WorldWideScience

Sample records for genome era gene-orchestrated

  1. Isotope-based medical research in the post genome era: Gene-orchestrated life functions in medicine seen and affected by isotopes. Workshop report

    International Nuclear Information System (INIS)

    Feinendegen, L.E.

    1997-01-01

    The US Department of Energy (DOE) and the National Institutes of Health (NIH) conducted a workshop on Isotope-Based Medical Research in the Post Genome Era at NIH, Bethesda, Maryland, November 12--14, 1997. The workshop aimed at identifying the role of stable and radioisotopes for advanced diagnosis and therapy of a wide range of illnesses using the new information that comes from the human genome program. In this sense, the agenda addressed the challenge of functional genomics in humans. The workshop addressed: functional genomics in clinical medicine; new diagnostic potentials; new therapy potentials; challenge to tracer- and effector-pharmaceutical chemistry; and project plans for joint ventures

  2. Isotope-based medical research in the post genome era: Gene-orchestrated life functions in medicine seen and affected by isotopes. Workshop report

    Energy Technology Data Exchange (ETDEWEB)

    Feinendegen, L.E.

    1997-12-31

    The US Department of Energy (DOE) and the National Institutes of Health (NIH) conducted a workshop on Isotope-Based Medical Research in the Post Genome Era at NIH, Bethesda, Maryland, November 12--14, 1997. The workshop aimed at identifying the role of stable and radioisotopes for advanced diagnosis and therapy of a wide range of illnesses using the new information that comes from the human genome program. In this sense, the agenda addressed the challenge of functional genomics in humans. The workshop addressed: functional genomics in clinical medicine; new diagnostic potentials; new therapy potentials; challenge to tracer- and effector-pharmaceutical chemistry; and project plans for joint ventures.

  3. Privacy in the Genomic Era.

    Science.gov (United States)

    Naveed, Muhammad; Ayday, Erman; Clayton, Ellen W; Fellay, Jacques; Gunter, Carl A; Hubaux, Jean-Pierre; Malin, Bradley A; Wang, Xiaofeng

    2015-09-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.

  4. Privacy in the Genomic Era

    Science.gov (United States)

    NAVEED, MUHAMMAD; AYDAY, ERMAN; CLAYTON, ELLEN W.; FELLAY, JACQUES; GUNTER, CARL A.; HUBAUX, JEAN-PIERRE; MALIN, BRADLEY A.; WANG, XIAOFENG

    2015-01-01

    Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. PMID:26640318

  5. Molecular anthropology in the genomic era.

    Science.gov (United States)

    Destro-Bisol, Giovanni; Jobling, Mark A; Rocha, Jorge; Novembre, John; Richards, Martin B; Mulligan, Connie; Batini, Chiara; Manni, Franz

    2010-01-01

    Molecular Anthropology is a relatively young field of research. In fact, less than 50 years have passed since the symposium "Classification and Human Evolution" (1962, Burg Wartenstein, Austria), where the term was formally introduced by Emil Zuckerkandl. In this time, Molecular Anthropology has developed both methodologically and theoretically and extended its applications, so covering key aspects of human evolution such as the reconstruction of the history of human populations and peopling processes, the characterization of DNA in extinct humans and the role of adaptive processes in shaping the genetic diversity of our species. In the current scientific panorama, molecular anthropologists have to face a double challenge. As members of the anthropological community, we are strongly committed to the integration of biological findings and other lines of evidence (e.g. linguistic and archaeological), while keeping in line with methodological innovations which are moving the approach from the genetic to the genomic level. In this framework, the meeting "DNA Polymorphisms in Human Populations: Molecular Anthropology in the Genomic Era" (Rome, December 3-5, 2009) offered an opportunity for discussion among scholars from different disciplines, while paying attention to the impact of recent methodological innovations. Here we present an overview of the meeting and discuss perspectives and prospects of Molecular Anthropology in the genomic era.

  6. Cardiovascular Precision Medicine in the Genomics Era

    Directory of Open Access Journals (Sweden)

    Alexandra M. Dainis, BS

    2018-04-01

    Full Text Available Summary: Precision medicine strives to delineate disease using multiple data sources—from genomics to digital health metrics—in order to be more precise and accurate in our diagnoses, definitions, and treatments of disease subtypes. By defining disease at a deeper level, we can treat patients based on an understanding of the molecular underpinnings of their presentations, rather than grouping patients into broad categories with one-size-fits-all treatments. In this review, the authors examine how precision medicine, specifically that surrounding genetic testing and genetic therapeutics, has begun to make strides in both common and rare cardiovascular diseases in the clinic and the laboratory, and how these advances are beginning to enable us to more effectively define risk, diagnose disease, and deliver therapeutics for each individual patient. Key Words: genome sequencing, genomics, precision medicine, targeted therapeutics

  7. Field protocols for the genomic era

    Directory of Open Access Journals (Sweden)

    N Bulatova

    2009-08-01

    Full Text Available For many decades karyotype was the only source of overall genomic information obtained from species of mammal. However, approaches have been developed in recent years to obtain molecular and ultimately genomic information directly from the extracted DNA of an organism. Molecular data have accumulated hugely for mammalian taxa. The growing volume of studies should motivate field researchers to collect suitable samples for molecular analysis from various species across all their ranges. This is the reason why we here include a molecular sampling procedure within a field work protocol, which also includes more traditional (including cytogenetic techniques. In this way we hope to foster the development of molecular and genomic studies in non-standard wild mammals.

  8. Endogenous Retroviruses in the Genomics Era.

    Science.gov (United States)

    Johnson, Welkin E

    2015-11-01

    Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.

  9. Genome projects and the functional-genomic era.

    Science.gov (United States)

    Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

    2005-12-01

    The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

  10. Holistic Nursing in the Genetic/Genomic Era.

    Science.gov (United States)

    Sharoff, Leighsa

    2016-06-01

    Holistic nursing practice is an ever-evolving transformative process with core values that require continued growth, professional leadership, and advocacy. Holistic nurses are required to stay current with all new required competencies, such as the Core Competencies in Genetics for Health Professional, and, as such, be adept at translating scientific evidence relating to genetics/genomics in the clinical setting. Knowledge of genetics/genomics in relation to nursing practice, policy, utilization, and research influence nurses' responsibilities. In addition to holistic nursing competencies, the holistic nurse must have basic knowledge and skills to integrate genetics/genomics aspects. It is important for holistic nurses to enhance their overall knowledge foundation, skills, and attitudes about genetics to prepare for the transformation in health care that is already underway. Holistic nurses can provide an important perspective to the application of genetics and genomics, focusing on health promotion, caring, and understanding the relationship between caring and families, community, and society. Yet there may be a lack of genetic and genomic knowledge to fully participate in the current genomic era. This article will explore the required core competencies for all health care professionals, share linkage of holistic nurses in practice with genetic/genomic conditions, and provide resources to further one's knowledge base. © The Author(s) 2015.

  11. Bordetella pertussis evolution in the (functional) genomics era

    Science.gov (United States)

    Belcher, Thomas; Preston, Andrew

    2015-01-01

    The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps. PMID:26297914

  12. Enhancement of Plant Productivity in the Post-Genomics Era.

    Science.gov (United States)

    Thao, Nguyen Phuong; Tran, Lam-Son Phan

    2016-08-01

    in mediating cellular ion homeostasis and plant tolerance to both biotic and abiotic stresses. In summary, with recent progresses in biological and biotechnological areas, especially rapid development of advanced technologies in biological system modeling, functional genomics, computer-based analyzing tools, genetic engineering and molecular breeding, biological control and biotechnological applications in agriculture have brought about an extraordinary revolution and have been considered the most powerful approaches in maintaining or even increasing crop yield. Therefore, in this issue, we would like to introduce to the audience a collection of various strategies used for enhancing crop productivity, with the focus on advanced biological-biotechnological platforms in the post-genomics era.

  13. The potential of metabolomics for Leishmania research in the post-genomics era

    NARCIS (Netherlands)

    Scheltema, Richard A.; Decuypere, Saskia; T'Kindt, Ruben; Dujardin, Jean-Claude; Coombs, Graham H.; Breitling, Rainer; T’Kindt, Ruben

    The post-genomics era has provided researchers with access to a new generation of tools for the global characterization and understanding of pathogen diversity. This review provides a critical summary of published Leishmania post-genomic research efforts to date, and discusses the potential impact

  14. Aspergillus and Penicillium in the Post-genomic Era

    DEFF Research Database (Denmark)

    and a whole genus genome sequencing project in progress for Aspergillus. This book highlights some of the changes in the studies into these fungi, since the availability of genome sequences. The contributions vary from insights in the taxonomy of these genera, use of genomics for forward genetics and genomic......Genome sequencing has affected studies into the biology of all classes of organisms and this is certainly true for filamentous fungi. The level with which biological systems can be studied since the availability of genomes and post-genomic technologies is beyond what most people could have imagined...... previously. The fungal genera Aspergillus and Penicillium contain some species that are amongst the most widely used industrial microorganisms and others that are serious pathogens of plants, animals and humans. These genera are also at the forefront of fungal genomics with many genome sequences available...

  15. Assessing the origin of species in the genomic era

    OpenAIRE

    Moyle, Leonie C

    2005-01-01

    Advances in genomics have rapidly accelerated research into the genetics of species differences, reproductive isolating barriers, and hybrid incompatibility. Recent genomic analyses in Drosophila species suggest that modified olfactory cues are involved in discrimination that is reinforced by natural selection.

  16. Perspectives of Integrative Cancer Genomics in Next Generation Sequencing Era

    Directory of Open Access Journals (Sweden)

    So Mee Kwon

    2012-06-01

    Full Text Available The explosive development of genomics technologies including microarrays and next generation sequencing (NGS has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research.

  17. Protein annotation in the era of personal genomics

    DEFF Research Database (Denmark)

    Holberg Blicher, Thomas; Gupta, Ramneek; Wesolowska, Agata

    2010-01-01

    the differences between many individuals of the same species-humans in particular-the focus needs be on the functional impact of individual residue variation. To fulfil the promises of personal genomics, we need to start asking not only what is in a genome but also how millions of small differences between......Protein annotation provides a condensed and systematic view on the function of individual proteins. It has traditionally dealt with sorting proteins into functional categories, which for example has proven to be successful for the comparison of different species. However, if we are to understand...... individual genomes affect protein function and in turn human health. Copyright © 2010 Elsevier Ltd. All rights reserved....

  18. Lampreys as Diverse Model Organisms in the Genomics Era.

    Science.gov (United States)

    McCauley, David W; Docker, Margaret F; Whyard, Steve; Li, Weiming

    2015-11-01

    Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.

  19. Tracing Monotreme Venom Evolution in the Genomics Era

    Directory of Open Access Journals (Sweden)

    Camilla M. Whittington

    2014-04-01

    Full Text Available The monotremes (platypuses and echidnas represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves.

  20. Tracing monotreme venom evolution in the genomics era.

    Science.gov (United States)

    Whittington, Camilla M; Belov, Katherine

    2014-04-02

    The monotremes (platypuses and echidnas) represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom) systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves.

  1. Pea (Pisum sativum L. in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Robert J. Redden

    2012-04-01

    Full Text Available Pea (Pisum sativum L. was the original model organism used in Mendel’s discovery (1866 of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species. Although the size and repetitive nature of the pea genome has so far restricted its sequencing, comprehensive genomic and post genomic resources already exist. These include BAC libraries, several types of molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. The availability of the full genome sequences of three legume species has offered significant opportunities for genome wide comparison revealing synteny and co-linearity to pea. A combination of a candidate gene and colinearity approach has successfully led to the identification of genes underlying agronomically important traits including virus resistances and plant architecture. Some of this knowledge has already been applied to marker assisted selection (MAS programs, increasing precision and shortening the breeding cycle. Yet, complete translation of marker discovery to pea breeding is still to be achieved. Molecular analysis of pea collections has shown that although substantial variation is present within the cultivated genepool, wild material offers the possibility to incorporate novel traits that may have been inadvertently eliminated. Association mapping analysis of diverse pea germplasm promises to identify genetic variation related to desirable agronomic traits, which are historically difficult to breed for in a traditional manner. The availability of high throughput ‘omics’ methodologies offers great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems.

  2. Genes, race, and psychology in the genome era: an introduction.

    Science.gov (United States)

    Anderson, Norman B; Nickerson, Kim J

    2005-01-01

    The mapping of the human genome has reawakened interest in the topic of race and genetics, especially the use of genetic technology to examine racial differences in complex outcomes such as health and intelligence. Advances in genomic research challenge psychology to address the myriad conceptual, methodological, and analytical issues associated with research on genetics and race. In addition, the field needs to understand the numerous social, ethical, legal, clinical, and policy implications of research in this arena. Addressing these issues should not only benefit psychology but could also serve to guide such thought in other fields, including molecular biology. The purpose of this special issue is to begin a discussion of this issue of race and genetics within the field of psychology. Several scholars who work in the fields of genetics, race, or related areas were invited to write (or had previously submitted) articles sharing their perspectives. (c) 2005 APA

  3. Future Translational Applications From the Contemporary Genomics Era

    Science.gov (United States)

    Fox, Caroline S.; Hall, Jennifer L.; Arnett, Donna K.; Ashley, Euan A.; Delles, Christian; Engler, Mary B.; Freeman, Mason W.; Johnson, Julie A.; Lanfear, David E.; Liggett, Stephen B.; Lusis, Aldons J.; Loscalzo, Joseph; MacRae, Calum A.; Musunuru, Kiran; Newby, L. Kristin; O’Donnell, Christopher J.; Rich, Stephen S.; Terzic, Andre

    2016-01-01

    The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care. PMID:25882488

  4. Leptospira species molecular epidemiology in the genomic era.

    Science.gov (United States)

    Caimi, K; Repetto, S A; Varni, V; Ruybal, P

    2017-10-01

    Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach. Bayesian phylogenetic analysis of concatenated sequences from R7-MLST loci allowed us to resolve taxonomic inconsistencies but also showed that events such as recombination, gene conversion or lateral gene transfer played an important role in the evolution of Leptospira genus. Whole genome sequencing allows us to contribute with suitable epidemiologic information useful to apply in the design of control strategies and also in diagnostic methods for this illness. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Fungal biology in the post-genomic era.

    Science.gov (United States)

    Scazzocchio, Claudio

    2014-01-01

    In this review I give a personal perspective of how fungal biology has changed since I started my Ph. D. in 1963. At that time we were working in the shadow of the birth of molecular biology as an autonomous and reductionistic discipline, embodied in Crick's central dogma. This first period was methodologically characterised by the fact that we knew what genes were, but we could not access them directly. This radically changed in the 70s-80s when gene cloning, reverse genetics and DNA sequencing become possible. The "next generation" sequencing techniques have produced a further qualitative revolutionary change. The ready access to genomes and transcriptomes of any microbial organism allows old questions to be asked in a radically different way and new questions to be approached. I provide examples chosen somewhat arbitrarily to illustrate some of these changes, from applied aspects to fundamental problems such as the origin of fungal specific genes, the evolutionary history of genes clusters and the realisation of the pervasiveness of horizontal transmission. Finally, I address how the ready availability of genomes and transcriptomes could change the status of model organisms.

  6. Evaluating Phylogenetic Congruence in the Post-Genomic Era

    Science.gov (United States)

    Leigh, Jessica W.; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

    2011-01-01

    Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures. PMID:21712432

  7. Transcriptional and chromatin regulation during fasting – The genomic era

    Science.gov (United States)

    Goldstein, Ido; Hager, Gordon L.

    2015-01-01

    An elaborate metabolic response to fasting is orchestrated by the liver and is heavily reliant upon transcriptional regulation. In response to hormones (glucagon, glucocorticoids) many transcription factors (TFs) are activated and regulate various genes involved in metabolic pathways aimed at restoring homeostasis: gluconeogenesis, fatty acid oxidation, ketogenesis and amino acid shuttling. We summarize the recent discoveries regarding fasting-related TFs with an emphasis on genome-wide binding patterns. Collectively, the summarized findings reveal a large degree of co-operation between TFs during fasting which occurs at motif-rich DNA sites bound by a combination of TFs. These new findings implicate transcriptional and chromatin regulation as major determinants of the response to fasting and unravels the complex, multi-TF nature of this response. PMID:26520657

  8. Macromolecular structure determination in the post-genome era

    CERN Document Server

    Kuhn, P

    2001-01-01

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system...

  9. [Research progress in neuropsychopharmacology updated for the post-genomic era].

    Science.gov (United States)

    Nakanishi, Toru

    2009-11-01

    Neuropsychopharmacological research in the post genomic (genomic sequence) era has been developing rapidly through the use of novel techniques including DNA chips. We have applied these techniques to investigate the anti-tumor effect of NSAIDs, isolate novel genes specifically expressed in rheumatoid arthritis, and analyze gene expression profiles in mesenchymal stem cells. Recently, we have developed a novel system of quantitative PCR for detection of BDNF mRNA isoforms. By using this system, we identified the exon-specific mode of expression in acute and chronic pain. In addition, we have made gene expression profiles of KO mice of beta2 subunits in acetylcholine receptors.

  10. Macromolecular structure determination in the post-genome era

    International Nuclear Information System (INIS)

    Kuhn, P.; Soltis, S.M.

    2001-01-01

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system for the structure determination steps of this process, starting with the initial characterization of the frozen sample, followed by data collection, data reduction, phase determination, and model building. This paper focuses on the data collection elements of this high-throughput system

  11. Personalized Medicine in a New Genomic Era: Ethical and Legal Aspects.

    Science.gov (United States)

    Shoaib, Maria; Rameez, Mansoor Ali Merchant; Hussain, Syed Ather; Madadin, Mohammed; Menezes, Ritesh G

    2017-08-01

    The genome of two completely unrelated individuals is quite similar apart from minor variations called single nucleotide polymorphisms which contribute to the uniqueness of each and every person. These single nucleotide polymorphisms are of great interest clinically as they are useful in figuring out the susceptibility of certain individuals to particular diseases and for recognizing varied responses to pharmacological interventions. This gives rise to the idea of 'personalized medicine' as an exciting new therapeutic science in this genomic era. Personalized medicine suggests a unique treatment strategy based on an individual's genetic make-up. Its key principles revolve around applied pharmaco-genomics, pharmaco-kinetics and pharmaco-proteomics. Herein, the ethical and legal aspects of personalized medicine in a new genomic era are briefly addressed. The ultimate goal is to comprehensively recognize all relevant forms of genetic variation in each individual and be able to interpret this information in a clinically meaningful manner within the ambit of ethical and legal considerations. The authors of this article firmly believe that personalized medicine has the potential to revolutionize the current landscape of medicine as it makes its way into clinical practice.

  12. Novel Features and Considerations for ERA and Regulation of Crops Produced by Genome Editing

    Directory of Open Access Journals (Sweden)

    Nina Duensing

    2018-06-01

    Full Text Available Genome editing describes a variety of molecular biology applications enabling targeted and precise alterations of the genomes of plants, animals and microorganisms. These rapidly developing techniques are likely to revolutionize the breeding of new crop varieties. Since genome editing can lead to the development of plants that could also have come into existence naturally or by conventional breeding techniques, there are strong arguments that these cases should not be classified as genetically modified organisms (GMOs and be regulated no differently from conventionally bred crops. If a specific regulation would be regarded necessary, the application of genome editing for crop development may challenge risk assessment and post-market monitoring. In the session “Plant genome editing—any novel features to consider for ERA and regulation?” held at the 14th ISBGMO, scientists from various disciplines as well as regulators, risk assessors and potential users of the new technologies were brought together for a knowledge-based discussion to identify knowledge gaps and analyze scenarios for the introduction of genome-edited crops into the environment. It was aimed to enable an open exchange forum on the regulatory approaches, ethical aspects and decision-making considerations.

  13. INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH

    Science.gov (United States)

    Genome sequencing efforts in the past decade were aimed at generating draft sequences of many prokaryotic and eukaryotic model organisms. Successful completion of unicellular eukaryotes, worm, fly and human genome have opened up the new field of molecular biology and function...

  14. Growing up at the intersection of the genomic era and the information age.

    Science.gov (United States)

    Driessnack, Martha

    2009-06-01

    Children actively seek to make sense of their worlds based on the information they receive and their experience. For children growing up at the intersection of genomic era and information age, the array of information and experience continues to expand. This article highlights the importance of exploring these early contexts for learning, including the children's exposure to books and mass media, and the impact of early learning on later health literacy and behaviors. This article presents a case study discussing the inheritance of cystic fibrosis using the Harry Potter book series.

  15. Description of Hymenolepis microstoma (Nottingham strain: a classical tapeworm model for research in the genomic era

    Directory of Open Access Journals (Sweden)

    Olson Peter D

    2010-12-01

    Full Text Available Abstract Background Hymenolepis microstoma (Dujardin, 1845 Blanchard, 1891, the mouse bile duct tapeworm, is a rodent/beetle-hosted laboratory model that has been used in research and teaching since its domestication in the 1950s. Recent characterization of its genome has prompted us to describe the specific strain that underpins these data, anchoring its identity and bringing the 150+ year-old original description up-to-date. Results Morphometric and ultrastructural analyses were carried out on laboratory-reared specimens of the 'Nottingham' strain of Hymenolepis microstoma used for genome characterization. A contemporary description of the species is provided including detailed illustration of adult anatomy and elucidation of its taxonomy and the history of the specific laboratory isolate. Conclusions Our work acts to anchor the specific strain from which the H. microstoma genome has been characterized and provides an anatomical reference for researchers needing to employ a model tapeworm system that enables easy access to all stages of the life cycle. We review its classification, life history and development, and briefly discuss the genome and other model systems being employed at the beginning of a genomic era in cestodology.

  16. Each cell counts: Hematopoiesis and immunity research in the era of single cell genomics.

    Science.gov (United States)

    Jaitin, Diego Adhemar; Keren-Shaul, Hadas; Elefant, Naama; Amit, Ido

    2015-02-01

    Hematopoiesis and immunity are mediated through complex interactions between multiple cell types and states. This complexity is currently addressed following a reductionist approach of characterizing cell types by a small number of cell surface molecular features and gross functions. While the introduction of global transcriptional profiling technologies enabled a more comprehensive view, heterogeneity within sampled populations remained unaddressed, obscuring the true picture of hematopoiesis and immune system function. A critical mass of technological advances in molecular biology and genomics has enabled genome-wide measurements of single cells - the fundamental unit of immunity. These new advances are expected to boost detection of less frequent cell types and fuzzy intermediate cell states, greatly expanding the resolution of current available classifications. This new era of single-cell genomics in immunology research holds great promise for further understanding of the mechanisms and circuits regulating hematopoiesis and immunity in both health and disease. In the near future, the accuracy of single-cell genomics will ultimately enable precise diagnostics and treatment of multiple hematopoietic and immune related diseases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Data analysis in the post-genome-wide association study era

    Directory of Open Access Journals (Sweden)

    Qiao-Ling Wang

    2016-12-01

    Full Text Available Since the first report of a genome-wide association study (GWAS on human age-related macular degeneration, GWAS has successfully been used to discover genetic variants for a variety of complex human diseases and/or traits, and thousands of associated loci have been identified. However, the underlying mechanisms for these loci remain largely unknown. To make these GWAS findings more useful, it is necessary to perform in-depth data mining. The data analysis in the post-GWAS era will include the following aspects: fine-mapping of susceptibility regions to identify susceptibility genes for elucidating the biological mechanism of action; joint analysis of susceptibility genes in different diseases; integration of GWAS, transcriptome, and epigenetic data to analyze expression and methylation quantitative trait loci at the whole-genome level, and find single-nucleotide polymorphisms that influence gene expression and DNA methylation; genome-wide association analysis of disease-related DNA copy number variations. Applying these strategies and methods will serve to strengthen GWAS data to enhance the utility and significance of GWAS in improving understanding of the genetics of complex diseases or traits and translate these findings for clinical applications. Keywords: Genome-wide association study, Data mining, Integrative data analysis, Polymorphism, Copy number variation

  18. Patient-physician alliance: from Hippocrates to Post-Genomic Era. Commentary.

    Science.gov (United States)

    Pulciani, Simonetta; Taruscio, Domenica

    2017-01-01

    Patients need clinical competence, appropriate diagnosis and therapies in overcoming their disease. Yet this is insufficient. The illness experience tends to frighten people and the resulting emotional aspects could become relevant factors in coping with a sickness and disability. Hippocrates was the first to urge physicians to look beyond the physical features of diseases and to consider the patient as a unique psychosomatic entity. Additionally, the scientist spurred physicians to make the patient an active participant in combating the disease. According to Hippocrates, "the Medical Art has three actors: the physician, the patients and the disease. The physician and the patient must be allied against the disease in order to fight it". In the "Post-Genomic Era", an effective therapeutic approach merits a patient-physician participation, based on scientific understandings and human considerations. These recommendations are even more urgent for Rare Diseases.

  19. Clinical biochemistry and laboratory medicine in the post-genome era

    International Nuclear Information System (INIS)

    Efremov, Georgi D.

    2001-01-01

    The last decades of the 20th century were a period of outstanding scientific achievements. The most significant discovery was the decoding of the human genome (Venter, J. et al., 2001; Dennis, C. et al., 2001; Baltimore, D., 2001). In this article the present view of the post genomic era is presented. The new analytical methods, such as micro arrays, bio chips, and nano technology, the discovery of SNPs, and the analysis of the proteome will lead to a greater understanding of the pathogenesis of inherited and acquired diseases. Their use in clinical chemistry and laboratory medicine, and the future of technological innovations are discussed. In the post genomic era the greatest interest will be devoted to the application of these scientific achievements in the diagnosis, prevention and therapy of human diseases. The advances in human genetics that have occurred during the past 20 years have revolutionized our knowledge of the role played by inheritance in health and disease. It is clear that our DNA determines not only single gene disorders but also interacts with environments to predispose individuals to cancer, allergy, hypertension, heart disease, diabetes, psychiatric disorders and even to some infectious diseases. The study of longevity and the demonstration of genes favouring a long lifespan suggest that such protective systems exist. The study of genetic polymorphisms has made clear that some alleles have beneficial effects. These discoveries will be of great help in our understanding of the interactions between genetics and environment. Gene array analysis has become the method of choice for identifying genes expressed at different levels in different samples. The mRNA expression profiles of normal and tumor tissues, treated and untreated cell cultures, and developmental stages of an organism can be compared quickly and easily with an appropriate array analysis system. A major task after a genome has been fully sequenced is to understand the functions

  20. Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

    Directory of Open Access Journals (Sweden)

    Arun Prabhu Dhanapal

    2015-01-01

    Full Text Available The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.

  1. Ocean acidification research in the 'post-genomic' era: Roadmaps from the purple sea urchin Strongylocentrotus purpuratus.

    Science.gov (United States)

    Evans, Tyler G; Padilla-Gamiño, Jacqueline L; Kelly, Morgan W; Pespeni, Melissa H; Chan, Francis; Menge, Bruce A; Gaylord, Brian; Hill, Tessa M; Russell, Ann D; Palumbi, Stephen R; Sanford, Eric; Hofmann, Gretchen E

    2015-07-01

    Advances in nucleic acid sequencing technology are removing obstacles that historically prevented use of genomics within ocean change biology. As one of the first marine calcifiers to have its genome sequenced, purple sea urchins (Strongylocentrotus purpuratus) have been the subject of early research exploring genomic responses to ocean acidification, work that points to future experiments and illustrates the value of expanding genomic resources to other marine organisms in this new 'post-genomic' era. This review presents case studies of S. purpuratus demonstrating the ability of genomic experiments to address major knowledge gaps within ocean acidification. Ocean acidification research has focused largely on species vulnerability, and studies exploring mechanistic bases of tolerance toward low pH seawater are comparatively few. Transcriptomic responses to high pCO₂ seawater in a population of urchins already encountering low pH conditions have cast light on traits required for success in future oceans. Secondly, there is relatively little information on whether marine organisms possess the capacity to adapt to oceans progressively decreasing in pH. Genomics offers powerful methods to investigate evolutionary responses to ocean acidification and recent work in S. purpuratus has identified genes under selection in acidified seawater. Finally, relatively few ocean acidification experiments investigate how shifts in seawater pH combine with other environmental factors to influence organism performance. In S. purpuratus, transcriptomics has provided insight into physiological responses of urchins exposed simultaneously to warmer and more acidic seawater. Collectively, these data support that similar breakthroughs will occur as genomic resources are developed for other marine species. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. A Dual-Promoter Gene Orchestrates the Sucrose-Coordinated Synthesis of Starch and Fructan in Barley

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Yunkai; Fei, Mingliang; Rosenquist, Sara; Jin, Lu; Gohil, Suresh; Sandström, Corine; Olsson, Helena; Persson, Cecilia; Höglund, Anna-Stina; Fransson, Gunnel; Ruan, Ying; Åman, Per; Jansson, Christer; Liu, Chunlin; Andersson, Roger; Sun, Chuanxin

    2017-12-01

    Starch and fructan are two important carbohydrates in many flowering plants and in human diets. Understanding how plants allocate photosynthates and how they prioritize synthesis of different carbohydrates during development is essential in efforts to improve cereals for increased stress tolerance and for desirable carbohydrate compositions in food and feed. We report the coordinated synthesis of starch and fructan in barley, orchestrated by two functionally opposing transcription factors encoded from two alternative promoters, one intronic/exonic, harbored on a single gene. . This dual-transcription factor system employs an autoregulatory, antagonsitic mechanism in sensing sucrose at one promoter, potentially via sucrose/glucose/fructose/trehalose 6-phosphate signaling, and conduct a coordinated synthesis of starch and fructan synthesis by competitive transcription factor binding to the second promoter The finding of an intron/exon-spanning promoter in a hosting gene, resulting in proteins with distinct functions, contributes to our appreciation of the complexity of the plant genome As a case in point for the physiological role of the antagonistic transcription factor system, we have demonstrated that it can be exploited in breeding barley with tailored amounts of fructan for production of specialty food ingredients.

  3. Global MLST of Salmonella Typhi Revisited in Post-Genomic Era: Genetic conservation, Population Structure and Comparative genomics of rare sequence types

    Directory of Open Access Journals (Sweden)

    Kien-Pong eYap

    2016-03-01

    Full Text Available Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus Sequence Typing (MLST is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2 co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC and tviD that may explain the variations that differentiate between seemingly successful (widespread and unsuccessful (poor dissemination S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

  4. Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.

    Science.gov (United States)

    Kim, Tae-Sung; He, Qiang; Kim, Kyu-Won; Yoon, Min-Young; Ra, Won-Hee; Li, Feng Peng; Tong, Wei; Yu, Jie; Oo, Win Htet; Choi, Buung; Heo, Eun-Beom; Yun, Byoung-Kook; Kwon, Soon-Jae; Kwon, Soon-Wook; Cho, Yoo-Hyun; Lee, Chang-Yong; Park, Beom-Seok; Park, Yong-Jin

    2016-05-26

    Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.

  5. Disease management in the genomics era - Summaries of focus issue papers

    Science.gov (United States)

    The genomics revolution has contributed enormously to research and disease management applications in plant pathology. This development has rapidly increased our understanding of the molecular mechanisms underpinning pathogenesis and resistance, contributed novel markers for rapid pathogen detectio...

  6. Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Cristiane C. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Amaral, Gilda R. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Campeão, Mariana [Univ. of Rio de Janeiro (UFRJ) (Brazil); Edwards, Robert A. [Univ. of Rio de Janeiro (UFRJ) (Brazil); San Diego State Univ., CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Polz, Martin F. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Dutilh, Bas E. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Radbould Univ., Nijmegen (Netherlands); Ussery, David W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sawabe, Tomoo [Hokkaido Univ., Hakodate (Japan); Swings, Jean [Univ. of Rio de Janeiro (UFRJ) (Brazil); Ghent Univ. (Belgium); Thompson, Fabiano L. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Advanced Systems Laboratory Production Management COPPE / UFRJ, Rio de Janeiro (Brazil)

    2014-12-23

    Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

  7. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S.; Fredrickson, J. K.; Stevens, R.

    2009-03-01

    Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

  8. Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

    Science.gov (United States)

    Robins-Browne, Roy M.; Holt, Kathryn E.; Ingle, Danielle J.; Hocking, Dianna M.; Yang, Ji; Tauschek, Marija

    2016-01-01

    The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods. PMID:27917373

  9. Use of γ-ray-induced mutations in the genome era in rice

    International Nuclear Information System (INIS)

    Kusaba, Makoto

    2007-01-01

    Ionizing radiation has been used for inducing mutations and improving crops since the discovery by STADLER (1928) that X-rays could induce mutations in barley. At the end of 2004, the whole genome sequence of rice was determined (INTERNATIONAL RICE GENOME SEQUENCING PROJECT, 2005). What can γ-ray-induced mutations contribute now that this has been achieved? One answer could be the elucidation of the functions of the numerous genes revealed by the complete sequence of the rice genome. This includes identification of mutants through reverse genetics and the isolation of genes containing mutations through forward genetics using molecular markers and sequence information. Another answer could be mutation breeding using reverse genetics. But first we must know what kind of DNA lesions are caused by γ-rays. In this article, I describe the production of DNA lesions, and then discuss how γ-ray-induced mutations can contribute to the elucidation of gene function and to mutation breeding. (author)

  10. Large inserts for big data: artificial chromosomes in the genomic era.

    Science.gov (United States)

    Tocchetti, Arianna; Donadio, Stefano; Sosio, Margherita

    2018-05-01

    The exponential increase in available microbial genome sequences coupled with predictive bioinformatic tools is underscoring the genetic capacity of bacteria to produce an unexpected large number of specialized bioactive compounds. Since most of the biosynthetic gene clusters (BGCs) present in microbial genomes are cryptic, i.e. not expressed under laboratory conditions, a variety of cloning systems and vectors have been devised to harbor DNA fragments large enough to carry entire BGCs and to allow their transfer in suitable heterologous hosts. This minireview provides an overview of the vectors and approaches that have been developed for cloning large BGCs, and successful examples of heterologous expression.

  11. Advancing Crop Transformation in the Era of Genome Editing[OPEN

    Science.gov (United States)

    Blechl, Ann E.; Brutnell, Thomas P.; Conrad, Liza J.; Gelvin, Stanton B.; Jackson, David P.; Kausch, Albert P.; Lemaux, Peggy G.; Medford, June I.; Orozco-Cárdenas, Martha L.; Tricoli, David M.; Van Eck, Joyce; Voytas, Daniel F.

    2016-01-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. PMID:27335450

  12. Molecular target discovery for neural repair in the functional genomics era

    NARCIS (Netherlands)

    Verhaagen, J.; van Kesteren, R.E.; Bossers, K.A.; Mac Gillavry, H.D.; Mason, M.R.; Smit, A.B.

    2012-01-01

    A comprehensive understanding of the molecular pathways activated by traumatic neural injury is of major importance for the development of treatments for spinal cord injury (SCI). High-throughput gene expression profiling is a powerful approach to reveal genome-wide changes in gene expression during

  13. Meiotic homoeologous recombination-based alien gene introgression in the genomics era of wheat

    Science.gov (United States)

    Wheat (Triticum spp.) has a narrow genetic basis due to its allopolyploid origin. However, wheat has numerous wild relatives usable for expanding genetic variability of its genome through meiotic homoeologous recombination. Traditionally, laborious cytological analyses have been employed to detect h...

  14. Germplasm Management in the Post-genomics Era-a case study with lettuce

    Science.gov (United States)

    High-throughput genotyping platforms and next-generation sequencing technologies revolutionized our ways in germplasm characterization. In collaboration with UC Davis Genome Center, we completed a project of genotyping the entire cultivated lettuce (Lactuca sativa L.) collection of 1,066 accessions ...

  15. Training future physicians in the era of genomic medicine: trends in undergraduate medical genetics education.

    Science.gov (United States)

    Plunkett-Rondeau, Jevon; Hyland, Katherine; Dasgupta, Shoumita

    2015-11-01

    Advances in genomic technologies are transforming medical practice, necessitating the expertise of genomically-literate physicians. This study examined 2013-2014 trends in genetics curricula in US and Canadian medical schools to ascertain whether and how curricula are keeping pace with this rapid evolution. Medical genetics course directors received a 60-item electronic questionnaire covering curriculum design, assessment, remediation of failing grades, and inclusion of specific topics. The response rate was 74%. Most schools teach the majority of genetics during the first 2 years, with an increase in the number of integrated curricula. Only 26% reported formal genetics teaching during years 3 and 4, and most respondents felt the amount of time spent on genetics was insufficient preparation for clinical practice. Most participants are using the Association of Professors of Human and Medical Genetics Core Curriculum(1) as a guide. Topics recently added include personalized medicine (21%) and direct-to-consumer testing (18%), whereas eugenics (17%), linkage analysis (16%), and evolutionary genetics (15%) have been recently eliminated. Remediation strategies were heterogeneous across institutions. These findings provide an important update on how genetics and genomics is taught at US and Canadian medical schools. Continuous improvement of educational initiatives will aid in producing genomically-literate physicians.

  16. Genetic gatekeepers: regulating direct-to-consumer genomic services in an era of participatory medicine.

    Science.gov (United States)

    Palmer, Jessica Elizabeth

    2012-01-01

    Should consumers be able to obtain information about their own bodies, even if it has no proven medical value? Direct-to-consumer ("DTC") genomic companies offer consumers two services: generation of the consumer's personal genetic sequence, and interpretation of that sequence in light of current research. Concerned that consumers will misunderstand genomic information and make ill-advised health decisions, regulators, legislators and scholars have advocated restricted access to DTC genomic services. The Food and Drug Administration, which has historically refrained from regulating most genetic tests, has announced its intent to treat DTC genomic services as medical devices because they make "medical claims." This Article argues that FDA regulation of genomic services as medical devices would be counterproductive. Clinical laboratories conducting genetic tests are already overseen by a federal regime administered by the Centers for Medicare and Medicaid Services. While consumers and clinicians would benefit from clearer communication of test results and their health implications, FDA's gatekeeping framework is ill-suited to weigh the safety and efficacy of genomic information that is not medically actionable in traditional ways. Playing gatekeeper would burden FDA's resources, conflict with the patient-empowering policies promoted by personalized medicine initiatives, impair individuals' access to information in which they have powerful autonomy interests, weaken novel participatory research infrastructures, and set a poor precedent for the future regulation of medical information. Rather than applying its risk-based regulatory framework to genetic information, FDA should ameliorate regulatory uncertainty by working with the Federal Trade Commission and Centers for Medicare and Medicaid Services to ensure that DTC genomic services deliver analytically valid data, market and implement their services in a truthful manner, and fully disclose the limitations of their

  17. Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding.

    Science.gov (United States)

    Bhat, Javaid A; Ali, Sajad; Salgotra, Romesh K; Mir, Zahoor A; Dutta, Sutapa; Jadon, Vasudha; Tyagi, Anshika; Mushtaq, Muntazir; Jain, Neelu; Singh, Pradeep K; Singh, Gyanendra P; Prabhu, K V

    2016-01-01

    Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

  18. Approaches to advancing quantitative human health risk assessment of environmental chemicals in the post-genomic era.

    Science.gov (United States)

    Chiu, Weihsueh A; Euling, Susan Y; Scott, Cheryl Siegel; Subramaniam, Ravi P

    2013-09-15

    The contribution of genomics and associated technologies to human health risk assessment for environmental chemicals has focused largely on elucidating mechanisms of toxicity, as discussed in other articles in this issue. However, there is interest in moving beyond hazard characterization to making more direct impacts on quantitative risk assessment (QRA)--i.e., the determination of toxicity values for setting exposure standards and cleanup values. We propose that the evolution of QRA of environmental chemicals in the post-genomic era will involve three, somewhat overlapping phases in which different types of approaches begin to mature. The initial focus (in Phase I) has been and continues to be on "augmentation" of weight of evidence--using genomic and related technologies qualitatively to increase the confidence in and scientific basis of the results of QRA. Efforts aimed towards "integration" of these data with traditional animal-based approaches, in particular quantitative predictors, or surrogates, for the in vivo toxicity data to which they have been anchored are just beginning to be explored now (in Phase II). In parallel, there is a recognized need for "expansion" of the use of established biomarkers of susceptibility or risk of human diseases and disorders for QRA, particularly for addressing the issues of cumulative assessment and population risk. Ultimately (in Phase III), substantial further advances could be realized by the development of novel molecular and pathway-based biomarkers and statistical and in silico models that build on anticipated progress in understanding the pathways of human diseases and disorders. Such efforts would facilitate a gradual "reorientation" of QRA towards approaches that more directly link environmental exposures to human outcomes. Published by Elsevier Inc.

