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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

    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.

  2. Vaccinology in the genome era

    OpenAIRE

    Rinaudo, C. Daniela; Telford, John L.; Rappuoli, Rino; Seib, Kate L.

    2009-01-01

    Vaccination has played a significant role in controlling and eliminating life-threatening infectious diseases throughout the world, and yet currently licensed vaccines represent only the tip of the iceberg in terms of controlling human pathogens. However, as we discuss in this Review, the arrival of the genome era has revolutionized vaccine development and catalyzed a shift from conventional culture-based approaches to genome-based vaccinology. The availability of complete bacterial genomes h...

  3. Microbiology in the post-genomic era.

    Science.gov (United States)

    Medini, Duccio; Serruto, Davide; Parkhill, Julian; Relman, David A; Donati, Claudio; Moxon, Richard; Falkow, Stanley; Rappuoli, Rino

    2008-06-01

    Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics. In this article, we review the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments, and address the implications of the genomic era for the future of microbiology.

  4. The Post-Genomic Era of Cassava

    Science.gov (United States)

    The genomics era revolutionized our efficiency at gathering and disseminating scientific information required for advancing our understanding of plant biology. In the case of cassava, the genomics revolution has not kept pace with other staple food and fiber crops important to global economies. As a...

  5. [Ethical issues in genome-era].

    Science.gov (United States)

    Kosugi, Shinji

    2016-06-01

    Handling of personal genome information is one of the most important current ethical issues in the era of next generation sequencer which is technically progressing at a furious speed, making it 100,000 times faster in only in five years. The author picked up topics of(1) research and clinical guidelines of handling of human genome information, (2) incidental and secondary findings of next generation sequencer in clinical exome and genome sequencing, and (3) so-called direct-to-consumer genetic testing services. In the topic(2), ACMG (American College of Medical Genetics and Genomics) recommendations inreporting incidental findings proposed in 2013 and 2014 are focused.

  6. 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

  7. Injury in the era of genomics.

    Science.gov (United States)

    Cobb, J P; Brownstein, B H; Watson, M A; Shannon, W D; Laramie, J M; Qiu, Y; Stormo, G D; Morrissey, J J; Buchman, T G; Karl, I E; Hotchkiss, R S

    2001-03-01

    The traditional approach to the study of biology employs small-scale experimentation that results in the description of a molecular sequence of known function or relevance. In the era of the genome the reverse is true, as large-scale cloning and gene sequencing come first, followed by the use of computational methods to systematically determine gene function and regulation. The overarching goal of this new approach is to translate the knowledge learned from a systematic, global analysis of genomic data into a complete understanding of biology. For investigators who study shock, the specific goal is to increase understanding of the adaptive response to injury at the level of the entire genome. This review describes our initial experience using DNA microarrays to profile stress-induced changes in gene expression. We conclude that efforts to apply genomics to the study of injury are best coordinated by multi-disciplinary groups, because of the extensive expertise required.

  8. 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.

  9. Kinesiogenomics: The Genomic Era in Kinesiology

    Directory of Open Access Journals (Sweden)

    Onur ORAL

    2015-08-01

    Full Text Available The application of genomics research in kinesiology may be characterized as kinesiogenomics or sport genetics. Therefore, kinesiogenomcs is generally known as the study of genetics in the various discipline of kinesiology which refer to the study of human movement. In the research field of Kinesiogenomics, the scientific goal is to clarify the role of genes in sport performance, identification of various genes with their different alleles that affect to the response and adaptation of the body systems and m etabolism . By thelp of the these genetic research studies in various disciplines of kinesiology, it will be possible to use genetic testing to predict sport performance or to individualize exercise prescription with the potential for genetic therapy. I t is supposed to enhance the sport performance because of that reason that the Interindividual variation of kinesiogenomic - related trait such as maximal oxygen consumption, muscle fibre composition and trainability has a strong genetic basis. Genetic res earch has a large potential for developing the area of kinesiology with the contribution of genetic factors for various phenotypes related to sport performance including aerobic and anaerobic performance, muscular endurance and strength, motor performance, and some determinant of performance such as morphological, cardiac and skeletal muscle characteristic. In the area of kinesiology, up till now kinesiogenomics research studies have moved into a new era utilizing well - phenotyped, large cohort and genomewide technologies. The main aim of this review is to summarize the most recent and significant genetic finding in the various discipline of kinesiology and to predict the future expectation and possibilities for kinesiogenomics.

