ in bovine mastitis, cattle were challenged with high (S1444) or intermediate (S1449, S1463) LukMF′-producing isolates. Only animals infected with S1444 developed severe clinical symptoms. Importantly, LukM was produced in vivo during the course of infection and levels in milk were associated with the severity of mastitis. Altogether, these findings underline the importance of LukMF′ as a virulence factor and support the development of therapeutic approaches targeting LukMF′ to control S. aureus mastitis in cattle. PMID:27886237

  11. Space Shuttle Program Primary Avionics Software System (PASS) Success Legacy -Major Accomplishments and Lessons Learned

    Science.gov (United States)

    Orr, James K.

    2010-01-01

    This presentation has shown the accomplishments of the PASS project over three decades and highlighted the lessons learned. Over the entire time, our goal has been to continuously improve our process, implement automation for both quality and increased productivity, and identify and remove all defects due to prior execution of a flawed process in addition to improving our processes following identification of significant process escapes. Morale and workforce instability have been issues, most significantly during 1993 to 1998 (period of consolidation in aerospace industry). The PASS project has also consulted with others, including the Software Engineering Institute, so as to be an early evaluator, adopter, and adapter of state-of-the-art software engineering innovations.

  12. Radiation safety training for industrial irradiators: What are we trying to accomplish?

    International Nuclear Information System (INIS)

    Smith, M.A.

    1998-01-01

    Radiation safety training at an industrial irradiator facility takes a different approach than the traditional methods and topics used at other facilities. Where the more routine industrial radiation users focus on standard training topics of contamination control, area surveys, and the traditional dogma of time, distance, and shielding, radiation safety in an industrial irradiation facility must be centered on preventing accidents. Because the primary methods for accomplishing that goal are engineering approaches such as safety system interlocks, training provided to facility personnel should address system operation and emergency actions. This presents challenges in delivering radiation safety training to an audience of varied educational and technical background where little to no commercially available training material specific to this type of operation exists

  13. Recent Accomplishments and Future Directions in US Fusion Safety & Environmental Program

    Energy Technology Data Exchange (ETDEWEB)

    David A. Petti; Brad J. Merrill; Phillip Sharpe; L. C. Cadwallader; L. El-Guebaly; S. Reyes

    2006-07-01

    The US fusion program has long recognized that the safety and environmental (S&E) potential of fusion can be attained by prudent materials selection, judicious design choices, and integration of safety requirements into the design of the facility. To achieve this goal, S&E research is focused on understanding the behavior of the largest sources of radioactive and hazardous materials in a fusion facility, understanding how energy sources in a fusion facility could mobilize those materials, developing integrated state of the art S&E computer codes and risk tools for safety assessment, and evaluating S&E issues associated with current fusion designs. In this paper, recent accomplishments are reviewed and future directions outlined.

  14. An accomplished teacher's use of scaffolding during a second-grade unit on designing games.

    Science.gov (United States)

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

    2012-06-01

    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.

  15. Status of selected ion flow tube MS: accomplishments and challenges in breath analysis and other areas.

    Science.gov (United States)

    Smith, David; Španěl, Patrik

    2016-06-01

    This article reflects our observations of recent accomplishments made using selected ion flow tube MS (SIFT-MS). Only brief descriptions are given of SIFT-MS as an analytical method and of the recent extensions to the underpinning analytical ion chemistry required to realize more robust analyses. The challenge of breath analysis is given special attention because, when achieved, it renders analysis of other air media relatively straightforward. Brief overviews are given of recent SIFT-MS breath analyses by leading research groups, noting the desirability of detection and quantification of single volatile biomarkers rather than reliance on statistical analyses, if breath analysis is to be accepted into clinical practice. A 'strengths, weaknesses, opportunities and threats' analysis of SIFT-MS is made, which should help to increase its utility for trace gas analysis.

  16. Accomplishing the Visions for Teacher Education Programs Advocated in the National Science Education Standards

    Science.gov (United States)

    Akcay, Hakan; Yager, Robert

    2010-10-01

    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.

  17. Tear and decohesion of bovine pericardial tissue.

    Science.gov (United States)

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

    2016-10-01

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Photodynamically generated bovine serum albumin radicals

    DEFF Research Database (Denmark)

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

    1998-01-01

    Porphyrin-sensitized photoxidation of bovine serum albumin (BSA) results in oxidation of the protein at (at least) two different, specific sites: the Cys-34 residue giving rise to a thiyl radical (RS.); and one or both of the tryptophan residues (Trp-134 and Trp-214) resulting in the formation...... of tertiary carbon-centred radicals and disruption of the tryptophan ring system. In the case of porphyrins such as hematoporphyrin, which bind at specific sites on BSA, these species appear to arise via long-range transfer of damage within the protein structure, as the binding site is some distance from...... the ultimate site of radical formation. This transfer of damage is shown to depend on a number of factors including the conformation of the protein, the presence of blocking groups and pH. Alteration of the protein conformation results in radical formation at additional (or alternative) sites, as does blocking...

  19. Radioimmunoassay for progesterone in bovine milk

    International Nuclear Information System (INIS)

    Ruiz, Miriam; Figueredo, Nancy; Castillo, Sonia; Pizarro

    2002-01-01

    A system for the measurement of progesterone in bovine milk by radioimmunoassay has been developed and validated. This assay includes an iodine tracer purified by HPLC, the standard prepared in fat-free milk and an antibody anti-progesterone combined with second antibody. The detection limit of the assay is at 0.2 nmol/L calculated from the maximum binding menus two standard deviations and the precision is satisfactory. In the recovery assay was used 4 milk different samples and the result was 98% of recuperation. The progesterone was determinate in milk samples from post-partum animals taking samples three times per week for 40 days. The assay is simple, rapid and possibility the progesterone measurement without sample dilution, distinguish the cyclic changes of this hormone that reflect the ovarian activity in the animals. (author)

  20. Radioimmunological progesteron determination in peripheral bovine blood

    International Nuclear Information System (INIS)

    Ender, M.