  19. Approaches to advancing quantitative human health risk assessment of environmental chemicals in the post-genomic era

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Weihsueh A., E-mail: chiu.weihsueh@epa.gov [National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington DC, 20460 (United States); Euling, Susan Y.; Scott, Cheryl Siegel; Subramaniam, Ravi P. [National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington DC, 20460 (United States)

    2013-09-15

    The contribution of genomics and associated technologies to human health risk assessment for environmental chemicals has focused largely on elucidating mechanisms of toxicity, as discussed in other articles in this issue. However, there is interest in moving beyond hazard characterization to making more direct impacts on quantitative risk assessment (QRA) — i.e., the determination of toxicity values for setting exposure standards and cleanup values. We propose that the evolution of QRA of environmental chemicals in the post-genomic era will involve three, somewhat overlapping phases in which different types of approaches begin to mature. The initial focus (in Phase I) has been and continues to be on “augmentation” of weight of evidence — using genomic and related technologies qualitatively to increase the confidence in and scientific basis of the results of QRA. Efforts aimed towards “integration” of these data with traditional animal-based approaches, in particular quantitative predictors, or surrogates, for the in vivo toxicity data to which they have been anchored are just beginning to be explored now (in Phase II). In parallel, there is a recognized need for “expansion” of the use of established biomarkers of susceptibility or risk of human diseases and disorders for QRA, particularly for addressing the issues of cumulative assessment and population risk. Ultimately (in Phase III), substantial further advances could be realized by the development of novel molecular and pathway-based biomarkers and statistical and in silico models that build on anticipated progress in understanding the pathways of human diseases and disorders. Such efforts would facilitate a gradual “reorientation” of QRA towards approaches that more directly link environmental exposures to human outcomes.

  20. Approaches to advancing quantitative human health risk assessment of environmental chemicals in the post-genomic era

    International Nuclear Information System (INIS)

    Chiu, Weihsueh A.; Euling, Susan Y.; Scott, Cheryl Siegel; Subramaniam, Ravi P.

    2013-01-01

    The contribution of genomics and associated technologies to human health risk assessment for environmental chemicals has focused largely on elucidating mechanisms of toxicity, as discussed in other articles in this issue. However, there is interest in moving beyond hazard characterization to making more direct impacts on quantitative risk assessment (QRA) — i.e., the determination of toxicity values for setting exposure standards and cleanup values. We propose that the evolution of QRA of environmental chemicals in the post-genomic era will involve three, somewhat overlapping phases in which different types of approaches begin to mature. The initial focus (in Phase I) has been and continues to be on “augmentation” of weight of evidence — using genomic and related technologies qualitatively to increase the confidence in and scientific basis of the results of QRA. Efforts aimed towards “integration” of these data with traditional animal-based approaches, in particular quantitative predictors, or surrogates, for the in vivo toxicity data to which they have been anchored are just beginning to be explored now (in Phase II). In parallel, there is a recognized need for “expansion” of the use of established biomarkers of susceptibility or risk of human diseases and disorders for QRA, particularly for addressing the issues of cumulative assessment and population risk. Ultimately (in Phase III), substantial further advances could be realized by the development of novel molecular and pathway-based biomarkers and statistical and in silico models that build on anticipated progress in understanding the pathways of human diseases and disorders. Such efforts would facilitate a gradual “reorientation” of QRA towards approaches that more directly link environmental exposures to human outcomes

  1. Future translational applications from the contemporary genomics era: a scientific statement from the American Heart Association.

    Science.gov (United States)

    Fox, Caroline S; Hall, Jennifer L; Arnett, Donna K; Ashley, Euan A; Delles, Christian; Engler, Mary B; Freeman, Mason W; Johnson, Julie A; Lanfear, David E; Liggett, Stephen B; Lusis, Aldons J; Loscalzo, Joseph; MacRae, Calum A; Musunuru, Kiran; Newby, L Kristin; O'Donnell, Christopher J; Rich, Stephen S; Terzic, Andre

    2015-05-12

    The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care. © 2015 American Heart Association, Inc.

  2. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies.

    Science.gov (United States)

    Potter, Sally; Bragg, Jason G; Blom, Mozes P K; Deakin, Janine E; Kirkpatrick, Mark; Eldridge, Mark D B; Moritz, Craig

    2017-01-01

    The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale . We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.

  3. Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”

    DEFF Research Database (Denmark)

    Herrgard, Markus; Panagiotou, Gianni

    2012-01-01

    The application of genome-scale technologies, both experimental and in silico, to industrial biotechnology has allowed improving the conversion of biomass-derived feedstocks to chemicals, materials and fuels through microbial fermentation. In particular, due to rapidly decreasing costs and its...... technologies for finding the underlying molecular mechanisms for (a) improved carbon source utilization, (b) increased product formation, and (c) stress tolerance. We also discuss the strengths and weaknesses of different strategies for mapping industrially relevant genotype-to-phenotype links including...

  4. Future Translational Applications From the Contemporary Genomics Era: A Scientific Statement From the American Heart Association

    OpenAIRE

    Fox, Caroline S.; Hall, Jennifer L.; Arnett, Donna K.; Ashley, Euan A.; Delles, Christian; Engler, Mary B.; Freeman, Mason W.; Johnson, Julie A.; Lanfear, David E.; Liggett, Stephen B.; Lusis, Aldons J.; Loscalzo, Joseph; MacRae, Calum A.; Musunuru, Kiran; Newby, L. Kristin

    2015-01-01

    The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardi...

  5. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Science.gov (United States)

    Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

    2009-01-01

    The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

  6. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-01-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  7. Ethnobotany genomics - discovery and innovation in a new era of exploratory research

    Directory of Open Access Journals (Sweden)

    Ragupathy Subramanyam

    2010-01-01

    Full Text Available Abstract We present here the first use of DNA barcoding in a new approach to ethnobotany we coined "ethnobotany genomics". This new approach is founded on the concept of 'assemblage' of biodiversity knowledge, which includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK and scientific knowledge (SK. We employed contemporary genomic technology, DNA barcoding, as an important tool for identifying cryptic species, which were already recognized ethnotaxa using the TK classification systems of local cultures in the Velliangiri Hills of India. This research is based on several case studies in our lab, which define an approach to that is poised to evolve quickly with the advent of new ideas and technology. Our results show that DNA barcoding validated several new cryptic plant species to science that were previously recognized by TK classifications of the Irulas and Malasars, and were lumped using SK classification. The contribution of the local aboriginal knowledge concerning plant diversity and utility in India is considerable; our study presents new ethnomedicine to science. Ethnobotany genomics can also be used to determine the distribution of rare species and their ecological requirements, including traditional ecological knowledge so that conservation strategies can be implemented. This is aligned with the Convention on Biological Diversity that was signed by over 150 nations, and thus the world's complex array of human-natural-technological relationships has effectively been re-organized.

  8. Persea americana (avocado): bringing ancient flowers to fruit in the genomics era.

    Science.gov (United States)

    Chanderbali, André S; Albert, Victor A; Ashworth, Vanessa E T M; Clegg, Michael T; Litz, Richard E; Soltis, Douglas E; Soltis, Pamela S

    2008-04-01

    The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary "outpost" among flowering plants, representing a basal lineage (the magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical-zone crop. Among the goals of avocado improvement are to develop varieties with fruit that will "store" better on the tree, show uniform ripening and have better post-harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non-flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms.

  9. Ethnobotany genomics - discovery and innovation in a new era of exploratory research.

    Science.gov (United States)

    Newmaster, Steven G; Ragupathy, Subramanyam

    2010-01-26

    We present here the first use of DNA barcoding in a new approach to ethnobotany we coined "ethnobotany genomics". This new approach is founded on the concept of 'assemblage' of biodiversity knowledge, which includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK) and scientific knowledge (SK). We employed contemporary genomic technology, DNA barcoding, as an important tool for identifying cryptic species, which were already recognized ethnotaxa using the TK classification systems of local cultures in the Velliangiri Hills of India. This research is based on several case studies in our lab, which define an approach to that is poised to evolve quickly with the advent of new ideas and technology. Our results show that DNA barcoding validated several new cryptic plant species to science that were previously recognized by TK classifications of the Irulas and Malasars, and were lumped using SK classification. The contribution of the local aboriginal knowledge concerning plant diversity and utility in India is considerable; our study presents new ethnomedicine to science. Ethnobotany genomics can also be used to determine the distribution of rare species and their ecological requirements, including traditional ecological knowledge so that conservation strategies can be implemented. This is aligned with the Convention on Biological Diversity that was signed by over 150 nations, and thus the world's complex array of human-natural-technological relationships has effectively been re-organized.

  10. Laser capture microdissection in the genomic and proteomic era: targeting the genetic basis of cancer.

    Science.gov (United States)

    Domazet, Barbara; Maclennan, Gregory T; Lopez-Beltran, Antonio; Montironi, Rodolfo; Cheng, Liang

    2008-03-15

    The advent of new technologies has enabled deeper insight into processes at subcellular levels, which will ultimately improve diagnostic procedures and patient outcome. Thanks to cell enrichment methods, it is now possible to study cells in their native environment. This has greatly contributed to a rapid growth in several areas, such as gene expression analysis, proteomics, and metabolonomics. Laser capture microdissection (LCM) as a method of procuring subpopulations of cells under direct visual inspection is playing an important role in these areas. This review provides an overview of existing LCM technology and its downstream applications in genomics, proteomics, diagnostics and therapy.

  11. Adrenocortical carcinoma: the dawn of a new era of genomic and molecular biology analysis.

    Science.gov (United States)

    Armignacco, R; Cantini, G; Canu, L; Poli, G; Ercolino, T; Mannelli, M; Luconi, M

    2018-05-01

    Over the last decade, the development of novel and high penetrance genomic approaches to analyze biological samples has provided very new insights in the comprehension of the molecular biology and genetics of tumors. The use of these techniques, consisting of exome sequencing, transcriptome, miRNome, chromosome alteration, genome, and epigenome analysis, has also been successfully applied to adrenocortical carcinoma (ACC). In fact, the analysis of large cohorts of patients allowed the stratification of ACC with different patterns of molecular alterations, associated with different outcomes, thus providing a novel molecular classification of the malignancy to be associated with the classical pathological analysis. Improving our knowledge about ACC molecular features will result not only in a better diagnostic and prognostic accuracy, but also in the identification of more specific therapeutic targets for the development of more effective pharmacological anti-cancer approaches. In particular, the specific molecular alteration profiles identified in ACC may represent targetable events by the use of already developed or newly designed drugs enabling a better and more efficacious management of the ACC patient in the context of new frontiers of personalized precision medicine.

  12. New Software for the Fast Estimation of Population Recombination Rates (FastEPRR in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Feng Gao

    2016-06-01

    Full Text Available Genetic recombination is a very important evolutionary mechanism that mixes parental haplotypes and produces new raw material for organismal evolution. As a result, information on recombination rates is critical for biological research. In this paper, we introduce a new extremely fast open-source software package (FastEPRR that uses machine learning to estimate recombination rate ρ (=4Ner from intraspecific DNA polymorphism data. When ρ>10 and the number of sampled diploid individuals is large enough (≥50, the variance of ρFastEPRR remains slightly smaller than that of ρLDhat. The new estimate ρcomb (calculated by averaging ρFastEPRR and ρLDhat has the smallest variance of all cases. When estimating ρFastEPRR, the finite-site model was employed to analyze cases with a high rate of recurrent mutations, and an additional method is proposed to consider the effect of variable recombination rates within windows. Simulations encompassing a wide range of parameters demonstrate that different evolutionary factors, such as demography and selection, may not increase the false positive rate of recombination hotspots. Overall, accuracy of FastEPRR is similar to the well-known method, LDhat, but requires far less computation time. Genetic maps for each human population (YRI, CEU, and CHB extracted from the 1000 Genomes OMNI data set were obtained in less than 3 d using just a single CPU core. The Pearson Pairwise correlation coefficient between the ρFastEPRR and ρLDhat maps is very high, ranging between 0.929 and 0.987 at a 5-Mb scale. Considering that sample sizes for these kinds of data are increasing dramatically with advances in next-generation sequencing technologies, FastEPRR (freely available at http://www.picb.ac.cn/evolgen/ is expected to become a widely used tool for establishing genetic maps and studying recombination hotspots in the population genomic era.

  13. Communicating genetic risk information for common disorders in the era of genomic medicine.

    Science.gov (United States)

    Lautenbach, Denise M; Christensen, Kurt D; Sparks, Jeffrey A; Green, Robert C

    2013-01-01

    Communicating genetic risk information in ways that maximize understanding and promote health is increasingly important given the rapidly expanding availability and capabilities of genomic technologies. A well-developed literature on risk communication in general provides guidance for best practices, including presentation of information in multiple formats, attention to framing effects, use of graphics, sensitivity to the way numbers are presented, parsimony of information, attentiveness to emotions, and interactivity as part of the communication process. Challenges to communicating genetic risk information include deciding how best to tailor it, streamlining the process, deciding what information to disclose, accepting that communications may have limited influence, and understanding the impact of context. Meeting these challenges has great potential for empowering individuals to adopt healthier lifestyles and improve public health, but will require multidisciplinary approaches and collaboration.

  14. Integrating population genetics and conservation biology in the era of genomics.

    Science.gov (United States)

    Ouborg, N Joop

    2010-02-23

    As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled 'Integrating Population Genetics and Conservation Biology' was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

  15. Back to the Future - Part 1. The medico-legal autopsy from ancient civilization to the post-genomic era.

    Science.gov (United States)

    Cecchetto, Giovanni; Bajanowski, Thomas; Cecchi, Rossana; Favretto, Donata; Grabherr, Silke; Ishikawa, Takaki; Kondo, Toshikazu; Montisci, Massimo; Pfeiffer, Heidi; Bonati, Maurizio Rippa; Shokry, Dina; Vennemann, Marielle; Ferrara, Santo Davide

    2017-07-01

    Part 1 of the review "Back to the Future" examines the historical evolution of the medico-legal autopsy and microscopy techniques, from Ancient Civilization to the Post-Genomic Era. In the section focusing on "The Past", the study of historical sources concerning the origins and development of the medico-legal autopsy, from the Bronze Age until the Middle Ages, shows how, as early as 2000 BC, the performance of autopsies for medico-legal purposes was a known and widespread practice in some ancient civilizations in Egypt, the Far East and later in Europe. In the section focusing on "The Present", the improvement of autopsy techniques by Friedrich Albert Zenker and Rudolf Virchow and the contemporary development of optical microscopy techniques for forensic purposes during the 19th and 20th centuries are reported, emphasizing, the regulation of medico-legal autopsies in diverse nations around the world and the publication of international guidelines or best practices elaborated by International Scientific Societies. Finally, in "The Future" section, innovative robotized and advanced microscopy systems and techniques, including their possible use in the bio-medicolegal field, are reported, which should lead to the improvement and standardization of the autopsy methodology, thereby achieving a more precise identification of natural and traumatic pathologies.

  16. Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

    Science.gov (United States)

    Apweiler, R; Gateau, A; Contrino, S; Martin, M J; Junker, V; O'Donovan, C; Lang, F; Mitaritonna, N; Kappus, S; Bairoch, A

    1997-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Ongoing genome sequencing projects have dramatically increased the number of protein sequences to be incorporated into SWISS-PROT. Since we do not want to dilute the quality standards of SWISS-PROT by incorporating sequences without proper sequence analysis and annotation, we cannot speed up the incorporation of new incoming data indefinitely. However, as we also want to make the sequences available as fast as possible, we introduced TREMBL (TRanslation of EMBL nucleotide sequence database), a supplement to SWISS-PROT. TREMBL consists of computer-annotated entries in SWISS-PROT format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in SWISS-PROT. While TREMBL is already of immense value, its computer-generated annotation does not match the quality of SWISS-PROTs. The main difference is in the protein functional information attached to sequences. With this in mind, we are dedicating substantial effort to develop and apply computer methods to enhance the functional information attached to TREMBL entries.

  17. The future of radiation therapy in the post-genomic era

    International Nuclear Information System (INIS)

    McBride, W. H.; Iwamoto, K. S.

    2003-01-01

    The cloning of the human genome has generated a tremendous resource of information that will improve treatment of cancer, and other diseases. Allied to these discoveries are powerful new investigative tools that have been, and are being, developed. These are being used to give a comprehensive biological profile of individuals and their cancer that will allow better classification, as well as identification of pathways that might be targeted with therapeutic benefit. The hope is that these approaches will allow intervention that is tailored to the needs of the individual patient and that the targeted cancer therapies will be associated with less toxicity than those currently used. This raises questions as to how best to use the new biotechnologies to predict responses to conventional therapies and indeed will conventional therapies, like radiation therapy, have a role in cancer treatment as specific biologically targeted drugs become commonplace. Here, it is argued that even the molecular staging of cancer that is currently being performed, if exploited correctly, will greatly aid patient selection for radiation therapy and that this should be the starting point for further studies aimed at developing predictive profiles for improving treatment outcome. It is also argued that because the biological anti-cancer agents target molecular pathways that overlap with those responsible for radiosensitivity, and because on their own they have little cytotoxic power, radiation therapists should incorporate biological agents into combined modality regimens and that this is likely to be a standard form of treatment in the next decade. (author)

  18. Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

    Science.gov (United States)

    O'Donnell, Christopher J; Nabel, Elizabeth G

    2008-10-01

    The inaugural issue of Circulation: Cardiovascular Genetics arrives at a remarkable time in the history of genetic research and cardiovascular medicine. Despite tremendous progress in knowledge gained, cardiovascular disease(CVD) remains the leading cause of death in the United States,1 and it has overcome infectious diseases as the leading cause of death worldwide.2 In addition, rates of CVD remain higher in black and Hispanic populations in the United States.1 The recent Strategic Plan of the National Heart, Lung,and Blood Institute (NHLBI) emphasizes research areas to fill the significant knowledge gaps needed to improve the diagnosis,treatment, and control of known risk factors and clinically apparent disease. Simultaneously, the NHLBI Strategic Plan recognizes a tremendous opportunity that is available for use of genetic and genomic research to generate new knowledge that might reduce the morbidity and mortality from CVD in US populations.3 Public availability of vast amounts of detailed sequence information about the human genome, completed sequence data on dozens of other animal genomes, and private sector development of high-throughput genetic technologies has transformed in a few short years the conduct of cardiovascular genetics and genomics research from a primary focus on mendelian disorders to a current emphasis on genome-wide association studies (GWAS; Figure1). In this review, we describe the rationale for the current emphasis on large-scale genomic studies, summarize the evolving approaches and progress to date, and identify immediate-term research needs. The National Institutes of Health (NIH) and the NHLBI are supporting a portfolio of large-scale genetic and genomic programs in diverse US populations with the longer-term objective of translating knowledge into the prediction, prevention, and preemption of CVD, as well as lung, sleep, and blood disorders. Underlying this portfolio is a strong commitment to make available participant-level data and

  19. Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era

    Science.gov (United States)

    Tebani, Abdellah; Abily-Donval, Lenaig; Afonso, Carlos; Marret, Stéphane; Bekri, Soumeya

    2016-01-01

    Inborn errors of metabolism (IEM) represent a group of about 500 rare genetic diseases with an overall estimated incidence of 1/2500. The diversity of metabolic pathways involved explains the difficulties in establishing their diagnosis. However, early diagnosis is usually mandatory for successful treatment. Given the considerable clinical overlap between some inborn errors, biochemical and molecular tests are crucial in making a diagnosis. Conventional biological diagnosis procedures are based on a time-consuming series of sequential and segmented biochemical tests. The rise of “omic” technologies offers holistic views of the basic molecules that build a biological system at different levels. Metabolomics is the most recent “omic” technology based on biochemical characterization of metabolites and their changes related to genetic and environmental factors. This review addresses the principles underlying metabolomics technologies that allow them to comprehensively assess an individual biochemical profile and their reported applications for IEM investigations in the precision medicine era. PMID:27447622

  20. The Environmental Acinetobacter baumannii Isolate DSM30011 Reveals Clues into the Preantibiotic Era Genome Diversity, Virulence Potential, and Niche Range of a Predominant Nosocomial Pathogen

    Science.gov (United States)

    Viale, Alejandro M.; Borges, Vítor; Cameranesi, María M.; Taib, Najwa; Espariz, Martín; Brochier-Armanet, Céline; Gomes, João Paulo; Salcedo, Suzana P.

    2017-01-01

    Abstract Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A. baumannii genomes revealed the presence of 12 unique accessory chromosomal regions in DSM30011 including five encompassing phage-related genes, five containing toxin genes of the type-6 secretion system, and one with an atypical CRISPRs/cas cluster. No antimicrobial resistance islands were identified in DSM30011 agreeing with a general antimicrobial susceptibility phenotype including folate synthesis inhibitors. The marginal ampicillin resistance of DSM30011 most likely derived from chromosomal ADC-type ampC and blaOXA-51-type genes. Searching for catabolic pathways genes revealed several clusters involved in the degradation of plant defenses including woody tissues and a previously unreported atu locus responsible of aliphatic terpenes degradation, thus suggesting that resinous plants may provide an effective niche for this organism. DSM30011 also harbored most genes and regulatory mechanisms linked to persistence and virulence in pathogenic Acinetobacter species. This strain thus revealed important clues into the genomic diversity, virulence potential, and niche ranges of the preantibiotic era A. baumannii population, and may provide an useful tool for our understanding of the processes that led to the recent evolution of this species toward an opportunistic pathogen of humans. PMID:28934377

  1. Perspectives in the control of infectious diseases by transgenic mosquitoes in the post-genomic era: a review

    Directory of Open Access Journals (Sweden)

    Márcia Aparecida Sperança

    2007-06-01

    Full Text Available Arthropod-borne diseases caused by a variety of microorganisms such as dengue virus and malaria parasites afflict billions of people worldwide imposing major economic and social burdens. Despite many efforts, vaccines against diseases transmitted by mosquitoes, with the exception of yellow fever, are not available. Control of such infectious pathogens is mainly performed by vector management and treatment of affected individuals with drugs. However, the numbers of insecticide-resistant insects and drug-resistant parasites are increasing. Therefore, inspired in recent years by a lot of new data produced by genomics and post-genomics research, several scientific groups have been working on different strategies to control infectious arthropod-borne diseases. This review focuses on recent advances and perspectives towards construction of transgenic mosquitoes refractory to malaria parasites and dengue virus transmission.

  2. Perspectives in the control of infectious diseases by transgenic mosquitoes in the post-genomic era--a review.

    Science.gov (United States)

    Sperança, Márcia Aparecida; Capurro, Margareth Lara

    2007-06-01

    Arthropod-borne diseases caused by a variety of microorganisms such as dengue virus and malaria parasites afflict billions of people worldwide imposing major economic and social burdens. Despite many efforts, vaccines against diseases transmitted by mosquitoes, with the exception of yellow fever, are not available. Control of such infectious pathogens is mainly performed by vector management and treatment of affected individuals with drugs. However, the numbers of insecticide-resistant insects and drug-resistant parasites are increasing. Therefore, inspired in recent years by a lot of new data produced by genomics and post-genomics research, several scientific groups have been working on different strategies to control infectious arthropod-borne diseases. This review focuses on recent advances and perspectives towards construction of transgenic mosquitoes refractory to malaria parasites and dengue virus transmission.

  3. Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine

    Science.gov (United States)

    Kumar, Avishek; Butler, Brandon M.; Kumar, Sudhir; Ozkan, S. Banu

    2016-01-01

    Summary Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. PMID:26684487

  4. Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.

    Science.gov (United States)

    Kumar, Avishek; Butler, Brandon M; Kumar, Sudhir; Ozkan, S Banu

    2015-12-01

    Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Research Guidelines in the Era of Large-scale Collaborations: An Analysis of Genome-wide Association Study Consortia

    Science.gov (United States)

    Austin, Melissa A.; Hair, Marilyn S.; Fullerton, Stephanie M.

    2012-01-01

    Scientific research has shifted from studies conducted by single investigators to the creation of large consortia. Genetic epidemiologists, for example, now collaborate extensively for genome-wide association studies (GWAS). The effect has been a stream of confirmed disease-gene associations. However, effects on human subjects oversight, data-sharing, publication and authorship practices, research organization and productivity, and intellectual property remain to be examined. The aim of this analysis was to identify all research consortia that had published the results of a GWAS analysis since 2005, characterize them, determine which have publicly accessible guidelines for research practices, and summarize the policies in these guidelines. A review of the National Human Genome Research Institute’s Catalog of Published Genome-Wide Association Studies identified 55 GWAS consortia as of April 1, 2011. These consortia were comprised of individual investigators, research centers, studies, or other consortia and studied 48 different diseases or traits. Only 14 (25%) were found to have publicly accessible research guidelines on consortia websites. The available guidelines provide information on organization, governance, and research protocols; half address institutional review board approval. Details of publication, authorship, data-sharing, and intellectual property vary considerably. Wider access to consortia guidelines is needed to establish appropriate research standards with broad applicability to emerging forms of large-scale collaboration. PMID:22491085

  6. ‘There and back again’: revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

    Science.gov (United States)

    Magiorkinis, Gkikas; Belshaw, Robert; Katzourakis, Aris

    2013-01-01

    Almost 8% of the human genome comprises endogenous retroviruses (ERVs). While they have been shown to cause specific pathologies in animals, such as cancer, their association with disease in humans remains controversial. The limited evidence is partly due to the physical and bioethical restrictions surrounding the study of transposons in humans, coupled with the major experimental and bioinformatics challenges surrounding the association of ERVs with disease in general. Two biotechnological landmarks of the past decade provide us with unprecedented research artillery: (i) the ultra-fine sequencing of the human genome and (ii) the emergence of high-throughput sequencing technologies. Here, we critically assemble research about potential pathologies of ERVs in humans. We argue that the time is right to revisit the long-standing questions of human ERV pathogenesis within a robust and carefully structured framework that makes full use of genomic sequence data. We also pose two thought-provoking research questions on potential pathophysiological roles of ERVs with respect to immune escape and regulation. PMID:23938753

  7. So many genes, so little time: A practical approach to divergence-time estimation in the genomic era.

    Science.gov (United States)

    Smith, Stephen A; Brown, Joseph W; Walker, Joseph F

    2018-01-01

    Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications. However, despite the recent explosion in genomic and transcriptomic data, the utility of these data sources for efficient divergence-time inference remains unexamined. Phylogenomic datasets pose two distinct problems for divergence-time estimation: (i) the volume of data makes inference of the entire dataset intractable, and (ii) the extent of underlying topological and rate heterogeneity across genes makes model mis-specification a real concern. "Gene shopping", wherein a phylogenomic dataset is winnowed to a set of genes with desirable properties, represents an alternative approach that holds promise in alleviating these issues. We implemented an approach for phylogenomic datasets (available in SortaDate) that filters genes by three criteria: (i) clock-likeness, (ii) reasonable tree length (i.e., discernible information content), and (iii) least topological conflict with a focal species tree (presumed to have already been inferred). Such a winnowing procedure ensures that errors associated with model (both clock and topology) mis-specification are minimized, therefore reducing error in divergence-time estimation. We demonstrated the efficacy of this approach through simulation and applied it to published animal (Aves, Diplopoda, and Hymenoptera) and plant (carnivorous Caryophyllales, broad Caryophyllales, and Vitales) phylogenomic datasets. By quantifying rate heterogeneity across both genes and lineages we found that every empirical dataset examined included genes with clock-like, or nearly clock-like, behavior. Moreover, many datasets had genes that were clock-like, exhibited reasonable evolutionary rates, and were mostly compatible with the species tree. We identified overlap in age estimates when analyzing these filtered genes under strict clock and uncorrelated

  8. Improving livestock for agriculture - technological progress from random transgenesis to precision genome editing heralds a new era.

    Science.gov (United States)

    Laible, Götz; Wei, Jingwei; Wagner, Stefan

    2015-01-01

    Humans have a long history in shaping the genetic makeup of livestock to optimize production and meet growing human demands for food and other animal products. Until recently, this has only been possible through traditional breeding and selection, which is a painstakingly slow process of accumulating incremental gains over a long period. The development of transgenic livestock technology offers a more direct approach with the possibility for making genetic improvements with greater impact and within a single generation. However, initially the technology was hampered by technical difficulties and limitations, which have now largely been overcome by progressive improvements over the past 30 years. Particularly, the advent of genome editing in combination with homologous recombination has added a new level of efficiency and precision that holds much promise for the genetic improvement of livestock using the increasing knowledge of the phenotypic impact of genetic sequence variants. So far not a single line of transgenic livestock has gained approval for commercialization. The step change to genome-edited livestock with precise sequence changes may accelerate the path to market, provided applications of this new technology for agriculture can deliver, in addition to economic incentives for producers, also compelling benefits for animals, consumers, and the environment. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. What’s old is new again: yeast mutant screens in the era of pooled segregant analysis by genome sequencing

    Directory of Open Access Journals (Sweden)

    Chris Curtin

    2016-04-01

    Full Text Available While once de-rigueur for identification of genes involved in biological processes, screening of chemically induced mutant populations is an approach that has largely been superseded for model organisms such as Saccharomyces cerevisiae. Availability of single gene deletion/overexpression libraries and combinatorial synthetic genetic arrays provide yeast researchers more structured ways to probe genetic networks. Furthermore, in the age of inexpensive DNA sequencing, methodologies such as mapping of quantitative trait loci (QTL by pooled segregant analysis and genome-wide association enable the identification of multiple naturally occurring allelic variants that contribute to polygenic phenotypes of interest. This is, however, contingent on the capacity to screen large numbers of individuals and existence of sufficient natural phenotypic variation within the available population. The latter cannot be guaranteed and non-selectable, industrially relevant phenotypes, such as production of volatile aroma compounds, pose severe limitations on the use of modern genetic techniques due to expensive and time-consuming downstream analyses. An interesting approach to overcome these issues can be found in Den Abt et al.[1] (this issue of Microbial Cell, where a combination of repeated rounds of chemical mutagenesis and pooled segregant analysis by whole genome sequencing was applied to identify genes involved in ethyl acetate formation, demonstrating a new path for industrial yeast strain development and bringing classical mutant screens into the 21st century.

  10. Integrated, multi-scale, spatial-temporal cell biology--A next step in the post genomic era.

    Science.gov (United States)

    Horwitz, Rick

    2016-03-01

    New microscopic approaches, high-throughput imaging, and gene editing promise major new insights into cellular behaviors. When coupled with genomic and other 'omic information and "mined" for correlations and associations, a new breed of powerful and useful cellular models should emerge. These top down, coarse-grained, and statistical models, in turn, can be used to form hypotheses merging with fine-grained, bottom up mechanistic studies and models that are the back bone of cell biology. The goal of the Allen Institute for Cell Science is to develop the top down approach by developing a high throughput microscopy pipeline that is integrated with modeling, using gene edited hiPS cell lines in various physiological and pathological contexts. The output of these experiments and models will be an "animated" cell, capable of integrating and analyzing image data generated from experiments and models. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry.

    Science.gov (United States)

    Atzmon, Gil; Hao, Li; Pe'er, Itsik; Velez, Christopher; Pearlman, Alexander; Palamara, Pier Francesco; Morrow, Bernice; Friedman, Eitan; Oddoux, Carole; Burns, Edward; Ostrer, Harry

    2010-06-11

    For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.

  12. Dissecting DNA repair in adult high grade gliomas for patient stratification in the post-genomic era

    Science.gov (United States)

    Perry, Christina; Agarwal, Devika; Abdel-Fatah, Tarek M.A.; Lourdusamy, Anbarasu; Grundy, Richard; Auer, Dorothee T.; Walker, David; Lakhani, Ravi; Scott, Ian S.; Chan, Stephen; Ball, Graham; Madhusudan, Srinivasan

    2014-01-01

    Deregulation of multiple DNA repair pathways may contribute to aggressive biology and therapy resistance in gliomas. We evaluated transcript levels of 157 genes involved in DNA repair in an adult glioblastoma Test set (n=191) and validated in ‘The Cancer Genome Atlas’ (TCGA) cohort (n=508). A DNA repair prognostic index model was generated. Artificial neural network analysis (ANN) was conducted to investigate global gene interactions. Protein expression by immunohistochemistry was conducted in 61 tumours. A fourteen DNA repair gene expression panel was associated with poor survival in Test and TCGA cohorts. A Cox multivariate model revealed APE1, NBN, PMS2, MGMT and PTEN as independently associated with poor prognosis. A DNA repair prognostic index incorporating APE1, NBN, PMS2, MGMT and PTEN stratified patients in to three prognostic sub-groups with worsening survival. APE1, NBN, PMS2, MGMT and PTEN also have predictive significance in patients who received chemotherapy and/or radiotherapy. ANN analysis of APE1, NBN, PMS2, MGMT and PTEN revealed interactions with genes involved in transcription, hypoxia and metabolic regulation. At the protein level, low APE1 and low PTEN remain associated with poor prognosis. In conclusion, multiple DNA repair pathways operate to influence biology and clinical outcomes in adult high grade gliomas. PMID:25026297

  13. ASPECTOS BIOÉTICOS DEL CONSEJO GENÉTICO EN LA ERA DEL PROYECTO DEL GENOMA HUMANO ASPECTOS BIOÉTICOS DO CONSELHO GENÉTICO NA ERA DO PROJETO DO GENOMA HUMANO THE GENETIC COUNCIL’S BIOETHIC ASPECTS IN THE HUMAN GENOME PROJECT’S ERA

    Directory of Open Access Journals (Sweden)

    Manuel J Santos Alcántara

    2004-01-01

    Full Text Available El conocimiento obtenido a la fecha acerca del Genoma Humano a través del Proyecto Genoma Humano (PGH, ha impactado profundamente en la medicina. La medicina en la era genómica se va tornando cada vez más preventiva que curativa. El conocimiento obtenido por el PGH ha permitido desarrollar tests de diagnóstico genético que pueden aplicarse a personas ya enfermas o a aquellas que todavía no han desarrollado una particular afección genética (diagnóstico presintomático. También estos tests pueden aplicarse para el diagnóstico antenatal y embrionario preimplantacional de enfermedades genéticas. En la aplicación de estos tests el Consejo Genético, en su calidad de acto médico, tiene un rol esencial. En este artículo se presentará el Proyecto del Genoma Humano, el proceso del Consejo Genético y sus implicancias bioéticas desde una perspectiva principialista y personalistaO conhecimento obtido até hoje acerca do Genoma Humano através do Projeto Genoma Humano (PGH, impactou profundamente na Medicina. A Medicina na era genómica vai se tornando cada vez mais curativa. O conhecimento obtido através do PGH permitiu desenvolver testes de diagnóstico genético, que podem aplicar-se a pessoas já enfermas ou a aquelas que todavia não desenvolveram uma afecção genética particular (diagnóstico pré-sintomático. Estes testes também podem ser aplicados para o diagnóstico pré-natal e embrionário de doenças genéticas. Na aplicação destes testes, o Conselho Genético, na sua qualidade de ato médico, tem um papel essencial. Neste artigo será apresentado o Projeto do Genoma Humano, o Processo do Conselho Genético e suas implicações bioéticas de uma perspectiva principialista e personalistaThe Human Genome Project has had a significant impact in Medicine. Genomic Medicine is becoming more preventive than curative. The knowledge obtained by the Human Genome Project has allowed the development of genetic diagnostic tests for

  14. ERA-40

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — ERA-40 project was to produce and promote the use of a comprehensive set of global analysis describing the state of the atmosphere and land and ocean-wave conditions...

  15. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  16. MEETING REPORT ASSESSING HUMAN GERM-CELL MUTAGENESIS IN THE POST-GENOME ERA: A CELEBRATION OF THE LEGACY OF WILLIAM LAWSON (BILL) RUSSELL

    Science.gov (United States)

    Although numerous germ-cell mutagens have been identified in animal model systems, to date, no human germ-cell mutagens have been confirmed. Because the genomic integrity of our germ cells is essential for the continuation of the human species, a resolution of this enduring conu...

  17. Meeting Report. Assessing Human Germ-Cell Mutagenesis in thePost-Genome Era: A Celebration of the Legacy of William Lawson (Bill)Russell

    Energy Technology Data Exchange (ETDEWEB)

    Wyrobek, Andrew J.; Mulvihill, John J.; Wassom, John S.; Malling,Heinrich V.; Shelby, Michael D.; Lewis, Susan E.; Witt, Kristine L.; Preston, R. Julian; Perreault-Darney, Sally; Allen, James W.; DeMarini,David M.; Woychik, Richard P.; Bishop Jack B; Workshop Presenters

    2006-04-18

    Although numerous germ-cell mutagens have been identified inanimal model systems, to date, no human germ-cell mutagens have beenconfirmed. Because the genomic integrity of our germ cells is essentialfor the continuation of the human species, a resolution of this enduringconundrum is needed. To facilitate such a resolution, we organized aworkshop at The Jackson Laboratory in Bar Harbor, Maine on September28-30, 2004. This interactive workshop brought together scientists from awide range of disciplines to assess the applicability of emergingmolecular methods for genomic analysis to the field of human germ-cellmutagenesis. Participants recommended that focused, coordinated humangerm-cell mutation studies be conducted in relation to important societalexposures. Because cancer survivors represent a unique cohort withwell-defined exposures, there was a consensus that studies should bedesigned to assess the mutational impact on children born to parents whohad received certain types of mutagenic cancer chemotherapy prior toconceiving their children. Within this high-risk cohort, parents andchildren could be evaluated for inherited changes in (a) gene sequencesand chromosomal structure, (b) repeat sequences and minisatelliteregions, and (c) global gene expression and chromatin. Participants alsorecommended studies to examine trans-generational effects in humansinvolving mechanisms such as changes in imprinting and methylationpatterns, expansion of nucleotide repeats, or induction of mitochondrialDNA mutations. Workshop participants advocated establishment of abio-bank of human tissue samples that could be used to conduct amultiple-endpoint, comprehensive, and collaborative effort to detectexposure-induced heritable alterations in the human genome. Appropriateanimal models of human germ-cell mutagenes is should be used in parallelwith human studies to provide insights into the mechanisms of mammaliangerm-cell mutagenesis. Finally, participants recommended that

  18. Moving into a new era of periodontal genetic studies: relevance of large case-control samples using severe phenotypes for genome-wide association studies.