  10. Current research status of immunology in the genomic era

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    This review updates the current status of immunology research under the influence of genomics,both conceptually and technologically.It particularly highlights the advantages of employing the high-throughput and large-scale technology,the large genomic database,and bioinformatic power in the immunology research.The fast development in the fields of basic immunology,clinical immunology(tumor and infectious immunology) and vaccine designing is illustrated with respect to the successful usage of genomic strategy.We also speculate the future research directions of immunology in the era of genomics and post-genomics.

  11. Current research status of immunology in the genomic era

    Institute of Scientific and Technical Information of China (English)

    LI HaoWen; LI dinZhi; ZHAO GuoPing; WANG Ying

    2009-01-01

    This review updates the current status of immunology research under the influence of genomics, both conceptually and technologically. It particularly highlights the advantages of employing the high-throughput and large-scale technology, the large genomic database, and bioinformatic power in the immunology research. The fast development in the fields of basic immunology, clinical immunology (tumor and infectious immunology) and vaccine designing is illustrated with respect to the successful usage of genomic strategy. We also speculate the future research directions of immunology in the era of genomics and post-genomics.

  12. Patient privacy in the genomic era.

    Science.gov (United States)

    Raisaro, Jean Louis; Ayday, Erman; Hubaux, Jean-Pierre

    2014-05-07

    According to many scientists and clinicians, genomics is taking on a key role in the field of medicine. Impressive advances in genome sequencing have opened the way to a variety of revolutionary applications in modern healthcare. In particular, the increasing understanding of the human genome, and of its relation to diseases and response to treatments brings promise of improvements in better preventive and personalized medicine. However, this progress raises important privacy and ethical concerns that need to be addressed. Indeed, each genome is the ultimate identifier of its owner and, due to its nature, it contains highly personal and privacy-sensitive data. In this article, after summarizing recent advances in genomics, we discuss some important privacy issues associated with human genomic information and methods put in place to address them.

  13. Proteomics in the genome engineering era.

    Science.gov (United States)

    Vandemoortele, Giel; Gevaert, Kris; Eyckerman, Sven

    2016-01-01

    Genome engineering experiments used to be lengthy, inefficient, and often expensive, preventing a widespread adoption of such experiments for the full assessment of endogenous protein functions. With the revolutionary clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 technology, genome engineering became accessible to the broad life sciences community and is now implemented in several research areas. One particular field that can benefit significantly from this evolution is proteomics where a substantial impact on experimental design and general proteome biology can be expected. In this review, we describe the main applications of genome engineering in proteomics, including the use of engineered disease models and endogenous epitope tagging. In addition, we provide an overview on current literature and highlight important considerations when launching genome engineering technologies in proteomics workflows.

  14. 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.

  15. Pharmacogenetic applications of the post genomic era.

    Science.gov (United States)

    Sengupta, L K; Sengupta, Susmita; Sarkar, Munna

    2002-06-01

    The human genome sequence has given us the view of the internal genetic scaffold around which human life is molded. We have inherited this heritage from our ancestors and through it we are connected to all life on earth. The sequencing of the human genome, amongst others, has led to the newer areas of healthcare and medicine. The human population is heterogeneous and consists of populations of immense ethnic diversity. There are considerable allelic differences between human populations as well as individuals within each ethnic group as a result of molecular heterogeneity of the genome. This, in turn, is responsible for differential allelic expression of genes endowing them with polymorphic characters. The molecular diversity within genes is responsible amongst others, of disease resistance or susceptibility or for that matter drug response. The objective of this article is to understand the nuances of the genetic repertoire and correlate it with disease gene identification, genes that have been or can be used as drug targets, identify candidate genes for drug development and recent trends in drug discovery. As regular clinical trials for drugs does not take into account the ethnic variations, it sometimes results in the differential response with respect to the efficacy and/or adverse reaction of the drug. Therefore the diverse ethnic populations of the world pose a challenge to the pharma industry. The concept of the personal medicine seems to be the answer to this problem. But it is a Herculean task requiring immense innovation in technology, is time consuming and is not a financially viable proposition at this point of time. An alternate approach would be to divide the populations in genetic cohorts and design drugs according to their genetic profile and haplotype. In addition, the ethical and legal bindings have also to be taken into consideration.