    1974-01-01

    A radioimmunological method of determination of the progesterone level in peripheral bovine blood is described which enables a monitoring of the corpus luteum function under varying conditions. There is no dependence of the corpus luteum function on the pituitary gland after endogenous prolactin inhibition with a synthetic prolactin inhibitor in the oestrus cycle and in the end-phase of gravidity. In hysterectomized animals, however, the inhibition of endogenous LH leads to luteolysis. The release of endogenous LH, induced by the administration of an LH release hormone, causes a short increase in progesterone production in the middle phase of the cycle only. The administration of exogenous glucocorticoids during the oestrus cycle did not influence the corpus luteum function. The method described is used in a field test to determine the right time for artificial insemination. There is a significant difference between the progesterone values of impregnated and non-pregnant animals at 16-18 days after insemination. (BSC/AK) [de

  1. Nucleolar ultrastructure in bovine nuclear transfer embryos

    DEFF Research Database (Denmark)

    Kanka, J; Smith, S D; Soloy, E

    1999-01-01

    in nuclear morphology as a transformation of the nucleolus precursor body into a functional rRNA synthesising nucleolus with a characteristic ultrastructure. We examined nucleolar ultrastructure in bovine in vitro produced (control) embryos and in nuclear transfer embryos reconstructed from a MII phase...... at 1 hr after fusion and, by 3 hr after fusion, it was restored again. At this time, the reticulated fibrillo-granular nucleolus had an almost round shape. The nucleolar precursor body seen in the two-cell stage nuclear transfer embryos consisted of intermingled filamentous components and secondary...... time intervals after fusion. In the two-cell stage nuclear transfer embryo, the originally reticulated nucleolus of the donor blastomere had changed into a typical nucleolar precursor body consisting of a homogeneous fibrillar structure. A primary vacuole appeared in the four-cell stage nuclear...

  2. Copy number variation in the bovine genome

    DEFF Research Database (Denmark)

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

    2010-01-01

    to genetic variation in cattle. Results We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation...... in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental...... duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences. Conclusions Together, this analysis provides a useful...

  3. Human bovine tuberculosis - remains in the differential.

    LENUS (Irish Health Repository)

    Bilal, Shaukat

    2010-11-01

    Mycobacterium bovis is a pathogen of cattle. The unpasteurized milk of affected cattle is a source of infection in humans. Despite the screening of cattle and the pasteurization of milk, M bovis has not been eradicated. A high index of clinical suspicion is needed in symptomatic patients with a history of possible exposure. At risk groups include animal workers, farmers, meat packers, vets and zoo keepers. Humans are usually infected by the aerosol route. We present two cases of human bovine tuberculosis. One was a presumptive case and the second was a confirmed case. Both responded well to antituberculous therapy. In the confirmed case, there was evidence of transmission to the partner living in the same house. Rifampicin prophylaxis was given to the exposed case. The M. bovis from the confirmed case was isoniazid resistant, in addition to having the well known resistance to pyrazinamide. Isoniazid resistance has been described before in those who are immunocompromised. We describe it in an immunocompetent patient.

  4. Affordability as a discursive accomplishment in a changing National Health Service.

    Science.gov (United States)

    Russell, Jill; Greenhalgh, Trisha

    2012-12-01

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

  5. Pathological studies on bovine viral diarrhea

    International Nuclear Information System (INIS)

    Elkady, A.A.M.A.

    2002-01-01

    Bovine viral diarrhea virus (BVDV) is classified as an RNA virus in the family flavin viride and is a member of the genus pest virus (Collet et al 1989). BVDV has a worldwide distribution and infections in cattle populations (Kahrs et al 1970). It was recognized since 50 years ago, the initial description of an acute enteric disease of cattle in North America, which was characterized by outbreaks of diarrhea and erosive of digestive tract (Olafsonp et al 1946). The disease and causative agent were named bovine viral diarrhea (B V D ) and (B V DV), respectively. This virus was subsequently associated with a sporadically occurring and highly fatal enteric disease that was termed mucosal disease (M D), (Ramsey and Chivers 1953). The initial isolate of BVDV did not produce cytopathic effect in cell culture, whereas an isolate from MD did produce cytopathic effects (Lee et al 1957). In vitro characteristic of non cytopathic or sytopathic effects of BVDV is referred to as the biotype of the virus. It has now been established that MD occurs only when xattle that are born immuno tolerant to and persistently infected with a noncyropathic BVDV become super infected with a cytopathic BVDV. The knowledge of the molecular biology. Pathogenesis and epidemiology of BVDV has greatly evolved in the past 10-15 years and has provided a better understanding of this complex infectious agent. Infection with BVDV can result in a wide spectrum of diseases ranging from subclinical infection s to a highly fatal from known as mucosal disease (ND). The clinical response to infection depends on multiple interactive factors. Host factors that influence the clinical outcome of BVDV infection include whether the host is immunocompetent or immuno tolerant to BVDV, pregnancy status, gestational age of the fetus, immune status (passively derived or actively derived from previous infection or vaccination) and concurrent level of environmental stress

  6. Nonenzymatic glycosylation of bovine myelin basic protein

    International Nuclear Information System (INIS)

    Hitz, J.B.

    1987-01-01

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

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

    Science.gov (United States)

    ... the CDC Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease Note: Javascript is disabled or is not ... spongiform encephalopathy) is a progressive neurological disorder of cattle that results from infection by an unusual transmissible ...

  8. Aspiration lung disorders in bovines: A case report and review

    Directory of Open Access Journals (Sweden)

    Anthony S. Shakespeare

    2012-04-01

    Full Text Available Lung aspiration disorders in bovines are invariably diagnosed as infectious aspiration pneumonias. There is a distinct differentiation between aspiration pneumonia and aspiration pneumonitis in humans that can be applied to bovines. The nature and quantity of the aspirate can result in differing pathogeneses which can require differing therapeutic approaches. Whilst blood gases were important in detecting and prognosticating lung problems, changes in barometric pressure with altitude have to be considered when interpreting partial pressures of oxygen. Anatomical differences in the lungs of bovines can explain why this species is more prone to certain pneumonic problems. Pulmonary physiotherapy is important in treating lung disorders in humans and should be considered as an adjunct therapy in bovine respiratory conditions. A case work-up was used to highlight some of the points discussed in this article.