    Science.gov (United States)

    Vaithilingam, R D; Safii, S H; Baharuddin, N A; Ng, C C; Cheong, S C; Bartold, P M; Schaefer, A S; Loos, B G

    2014-12-01

    Studies to elucidate the role of genetics as a risk factor for periodontal disease have gone through various phases. In the majority of cases, the initial 'hypothesis-dependent' candidate-gene polymorphism studies did not report valid genetic risk loci. Following a large-scale replication study, these initially positive results are believed to be caused by type 1 errors. However, susceptibility genes, such as CDKN2BAS (Cyclin Dependend KiNase 2B AntiSense RNA; alias ANRIL [ANtisense Rna In the Ink locus]), glycosyltransferase 6 domain containing 1 (GLT6D1) and cyclooxygenase 2 (COX2), have been reported as conclusive risk loci of periodontitis. The search for genetic risk factors accelerated with the advent of 'hypothesis-free' genome-wide association studies (GWAS). However, despite many different GWAS being performed for almost all human diseases, only three GWAS on periodontitis have been published - one reported genome-wide association of GLT6D1 with aggressive periodontitis (a severe phenotype of periodontitis), whereas the remaining two, which were performed on patients with chronic periodontitis, were not able to find significant associations. This review discusses the problems faced and the lessons learned from the search for genetic risk variants of periodontitis. Current and future strategies for identifying genetic variance in periodontitis, and the importance of planning a well-designed genetic study with large and sufficiently powered case-control samples of severe phenotypes, are also discussed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  19. O desafio da malária: o caso brasileiro e o que se pode esperar dos progressos da era genômica The malaria challenge: the Brazilian case and what can be expected from progress in genomics

    Directory of Open Access Journals (Sweden)

    Luiz Hildebrando Pereira da Silva

    2002-01-01

    Full Text Available A área endêmica de malária no Brasil se estende atualmente à totalidade da região amazônica, com cerca de 500 mil casos anuais, em geral com situações de baixa e média endemicidade mas ainda apresentando focos de alto risco. Fatores demográficos e socioeconômicos são dominantes nos desafios que enfrentam os Serviços de Saúde Pública no controle da malária. No presente artigo são discutidos fatores determinantes da instabilidade da situação endêmica bem como a necessidade de ações permanentes de vigilância e de intervenção dos Serviços de Saúde para que se evitem surtos epidêmicos e alastramento das áreas endêmicas. No artigo, em seguida, apresenta-se uma síntese de progressos recentes nos estudos da era genômica e pós-genômica sobre o parasita, o vetor e o hospedeiro humano que podem favorecer, no futuro, o desenvolvimento e a melhoria dos métodos de controle da malária.Malaria endemic areas in Brazil are restricted to the Amazon Region, with an average of 500 thousand new cases every year. The situation can be defined as unstable hipoendemic with, however, foci of high endemicity. Demographic and socio economic factors are main determinants in the malaria challenge for the Public Health System. In the present paper, biological and social factors responsible for the unstable endemic situation are discussed. The need for a permanent surveillance and intervention of Public Health Services are stressed to avoid the occurrence of local epidemics and spreading of endemic areas. In the paper, are also summarised recent lines of research developed in the post genomic era in the studies of parasite, vector and human molecular genetics that would favour the development, in the future, of new tools and procedures for malaria control

  20. Insect Immunity: The Post-Genomic Era

    OpenAIRE

    Bangham, Jenny; Jiggins, Frank; Lemaitre, Bruno

    2006-01-01

    Insects have a complex and effective immune system, many components of which are conserved in mammals. But only in the last decade have the molecular mechanisms that regulate the insect immune response--and their relevance to general biology and human immunology--become fully appreciated. A meeting supported by the Centre National de la Récherche Scientifique (France) was held to bring together the whole spectrum of researchers working on insect immunity. The meeting addressed diverse aspects...

  1. ERA`s Ranger uranium mine

    Energy Technology Data Exchange (ETDEWEB)

    Davies, W. [Energy Resources of Australia Ltd., Sydney, NSW (Australia)

    1997-12-31

    Energy Resource of Australia (ERA) is a public company with 68% of its shares owned by the Australian company North Limited. It is currently operating one major production centre - Ranger Mine which is 260 kilometres east of Darwin, extracting and selling uranium from the Ranger Mine in the Northern Territory to nuclear electricity utilities in Japan, South Korea, Europe and North America. The first drum of uranium oxide from Ranger was drummed in August 1981 and operations have continued since that time. ERA is also in the process of working towards obtaining approvals for the development of a second mine - Jabiluka which is located 20 kilometres north of Ranger. The leases of Ranger and Jabiluka adjoin. The Minister for the Environment has advised the Minister for Resources and Energy that there does not appear to be any environmental issue which would prevent the preferred Jabiluka proposal from proceeding. Consent for the development of ERA`s preferred option for the development of Jabiluka is being sought from the Aboriginal Traditional Owners. Ranger is currently the third largest producing uranium mine in the world producing 4,237 tonnes of U{sub 3}O{sub 8} in the year to June 1997.

  2. Population genomics of fungal and oomycete pathogens

    Science.gov (United States)

    We are entering a new era in plant pathology where whole-genome sequences of many individuals of a pathogen species are becoming readily available. This era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. Population gen...

  3. Dakwah di Era Digital

    OpenAIRE

    Budiantoro, Wahyu

    2018-01-01

    These days dakwah is not only interpreted as transformation of a pure religious value, but also transformation of a more relevant value including many aspects in digital era. Digital era is when society succumbed into the flow of information causing cultural shock and difficulties on synthesizing meaning from those scattered information. Dakwah on Digital age must accommodate societal needs which tend to move into a mass society. It results in strategy and more humane and innovative dakwah me...

  4. Ecological recovery in ERA

    DEFF Research Database (Denmark)

    EFSA Scientific Committee (Scientific Committee); Topping, Christopher John

    2016-01-01

    knowledge and data retrieved from the literature. Finally, the information presented in this opinion was reviewed by experts from the relevant EFSA Panels, European risk assessment bodies and through an open consultation requesting input from stakeholders. A conceptual framework was developed to address...... recognises the importance of more integrated ERAs considering both the local and landscape scales, as well as the possible co-occurrence of multiple potential stressors that fall under the remit of EFSA, which are important when addressing ecological recovery. In this scientific opinion, the Scientific...... Committee gathered scientific knowledge on the potential for the recovery of non-target organisms for the further development of ERA. Current EFSA guidance documents and opinions were reviewed on how ecological recovery is addressed in ERA schemes. In addition, this scientific opinion is based on expert...

  5. ERA: Adverse Consequences

    Science.gov (United States)

    Martin, Brian

    2011-01-01

    Excellence in Research for Australia has a number of limitations: inputs are counted as outputs, time is wasted, disciplinary research is favoured and public engagement is discouraged. Most importantly, by focusing on measurement and emphasising competition, ERA may actually undermine the cooperation and intrinsic motivation that underpin research…

  6. Energy: a new era

    International Nuclear Information System (INIS)

    Moore, Curtis.

    1995-01-01

    The world appears on the verge of a new era of advanced technologies and new fuels. Although such a transformation is unlikely to take place overnight, change is clearly coming. The question is how much and how fast: Will energy transition amount to a technological revolution, or merely an evolution? A detailed evaluation of the various aspects is given. (author). 23 refs

  7. ERA's Ranger uranium mine

    International Nuclear Information System (INIS)

    Davies, W.

    1997-01-01

    Energy Resource of Australia (ERA) is a public company with 68% of its shares owned by the Australian company North Limited. It is currently operating one major production centre - Ranger Mine which is 260 kilometres east of Darwin, extracting and selling uranium from the Ranger Mine in the Northern Territory to nuclear electricity utilities in Japan, South Korea, Europe and North America. The first drum of uranium oxide from Ranger was drummed in August 1981 and operations have continued since that time. ERA is also in the process of working towards obtaining approvals for the development of a second mine - Jabiluka which is located 20 kilometres north of Ranger. The leases of Ranger and Jabiluka adjoin. The Minister for the Environment has advised the Minister for Resources and Energy that there does not appear to be any environmental issue which would prevent the preferred Jabiluka proposal from proceeding. Consent for the development of ERA's preferred option for the development of Jabiluka is being sought from the Aboriginal Traditional Owners. Ranger is currently the third largest producing uranium mine in the world producing 4,237 tonnes of U 3 O 8 in the year to June 1997

  8. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

    Directory of Open Access Journals (Sweden)

    James B Pettengill

    Full Text Available The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis. In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples and computational (petabytes of sequence data issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST scheme. When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates there are features (e.g., genomic, assembly, and contamination that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

  9. Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

    Science.gov (United States)

    Pettengill, James B; Pightling, Arthur W; Baugher, Joseph D; Rand, Hugh; Strain, Errol

    2016-01-01

    The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases of whole-genome sequence data are being populated. These databases currently contain tens of thousands of samples and are expected to grow to hundreds of thousands within a few years. For these databases to be of optimal use one must be able to quickly interrogate them to accurately determine the genetic distances among a set of samples. Being able to do so is challenging due to both biological (evolutionary diverse samples) and computational (petabytes of sequence data) issues. We evaluated seven measures of genetic distance, which were estimated from either k-mer profiles (Jaccard, Euclidean, Manhattan, Mash Jaccard, and Mash distances) or nucleotide sites (NUCmer and an extended multi-locus sequence typing (MLST) scheme). When analyzing empirical data (whole-genome sequence data from 18,997 Salmonella isolates) there are features (e.g., genomic, assembly, and contamination) that cause distances inferred from k-mer profiles, which treat absent data as informative, to fail to accurately capture the distance between samples when compared to distances inferred from differences in nucleotide sites. Thus, site-based distances, like NUCmer and extended MLST, are superior in performance, but accessing the computing resources necessary to perform them may be challenging when analyzing large databases.

  10. Dakwah di Era Digital

    Directory of Open Access Journals (Sweden)

    Wahyu Budiantoro

    2018-04-01

    Full Text Available These days dakwah is not only interpreted as transformation of a pure religious value, but also transformation of a more relevant value including many aspects in digital era. Digital era is when society succumbed into the flow of information causing cultural shock and difficulties on synthesizing meaning from those scattered information. Dakwah on Digital age must accommodate societal needs which tend to move into a mass society. It results in strategy and more humane and innovative dakwah methods. One of innovative dakwah methods is conducted dakwah activities through digital media,with the consequences of this is that da’i must developed soft skill and technological capabilities. Another beneficial comes from this is that dakwah could become more modern and practical in terms of methods and material. On the other hand, citizen Journalism as a mass cultural product and the results of technological development, gives an opportunity for da’i to able to record the entire activities, including the dynamics of islamic life. In terms of learning curriculum, dakwah in digital format must be included, so then the intellectual and cultural spirit which flourished in pesantren could be adapted and competed in a global world.

  11. Second Nuclear Era

    International Nuclear Information System (INIS)

    Weinberg, A.M.; Spiewak, I.; Barkenbus, J.N.; Livingston, R.S.; Phung, D.L.

    1984-03-01

    The Institute for Energy Analysis with support from The Andrew W. Mellon Foundation has studied the decline of the present nuclear era in the United States and the characteristics of a Second Nuclear Era which might be instrumental in restoring nuclear power to an appropriate place in the energy options of our country. The study has determined that reactors operating today are much safer than they were at the time of the TMI accident. A number of concepts for a supersafe reactor were reviewed and at least two were found that show considerable promise, the PIUS, a Swedish pressurized water design, and a gas-cooled modular design of German and US origin. Although new, safer, incrementally improved, conventional reactors are under study by the nuclear industry, the complete lack of new orders in the United States will slow their introduction and they are likely to be more expensive than present designs. The study recommends that supersafe reactors be taken seriously and that federal and private funds both be used to design and, if feasible, to build a prototype reactor of substantial size. 146 references, 8 figures, 2 tables

  12. Rework of the ERA software system: ERA-8

    Science.gov (United States)

    Pavlov, D.; Skripnichenko, V.

    2015-08-01

    The software system that has been powering many products of the IAA during decades has undergone a major rework. ERA has capabilities for: processing tables of observations of different kinds, fitting parameters to observations, integrating equations of motion of the Solar system bodies. ERA comprises a domain-specific language called SLON, tailored for astronomical tasks. SLON provides a convenient syntax for reductions of observations, choosing of IAU standards to use, applying rules for filtering observations or selecting parameters for fitting. Also, ERA includes a table editor and a graph plotter. ERA-8 has a number of improvements over previous versions such as: integration of the Solar system and TT xA1 TDB with arbitrary number of asteroids; option to use different ephemeris (including DE and INPOP); integrator with 80-bit floating point. The code of ERA-8 has been completely rewritten from Pascal to C (for numerical computations) and Racket (for running SLON programs and managing data). ERA-8 is portable across major operating systems. The format of tables in ERA-8 is based on SQLite. The SPICE format has been chosen as the main format for ephemeris in ERA-8.

  13. Nasionalisme di Era Internet

    Directory of Open Access Journals (Sweden)

    Danu Widhyatmoko

    2015-04-01

    Full Text Available Nationalism and nationality of a country life are moving into the new phase. Internet has become a new medium that opens up so many opportunities to create a sense of nationalism for the country. This paper contains a review of nationalism in the age of the Internet. This paper begins with understanding nationalism, the character of the Internet, social media and nationalism in the era of the Internet. Research method used in this paper is literature study, continued with reflective data analysis. With reflective analysis method, the authors analyzed data from the data collection has been carried out for comparison between the existing literature by circumstances or phenomena that occur, so that the conclusions of rational and scientific data can be obtained. 

  14. Harvesting Legume Genomes: Plant Genetic Resources

    Science.gov (United States)

    Genomics and high through-put phenotyping are ushering in a new era of accessing genetic diversity held in plant genetic resources, the cornerstone of both traditional and genomics-assisted breeding efforts of food legume crops. Acknowledged or not, yield plateaus must be broken given the daunting ...

  15. Introduction to the Post-Human Genome Project era, a target for interactions between polygenic and/or multiphenotypical components in cancer control in South America Introducción a la post era del Proyeto Genoma Humano: la interrelación entre componentes multi-genéticos y multi-fenotípicos en el control del cáncer en América Latina como una meta

    Directory of Open Access Journals (Sweden)

    José Iscovich

    1998-01-01

    Full Text Available Epidemiological studies have suggested that the propensity to develop malignancy involves a complex mix of genetic and environmental determinants, however both older and innovative techniques display unresolved questions regarding etiology. Current barriers to achieving the potential benefit from this understanding are: 1 incomplete background on the various environmental and genetic factors involved in the carcinogenesis mechanism; 2 difficulties in accurately differentiating specific molecular subtypes and measuring the effective cellular exposure dose; and 3 difficulties in determining the multifactorial interaction between genetic and environmental factors. To extrapolate Human Genome Project research findings to the Post-Human Genome Project era, South America provides a large population and large-pedigree families, thus including genetically heterogeneous and less heterogeneous groups. An initial strategy might be to trace high risk populations and the respective exposures to which they are susceptible, such as: 1 migration, identifying rural migrant populations; 2 inherent susceptibility, studying "long term homogeneous populations" or large families living in similar rural environments; and 3 dissection of gene-environmental interaction.Estudios epidemiológicos han demonstrado que la susceptibilidad de la población a las enfermedades malignas está basada en interrelaciones genéticas hereditarias y no hereditarias. Las técnicas epidemiológicas tradicionales no han resuelto los problemas básicos de los mecanismos etiológicos. Las barreras existentes son: 1 el conocimiento incompleto de las etapas del mecanismo de la carcinogénesis accionada por factores genéticos y ambientales; 2 la dificultad en delimitar subtipos específicos de neoplasmas basados en mecanismos moleculares definidos, y las dosis efectivas de exposición celular; y 3 la capacidad en determinar la interrelación en el mecanismo genético-ambiental. Anticipandose

  16. Saúde pública e ética na era da medicina genômica: rastreamentos genéticos Public health and ethics in the age of genomic medicine: genetic screening

    Directory of Open Access Journals (Sweden)

    Flavia Miranda Gomes de Constantino Bandeira

    2006-03-01

    Full Text Available O presente artigo tem como objetivo contextualizar o campo da saúde pública diante dos grandes avanços da biotecnologia e genética aplicada, destacando elementos para a problematização do tema tais como benefícios e questões éticas relacionados aos rastreamentos genéticos. O Projeto Genoma Humano gerou várias expectativas, dentre elas, a possibilidade de rastrear genes associados a doenças e comportamentos, e mais ainda, de intervir geneticamente no ser humano, levantando preocupações relativas ao renascimento da eugenia, ao aconselhamento genético, e ao uso da informação genética como critério de acesso aos planos de saúde e postos de trabalho. Uma discussão de todos esses tópicos é essencial para que a saúde pública seja beneficiada com as informações obtidas através da análise genômica das populações.This article has the objective to bring the field of public health into context in the face of the great advances of biotechnology and applied genetics, focusing on issues related to the theme such as benefits and ethics concerning genetic screening. The Human Genome Project has generated many expectations among which the possibility of screening genes associated to diseases and behaviors, moreover, the possibility of genetic interventions on humans, creating concerns related to the resurgence of Eugenia, of genetic counseling and the use of genetic information as a standard for access to healthcare clinics and jobs. The discussion of all these issues is essential to benefit public health with information obtained through population genomic analysis.

  17. The forthcoming era of precision medicine.

    Science.gov (United States)

    Gamulin, Stjepan

    2016-11-01

    The aim of this essay is to present the definition and principles of personalized or precision medicine, the perspective and barriers to its development and clinical application. The implementation of precision medicine in health care requires the coordinated efforts of all health care stakeholders (the biomedical community, government, regulatory bodies, patients' groups). Particularly, translational research with the integration of genomic and comprehensive data from all levels of the organism ("big data"), development of bioinformatics platforms enabling network analysis of disease etiopathogenesis, development of a legislative framework for handling personal data, and new paradigms of medical education are necessary for successful application of the concept of precision medicine in health care. In the present and future era of precision medicine, the collaboration of all participants in health care is necessary for its realization, resulting in improvement of diagnosis, prevention and therapy, based on a holistic, individually tailored approach. Copyright © 2016 by Academy of Sciences and Arts of Bosnia and Herzegovina.

  18. The forthcoming era of precision medicine

    Directory of Open Access Journals (Sweden)

    Stjepan Gamulin

    2016-11-01

    Full Text Available Abstract. The aim of this essay is to present the definition and principles of personalized or precision medicine, the perspective and barriers to its development and clinical application. The implementation of precision medicine in health care requires the coordinated efforts of all health care stakeholders (the biomedical community, government, regulatory bodies, patients’ groups. Particularly, translational research with the integration of genomic and comprehensive data from all levels of the organism (“big data”, development of bioinformatics platforms enabling network analysis of disease etiopathogenesis, development of a legislative framework for handling personal data, and new paradigms of medical education are necessary for successful application of the concept of precision medicine in health care. Conclusion. In the present and future era of precision medicine, the collaboration of all participants in health care is necessary for its realization, resulting in improvement of diagnosis, prevention and therapy, based on a holistic, individually tailored approach.

  19. VALUATION IN THE CONSTITUTIONAL ERA

    African Journals Online (AJOL)

    Brimer

    16 ..... stem from the pre-constitutional era, and the constitutional framework and its legitimate reform efforts. A decision on what is just ...... Carroll L Alice's Adventures in Wonderland (Digital Scanning Scituate MA. 2007). Dagan 1999 Va L Rev.

  20. Three eras of climate change

    Energy Technology Data Exchange (ETDEWEB)

    Huq, Saleemul; Toulmin, Camilla

    2006-10-15

    Climate change as a global challenge has evolved through a series of stages in the last few decades. We are now on the brink of a new era which will see the terms of the debate shift once again. The different eras are characterised by the scientific evidence, public perceptions, responses and engagement of different groups to address the problem. In the first era, from the late 1980s to 2000, climate change was seen as an “environmental” problem to do with prevention of future impacts on the planet's climate systems over the next fifty to hundred years, through reductions in emissions of greenhouse gases, known as “mitigation”. The second era can be said to have started around the turn of the millennium, with the recognition that there will be some unavoidable impacts from climate change in the near term (over the next decade or two). These impacts must be coped with through “adaptation”, as well as mitigation, to prevent much more severe and possibly catastrophic impacts in the longer term. It has become clear that many of the impacts of climate change in the near term are likely to fall on the poorest countries and communities. The third era, which we are just about to enter, will see the issue change from tackling an environmental or development problem to a question of “global justice”. It will engage with a much wider array of citizens from around the world than previous eras.

  1. Genome-derived vaccines.

    Science.gov (United States)

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  2. Desafios na era pós genômica para o desenvolvimento de testes laboratoriais para o diagnóstico da hanseníase Challenges in the post genomic era for the development of tests for leprosy diagnosis

    Directory of Open Access Journals (Sweden)

    Mariane Martins de Araújo Stefani

    2008-01-01

    Full Text Available O diagnóstico da hanseníase se baseia em manifestações clínicas e não existe teste laboratorial para diagnosticar casos assintomáticos ou para prever progressão da doença entre indivíduos expostos. Novas análises genômicas comparativas in silico e ferramentas de biologia molecular têm sido empregadas para revelar proteínas exclusivas do Mycobacterium leprae que apresentem potencial aplicação diagnóstica. A hanseníase tuberculóide paucibacilar (PB apresenta baixo nível de anticorpos e forte resposta imune celular (RIC tipo Th1/interferon gamma (IFN-γ. A doença lepromatosa multibacilar (MB apresenta sorologia positiva e fraca RIC. Portanto, testes laboratoriais para diagnosticar hanseníase PB e MB devem contemplar testes de RIC e sorologia. Proteínas recombinantes do Mycobacterium leprae sorologicamente reativas podem ser incorporadas ao antígeno PGLI para melhorar o diagnóstico sorológico de pacientes MB. Proteínas recombinantes e peptídeos sintéticos do Mycobacterium leprae têm sido testados em ensaios de RIC/IFN-γ para diagnosticar casos PB. Sorologia anti-PGLI modificada incorporando novos antígenos do Mycobacterium leprae e ensaios baseados na RIC/produção de IFN-γ devem permitir a detecção precoce de casos MB e PB em países endêmicos.Leprosy diagnosis is based mainly on clinical manifestations and no laboratory test is available to diagnose asymptomatic disease or to predict disease progression among exposed individuals. Novel comparative genomic in silico analyses and molecular biology tools have discovered unique Mycobacterium leprae proteins with potential diagnostic application. Tuberculoid paucibacillary leprosy (PB shows low antibodies titers and strong Th1 type/ IFN-γ specific cell mediated immunity (CMI, while lepromatous multibacillary patients (MB show high antibody titers and low CMI. Therefore, laboratory tests for PB and MB leprosy diagnosis will require CMI and antibody based assays

  3. METODE MUHADDITSIN DI ERA MODERN

    Directory of Open Access Journals (Sweden)

    Adriansyah Adriansyah

    2016-05-01

    Full Text Available After the era of tadwin, almost all disciplines of knowledge in the Islamic world, including the study of hadith, was considered “running on the spot.” Yet, attention and maintenance of the hadith was still favored by intellectuals. Similarly, in the modern era, the hadith remains the object of criticism by not only Muslim intellectuals but also outsiders, such as the West. Western imperialism against the Islamic world in the past was now the beginning of the history of how Muslims are only able to “survive” rather than “attack.” The emergence of defensive and reactive works against trends of the West in criticizing and blasphemed the hadith, then, such works became trends and supporting methodologies among Muslim observers of the hadith in today’s modern era

  4. The Chlamydomonas genome project: a decade on

    Science.gov (United States)

    Blaby, Ian K.; Blaby-Haas, Crysten; Tourasse, Nicolas; Hom, Erik F. Y.; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George; Stanke, Mario; Harris, Elizabeth H.; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S.; Prochnik, Simon

    2014-01-01

    The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis and micronutrient homeostasis. Ten years since its genome project was initiated, an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the “omics” era. Housed at Phytozome, the Joint Genome Institute’s (JGI) plant genomics portal, the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of RNA-Seq data. Here, we present the past, present and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. PMID:24950814

  5. Genomic research perspectives in Kazakhstan

    Directory of Open Access Journals (Sweden)

    Ainur Akilzhanova

    2014-01-01

    Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

  6. Biomarkers in molecular epidemiology study of oral squamous cell carcinoma in the era of precision medicine

    Directory of Open Access Journals (Sweden)

    Qing-Hao Zhu

    2017-01-01

    Full Text Available Oral cancer, which occurs in the mouth, lips, and tongue, is a multifactorial disease whose etiology involves environment, genetic, and epigenetic factors. Tobacco use and alcohol consumption are regarded as the primary risk factors for oral squamous cell carcinoma (OSCC, and betel use, other chemicals, radiation, environmental, and genetics are reported as relevant risk factors for oral carcinogenesis. The human papillomavirus infection is an independent risk factor. Traditional epidemiology studies have revealed that environmental carcinogens are risk factors for OSCC. Molecular epidemiology studies have revealed that the susceptibility to OSCC is influenced by both environmental and genetic risk factors. However, the details and mechanisms of risk factors involved in OSCC are unclear. Advanced methods and techniques used in human genome studies provide great opportunities for researchers to explore and identify (a the details of such risk factors and (b genetic susceptibility involved in OSCC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era into the era of genome-wide association study. In the era of precision medicine, molecular epidemiology studies should focus on biomarkers for cancer genomics and their potential utility in clinical practice. Here, we briefly reviewed several molecular epidemiology studies of OSCC, focusing on biomarkers as valuable utility in risk assessment, clinical screening, diagnosis, and prognosis prediction of OSCC in the era of precision medicine.

  7. Survival of Er(a+) red cells in a patient with allo-anti-Era

    International Nuclear Information System (INIS)

    Thompson, H.W.; Skradski, K.J.; Thoreson, J.R.; Polesky, H.F.

    1985-01-01

    51 Chromium-labeled Er(a+) red cells survived nearly normally (T1/2 of 21 days) in a patient with allo-anti-Era. Transfusion of Er(a+) blood was without significant reaction and did not affect the anti-Era titer

  8. Ecology and genomics of Bacillus subtilis.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2008-06-01

    Bacillus subtilis is a remarkably diverse bacterial species that is capable of growth within many environments. Recent microarray-based comparative genomic analyses have revealed that members of this species also exhibit considerable genomic diversity. The identification of strain-specific genes might explain how B. subtilis has become so broadly adapted. The goal of identifying ecologically adaptive genes could soon be realized with the imminent release of several new B. subtilis genome sequences. As we embark upon this exciting new era of B. subtilis comparative genomics we review what is currently known about the ecology and evolution of this species.

  9. Phenotyping for drought tolerance of crops in the genomics era

    Directory of Open Access Journals (Sweden)

    Roberto eTuberosa

    2012-09-01

    Full Text Available Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognised obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.

  10. Cancer classification in the genomic era: five contemporary problems.

    Science.gov (United States)

    Song, Qingxuan; Merajver, Sofia D; Li, Jun Z

    2015-10-19

    Classification is an everyday instinct as well as a full-fledged scientific discipline. Throughout the history of medicine, disease classification is central to how we develop knowledge, make diagnosis, and assign treatment. Here, we discuss the classification of cancer and the process of categorizing cancer subtypes based on their observed clinical and biological features. Traditionally, cancer nomenclature is primarily based on organ location, e.g., "lung cancer" designates a tumor originating in lung structures. Within each organ-specific major type, finer subgroups can be defined based on patient age, cell type, histological grades, and sometimes molecular markers, e.g., hormonal receptor status in breast cancer or microsatellite instability in colorectal cancer. In the past 15+ years, high-throughput technologies have generated rich new data regarding somatic variations in DNA, RNA, protein, or epigenomic features for many cancers. These data, collected for increasingly large tumor cohorts, have provided not only new insights into the biological diversity of human cancers but also exciting opportunities to discover previously unrecognized cancer subtypes. Meanwhile, the unprecedented volume and complexity of these data pose significant challenges for biostatisticians, cancer biologists, and clinicians alike. Here, we review five related issues that represent contemporary problems in cancer taxonomy and interpretation. (1) How many cancer subtypes are there? (2) How can we evaluate the robustness of a new classification system? (3) How are classification systems affected by intratumor heterogeneity and tumor evolution? (4) How should we interpret cancer subtypes? (5) Can multiple classification systems co-exist? While related issues have existed for a long time, we will focus on those aspects that have been magnified by the recent influx of complex multi-omics data. Exploration of these problems is essential for data-driven refinement of cancer classification and the successful application of these concepts in precision medicine.

  11. Pea (Pisum sativum L.) in the Genomic Era

    Czech Academy of Sciences Publication Activity Database

    Smýkal, P.; Aubert, G.; Burstin, J.; Coyne, C.J.; Ellis, N.T.H.; Flavell, A.J.; Ford, R.; Hýbl, M.; Macas, Jiří; Neumann, Pavel; McPhee, K.E.; Redden, R.J.; Rubiales, D.; Weller, J.L.; Warkentin, T.D.

    2012-01-01

    Roč. 2, č. 2 (2012), s. 74-115 ISSN 2073-4395 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : breeding * germplasm * genetic diversity * pea Subject RIV: EB - Genetics ; Molecular Biology

  12. Newborn Screening in the Era of Precision Medicine.

    Science.gov (United States)

    Yang, Lan; Chen, Jiajia; Shen, Bairong

    2017-01-01

    As newborn screening success stories gained general confirmation during the past 50 years, scientists quickly discovered diagnostic tests for a host of genetic disorders that could be treated at birth. Outstanding progress in sequencing technologies over the last two decades has made it possible to comprehensively profile newborn screening (NBS) and identify clinically relevant genomic alterations. With the rapid developments in whole-genome sequencing (WGS) and whole-exome sequencing (WES) recently, we can detect newborns at the genomic level and be able to direct the appropriate diagnosis to the different individuals at the appropriate time, which is also encompassed in the concept of precision medicine. Besides, we can develop novel interventions directed at the molecular characteristics of genetic diseases in newborns. The implementation of genomics in NBS programs would provide an effective premise for the identification of the majority of genetic aberrations and primarily help in accurate guidance in treatment and better prediction. However, there are some debate correlated with the widespread application of genome sequencing in NBS due to some major concerns such as clinical analysis, result interpretation, storage of sequencing data, and communication of clinically relevant mutations to pediatricians and parents, along with the ethical, legal, and social implications (so-called ELSI). This review is focused on these critical issues and concerns about the expanding role of genomics in NBS for precision medicine. If WGS or WES is to be incorporated into NBS practice, considerations about these challenges should be carefully regarded and tackled properly to adapt the requirement of genome sequencing in the era of precision medicine.

  13. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

    Science.gov (United States)

    Brister, James Rodney; Bao, Yiming; Kuiken, Carla; Lefkowitz, Elliot J; Le Mercier, Philippe; Leplae, Raphael; Madupu, Ramana; Scheuermann, Richard H; Schobel, Seth; Seto, Donald; Shrivastava, Susmita; Sterk, Peter; Zeng, Qiandong; Klimke, William; Tatusova, Tatiana

    2010-10-01

    Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

  14. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

    Directory of Open Access Journals (Sweden)

    Qiandong Zeng

    2010-10-01

    Full Text Available Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

  15. Agricultural genomics and sustainable development: perspectives ...

    African Journals Online (AJOL)

    Administrator

    era is to establish how genes and proteins function to bring about changes in phenotype. Some of ... within the context of sustainable development of African economies. The greatest .... these strategies, the genomes of many organisms have now been ... gene structure and order, e.g. between rice, wheat, corn, millets and ...

  16. Genome sequences of Phytophthora enable translational plant disease management and accelerate research

    Science.gov (United States)

    Niklaus J. Grünwald

    2012-01-01

    Whole and partial genome sequences are becoming available at an ever-increasing pace. For many plant pathogen systems, we are moving into the era of genome resequencing. The first Phytophthora genomes, P. ramorum and P. sojae, became available in 2004, followed shortly by P. infestans...

  17. Tarbijalepingud rahvusvahelises eraõiguses / Margus Kingisepp

    Index Scriptorium Estoniae

    Kingisepp, Margus, 1969-

    1997-01-01

    Tarbijalepingute reguleerimisest erinevates riikides, 1955. a. Haagi konventsioonist ja 1980. a. Rooma konventsioonist, rahvusvahelisest jurisdiktsioonist tarbijalepingute puhul ning rahvusvahelise eraõiguse sätetest Eesti õiguses

  18. Understanding patient and provider perceptions and expectations of genomic medicine.

    Science.gov (United States)

    Hall, Michael J; Forman, Andrea D; Montgomery, Susan V; Rainey, Kim L; Daly, Mary B

    2015-01-01

    Advances in genome sequencing technology have fostered a new era of clinical genomic medicine. Genetic counselors, who have begun to support patients undergoing multi-gene panel testing for hereditary cancer risk, will review brief clinical vignettes, and discuss early experiences with clinical genomic testing. Their experiences will frame a discussion about how current testing may challenge patient understanding and expectations toward the evaluation of cancer risk and downstream preventive behaviors. © 2014 Wiley Periodicals, Inc.

  19. The New Era of Counterforce

    Science.gov (United States)

    Lieber, Keir

    Nuclear deterrence rests on the survivability of nuclear arsenals. For much of the nuclear age, counterforce disarming attacks those aimed at eliminating nuclear forces were nearly impossible because of the ability of potential victims to hide and protect their weapons. However, technological developments are eroding this foundation of nuclear deterrence. Advances rooted in the computer revolution have made nuclear forces around the world far more vulnerable than before. Specifically, two key approaches that countries have relied on to ensure arsenal survivability since the dawn of the nuclear age hardening and concealment have been undercut by leaps in weapons accuracy and a revolution in remote sensing. Various models, methods, and evidence demonstrate the emergence of new possibilities for counterforce disarming strikes. In short, the task of securing nuclear arsenals against attack is a far greater challenge than it was in the past. The new era of counterforce challenges the basis for confidence in contemporary deterrence stability, raises critical issues for national and international security policy, and sheds light on one of the enduring theoretical puzzles of the nuclear era: why international security competition has endured in the shadow of the nuclear revolution.

  20. Characterization of ERAS, a putative novel human oncogene, in skin and breast

    Energy Technology Data Exchange (ETDEWEB)

    Peña Avalos, B.L. de la

    2014-07-01

    Most human tumors have mutations in genes of the RAS small GTPase protein family. RAS works as a molecular switch for signaling pathways that modulate many aspects of cell behavior, including proliferation, differentiation, motility and death. Oncogenic mutations in RAS prevent GTP hydrolysis, locking RAS in a permanently active state, being the most common mutations in HRAS, KRAS and NRAS. The human RAS family consists of at least 36 different genes, many of which have been scarcely studied. One of these relatively unknown genes is ERAS (ES cell-expressed RAS), which is a constitutively active RAS protein, localized in chromosome X and expressed only in embryonic cells, being undetectable in adult tissues. New high throughput technologies have made it possible to screen complete cancer genomes for identification of mutations associated to cancer. Using the Sleeping Beauty (SB) transposon system, ERAS was identified as a putative novel oncogene in non-melanoma skin and breast cancers. The major aim of this project is to determine the general characteristics of ERAS as a putative novel human oncogene in skin and breast cells. Forced expression of ERAS results in drastic changes in cell shape, proliferation and motility. When ERAS is overexpressed in skin and breast human cells it is mainly localized in the cytoplasmic membrane. ERAS activates the phosphatidylinositol-3-OH kinase (PI3K) pathway but not the mitogen-activated protein kinase (MAPK) pathway. ERAS-expressing cells suffer spontaneous morphologic and phenotypic EMT-like changes, including cytoskeleton reorganization, vimentin and N-cadherin up-regulation and down-regulation of E-cadherin, which can be associated with increased malignancy, and invasive and metastatic potential. Our results suggest that inappropriate expression of ERAS lead to transformation of human cells. (Author)

  1. Annotation-Based Whole Genomic Prediction and Selection

    DEFF Research Database (Denmark)

    Kadarmideen, Haja; Do, Duy Ngoc; Janss, Luc

    Genomic selection is widely used in both animal and plant species, however, it is performed with no input from known genomic or biological role of genetic variants and therefore is a black box approach in a genomic era. This study investigated the role of different genomic regions and detected QTLs...... in their contribution to estimated genomic variances and in prediction of genomic breeding values by applying SNP annotation approaches to feed efficiency. Ensembl Variant Predictor (EVP) and Pig QTL database were used as the source of genomic annotation for 60K chip. Genomic prediction was performed using the Bayes...... classes. Predictive accuracy was 0.531, 0.532, 0.302, and 0.344 for DFI, RFI, ADG and BF, respectively. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP...

  2. Entrepreneurship in the Digital Era

    Directory of Open Access Journals (Sweden)

    Nur Achmad

    2016-12-01

    Full Text Available This research aims to know about the entrepreneurship as one of the key issues related to many aspects, including its relevance to the economic, business and employment. The researches on entrepreneurship are the references to identify the success factors which supported the entrepreneurial success. The internet development in the digital age indirectly influenced the entrepreneurial ethos. It is not only influenced by the market potential and product innovation, but also by the commitments to entrepreneurship education and training model. Therefore, the studies on entrepreneurship in the industrial and developing countries are attractive. It is relevant to the internet era which provided opportunities for the development of entrepreneurial ethos, especially for the younger generation.

  3. TANTANGAN DAKWAH DI ERA POSMODERNISME

    Directory of Open Access Journals (Sweden)

    Elya Munfarida

    2016-11-01

    Full Text Available As a criticism to modemism, posmodemism has created new cultural realities different from the previous. Through its political acts and strategies, postmodernism has constructed cultural hypereality and complexity. This change becomes a chance and also threat that we need to be critical to anticipate the negative effects. One of its strategies is cultural deconstruction, which denies transcendental signs, meanings, and values, represents one of its negative effects. It will eliminate religious values which by contrast place transcendental values as its principle. For that reason, we need to contextualize Islamic teachings in order not to make postmodernism eliminate Muslims’ sense of religiousity. Da’wa, as a means of communication and transformation of Islamic values, plays a significantrole in this postmodernism era. Consequently, reconstruction of contextual da’wa strategy should be committed to balance the domination of postmodernism cultures.

  4. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  5. Value-based genomics.

    Science.gov (United States)

    Gong, Jun; Pan, Kathy; Fakih, Marwan; Pal, Sumanta; Salgia, Ravi

    2018-03-20

    Advancements in next-generation sequencing have greatly enhanced the development of biomarker-driven cancer therapies. The affordability and availability of next-generation sequencers have allowed for the commercialization of next-generation sequencing platforms that have found widespread use for clinical-decision making and research purposes. Despite the greater availability of tumor molecular profiling by next-generation sequencing at our doorsteps, the achievement of value-based care, or improving patient outcomes while reducing overall costs or risks, in the era of precision oncology remains a looming challenge. In this review, we highlight available data through a pre-established and conceptualized framework for evaluating value-based medicine to assess the cost (efficiency), clinical benefit (effectiveness), and toxicity (safety) of genomic profiling in cancer care. We also provide perspectives on future directions of next-generation sequencing from targeted panels to whole-exome or whole-genome sequencing and describe potential strategies needed to attain value-based genomics.

  6. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  7. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  8. Nutrigenomics in the modern era.

    Science.gov (United States)

    Mathers, John C

    2017-08-01

    The concept that interactions between nutrition and genetics determine phenotype was established by Garrod at the beginning of the 20th century through his ground-breaking work on inborn errors of metabolism. A century later, the science and technologies involved in sequencing of the human genome stimulated development of the scientific discipline which we now recognise as nutritional genomics (nutrigenomics). Much of the early hype around possible applications of this new science was unhelpful and raised expectations, which have not been realised as quickly as some would have hoped. However, major advances have been made in quantifying the contribution of genetic variation to a wide range of phenotypes and it is now clear that for nutrition-related phenotypes, such as obesity and common complex diseases, the genetic contribution made by SNP alone is often modest. There is much scope for innovative research to understand the roles of less well explored types of genomic structural variation, e.g. copy number variants, and of interactions between genotype and dietary factors, in phenotype determination. New tools and models, including stem cell-based approaches and genome editing, have huge potential to transform mechanistic nutrition research. Finally, the application of nutrigenomics research offers substantial potential to improve public health e.g. through the use of metabolomics approaches to identify novel biomarkers of food intake, which will lead to more objective and robust measures of dietary exposure. In addition, nutrigenomics may have applications in the development of personalised nutrition interventions, which may facilitate larger, more appropriate and sustained changes in eating (and other lifestyle) behaviours and help to reduce health inequalities.

  9. Genome engineering for microbial natural product discovery.

    Science.gov (United States)

    Choi, Si-Sun; Katsuyama, Yohei; Bai, Linquan; Deng, Zixin; Ohnishi, Yasuo; Kim, Eung-Soo

    2018-03-03

    The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Human Genome Sequencing in Health and Disease

    Science.gov (United States)

    Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

    2013-01-01

    Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

  11. Nuclear energy and the new era

    International Nuclear Information System (INIS)

    Sefidvash, F.

    1992-01-01

    The problem of the utilization of nuclear energy is not only technical but also has important social, economic, political and ethical ramifications. Therefore, to discuss nuclear energy for the future, a vision of the new era needs to be identified. A model for the new era, as a natural consequence of growing interdependence among nations and the process of human evolution is described. The problems of inherent and passive safety, waste disposal, ecology, proliferation, economy and regulatory institutions in the new era are discussed. The particular role of small nuclear power reactors and their potential advantages are described. (author). 12 refs

  12. El lenguaje en la era digital

    Directory of Open Access Journals (Sweden)

    Juan Carlos Vergara Silva

    1998-02-01

    Con base en la interrelación entre lenguaje y pensamiento se plantea el papel fundamental que el lenguaje ocupa en el modelo económico, educativo y cultural generado por la aparición de la era digital o era del conocimiento. en este artículo se evidencian los retos que genera una era marcada por un esquema digital en el desarrollo y uso de habilidades comunicativas tanto en la docencia superior como en el ejercicio profesional eficiente.