  16. The Post-genomic Era of Trichoderma reesei: What's Next?

    Science.gov (United States)

    Gupta, Vijai Kumar; Steindorff, Andrei Stecca; de Paula, Renato Graciano; Silva-Rocha, Rafael; Mach-Aigner, Astrid R; Mach, Robert L; Silva, Roberto N

    2016-12-01

    The ascomycete Trichoderma reesei is one of the most well studied cellulolytic microorganisms. This fungus is widely used in the biotechnology industry, mainly in the production of biofuels. Due to its importance, its genome was sequenced in 2008, opening new avenues to study this microorganism. In this 'post-genomic' era, a transcriptomic and proteomic era has emerged. Here, we present an overview of new findings in the gene expression regulation network of T. reesei. We also discuss new rational strategies to obtain mutants that produce hydrolytic enzymes with a higher yield, using metabolic engineering. Finally, we present how synthetic biology strategies can be used to create engineered promoters to efficiently synthesize enzymes for biomass degradation to produce bioethanol.

  17. Heritability in the genomics era--concepts and misconceptions.

    Science.gov (United States)

    Visscher, Peter M; Hill, William G; Wray, Naomi R

    2008-04-01

    Heritability allows a comparison of the relative importance of genes and environment to the variation of traits within and across populations. The concept of heritability and its definition as an estimable, dimensionless population parameter was introduced by Sewall Wright and Ronald Fisher nearly a century ago. Despite continuous misunderstandings and controversies over its use and application, heritability remains key to the response to selection in evolutionary biology and agriculture, and to the prediction of disease risk in medicine. Recent reports of substantial heritability for gene expression and new estimation methods using marker data highlight the relevance of heritability in the genomics era.

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

    Science.gov (United States)

    Belcher, Thomas; Preston, Andrew

    2015-11-01

    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.

  19. Drosophila and experimental neurology in the post-genomic era.

    Science.gov (United States)

    Shulman, Joshua M

    2015-12-01

    For decades, the fruit fly, Drosophila melanogaster, has been among the premiere genetic model systems for probing fundamental neurobiology, including elucidation of mechanisms responsible for human neurologic disorders. Flies continue to offer virtually unparalleled versatility and speed for genetic manipulation, strong genomic conservation, and a nervous system that recapitulates a range of cellular and network properties relevant to human disease. I focus here on four critical challenges emerging from recent advances in our understanding of the genomic basis of human neurologic disorders where innovative experimental strategies are urgently needed: (1) pinpointing causal genes from associated genomic loci; (2) confirming the functional impact of allelic variants; (3) elucidating nervous system roles for novel or poorly studied genes; and (4) probing network interactions within implicated regulatory pathways. Drosophila genetic approaches are ideally suited to address each of these potential translational roadblocks, and will therefore contribute to mechanistic insights and potential breakthrough therapies for complex genetic disorders in the coming years. Strategic collaboration between neurologists, human geneticists, and the Drosophila research community holds great promise to accelerate progress in the post-genomic era.

  20. Defining "mutation" and "polymorphism" in the era of personal genomics.

    Science.gov (United States)

    Karki, Roshan; Pandya, Deep; Elston, Robert C; Ferlini, Cristiano

    2015-07-15

    The growing advances in DNA sequencing tools have made analyzing the human genome cheaper and faster. While such analyses are intended to identify complex variants, related to disease susceptibility and efficacy of drug responses, they have blurred the definitions of mutation and polymorphism. In the era of personal genomics, it is critical to establish clear guidelines regarding the use of a reference genome. Nowadays DNA variants are called as differences in comparison to a reference. In a sequencing project Single Nucleotide Polymorphisms (SNPs) and DNA mutations are defined as DNA variants detectable in >1 % or genomic sequence. We propose to solve this nomenclature dilemma by defining mutations as DNA variants obtained in a paired sequencing project including the germline DNA of the same individual as a reference. Moreover, the term mutation should be accompanied by a qualifying prefix indicating whether the mutation occurs only in somatic cells (somatic mutation) or also in the germline (germline mutation). We believe this distinction in definition will help avoid confusion among researchers and support the practice of sequencing the germline and somatic tissues in parallel to classify the DNA variants thus defined as mutations.