  9. Aspiration lung disorders in bovines: A case report and review

    Directory of Open Access Journals (Sweden)

    Anthony S. Shakespeare

    2012-11-01

    Full Text Available Lung aspiration disorders in bovines are invariably diagnosed as infectious aspiration pneumonias. There is a distinct differentiation between aspiration pneumonia and aspiration pneumonitis in humans that can be applied to bovines. The nature and quantity of the aspirate can result in differing pathogeneses which can require differing therapeutic approaches. Whilst blood gases were important in detecting and prognosticating lung problems, changes in barometric pressure with altitude have to be considered when interpreting partial pressures of oxygen. Anatomical differences in the lungs of bovines can explain why this species is more prone to certain pneumonic problems. Pulmonary physiotherapy is important in treating lung disorders in humans and should be considered as an adjunct therapy in bovine respiratory conditions. A case work-up was used to highlight some of the points discussed in this article.

  10. Histologic and Immunohistochemical classification of 41 bovine adrenal gland neoplasms

    DEFF Research Database (Denmark)

    Grossi, Anette Blak; Leifsson, Páll S.; Jensen, Henrik Elvang

    2013-01-01

    . An immunohistochemistry panel consisting of antibodies against melan A, synaptophysin, and CNPase was considered most useful to classify bovine adrenal tumors. However, the distinction between benign and malignant adrenocortical tumors was based on histologic features as in human medicine....

  11. Cartilage (Bovine and Shark) (PDQ®)—Health Professional Version

    Science.gov (United States)

    Expert-reviewed information summary about the use of bovine and shark cartilage as a treatment for people with cancer. Note: The information in this summary is no longer being updated and is provided for reference purposes only.

  12. Recognizing the radiographic features of some common bovine foot problems

    International Nuclear Information System (INIS)

    Ebeid, M.; Steiner, A.

    1996-01-01

    Radiographs of an injured or infected bovine foot can be tricky to interpret - the anatomy is complex, and the signs may be subtle. This guide leads you through the classic radiographic features of several common foot conditions

  13. Prevalence of bovine mastitis and multi-antibiotic resistant ...

    African Journals Online (AJOL)

    Prevalence of bovine mastitis and multi-antibiotic resistant Staphylococcus and ... Bulletin of Animal Health and Production in Africa ... their antibiotic sensitivities and management practices of sahiwal and dairy cattle kept at a centre of Kenya ...

  14. Aspiration lung disorders in bovines: a case report and review.

    Science.gov (United States)

    Shakespeare, Anthony S

    2012-11-01

    Lung aspiration disorders in bovines are invariably diagnosed as infectious aspiration pneumonias. There is a distinct differentiation between aspiration pneumonia and aspiration pneumonitis in humans that can be applied to bovines. The nature and quantity of the aspirate can result in differing pathogeneses which can require differing therapeutic approaches. Whilst blood gases were important in detecting and prognosticating lung problems, changes in barometric pressure with altitude have to be considered when interpreting partial pressures of oxygen. Anatomical differences in the lungs of bovines can explain why this species is more prone to certain pneumonic problems. Pulmonary physiotherapy is important in treating lung disorders in humans and should be considered as an adjunct therapy in bovine respiratory conditions. A case work-up was used to highlight some of the points discussed in this article.

  15. Detection of genes associated with developmental competence of bovine oocytes

    Czech Academy of Sciences Publication Activity Database

    Němcová, Lucie; Jansová, Denisa; Vodičková Kepková, Kateřina; Vodička, Petr; Jeseta, M.; Machatková, M.; Kaňka, Jiří

    2016-01-01

    Roč. 166, č. 1 (2016), s. 58-71 ISSN 0378-4320 Institutional support: RVO:67985904 Keywords : oocyte * embryo * bovine * developmental competence * transcription Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.605, year: 2016

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

    Czech Academy of Sciences Publication Activity Database

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

    2012-01-01

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

  17. Characterization Of Bovine Adipose-Derived Stem Cells

    OpenAIRE

    Daniel Cebo

    2017-01-01

    Bovine adipose-derived stem cells were obtained from the subcutaneous abdominal adipose tissue. The cells were cultured by the modified tissue-explants method developed in our laboratory and then analyzed using optical microscopy and flow cytometry. These cells were able to replicate in our cell culture conditions. cell Flow cytometry showed that bovine adipose-derived stem cells expressed mesenchymal stem cell markers CD73 and CD90. Meanwhile haematopoietic markers CD45 and CD34 are absent f...

  18. Gabor Weber Local Descriptor for Bovine Iris Recognition

    OpenAIRE

    Sun, Shengnan; Zhao, Lindu; Yang, Shicai

    2013-01-01

    Iris recognition is a robust biometric technology. This paper proposes a novel local descriptor for bovine iris recognition, named Gabor Weber local descriptor (GWLD). We first compute the Gabor magnitude maps for the input bovine iris image, and then calculate the differential excitation and orientation for each pixel over each Gabor magnitude map. After that, we use these differential excitations and orientations to construct the GWLD histogram representation. Finally, histogram intersectio...

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

    African Journals Online (AJOL)

    Traitement De La Peripneumonie Contagieuse Bovine Par L'oxyteTracycline Longe Action Et Transmission Experimentale de la Maladie A Partir de Bovins Traites. ... Tous les 14 animaux ont séroconverti et l'analyse post-mortem a montré la présence des lésions chroniques dont des séquestres pulmonaires chez 4 d'entre ...