  13. Periodistas para la era digital

    Directory of Open Access Journals (Sweden)

    Fernando Villalobos G.

    2014-12-01

    Full Text Available La formación de los periodistas del siglo XXI en la era digital se concibe como un reto y el mayor desafío. Los medios digitales demandan especialización y dominio de las nuevas tecnologías. Las universidades, principales gestores de este cambio, en la sociedad del conocimiento, requieren trabajar en la reformulación de nuevos pensum y en tres terrenos fundamentales: el perfil del egresado, el estilo pedagógico y el nuevo modo de relacionarse con el mundo exterior. Se necesita de una oferta académica referida al ciberperiodismo y a la cibercomunicación. La profesión periodística, y específicamente la formación de los comunicadores registra cambios importantes debido a las nuevas tecnologías, ahora el aula es el mundo globalizado e interconectado por la gran autopista de la información, por ello, la formación del comunicador social, demanda renovadas prácticas educativas. Las universidades deben repensar el papel que están obligadas a desempeñar, reformular los pensum académicos y ofertar la cibercomunicación y el ciberperiodismo para estar al día de las grandes transformaciones.

  14. A THIRD ERA OF MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Liviu NEAMŢU

    2009-12-01

    Full Text Available Management like any social activity through specific stages of development trends from general society. Following these historical trends, this study summarizes the evolution of management at four stages of a full cycle of development, from a informal management to one perfect formalized. These stages of development are found differential represented at the various economic development regions in the world. Evolution increasingly grouped patterns of management and generalization for schools of thought management determines the current global development of worldwide management. For the current stage of evolution may be called as "the third era of management" or "imperial period” in which management pressures on individuals, employers or subordinate, are enormous. Evolution of companies, of markets and national economies also the global economy is driven by the current trend in management, leading to very strong mutations in the relationship of forces. The world economy is in what is called "war of resources" and the alternative that we believe is necessary in this "human management" although speculative trends of concentration of capital are binding on any plans or state regulators global ethical management.

  15. The Performing Arts in a New Era

    National Research Council Canada - National Science Library

    McCarthy, Kevin

    2001-01-01

    The Pew Charitable Trust commissioned The Performing Arts in a New Era from RAND in 1999 as part of a broad initiative aimed at increasing policy and financial support for nonprofit culture in the United States...

  16. MEMAKNAI SUMPAH PEMUDA DI ERA REFORMASI

    Directory of Open Access Journals (Sweden)

    Sutejo K. Widodo

    2013-03-01

    Full Text Available The moment of Sumpah Pemuda (Young Man Oath took place 84 years ago, reflecting the spirit of nationalism that is still very important in this Reformation era. This paper endeavors to dig deeper meaning of Sumpah Pemuda in its pre-independence era and applying it to our contemporary situation. The method used here is historical research using literature resources, such as articles, books, and other readings in internet. It is then concluded that the spirit of Sumpah Pemuda should be our contemplative materials and valuable Iesson so that Reformation era may succeed in achieving national goals stated in the Constitution, a society that is fair, prosperous, and democratic. Keywords: Sumpah Pemuda, Reformation era, nationalism.

  17. Technology: A New Era in Education

    Science.gov (United States)

    Cunningham, William G.

    1977-01-01

    Teachers and technologists have lived apart, with much doubt on both sides. The author suggests that collaboration, mutual trust, and respect, will usher in a new era for effective education. (Editor)

  18. A new era of competitiveness.

    Science.gov (United States)

    Theadore, Jason C

    2011-01-01

    Many of my family, friends, and colleagues would describe me as competitive and that at times I overuse this skill with a win-at-all-costs attitude. I would tend to agree. I love to win. Yet for me winning is not about me, it is as our coaches suggest, about others. I was recently asked by a new clinical leader if I missed taking care of patients. Without thinking, my response was that I take part in the care (add value) of every patient as a leader. Every decision we make as leaders (coaches) impacts many others regardless of the magnitude of our decision and, at times, our direct involvement. Operational excellence, in any field, is about winning. We all have different definitions of winning, defined by the strategic vision for our organizations. An organization's managers, supervisors, and employees all play an important role in the team to achieve the vision of the organization. As some elite coaches have suggested, winning starts with each of us being our best. Today's environment requires consistent change. Yet many in the radiology field change the wrong things for the wrong reasons. Many organizations and individuals look for instant gratification, specifically in this new era of competitiveness. Many evaluate what their competitors are doing in the market, what cars their neighbors are buying, or become jealous over a friend's success. Focusing on others and not improving yourself takes your focus away from what is important-you and the team you lead. Keeping your focus on your operations and what you can control may very well help you coach a winning team.

  19. Era Transmídia

    Directory of Open Access Journals (Sweden)

    Rodrigo Dias Arnaut

    2011-12-01

    Full Text Available A abordagem transmídia se mostra cada vez mais atual e interessante por integrar todos os conceitos de produção de conteúdos em uma única metodologia e processo de criação e distribuição. Atualmente, e cada vez mais, as pessoas, o público em geral é um potencial produtor de conteúdo nas novas mídias, seja através de uma simples câmera fotográfica, um telefone celular, um PC ou mesmo do mais sofisticado tablet. Nesta nova dinâmica, o mercado (conjunto de: audiência, mídia, concorrência e demais agentes apresenta novas plataformas de comuni-cação que, devido a sua abertura e amplo acesso, trazem consigo uma grande perda de controle do que é publi-cado e do próprio contexto originalmente planejado, pois a mídia espontânea e a interpretação do público criam novos caminhos para a história principal do projeto.A necessidade do mercado em estreitar relacionamento com seus clientes ou públicos (cada segmento de mercado é considerado um público diferente passa por uma grande transformação, que se implementada de forma impul-siva e despreparada, no que diz respeito à análise do público-alvo, aos formatos de distribuição e à mensagem enviada, pode acarretar na perda de oportunidades e propostas de comunicação. O foco dos projetos transmídia é utilizar  metodologias e  processos mais completos e abrangentes, do ponto de vista das áreas de criação de con-teúdo, tecnologia, marketing e outras, utilizando as melhores plataformas de mídia para o sucesso do projeto. De forma resumida o grupo de estudos em transmídia, #EraTransmídia, irá apresentar seus conceitos com o objetivo de proporcionar o engajamento social multiplataforma para resultados positivos.

  20. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  1. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  2. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  3. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  4. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  5. Advances in Miniaturized Instruments for Genomics

    Directory of Open Access Journals (Sweden)

    Cihun-Siyong Alex Gong

    2014-01-01

    Full Text Available In recent years, a lot of demonstrations of the miniaturized instruments were reported for genomic applications. They provided the advantages of miniaturization, automation, sensitivity, and specificity for the development of point-of-care diagnostics. The aim of this paper is to report on recent developments on miniaturized instruments for genomic applications. Based on the mature development of microfabrication, microfluidic systems have been demonstrated for various genomic detections. Since one of the objectives of miniaturized instruments is for the development of point-of-care device, impedimetric detection is found to be a promising technique for this purpose. An in-depth discussion of the impedimetric circuits and systems will be included to provide total consideration of the miniaturized instruments and their potential application towards real-time portable imaging in the “-omics” era. The current excellent demonstrations suggest a solid foundation for the development of practical and widespread point-of-care genomic diagnostic devices.

  6. Functional genomics for food microbiology: Molecular mechanisms of weak organic acid preservative adaptation in yeast

    NARCIS (Netherlands)

    Brul, S.; Kallemeijn, W.; Smits, G.

    2008-01-01

    The recent era of genomics has offered tremendous possibilities to biology. This concise review describes the possibilities of applying (functional) genomics studies to the field of microbial food stability. In doing so, the studies on weak-organic-acid stress response in yeast are discussed by way

  7. ERA: Efficient serial and parallel suffix tree construction for very long strings

    KAUST Repository

    Mansour, Essam

    2011-09-01

    The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix tree are too large to fit into the main memory, most existing construction algorithms become very inefficient. This paper presents a disk-based suffix tree construction method, called Elastic Range (ERa), which works efficiently with very long strings that are much larger than the available memory. ERa partitions the tree construction process horizontally and vertically and minimizes I/Os by dynamically adjusting the horizontal partitions independently for each vertical partition, based on the evolving shape of the tree and the available memory. Where appropriate, ERa also groups vertical partitions together to amortize the I/O cost. We developed a serial version; a parallel version for shared-memory and shared-disk multi-core systems; and a parallel version for shared-nothing architectures. ERa indexes the entire human genome in 19 minutes on an ordinary desktop computer. For comparison, the fastest existing method needs 15 minutes using 1024 CPUs on an IBM BlueGene supercomputer.

  8. Recent Reanalysis Activities at ECMWF: Results from ERA-20C and Plans for ERA5

    Science.gov (United States)

    Dragani, R.; Hersbach, H.; Poli, P.; Pebeuy, C.; Hirahara, S.; Simmons, A.; Dee, D.

    2015-12-01

    This presentation will provide an overview of the most recent reanalysis activities performed at the European Centre for Medium-Range Weather Forecasts (ECMWF). A pilot reanalysis of the 20th-century (ERA-20C) has recently been completed. Funded through the European FP7 collaborative project ERA-CLIM, ERA-20C is part of a suite of experiments that also includes a model-only integration (ERA-20CM) and a land-surface reanalysis (ERA-20CL). Its data assimilation system is constrained by only surface observations obtained from ISPD (3.2.6) and ICOADS (2.5.1). Surface boundary conditions are provided by the Hadley Centre (HadISST2.1.0.0) and radiative forcing follows CMIP5 recommended data sets. First-guess uncertainty estimates are based on a 10-member ensemble of Data Assimilations, ERA-20C ensemble, run prior to ERA-20C using ten SST and sea-ice realizations from the Hadley Centre. In November 2014, the European Commission entrusted ECMWF to run on its behalf the Copernicus Climate Change Service (C3S) aiming at producing quality-assured information about the past, current and future states of the climate at both European and global scales. Reanalysis will be one of the main components of the C3S portfolio and the first one to be produced is a global modern era reanalysis (ERA5) covering the period from 1979 onwards. Based on a recent version of the ECMWF data assimilation system, ERA5 will replace the widely used ERA-Interim dataset. This new production will benefit from a much improved model, and better characterized and exploited observations compared to its predecessor. The first part of the presentation will focus on the ERA-20C production, provide an overview of its main characteristics and discuss some of the key results from its assessment. The second part of the talk will give an overview of ERA5, and briefly discuss some of its challenges.

  9. Communicating mathematics in the digital era

    CERN Document Server

    Borwein, Jonathan; Rodrigues, Jose Francisco

    2008-01-01

    The digital era has dramatically changed the ways that researchers search, produce, publish, and disseminate their scientific work. These processes are still rapidly evolving due to improvements in information science, new achievements in computer science technologies, and initiatives such as DML and open access journals, digitization projects, scientific reference catalogs, and digital repositories. These changes have prompted many mathematicians to play an active part in the developments of the digital era, and have led mathematicians to promote and discuss new ideas with colleagues from other fields, such as technology developers and publishers. This book is a collection of contributions by key leaders in the field, offering the paradigms and mechanisms for producing, searching, and exploiting scientific and technical scholarship in mathematics in the digital era.

  10. Chinese librarianship in the digital era

    CERN Document Server

    Fang, Conghui

    2013-01-01

    The library in China has been transformed by rapid socioeconomic development, and the proliferation of the Internet. The issues faced by Chinese libraries andlibrarians are those faced by library practitioners more globally, however, China also has its own unique set of issues in the digital era, including developmental imbalance between East and West, urban and rural areas, and availability of skilled practitioners. Chinese Librarianship in the Digital Era is the first book on Chinese libraries responding to these issues, and more.The first part of the book places discussion in historical con

  11. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  12. New criteria for supplementation of selected micronutrients in the era of nutrigenetics and nutrigenomics.

    Science.gov (United States)

    Schwartz, Betty

    2014-08-01

    Advances in molecular biology, emergence of novel techniques and huge amount of information generated in the post-Human Genome Project era have fostered the emergence of new disciplines in the field of nutritional research: Nutrigenomics deals with the effect of diet on gene expression whereas nutrigenetics refers to the impact of inherited traits on the response to a specific dietary pattern, functional food or supplement. Understanding the role of micronutrient supplementation with specific genetic backgrounds may provide an important contribution to a new optimum health strategy based on individualized nutritional treatment and may provide the strategies for the development of safer and more effective dietary interventions. This overview of the various aspects of supplementation of micronutrients in the era of nutrigenetics and nutrigenomics may provide a better understanding of novel nutritional research approach and provide an additional insight that can be applied to the daily dietary practice.

  13. Human genetics and genomics a decade after the release of the draft sequence of the human genome

    Science.gov (United States)

    2011-01-01

    Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade. PMID:22155605

  14. Family Health in an Era of Stress.

    Science.gov (United States)

    USA Today, 1979

    1979-01-01

    Summarizes major findings of a national survey, "The General Mills American Family Report 1978/79: Family Health in an Era of Stress," conducted by Yankelovich, Skelly and White. Topics covered include attitudes toward medical costs, mental illness, and good health practices, as well as expressed interest in health information. (SJL)

  15. Biotechnology: An Era of Hopes and Fears

    Science.gov (United States)

    2016-01-01

    Strategic Studies Quarterly ♦ Fall 2016 23 Biotechnology An Era of Hopes and Fears LTC Douglas R. Lewis, PhD, US Army Abstract Biotechnology ......ignored. The idea of advances in biotechnology increasing the biological weapons threat is not new. In 2003 an analysis of gene sequencing and

  16. Time Management in the Digital Era

    Science.gov (United States)

    Wodarz, Nan

    2013-01-01

    School business officials can strike a balance between setting a long-term strategy and responding to short-term situations by implementing time management strategies. This article presents tips for time management that could help boost productivity and save time in this digital era. Tips include decreasing meeting times via Skype or…

  17. Aplikasi Citizen Journalism di Era Konvergensi Media

    Directory of Open Access Journals (Sweden)

    Rahmat Edi Irawan

    2014-10-01

    Full Text Available Citizen journalism has now become one of the most developed television program concepts. If the concept was initially more widely used in radio and online media, this time with easier and cheaper technology coverage and delivery of images, it is a concept that provides a place for people to become amateur journalist that can also be easily applied in the medium of television. Research raised the issue on how the concept and implementation of citizen journalism on television in the era of media convergence. The purpose of this study is to explain concepts and demonstrate the implementation of citizen journalism on television in the era of media convergence. Research used qualitative method in which data were obtained using literature study. Results of the study showed that the implementation of citizen journalism on television is also increasingly facilitated by the entry of the television in the era of media convergence, or different media mingle, such as television with printed, radio, and Internet media. The era of media convergence makes the concept of citizen journalism can be more developed, because the platform or media distribution is also increasingly varied for amateur journalist. However, the system equipment that must be provided, human resources that must be owned, as well as huge capital to be owned make a few television stations open a lot of platforms to provide space for amateur journalist in citizen journalism. 

  18. Rethinking Education in an Era of Globalisation

    Science.gov (United States)

    Wrigley, Terry

    2007-01-01

    This article reflects on the historic tensions of education under capitalism, arguing that they have been exacerbated in our era of neo-liberal globalisation. Government drives for greater "accountability" and "effectiveness" are a blinkered response to the threefold global crisis we face: poverty and debt; a collapse of the…

  19. Global Learning in a New Era

    Science.gov (United States)

    Ramaley, Judith

    2016-01-01

    Our nation's colleges and universities frequently adapt their approach to education in response to the reality of social, economic and environmental challenges. Today the reality is that we are increasingly interconnected on a global scale. This new era of globalization impacts every facet of society, and it offers both an exciting blend of…

  20. Scandinavian neuroscience during the Nazi era

    DEFF Research Database (Denmark)

    Kondziella, Daniel; Hansen, Klaus; Zeidman, Lawrence A

    2013-01-01

    Although Scandinavian neuroscience has a proud history, its status during the Nazi era has been overlooked. In fact, prominent neuroscientists in German-occupied Denmark and Norway, as well as in neutral Sweden, were directly affected. Mogens Fog, Poul Thygesen (Denmark) and Haakon Sæthre (Norway...

  1. Family Therapy in the Postmodern Era.

    Science.gov (United States)

    Mills, Steven D.; Sprenkle, Douglas H.

    1995-01-01

    Discusses theoretical and clinical developments that have accompanied family therapy's entry into the postmodern era. Clinical trends, including use of reflecting teams, self-of-the-therapist issues, increased therapist self-disclosure, and postmodern supervision are examined. Feminist critiques, health-care reform, and increasing collaboration…

  2. Faculty Recruitment in an Era of Change

    Science.gov (United States)

    Levine, Marilyn; Schimpf, Martin

    2010-01-01

    Faculty recruitment is a challenge for administration and departments, especially in an era of change in the academy. This article builds on information from an interactive conference panel session that focused on faculty recruitment best practices. The article addresses faculty recruitment strategies that focus on the optimization of search…

  3. Multiscale computing in the exascale era

    NARCIS (Netherlands)

    Alowayyed, S.; Groen, D.; Coveney, P.V.; Hoekstra, A.G.

    We expect that multiscale simulations will be one of the main high performance computing workloads in the exascale era. We propose multiscale computing patterns as a generic vehicle to realise load balanced, fault tolerant and energy aware high performance multiscale computing. Multiscale computing

  4. Use of genome-scale microbial models for metabolic engineering

    DEFF Research Database (Denmark)

    Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

    2004-01-01

    Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....

  5. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  6. Interpretation of Genomic Data Questions and Answers

    Science.gov (United States)

    Simon, Richard

    2008-01-01

    Using a question and answer format we describe important aspects of using genomic technologies in cancer research. The main challenges are not managing the mass of data, but rather the design, analysis and accurate reporting of studies that result in increased biological knowledge and medical utility. Many analysis issues address the use of expression microarrays but are also applicable to other whole genome assays. Microarray based clinical investigations have generated both unrealistic hyperbole and excessive skepticism. Genomic technologies are tremendously powerful and will play instrumental roles in elucidating the mechanisms of oncogenesis and in devlopingan era of predictive medicine in which treatments are tailored to individual tumors. Achieving these goals involves challenges in re-thinking many paradigms for the conduct of basic and clinical cancer research and for the organization of interdisciplinary collaboration. PMID:18582627

  7. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  8. Electra en Piñera

    Directory of Open Access Journals (Sweden)

    Elina Miranda Cancela

    1991-12-01

    Full Text Available Este artigo e uma análise da Electra Garrigó de Virgilio Piñera, teatrólogo cubano, e das suas vinculações com o teatro trágico grego, sobretudo com a Electra de Sófocles, acrescida ainda de aproximações com autores modernos que trataram do mesmo tema. Apesar da inspiração grega, Piñera permanece um típico teatrólogo nacional, marcado pelos momentos de grande tensão social da sua época (a tragédia em apreço data de 1941. O conflito produzido pela excessiva autoridade dos pais sobre os filhos, latente neste mito, interessa-o por seu significado dentro da família cubana.

  9. Menertawakan Fobia Komunis di Era Reproduksi Digital

    Directory of Open Access Journals (Sweden)

    Triyono Lukmantoro

    2017-04-01

    Full Text Available Abstract. In May-June 2016 issue of the rise of the Indonesian Communist Party (PKI and the latent danger of communism appeared again. Excessive fear of PKI and communism continues propagated. That is what is referred to as a communist phobia. But, the issue is considered sensitive that it gave birth to criticism. The phenomenon is the presence of a number of memes comics whose contents laugh hammer and sickle symbol and three communist iconic figures, namely D.N. Aidit, Tan Malaka, and Mao Zedong. Meme comics containing parody to show incongruities that can only happen to the era of digital reproduction. The idea of meme comics can be traced to the thought Walter Benjamin about the works of art in the age of mechanical reproduction. In that era, aura was declining. The crisis and the disappearance of aura increasingly occurs to the time of digital reproduction.

  10. Lessons from a phenotyping center revealed by the genome-guided mapping of powdery mildew resistance loci

    Science.gov (United States)

    The genomics era brought unprecedented tools for genetic analysis of host resistance, but careful attention is needed on obtaining accurate and reproducible phenotypes so that genomic results appropriately reflect biology. Phenotyping host resistance by natural infection in the field can produce var...

  11. Flavour physics in the LHC era

    CERN Document Server

    Gershon, Tim

    2014-01-01

    These lectures give a topical review of heavy flavour physics, in particular \\CP violation and rare decays, from an experimental point of view. They describe the ongoing motivation to study heavy flavour physics in the LHC era, the current status of the field emphasising key results from previous experiments, some selected topics in which new results are expected in the near future, and a brief look at future projects.

  12. The Molecular Era of Surfactant Biology

    OpenAIRE

    Whitsett, Jeffrey A.

    2014-01-01

    Advances in the physiology, biochemistry, molecular and cell biology of the pulmonary surfactant system transformed the clinical care and outcome of preterm infants with respiratory distress syndrome. The molecular era of surfactant biology provided genetic insights into the pathogenesis of pulmonary disorders, previously termed “idiopathic” that affect newborn infants, children and adults. Knowledge related to the structure and function of the surfactant proteins and their roles in alveolar ...

  13. A New Era for Jefferson Lab

    International Nuclear Information System (INIS)

    McKeown, R. D.; Montgomery, H. E.; Pennington, M. R.

    2016-01-01

    On a cool Saturday morning in late April a seemingly endless stream of cars turned off Jefferson Avenue in Newport News, Virginia, bringing 12,000 people ages 1 to 91 to the Open House to learn more about “the new era in science” at the Thomas Jefferson National Accelerator Facility. Here, the visitors were dazzled by the complex equipment, the enthusiastic staff, and the advanced technology at the Laboratory.

  14. Creative clusters: a new era for SMEs?

    OpenAIRE

    Oxborrow, L

    2012-01-01

    Objectives: The paper illustrates how the characteristics of industry clusters are revived in a new era for SME networks. It explores how a succession of industry shocks - increased global competition, recession and reduced policy support - have stimulated an innovative response in creative SMEs. The paper goes on to investigate the clustering experience of a small group of creative entrepreneurs in pursuing networked activities, with a view to identifying lessons that can be learnt to suppor...

  15. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  16. Clinical research of traditional Chinese medicine in big data era.

    Science.gov (United States)

    Zhang, Junhua; Zhang, Boli

    2014-09-01

    With the advent of big data era, our thinking, technology and methodology are being transformed. Data-intensive scientific discovery based on big data, named "The Fourth Paradigm," has become a new paradigm of scientific research. Along with the development and application of the Internet information technology in the field of healthcare, individual health records, clinical data of diagnosis and treatment, and genomic data have been accumulated dramatically, which generates big data in medical field for clinical research and assessment. With the support of big data, the defects and weakness may be overcome in the methodology of the conventional clinical evaluation based on sampling. Our research target shifts from the "causality inference" to "correlativity analysis." This not only facilitates the evaluation of individualized treatment, disease prediction, prevention and prognosis, but also is suitable for the practice of preventive healthcare and symptom pattern differentiation for treatment in terms of traditional Chinese medicine (TCM), and for the post-marketing evaluation of Chinese patent medicines. To conduct clinical studies involved in big data in TCM domain, top level design is needed and should be performed orderly. The fundamental construction and innovation studies should be strengthened in the sections of data platform creation, data analysis technology and big-data professionals fostering and training.

  17. The Past, Present, and Future of Human Centromere Genomics

    Directory of Open Access Journals (Sweden)

    Megan E. Aldrup-MacDonald

    2014-01-01

    Full Text Available The centromere is the chromosomal locus essential for chromosome inheritance and genome stability. Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Contiguous alpha satellite DNA sequence is absent from the assembled reference genome, limiting current understanding of centromere organization and function. Here, we review the progress in centromere genomics spanning the discovery of the sequence to its molecular characterization and the work done during the Human Genome Project era to elucidate alpha satellite structure and sequence variation. We discuss exciting recent advances in alpha satellite sequence assembly that have provided important insight into the abundance and complex organization of this sequence on human chromosomes. In light of these new findings, we offer perspectives for future studies of human centromere assembly and function.

  18. A Roadmap for Tick-Borne Flavivirus Research in the “Omics” Era

    Directory of Open Access Journals (Sweden)

    Jeffrey M. Grabowski

    2017-12-01

    Full Text Available Tick-borne flaviviruses (TBFs affect human health globally. Human vaccines provide protection against some TBFs, and antivirals are available, yet TBF-specific control strategies are limited. Advances in genomics offer hope to understand the viral complement transmitted by ticks, and to develop disruptive, data-driven technologies for virus detection, treatment, and control. The genome assemblies of Ixodes scapularis, the North American tick vector of the TBF, Powassan virus, and other tick vectors, are providing insights into tick biology and pathogen transmission and serve as nucleation points for expanded genomic research. Systems biology has yielded insights to the response of tick cells to viral infection at the transcript and protein level, and new protein targets for vaccines to limit virus transmission. Reverse vaccinology approaches have moved candidate tick antigenic epitopes into vaccine development pipelines. Traditional drug and in silico screening have identified candidate antivirals, and target-based approaches have been developed to identify novel acaricides. Yet, additional genomic resources are required to expand TBF research. Priorities include genome assemblies for tick vectors, “omic” studies involving high consequence pathogens and vectors, and emphasizing viral metagenomics, tick-virus metabolomics, and structural genomics of TBF and tick proteins. Also required are resources for forward genetics, including the development of tick strains with quantifiable traits, genetic markers and linkage maps. Here we review the current state of genomic research on ticks and tick-borne viruses with an emphasis on TBFs. We outline an ambitious 10-year roadmap for research in the “omics era,” and explore key milestones needed to accomplish the goal of delivering three new vaccines, antivirals and acaricides for TBF control by 2030.

  19. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  20. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  1. STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

    OpenAIRE

    Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

    2014-01-01

    The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technic...

  2. Pipeline to upgrade the genome annotations

    Directory of Open Access Journals (Sweden)

    Lijin K. Gopi

    2017-12-01

    Full Text Available Current era of functional genomics is enriched with good quality draft genomes and annotations for many thousands of species and varieties with the support of the advancements in the next generation sequencing technologies (NGS. Around 25,250 genomes, of the organisms from various kingdoms, are submitted in the NCBI genome resource till date. Each of these genomes was annotated using various tools and knowledge-bases that were available during the period of the annotation. It is obvious that these annotations will be improved if the same genome is annotated using improved tools and knowledge-bases. Here we present a new genome annotation pipeline, strengthened with various tools and knowledge-bases that are capable of producing better quality annotations from the consensus of the predictions from different tools. This resource also perform various additional annotations, apart from the usual gene predictions and functional annotations, which involve SSRs, novel repeats, paralogs, proteins with transmembrane helices, signal peptides etc. This new annotation resource is trained to evaluate and integrate all the predictions together to resolve the overlaps and ambiguities of the boundaries. One of the important highlights of this resource is the capability of predicting the phylogenetic relations of the repeats using the evolutionary trace analysis and orthologous gene clusters. We also present a case study, of the pipeline, in which we upgrade the genome annotation of Nelumbo nucifera (sacred lotus. It is demonstrated that this resource is capable of producing an improved annotation for a better understanding of the biology of various organisms.

  3. Biobanks in the Era of Digital Medicine.

    Science.gov (United States)

    Jacobs, Gunnar; Wolf, Andreas; Krawczak, Michael; Lieb, Wolfgang

    2018-05-01

    Digitalization is currently permeating virtually all sectors of modern societies, including biomedical research and medical care. At the same time, biobanks engaged in the long-term storage of biological samples that are fit for purpose have become key drivers in both fields. The present article highlights some of the challenges and opportunities that biobanking is facing in the current proverbial "era of digitalization." © 2017 The Authors Clinical Pharmacology & Therapeutics published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  4. Superbend era begins swiftly at the ALS

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, Art; Tamura, Lori

    2001-11-29

    The successful installation and commissioning of high-field superconducting bend magnets (superbends) in three curved sectors of ALS storage ring was the first time the magnet lattice of an operating synchrotron light source has been retrofitted in this fundamental way. As a result, the ALS now offers an expanded spectral range well into the hard x-ray region without compromising either the number of undulators or their high brightness in the soft x-ray region for which the ALS design was originally optimized. In sum, when the superbend-enhanced ALS started up for user operations in October 2001, it marked the beginning of a new era in its history.

  5. Evolusi Saluran Interaksi di Era Internet

    Directory of Open Access Journals (Sweden)

    Benedictus Arnold Simangunsong

    2011-07-01

    Full Text Available The development and advancement of technology affects how man interacts with others. The revolution of society interaction which was proposed by Straubhaar and LaRose, from pre-farming society to a farming society, into an industrial society, which was marked by the label of industrial revolution, to the information society, which is marked by the information revolution, shifted the way and man’s attitudes both in terms of economy and interaction. In the information society, the revolution also takes place in message delivery, where face-to-face was common at first, to textual and visual delivery, which is a change in the internet era.

  6. Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine.

    Science.gov (United States)

    Ji, Yuan; Si, Yue; McMillin, Gwendolyn A; Lyon, Elaine

    2018-04-23

    The rapid development and dramatic decrease in cost of sequencing techniques have ushered the implementation of genomic testing in patient care. Next generation DNA sequencing (NGS) techniques have been used increasingly in clinical laboratories to scan the whole or part of the human genome in order to facilitate diagnosis and/or prognostics of genetic disease. Despite many hurdles and debates, pharmacogenomics (PGx) is believed to be an area of genomic medicine where precision medicine could have immediate impact in the near future. Areas covered: This review focuses on lessons learned through early attempts of clinically implementing PGx testing; the challenges and opportunities that PGx testing brings to precision medicine in the era of NGS. Expert commentary: Replacing targeted analysis approach with NGS for PGx testing is neither technically feasible nor necessary currently due to several technical limitations and uncertainty involved in interpreting variants of uncertain significance for PGx variants. However, reporting PGx variants out of clinical whole exome or whole genome sequencing (WES/WGS) might represent additional benefits for patients who are tested by WES/WGS.

  7. 77 FR 40644 - ERA Systems, LLC, Formerly ERA Systems Corporation, a Subsidiary of Systems Research and...

    Science.gov (United States)

    2012-07-10

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-81,047, TA-W-81,047A] ERA Systems..., 2011, resulted in a negative determination, issued on January 13, 2012. The determination was... partial separation from employment on the date of certification through two years from the date of...

  8. A comprehensive and quantitative exploration of thousands of viral genomes

    Science.gov (United States)

    Mahmoudabadi, Gita

    2018-01-01

    The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends. PMID:29624169

  9. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  10. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  11. Mempertanyakan Privasi di Era Selebgram: Masih Adakah?

    Directory of Open Access Journals (Sweden)

    Ester Krisnawati

    2017-01-01

    Full Text Available Abstract: Instagram marks the importance of participatory culture in the era of new media. This paper aims to examine the complex notion of privacy in regards to children’s privacy that were made famous (by their parents through Instagram with the selebgram phenomenon. By examining the data gathered using #selebgram and underlining the self-presentation perspective in the study of the psychological communication, the results show that parents have their own motives and goal when uploading their child’s fotos on Instagram. Consequently, the childs have to lose their privacy in cyberspace and of course, the information is vulnerable to crime. Keywords: children’s privacy, Instagram, selebgram, self-presentation Abstrak: Instagram menandai gagasan pentingnya budaya partisipatif dalam era media baru. Tujuan dari paper ini adalah untuk menganalisa konsep Instagram sebagai forum dan sarana komunikasi dengan melihat fenomena selebgram. Paper ini meneliti gagasan kompleks privasi dalam hal privasi anak-anak yang dibuat terkenal (oleh orang tua mereka melalui Instagram dengan memeriksa data yang dikumpulkan menggunakan #selebgram dan menggarisbawahi perspektif presentasi diri dalam kajian psikologi komunikasi. Hasil analisa menunjukkan bahwa ada motif dan tujuan orang tua memuat foto anaknya di akun Instagram. Sedangkan dampaknya, anak tidak mempunyai privasi di dunia maya dan tentunya informasi tersebut akan rentan disalahgunakan untuk kejahatan. Kata Kunci: Instagram, presentasi diri, privasi anak, selebgram

  12. CENTRAL BANKING IN THE NEW ERA

    Directory of Open Access Journals (Sweden)

    Bilal Bagis

    2017-12-01

    Full Text Available This paper analyzes the evolution of central banking, and in particular the American experience of central banking. It provides projections for the future of central banking in the new era of post 2008. The paper initially demonstrates recent improvements in the financial and banking sectors, regulations and different measures of monetary and financial rules both in the USA and the rest of the advanced economies. Then, it claims institutions, such as central banks, will gain new objectives and more significance in this new era and thus will be given new roles, over time and along with the improvements and deepening in the financial system. The paper argues centuries long central bank evolution is not complete yet and that more objectives should be expected to come forward. In that line, there is need for a shift in the conventional policy measures. New trends in central banking such as the helicopter money, popular nominal GDP targeting regime and the retro developmental central banking are all critically analyzed. The paper provides a breakdown of financial development and central banking activities in a historical context and provides a rationale and a new basis for possible future innovations.

  13. The end of a remarkable era

    CERN Multimedia

    2011-01-01

    An important era in particle physics is coming to an end: the US Department of Energy announced on Monday that it will not fund an extension to Tevatron running beyond 2011. It is a poignant moment for particle physics as we prepare to bid farewell to a machine that has changed our view of the Universe, and played a significant role in paving the way for the new era that is opening up with the LHC.   The Tevatron has been at the high-energy frontier of particle physics for over a quarter of a century. That’s a remarkable achievement by any account, and the physics results are there to prove it. As well as bringing us the discovery of the top quark in 1995, the Tevatron’s experiments have provided vitally important precision measurements covering the full spectrum of Standard Model physics, not to mention hints of what may lie beyond. With several months of running still to come, it would be a foolish gambler who bet against further new physics emerging before the Teva...

  14. Reprogramming neurodegeneration in the big data era.

    Science.gov (United States)

    Zhou, Lujia; Verstreken, Patrik

    2018-02-01

    Recent genome-wide association studies (GWAS) have identified numerous genetic risk variants for late-onset Alzheimer's disease (AD) and Parkinson's disease (PD). However, deciphering the functional consequences of GWAS data is challenging due to a lack of reliable model systems to study the genetic variants that are often of low penetrance and non-coding identities. Pluripotent stem cell (PSC) technologies offer unprecedented opportunities for molecular phenotyping of GWAS variants in human neurons and microglia. Moreover, rapid technological advances in whole-genome RNA-sequencing and epigenome mapping fuel comprehensive and unbiased investigations of molecular alterations in PSC-derived disease models. Here, we review and discuss how integrated studies that utilize PSC technologies and genome-wide approaches may bring new mechanistic insight into the pathogenesis of AD and PD. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Personalized therapies in the cancer "omics" era

    Directory of Open Access Journals (Sweden)

    Pandiella Atanasio

    2010-07-01

    Full Text Available Abstract A molecular hallmark of cancer is the presence of genetic alterations in the tumoral DNA. Understanding how these alterations translate into the malignant phenotype is critical for the adequate treatment of oncologic diseases. Several cancer genome sequencing reports have uncovered the number and identity of proteins and pathways frequently altered in cancer. In this article we discuss how integration of these genomic data with other biological and proteomic studies may help in designing anticancer therapies "a la carte". An important conclusion is that next generation treatment of neoplasias must be based on rational drug combinations that target various pathways and cellular entities that sustain the survival of cancer cells.

  16. Functional genomics approaches in parasitic helminths.

    Science.gov (United States)

    Hagen, J; Lee, E F; Fairlie, W D; Kalinna, B H

    2012-01-01

    As research on parasitic helminths is moving into the post-genomic era, an enormous effort is directed towards deciphering gene function and to achieve gene annotation. The sequences that are available in public databases undoubtedly hold information that can be utilized for new interventions and control but the exploitation of these resources has until recently remained difficult. Only now, with the emergence of methods to genetically manipulate and transform parasitic worms will it be possible to gain a comprehensive understanding of the molecular mechanisms involved in nutrition, metabolism, developmental switches/maturation and interaction with the host immune system. This review focuses on functional genomics approaches in parasitic helminths that are currently used, to highlight potential applications of these technologies in the areas of cell biology, systems biology and immunobiology of parasitic helminths. © 2011 Blackwell Publishing Ltd.

  17. Genomics-based plant germplasm research (GPGR)

    Institute of Scientific and Technical Information of China (English)

    Jizeng Jia; Hongjie Li; Xueyong Zhang; Zichao Li; Lijuan Qiu

    2017-01-01

    Plant germplasm underpins much of crop genetic improvement. Millions of germplasm accessions have been collected and conserved ex situ and/or in situ, and the major challenge is now how to exploit and utilize this abundant resource. Genomics-based plant germplasm research (GPGR) or "Genoplasmics" is a novel cross-disciplinary research field that seeks to apply the principles and techniques of genomics to germplasm research. We describe in this paper the concept, strategy, and approach behind GPGR, and summarize current progress in the areas of the definition and construction of core collections, enhancement of germplasm with core collections, and gene discovery from core collections. GPGR is opening a new era in germplasm research. The contribution, progress and achievements of GPGR in the future are predicted.

  18. Genetic counselors: translating genomic science into clinical practice

    OpenAIRE

    Bennett, Robin L.; Hampel, Heather L.; Mandell, Jessica B.; Marks, Joan H.

    2003-01-01

    In a time of emerging genetic tests and technologies, genetic counselors are faced with the challenge of translating complex genomic data into information that will aid their client’s ability to learn about, understand, make, and cope with decisions relating to genetic diagnoses. The first of two companion articles in this issue examines the role of the genetic counselor, particularly in counseling individuals at risk for or diagnosed with breast cancer, in an era of high-tech health care and...

  19. Databases and web tools for cancer genomics study.

    Science.gov (United States)

    Yang, Yadong; Dong, Xunong; Xie, Bingbing; Ding, Nan; Chen, Juan; Li, Yongjun; Zhang, Qian; Qu, Hongzhu; Fang, Xiangdong

    2015-02-01

    Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  20. The human Genome project and the future of oncology

    International Nuclear Information System (INIS)

    Collins, Francis S.

    1996-01-01

    The Human Genome Project is an ambitious 15-year effort to devise maps and sequence of the 3-billion base pair human genome, including all 100,000 genes. The project is running ahead of schedule and under budget. Already the effects on progress in disease gene discovery have been dramatic, especially for cancer. The most appropriate uses of susceptibility testing for breast, ovarian, and colon cancer are being investigated in research protocols, and the need to prevent genetic discrimination in employment and health insurance is becoming more urgent. In the longer term, these gene discoveries are likely to usher in a new era of therapeutic molecular medicine

  1. A New Era for Research Education in Australia?

    Science.gov (United States)

    Marsh, Helene; Smith, Bradley; King, Max; Evans, Terry

    2012-01-01

    Use of the Australian research assessment exercise, Excellence in Research for Australia (ERA) to influence the policy and practice of research education in Australia will undoubtedly have many consequences, some of them unintended and potentially deleterious. ERA is a retrospective measure of research quality; research education is prospective.…

  2. Progressive-Era Resources on the World Wide Web.

    Science.gov (United States)

    Howenstein, Amanda

    1999-01-01

    Provides a list of Progressive-era websites with the address and a detailed description of each of the websites. Includes topics such as the womens suffrage movement, the Triangle Shirtwaist Factory fire, the Prohibition, labor-management conflicts, the Hull House, the Chicago fire, Emma Goldman, Progressive-era entertainment, and the Worlds Fair.…

  3. Enhanced recovery after surgery (ERAS) in penetrating abdominal ...

    African Journals Online (AJOL)

    Background: Enhanced recovery after surgery (ERAS) programmes employed in elective surgery have provided strong evidence for decreased lengths of hospital stay without increase in postoperative complications. The aim of this study was to explore the role and benefits of ERAS implemented in patients undergoing ...