  1. Healthcare management-training and education in the genomic era.

    Science.gov (United States)

    Betta, Michela; Clulow, Val

    2005-01-01

    Increasingly the rapid developments by scientists working in the new business sector of biotechnology are being thrust into mainstream news reports. The incredible pace of the creation of neo-knowledge recently leads us to believe there has not been enough time between events for the healthcare sector, the general public, the legislators or the ethicists to reflect and conduct the checks and balances required for thoughtful progress. The decline of the hospital and the emergence of the laboratory as a consequence of the advent of the genomic era signal a profound shift, which will have unprecedented impacts on professionals in the healthcare system and its repercussions will force explicit changes in their education.

  2. Elucidating endometrial function in the post-genomic era.

    Science.gov (United States)

    Giudice, Linda C

    2003-01-01

    The post-genomic era has now arrived, and science and biology are on the threshold of a transition from understanding functions of single molecules and pathways in cells, tissues and whole organisms to understanding integrative systems. The endometrium is a dynamic tissue that responds to multiple stimuli, depending on physiological and environmental conditions, including steroid hormones, an implanting conceptus, withdrawal of steroid hormones, contraceptive steroids, selective steroid hormone receptor modulators, infection, transient cell populations, and metaplastic and neoplastic agents. High throughput technologies with regard to DNA, RNA and proteins are well positioned to enable a thorough understanding of the dynamic changes and integrative systems involved in endometrial maturation, desquamation, receptivity to implantation, infertility, pregnancy maintenance and failure, inflammation and infection, and malignant transformation. This monograph reviews some of the salient features of the new technologies and summarizes current information on endometrial biology derived from these approaches.

  3. Plant microbe interactions in post genomic era: perspectives and applications

    Directory of Open Access Journals (Sweden)

    Jahangir Imam

    2016-09-01

    Full Text Available Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.

  4. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications.

    Science.gov (United States)

    Imam, Jahangir; Singh, Puneet K; Shukla, Pratyoosh

    2016-01-01

    Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.

  5. 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.

  6. Towards a new era in medicine: therapeutic genome editing.

    Science.gov (United States)

    Porteus, Matthew H

    2015-12-22

    Genome editing is the process of precisely modifying the nucleotide sequence of the genome. It has provided a powerful approach to research questions but, with the development of a new set of tools, it is now possible to achieve frequencies of genome editing that are high enough to be useful therapeutically. Genome editing is being developed to treat not only monogenic diseases but also infectious diseases and diseases that have both a genetic and an environmental component.

  7. Methods of Genome Engineering: a New Era of Molecular Biology.

    Science.gov (United States)

    Chugunova, A A; Dontsova, O A; Sergiev, P V

    2016-07-01

    Genome sequencing now progressing much faster than our understanding of the majority of gene functions. Studies of physiological functions of various genes would not be possible without the ability to manipulate the genome. Methods of genome engineering can now be used to inactivate a gene to study consequences, introduce heterologous genes into the genome for scientific and biotechnology applications, create genes coding for fusion proteins to study gene expression, protein localization, and molecular interactions, and to develop animal models of human diseases to find appropriate treatment. Finally, genome engineering might present the possibility to cure hereditary diseases. In this review, we discuss and compare the most important methods for gene inactivation and editing, as well as methods for incorporation of heterologous genes into the genome.

  8. 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.

  9. Genome Project Standards in a New Era of Sequencing

    Energy Technology Data Exchange (ETDEWEB)

    GSC Consortia; HMP Jumpstart Consortia; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G.; Hostetler, J.; Muzny, D.; Detter, J. C.; Ali, J.; Birren, B.; Bruce, D. C.; Buhay, C.; Cole, J. R.; Ding, Y.; Dugan, S.; Field, D.; Garrity, G. M.; Gibbs, R.; Graves, T.; Han, C. S.; Harrison, S. H.; Highlander, S.; Hugenholtz, P.; Khouri, H. M.; Kodira, C. D.; Kolker, E.; Kyrpides, N. C.; Lang, D.; Lapidus, A.; Malfatti, S. A.; Markowitz, V.; Metha, T.; Nelson, K. E.; Parkhill, J.; Pitluck, S.; Qin, X.; Read, T. D.; Schmutz, J.; Sozhamannan, S.; Strausberg, R.; Sutton, G.; Thomson, N. R.; Tiedje, J. M.; Weinstock, G.; Wollam, A.