  20. Epidemiology of Bovine Mastitis in Cows of Dharwad District

    OpenAIRE

    Kurjogi, Mahantesh M.; Kaliwal, Basappa B.

    2014-01-01

    Bovine mastitis is very common in cows of both developed and developing countries. The prevalence of clinical and subclinical mastitis (SCM) varies from region to region. Hence, the present study was carried out to determine the prevalence of mastitis using three diagnostic tests by considering different risk factors like age, lactation, breed, season, quarters, and herd. The results showed that surf field mastitis test (SFMT) is the most sensitive test for diagnosis of bovine mastitis, the o...

  1. No evidence for a bovine mastitis Escherichia coli pathotype.

    Science.gov (United States)

    Leimbach, Andreas; Poehlein, Anja; Vollmers, John; Görlich, Dennis; Daniel, Rolf; Dobrindt, Ulrich

    2017-05-08

    Escherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result in the identification of common traits. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype has been proposed suggesting virulence traits that differentiate MAEC from commensal E. coli. The present study was designed to investigate the MPEC pathotype hypothesis by comparing the genomes of MAEC and commensal bovine E. coli. We sequenced the genomes of eight E. coli isolated from bovine mastitis cases and six fecal commensal isolates from udder-healthy cows. We analyzed the phylogenetic history of bovine E. coli genomes by supplementing this strain panel with eleven bovine-associated E. coli from public databases. The majority of the isolates originate from phylogroups A and B1, but neither MAEC nor commensal strains could be unambiguously distinguished by phylogenetic lineage. The gene content of both MAEC and commensal strains is highly diverse and dominated by their phylogenetic background. Although individual strains carry some typical E. coli virulence-associated genes, no traits important for pathogenicity could be specifically attributed to MAEC. Instead, both commensal strains and MAEC have very few gene families enriched in either pathotype. Only the aerobactin siderophore gene cluster was enriched in commensal E. coli within our strain panel. This is the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates. With our comparative genomics approach we could not confirm previous studies that argue for a positive selection of specific traits enabling MAEC to elicit bovine mastitis. Instead, MAEC are facultative and opportunistic pathogens recruited from the highly diverse bovine gastrointestinal microbiota. Virulence-associated genes implicated in mastitis are a by-product of commensalism with the primary function

  2. Bovine origin Staphylococcus aureus: A new zoonotic agent?

    Science.gov (United States)

    Rao, Relangi Tulasi; Jayakumar, Kannan; Kumar, Pavitra

    2017-10-01

    The study aimed to assess the nature of animal origin Staphylococcus aureus strains. The study has zoonotic importance and aimed to compare virulence between two different hosts, i.e., bovine and ovine origin. Conventional polymerase chain reaction-based methods used for the characterization of S. aureus strains and chick embryo model employed for the assessment of virulence capacity of strains. All statistical tests carried on R program, version 3.0.4. After initial screening and molecular characterization of the prevalence of S. aureus found to be 42.62% in bovine origin samples and 28.35% among ovine origin samples. Meanwhile, the methicillin-resistant S. aureus prevalence is found to be meager in both the hosts. Among the samples, only 6.8% isolates tested positive for methicillin resistance. The biofilm formation quantified and the variation compared among the host. A Welch two-sample t -test found to be statistically significant, t=2.3179, df=28.103, and p=0.02795. Chicken embryo model found effective to test the pathogenicity of the strains. The study helped to conclude healthy bovines can act as S. aureus reservoirs. Bovine origin S. aureus strains are more virulent than ovine origin strains. Bovine origin strains have high probability to become zoonotic pathogen. Further, gene knock out studies may be conducted to conclude zoonocity of the bovine origin strains.

  3. Bovine coronavirus antibody titers at weaning negatively correlate with incidence of bovine respiratory disease in the feed yard

    Science.gov (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. Professional conceptualisation and accomplishment of patient safety in mental healthcare: an ethnographic approach

    Directory of Open Access Journals (Sweden)

    Braithwaite Jeffrey

    2011-05-01

    Full Text Available Abstract Background This study seeks to broaden current understandings of what patient safety means in mental healthcare and how it is accomplished. We propose a qualitative observational study of how safety is produced or not produced in the complex context of everyday professional mental health practice. Such an approach intentionally contrasts with much patient safety research which assumes that safety is achieved and improved through top-down policy directives. We seek instead to understand and articulate the connections and dynamic interactions between people, materials, and organisational, legal, moral, professional and historical safety imperatives as they come together at particular times and places to perform safe or unsafe practice. As such we advocate an understanding of patient safety 'from the ground up'. Methods/Design The proposed project employs a six-phase data collection framework in two mental health settings: an inpatient unit and a community team. The first four phases comprise multiple modes of focussed, unobtrusive observation of professionals at work, to enable us to trace the conceptualisation and enactment of safety as revealed in dialogue and narrative, use of artefacts and space, bodily activity and patterns of movement, and in the accomplishment of specific work tasks. An interview phase and a social network analysis phase will subsequently be conducted to offer comparative perspectives on the observational data. This multi-modal and holistic approach to studying patient safety will complement existing research, which is dominated by instrumentalist approaches to discovering factors contributing to error, or developing interventions to prevent or manage adverse events. Discussion This ethnographic research framework, informed by the principles of practice theories and in particular actor-network ideas, provides a tool to aid the understanding of patient safety in mental healthcare. The approach is novel in that it

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

    Science.gov (United States)

    2011-01-01

    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 seeks to articulate an 'anatomy

  6. Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

    Science.gov (United States)

    Zhang, Yan-Cong; Lin, Kui

    2015-01-01

    Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

  7. Proteomic characterisation of bovine and avian purified protein derivatives and identification of specific antigens for serodiagnosis of bovine tuberculosis

    OpenAIRE

    Infantes-Lorenzo, José Antonio; Moreno, Inmaculada; Risalde, María de los Ángeles; Roy, Álvaro; Villar, Margarita; Romero, Beatriz; Ibarrola, Nieves; de la Fuente, José; Puentes, Eugenia; de Juan, Lucía; Gortázar, Christian; Bezos, Javier; Domínguez, Lucas; Domínguez, Mercedes

    2017-01-01

    Background Bovine purified protein derivative (bPPD) and avian purified protein derivative (aPPD) are widely used for bovine tuberculosis diagnosis. However, little is known about their qualitative and quantitative characteristics, which makes their standardisation difficult. In addition, bPPD can give false-positive tuberculosis results because of sequence homology between Mycobacterium bovis (M. bovis) and M. avium proteins. Thus, the objective of this study was to carry out a proteomic cha...