  4. Pengelolaan Kepegawaian pada Era Otonomi Daerah

    Directory of Open Access Journals (Sweden)

    Erlanda Juliansyah Putra

    2015-04-01

    ABSTRACTPersonnel management in the era of regional autonomy in essence , has experienced rapid growth , especially in the case of the preparation of the needs of employees , along with the procurement process and the appointment of civil servants. In developing the needs of employees , management personnel requirements determination is based on job analysis and workload that is based on the priority needs of the region . Besides the procurement process and the appointment of civil servants has also contains a provision that puts the professionalism system based on the ability of each candidate civil servants as well as some of the qualification requirements to enable the civil servants to be able to compete boost development in the region , accompanied by the management salary and allowances are based on the management of the budget needs of each region.

  5. Laplace and the era of differential equations

    Science.gov (United States)

    Weinberger, Peter

    2012-11-01

    Between about 1790 and 1850 French mathematicians dominated not only mathematics, but also all other sciences. The belief that a particular physical phenomenon has to correspond to a single differential equation originates from the enormous influence Laplace and his contemporary compatriots had in all European learned circles. It will be shown that at the beginning of the nineteenth century Newton's "fluxionary calculus" finally gave way to a French-type notation of handling differential equations. A heated dispute in the Philosophical Magazine between Challis, Airy and Stokes, all three of them famous Cambridge professors of mathematics, then serves to illustrate the era of differential equations. A remark about Schrödinger and his equation for the hydrogen atom finally will lead back to present times.

  6. Russian Gas Market: Entering New Era

    International Nuclear Information System (INIS)

    Mitrova, Tatiana; Molnar, Gergely

    2015-04-01

    After a period of extensive growth in the 2000's, the Russian gas industry is now facing numerous challenges. Mounting competition by independent producers and the development of new production by Gazprom, combined with stagnating domestic demand and weakening export markets, have created a situation of overproduction, made worse by western sanctions and low oil and gas prices. Expansion to the East thanks to the recent China deal is not expected to provide much relief before 2024. The coming decade will be critical for the industry and its outcome will largely depend on the government's pricing and institutional policies but the role of the state should remain essential. This document presents the key findings of the New CEDIGAZ report 'Russian Gas Market: Entering New Era'. The report analyses the ongoing changes in the Russian industry and the challenges to be met

  7. Engineering Education for a New Era

    Science.gov (United States)

    Ohgaki, Shinichiro

    Engineering education is composed of five components, the idea what engineering education ought to be, the knowledge in engineering fields, those who learn engineering, those who teach engineering and the stakeholders in engineering issues. The characteristics of all these five components are changing with the times. When we consider the engineering education for the next era, we should analyze the changes of all five components. Especially the knowledge and tools in engineering fields has been expanding, and advanced science and technology is casting partly a dark shadow on the modern convenient life. Moral rules or ethics for developing new products and engineering systems are now regarded as most important in engineering fields. All those who take the responsibility for engineering education should understand the change of all components in engineering education and have a clear grasp of the essence of engineering for sustainable society.

  8. The Rejuvenation of Cartography in ICT Era

    Directory of Open Access Journals (Sweden)

    GUO Renzhong

    2017-10-01

    Full Text Available With the impetus of ICT, cartography faces the unprecedented challenges. The paper discusses the problems and changes of cartography facing the digital technology, analyzes the constraints of traditional cartography that are mainly delimited by 2D physical paper map. Diverseness of modern cartography shows various map products, and the paper illustrates the digital freedom in information space of modern cartography from eight aspects, including physical reality VS virtual reality, paper map VS digital map, superficial visualization VS inner visualization and so on. Modern cartography encounters the new development opportunities and fresh demands in digital era, and it's necessary to extend the framework of cartography and to assimilate newly sprouted things to promote the rejuvenation of cartography.

  9. Astronomy in the Big Data Era

    Directory of Open Access Journals (Sweden)

    Yanxia Zhang

    2015-05-01

    Full Text Available The fields of Astrostatistics and Astroinformatics are vital for dealing with the big data issues now faced by astronomy. Like other disciplines in the big data era, astronomy has many V characteristics. In this paper, we list the different data mining algorithms used in astronomy, along with data mining software and tools related to astronomical applications. We present SDSS, a project often referred to by other astronomical projects, as the most successful sky survey in the history of astronomy and describe the factors influencing its success. We also discuss the success of Astrostatistics and Astroinformatics organizations and the conferences and summer schools on these issues that are held annually. All the above indicates that astronomers and scientists from other areas are ready to face the challenges and opportunities provided by massive data volume.

  10. Scandinavian neuroscience during the Nazi era.

    Science.gov (United States)

    Kondziella, Daniel; Hansen, Klaus; Zeidman, Lawrence A

    2013-07-01

    Although Scandinavian neuroscience has a proud history, its status during the Nazi era has been overlooked. In fact, prominent neuroscientists in German-occupied Denmark and Norway, as well as in neutral Sweden, were directly affected. Mogens Fog, Poul Thygesen (Denmark) and Haakon Sæthre (Norway) were resistance fighters, tortured by the Gestapo: Thygesen was imprisoned in concentration camps and Sæthre executed. Jan Jansen (Norway), another neuroscientist resistor, escaped to Sweden, returning under disguise to continue fighting. Fritz Buchthal (Denmark) was one of almost 8000 Jews escaping deportation by fleeing from Copenhagen to Sweden. In contrast, Carl Værnet (Denmark) became a collaborator, conducting inhuman experiments in Buchenwald concentration camp, and Herman Lundborg (Sweden) and Thorleif Østrem (Norway) advanced racial hygiene in order to maintain the "superior genetic pool of the Nordic race." Compared to other Nazi-occupied countries, there was a high ratio of resistance fighters to collaborators and victims among the neuroscientists in Scandinavia.

  11. Chirurgie in die Grieks-Romeinse era

    Directory of Open Access Journals (Sweden)

    François P. Retief

    2006-09-01

    Full Text Available In die Grieks-Romeinse era het mediese behandeling kenmerkend uit drie elemente bestaan, naamlik regimen (dieet en gesonde leefwyse, geneesmiddels en chirurgie – laasgenoemde alleen toegepas indien regimen en geneesmiddels onsuksesvol was. Bewyse van primitiewe chirurgie dateer terug na die Bronstydperk, en in Homerus se eposse is heelwat vermelding van die chirurgiese hantering van oorlogswonde, met tussenkoms van die gode. Met die koms van empiriese geneeskunde in die 5de eeu v.C. het chirurgie in die Hippokratiese Corpus prominent gefigureer met beduidende bydraes in veral die ortopediese veld en hoofbeserings. Uitbouing van anatomiese en fisiologiese kennis, gebaseer op disseksie van menslike kadawers in Alexandrië vanaf die laat 4de eeu v.C., het chirurgie ’n hupstoot gegee. Teen die Romeinse era vanaf die 2de eeu v.C. het snykundetegnieke (en -instrumente beduidend verbeter, maar is steeds oorwegend deur Griekse geneeshere beoefen. Van geneeshere is steeds verwag om al drie bovermelde terapeutiese modaliteite te bemeester, maar chirurgie het meer aansien verwerf en daar is al meer in onderafdelings van chirurgie soos oogheelkunde, vrouesiektes en verloskunde, blaaskwale en mond- en keelsnykunde gespesialiseer. Militêre geneeskunde was in die Romeinse Ryk ’n belangrike aktiwiteit, en het veral traumachirurgie uitgebou. Betreding van die buik- en toraksholtes was nie meer noodwendig fataal nie, en veeartsenykunde het tot stand gekom. Die eerste beduidende chirurgiehandboek ná die Hippokratiese Corpus is in die 1ste eeu n.C. deur Celsus opgestel. Vanaf die 3de eeu het die chirurgieberoep min vordering gemaak, die beroepstaal het mettertyd van Grieks na Latyn verander en kundigheid is later veral deur Islam-geneeshere na die Middeleeue en later oorgedra.

  12. Long-memory exchange rate dynamics in the euro era

    International Nuclear Information System (INIS)

    Barkoulas, John T.; Barilla, Anthony G.; Wells, William

    2016-01-01

    We investigate the long-run dynamics of a system of eight major exchange rates in the euro era using both integer and fractional cointegration methodologies. Contrary to the fragile evidence in the pre-euro era, robust evidence of linear cointegratedness is obtained in the foreign exchange market during the euro era. Upon closer examination, deviations from the cointegrating relationship exhibit nonstationary, long-memory dynamic behavior (Joseph effect). We find the long-memory evidence to be temporally stable in the most recent era. Finally, the foreign exchange system dynamics appears to be characterized by less persistence (smaller fractional exponent) in the euro era (as compared to pre-euro time periods), potentially indicating increased policy coordination by central banks in the recent period.

  13. Variability of Iberian upwelling implied by ERA-40 and ERA-Interim reanalyses

    Directory of Open Access Journals (Sweden)

    José M. R. Alves

    2013-05-01

    Full Text Available The Regional Ocean Modeling System ocean model is used to simulate the decadal evolution of the regional waters in offshore Iberia in response to atmospheric fields given by ECMWF ERA-40 (1961–2001 and ERA-Interim (1989–2008 reanalyses. The simulated sea surface temperature (SST fields are verified against satellite AVHRR SST, and they are analysed to characterise the variability and trends of coastal upwelling in the region. Opposing trends in upwelling frequency are found at the northern limit, where upwelling has been decreasing in recent decades, and at its southern edge, where there is some evidence of increased upwelling. These results confirm previous observational studies and, more importantly, indicate that observed SST trends are not only due to changes in radiative or atmospheric heat fluxes alone but also due to changes in upwelling dynamics, suggesting that such a process may be relevant in climate change scenarios.

  14. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  16. The ERA-EDTA today and tomorrow: a progress document by the ERA-EDTA Council.

    Science.gov (United States)

    Zoccali, Carmine; Arici, Mustafa; Blankestijn, Peter J; Bruchfeld, Annette; Capasso, Giovambattista; Fliser, Danilo; Fouque, Denis; Goumenos, Dimitrios; Ketteler, Markus; Malyszko, Jolanta; Massy, Ziad; Rychlík, Ivan; Spasovski, Goce

    2018-05-23

    Scientific societies are increasingly seen as central to the advancement of information sharing and collaboration among scientists and clinical investigators for the progress of medical research and the promotion of education, professional competence, integrity and quality studies. To more effectively serve the practicing nephrologists and investigators dedicated to renal science, the Council of the European Renal Association and European Dialysis and Transplantation Association (ERA-EDTA) reorganized and integrated the various activities of the society into two branches, the Clinical Nephrology Governance branch and the Renal Science branch. New affordable initiatives to promote research, education and professional development and to advocate for the recognition of chronic kidney disease as a major public health issue at the European level will be put in place and/or potentiated in the new organizational frame. Educational initiatives will be espoused to Continuous Professional Development and, starting from 2019, 14 Education & Continuous Professional Development courses will be held covering the full range of knowledge areas of modern nephrology. Consolidation and development is the short- and medium-term mantra of the ERA-EDTA. The society has a rich portfolio of successful activities and brilliant, creative scientists among its members. Integrating the various activities of the ERA-EDTA and treasuring the expertise and wisdom of its most accomplished members will facilitate collaborative research, education and its public impact at large.

  17. Recommended Capacities for Educational Leadership: Pre-Reform Era Scholars versus Reform-Era Scholars versus National Standards

    Science.gov (United States)

    Gordon, Stephen P.; Taylor-Backor, Karen; Croteau, Susan

    2017-01-01

    We reviewed the scholarship on capacities for educational leadership for the past decade of the pre-reform era (1976-1985), as well as a recent decade of the reform era (2005-2015), and compared scholarship from both decades with the current Professional Standards for Educational Leaders. We found that scholars in the past decade of the pre-reform…

  18. Agrobacterium-mediated transformation as a tool for functional genomics in fungi

    NARCIS (Netherlands)

    Michielse, C.B.; Hooykaas, P.J.J.; Hondel, C.A.M.J.J. van den; Ram, A.F.J.

    2005-01-01

    In the era of functional genomics, the need for tools to perform large-scale targeted and random mutagenesis is increasing. A potential tool is Agrobacterium-mediated fungal transformation. A. tumefaciens is able to transfer a part of its DNA (transferred DNA; T-DNA) to a wide variety of fungi and

  19. Toward genome-scale models of the Chinese hamster ovary cells: incentives, status and perspectives

    DEFF Research Database (Denmark)

    Kaas, Christian Schrøder; Fan, Yuzhou; Weilguny, Dietmar

    2014-01-01

    Bioprocessing of the important Chinese hamster ovary (CHO) cell lines used for the production of biopharmaceuticals stands at the brink of several redefining events. In 2011, the field entered the genomics era, which has accelerated omics-based phenotyping of the cell lines. In this review we...

  20. Can Genetics and Genomics Nursing Competencies Be Successfully Taught in a Prenursing Microbiology Course?

    Science.gov (United States)

    Shuster, Michele

    2011-01-01

    In recognition of the entry into the era of personalized medicine, a new set of genetics and genomics competencies for nurses was introduced in 2006. Since then, there have been a number of reports about the critical importance of these competencies for nursing practices and about the challenges of addressing these competencies in the preservice…

  1. Genome sequence analysis with MonetDB - A case study on Ebola virus diversity

    NARCIS (Netherlands)

    Cijvat, R.; Manegold, S.; Kersten, M.; Klau, G.W.; Schönhuth, A.; Marschall, T.; Zhang, Y.

    2015-01-01

    Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but yields terabytes of data to be stored and analyzed. Biologists are often exposed to excessively time consuming and error-prone data management and

  2. Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

    Science.gov (United States)

    Fazal, Mohammed-Abbas; Alexander, Sarah; Burnett, Edward; Deheer-Graham, Ana; Oliver, Karen; Holroyd, Nancy; Parkhill, Julian; Russell, Julie E

    2016-11-03

    Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for Salmonella enterica subsp. enterica serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939. © Crown copyright 2016.

  3. Functional annotation of rare gene aberration drivers of pancreatic cancer | Office of Cancer Genomics

    Science.gov (United States)

    As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC).

  4. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  5. Convergence of advances in genomics, team science, and repositories as drivers of progress in psychiatric genomics.

    Science.gov (United States)

    Lehner, Thomas; Senthil, Geetha; Addington, Anjené M

    2015-01-01

    After many years of unfilled promise, psychiatric genetics has seen an unprecedented number of successes in recent years. We hypothesize that the field has reached an inflection point through a confluence of four key developments: advances in genomics; the orientation of the scientific community around large collaborative team science projects; the development of sample and data repositories; and a policy framework for sharing and accessing these resources. We discuss these domains and their effect on scientific progress and provide a perspective on why we think this is only the beginning of a new era in scientific discovery. Published by Elsevier Inc.

  6. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  7. Implementation of the Spanish ERAS program in bariatric surgery.

    Science.gov (United States)

    Ruiz-Tovar, Jaime; Muñoz, José Luis; Royo, Pablo; Duran, Manuel; Redondo, Elisabeth; Ramirez, Jose Manuel

    2018-03-08

    The essence of Enhanced Recovery After Surgery (ERAS) programs is the multimodal approach, and many authors have demonstrated safety and feasibility in fast track bariatric surgery. According to this concept, a multidisciplinary ERAS program for bariatric surgery has been developed by the Spanish Fast Track Group (ERAS Spain). The aim of this study was to analyze the initial implementation of this Spanish National ERAS protocol in bariatric surgery, comparing it with a historical cohort receiving standard care. A multi-centric prospective study was performed, including 233 consecutive patients undergoing bariatric surgery during 2015 and following ERAS protocol. It was compared with a historical cohort of 286 patients, who underwent bariatric surgery at the same institutions between 2013 and 2014 and following standard care. Compliance with the protocol, morbidity, mortality, hospital stay and readmission were evaluated. Bariatric techniques performed were Roux-en-Y gastric bypass and sleeve gastrectomy. There were no significant differences in complications, mortality and readmission. Postoperative pain and hospital stay were significantly lower in the ERAS group. The total compliance to protocol was 80%. The Spanish National ERAS protocol is a safe issue, obtaining similar results to standard care in terms of complications, reoperations, mortality and readmissions. It is associated with less postoperative pain and earlier hospital discharge.

  8. The spectrum of genomic signatures: from dinucleotides to chaos game representation.

    Science.gov (United States)

    Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

    2005-02-14

    In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

  9. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  10. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  11. Epigenetics in the Vascular Endothelium: Looking From a Different Perspective in the Epigenomics Era.

    Science.gov (United States)

    Yan, Matthew S; Marsden, Philip A

    2015-11-01

    Cardiovascular diseases are commonly thought to be complex, non-Mendelian diseases that are influenced by genetic and environmental factors. A growing body of evidence suggests that epigenetic pathways play a key role in vascular biology and might be involved in defining and transducing cardiovascular disease inheritability. In this review, we argue the importance of epigenetics in vascular biology, especially from the perspective of endothelial cell phenotype. We highlight and discuss the role of epigenetic modifications across the transcriptional unit of protein-coding genes, especially the role of intragenic chromatin modifications, which are underappreciated and not well characterized in the current era of genome-wide studies. Importantly, we describe the practical application of epigenetics in cardiovascular disease therapeutics. © 2015 American Heart Association, Inc.

  12. Astrometric surveys in the Gaia era

    Science.gov (United States)

    Zacharias, Norbert

    2018-04-01

    The Gaia first data release (DR1) already provides an almost error free optical reference frame on the milli-arcsecond (mas) level allowing significantly better calibration of ground-based astrometric data than ever before. Gaia DR1 provides positions, proper motions and trigonometric parallaxes for just over 2 million stars in the Tycho-2 catalog. For over 1.1 billion additional stars DR1 gives positions. Proper motions for these, mainly fainter stars (G >= 11.5) are currently provided by several new projects which combine earlier epoch ground-based observations with Gaia DR1 positions. These data are very helpful in the interim period but will become obsolete with the second Gaia data release (DR2) expected in April 2018. The era of traditional, ground-based, wide-field astrometry with the goal to provide accurate reference stars has come to an end. Future ground-based astrometry will fill in some gaps (very bright stars, observations needed at many or specific epochs) and mainly will go fainter than the Gaia limit, like the PanSTARRS and the upcoming LSST surveys.

  13. ETIKA DRIYARKARA DAN RELEVANSINYA DI ERA POSTMODERN

    Directory of Open Access Journals (Sweden)

    Banin Diar Sukmono

    2013-04-01

    Full Text Available Driyarkara is an Indonesian philosopher who has original way of thinking. This paper aims to explore and analyze his ideas of moral and decency. According to Driyarkara, moral is a human need. Without moral, humanity will be in chaos. Based on Driyarkara's point of view, moral is a consequence of consciousness; therefore, having high moral standard is a human nature. Furthermore, conscience can be a moral standard for determining right or wrong as long as the conscience itself has not been “raped”. When conducting a moral consideration, every human has to use his own reason which is reflected in Driyarkara's Purity of Reason Dialectic. For him, all moral efforts show that human always want to achieve the perfection which is considered as God. The Driyarkara ethics could be classified as the deontological ethics. But it is the deontological ethics which has theological, humanist-naturalist, and axiological dimensions so that it can be defined as teleological as well. If we correlate the Driyarkara ethics and the Postmodern Era where morality has already been blurring, we can place the Driyarkara ethics which is considered teleological and deontological as a solid alternative of morality.

  14. CERN moves into the LHC era

    CERN Multimedia

    2001-01-01

    Dr Hans Eschelbacher (on the left), President of the CERN Council for the last three years, hands over to his successor Maurice Bourquin.  The CERN Council, where the representatives of the 20 Member States of the Organization decide on scientific programmes and financial resources, held its 116th session on 15 December under the chairmanship of Dr. Hans C. Eschelbacher (DE). 'Le Roi est mort. Vive le Roi !' The Large Electron Positron Collider (LEP) era has ended and CERN's future is the Large Hadron Collider (LHC), stated Director General, Prof. Luciano Maiani. He opened his report to Council with a 'homage to LEP', which reached the end of its career during 2000 and is now being dismantled to make way for CERN's next major machine, the LHC collider, in the same 27-kilometre tunnel. The strong indications of a Higgs boson at 115 GeV found during the year were the culmination of LEP's long and distinguished physics career, during which the machine opened up new regimes of precision physics, involvi...

  15. Global Learning in a New Era

    Directory of Open Access Journals (Sweden)

    Judith Ramaley

    2016-06-01

    Full Text Available Our nation’s colleges and universities have frequently adapted their educational approaches and their relationships with society to respond to new social, economic and environmental challenges. The increasingly interconnected patterns that link together our lives on a global scale have created a new reality. Globalization offers an especially exciting and challenging blend of generational change combined with the emergence of a set of complex, multi-faceted problems created by the global context in which we all now live and work. How shall we educate our students for life in this new era? What can we expect of our graduates in a global world? The answer to these questions is straightforward but will require our institutions to make significant changes in their approach to educating their students and in their interactions with the broader communities that they serve. The approach is shaped by a clear sense of what a globally prepared graduate knows and can do, guided by clear learning outcomes exercised along a sequential pathway of experiences extending from the first year of college through to graduation. These experiences are supported by the use of engaged learning practices that draw students into work that is both personally and socially meaningful cross-disciplinary inquiry that focuses on Big Questions with the goal of finding ways to address those questions in ethical and responsible and effective ways.

  16. Flavour in the era of the LHC

    CERN Multimedia

    2006-01-01

    The 4th meeting of the 'Flavour in the era of the LHC' workshop will take place at CERN on 9-11 October, 2006. The goal of this workshop is to outline and document a programme for flavour physics for the next decade, addressing in particular the complementarity and synergy between the discoveries we expect to emerge from the LHC and the potential for accurate measurements of future flavour factories. Over 150 physicists will join in the discussions of the three working groups dedicated to 'Flavour physics at high Q', 'B/D/K decays' and 'Flavour in the lepton sector, EDM's, g-2, etc'. The previous meetings took place in November 2005, and in February and May this year. In addition to the working group sessions, a special miniworkshop dedicated to future prospects for electric dipole moment (EDM) searches and g-2 measurements will be held on 9-10 October. Sensitive EDM and g-2 experiments probe physics in an integral way, and in many cases their physics reach is much higher than the spectrometer searches at th...

  17. Flavour in the era of the LHC

    CERN Multimedia

    2006-01-01

    The 4th meeting of the 'Flavour in the era of the LHC'workshop will take place at CERN on 9-11 October, 2006. The goal of this workshop is to outline and document a programme for flavour physics for the next decade, addressing in particular the complementarity and synergy between the discoveries we expect to emerge from the LHC and the potential for accurate measurements of future flavour factories. Over 150 physicists will join in the discussions of the three working groups dedicated to 'Flavour physics at high Q', 'B/D/K decays'and 'Flavour in the lepton sector, EDM's, g-2, etc'. The previous meetings took place in November 2005, and in February and May this year. In addition to the working group sessions, a special miniworkshop dedicated to future prospects for electric dipole moment (EDM) searches and g-2 measurements will be held on 9-10 October. Sensitive EDM and g-2 experiments probe physics in an integral way, and in many cases their physics reach is much higher than the spectrometer searches at th...

  18. Cancer Genomics: Diversity and Disparity Across Ethnicity and Geography.

    Science.gov (United States)

    Tan, Daniel S W; Mok, Tony S K; Rebbeck, Timothy R

    2016-01-01

    Ethnic and geographic differences in cancer incidence, prognosis, and treatment outcomes can be attributed to diversity in the inherited (germline) and somatic genome. Although international large-scale sequencing efforts are beginning to unravel the genomic underpinnings of cancer traits, much remains to be known about the underlying mechanisms and determinants of genomic diversity. Carcinogenesis is a dynamic, complex phenomenon representing the interplay between genetic and environmental factors that results in divergent phenotypes across ethnicities and geography. For example, compared with whites, there is a higher incidence of prostate cancer among Africans and African Americans, and the disease is generally more aggressive and fatal. Genome-wide association studies have identified germline susceptibility loci that may account for differences between the African and non-African patients, but the lack of availability of appropriate cohorts for replication studies and the incomplete understanding of genomic architecture across populations pose major limitations. We further discuss the transformative potential of routine diagnostic evaluation for actionable somatic alterations, using lung cancer as an example, highlighting implications of population disparities, current hurdles in implementation, and the far-reaching potential of clinical genomics in enhancing cancer prevention, diagnosis, and treatment. As we enter the era of precision cancer medicine, a concerted multinational effort is key to addressing population and genomic diversity as well as overcoming barriers and geographical disparities in research and health care delivery. © 2015 by American Society of Clinical Oncology.

  19. Storm-Tracks in ERA-40 and ERA-Interim Reanalyses

    Science.gov (United States)

    Liberato, M. L. R.; Trigo, I. F.; Trigo, R. M.

    2009-04-01

    Extratropical cyclones, their dominant paths, frequency and intensity have long been the object of climatological studies. The analysis of cyclone characteristics for the Euro-Atlantic sector (85°W-70°E; 20°N-75°N) presented here is based on the cyclone detecting and tracking algorithm first developed for the Mediterranean region (Trigo et al., 1999, 2002) and recently extended to a larger Euro-Atlantic region (Trigo, 2006). The objective methodology, which identifies and follows individual lows (Trigo et al. 1999), is applied to 6-hourly geopotential data at 1000-hPa from two reanalyses datasets provided by the European Centre for Medium-Range Weather Forecasts (ECMWF): ERA-40 and ERA-Interim reanalyses. Two storm-track databases are built over the Northern Atlantic European area, spanning the common available extended winter seasons from October 1989 to March 2002. Although relatively short, this common period allows a comparison of systems represented in reanalyses datasets with distinct horizontal resolutions (T106 and T255, respectively). This exercise is mostly focused on the key areas of cyclone formation and dissipation and main cyclone characteristics for the Euro-Atlantic sector. Trigo, I. F., T. D. Davies, and G. R. Bigg, 1999: Objective climatology of cyclones in the Mediterranean region. J. Climate, 12, 1685-1696. Trigo I. F., G. R. Bigg and T. D. Davies, 2002: Climatology of Cyclogenesis Mechanisms in the Mediterranean. Mon. Weather Rev. 130, 549-569. Trigo, I. F. 2006: Climatology and Interannual Variability of Storm-Tracks in the Euro-Atlantic sector: a comparison between ERA-40 and NCEP/NCAR Reanalyses. Clim. Dyn. DOI 10.1007/s00382-005-0065-9.

  20. Molecular identification, genetic diversity, population genetics and genomics of Rhizoctonia solani. In:perspective of plant pathology in genomic era

    Science.gov (United States)

    The basidiomycetous soilborne fungus Rhizoctonia (sensu lato) is an economically important pathogen of worldwide distribution and it is known to attack at least 188 species of higher plants, including agronomic crops, vegetables, ornamentals, forest trees and turfgrasses. The pathogenic isolates may...

  1. Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms.

    Science.gov (United States)

    Johnson, Brant R; Klaenhammer, Todd R

    2014-07-01

    For thousands of years, humans have safely consumed microorganisms through fermented foods. Many of these bacteria are considered probiotics, which act through diverse mechanisms to confer a health benefit to the host. However, it was not until the availability of whole-genome sequencing and the era of genomics that mechanisms of probiotic efficacy could be discovered. In this review, we explore the history of the probiotic concept and the current standard of integrated genomic techniques to discern the complex, beneficial relationships between probiotic microbes and their hosts.

  2. The new survivors and a new era for trauma research.

    Science.gov (United States)

    Brohi, Karim; Schreiber, Martin

    2017-07-01

    Karim Brohi and Martin Schreiber, Guest Editors of the Special Issue on Trauma, describe a new era in exploration of the biology of injury response and translation of new opportunities into clinical practice.

  3. The new survivors and a new era for trauma research

    OpenAIRE

    Brohi, Karim; Schreiber, Martin

    2017-01-01

    Karim Brohi and Martin Schreiber, Guest Editors of the Special Issue on Trauma, describe a new era in exploration of the biology of injury response and translation of new opportunities into clinical practice.

  4. CENET: Cost Efficiency in a New Era with new Technology

    Energy Technology Data Exchange (ETDEWEB)

    Karlsen, Jan E.; Lund, Bjoernar; Bos, Christian F.M.; Stokka, Sigmund

    1997-12-31

    This report relates to the CENET (Cost Efficiency in a New Era with new Technology) project the oil and gas in Europe. Key objectives of the CENET project are to determine the role of RTD (Research and Technology Development) in European oil and gas industry towards improved value and cost reduction with a particular focus on the means of developing offshore European marginal fields commercially, to identify RTD areas with the largest potential for improved value and cost reduction and technological developments and advances which are likely to increase European competitiveness internationally, and to provide guidance to European governments when deciding RTD priorities. A new era with new technology concerns increased oil and gas potential during the next century, a new era with clean, safe and cost efficient energy production, a new era with a new business structure, and globalization of the industry. 44 tabs., 5 figs., 23 tabs.

  5. Eraõigusliku juriidilise isiku organi liikmete õigussuhted / Kalev Saare

    Index Scriptorium Estoniae

    Saare, Kalev, 1974-

    2010-01-01

    Eraõiguslike juriidiliste isikute organi mõistest aktsiaseltsi ja osaühingu näitel, organiliikmete sisesuhte tekkimisest ja tsiviilseadustiku üldosa seaduse poolt määratud sisesuhte sisusse kuuluvatest peamistest kohustustest

  6. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  7. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  8. Evaluation of ERA-Interim precipitation data in complex terrain

    Science.gov (United States)

    Gao, Lu; Bernhardt, Matthias; Schulz, Karsten

    2013-04-01

    Precipitation controls a large variety of environmental processes, which is an essential input parameter for land surface models e.g. in hydrology, ecology and climatology. However, rain gauge networks provides the necessary information, are commonly sparse in complex terrains, especially in high mountainous regions. Reanalysis products (e.g. ERA-40 and NCEP-NCAR) as surrogate data are increasing applied in the past years. Although they are improving forward, previous studies showed that these products should be objectively evaluated due to their various uncertainties. In this study, we evaluated the precipitation data from ERA-Interim, which is a latest reanalysis product developed by ECMWF. ERA-Interim daily total precipitation are compared with high resolution gridded observation dataset (E-OBS) at 0.25°×0.25° grids for the period 1979-2010 over central Alps (45.5-48°N, 6.25-11.5°E). Wet or dry day is defined using different threshold values (0.5mm, 1mm, 5mm, 10mm and 20mm). The correspondence ratio (CR) is applied for frequency comparison, which is the ratio of days when precipitation occurs in both ERA-Interim and E-OBS dataset. The result shows that ERA-Interim captures precipitation occurrence very well with a range of CR from 0.80 to 0.97 for 0.5mm to 20mm thresholds. However, the bias of intensity increases with rising thresholds. Mean absolute error (MAE) varies between 4.5 mm day-1 and 9.5 mm day-1 in wet days for whole area. In term of mean annual cycle, ERA-Interim almost has the same standard deviation of the interannual variability of daily precipitation with E-OBS, 1.0 mm day-1. Significant wet biases happened in ERA-Interim throughout warm season (May to August) and dry biases in cold season (November to February). The spatial distribution of mean annual daily precipitation shows that ERA-Interim significant underestimates precipitation intensity in high mountains and northern flank of Alpine chain from November to March while pronounced

  9. THE APPEARANCE OF GOVERNMENT BUREAUCRACY IN QUANTUM ERA

    OpenAIRE

    Kadir, Gau

    2015-01-01

    This study will answer three main questions: 1) how is the reduction of Weber???s theory in the bureaucracy appearance?; 2) How is the model of government bureaucracy in rationalistic and quantum era?; and 3) how is the reality of government bureaucracy reformation model in rationalistic and quantum era? This study was employed empirically by using qualitative method and content analysis techniques with the focus on the bureaucracy reformation as a result of rational thinking application in q...

  10. Era of superheavy-particle dominance and big bang nucleosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Polnarev, A.G.; Khlopov, M.Y.

    1982-01-01

    The observed primordial He/sup 4/ abundance imposes astrophysical constraints on the possible departures from radiation dominance in the big bang universe during the neutron hardening era (at epoch t roughly-equal1 sec). Limits are obtained which, along with the data on the spectrum of the cosmic background radiation, practically rule out any stages of superheavy stable-particle dominance in the era 1< or approx. =t<10/sup 10/ sec, thereby setting restrictions on current elementary-particle theories.

  11. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  12. War and peace in the Internet era

    Directory of Open Access Journals (Sweden)

    Josep M. Porta Fabregat

    2004-04-01

    Full Text Available This article looks to find the ideological causes that lead human beings to war or peace nowadays, in the Internet era. This proposal is worthy of study as war is not a need in terms of human nature or history: we are capable of war and peace simultaneously. However, why does war survive if we are able to live in peace? In our opinion, the actual cause of conflict is fanaticism. This phenomenon comes from the perversion of the two bases of our civilisation: liberty and rationality. This twofold perversion leads us to believe that we are the Absolute, or at least its instrument.Since the fall of the Berlin wall, this kind of fanaticism has come from the generalised conviction that we are at the "end of history"; in this light, one can conclude that this irrationality is definitive and, thus, that any efforts to achieve world peace are useless. However, we believe that the formula for peace can only be derived from reflection and the effective extension around the world of a technical medium that makes communication between all men possible. This would be able to resolve all the perversions of liberty and rationality and make people aware of the infinite distance between us and the Absolute. However, this reflection is not enough. For this awareness to triumph, the technical and ideological situation represented by the Internet has to spread over the whole planet: liberty for those taking part, rationality to allow for communication among all those connected and universal access. This is the moral trend for the Internet, which in itself encourages progress towards world peace.

  13. A new Era in Sustainable Development

    Energy Technology Data Exchange (ETDEWEB)

    Bass, Steve

    2007-03-15

    It is 20 years since the World Commission on Environment and Development — the Brundtland Commission — released its influential report on sustainable development. This is now the declared intention of most governments, many international organisations, and an increasing number of businesses and civil society groups. High profile 'intentions' have given rise to a bewildering array of sustainable development plans, tools and business models. But these have not yet triggered the pace, scale, scope and depth of change that is needed to make development sustainable. They leave the underlying causes of unsustainable development largely undisturbed. They include few means for anticipating non-linear changes – from climate change to economic cycles – and for building resilience to them. Consequently, most environmental and welfare measures continue to decline in almost all countries. Much energy has been spent crafting the sustainable development 'toolkit'. But that energy has been channelled largely through a narrow set of international processes and 'elite' national actors. The results are not yet integral to the machinery of government or business, or people's daily lives. This paper calls for energies to be directed in new ways, constructing a truly global endeavour informed by diverse local actors' evidence of 'what works', and focusing more keenly on long-term futures. The key drivers and challenges of a 'new era in sustainable development' are suggested, to elicit ideas and leadership from a richer vein of experience than has been embraced by the formal international endeavours to date. This paper is the first in a series on the sustainable development futures that face key sectors and stakeholder groups.

  14. Politisasi Birokrasi Pemerintahan Desa Pada Era Reformasi

    Directory of Open Access Journals (Sweden)

    R Widodo Triputro

    2015-12-01

    Full Text Available Public bureaucracy holds a strategic position in government implementation as well as to effort of democratization and autonomy in local and village government scope. Professional bureaucracy apparatus intensely support the increase of public service quality, particular yfor social empowerment as the realization of local and village autonomy essence. The concept of bureaucracy neutrality needs to be bought into reality in order to urge a bureaucracy that more oriented to its main function, namely as public service apparatus. Long history oflndonesian bureaucracy reflects the occuring bureaucracy politization by government regime, with the result that all bureaucracy's line become an administration tool in performing is authority centralization. As the consequence, service tends to be addressed to government (patron by neglecting public service function. It includes in village government scope, in which bureaucracy becomes a political machine, meanwlile serves as an effective controlling tool that limits social access to public arena. The outcome of case study conducted in one village of Bantul Regency with data resource was gained from government official and prominent figures both in regency or village government area, reveals that bureaucracy politization in village government nowdays is much stronger than under new orde era. On the pretext of democratization and social empowerment, government (red : regent and his political party performs a set of bureaucracy politization in village government. With limited village resource condition, politic euphoria, and conflict as the result of election proces of village government bureaucracy apparatus, government intervences village government and its community. The patron-client relation is between the government with village government and its community. It is evidenced that bureaucracy politization of villlage government is re-carried out, among others is the estabilish of "Paguyuban Pamong" with its

  15. Prolactinoma treatment status in the cabergoline era

    International Nuclear Information System (INIS)

    Watanabe, Shinya; Takano, Shingo; Akutsu, Hiroyoshi; Sato, Hiroshige; Matsumura, Akira

    2011-01-01

    The aim of our study is to report the most adequate therapy for prolactinoma in the cabergoline era. From 2003 to 2009, 27 patients with prolactinoma were treated at our hospital. Patients are categorized into 2 groups. The Cabergoline Group: Cabergoline was administered for 5 years and discontinued. Using this protocol, the case with normal prolactin level in addition to having no visible tumor more than 24 months after the discontinuation of cabergoline was judged as cured. The Operation Group: Transsphenoidal surgery (TSS) was performed first. In the Cabergoline group, 12 cases were cured with 5 years cabergoline treatment (Cure) and 6 cases were not cured (Not cure). We compared the pretreatment prolactin level, the normalization of the serum level of prolactin, the degree of invasiveness on MRI, regression of the tumor during treatment on MRI, max dose of cabergoline, degree of pituitary hormone replacement, frequency of pregnancy, and follow up periods between the Cabergoline-cure group, the Cabergoline-not-cure group, and the Operation group. Normalization rate in serum level of prolactin and cure rate were 91% and 63% in the Cabergoline group. Pretreatment prolactine level and the frequency of tumor invasiveness on initial MRI were significantly higher in the Cabergoline-not-cure group compared to the Cabergoline-cure group. All of the five woman accompanied with pregnancy after the treatment belonged to the Cabergoline-cure group. In the Operation group, all 4 cases achieved normalization of serum prolactin level without visible tumor and with normal pituitary function. Cabergoline for prolactinoma is effective, but the cure rate by continuous usage of cabergoline for 5 years was 67%. The factors that cabergoline and/or TSS can cure prolactinoma are non-invasive tumor and prolactin level under 200 ng/mL at pretreatment. (author)

  16. Space Weather Drivers in the ACE Era

    Science.gov (United States)

    Vogt, M.; Puhl-Quinn, P.; Jordanova, V. K.; Smith, C. W.; Cohen, C. M.

    2004-12-01

    The Advanced Composition Explorer (ACE) spacecraft was launched Aug.~25, 1997 [Stone et al., 1998]. Beginning shortly after launch and continuing to the present day ACE has provided real-time data telemetry of solar wind conditions upstream of the Earth. The real-time data includes solar wind speed and density, magnetic field direction and magnitude, and a range of energetic particle intensities [Zwickl et al., 1999]. The real-time data product is provided within 5 minutes of observation and many partners from both industry and science use these data for a variety of purposes. The most common purpose of practical industrial application involves mitigation of lost services arising from magnetospheric storm activity. Many space weather efforts are directed at providing improved predictions of magnetospheric response that can be applied to real-time data in the hope of better predicting the vulnerability and required action of industry to approaching disturbances. It therefore seems prudent that following 6 years of activity including one solar maximum period we should evaluate the nature and strength of the largest disturbances observed with the hope of better assessing the industrial response. Simply put: ``Did ACE observe disturbances that were as large as those seen previously during the space age?'' If not, it may be the case that industry must evaluate its response to the real-time warnings and not become complacent by the simple act of survival. We compare the most intense space weather events of the ACE era with those recorded on the Omnitape data set spanning 40+ years of spacecraft measurements in the near-Earth environment. We compare both magnetospheric response parameters and solar wind drivers. In addition, we compare the large energetic particle events over the same time frame. Stone, E.~C., et al., Space Science Rev., 86(1-4), 357-408, 1998. Zwickl, R.~D., et al., Space Science Rev., 86(1-4), 633-648, 1998.

  17. Genomics, transcriptomics and proteomics: enabling insights into social evolution and disease challenges for managed and wild bees.

    Science.gov (United States)

    Trapp, Judith; McAfee, Alison; Foster, Leonard J

    2017-02-01

    Globally, there are over 20 000 bee species (Hymenoptera: Apoidea: Anthophila) with a host of biologically fascinating characteristics. Although they have long been studied as models for social evolution, recent challenges to bee health (mainly diseases and pesticides) have gathered the attention of both public and research communities. Genome sequences of twelve bee species are now complete or under progress, facilitating the application of additional 'omic technologies. Here, we review recent developments in honey bee and native bee research in the genomic era. We discuss the progress in genome sequencing and functional annotation, followed by the enabled comparative genomics, proteomics and transcriptomics applications regarding social evolution and health. Finally, we end with comments on future challenges in the postgenomic era. © 2016 John Wiley & Sons Ltd.