    2009-06-01

    For over a decade, genome 43 sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole genome sequencing that requires a careful reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker 'draft', however these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and contributed to many wasted hours of (mis)interpretation. These same novel sequencing technologies have also brought an exponential leap in raw sequencing capability, and at greatly reduced prices that have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The resulting effect is an ever-widening gap between drafted and finished genomes that only promises to continue (Figure 1), hence there is an urgent need to distinguish good and poor datasets. The sequencing institutes in the authorship, along with the NIH's Human Microbiome Project Jumpstart Consortium (3), strongly believe that a new set of standards is required for genome sequences. The following represents a set of six community-defined categories of genome sequence standards that better

  10. RNomics: The New Frontier in the post-genomic era

    Institute of Scientific and Technical Information of China (English)

    Liang-Hu Qu

    2009-01-01

    @@ It has been shown that whenever there is breakthrough in DNA structure there follows a bloom period of RNA re-search. The decipherment of the DNA double-helix structure in 1953 initiated the new era of interpreting genetic in-formation at the transcriptional and translational level, which directly resulted in the discovery of mRNAs, tRNAs, rRNAs, as well as the establishment of the "Genetic Code" and the "'Central Dogma".

  11. [Industrial biotechnology in the post-genomic era].

    Science.gov (United States)

    Zhang, Yanping; Li, Yin

    2010-09-01

    The background and the importance of developing industrial biotechnology were illustrated, followed by a brief analysis on the driving effect of genomics and functional genomics. Seventeen papers covering metabolic engineering, fermentation engineering, industrial enzymes and biocatalysis are published in this special issue. These papers were briefly introduced to show the most recent developments of industrial biotechnology.

  12. 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...

  13. Neuroscience in the era of functional genomics and systems biology.

    Science.gov (United States)

    Geschwind, Daniel H; Konopka, Genevieve

    2009-10-15

    Advances in genetics and genomics have fuelled a revolution in discovery-based, or hypothesis-generating, research that provides a powerful complement to the more directly hypothesis-driven molecular, cellular and systems neuroscience. Genetic and functional genomic studies have already yielded important insights into neuronal diversity and function, as well as disease. One of the most exciting and challenging frontiers in neuroscience involves harnessing the power of large-scale genetic, genomic and phenotypic data sets, and the development of tools for data integration and mining. Methods for network analysis and systems biology offer the promise of integrating these multiple levels of data, connecting molecular pathways to nervous system function.

  14. Advancing Crop Transformation in the Era of Genome Editing

    Science.gov (United States)

    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 thirty years of technological advances. Genome editing provides new opportunities to...

  15. The role of the toxicologic pathologist in the post-genomic era(#).

    Science.gov (United States)

    Maronpot, Robert R

    2013-06-01

    An era can be defined as a period in time identified by distinctive character, events, or practices. We are now in the genomic era. The pre-genomic era: There was a pre-genomic era. It started many years ago with novel and seminal animal experiments, primarily directed at studying cancer. It is marked by the development of the two-year rodent cancer bioassay and the ultimate realization that alternative approaches and short-term animal models were needed to replace this resource-intensive and time-consuming method for predicting human health risk. Many alternatives approaches and short-term animal models were proposed and tried but, to date, none have completely replaced our dependence upon the two-year rodent bioassay. However, the alternative approaches and models themselves have made tangible contributions to basic research, clinical medicine and to our understanding of cancer and they remain useful tools to address hypothesis-driven research questions. The pre-genomic era was a time when toxicologic pathologists played a major role in drug development, evaluating the cancer bioassay and the associated dose-setting toxicity studies, and exploring the utility of proposed alternative animal models. It was a time when there was shortage of qualified toxicologic pathologists. The genomic era: We are in the genomic era. It is a time when the genetic underpinnings of normal biological and pathologic processes are being discovered and documented. It is a time for sequencing entire genomes and deliberately silencing relevant segments of the mouse genome to see what each segment controls and if that silencing leads to increased susceptibility to disease. What remains to be charted in this genomic era is the complex interaction of genes, gene segments, post-translational modifications of encoded proteins, and environmental factors that affect genomic expression. In this current genomic era, the toxicologic pathologist has had to make room for a growing population of