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

    DEFF Research Database (Denmark)

    Fredslund, Jakob

    2006-01-01

    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...... 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...... 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...

  9. Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China.

    Science.gov (United States)

    Feng, Shang-Guo; Lu, Jiang-Jie; Gao, Ling; Liu, Jun-Jun; Wang, Hui-Zhong

    2014-04-01

    Dendrobium plants are important commercial herbs in China, widely used in traditional medicine and ornamental horticulture. In this study, sequence-related amplified polymorphism (SRAP) markers were applied to molecular phylogeny analysis and species identification of 31 Chinese Dendrobium species. Fourteen SRAP primer pairs produced 727 loci, 97% of which (706) showed polymorphism. Average polymorphism information content of the SRAP pairs was 0.987 (0.982-0.991), showing that plenty of genetic diversity exists at the interspecies level of Chinese Dendrobium. The molecular phylogeny analysis (UPGMA) grouped the 31 Dendrobium species into six clusters. We obtained 18 species-specific markers, which can be used to identify 10 of the 31 species. Our results indicate the SRAP marker system is informative and would facilitate further application in germplasm appraisal, evolution, and genetic diversity studies in the genus Dendrobium.

  10. KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

    Science.gov (United States)

    Wang, Dapeng; Xu, Jiayue; Yu, Jun

    2015-09-16

    The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

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

    Science.gov (United States)

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

    2003-01-01

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

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

    Science.gov (United States)

    Suh, Siri

    2018-06-01

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

  13. International Space Station Research for the Next Decade: International Coordination and Research Accomplishments

    Science.gov (United States)

    Thumm, Tracy L.; Robinson, Julie A.; Johnson-Green, Perry; Buckley, Nicole; Karabadzhak, George; Nakamura, Tai; Sorokin, Igor V.; Zell, Martin; Sabbagh, Jean

    2011-01-01

    During 2011, the International Space Station reached an important milestone in the completion of assembly and the shift to the focus on a full and continuous utilization mission in space. The ISS partnership itself has also met a milestone in the coordination and cooperation of utilization activities including research, technology development and education. We plan and track all ISS utilization activities jointly and have structures in place to cooperate on common goals by sharing ISS assets and resources, and extend the impacts and efficiency of utilization activities. The basic utilization areas on the ISS include research, technology development and testing, and education/outreach. Research can be categorized as applied research for future exploration, basic research taking advantage of the microgravity and open space environment, and Industrial R&D / commercial research focused at industrial product development and improvement. Technology development activities range from testing of new spacecraft systems and materials to the use of ISS as an analogue for future exploration missions to destinations beyond Earth orbit. This presentation, made jointly by all ISS international partners, will highlight the ways that international cooperation in all of these areas is achieved, and the overall accomplishments that have come as well as future perspectives from the cooperation. Recently, the partnership has made special efforts to increase the coordination and impact of ISS utilization that has humanitarian benefits. In this context the paper will highlight tentative ISS utilization developments in the areas of Earth remote sensing, medical technology transfer, and education/outreach.

  14. Task III: UCSD/DIII-D/Textor FY-97-98 Accomplishments

    International Nuclear Information System (INIS)

    Boedo, J.A.

    2000-01-01

    OAK (B204) Task III: UCSD/DIII-D/Textor FY-97-98 Accomplishments. A comprehensive report on the physics of pump limiters and particularly, the characterization of ALT-II, was published in Nuclear Fusion, bringing the project to a closure. The performance of the toroidal pump limiter was characterized under full auxiliary heating of 7 MW of NBI and ICRH and full pumping, as stated in the project milestones. Relevant highlights are: (1) Pumping with ALT-II allows for density control. (2) The achieved exhaust efficiency is 4% during NBI operation and near 2% during OH or ICRH operation. (3) We have shown that an exhaust efficiency of 2% is sufficient to satisfy the ash removal requirements of fusion reactors. (4) The plasma particle efflux and the pumped flux both increase with density and heating power. (5) The particle confinement time is less than the energy confinement time by a factor of 4. In summary, pumped belt limiters could provide the density control and ash exhaust requirements of fusion reactors

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    In April 1992, Argonne National Laboratory (ANL) launched the implementation of quality management (QM) as an initiative of the Laboratory Director. The goal of the program is to seek ways of improving Laboratory performance and effectiveness by drawing from the realm of experiences in the global total quality management movement. The Argonne QM initiative began with fact finding and formulating a strategy for implementation; the emphasis is that the underlying principles of QM should be an integral part of how the Laboratory is managed and operated. A primary theme that has guided the Argonne QM initiative is to consider only those practices that offer the potential for real improvement, make sense, fit the culture, and would be credible to the broad population. In October 1993, the Laboratory began to pilot a targeted set of QM activities selected to produce outcomes important to the Laboratory--strengthening the customer focus, improving work processes, enhancing employee involvement and satisfaction, and institutionalizing QM. This report describes the results of the just-concluded QM development and demonstration phase in terms of detailed strategies, accomplishments, and lessons learned. These results are offered as evidence to support the conclusion that the Argonne QM initiative has achieved value-added results and credibility and is well positioned to support future deployment across the entire Laboratory as an integrated management initiative. Recommendations for follow-on actions to implement future deployment are provided separately.