  18. Biodiversity analysis in the digital era

    Science.gov (United States)

    2016-01-01

    This paper explores what the virtual biodiversity e-infrastructure will look like as it takes advantage of advances in ‘Big Data’ biodiversity informatics and e-research infrastructure, which allow integration of various taxon-level data types (genome, morphology, distribution and species interactions) within a phylogenetic and environmental framework. By overcoming the data scaling problem in ecology, this integrative framework will provide richer information and fast learning to enable a deeper understanding of biodiversity evolution and dynamics in a rapidly changing world. The Atlas of Living Australia is used as one example of the advantages of progressing towards this future. Living in this future will require the adoption of new ways of integrating scientific knowledge into societal decision making. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481789

  19. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  20. Nutrition in the genomics era: Cardiovascular disease risk and the Mediterranean diet

    Science.gov (United States)

    The effect of dietary changes on phenotypes (i.e., plasma lipid measures, body weight and blood pressure)differs significantly between individuals. This phenomenon has been more extensively researched in relation to changes in dietary fat and plasma lipid concentrations for the prevention of cardiov...

  1. The genomic era and serious mental illness: a potential application for psychiatric genetic counseling.

    Science.gov (United States)

    Austin, Jehannine C; Honer, William G

    2007-02-01

    Genetic counseling is an important clinical service that is routinely offered to families affected by genetic disorders or by complex disorders for which genetic testing is available. It is not yet routinely offered to individuals with serious mental illnesses and their families, but recent findings that beliefs about the cause of mental illness can affect an individual's adaptation to the illness suggest that genetic counseling may be a useful intervention for this population. In a genetic counseling session the counselor discusses genetic and environmental contributors to disease pathogenesis; helps individuals explore conceptions, fears, and adaptive strategies; and provides nondirective support for decision making. Expected outcomes may include reductions in fear, stigma, and guilt associated with a psychiatric diagnosis; improvements in adherence to prescribed medications; declines in risk behaviors; and reductions in misconceptions about the illness. The authors endorse a multidisciplinary approach in which a psychiatrist and genetic counselor collaborate to provide comprehensive psychiatric genetic counseling.

  2. Congenital neutropenia in the era of genomics: classification, diagnosis, and natural history.

    Science.gov (United States)

    Donadieu, Jean; Beaupain, Blandine; Fenneteau, Odile; Bellanné-Chantelot, Christine

    2017-11-01

    This review focuses on the classification, diagnosis and natural history of congenital neutropenia (CN). CN encompasses a number of genetic disorders with chronic neutropenia and, for some, affecting other organ systems, such as the pancreas, central nervous system, heart, bone and skin. To date, 24 distinct genes have been associated with CN. The number of genes involved makes gene screening difficult. This can be solved by next-generation sequencing (NGS) of targeted gene panels. One of the major complications of CN is spontaneous leukaemia, which is preceded by clonal somatic evolution, and can be screened by a targeted NGS panel focused on somatic events. © 2017 John Wiley & Sons Ltd.

  3. Traditional Chinese medicine research in the post-genomic era: good practice, priorities, challenges and opportunities.

    Science.gov (United States)

    Uzuner, Halil; Bauer, Rudolf; Fan, Tai-Ping; Guo, De-An; Dias, Alberto; El-Nezami, Hani; Efferth, Thomas; Williamson, Elizabeth M; Heinrich, Michael; Robinson, Nicola; Hylands, Peter J; Hendry, Bruce M; Cheng, Yung-Chi; Xu, Qihe

    2012-04-10

    GP-TCM is the 1st EU-funded Coordination Action consortium dedicated to traditional Chinese medicine (TCM) research. This paper aims to summarise the objectives, structure and activities of the consortium and introduces the position of the consortium regarding good practice, priorities, challenges and opportunities in TCM research. Serving as the introductory paper for the GP-TCM Journal of Ethnopharmacology special issue, this paper describes the roadmap of this special issue and reports how the main outputs of the ten GP-TCM work packages are integrated, and have led to consortium-wide conclusions. Literature studies, opinion polls and discussions among consortium members and stakeholders. By January 2012, through 3 years of team building, the GP-TCM consortium had grown into a large collaborative network involving ∼200 scientists from 24 countries and 107 institutions. Consortium members had worked closely to address good practice issues related to various aspects of Chinese herbal medicine (CHM) and acupuncture research, the focus of this Journal of Ethnopharmacology special issue, leading to state-of-the-art reports, guidelines and consensus on the application of omics technologies in TCM research. In addition, through an online survey open to GP-TCM members and non-members, we polled opinions on grand priorities, challenges and opportunities in TCM research. Based on the poll, although consortium members and non-members had diverse opinions on the major challenges in the field, both groups agreed that high-quality efficacy/effectiveness and mechanistic studies are grand priorities and that the TCM legacy in general and its management of chronic diseases in particular represent grand opportunities. Consortium members cast their votes of confidence in omics and systems biology approaches to TCM research and believed that quality and pharmacovigilance of TCM products are not only grand priorities, but also grand challenges. Non-members, however, gave priority to integrative medicine, concerned on the impact of regulation of TCM practitioners and emphasised intersectoral collaborations in funding TCM research, especially clinical trials. The GP-TCM consortium made great efforts to address some fundamental issues in TCM research, including developing guidelines, as well as identifying priorities, challenges and opportunities. These consortium guidelines and consensus will need dissemination, validation and further development through continued interregional, interdisciplinary and intersectoral collaborations. To promote this, a new consortium, known as the GP-TCM Research Association, is being established to succeed the 3-year fixed term FP7 GP-TCM consortium and will be officially launched at the Final GP-TCM Congress in Leiden, the Netherlands, in April 2012. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  4. Tomato breeding in the genomics era: insights from a SNP array

    NARCIS (Netherlands)

    Víquez-Zamora, M.; Vosman, B.; Geest, van H.; Bovy, A.G.; Visser, R.G.F.; Finkers, H.J.; Heusden, van A.W.

    2013-01-01

    Background - The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them

  5. Erythropoietin abuse and erythropoietin gene doping: detection strategies in the genomic era.

    Science.gov (United States)

    Diamanti-Kandarakis, Evanthia; Konstantinopoulos, Panagiotis A; Papailiou, Joanna; Kandarakis, Stylianos A; Andreopoulos, Anastasios; Sykiotis, Gerasimos P

    2005-01-01

    The administration of recombinant human erythropoietin (rhEPO) increases the maximum oxygen consumption capacity, and is therefore abused as a doping method in endurance sports. The detection of erythropoietin (EPO) abuse is based on direct pharmacological and indirect haematological approaches, both of which have several limitations. In addition, current detection methods cannot cope with the emerging doping strategies of EPO mimicry, analogues and gene doping, and thus novel detection strategies are urgently needed. Direct detection methods for EPO misuse can be either pharmacological approaches that identify exogenous substances based on their physicochemical properties, or molecular methods that recognise EPO transgenes or gene transfer vectors. Since direct detection with molecular methods requires invasive procedures, it is not appropriate for routine screening of large numbers of athletes. In contrast, novel indirect methods based on haematological and/or molecular profiling could be better suited as screening tools, and athletes who are suspect of doping would then be submitted to direct pharmacological and molecular tests. This article reviews the current state of the EPO doping field, discusses available detection methods and their shortcomings, outlines emerging pharmaceutical and genetic technologies in EPO misuse, and proposes potential directions for the development of novel detection strategies.

  6. Studying stress responses in the post-genomic era: its ecological ...

    Indian Academy of Sciences (India)

    Madhu Sudhan

    2007-03-26

    Mar 26, 2007 ... stress is regarded as an “environmental factor causing a change in a biological ... and evolutionary perspective and to investigate the role of stress ... and here more specifically, which genes affect acclimation and adaptation ...

  7. Conceptualizing genetic counseling as psychotherapy in the era of genomic medicine.

    Science.gov (United States)

    Austin, Jehannine; Semaka, Alicia; Hadjipavlou, George

    2014-12-01

    Discussions about genetic contributions to medical illness have become increasingly commonplace. Physicians and other health-care providers in all quarters of medicine, from oncology to psychiatry, routinely field questions about the genetic basis of the medical conditions they treat. Communication about genetic testing and risk also enter into these conversations, as knowledge about genetics is increasingly expected of all medical specialists. Attendant to this evolving medical landscape is some uncertainty regarding the future of the genetic counseling profession, with the potential for both increases and decreases in demand for genetic counselors being possible outcomes. This emerging uncertainty provides the opportunity to explicitly conceptualize the potentially distinct value and contributions of the genetic counselor over and above education about genetics and risk that may be provided by other health professionals. In this paper we suggest conceptualizing genetic counseling as a highly circumscribed form of psychotherapy in which effective communication of genetic information is a central therapeutic goal. While such an approach is by no means new--in 1979 Seymour Kessler explicitly described genetic counseling as a "kind of psychotherapeutic encounter," an "interaction with a psychotherapeutic potential"--we expand on his view, and provide research evidence in support of our position. We review available evidence from process and outcome studies showing that genetic counseling is a therapeutic encounter that cannot be reduced to one where the counselor performs a simple "conduit for information" function, without losing effectiveness. We then discuss potential barriers that may have impeded greater uptake of a psychotherapeutic model of practice, and close by discussing implications for practice.

  8. Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Baell, Jonathan B.; Fernández-Recio, Juan

    2012-01-01

    Bioinformatics and chemoinformatics approaches contribute to hit discovery, hit-to-lead optimization, safety profiling, and target identification and enhance our overall understanding of the health and disease states. A vast repertoire of computational methods has been reported and increasingly...

  9. 51. Brazilian congress on genetics. From biostatistics to bioinformatics. Genomic era. Abstracts

    International Nuclear Information System (INIS)

    2005-01-01

    Use of radioisotopes and ionizing radiations in genetics is presented. Several aspects related to men, animals, plants and microorganisms are reported highlighting biological radiation effects, evolution, mutagenesis and genetic engineering. Genetic mapping, polymerase chain reaction, gene mutations, genetic diversity, DNA hybridization, DNA sequencing, plant cultivation and plant grow are studied as well. Goiania radiation accident is mentioned and biological radiation effects of Cesium 137 are evaluated by biological indicators and radiation environmental monitoring

  10. Patients-in-Waiting: Living between Sickness and Health in the Genomics Era

    Science.gov (United States)

    Timmermans, Stefan; Buchbinder, Mara

    2010-01-01

    What are the social consequences of the recent expansion of newborn screening in the United States? The adoption of new screening technologies has generated diagnostic uncertainty about the nature of screening targets, making it unclear not only whether a newborn will develop a disease but also what the condition actually is. Based on observations…

  11. Constructing linkage maps in the genomics era with MapDisto 2.0.

    Science.gov (United States)

    Heffelfinger, Christopher; Fragoso, Christopher A; Lorieux, Mathias

    2017-07-15

    Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. The program is available free of charge at mapdisto.free.fr. mapdisto@gmail.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  12. Coastal Change Analysis Program (C-CAP) zone 66 1995-era and 2000-era land cover change analysis (NODC Accession 0042136)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains the 1995-era and 2000-era classifications of US Coast zone 66 and can be used to analyze change. This imagery was collected as part of the...

  13. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  14. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  15. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  16. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  17. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  18. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

    Science.gov (United States)

    Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

    2016-01-01

    Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and

  19. Molecular Tumor Boards: Ethical Issues in the New Era of Data Medicine.

    Science.gov (United States)

    Stoeklé, Henri-Corto; Mamzer-Bruneel, Marie-France; Frouart, Charles-Henry; Le Tourneau, Christophe; Laurent-Puig, Pierre; Vogt, Guillaume; Hervé, Christian

    2018-02-01

    The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with "genomic medicine" nor with "precision medicine", but with "data medicine" (DM) (big data, data mining). The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The "transformation" of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a new vision of care. Molecular tumor boards (MTB) are one response to these changes and are now providing better access to next-generation sequencing (NGS) and new cancer treatments to patients with inoperable or metastatic cancers, and those for whom the usual treatment has failed. However, MTB face a crucial ethical challenge: maintaining and improving the trust of patients, clinicians, researchers and industry in academic medical centers supported by private or public funding rather than providing genetic data directly to private companies. We believe that, in this era of DM, appropriate modern digital communication networks will be required to maintain this trust and to improve the organization and effectiveness of the system. There is, therefore, a need to reconsider the form and content of informed consent (IC) documents at all academic medical centers and to introduce dynamic and electronic informed consent (e-IC).

  20. The Functional Genomics Initiative at Oak Ridge National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Dabney; Justice, Monica; Beattle, Ken; Buchanan, Michelle; Ramsey, Michael; Ramsey, Rose; Paulus, Michael; Ericson, Nance; Allison, David; Kress, Reid; Mural, Richard; Uberbacher, Ed; Mann, Reinhold

    1997-12-31

    The Functional Genomics Initiative at the Oak Ridge National Laboratory integrates outstanding capabilities in mouse genetics, bioinformatics, and instrumentation. The 50 year investment by the DOE in mouse genetics/mutagenesis has created a one-of-a-kind resource for generating mutations and understanding their biological consequences. It is generally accepted that, through the mouse as a surrogate for human biology, we will come to understand the function of human genes. In addition to this world class program in mammalian genetics, ORNL has also been a world leader in developing bioinformatics tools for the analysis, management and visualization of genomic data. Combining this expertise with new instrumentation technologies will provide a unique capability to understand the consequences of mutations in the mouse at both the organism and molecular levels. The goal of the Functional Genomics Initiative is to develop the technology and methodology necessary to understand gene function on a genomic scale and apply these technologies to megabase regions of the human genome. The effort is scoped so as to create an effective and powerful resource for functional genomics. ORNL is partnering with the Joint Genome Institute and other large scale sequencing centers to sequence several multimegabase regions of both human and mouse genomic DNA, to identify all the genes in these regions, and to conduct fundamental surveys to examine gene function at the molecular and organism level. The Initiative is designed to be a pilot for larger scale deployment in the post-genome era. Technologies will be applied to the examination of gene expression and regulation, metabolism, gene networks, physiology and development.

  1. The diploid genome sequence of an individual human.

    Directory of Open Access Journals (Sweden)

    Samuel Levy

    2007-09-01

    Full Text Available Presented here is a genome sequence of an individual human. It was produced from approximately 32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel included 3,213,401 single nucleotide polymorphisms (SNPs, 53,823 block substitutions (2-206 bp, 292,102 heterozygous insertion/deletion events (indels(1-571 bp, 559,473 homozygous indels (1-82,711 bp, 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.

  2. Genomic signals of migration and continuity in Britain before the Anglo-Saxons.

    Science.gov (United States)

    Martiniano, Rui; Caffell, Anwen; Holst, Malin; Hunter-Mann, Kurt; Montgomery, Janet; Müldner, Gundula; McLaughlin, Russell L; Teasdale, Matthew D; van Rheenen, Wouter; Veldink, Jan H; van den Berg, Leonard H; Hardiman, Orla; Carroll, Maureen; Roskams, Steve; Oxley, John; Morgan, Colleen; Thomas, Mark G; Barnes, Ian; McDonnell, Christine; Collins, Matthew J; Bradley, Daniel G

    2016-01-19

    The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼ 1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

  3. Lunar geodesy and cartography: a new era

    Science.gov (United States)

    Duxbury, Thomas; Smith, David; Robinson, Mark; Zuber, Maria T.; Neumann, Gregory; Danton, Jacob; Oberst, Juergen; Archinal, Brent; Glaeser, Philipp

    The Lunar Reconnaissance Orbiter (LRO) ushers in a new era in precision lunar geodesy and cartography. LRO was launched in June, 2009, completed its Commissioning Phase in Septem-ber 2009 and is now in its Primary Mission Phase on its way to collecting high precision, global topographic and imaging data. Aboard LRO are the Lunar Orbiter Laser Altimeter (LOLA -Smith, et al., 2009) and the Lunar Reconnaissance Orbiter Camera (LROC -Robinson, et al., ). LOLA is a derivative of the successful MOLA at Mars that produced the global reference surface being used for all precision cartographic products. LOLA produces 5 altimetry spots having footprints of 5 m at a frequency of 28 Hz, significantly bettering MOLA that produced 1 spot having a footprint of 150 m at a frequency of 10 Hz. LROC has twin narrow angle cameras having pixel resolutions of 0.5 meters from a 50 km orbit and a wide-angle camera having a pixel resolution of 75 m and in up to 7 color bands. One of the two NACs looks to the right of nadir and the other looks to the left with a few hundred pixel overlap in the nadir direction. LOLA is mounted on the LRO spacecraft to look nadir, in the overlap region of the NACs. The LRO spacecraft has the ability to look nadir and build up global coverage as well as looking off-nadir to provide stereo coverage and fill in data gaps. The LROC wide-angle camera builds up global stereo coverage naturally from its large field-of-view overlap from orbit to orbit during nadir viewing. To date, the LROC WAC has already produced global stereo coverage of the lunar surface. This report focuses on the registration of LOLA altimetry to the LROC NAC images. LOLA has a dynamic range of tens of km while producing elevation data at sub-meter precision. LOLA also has good return in off-nadir attitudes. Over the LRO mission, multiple LOLA tracks will be in each of the NAC images at the lunar equator and even more tracks in the NAC images nearer the poles. The registration of LOLA

  4. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  5. Bremsstrahlung: an experimentalists personal perspective on the post modern era

    International Nuclear Information System (INIS)

    Quarles, C.A.

    2000-01-01

    In this brief review I will discuss the recent experimental work on the doubly differential cross section, i.e. the photon energy and angular distribution, for electron Bremsstrahlung from thin solid film and gas targets. Since the beginning of the modern era in the study of Bremsstrahlung with the publication of the 1971 paper by Ts eng and Pratt, Professor Pratt has been the dominant influence in Bremsstrahlung research. Most, if not all, experimental research during the modern era has been motivated by the interest in comparing data with the theory of Pratt and his coworkers. As Bremsstrahlung research has moved into its post modern era, new experiments with increasing precision are concentrating on determining under what conditions ordinary Bremsstrahlung theory needs to be supplemented by a contribution from polarization Bremsstrahlung. Efforts to improve the comparison of thin-target experiment with theory have also led to new experimental and modeling work on Bremsstrahlung from thick solid targets. Thick-target Bremsstrahlung is interesting in its own right, but we also want to understand it better since it is the ever-present background in the thin-target experiments and the limiting factor in the effort to distinguish the polarization contribution to the total Bremsstrahlung spectrum. Professor Pratt ushered in the modern era in Bremsstrahlung research and has recently guided the transition into the post modern era. It can be expected that he will continue to have a formative influence on the developments of Bremsstrahlung research into the foreseeable future.

  6. Data mining and the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Abarbanel, Henry [The MITRE Corporation, McLean, VA (US). JASON Program Office; Callan, Curtis [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, William [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, Freeman [The MITRE Corporation, McLean, VA (US). JASON Program Office; Hwa, Terence [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, Steven [The MITRE Corporation, McLean, VA (US). JASON Program Office; Levine, Herbert [The MITRE Corporation, McLean, VA (US). JASON Program Office; Rothaus, Oscar [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, Roy [The MITRE Corporation, McLean, VA (US). JASON Program Office; Stubbs, Christopher [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, Peter [The MITRE Corporation, McLean, VA (US). JASON Program Office

    2000-01-07

    As genomics research moves from an era of data acquisition to one of both acquisition and interpretation, new methods are required for organizing and prioritizing the data. These methods would allow an initial level of data analysis to be carried out before committing resources to a particular genetic locus. This JASON study sought to delineate the main problems that must be faced in bioinformatics and to identify information technologies that can help to overcome those problems. While the current influx of data greatly exceeds what biologists have experienced in the past, other scientific disciplines and the commercial sector have been handling much larger datasets for many years. Powerful datamining techniques have been developed in other fields that, with appropriate modification, could be applied to the biological sciences.

  7. Biomonitoring in the Era of the Exposome.

    Science.gov (United States)

    Dennis, Kristine K; Marder, Elizabeth; Balshaw, David M; Cui, Yuxia; Lynes, Michael A; Patti, Gary J; Rappaport, Stephen M; Shaughnessy, Daniel T; Vrijheid, Martine; Barr, Dana Boyd

    2017-04-01

    The term "exposome" was coined in 2005 to underscore the importance of the environment to human health and to bring research efforts in line with those on the human genome. The ability to characterize environmental exposures through biomonitoring is key to exposome research efforts. Our objectives were to describe why traditional and nontraditional (exposomic) biomonitoring are both critical in studies aiming to capture the exposome and to make recommendations on how to transition exposure research toward exposomic approaches. We describe the biomonitoring needs of exposome research and approaches and recommendations that will help fill the gaps in the current science. Traditional and exposomic biomonitoring approaches have key advantages and disadvantages for assessing exposure. Exposomic approaches differ from traditional biomonitoring methods in that they can include all exposures of potential health significance, whether from endogenous or exogenous sources. Issues of sample availability and quality, identification of unknown analytes, capture of nonpersistent chemicals, integration of methods, and statistical assessment of increasingly complex data sets remain challenges that must continue to be addressed. To understand the complexity of exposures faced throughout the lifespan, both traditional and nontraditional biomonitoring methods should be used. Through hybrid approaches and the integration of emerging techniques, biomonitoring strategies can be maximized in research to define the exposome.

  8. EN LA ERA DEL CADUCEO DE MERCURIO

    Directory of Open Access Journals (Sweden)

    Hernán Urbina Joiro

    2010-06-01

    Full Text Available

    En un momento extraño el bastón de Asclepio, dios de la medicina, fue cambiado por el caduceo de Mercurio, dios del comercio y también de los ladrones.

    Distintas tradiciones griegas dicen que Asclepio se servía de un bastón y de la serpiente para sanar enfermos, enseñar y resucitar difuntos1,2 y que cuando volvió a la vida a Hipólito, hijo de Teseo, le había restado tantos muertos a Hades, rey de los infiernos, que el propio Hades fue a querellarse ante Zeus, quien convencido de la amenaza que representaría Asclepio para mantener el orden establecido, lo hirió con un rayo3,4. La vara de Asclepio —Esculapio para los romanos— con una serpiente enrollada simbolizó la sanación mediada por el médico5.

    De Hermes —Mercurio para los romanos—, dios griego del comercio, las comunicaciones, la astucia y los ladrones6, la tradición afirma que su caduceo consistía en un bastón de oro con alas y dos serpientes enrolladas, y que le fue regalado por Apolo a cambio de la flauta del dios Pan7. Una práctica anglosajona del siglo XVI, iniciada por el doctor William Butts, médico del rey Enrique VIII, introdujo el caduceo de Mercurio —en lugar de lavara de Asclepio— como símbolo entre médicos británicos8 y de allí pasó a galenos del cuerpo médico del ejército de los Estados Unidos y de diversas otras comunidades médicas. Por cierto, Mrs. Butts aparece en Enrique VIII, de William Shakespeare, como «El doctor Butts, médico del Rey»9.

    Sin embargo, de acuerdo con Michel Foucault, sólo en el siglo XVIII se expresaría en pleno la era de la «economía política»10 como el eje del arte de gobernar y en donde la medicina jugaría un papel central para vigilar a los pueblos, perseguir amenazas como la locura, los descarríos sexuales, las infecciones e incluso a la propia delincuencia11. En La vida de los hombres infames12, Foucault sostiene que fue en la Alemania de finales del siglo XVIII donde surgi

  9. CERN: End of LEP's Z era

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1995-11-15

    Full text: Achapter of history at CERN's LEP electron-positron collider closed in October when the four big experiments, Aleph, Delphi, L3 and Opal, logged their final data at the Z energy, just over six years after LEP's first Z was detected. The LEP Z era has been one of great success, both in terms of physics results and the advances which have been made with the machine itself. LEP now takes a step towards becoming LEP2, when the energy is wound up from around 45 GeV to about 70 GeV per beam (September, page 6). By the end of LEP's 1995 run, each of the four LEP experiments had seen almost five million Zs. Now the spotlight at LEP shifts to producing pairs of W particles, the electrically charged counterparts of the Z. LEP's first Zs were recorded in August 1989, one month after the machine's first circulating beam. The 30,000 Z decays recorded by each experiment in 1989 confirmed that matter comes in just three distinct families of quarks and leptons. The values of the Z mass and width quoted in 1990 were 91.161 ± 0.031 GeV and 2.534 ± 0.027 GeV. By the beginning of 1995, these had been fine-tuned to the extraordinary accuracy of 91.1884 ± 0.0022 GeV and 2.4963 ± 0.0032 GeV, and when data from this year's run is included, will be even better. These results, combined with precision data from neutrino experiments and from Fermilab's Tevatron protonantiproton collider, have put the Standard Model of quarks and leptons through its most gruelling test yet. Right from the start, collaboration between LEP experiments and the accelerator team has been close, with frequent scheduling meetings determining how the machine is run. For the first few years, LEP ran on a diet of four bunches of electrons and four of positrons, but by the end of 1992, a way had been found to increase the luminosity by squeezing in more bunches. In 1993, the 'pretzel' scheme (October 1992, page 17), so called because of the shape traced out by the circulating beams, was running with eight

  10. System and software safety analysis for the ERA control computer

    International Nuclear Information System (INIS)

    Beerthuizen, P.G.; Kruidhof, W.

    2001-01-01

    The European Robotic Arm (ERA) is a seven degrees of freedom relocatable anthropomorphic robotic manipulator system, to be used in manned space operation on the International Space Station, supporting the assembly and external servicing of the Russian segment. The safety design concept and implementation of the ERA is described, in particular with respect to the central computer's software design. A top-down analysis and specification process is used to down flow the safety aspects of the ERA system towards the subsystems, which are produced by a consortium of companies in many countries. The user requirements documents and the critical function list are the key documents in this process. Bottom-up analysis (FMECA) and test, on both subsystem and system level, are the basis for safety verification. A number of examples show the use of the approach and methods used

  11. Leprosy: International Public Health Policies and Public Health Eras

    Directory of Open Access Journals (Sweden)

    Niyi Awofeso

    2011-09-01

    Full Text Available Public health policies continue to play important roles in national and international health reforms. However, the influence and legacies of the public health eras during which such policies are formulated remain largely underappreciated. The limited appreciation of this relationship may hinder consistent adoption of public health policies by nation-states, and encumber disinvestment from ineffective or anachronistic policies. This article reviews seven public health eras and highlights how each era has influenced international policy formulation for leprosy control—“the fertile soil for policy learning”. The author reiterates the role of health leadership and health activism in facilitating consistency in international health policy formulation and implementation for leprosy control.

  12. Participatory Design in an Era of Participation, Special Issue

    DEFF Research Database (Denmark)

    This special issue on participatory design in an era of participation presents emerging topics and discussions from the thirteenth Participatory Design conference (PDC), held at Aarhus University in August 2016. The PDC 2016 marked the twenty-fifth anniversary of the Participatory Design conference...... series, which began in 1990 with the first biannual conference in Seattle. Since then, the PDC conferences have continued to bring together a multidisciplinary, international community of researchers and practitioners around issues of cooperative design. The theme for the 2016 PDC conference...... was ‘Participatory Design in an Era of Participation.’ Critical and constructive discussions were invited on the values, characteristics, politics and future practices of participatory design in an era in which participation has now become pervasive (Bossen, Smith, Kanstrup, McDonnell, et al. 2016, Bossen, Smith...

  13. [A review of the genomic and gene cloning studies in trees].

    Science.gov (United States)

    Yin, Tong-Ming

    2010-07-01

    Supported by the Department of Energy (DOE) of U.S., the first tree genome, black cottonwood (Populus trichocarpa), has been completely sequenced and publicly release. This is the milestone that indicates the beginning of post-genome era for forest trees. Identification and cloning genes underlying important traits are one of the main tasks for the post-genome-era tree genomic studies. Recently, great achievements have been made in cloning genes coordinating important domestication traits in some crops, such as rice, tomato, maize and so on. Molecular breeding has been applied in the practical breeding programs for many crops. By contrast, molecular studies in trees are lagging behind. Trees possess some characteristics that make them as difficult organisms for studying on locating and cloning of genes. With the advances in techniques, given also the fast growth of tree genomic resources, great achievements are desirable in cloning unknown genes from trees, which will facilitate tree improvement programs by means of molecular breeding. In this paper, the author reviewed the progress in tree genomic and gene cloning studies, and prospected the future achievements in order to provide a useful reference for researchers working in this area.

  14. Cancer Prevention in the Precision Medicine Era

    Science.gov (United States)

    Dr. Rebbeck’s research focuses on the etiology and prevention of cancer, with an emphasis on cancers with a genetic etiology and those that are associated with disparities in incidence or mortality by race. He has directed multiple large molecular epidemiologic studies and international consortia that have been used to identify and characterize genes involved in cancer etiology, understand the relationship of allelic variation with biochemical or physiological traits, explore interactions of inherited and somatic genomic variation with epidemiological risk factors. His research also focuses on the roles of biological and social factors on prostate cancer disparities and prostate cancer in Africa through the Men of African Descent and Carcinoma of the Prostate (MADCaP) consortium. He has also led a number of consortia that study carriers of BRCA1 or BRCA2 mutations to understand breast, ovarian, and prostate cancer risk and precision prevention interventions that may reduce that risk. In addition to his research activities, Dr. Rebbeck leads a number of initiatives on the Harvard Campus. He serves as Associate Director for Equity and Engagement in the Dana-Farber / Harvard Cancer Center and Co-Director for the Collective Impact Program of Harvard Catalyst. In this role, he prioritizes the cancer research agenda to maximize disease prevention and risk reduction in Massachusetts. He also oversees a team charged with ensuring that this research engages with and positively impacts communities with the greatest disease burden.  As Director of Global Oncology at the Dana Farber Cancer Institute, Dr. Rebbeck oversees formal and informal training and research partnerships between Dana Farber investigators and trainees with international partners.

  15. [Embracing medical innovation in the era of big data].

    Science.gov (United States)

    You, Suning

    2015-01-01

    Along with the advent of big data era worldwide, medical field has to place itself in it inevitably. The current article thoroughly introduces the basic knowledge of big data, and points out the coexistence of its advantages and disadvantages. Although the innovations in medical field are struggling, the current medical pattern will be changed fundamentally by big data. The article also shows quick change of relevant analysis in big data era, depicts a good intention of digital medical, and proposes some wise advices to surgeons.

  16. Governments, contractors seen headed for era of cooperation

    International Nuclear Information System (INIS)

    McHaffie, E.R.; Jarvis, M.G.; Barber, S.A.

    1993-01-01

    The oil and gas industry is on the threshold of a new era in international oil and gas investments. It will be an era of increasing flexibility and cooperation among investors, oil companies, and host governments. And it will develop as a necessary response to flat oil prices and the growing mobility of capital. This article will cover three essential elements of this topic: the effect of fiscal terms on the economics of a project investment; how recent changes in global economies have impacted the economics of the projects the authors evaluated at Amoco; some potential trends that fiscal provisions, and the pattern of investment in the upstream petroleum industry, may take

  17. La era de la información

    OpenAIRE

    Florez Calderón, Mauro

    2011-01-01

    La revolución de la información basada en la información tiene como límite las fronteras del conocimiento. La información a diferencia de un bien material es inalienable, acumulativa y no produce los tipos de deterioro ambiental creados por la industria; por lo anterior, algunos especialistas, a la era de la información la denominan era Post-industrial. Si es necio pretender entender los procesos producidos por la revolución industrial, con una mentalidad pastoril, mucho más necio será tratar...

  18. E-Polmas: Paradigma Baru Pemolisian Masyarakat Era Digital

    Directory of Open Access Journals (Sweden)

    Bayu Suseno

    2016-05-01

    Full Text Available Tulisan ini memberikan perpekstif baru tentang polmas di era digital dengan menggunakan studi kasus kejahatan cyber crime di Polrestabes Semarang. Berdasarkan tingginya angka kejahatan berbasis teknologi yang ditangani kepolisian maka ada kebutuhan mendesak untuk melakukan kajian ulang terhadap pendekatan polmas yang selama ini ada. Penulis memberikan sebuah pandangan baru konsep polmas era digital atau E-Polmas. E-Polmas merupakan pengembangan dari konsep Polmas yang sudah ada, akan tetapi menitikberatkan kepada media yang digunakan untuk menyampaikan pesan kamtibmas kepada masyarakat. Yang semula dilaksanakan secara manual konvensional, dirubah menjadi cara online dengan memanfaatkan media sosial yang sudah ada.

  19. Identitas Moral: Rekonstruksi Identitas Keindonesiaan pada Era Globalisasi Budaya

    Directory of Open Access Journals (Sweden)

    Leonardus Pandu Hapsoro

    2016-06-01

    Full Text Available Tulisan ini membahas mengenai proses rekonstruksi identitas keindonesiaan para aktor dalam komunitas Kultura Indonesia Star Society (KISS pada era globalisasi budaya. Dengan menggunakan metode penelitian kualitatif dan kerangka pemikiran Zygmunt Bauman antara modernitas cair dan agensi moral, tulisan ini menunjukkan bagaimana proses rekonstruksi identitas moral berawal dari keresahan aktor terhadap kondisi budaya tradisional pada era globalisasi. Penulis berpendapat bahwa ekspresi dari identitas aktor melalui gerakan sosial ini akan berperan menciptakan keberagaman budaya pada era globalisasi dan modernitas cair. Penulis ingin bergerak menjauh dari pandangan agentless dalam proses globalisasi dengan melihat dinamika agensi. Melalui agen dan bentuk agensi moral, penulis berpendapat bahwa di dalam proses dan dampak globalisasi, manusia tidak tertahan pada kondisi "adalah" atau tekanan struktural, melainkan terdapat optimisme untuk melihat suatu harapan atas kondisi yang "seharusnya" atau lebih baik melalui kesadaran identitas dan moral.This study discusses about the process of identity construction of actor  in the KISS community in an era of cultural globalization. This study will explain how the construction process of moral identity actor is formed in the era of cultural globalization. Moral identity construction of the actor in the era of globalization will be the anchor for agents to act and preserve the traditional culture with motivation, passion, and hope. This study used a qualitative approach by using the framework of Zygmunt Bauman concept of liquid modernity and moral agency. Through the framework of moral agency, this study shows how the construction of moral identity process begins with the actor disquite over the state of traditional culture in globalization era. Moral identity of the actor is capable of forming social practices agent in a daily life. First, by forming a community KISS. Second, as the cornerstone of actors to act

  20. Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

    Directory of Open Access Journals (Sweden)

    Claudia Bartoli

    2017-05-01

    Full Text Available The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes. In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.

  1. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  2. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  3. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  4. Advances in genome editing for improved animal breeding: A review

    Directory of Open Access Journals (Sweden)

    Shakil Ahmad Bhat

    2017-11-01

    Full Text Available Since centuries, the traits for production and disease resistance are being targeted while improving the genetic merit of domestic animals, using conventional breeding programs such as inbreeding, outbreeding, or introduction of marker-assisted selection. The arrival of new scientific concepts, such as cloning and genome engineering, has added a new and promising research dimension to the existing animal breeding programs. Development of genome editing technologies such as transcription activator-like effector nuclease, zinc finger nuclease, and clustered regularly interspaced short palindromic repeats systems begun a fresh era of genome editing, through which any change in the genome, including specific DNA sequence or indels, can be made with unprecedented precision and specificity. Furthermore, it offers an opportunity of intensification in the frequency of desirable alleles in an animal population through gene-edited individuals more rapidly than conventional breeding. The specific research is evolving swiftly with a focus on improvement of economically important animal species or their traits all of which form an important subject of this review. It also discusses the hurdles to commercialization of these techniques despite several patent applications owing to the ambiguous legal status of genome-editing methods on account of their disputed classification. Nonetheless, barring ethical concerns gene-editing entailing economically important genes offers a tremendous potential for breeding animals with desirable traits.

  5. The Global Genome Biodiversity Network (GGBN) Data Standard specification

    Science.gov (United States)

    Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

    2016-01-01

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

  6. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  7. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  8. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  9. Formalities in the digital era: an obstacle or opportunity?

    NARCIS (Netherlands)

    van Gompel, S.; Bently, L.; Suthersanen, U.; Torremans, P.

    2010-01-01

    This paper, which was presented at the 2009 ALAI conference in London, examines the possible reintroduction of copyright formalities against the background of the challenges that copyright law faces in the digital era. It does so by contrasting the current calls for reintroducing formalities with

  10. First results from stellar occultations in the "GAIA era"

    Science.gov (United States)

    Benedetti-Rossi, G.; Vieira-Martins, R.; Sicardy, B.

    2017-09-01

    Stellar occultation is a powerful technique to study distant solar system bodies. It allows high angular resolution of the occulting body from the analysis of a light curve acquired with high temporal resolution with uncertainties comparable as probes. In the "GAIA era", stellar occultations is now able to obtain even more impressive results such as the presence of atmosphere, rings and topographic features.

  11. NASA EOSDIS Evolution in the BigData Era

    Science.gov (United States)

    Lynnes, Christopher

    2015-01-01

    NASA's EOSDIS system faces several challenges in the Big Data Era. Although volumes are large (but not unmanageably so), the variety of different data collections is daunting. That variety also brings with it a large and diverse user community. One key evolution EOSDIS is working toward is to enable more science analysis to be performed close to the data.

  12. Culturally Responsive: Art Education in a Global Era

    Science.gov (United States)

    Lai, Alice

    2012-01-01

    Facing the era of globalization, culturally responsive art teachers must recognize that students' home culture, including local artistic expression, is inevitably influenced by global forces. They should strive to engage with students systems and issues of globalization and its impact on their community culture and art. In this article, the author…

  13. THE UNECIC: INTERNATIONAL TRADE IN THE DIGITAL ERA

    African Journals Online (AJOL)

    Dr Tanya du Plessis

    THE UNECIC: INTERNATIONAL TRADE IN THE DIGITAL ERA. S Eiselen. *. 1. Introduction. The use of electronic means of communication such as e-mail, SMS and the internet in the last decade has outstripped and replaced other more traditional forms of communications such as post, telex and telegram. The only other ...

  14. Gender prejudice in the Victorian Era: an elucidation of Thomas ...

    African Journals Online (AJOL)

    The more intriguing character of the Victorian society was that women bore the brunt of the society's inequality, injustice and unfairness. This paper examines British history with the intent of exposing the variables that shaped and defined the Victorian era consciousness, especially the collective perspective about gender ...

  15. systemic chemical education reform [scer] in the global era

    African Journals Online (AJOL)

    IICBA01

    growing the systemic way of thinking of our students that is one of the most important characteristics of Global Era. Here is the systemic education reform which means the change of our educational system from linearity to systemic in which we design the curriculum and write content systemically, which presented by SATL ...

  16. Professional Boundaries in the Era of the Internet

    Science.gov (United States)

    Gabbard, Glen O.; Kassaw, Kristin A.; Perez-Garcia, Gonzalo

    2011-01-01

    Objective: The era of the Internet presents new dilemmas in educating psychiatrists about professional boundaries. The objective of this overview is to clarify those dilemmas and offer recommendations for dealing with them. Method: The characteristics of social networking sites, blogs, and search engines are reviewed with a specific focus on their…

  17. Not invented here : managing corporate innovation in a new era

    NARCIS (Netherlands)

    Vrande, van de V.J.A.