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

    International Nuclear Information System (INIS)

    1994-06-01

    This proposal presents the research accomplishments and ongoing activities of Boston University researchers in high energy physics. Some changes have been made in the structure of the program from the previous arrangement of tasks. Task B, Accelerator Design Physics, is being submitted as a separate proposal for an independent grant; this will be consistent with the nature of the research and the source of funding. Boston University is active in seven principal areas: (1) Task A: Colliding Beams -- physics of e + e - and anti pp collisions; (2) Task C: MACRO Experiment -- search for magnetic monopoles and study of cosmic rays; (3) Task D: Proton Decay -- search for nucleon instability and study of neutrino interactions; (4) Tasks E, J, and N: Particle Theory -- theoretical high energy particle physics, including two Outstanding Junior Investigator awards; (5) Task F: Muon G-2 -- measurement of the anomalous magnetic moment of the muon; (6) Task K: SSCintcal -- calorimetry for the GEM Experiment; (7) Task L: Muon Detectors for the GEM Experiment. The body of the proposal is devoted to detailed discussions of each of the tasks. The total budget request for the program appears in a summary chapter that includes a general budget discussion and individual budget requests and explanations for each of the tasks

  17. Predictors of systolic BP benazepril plus amlodipine or hydrochlorothiazide) in the ACCOMPLISH Study.

    Science.gov (United States)

    Kjeldsen, Sverre E; Jamerson, Kenneth A; Bakris, George L; Pitt, Bertram; Dahlöf, Björn; Velazquez, Eric J; Hua, Tsushung A; Kelly, Roxzana Y; Zappe, Dion; Hester, Allen; Tuomilehto, Jaakko; Ostergren, Jan; Ibsen, Hans; Weber, Michael

    2012-04-01

    The ACCOMPLISH Trial investigated intensive antihypertensive combination treatment with benazepril + amlodipine (B+A) or benazepril + hydrochlorothiazide (B+H) on cardiovascular outcomes in patients with systolic hypertension. We analyzed the baseline predictors of achieving a systolic blood pressure (SBP) Nordic region) and Caucasian ethnicity in both randomization arms. A higher diastolic BP and the use of lipid lowering agents indicated favorable effects in the B+H arm only. The predictors of uncontrolled SBP were: (i) higher baseline SBP values, (ii) higher number of previous antihypertensive medications in both arms, (iii) the previous use of insulin in the B+A arm, and (iv) pre-trial calcium channel blocker (CCB) use in the B+H arm. Additionally, pre-trial use of thiazides and electrocardiogram (ECG)-left ventricular hypertrophy (LVH) at baseline predicted higher, and smoking lower absolute SBP in the B+A arm and the use of thiazides and proteinuria a higher SBP in the B+H arm. Irrespective of treatment, patients in the USA and Caucasians achieved better SBP control, whereas higher baseline SBP and more previous antihypertensive medications indicated less control. Concomitant use of lipid lowering treatment indicated a better SBP control in the benazepril + hydrochlorothiazide arm. Lastly, insulin use and ECG-LVH in the benazepril + amlodipine arm and proteinuria in the benazepril + hydrochlorothiazide arm indicated poor control.

  18. Task V of the IEA Photovoltaic Power Systems Program: Accomplishments and Activities

    International Nuclear Information System (INIS)

    Bower, Ward

    1999-01-01

    The International Energy Agency (IEA) is an energy forum for 24 industrialized countries and was established in 1974 as an autonomous body within the Organization for Economic Cooperation and Development (OECD). The IEA Photovoltaic Power Systems (PVPS) program implementing agreement was signed in 1993, and renewed for another five years in 1998. Twenty-two countries are collaborating under the auspices of the IEA in the PVPS to address common technical and informational barriers that often limit the rate at which photovoltaic technologies advance into the markets. Task V of the IEA PVPS is entitled ''Grid Interconnection of Building-Integrated and Other Dispersed Photovoltaic Power Systems.'' The task sponsored a workshop in September 1997 on grid-interconnection of photovoltaic systems and is planning a second workshop to address impacts of more penetration of dispersed systems into the utility grid. This paper will summarize the accomplishments of Task V over the last five years and will detail the planned work for the next three years

  19. Preliminary quality assessment of bovine colostrum

    Directory of Open Access Journals (Sweden)

    Alessandro Taranto

    2013-02-01

    Full Text Available Data on bovine colostrum quality are scarce or absent, although Commission Regulations No 1662/2006 and No 1663/2006 include colostrum in the context of chapters on milk. Thus the aim of the present work is to study some physical, chemical, hygiene and safety quality parameters of bovine colostrum samples collected from Sicily and Calabria dairy herds. Thirty individual samples were sampled after 2-3 days from partum. The laboratory tests included: pH, fat (FT, total nitrogen (TN, lactose (LTS and dry matter (NM percentage (Lactostar and somatic cell count (CCS (DeLaval cell counter DCC. Bacterial counts included: standard plate count (SPC, total psychrophilic aerobic count (PAC, total, fecal coliforms by MPN (Most Probable Number, sulphite-reducing bacteria (SR. Salmonella spp. was determined. Bacteriological examinations were performed according to the American Public Health Association (APHA methods, with some adjustements related to the requirements of the study. Statistical analysis of data was performed by Spearman’s rank correlation coefficient. The results showed a low variability of pH values and FT, TN and DM percentage between samples; whereas LTS trend was less noticeable. A significant negative correlation (P<0.01 was observed between pH, TN and LTS amount. The correlation between LTS and TN contents was highly significant (P<0.001. Highly significant and negative was the correlation (P<0.001 between DM, NT and LTS content. SPC mean values were 7.54 x106 CFU/mL; PAC mean values were also high (3.3x106 CFU/mL. Acceptable values of coagulase positive staphylococci were showed; 3 Staphylococcus aureus and 1 Staphylococcus epidermidis strains was isolated. Coagulase negative staphylococci counts were low. A high variability in the number of TC, as for FC was observed; bacterial loads were frequently fairly high. Salmonella spp. and SR bacteria were absent. It was assumed that bacteria from samples had a prevailing environmental origin

  20. Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

    Czech Academy of Sciences Publication Activity Database

    Musilová, Zuzana; Říčan, Oldřich; Janko, Karel; Novák, J.

    2008-01-01

    Roč. 46, - (2008), s. 659-672 ISSN 1055-7903 R&D Projects: GA MŠk LC06073 Grant - others:GA UK(CZ) 182/2004/B-BIO; GA UK(CZ) 139407 Institutional research plan: CEZ:AV0Z50450515 Keywords : molecular phylogeny * Cichlids * south America Subject RIV: EG - Zoology Impact factor: 3.871, year: 2008

  1. The phylogeny of Goussia and Choleoeimeria (Apicomplexa; Eimeriorina) and the evolution of excystation structures in coccidia

    Czech Academy of Sciences Publication Activity Database

    Jirků, Milan; Modrý, David; Šlapeta, Jan Roger; Koudela, Břetislav; Lukeš, Julius

    2002-01-01

    Roč. 153, č. 4 (2002), s. 379-390 ISSN 1434-4610 R&D Projects: GA AV ČR KSK6005114; GA ČR GA524/00/P015 Institutional research plan: CEZ:AV0Z6022909 Keywords : SSU rDNA * coccidia * phylogeny Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.617, year: 2002

  2. Morphology, ecology and phylogeny of cyanobacteria belonging to genera Nostoc and Desmonostoc in Lithuania

    OpenAIRE

    Špakaitė, Ina

    2014-01-01

    The aim of the study was to investigate the morphology, ecology and phylogeny of cyanobacteria belonging to genera Nostoc and Desmonostoc in Lithuania. The detailed research of freshwater and terrestrial Nostoc and Desmonostoc species provided new data on taxonomy, biology and ecology of these cyanobacteria and the overall diversity of algae in Lithuania. 20 Nostoc species and two intraspecific taxa, and 18 taxa to the Nostoc genus level were identified. Twelve Nostoc species and intraspecifi...

  3. The phylogeny of Myxosporea (Myxozoa) based on small subunit ribosomal RNA gene analysis

    Czech Academy of Sciences Publication Activity Database

    Fiala, Ivan

    2006-01-01

    Roč. 36, č. 14 (2006), s. 1521-1534 ISSN 0020-7519 R&D Projects: GA MŠk LC522 Grant - others:Grantová agentura Jihočeské univerzity(CZ) 58/2002//P-BF Institutional research plan: CEZ:AV0Z60220518 Keywords : Myxosporea * SSU rDNA * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.337, year: 2006

  4. Phylogeny and sequence variability of the Sarcocystis singaporensis Zaman and Colley, (1975) 1976 ssrDNA

    Czech Academy of Sciences Publication Activity Database

    Šlapeta, Jan Roger; Kyselová, Iveta; Richardson, A. O.; Modrý, David; Lukeš, Julius

    2002-01-01

    Roč. 88, č. 9 (2002), s. 810-815 ISSN 0932-0113 R&D Projects: GA ČR GA524/00/P015; GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6022909 Keywords : Sarcocystis * phylogeny * ssrDNA Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.046, year: 2002

  5. Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers

    OpenAIRE

    Khan, Haseeb A.; Arif, Ibrahim A.; Bahkali, Ali H.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.

    2008-01-01

    This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to B...

  6. PHY·FI: fast and easy online creation and manipulation of phylogeny color figures

    Directory of Open Access Journals (Sweden)

    Fredslund Jakob

    2006-06-01

    Full Text Available Abstract Background The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. Results This paper presents an online tool, PHY·FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY·FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates". The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. Conclusion PHY·FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY·FI is free for all and is available from this web address: http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go

  7. Evidence of host specificity and congruence between phylogenies of bitterling and freshwater mussels

    Czech Academy of Sciences Publication Activity Database

    Liu, H.-Z.; Zhu, Y.-R.; Smith, C.; Reichard, Martin

    2006-01-01

    Roč. 45, č. 3 (2006), s. 428-434 ISSN 1021-5506 Grant - others:NSFC(CN) 30470237; NSFC(CN) 40432003; Innovation Program of the Chinese Academy of Sciences(CN) KZCX3-SW-126 Institutional research plan: CEZ:AV0Z60930519 Keywords : bitterling * host specificity * coevolution * phylogeny Subject RIV: EG - Zoology Impact factor: 0.943, year: 2006 http://zoolstud.sinica.edu.tw/Journals/45.3/428.pdf

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

    Czech Academy of Sciences Publication Activity Database

    Doležalová, J.; Vallo, P.; Petrželková, Klára Judita; Foitová, I.; Nurcahyo, W.; Mudakikwa, A.; Hashimoto, C.; Jirků, Milan; Lukeš, Julius; Scholz, Tomáš; Modrý, David

    2015-01-01

    Roč. 142, č. 10 (2015), s. 1278-1289 ISSN 0031-1820 R&D Projects: GA MŠk(CZ) EE2.3.30.0032; GA ČR GA206/09/0927 Institutional support: RVO:60077344 Keywords : Bertiella * Anoplocephala * phylogeny * primates * zoonotic potential Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.031, year: 2015

  9. Phylogeny of the Southeast Asian freshwater fish genus Pangio (Cypriniformes, Cobitidae)

    Czech Academy of Sciences Publication Activity Database

    Bohlen, Jörg; Šlechtová, Vendula; Tan, H. H.; Britz, R.

    2011-01-01

    Roč. 61, č. 3 (2011), s. 854-865 ISSN 1055-7903 R&D Projects: GA ČR GA206/05/2556; GA ČR GA206/08/0637; GA AV ČR IAA600450508; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z50450515 Keywords : pangio * eel loaches * phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.609, year: 2011

  10. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.

    Directory of Open Access Journals (Sweden)

    Emmanuelle Lerat

    2003-10-01

    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.