    2007-01-01

    Not Invented here: Managing Corporate Innovation in a New Era External technology sourcing as a means to develop new businesses is taking a more central role in established companies. Acquiring new technologies from outside the firm which speeds up the innovation process and complements internal R&D

  18. Customer to Consumer: The New Consumption in the Progressive Era.

    Science.gov (United States)

    Strasser, Susan

    1999-01-01

    Discusses the transformation of the U.S. consumption habits and the creation of the consumer during the Progressive Era. Describes the relationships among the production of goods, advertising, and progress. Focuses on the role advertising played in altering U.S. cultural beliefs and the continued attachment to the past. (CMK)

  19. Health Education Films of the Silent Era: A Historical Analysis

    Science.gov (United States)

    Sofalvi, Alan

    2011-01-01

    Films have been used to present health messages throughout the history of the medium. The purpose of this article is to describe pictures from the silent film era that were designed to educate people about health issues. Films still available in at least one format were reviewed. Published reviews were also used to obtain information about these…

  20. La era de la información

    Directory of Open Access Journals (Sweden)

    Mauro Florez Calderón

    1991-01-01

    Full Text Available La revolución de la información basada en la información tiene como límite las fronteras del conocimiento. La información a diferencia de un bien material es inalienable, acumulativa y no produce los tipos de deterioro ambiental creados por la industria; por lo anterior, algunos especialistas, a la era de la información la denominan era Post-industrial. Si es necio pretender entender los procesos producidos por la revolución industrial, con una mentalidad pastoril, mucho más necio será tratar de comprender la era informacional con una concepción industrial. La nueva era implica formas y estructuras del pensamiento radicalmente diferentes, pues las profundas transformaciones sociales, técnicas, políticas, económicas que conlleva, no conducirán necesariamente por si mismos a un mayor bienestar para la humanidad. En el presente artículo pretendo dar una visión general sobre este apasionante y delicado tema.

  1. ERA-pankurid võivad pattu kahetseda / Nils Niitra

    Index Scriptorium Estoniae

    Niitra, Nils, 1975-

    2002-01-01

    Tartu maakohtu kohtunik andis ERA Grupi üheksa eksjuhi suurprotsessil riiklikule süüdistajale ja kohtualustele kaks nädalat aega protsessi lahendamiseks lihtmenetluse teel, kuid selleks peavad endised pankurid end süüdi tunnistama

  2. Radiation oncology in the era of precision medicine

    DEFF Research Database (Denmark)

    Baumann, Michael; Krause, Mechthild; Overgaard, Jens

    2016-01-01

    with preservation of health-related quality of life can be achieved in many patients. Two major strategies, acting synergistically, will enable further widening of the therapeutic window of radiation oncology in the era of precision medicine: technology-driven improvement of treatment conformity, including advanced...

  3. Op pad na 'n omvattende woordeboekkultuur in die digitale era ...

    African Journals Online (AJOL)

    Many potential dictionary users within the digital era belong to Generation Z. Some features of this generation are briefly discussed. The need is indicated for an adaptation in lexicography that could motivate this generation to use dictionaries. It is argued that dictionary didactics should play an important role in establishing ...

  4. Attractions to radiation-like eras in superstring cosmologies

    CERN Document Server

    Partouche, Herve

    2010-01-01

    We review the cosmology induced by finite temperature and quantum effects on non-supersymmetric string models. We show the evolution is attracted to radiation-like solutions after the Hagedorn era and before the electroweak phase transition. This mechanism generates a hierarchy between the Planck mass and the supersymmetry breaking scale. A dynamical change of space-time dimension can take place.

  5. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  6. Results of ERAS protocol in patients with colorectal cancer

    Directory of Open Access Journals (Sweden)

    A. O. Rasulov

    2016-01-01

    Full Text Available Objective: explore the use of enhanced recovery after surgery (ERAS in the treatment of patients with colorectal cancer, evaluate its efficacy and safety.Materials and methods. Prospective, single-site, randomized study for the implementation of enhanced recovery after surgery in patients with colorectal cancer has been conducted from October 2014 till the present time. All patients after laparoscopic surgeries undergo treatment according to ERAS protocol, patients after open surgeries are randomized (1:1 in groups of the standard treatment or treatment according to ERAS protocol. The study included patients with localized and locally disseminated colorectal cancer aged from 18 to 75 years, ECOG score ≤ 2. The primary evaluated parameters were the following: the number of postoperative complications (according to Clavien– Dindo classification, postoperative hospital days, incidence of complications and mortality in the 30-day period, timing of activation.Results. Up to date, the study includes 105 patients: laparoscopic group – 51 patients, open-surgery group of patients treated by ERAS protocol – 27 patients, open-surgery group of patients with the standard post-op treatment – 26 patients. Complications requiring emergency surgery for anastomotic leak (p = 0.159 developed in 3.7 % of patients with the standard post-op treatment and in 3.9 % of patients after laparoscopic surgery, while 1 patient required repeat hospitalization. The total number of complications was significantly lower in opensurgery group of patients treated by ERAS protocol compared with the standard post-op treatment (p = 0.021. However, there were no differences between laparoscopic and open-surgery group with the standard post-op treatment (p = 0.159. An average hospitalization stay in patients with the standard post-op treatment was equal to 10 days compared to 7 days in patients treated by ERAS protocol (p = 0.067 and 6 days after laparoscopic

  7. ERA Panga pankrotiprotsess on lõppenud / Väinu Rozental

    Index Scriptorium Estoniae

    Rozental, Väinu, 1957-

    2005-01-01

    Viis ja pool aastat kestnud ERA Panga pankrotimenetlus on lõppenud ning mõlemad pankrotihaldurid said 3,53 miljonit krooni. Vt. samas: Järgmisena saab joone alla EVEA Panga pankrot. Lisa: ERA Panga pankrotil joon all

  8. Power Laws, Scale-Free Networks and Genome Biology

    CERN Document Server

    Koonin, Eugene V; Karev, Georgy P

    2006-01-01

    Power Laws, Scale-free Networks and Genome Biology deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features. The collection of chapters, contributed by both physicists and biologists, strives to address the problems in this field in a rigorous but not excessively mathematical manner and to represent different viewpoints, which is crucial in this emerging discipline. Each chapter includes, in addition to technical descriptions of properties of biological networks and evolutionary models, a more general and accessible introduction to the respective problems. Most chapters emphasize the potential of theoretical systems biology for disco...

  9. Avian genomics lends insights into endocrine function in birds.

    Science.gov (United States)

    Mello, C V; Lovell, P V

    2018-01-15

    The genomics era has brought along the completed sequencing of a large number of bird genomes that cover a broad range of the avian phylogenetic tree (>30 orders), leading to major novel insights into avian biology and evolution. Among recent findings, the discovery that birds lack a large number of protein coding genes that are organized in highly conserved syntenic clusters in other vertebrates is very intriguing, given the physiological importance of many of these genes. A considerable number of them play prominent endocrine roles, suggesting that birds evolved compensatory genetic or physiological mechanisms that allowed them to survive and thrive in spite of these losses. While further studies are needed to establish the exact extent of avian gene losses, these findings point to birds as potentially highly relevant model organisms for exploring the genetic basis and possible therapeutic approaches for a wide range of endocrine functions and disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Childhood Acute Lymphoblastic Leukemia: Integrating Genomics into Therapy

    Science.gov (United States)

    Tasian, Sarah K; Loh, Mignon L; Hunger, Stephen P

    2015-01-01

    Acute lymphoblastic leukemia (ALL), the most common malignancy of childhood, is a genetically complex entity that remains a major cause of childhood cancer-related mortality. Major advances in genomic and epigenomic profiling during the past decade have appreciably enhanced knowledge of the biology of de novo and relapsed ALL and have facilitated more precise risk stratification of patients. These achievements have also provided critical insights regarding potentially targetable lesions for development of new therapeutic approaches in the era of precision medicine. This review delineates the current genetic landscape of childhood ALL with emphasis upon patient outcomes with contemporary treatment regimens, as well as therapeutic implications of newly identified genomic alterations in specific subsets of ALL. PMID:26194091

  11. Energy revolution: From a fossil energy era to a new energy era

    Directory of Open Access Journals (Sweden)

    Caineng Zou

    2016-01-01

    Full Text Available This paper aims to predict the future situation of global energy development. In view of this, we reviewed the history of energy use and understood that new energy sources will usher in a new era following oil & gas, coal and wood one after another in the past time. Although the fossil energy sources are still plenty in the world, great breakthroughs made in some key technologies and the increasing demand for ecological environmental protection both impel the third time of transformation from oil & gas to new energy sources. Sooner or later, oil, gas, coal and new energy sources will each account for a quarter of global energy consumption in the new era, specifically speaking, accounting for 32.6%, 23.7%, 30.0% and 13.7% respectively. As one of the largest coal consumer, China will inevitably face up to the situation of tripartite confrontation of the coal, oil & gas and new energy. The following forecasting results were achieved. First, the oil will be in a stable period and its annual production peak will be around 2040, reaching up to 45 × 108 t. Second, the natural gas will enter the heyday period and its annual production peak will be around 2060, reaching up to 4.5 × 1012 m3, which will play a pivotal role in the future energy sustainable development. Third, the coal has entered a high-to-low-carbon transition period, and its direct use and the discharged pollutants will be significantly reduced. In 2050, the coal will be dropped to 25% of the primary energy mix. Last, the development and utilization of new energy sources has been getting into the golden age and its proportion in the primary energy mix will be substantially enhanced. On this basis, we presented some proposals for the future energy development in China. At first, we should understand well that China's energy production and consumption has its own characteristics. Under the present situation, we should strengthen the clean and efficient use of coal resources, which

  12. Genome sequence diversity and clues to the evolution of variola (smallpox) virus.

    Science.gov (United States)

    Esposito, Joseph J; Sammons, Scott A; Frace, A Michael; Osborne, John D; Olsen-Rasmussen, Melissa; Zhang, Ming; Govil, Dhwani; Damon, Inger K; Kline, Richard; Laker, Miriam; Li, Yu; Smith, Geoffrey L; Meyer, Hermann; Leduc, James W; Wohlhueter, Robert M

    2006-08-11

    Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.

  13. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  14. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  15. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  16. CRISPR/Cas9-mediated genome engineering of CHO cell factories: application and perspectives

    DEFF Research Database (Denmark)

    Lee, Jae Seong; Grav, Lise Marie; Lewis, Nathan E.

    2015-01-01

    repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system enables rapid,easy and efficient engineering of mammalian genomes. It has a wide range of applications frommodification of individual genes to genome-wide screening or regulation of genes. Facile genomeediting using CRISPR/Cas9 empowers...... researchers in the CHO community to elucidate the mechanisticbasis behind high level production of proteins and product quality attributes of interest. Inthis review, we describe the basis of CRISPR/Cas9-mediated genome editing and its applicationfor development of next generation CHO cell factories while...... highlighting both future perspectivesand challenges. As one of the main drivers for the CHO systems biology era, genome engineeringwith CRISPR/Cas9 will pave the way for rational design of CHO cell factories....

  17. [Genomics and transcriptomics of the Chinese liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda)].

    Science.gov (United States)

    Chelomina, G N

    2017-01-01

    The review summarizes the results of first genomic and transcriptomic investigations of the liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda). The studies mark the dawn of the genomic era for opisthorchiids, which cause severe hepatobiliary diseases in humans and animals. Their results aided in understanding the molecular mechanisms of adaptation to parasitism, parasite survival in mammalian biliary tracts, and genome dynamics in the individual development and the development of parasite-host relationships. Special attention is paid to the achievements in studying the codon usage bias and the roles of mobile genetic elements (MGEs) and small interfering RNAs (siRNAs). Interspecific comparisons at the genomic and transcriptomic levels revealed molecular differences, which may contribute to understanding the specialized niches and physiological needs of the respective species. The studies in C. sinensis provide a basis for further basic and applied research in liver flukes and, in particular, the development of efficient means to prevent, diagnose, and treat clonorchiasis.

  18. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes.

    Science.gov (United States)

    Angelbello, Alicia J; Chen, Jonathan L; Childs-Disney, Jessica L; Zhang, Peiyuan; Wang, Zi-Fu; Disney, Matthew D

    2018-02-28

    Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.

  19. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  20. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  1. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  2. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  3. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  4. Plant molecular biology and biotechnology research in the post-recombinant DNA era.

    Science.gov (United States)

    Tyagi, Akhilesh K; Khurana, Jitendra P

    2003-01-01

    After the beginning of the recombinant DNA era in the mid-1970s, researchers in India started to make use of the new technology to understand the structure of plant genes and regulation of their expression. The outcome started to appear in print in early the 1980s and genes for histones, tubulin, photosynthetic membrane proteins, phototransduction components, organelles and those regulated differentially by developmental and extrinsic signals were sequenced and characterized. Some genes of biotechnological importance like those encoding an interesting seed protein and the enzyme glyoxalase were also isolated. While work on the characterization of genome structure and organization was started quite early, it remained largely focused on the identification of DNA markers and genetic variability. In this context, the work on mustard, rice and wheat is worth mentioning. In the year 2000, India became a member of the international consortium to sequence entire rice genome. Several laboratories have also given attention to regulated expression of plastid and nuclear genes as well as to isolate target-specific promoters or design promoters with improved potential. Simultaneously, transgenic systems for crops like mustard, rice, wheat, cotton, legumes and several vegetables have been established. More recently, genes of agronomic importance like those for insect resistance, abiotic stress tolerance, nutritional improvement and male sterility, isolated in India or abroad, have been utilized for raising transgenics for crop improvement. Some of these transgenics have already shown their potential in containment facility or limited field trials conducted under the stipulated guidelines. Plant molecular biology and biotechnology are thus clearly poised to make an impact on research in basic biology and agriculture in the near future.

  5. Keeping up with the times: revising the dermatology residency curriculum in the era of molecular diagnostics and personalized medicine.

    Science.gov (United States)

    LaChance, Avery; Murphy, Michael J

    2014-11-01

    The clinical use of molecular diagnostics, genomics, and personalized medicine is increasing and improving rapidly over time. However, medical education incorporating the practical application of these techniques is lagging behind. Although instruction in these areas should be expanded upon and improved at all levels of training, residency provides a concentrated period of time in which to hone in on skills that are practically applicable to a trainee's specialty of choice. Although residencies in some fields, such as pathology, have begun to incorporate practical molecular diagnostics training, this area remains a relative gap in dermatology residency programs. Herein, we advocate for the incorporation of training in molecular diagnostics and personalized medicine into dermatology residency programs and propose a basic curriculum template for how to begin approaching these topics. By incorporating molecular diagnostics into dermatology residency training, dermatologists have the opportunity to lead the way and actively shape the specialty's transition into the era of personalized medicine. © 2014 The International Society of Dermatology.

  6. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  7. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  8. Islamism and Democratization in Indonesia Post-Reformation Era:

    Directory of Open Access Journals (Sweden)

    SYAHRIR KARIM

    2014-12-01

    Full Text Available In general, this paper will explore features and patterns of Islamism in Indonesia after the downfall of Suharto’s regime in which people called it as reformation era. In Indonesian context, the Islamism at least have four characteristics; (i promoting Islam as a sole basis in transforming society, (ii acknowledging Islam as an ideology, (iii among at the establishment of Islamic state, (iv which is characterised by implementing Shari`ah laws in daily lives. These four attributes may be used in capturing the growth of Muslim’s perception on state and democracy in the era of Islamic revival. The above views spread in the various streams or any schools existed in Indonesia, both Islamic movements and other form that is very influential in the process of democracy in Indonesia.

  9. Role of Imaging in the Era of Precision Medicine.

    Science.gov (United States)

    Giardino, Angela; Gupta, Supriya; Olson, Emmi; Sepulveda, Karla; Lenchik, Leon; Ivanidze, Jana; Rakow-Penner, Rebecca; Patel, Midhir J; Subramaniam, Rathan M; Ganeshan, Dhakshinamoorthy

    2017-05-01

    Precision medicine is an emerging approach for treating medical disorders, which takes into account individual variability in genetic and environmental factors. Preventive or therapeutic interventions can then be directed to those who will benefit most from targeted interventions, thereby maximizing benefits and minimizing costs and complications. Precision medicine is gaining increasing recognition by clinicians, healthcare systems, pharmaceutical companies, patients, and the government. Imaging plays a critical role in precision medicine including screening, early diagnosis, guiding treatment, evaluating response to therapy, and assessing likelihood of disease recurrence. The Association of University Radiologists Radiology Research Alliance Precision Imaging Task Force convened to explore the current and future role of imaging in the era of precision medicine and summarized its finding in this article. We review the increasingly important role of imaging in various oncological and non-oncological disorders. We also highlight the challenges for radiology in the era of precision medicine. Published by Elsevier Inc.

  10. Will ALICE run in the HL-LHC era?

    International Nuclear Information System (INIS)

    Wessels, J.P.

    2012-01-01

    We will present the perspectives for ion running in the HL-LHC era. In particular, ALICE is preparing a significant upgrade of its rate capabilities and is further extending its particle identification potential. This paves the way for heavy ion physics at unprecedented luminosities, which are expected in the HL-LHC era with the heaviest ions. Here, we outline a scenario, in which ALICE will be taking data at a luminosity of L > 6*10 27 cm -2 *s -1 for Pb-Pb with the aim of collecting at least 10 nb -1 . The potential interest of data-taking during high luminosity proton runs for ATLAS and CMS will also be commented. (author)

  11. Enforcing patents in the era of 3D printing

    DEFF Research Database (Denmark)

    Ballardini, Rosa Maria; Norrgård, Marcus; Minssen, Timo

    2015-01-01

    This article explores relevant laws and doctrines of patent infringement in Europe with a special emphasis on 3D printing (3DP) technologies. Considering the difficulties that patent owners might face in pursuing direct patent infringement actions in the rapidly evolving era of 3DP, we suggest...... of IP law. Enforcing patents in the era of 3D printing Rosa Maria Ballardini, Marcus Norrgård, and Timo Minssen Journal of Intellectual Property Law & Practice 2015 10: 850-866......, although the internet platforms and CAD files repositories will play a major role in the development and spreading of the 3DP technology, they will likely to be at the center of major law disputes unless they carefully consider the scope of their activities (host and/or customize and/or print) in light...

  12. The Anthropocene era. The Earth, the history and us

    International Nuclear Information System (INIS)

    Bonneuil, Christophe; Fressoz, Jean-Baptiste

    2013-01-01

    As some scientists state that the Earth entered the Anthropocene era which is an anthropogenic geological revolution: the traces of our urban, consumption, chemical and nuclear era will remain in the planet geological archives for thousands and even millions of years, and will result in huge difficulties for human societies. Between science and history, the authors give an overview of a development model which has become unsustainable: studies which highlighted the impossibility of an indefinite growth in the 1970's have been ignored, and instead of taking the three dimensions involved in sustainable development (economy, social, environment), into account, environment tends to become only a new item in firm accounting (markets of eco-systemic services, the biosphere, hydrosphere and atmosphere about to become simple subsystems of the financial and merchandising sphere)

  13. Carbon tetrachloride ERA soil-gas baseline monitoring

    International Nuclear Information System (INIS)

    Fancher, J.D.

    1994-01-01

    From December 1991 through December 1993, Westinghouse Hanford Company performed routine baseline monitoring of selected wells ad soil-gas points twice weekly in the 200 West Area of the Hanford Site. This work supported the carbon Tetrachloride Expedited Response Action (ERA) and provided a solid baseline of volatile organic compound (VOC) concentrations in wells and in the subsurface at the ERA site. As site remediation continues, comparisons to this baseline can be one means of measuring the success of carbon tetrachloride vapor extraction. This report contains observations of the patterns and trends associated with data obtained during soil-gas monitoring at the 200 West Area: Monitoring performed since late 1991 includes monitoring soil-gas probes ad wellheads for volatile organic compounds (VOCs). This report reflects monitoring data collected from December 1991 through December 1993

  14. Human action in a Genomic Era: debates on human nature Ação humana na Era do Genoma: debates sobre a natureza humana

    Directory of Open Access Journals (Sweden)

    Tatiana Gomes Rotondaro

    2009-03-01

    Full Text Available The supposed properties of 'genes' have led natural scientists to claim authority to explain the reasons of human action, behavior, and even human nature, which has traditionally been the object of study of the humanities. The aim of this paper is to discuss the possibilities of sociological theory dealing with the biological reductionism that establishes the strict articulation between 'human nature' and 'human action', presented in several speeches and papers by scientists and journalists and supported by features of 'genes'. I intend to argue that sociological theories may broaden their scope of analysis by encompassing biological dimensions, which does not necessarily mean adopting a biological reductionist approach.As supostas propriedades dos 'genes' levam os cientistas naturais a reivindicar autoridade para explicar as razões de atos, comportamentos e até a natureza humana, tradicional objeto de estudo das ciências humanas. O objetivo deste artigo é discutir as possibilidades de a teoria sociológica lidar com o reducionismo biológico, que estabelece uma articulação exata entre 'natureza humana' e 'ação humana'. Tal reducionismo está presente em discursos e artigos de cientistas e jornalistas, e é embasado por características dos 'genes'. Argumento que as teorias sociológicas podem ampliar suas possibilidades de análise se incorporarem dimensões biológicas, o que não implica necessariamente adotar uma abordagem reducionista.

  15. G×E Interaction and Pluralism in the Postgenomic Era

    OpenAIRE

    Perbal, Laurence

    2013-01-01

    Behavioral genetics is in a postgenomic era, and this paper illustrates this epistemological evolution using the debate between developmental criticism and traditional biometric genetics about gene x environment interaction. Quantitative geneticists are blamed for failing to respect the complexity of development; as a response, they claim a defensive position, called isolationist pluralism, which supports the idea that studying development is not their problem. But postgenomics seems to have ...

  16. CAPITALISM EMERGING ERA TAX SYSTEMS OF THE EUROPEAN COUNTRIES

    Directory of Open Access Journals (Sweden)

    Tsokova Viktoria Aleksandrovna

    2013-04-01

    Full Text Available Three phases should be distinguished in the development of tax systems: I. The Ancient World and Middle Ages (from the IV - III centuries. BC. till. XVII - XVIII centuries AD. II. The new time (from the XVII - XVIII centuries till the end of XIX century. - the era of the emerging capitalism. III. Modern History (from the XX century and up to the present time. The capitalism emerging era scientific ideas and tax systems research relevance (importance is caused by the emergence of the main distinct characteristics of any state, that is by the permanently increasing demand of that institution for money. This fact, in its turn, contributes to the formation of the state tax system, and, of course, the evolution of scientific views on taxation. Nowadays, some theoretical ideas in the field of taxation, clarifying the nature and the role of taxes in the European countries budget formation begin to appear in Europe, especially in the UK. The development of tax systems in England, France and Germany have been analyzed; and , basing on the dialectical, historical and logical approaches, and the method of scientific abstraction, the authors identify the following common features of the capitalism emerging era tax systems in the European countries: the taxation on a regular (permanent basis, the expansion of the tax-payers range – all citizens of the state are becoming tax payers, the introduction of the income tax and the abolishment of the revenue leasing – creation of government agencies system responsible for the administration of taxes, to establishing and collecting taxes only with the Parliament approval and permission. Classical theoretical and practical approaches to creation of tax systems of the states have been formulated in Europe in the era of nascent capitalism and they haven’t lost the relevance yet.

  17. SYNESTHETIC ARTISTIC PERCEPTION IN THE ERA OF POST LITERACY

    OpenAIRE

    Margarita, Gudova; Irina, Lisovetc

    2017-01-01

    In the era of post-literacy, the development ofinformation technology and the technological basis of art as well as the mechanismsof not only artistic creativity, but also its perception, change. Thetransformation peculiarities of artistic perception of the new polymorphic andmultimedia art require their scientific and theoretical comprehension in theconditions of post-literacy that have developed in the last 50 years.In this case, we are interested in the nuancescharacterizing the changes in...

  18. A New Era for Command and Control of Aerospace Operations

    Science.gov (United States)

    2014-08-01

    PRISM]) and force ap- plication (Theater Battle Management Core Systems [ TBMCS ]). How- ever, we are now operating in an era when the platforms that...PRISM and TBMCS were designed to manage can now perform either mis- July–August 2014 Air & Space Power Journal | 13 Senior Leader Perspective sion—or...through TBMCS . However, evolv- ing technologies now afford us the opportunity to ensure that most of the aircraft in the Air Force’s inventory can

  19. [Overall digitalization: leading innovation of endodontics in big data era].

    Science.gov (United States)

    Ling, J Q

    2016-04-09

    In big data era, digital technologies bring great challenges and opportunities to modern stomatology. The applications of digital technologies, such as cone-beam CT(CBCT), computer aided design,(CAD)and computer aided manufacture(CAM), 3D printing and digital approaches for education , provide new concepts and patterns to the treatment and study of endodontic diseases. This review provides an overview of the application and prospect of commonly used digital technologies in the development of endodontics.

  20. Assisted diversification for an era of habitat extinction

    Science.gov (United States)

    Charles H. Cannon

    2017-01-01

    How do we conserve tree diversity in a rapidly changing world, dominated by intensive human impact on the landscape? The Anthropocene is a useful term to describe a new era in Earth’s history, where we dominate the globe’s resources so completely that our activities alter basic nutrient, water, climate, and energy cycles. These rapid environmental changes and the...

  1. Publishing in open access era: focus on respiratory journals.

    Science.gov (United States)

    Dai, Ni; Xu, Dingyao; Zhong, Xiyao; Li, Li; Ling, Qibo; Bu, Zhaode

    2014-05-01

    We have entered an open access publishing era. The impact and significance of open access is still under debate after two decades of evolution. Open access journals benefit researchers and the general public by promoting visibility, sharing and communicating. Non-mainstream journals should turn the challenge of open access into opportunity of presenting best research articles to the global readership. Open access journals need to optimize their business models to promote the healthy and continuous development.

  2. Wireless Communications in the Era of Big Data

    OpenAIRE

    Bi, Suzhi; Zhang, Rui; Ding, Zhi; Cui, Shuguang

    2015-01-01

    © 1979-2012 IEEE. The rapidly growing wave of wireless data service is pushing against the boundary of our communication network's processing power. The pervasive and exponentially increasing data traffic present imminent challenges to all aspects of wireless system design, such as spectrum efficiency, computing capabilities, and fronthaul/backhaul link capacity. In this article, we discuss the challenges and opportunities in the design of scalable wireless systems to embrace the big data era...

  3. BRAIN DRAIN IN THE GLOBALIZATION ERA: THE CASE OF ROMANIA

    OpenAIRE

    MARIANA BĂLAN; COSMIN OLTEANU

    2017-01-01

    Migration is an old phenomenon in the history of humankind. However, the magnitude, complexity, and structure of migration flows in the global era are all unprecedented. According to the United Nations Report “Trends in International Migrant Stock: the 2015 Revision” at world level 244 million international migrants were recorded in 2015. With the increase in the number of migrants, the emigration of ‘high-skilled’ individuals is also growing. OECD and United Nation Statistics sho...

  4. Not invented here : managing corporate innovation in a new era

    OpenAIRE

    Vrande, van de, V.J.A.

    2007-01-01

    Not Invented here: Managing Corporate Innovation in a New Era External technology sourcing as a means to develop new businesses is taking a more central role in established companies. Acquiring new technologies from outside the firm which speeds up the innovation process and complements internal R&D is an important aspect of new business development within the paradigm of open innovation. It is becoming a requirement to create and sustain competitive advantage in different product markets, an...

  5. Gravitational Physics: the birth of a new era

    Science.gov (United States)

    Sakellariadou, Mairi

    2017-11-01

    We live the golden age of cosmology, while the era of gravitational astronomy has finally begun. Still, fundamental puzzles remain. Standard cosmology is formulated within the framework of Einstein's General theory of Relativity. Notwithstanding, General Relativity is not adequate to explain the earliest stages of cosmic existence, and cannot provide an explanation for the Big Bang itself. Modern early universe cosmology is in need of a rigorous underpinning in Quantum Gravity.

  6. Towards Geo-spatial Information Science in Big Data Era

    Directory of Open Access Journals (Sweden)

    LI Deren

    2016-04-01

    Full Text Available Since the 1990s, with the advent of worldwide information revolution and the development of internet, geospatial information science have also come of age, which pushed forward the building of digital Earth and cyber city. As we entered the 21st century, with the development and integration of global information technology and industrialization, internet of things and cloud computing came into being, human society enters into the big data era. This article covers the key features (ubiquitous, multi-dimension and dynamics, internet+networking, full automation and real-time, from sensing to recognition, crowdsourcing and VGI, and service-oriented of geospatial information science in the big data era and addresses the key technical issues (non-linear four dimensional Earth reference frame system, space based enhanced GNSS, space-air and land unified network communication techniques, on board processing techniques for multi-sources image data, smart interface service techniques for space-borne information, space based resource scheduling and network security, design and developing of a payloads based multi-functional satellite platform. That needs to be resolved to provide a new definition of geospatial information science in big data era. Based on the discussion in this paper, the author finally proposes a new definition of geospatial information science (geomatics, i.e. Geomatics is a multiple discipline science and technology which, using a systematic approach, integrates all the means for spatio-temporal data acquisition, information extraction, networked management, knowledge discovering, spatial sensing and recognition, as well as intelligent location based services of any physical objects and human activities around the earth and its environment. Starting from this new definition, geospatial information science will get much more chances and find much more tasks in big data era for generation of smart earth and smart city . Our profession

  7. Challenges of the Audit Profession in the Globalization Era

    OpenAIRE

    Victor Munteanu; Mihaela Cornelia Berechet (Dragnea)

    2016-01-01

    Massive unprecedented changes, that best describe this era, are affecting the accountant and auditor profession, as well as the global business environment. The traditional role of the financial auditor will change, but if it will adapt and provide new services, may become a trusted councillor for its clients. The way financial auditors approach future tendencies will shape the destiny of the accountant and auditor profession. Financial auditors must understand innovation, to be open towar...

  8. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  9. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  10. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  11. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  12. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  13. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  14. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  15. MEMILIH PEMIMPIN DALAM PRAKTIK KEPEMIMPINAN ORGANISASI SEKOLAH DI ERA GLOBAL

    Directory of Open Access Journals (Sweden)

    Sunarta sunarta

    2013-01-01

    Full Text Available The leader and leadership courses have produced many hypotheses which haven’t been solved from time to time. With regard to the demands of the globalization era recently, the successful organizations are those which are ruled by figures who have comparative and competitiveness strengths in many fields. In educational context, a leadership can be seen from the practice of school management starting from the basic educational level to the higher one. Educational leadership in the practice of school management expects that the one who plays roles and mandated as a leader must have specific requirements of a leader. Social life in the globalization era has changed the mindsets and views of the people in the world at any level. This influences the awareness of striking for their personal and social rights in the organization. A leader is someone or subject that leads as leadership manifestation such as authority, responsibility, commands, and delegation to the subordinates in an organization. Meanwhile a leadership is an art of persuading, directing people through obedience, belief, respect, and cooperation based on enthusiasm to meet the goals, A Dale Timpe, (1987. In order to give influence to the development of the organization, there are four leadership aspects that should be developed, such as (1 follower, (2 situation (3 communication and (4 leader.   Key words: leader, leadership, school organization, globalization era.

  16. PENGELOLAAN SANGGAR KEGIATAN BELAJAR (SKB PADA ERA OTONOMI DAERAH

    Directory of Open Access Journals (Sweden)

    Widodo Widodo

    2015-03-01

    Full Text Available This study aimed to describe the management implementation of Learning Activities Gallery (LAG in the autonomy era. Description of Non-formal Education program management, Human Resources management, and financial management. Its purpose is able to create (1 facilities and able to bridge regions to the center, (2 the emergence of creativity in the construc-tion area, (3 political stability and regional centers, (4 the assurance of business continuity, and (5 open communication. But in fact the management of LAG was facing problems regarding the amount of funding that was not sufficient, human resources was not professional, and the prog-ram did not develop. Research used qualitative case studies approach of various problems in some LAG. Then dialogic analyzed by Milles and Huberman included; data collection, data reduc-tion, data display and conclusions. The study found that LAG management in the autonomy era, there was already successful and the support of the local government, but most of the LAG was not growing even threatened dissolved or merged. LAG institutional management were not well developed caused by the lack of professional Human Resources, the lack of funding support. So from some of these problems were concluded that LAG management in the era of regional auto-nomy had a tendency to decrease or even unprofessional. Regional autonomy must consider LAG as a unit organizer non-formal and informal education programs with the full support of the government both funds and human resources professionals.

  17. Research on intact marine ecosystems: a lost era.

    Science.gov (United States)

    Stachowitsch, Michael

    2003-07-01

    It is proposed that a new, fifth era should be added to the four historical phases of marine research identified by Rupert Riedl, specifically an era devoted to studying and ameliorating disturbed marine ecosystems. In an age of global environmental deterioration, many marine ecosystems and organisms are high on the list of threatened entities. This poor status prompts research that would otherwise have been unnecessary and hinders research that would normally have been conducted. I argue that research into intact marine ecosystems is becoming increasingly difficult, and that most of our future insights into marine habitats will stem from knowledge gained by examining various disfunctions of those systems rather than their functions. The new era will therefore differ from past research in its underlying aim, the range of topics studied, the selection and funding of those topics, the validity of its conclusions, and in its urgency. Sea turtles and cetaceans are cited as case studies at the organismic level, shallow-water benthic communities, including coral reefs, at the ecosystem level.

  18. Are we ready for the ERAS protocol in colorectal surgery?

    Science.gov (United States)

    Kisielewski, Michał; Rubinkiewicz, Mateusz; Pędziwiatr, Michał; Pisarska, Magdalena; Migaczewski, Marcin; Dembiński, Marcin; Major, Piotr; Rembiasz, Kazimierz; Budzyński, Andrzej

    2017-01-01

    Modern perioperative care principles in elective colorectal surgery have already been established by international surgical authorities. Nevertheless, barriers to the introduction of routine evidence-based clinical care and changing dogmas still exist. One of the factors is the surgeon. To assess perioperative care trends in elective colorectal surgery among general surgery consultants in surgical departments in Malopolska Voivodeship, Poland. An anonymous standardized 20-question questionnaire was developed based on ERAS principles and sent out to Malopolska Voivodeship general surgery departments. Answers of general surgery consultants showed the level of acceptance of elements of perioperative care. The overall response rate was 66%. Several elements (antibiotic and antithrombotic prophylaxis, postoperative oxygen therapy, no nasogastric tubes) had quite a high acceptance rate. On the other hand, most crucial surgical perioperative elements (lack of mechanical bowel preparation, preoperative oral carbohydrate loading, use of laparoscopy and lack of drains, early fluid and oral diet intake, early mobilization) were not followed according to evidence-based ERAS protocol recommendations. Surgeons were not willing to change their practice, but were supportive of changes in anesthesiologist-dependent elements of perioperative care, such as restrictive fluid therapy, use of transversus abdominis plane blocks, etc. Many elements of perioperative care in elective colorectal surgery in Malopolska Voivodeship are still dictated by dogma and are not evidence-based. The level of acceptance of many important ERAS protocol elements is low. Surgeons are ready to accept only changes that do not interfere with their practice.

  19. MOOCs 2.0: THE SOCIAL ERA OF EDUCATION

    Directory of Open Access Journals (Sweden)

    Arda SOYLEV

    2017-04-01

    Full Text Available The improvements in the Internet technology led an evolution in education. Some students’ lives have changed since 2012 when the MOOCs gained popularity among the academia. The students now take courses from the top universities all around the world without time limitations and they even earn credits for their courses. They are able to discuss lecture topics not only with their instructors in the class but also with thousands of other online students and can get just-in-time help regarding to their questions from teaching assistants. These are some of the practices from the new era of MOOCs called “social MOOCs” or MOOC 2.0. The concepts of collaboration, blended learning and TAs are the new consequences. In this paper, we review the problems and the current solutions associated with MOOC 1.0 era. In the light of these, we analyze the MOOC 2.0 era and discuss its present and possible future affects to our lives.

  20. Genomic growth curves of an outbred pig population

    Directory of Open Access Journals (Sweden)

    Fabyano Fonseca e Silva

    2013-01-01

    Full Text Available In the current post-genomic era, the genetic basis of pig growth can be understood by assessing SNP marker effects and genomic breeding values (GEBV based on estimates of these growth curve parameters as phenotypes. Although various statistical methods, such as random regression (RR-BLUP and Bayesian LASSO (BL, have been applied to genomic selection (GS, none of these has yet been used in a growth curve approach. In this work, we compared the accuracies of RR-BLUP and BL using empirical weight-age data from an outbred F2 (Brazilian Piau X commercial population. The phenotypes were determined by parameter estimates using a nonlinear logistic regression model and the halothane gene was considered as a marker for evaluating the assumptions of the GS methods in relation to the genetic variation explained by each locus. BL yielded more accurate values for all of the phenotypes evaluated and was used to estimate SNP effects and GEBV vectors. The latter allowed the construction of genomic growth curves, which showed substantial genetic discrimination among animals in the final growth phase. The SNP effect estimates allowed identification of the most relevant markers for each phenotype, the positions of which were coincident with reported QTL regions for growth traits.

  1. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  2. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  3. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  4. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  5. Structural genomics in endocrinology

    NARCIS (Netherlands)

    Smit, J. W.; Romijn, J. A.

    2001-01-01

    Traditionally, endocrine research evolved from the phenotypical characterisation of endocrine disorders to the identification of underlying molecular pathophysiology. This approach has been, and still is, extremely successful. The introduction of genomics and proteomics has resulted in a reversal of

  6. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  7. Annotating individual human genomes.

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  9. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  10. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  11. The human genome project

    International Nuclear Information System (INIS)

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  12. Decoding the human genome

    CERN Multimedia

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  13. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  14. Human Germline Genome Editing

    OpenAIRE

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  15. RadGenomics project

    Energy Technology Data Exchange (ETDEWEB)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  16. Comparative Genome Viewer

    International Nuclear Information System (INIS)

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  17. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  18. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  19. Ultrafast comparison of personal genomes

    OpenAIRE

    Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

    2017-01-01

    We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

  20. Genomics using the Assembly of the Mink Genome

    DEFF Research Database (Denmark)

    Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

    2018-01-01

    The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

  1. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Science.gov (United States)

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  2. UPAYA PENINGKATAN EXPORT DRIVE INDUSTRI FASHION DI ERA GLOBALISASI

    Directory of Open Access Journals (Sweden)

    Idah Hadijah

    2014-05-01

    Full Text Available The Efforts to Increase Export Drives of Fashion Industy in the Globali­sation Era. The fashion industry is inseparable from the development of fashion, cultural element/national culture, and the influence of fashion in many aspects of human life. Thus, fashion industry is a positive business opportunities in globalization era. Fashion industry involves various parties such as the resource of fabric thread, fabric manufacturers, designer, producers to distributors, starts from small business to large business, and also involves a lot of workers with various skills and talents. In order to support fashion industry producers having positive export drives, it is necessary to to pay attention to many components, such as production, supplier, and the final products that are distributed to the retailers. These components are also related to the quality of human resources, material resources, fashion forecasting, and the multimedia of fashion industry. : Industri fashion, tidak terlepas dari perkembangan busana, unsur budaya/ kultur suatu bangsa, serta pengaruh busana dalam berbagai aspek kehidupan manusia. Dengan demikian industri fashion merupakan peluang bisnis yang positif di era globalisasi. Industri fashion melibatkan berbagai pihak mulai dari asal serat, pem­buatan kain, desainer, produsen sampai distributor, mulai dari bisnis kecil sampai bisnis besar, juga melibatkan banyak pekerja dengan berbagai keahlian dan bakat. Upaya produsen industri fashion agar memiliki export drive yang positif, perlu memperhatikan komponen produksi, komponen supplier, produk akhir yang didistri­busikan pada retailer. Komponen-komponen tersebut terkait dengan kualitas: sumber daya manusia, sumber daya material, fashion forecasting, dan multimedia industri fashion.

  3. Cecal intubation rates in different eras of endoscopic technological development.

    Science.gov (United States)

    Matyja, Maciej; Pasternak, Artur; Szura, Mirosław; Pędziwiatr, Michał; Major, Piotr; Rembiasz, Kazimierz

    2018-03-01

    Colonoscopy plays a critical role in colorectal cancer (CRC) screening and has been widely regarded as the gold standard. Cecal intubation rate (CIR) is one of the well-defined quality indicators used to assess colonoscopy. To assess the impact of new technologies on the quality of colonoscopy by assessing completion rates. This was a dual-center study at the 2 nd Department of Surgery at Jagiellonian University Medical College and at the Specialist Center "Medicina" in Krakow, Poland. The CIR and cecal intubation time (CIT) in three different eras of technological advancement were determined. The study enrolled 27 463 patients who underwent colonoscopy as part of a national CRC screening program. The patients were divided into three groups: group I - 3408 patients examined between 2000 and 2003 (optical endoscopes); group II - 10 405 patients examined between 2004 and 2008 (standard electronic endoscopes); and group III - 13 650 patients examined between 2009 and 2014 (modern endoscopes). There were statistically significant differences in the CIR between successive eras. The CIR in group I (2000-2003) was 69.75%, in group II (2004-2008) was 92.32%, and in group III (2009-2014) was 95.17%. The mean CIT was significantly reduced in group III. Our study shows that the technological innovation of novel endoscopy devices has a great influence on the effectiveness of the CRC screening program. The new era of endoscopic technological development has the potential to reduce examination-related patient discomfort, obviate the need for sedation and increase diagnostic yields.