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

    Science.gov (United States)

    2013-01-01

    Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. PMID:23627680

  12. Identification and phylogeny of the tomato receptor-like proteins family

    OpenAIRE

    Ermis Yanes-Paz; Gioser María Ramos-Echazábal; Glay Chinea; Yanelis Capdesuñer Ruiz; Ramón Santos Bermúdez

    2017-01-01

    The receptor-like proteins (RLPs) play multiple roles in development and defense. In the current work 75 RLPs were identified in tomato (Solanum lycopersicum L.) using iterative BLAST searches and domain prediction. A phylogenetic tree including all the identified RLPs from tomato and some functionally characterized RLPs from other species was built to identify their putative homologues in tomato. We first tested whether C3-F-based phylogeny was a good indicator of functional relation between...

  13. Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy.

    Science.gov (United States)

    Xia, Rong; Durand, Jean-Dominique; Fu, Cuizhang

    2016-03-01

    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. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. A preliminary molecular phylogeny of shield-bearer moths (Lepidoptera: Adeloidea: Heliozelidae) highlights rich undescribed diversity.

    Science.gov (United States)

    Milla, Liz; van Nieukerken, Erik J; Vijverberg, Ruben; Doorenweerd, Camiel; Wilcox, Stephen A; Halsey, Mike; Young, David A; Jones, Therésa M; Kallies, Axel; Hilton, Douglas J

    2018-03-01

    Heliozelidae are a widespread, evolutionarily early diverging family of small, day-flying monotrysian moths, for which a comprehensive phylogeny is lacking. We generated the first molecular phylogeny of the family using DNA sequences of two mitochondrial genes (COI and COII) and two nuclear genes (H3 and 28S) from 130 Heliozelidae specimens, including eight of the twelve known genera: Antispila, Antispilina, Coptodisca, Heliozela, Holocacista, Hoplophanes, Pseliastis, and Tyriozela. Our results provide strong support for five major Heliozelidae clades: (i) a large widespread clade containing the leaf-mining genera Antispilina, Coptodisca and Holocacista and some species of Antispila, (ii) a clade containing most of the described Antispila, (iii) a clade containing the leaf-mining genus Heliozela and the monotypic genus Tyriozela, (iv) an Australian clade containing Pseliastis and (v) an Australian clade containing Hoplophanes. Each clade includes several new species and potentially new genera. Collectively, our data uncover a rich and undescribed diversity that appears to be especially prevalent in Australia. Our work highlights the need for a major taxonomic revision of the family and for generating a robust molecular phylogeny using multi-gene approaches in order to resolve the relationships among clades. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Synthesis of phylogeny and taxonomy into a comprehensive tree of life

    Science.gov (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.

    2015-01-01

    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. PMID:26385966

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

    Directory of Open Access Journals (Sweden)

    Michelle Klein Sercundes

    2016-03-01

    Full Text Available Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC and beta subunit of RNA polymerase (rpoB, and mitochondrial gene coding for cytochrome B (cytB were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG, Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

  17. Using genomic data to unravel the root of the placental mammal phylogeny.

    Science.gov (United States)

    Murphy, William J; Pringle, Thomas H; Crider, Tess A; Springer, Mark S; Miller, Webb

    2007-04-01

    The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals approximately 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.

  18. Host and parasite morphology influence congruence between host and parasite phylogenies.

    Science.gov (United States)

    Sweet, Andrew D; Bush, Sarah E; Gustafsson, Daniel R; Allen, Julie M; DiBlasi, Emily; Skeen, Heather R; Weckstein, Jason D; Johnson, Kevin P

    2018-03-23

    Comparisons of host and parasite phylogenies often show varying degrees of phylogenetic congruence. However, few studies have rigorously explored the factors driving this variation. Multiple factors such as host or parasite morphology may govern the degree of phylogenetic congruence. An ideal analysis for understanding the factors correlated with congruence would focus on a diverse host-parasite system for increased variation and statistical power. In this study, we focused on the Brueelia-complex, a diverse and widespread group of feather lice that primarily parasitise songbirds. We generated a molecular phylogeny of the lice and compared this tree with a phylogeny of their avian hosts. We also tested for the contribution of each host-parasite association to the overall congruence. The two trees overall were significantly congruent, but the contribution of individual associations to this congruence varied. To understand this variation, we developed a novel approach to test whether host, parasite or biogeographic factors were statistically associated with patterns of congruence. Both host plumage dimorphism and parasite ecomorphology were associated with patterns of congruence, whereas host body size, other plumage traits and biogeography were not. Our results lay the framework for future studies to further elucidate how these factors influence the process of host-parasite coevolution. Copyright © 2018 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  19. Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

    Science.gov (United States)

    Covain, Raphaël; Fisch-Muller, Sonia; Oliveira, Claudio; Mol, Jan H; Montoya-Burgos, Juan I; Dray, Stéphane

    2016-01-01

    The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

    Science.gov (United States)

    Hale, Vanessa L; Tan, Chia L; Niu, Kefeng; Yang, Yeqin; Knight, Rob; Zhang, Qikun; Cui, Duoying; Amato, Katherine R

    2018-02-01

    Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza). Monkeys were housed at five different captive institutes: Panxi Wildlife Rescue Center (Guizhou, China), Beijing Zoo, Beijing Zoo Breeding Center, Singapore Zoo, and Singapore Zoo Primate Conservation Breeding Center. Captive diets varied widely between institutions, but within an institution, all colobine monkey species were fed nearly identical or identical diets. In addition, four monkey species were present at multiple captive institutes. This allowed us to parse the effects of diet and phylogeny in these captive colobines. Gut microbial communities clustered weakly by host species and strongly by diet, and overall, colobine phylogenetic relationships were not reflected in gut microbiota analyses. Core microbiota analyses also identified several key taxa-including microbes within the Ruminococcaceae and Lachnospiraceae families-that were shared by over 90% of the monkeys in this study. Microbial species within these families include many butyrate producers that are important for GI health. These results highlight the importance of diet in captive colobines.