  4. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  5. Experimental Induction of Genome Chaos.

    Science.gov (United States)

    Ye, Christine J; Liu, Guo; Heng, Henry H

    2018-01-01

    Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

  6. An artificial intelligence approach fit for tRNA gene studies in the era of big sequence data.

    Science.gov (United States)

    Iwasaki, Yuki; Abe, Takashi; Wada, Kennosuke; Wada, Yoshiko; Ikemura, Toshimichi

    2017-09-12

    Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions. This unsupervised clustering can reveal combinatorial oligonucleotide motifs that are responsible for the amino acid-dependent clustering, as well as other functionally and structurally important consensus motifs, which have been evolutionarily conserved. BLSOM is also useful for identifying tDNAs as phylogenetic markers for special phylotypes. When we constructed BLSOM with 'species-unknown' tDNAs from metagenomic sequences plus 'species-known' microbial tDNAs, a large portion of metagenomic tDNAs self-organized with species-known tDNAs, yielding information on microbial communities in environmental samples. BLSOM can also enhance accuracy in the tDNA database obtained from big sequence data. This unsupervised data mining should become important for studying numerous functionally unclear RNAs obtained from a wide range of organisms.

  7. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  8. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  9. CAPITALISM EMERGING ERA TAX SYSTEMS OF THE EUROPEAN COUNTRIES

    Directory of Open Access Journals (Sweden)

    Виктория Александровна Цокова

    2013-05-01

    Full Text Available Three phases should be distinguished in the development of tax systems:I. The Ancient World and Middle Ages (from the IV - III centuries. BC. till. XVII - XVIII centuries AD.II. The new time (from the XVII - XVIII centuries till the end of XIX century. - the era of the emerging capitalism.III. Modern History (from the XX century and up to the present time. The capitalism emerging era scientific ideas and tax systems research relevance (importance is caused by the emergence of the main distinct characteristics of any state, that is by the permanently increasing demand of that institution for money. This fact, in its turn, contributes to the formation of the state tax system, and, of course, the evolution of scientific views on taxation.Nowadays, some theoretical ideas in the field of taxation, clarifying the nature and the role of taxes in the European countries budget formation begin to appear in Europe, especially in theUK. The development of tax systems in England, France and Germany have  been analyzed;  and , basing on the  dialectical, historical and logical approaches, and the method of scientific abstraction, the authors identify the following common features of the  capitalism emerging era tax systems in the European countries: the taxation on a regular (permanent basis, the expansion of the tax-payers  range – all citizens of the state are becoming tax payers, the introduction of the income tax and the abolishment  of the revenue leasing – creation of government agencies system responsible for the administration of taxes, to establishing and collecting taxes only with the Parliament approval and permission.Classical theoretical and practical approaches to creation of tax systems of the states have been formulated in Europe in the era of nascent capitalism and they haven’t lost the relevance yet.DOI: http://dx.doi.org/10.12731/2218-7405-2013-4-55

  10. Nusantara dalam era niaga sebelum abad ke-19

    Directory of Open Access Journals (Sweden)

    Mohammad Iskandar

    2005-10-01

    Full Text Available Trading activities in the Nusantara archipelago had developed into an international trade. According to Ricklef, Europe was not the most developed region in the world. The developing world at the time was in fact the Islamic world, stretching from the Middle East to the Nusantara. If we trace it further back into the past, to the pre-Islamic age, trade in the Nusantara region had developed, espcially during the golden eras of Sriwijaya and Majapahit. This paper describes the economic and trade development in the Nusantara before the 19th century.

  11. L’immaginario collettivo nell’era biomediatica

    Directory of Open Access Journals (Sweden)

    Massimiliano Valerii

    2017-12-01

    Full Text Available Grazie alla diffusione delle tecnologie digitali, nel giro di un decennio la grande trasformazione dei media ha determinato una rivoluzione copernicana, che ha posto l’io-utente al centro del sistema. Questo lavoro prende spunto dal 14° Rapporto sulla comunicazione del Censis per analizzare i processi in corso. In particolare, ci si focalizza sull’ingresso nella cosiddetta era biomediatica, caratterizzata dalla trascrizione virtuale e dalla condivisione telematica in tempo reale delle biografie personali attraverso i social network, che sanciscono il primato dell’io-utente, produttore esso stesso – oltre che fruitore – di contenuti.

  12. Designing network on-chip architectures in the nanoscale era

    CERN Document Server

    Flich, Jose

    2010-01-01

    Going beyond isolated research ideas and design experiences, Designing Network On-Chip Architectures in the Nanoscale Era covers the foundations and design methods of network on-chip (NoC) technology. The contributors draw on their own lessons learned to provide strong practical guidance on various design issues.Exploring the design process of the network, the first part of the book focuses on basic aspects of switch architecture and design, topology selection, and routing implementation. In the second part, contributors discuss their experiences in the industry, offering a roadmap to recent p

  13. AN URBAN TYPOLOGY WITH THE DIMENSIONS OF KNOWLEDGE ERA

    Directory of Open Access Journals (Sweden)

    Flavio Numata Junior

    2014-07-01

    Full Text Available Starting from geographical issues to globalization of the economy, cities have come to play multiple roles as the center of life for most people. The paper aims to propose an urban typology with the main features of development strategies for innovation and internationalization. The research literature is essentially exploratory in nature and qualitative approach. The literature review shows the cities in different dimensions and its relationship to the knowledge era. Shows an urban prospective design, the Project Curitiba 2030, which is used for analysis with the relevant literature. At the end of the research we propose a urban typology with potential to experience the competitive dynamics of cities.

  14. Political Evolution at NATO Level in Post Cold War Era

    Directory of Open Access Journals (Sweden)

    Tomescu Cătălin Tomiţă

    2015-06-01

    Full Text Available The beginning of the post Cold era sounds like that: „The world has changed dramatically. The Alliance has made an essential contribution. The peoples of North America and the whole of Europe can now join in a community of shared values based on freedom, democracy, human rights and the rule of law. As an agent of change, a source of stability and the indispensable guarantor of its members' security, our Alliance will continue to play a key role in building a new, lasting order of peace in Europe: a Europe of cooperation and prosperity”[1].

  15. Banking marketing mix trends in a digital era

    Directory of Open Access Journals (Sweden)

    Catalina Ioana Chirica

    2012-10-01

    Full Text Available We live in a dynamic world, with everything changing more rapidly than perhaps ever before. Changes are simultaneously a cause and an effect in this world, triggered and affecting both companies (inclusing banks and consumers. Pro-activity and reactivity are key words. Adaptation of strategies, focused consumer targeting, extended usage of new technologies, rapid growth of online environment, breakthrough of social networks and smartphones, all represent factors that converge to one direction: a digital era, when companies/banks should focus on their clients' fidelity and have an in-depth understanding of their market in order to create a real competitive advantage.

  16. New era of neutron scattering research on advanced materials

    International Nuclear Information System (INIS)

    Ikeda, Susumu

    2001-01-01

    The projects of the next generation of pulsed spallation neutron source are planed in USA, Europe and Japan. They are one order of magnitude more powerful than the most powerful existing neutron source, ISIS in UK. They offer the exciting prospects for the future, and will open the new era of neutron scattering research on advanced materials. The Japanese project is named as the 'Joint project' between JAERI and KEK on high-intensity proton accelerators. The details of the neutron science facility in the 'Joint project' and the sciences to be developed are summarized. (author)

  17. Advancing STI priorities in the SDG era: priorities for action.

    Science.gov (United States)

    Chersich, Matthew F; Delany-Moretlwe, Sinead; Martin, Greg; Rees, Helen

    2018-01-16

    The Sustainable Development Goals present an opportunity to reimagine and then reconfigure the approach to controlling sexually transmitted infections (STIs). The predilection of STIs for women and for vulnerable populations means that services that ameliorate STIs, by their nature, enhance equity, a key focus of the goals. Given the considerable breadth and depth of the goals, it is important to locate points of convergence between the SDGs and STIs, further craft synergies with HIV and select a few population groups and settings to prioritise. There are many opportunities for STI aficionados in this era to advance the field and global control of these infections.

  18. A model for C-14 tracer evaporative rate analysis (ERA)

    International Nuclear Information System (INIS)

    Gardner, R.P.; Verghese, K.

    1993-01-01

    A simple model has been derived and tested for the C-14 tracer evaporative rate analysis (ERA) method. It allows the accurate determination of the evaporative rate coefficient of the C-14 tracer detector in the presence of variable evaporation rates of the detector solvent and variable background counting rates. The evaporation rate coefficient should be the most fundamental parameter available in this analysis method and, therefore, its measurements with the proposed model should allow the most direct correlations to be made with the system properties of interest such as surface cleanliness. (author)

  19. Challenges of the Audit Profession in the Globalization Era

    Directory of Open Access Journals (Sweden)

    Victor Munteanu

    2016-06-01

    Full Text Available Massive unprecedented changes, that best describe this era, are affecting the accountant and auditor profession, as well as the global business environment. The traditional role of the financial auditor will change, but if it will adapt and provide new services, may become a trusted councillor for its clients. The way financial auditors approach future tendencies will shape the destiny of the accountant and auditor profession. Financial auditors must understand innovation, to be open towards globalization, to be prepared as human resources that are competing not only nationally but also globally.

  20. Research on information security in big data era

    Science.gov (United States)

    Zhou, Linqi; Gu, Weihong; Huang, Cheng; Huang, Aijun; Bai, Yongbin

    2018-05-01

    Big data is becoming another hotspot in the field of information technology after the cloud computing and the Internet of Things. However, the existing information security methods can no longer meet the information security requirements in the era of big data. This paper analyzes the challenges and a cause of data security brought by big data, discusses the development trend of network attacks under the background of big data, and puts forward my own opinions on the development of security defense in technology, strategy and product.

  1. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø

    2012-01-01

    casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...... for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed Results...

  2. Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

    Science.gov (United States)

    Seoane-Zonjic, Pedro; Cañas, Rafael A; Bautista, Rocío; Gómez-Maldonado, Josefa; Arrillaga, Isabel; Fernández-Pozo, Noé; Claros, M Gonzalo; Cánovas, Francisco M; Ávila, Concepción

    2016-02-27

    In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82% of the gene structures, and a high proportion (85%) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members. The experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a

  3. Detrending career statistics in professional baseball: Accounting for the steroids era and beyond

    OpenAIRE

    Petersen, Alexander M.; Penner, Orion; Stanley, H. Eugene

    2010-01-01

    There is a long standing debate over how to objectively compare the career achievements of professional athletes from different historical eras. Developing an objective approach will be of particular importance over the next decade as Major League Baseball (MLB) players from the "steroids era" become eligible for Hall of Fame induction. Here we address this issue, as well as the general problem of comparing statistics from distinct eras, by detrending the seasonal statistics of professional b...

  4. Genomics of Volvocine Algae

    Science.gov (United States)

    Umen, James G.; Olson, Bradley J.S.C.

    2015-01-01

    Volvocine algae are a group of chlorophytes that together comprise a unique model for evolutionary and developmental biology. The species Chlamydomonas reinhardtii and Volvox carteri represent extremes in morphological diversity within the Volvocine clade. Chlamydomonas is unicellular and reflects the ancestral state of the group, while Volvox is multicellular and has evolved numerous innovations including germ-soma differentiation, sexual dimorphism, and complex morphogenetic patterning. The Chlamydomonas genome sequence has shed light on several areas of eukaryotic cell biology, metabolism and evolution, while the Volvox genome sequence has enabled a comparison with Chlamydomonas that reveals some of the underlying changes that enabled its transition to multicellularity, but also underscores the subtlety of this transition. Many of the tools and resources are in place to further develop Volvocine algae as a model for evolutionary genomics. PMID:25883411

  5. Genomics of Preterm Birth

    Science.gov (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  6. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  7. Genome Sequencing of Streptomyces atratus SCSIOZH16 and Activation Production of Nocardamine via Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Yan Li

    2018-06-01

    Full Text Available The Actinomycetes are metabolically flexible microorganisms capable of producing a wide range of interesting compounds, including but by no means limited to, siderophores which have high affinity for ferric iron. In this study, we report the complete genome sequence of marine-derived Streptomyces atratus ZH16 and the activation of an embedded siderophore gene cluster via the application of metabolic engineering methods. The S. atratus ZH16 genome reveals that this strain has the potential to produce 26 categories of natural products (NPs barring the ilamycins. Our activation studies revealed S. atratus SCSIO ZH16 to be a promising source of the production of nocardamine-type (desferrioxamine compounds which are important in treating acute iron intoxication and performing ecological remediation. We conclude that metabolic engineering provides a highly effective strategy by which to discover drug-like compounds and new NPs in the genomic era.

  8. Ebolavirus comparative genomics

    Science.gov (United States)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  9. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

  10. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina....... Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  11. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  12. Innovacion en servicios en la era del conocimiento.

    Directory of Open Access Journals (Sweden)

    Cruz, R.

    2008-01-01

    Full Text Available Now a day the world economy is based in knowledge, we are living and making business in an entirely new era with new rules, where services sector is taking a more important place and a more relevant roll than previously were, and the innovation becomes the way this kind of firms can compete, access to new markets and gain long term growing. Usually, innovation research, definitions and typologies developed were done for tangible products, a legacy from an earlier economic age (based on manufacturing industry, however, Services has they own particularities and distinctive characteristics from products. The understanding of this issue is very important to service providers companies, because they could adjust their innovation process more according to a service development model than an adapted product development one. This article points out the characteristics of the new knowledge era, the importance of innovation in services sector in this new economy and the typologies available for services with the purpose to help in the evaluation or adjustment of the firm’s innovation process that fall in this segment.

  13. [Precision nutrition in the era of precision medicine].

    Science.gov (United States)

    Chen, P Z; Wang, H

    2016-12-06

    Precision medicine has been increasingly incorporated into clinical practice and is enabling a new era for disease prevention and treatment. As an important constituent of precision medicine, precision nutrition has also been drawing more attention during physical examinations. The main aim of precision nutrition is to provide safe and efficient intervention methods for disease treatment and management, through fully considering the genetics, lifestyle (dietary, exercise and lifestyle choices), metabolic status, gut microbiota and physiological status (nutrient level and disease status) of individuals. Three major components should be considered in precision nutrition, including individual criteria for sufficient nutritional status, biomarker monitoring or techniques for nutrient detection and the applicable therapeutic or intervention methods. It was suggested that, in clinical practice, many inherited and chronic metabolic diseases might be prevented or managed through precision nutritional intervention. For generally healthy populations, because lifestyles, dietary factors, genetic factors and environmental exposures vary among individuals, precision nutrition is warranted to improve their physical activity and reduce disease risks. In summary, research and practice is leading toward precision nutrition becoming an integral constituent of clinical nutrition and disease prevention in the era of precision medicine.

  14. Pemberantasan korupsi anggota DPRD di era otonomi daerah

    Directory of Open Access Journals (Sweden)

    Mukhamad Murdiono

    2004-12-01

    Full Text Available Since the implementation of decentralization, the drastic changes of politic and governmental system has been occurred in Indonesia. One of those changes is the growing significant of legislature role. In autonomy of district era, legislature was growing to be powerful marked by the function of its role, as aspiration channel and executive controller. The empowerment of legislature role in autonomy era brings some problems, not only connected with legislature themselves but also with executive. The problem connected with legislature can be cited such as bad behaviors (manipulation of graduation, money politics, corruption, etc.. Those bad behaviors have been caused the degradation of DPRD image and decadency moral. Therefore, it is necessary to rebuild politic morality and to change the image of legislative members. In order to change the image of DPRD the things can be done are reformation and radical change of DPRD by all element of society. Besides that, it is necessary to review the relationship between DPRD and people. The members of DPRD should compromise their views as well as their own needs with the people's aspirations and needs.

  15. Film piracy in the era of digital technology

    Directory of Open Access Journals (Sweden)

    Petrović Vukašin

    2015-01-01

    Full Text Available Reproduction of films in the era of analog technology has been connected with a number of difficulties, involving, inter alia, technically complex process of reproduction, as well as high cash expenditures. In that sense, the very analog technology presented a barrier to reproduction of films by unauthorized persons. By switching to digital technology, the reproduction of mentioned copyright works became much easier, in terms of enabling individuals to, with easily available and relatively cheap technical means, in a fast and high quality way, make a large number of film copies. Since the digital era reflects progress of technology in the field of reproduction and distribution of films, as well as copyright works in general, the introduction of new exclusive rights in copyright law is very significant, as well as narrowing the existing limitations of copyright law rights and extension of duration of the protection. Effective enforcement of copyright protection in the new conditions opened a range of numerous issues, out of which the question of piracy in the field of film production is one of the most important, which presented the motivation for the author to cover this issue.

  16. Emerging interdisciplinary fields in the coming intelligence/convergence era

    Science.gov (United States)

    Noor, Ahmed K.

    2012-09-01

    Dramatic advances are in the horizon resulting from rapid pace of development of several technologies, including, computing, communication, mobile, robotic, and interactive technologies. These advances, along with the trend towards convergence of traditional engineering disciplines with physical, life and other science disciplines will result in the development of new interdisciplinary fields, as well as in new paradigms for engineering practice in the coming intelligence/convergence era (post-information age). The interdisciplinary fields include Cyber Engineering, Living Systems Engineering, Biomechatronics/Robotics Engineering, Knowledge Engineering, Emergent/Complexity Engineering, and Multiscale Systems engineering. The paper identifies some of the characteristics of the intelligence/convergence era, gives broad definition of convergence, describes some of the emerging interdisciplinary fields, and lists some of the academic and other organizations working in these disciplines. The need is described for establishing a Hierarchical Cyber-Physical Ecosystem for facilitating interdisciplinary collaborations, and accelerating development of skilled workforce in the new fields. The major components of the ecosystem are listed. The new interdisciplinary fields will yield critical advances in engineering practice, and help in addressing future challenges in broad array of sectors, from manufacturing to energy, transportation, climate, and healthcare. They will also enable building large future complex adaptive systems-of-systems, such as intelligent multimodal transportation systems, optimized multi-energy systems, intelligent disaster prevention systems, and smart cities.

  17. ERA Ranger tailings corridor review. Supervising Scientist report 154

    International Nuclear Information System (INIS)

    Merz, S.K.

    2000-01-01

    Sinclair Knight Merz (SKM) were commissioned by the Office of the Supervising Scientist on 25 May 2000 to undertake a review and complete a report on the tailings corridor at the ERA Ranger Mine. The objective of the study was to undertake an 'as is' and to some extent historic and look ahead, review of the corridor system sufficient to: assess the current suitability of key aspects of the design; assess the suitability of current operating, maintenance and system development regimes and responsibilities; and record any recommended actions or further investigations arising out of the review; in order to ensure the adequacy of the design, operation and maintenance. The scope of the study report was limited to the corridor itself, its associated sump and sump contents discharge and the branch corridors carrying pipelines to Pit 1. A representative report contents was discussed and agreed with the Office of the Supervising Scientist prior to commencement of the study and this is included as appendix A to this report. The originally agreed content is, with only minor amendment, reflected in this report. The study methodology comprised a review and assessment by SKM of the design of the existing system and current operations documentation and information obtained from investigations on site and discussions with ERA site personnel. Whilst, a number of modifications affecting the corridor are recommended for further consideration, the main findings of the report relate to operating and maintenance practices which should be adopted for the remainder of the mine/mill life

  18. Synergetic Paradigm of Geopolitical Confrontation in the Postmodern Era

    Directory of Open Access Journals (Sweden)

    Sergey N. Teplyakov

    2014-01-01

    Full Text Available The article analyzes current state and mechanisms of geopolitical struggle in postmodern information age that has come. The author judges from assumption that entirely new postmodern society appeared with expansion of information technology, accompanied by cardinal changes in mechanisms of political power. Information technologies have become one of the most important factors contributing to the transformation of modern society from industrial to informational (post-industrial. In modern conditions, ensuring national and global security is a comprehensive process that includes not only measures to ensure information and economic security individually, but also such an integrated component as providing both information and economic security. The author suggests that modem geopolitical confrontation is carried out based on the synergetic paradigm. The main tool is information and energy influence on enemy system weaknesses using information space control, organizing negative information campaigns and applying economic sanctions. If the main focus of geopolitical struggle in modern era was forced expansion of the territory, in information postmodern age control over economic and information space has become priority among forms of geopolitical struggle. Military expansion of modern era becomes substituted by information and economic expansionism of postmodern using synergetic paradigm of geopolitical confrontation in order to control and capture the opponent's political space.

  19. How to Perform an Ethical Risk Analysis (eRA).

    Science.gov (United States)

    Hansson, Sven Ove

    2018-02-26

    Ethical analysis is often needed in the preparation of policy decisions on risk. A three-step method is proposed for performing an ethical risk analysis (eRA). In the first step, the people concerned are identified and categorized in terms of the distinct but compatible roles of being risk-exposed, a beneficiary, or a decisionmaker. In the second step, a more detailed classification of roles and role combinations is performed, and ethically problematic role combinations are identified. In the third step, further ethical deliberation takes place, with an emphasis on individual risk-benefit weighing, distributional analysis, rights analysis, and power analysis. Ethical issues pertaining to subsidiary risk roles, such as those of experts and journalists, are also treated in this phase. An eRA should supplement, not replace, a traditional risk analysis that puts emphasis on the probabilities and severities of undesirable events but does not cover ethical issues such as agency, interpersonal relationships, and justice. © 2018 Society for Risk Analysis.

  20. Geography, Islands and Migration in an Era of Global Mobility

    Directory of Open Access Journals (Sweden)

    Russell King

    2009-05-01

    Full Text Available This paper examines the changing role of islands in the age of globalization and in an era of enhanced and diversified mobility. There are many types of islands, many metaphors of insularity, and many types of migration, so the interactions are far from simple. The ‘mobilities turn’ in migration studies recognizes the diversification in motivations and time-space regimes of human migration. After brief reviews of island studies and of migration studies, and the power of geography to capture and distil the interdisciplinarity and relationality of these two study domains, the paper explores various facets of the generally intense engagement that islands have with migration. Two particular scenarios are identified for islands and migration in the global era: the heuristic role of islands as ‘spatial laboratories’ for the study of diverse migration processes in microcosm; and the way in which, especially in the Mediterranean and near-Atlantic regions, islands have become critical locations in the geopolitics of irregular migration routes. The case of Malta is taken to illustrate some of these new insular migration dynamics.

  1. BRAIN DRAIN IN THE GLOBALIZATION ERA: THE CASE OF ROMANIA

    Directory of Open Access Journals (Sweden)

    MARIANA BĂLAN

    2017-06-01

    Full Text Available Migration is an old phenomenon in the history of humankind. However, the magnitude, complexity, and structure of migration flows in the global era are all unprecedented. According to the United Nations Report “Trends in International Migrant Stock: the 2015 Revision” at world level 244 million international migrants were recorded in 2015. With the increase in the number of migrants, the emigration of ‘high-skilled’ individuals is also growing. OECD and United Nation Statistics show that in the last decade the number of migrants with tertiary education increased by about 70%. Brain drain is also a well-known phenomenon. Highly educated individuals and scientists have travelled the world in all centuries in search of better study and research, and working conditions, and of new opportunities. Nowadays, in the era of globalisation and, implicitly, of swifter development of international markets, the emigration rate of high-skilled experts exceeds the total emigration rate, which shows the selectiveness of migration at educational level. The paper presents a brief analysis of the interdependencies between migration and globalisation and of the effects of globalisation on the migration of high-skilled individuals. The trends, structure, and volume of high-skilled labour force from Romania are analysed along with the effects generated by them.

  2. Safety in the nuclear era. Politics - strategy - arms control

    International Nuclear Information System (INIS)

    Siebel, G.

    1988-01-01

    Details are given on safety and the factors specifying safety in Europe; the history of the NATO and development of an alliance of sovereign states; nuclear deterrence - the politico-strategic standard of the nuclear era; the East/West struggle for military power; co-operative arms control - theory and practice of stability in the nuclear era; alternative schemes and models; SDI and EURECA - present and future chances and risks. The world is at the beginning of a fascinating development likely to be culminating in the control over and utilization of space, and the mastering of various technical problems be they of a civil or military nature. It remains to be seen whether man will be able to handle the new additional technical capacities in an ethically and politically responsible way. Be that as it may, political scepticism and negative reactions will not succeed in blocking the dynamic forces inherent in the development described. This is especially true for SDI and EURECA. Both schemes are full of both chances and risks. While chances ought to be made the most of risks must be controlled through policies guided by reason. (orig./HSCH) [de

  3. Switchyard in the Main Injector era conceptual design report

    International Nuclear Information System (INIS)

    Brown, C.; Kobilarcik, T.; Lucas, P.; Malensek, A.; Murphy, C.T.; Yang, M.-J.

    1997-08-01

    This report presents elements of a design of the Switchyard and of the present fixed target beamlines in the era of the Main Injector (MI). It presumes that 800 GeV Tevatron beam will be transported to this area in the MI era, and permits it to share cycles with 120 GeV Main Injector beam if this option is desired. Geographically, the region discussed extends from the vicinity of AO to downstream points beyond which beam properties will be determined by the requirements of specific experiments. New neutrino lines not utilizing the present Switchyard (NuMI, BooNE) are not addressed. Similarly Main Injector beams upstream of AO are described fully in MI documentation and are unaffected by what is presented here. The timing both of the preparation of this report and of its recommendations for proceeding with construction relate to a desire to do required work in Transfer Hall and Enclosure B during the Main Injector construction shutdown (September 1997 - September 1998). As these areas are off-limits during any Tevatron operation, it is necessary for the fixed target program that work be completed here during this extended down period. The design presented here enables the operation of all beamlines in the manner specified in the current Laboratory plans for future fixed- target physics

  4. Genome mining of the genetic diversity in the Aspergillus genus - from a collection of more than 30 Aspergillus species

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Theobald, Sebastian

    In the era of high-throughput sequencing, comparative genomics can be applied for evaluating species diversity. In this project we aim to compare the genomes of 300 species of filamentous fungi from the Aspergillus genus, a complex task. To be able to define species, clade, and core features......, this project uses BLAST on the amino acid level to discover orthologs. With a potential of 300 Aspergillus species each having ~12,000 annotated genes, traditional clustering will demand supercomputing. Instead, our approach reduces the search space by identifying isoenzymes within each genome creating...... intragenomic protein families (iPFs), and then connecting iPFs across all genomes. The initial findings in a set of 31 species show that ~48% of the annotated genes are core genes (genes shared between all species) and 2-24% of the genes are defining the individual species. The methods presented here...

  5. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

    Directory of Open Access Journals (Sweden)

    Konrad J Karczewski

    Full Text Available The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping, a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

  6. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

    Science.gov (United States)

    Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

    2014-01-01

    The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

  7. phiGENOME: an integrative navigation throughout bacteriophage genomes.

    Science.gov (United States)

    Stano, Matej; Klucar, Lubos

    2011-11-01

    phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Revisiting Respect for Persons in Genomic Research

    Directory of Open Access Journals (Sweden)

    Debra J. H. Mathews

    2014-01-01

    Full Text Available The risks and benefits of research using large databases of personal information are evolving in an era of ubiquitous, internet-based data exchange. In addition, information technology has facilitated a shift in the relationship between individuals and their personal data, enabling increased individual control over how (and how much personal data are used in research, and by whom. This shift in control has created new opportunities to engage members of the public as partners in the research enterprise on more equal and transparent terms. Here, we consider how some of the technological advances driving and paralleling developments in genomics can also be used to supplement the practice of informed consent with other strategies to ensure that the research process as a whole honors the notion of respect for persons upon which human research subjects protections are premised. Further, we suggest that technological advances can help the research enterprise achieve a more thoroughgoing respect for persons than was possible when current policies governing human subject research were developed. Questions remain about the best way to revise policy to accommodate these changes.

  9. A primer on high-throughput computing for genomic selection.

    Science.gov (United States)

    Wu, Xiao-Lin; Beissinger, Timothy M; Bauck, Stewart; Woodward, Brent; Rosa, Guilherme J M; Weigel, Kent A; Gatti, Natalia de Leon; Gianola, Daniel

    2011-01-01

    genetic gain). Eventually, HTC may change our view of data analysis as well as decision-making in the post-genomic era of selection programs in animals and plants, or in the study of complex diseases in humans.

  10. Illuminating the Druggable Genome (IDG)

    Data.gov (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  11. National Human Genome Research Institute

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  12. Genomic prediction using subsampling.

    Science.gov (United States)

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-03-24

    Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo. We evaluated the effect of subsampling bootstrap on prediction and computational parameters. Across datasets, we observed an optimal subsampling proportion of observations around 50% with replacement, and around 33% without replacement. Subsampling provided a substantial decrease in computation time, reducing the time to fit the model by half. On average, losses on predictive properties imposed by subsampling were negligible, usually below 1%. For each dataset, an optimal subsampling point that improves prediction properties was observed, but the improvements were also negligible. Combining subsampling with Gibbs sampling is an interesting ensemble algorithm. The investigation indicates that the subsampling bootstrap Markov chain algorithm substantially reduces computational burden associated with model fitting, and it may slightly enhance prediction properties.

  13. The Lotus japonicus genome

    DEFF Research Database (Denmark)

    Fabaceae, groundbreaking genetic and genomic research has established a significant body of knowledge on Lotus japonicus, which was adopted as a model species more than 20 years ago. The diverse nature of legumes means that such research has a wide potential and agricultural impact, for example...

  14. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of...

  15. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  16. Genomic Signatures of Reinforcement

    Directory of Open Access Journals (Sweden)

    Austin G. Garner

    2018-04-01

    Full Text Available Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.

  17. Better chocolate through genomics

    Science.gov (United States)

    Theobroma cacao, the cacao or chocolate tree, is a tropical understory tree whose seeds are used to make chocolate. And like any important crop, cacao is the subject of much research. On September 15, 2010, scientists publicly released a preliminary sequence of the cacao genome--which contains all o...

  18. Functional genomics of tomato

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... 1Repository of Tomato Genomics Resources, Department of Plant Sciences, School .... Due to its position at the crossroads of Sanger's sequencing .... replacement for the microarray-based expression profiling. .... during RNA fragmentation step prior to library construction, ...... tomato pollen as a test case.

  19. Genomic Signatures of Reinforcement

    Science.gov (United States)

    Goulet, Benjamin E.

    2018-01-01

    Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved. PMID:29614048

  20. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  1. Comparative Genomics of Eukaryotes.

    NARCIS (Netherlands)

    Noort, V. van

    2007-01-01

    This thesis focuses on developing comparative genomics methods in eukaryotes, with an emphasis on applications for gene function prediction and regulatory element detection. In the past, methods have been developed to predict functional associations between gene pairs in prokaryotes. The challenge

  2. Searching for genomic constraints

    Energy Technology Data Exchange (ETDEWEB)

    Lio` , P [Cambridge, Univ. (United Kingdom). Genetics Dept.; Ruffo, S [Florence, Univ. (Italy). Fac. di Ingegneria. Dipt. di Energetica ` S. Stecco`

    1998-01-01

    The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call `genomic constraints` from the rules that depend on the `external natural selection` acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour.

  3. Searching for genomic constraints

    International Nuclear Information System (INIS)

    Lio', P.; Ruffo, S.

    1998-01-01

    The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call 'genomic constraints' from the rules that depend on the 'external natural selection' acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour

  4. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  5. Statistical Methods in Integrative Genomics

    Science.gov (United States)

    Richardson, Sylvia; Tseng, George C.; Sun, Wei

    2016-01-01

    Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

  6. From plant genomes to phenotypes

    OpenAIRE

    Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

    2017-01-01

    Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

  7. The role of the clinician in the multi-omics era: are you ready?

    Science.gov (United States)

    van Karnebeek, Clara D M; Wortmann, Saskia B; Tarailo-Graovac, Maja; Langeveld, Mirjam; Ferreira, Carlos R; van de Kamp, Jiddeke M; Hollak, Carla E; Wasserman, Wyeth W; Waterham, Hans R; Wevers, Ron A; Haack, Tobias B; Wanders, Ronald J A; Boycott, Kym M

    2018-01-23

    Since Garrod's first description of alkaptonuria in 1902, and newborn screening for phenylketonuria introduced in the 1960s, P4 medicine (preventive, predictive, personalized, and participatory) has been a reality for the clinician serving patients with inherited metabolic diseases. The era of high-throughput technologies promises to accelerate its scale dramatically. Genomics, transcriptomics, epigenomics, proteomics, glycomics, metabolomics, and lipidomics offer an amazing opportunity for holistic investigation and contextual pathophysiologic understanding of inherited metabolic diseases for precise diagnosis and tailored treatment. While each of the -omics technologies is important to systems biology, some are more mature than others. Exome sequencing is emerging as a reimbursed test in clinics around the world, and untargeted metabolomics has the potential to serve as a single biochemical testing platform. The challenge lies in the integration and cautious interpretation of these big data, with translation into clinically meaningful information and/or action for our patients. A daunting but exciting task for the clinician; we provide clinical cases to illustrate the importance of his/her role as the connector between physicians, laboratory experts and researchers in the basic, computer, and clinical sciences. Open collaborations, data sharing, functional assays, and model organisms play a key role in the validation of -omics discoveries. Having all the right expertise at the table when discussing the diagnostic approach and individualized management plan according to the information yielded by -omics investigations (e.g., actionable mutations, novel therapeutic interventions), is the stepping stone of P4 medicine. Patient participation and the adjustment of the medical team's plan to his/her and the family's wishes most certainly is the capstone. Are you ready?

  8. Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species

    Directory of Open Access Journals (Sweden)

    Suliman Khan

    2016-01-01

    Full Text Available In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

  9. Kernel-based whole-genome prediction of complex traits: a review.

    Science.gov (United States)

    Morota, Gota; Gianola, Daniel

    2014-01-01

    Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways), thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics.

  10. Kernel-based whole-genome prediction of complex traits: a review

    Directory of Open Access Journals (Sweden)

    Gota eMorota

    2014-10-01

    Full Text Available Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways, thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics.

  11. Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences.

    Science.gov (United States)

    Kobeissy, Firas H; Gulbakan, Basri; Alawieh, Ali; Karam, Pierre; Zhang, Zhiqun; Guingab-Cagmat, Joy D; Mondello, Stefania; Tan, Weihong; Anagli, John; Wang, Kevin

    2014-02-01

    The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.

  12. Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species.

    Science.gov (United States)

    Khan, Suliman; Nabi, Ghulam; Ullah, Muhammad Wajid; Yousaf, Muhammad; Manan, Sehrish; Siddique, Rabeea; Hou, Hongwei

    2016-01-01

    In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a "sixth" mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

  13. GPM Ground Validation: Pre to Post-Launch Era

    Science.gov (United States)

    Petersen, Walt; Skofronick-Jackson, Gail; Huffman, George

    2015-04-01

    NASA GPM Ground Validation (GV) activities have transitioned from the pre to post-launch era. Prior to launch direct validation networks and associated partner institutions were identified world-wide, covering a plethora of precipitation regimes. In the U.S. direct GV efforts focused on use of new operational products such as the NOAA Multi-Radar Multi-Sensor suite (MRMS) for TRMM validation and GPM radiometer algorithm database development. In the post-launch, MRMS products including precipitation rate, accumulation, types and data quality are being routinely generated to facilitate statistical GV of instantaneous (e.g., Level II orbit) and merged (e.g., IMERG) GPM products. Toward assessing precipitation column impacts on product uncertainties, range-gate to pixel-level validation of both Dual-Frequency Precipitation Radar (DPR) and GPM microwave imager data are performed using GPM Validation Network (VN) ground radar and satellite data processing software. VN software ingests quality-controlled volumetric radar datasets and geo-matches those data to coincident DPR and radiometer level-II data. When combined MRMS and VN datasets enable more comprehensive interpretation of both ground and satellite-based estimation uncertainties. To support physical validation efforts eight (one) field campaigns have been conducted in the pre (post) launch era. The campaigns span regimes from northern latitude cold-season snow to warm tropical rain. Most recently the Integrated Precipitation and Hydrology Experiment (IPHEx) took place in the mountains of North Carolina and involved combined airborne and ground-based measurements of orographic precipitation and hydrologic processes underneath the GPM Core satellite. One more U.S. GV field campaign (OLYMPEX) is planned for late 2015 and will address cold-season precipitation estimation, process and hydrology in the orographic and oceanic domains of western Washington State. Finally, continuous direct and physical validation

  14. Opening plenary speaker: Human genomics, precision medicine, and advancing human health.

    Science.gov (United States)

    Green, Eric D

    2016-08-01

    Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases. Together, these developments are ushering in the era of genomic medicine. Augmenting the advances in human genomics have been innovations in technologies for measuring environmental and lifestyle information, electronic health records, and data science; together, these provide opportunities of unprecedented scale and scope for investigating the underpinnings of health and disease. To capitalize on these opportunities, U.S. President Barack Obama recently announced a major new research endeavor - the U.S. Precision Medicine Initiative. This bold effort will be framed around several key aims, which include accelerating the use of genomically informed approaches to cancer care, making important policy and regulatory changes, and establishing a large research cohort of >1 million volunteers to facilitate precision medicine research. The latter will include making the partnership with all participants a centerpiece feature in the cohort's design and development. The Precision Medicine Initiative represents a broad-based research program that will allow new approaches for individualized medical care to be rigorously tested, so as to establish a new evidence base for advancing clinical practice and, eventually, human health.

  15. A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

    Science.gov (United States)

    Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

    2016-12-01

    The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Variability in clinical diagnoses during the ICD-8 and ICD-10 era

    DEFF Research Database (Denmark)

    Frederiksen, Julie E Nordgaard; Jessen, Kasper; Sæbye, Ditte

    2016-01-01

    university-affiliated departments of psychiatry in Denmark in two time periods: 1980-1985 (ICD-8) and 2001-2010 (ICD-10). RESULTS: The synchronic inter-departmental diagnostic differences did not decrease in the ICD-10 era compared with ICD-8 era. Nor did the diachronic stability within each department...

  17. Interdisciplinarity in an Era of New Public Management: A Case Study of Graduate Business Schools

    Science.gov (United States)

    Ryan, Suzanne; Neumann, Ruth

    2013-01-01

    In an era of rapid knowledge transmission and creation spurred on by advances in technology and globalisation, calls for interdisciplinarity to solve "wicked" problems are common. In the same era, universities are increasingly adopting new public management practices. The extent to which these practices affect knowledge production is an…

  18. The Struggles of Women Industrial Workers To Improve Work Conditions in the Progressive Era.

    Science.gov (United States)

    Barrett, Nancy J.

    1999-01-01

    Offers a lesson plan that addresses the working conditions endured by women in the Progressive Era and their struggles for womens rights in the workplace. Strives to demonstrate the similarities between the plights of the Progressive Era women to those of women workers in the 1990s. (CMK)

  19. 75 FR 13319 - NextEra Energy Seabrook, LLC, et al.

    Science.gov (United States)

    2010-03-19

    ... NUCLEAR REGULATORY COMMISSION [Docket No. 50-443; NRC-2010-0108] NextEra Energy Seabrook, LLC, et al.,* Seabrook Station, Unit No. 1 Environmental Assessment and Finding of No Significant Impact * NextEra Energy Seabrook, LLC is authorized to act as agent for the Hudson Light & Power Department...

  20. Aare Sosaar nõuab sisse ERA Panga halbu laene / Tiit Elner

    Index Scriptorium Estoniae

    Elner, Tiit

    2000-01-01

    Ekspankur Aare Sosaare juhitav teadmata omanikega ERA Liising ostis pankrotis ERA Pangalt probleemseid laene, suurem nõuete ostja oli ka Krediidipank. Kokku on müüdud laenude lepingujärgne väärtus kuni 100 mln. kr.