  16. Neuroscience in the era of functional genomics and systems biology

    OpenAIRE

    Geschwind, Daniel H.; Konopka, Genevieve

    2009-01-01

    Advances in genetics and genomics have fuelled a revolution in discovery-based, or hypothesis-generating, research that provides a powerful complement to the more directly hypothesis-driven molecular, cellular and systems neuroscience. Genetic and functional genomic studies have already yielded important insights into neuronal diversity and function, as well as disease. One of the most exciting and challenging frontiers in neuroscience involves harnessing the power of large-scale genetic, gen...

  17. Chapter 13: Mining electronic health records in the genomics era.

    Directory of Open Access Journals (Sweden)

    Joshua C Denny

    Full Text Available The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare observations, combinations of simple free-text searches and billing codes may prove adequate when followed by manual chart review. However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed. Combinations of structured and unstructured textual data can be mined to generate high-validity collections of cases and controls for a given condition. Once high-quality cases and controls are identified, EHR-derived cases can be used for genomic discovery and validation. Since EHR data includes a broad sampling of clinically-relevant phenotypic information, it may enable multiple genomic investigations upon a single set of genotyped

  18. Tracing Monotreme Venom Evolution in the Genomics Era

    Science.gov (United States)

    Whittington, Camilla M.; Belov, Katherine

    2014-01-01

    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. PMID:24699339

  19. 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.

  20. Pea (Pisum sativum L.) in the genomics era

    Science.gov (United States)

    Pea (Pisum sativum L.) was the original model organism for Mendel´s discovery 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, largely as a consequence of its low multiplication rat...

  1. Advancing Crop Transformation in the Era of Genome Editing.

    Science.gov (United States)

    Altpeter, Fredy; Springer, Nathan M; Bartley, Laura E; Blechl, Ann E; Brutnell, Thomas P; Citovsky, Vitaly; 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; Walbot, Virginia; Wang, Kan; Zhang, Zhanyuan J; Stewart, C Neal

    2016-07-01

    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.

  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.

  3. Gene mutations of acute myeloid leukemia in the genome era.

    Science.gov (United States)

    Naoe, Tomoki; Kiyoi, Hitoshi

    2013-02-01

    Ten years ago, gene mutations found in acute myeloid leukemia (AML) were conceptually grouped into class I mutation, which causes constitutive activation of intracellular signals that contribute to the growth and survival, and class II mutation, which blocks differentiation and/or enhance self-renewal by altered transcription factors. A cooperative model between two classes of mutations has been suggested by murine experiments and partly supported by epidemiological findings. In the last 5 years, comprehensive genomic analysis proceeded to find new gene mutations, which are found in the epigenome-associated enzymes and the molecules never noticed so far. These new mutations apparently increase the complexity and heterogeneity of AML. Although a long list of gene mutations might have been compiled, the entire picture of molecular pathogenesis in AML remains to be elucidated because gene rearrangement, gene copy number, DNA methylation and expression profiles are not fully studied in conjunction with gene mutations. Comprehensive genome research will deepen the understanding of AML to promote the development of new classification and treatment. This review focuses on gene mutations that were recently discovered by genome sequencing.

  4. Epidemiological studies of esophageal cancer in the era of genome-wide association studies

    Institute of Scientific and Technical Information of China (English)

    An-Hui; Wang; Yuan; Liu; Bo; Wang; Yi-Xuan; He; Ye-Xian; Fang; Yong-Ping; Yan

    2014-01-01

    Esophageal cancer(EC) caused about 395000 deaths in 2010. China has the most cases of EC and EC is the fourth leading cause of cancer death in China. Esophageal squamous cell carcinoma(ESCC) is the predominant histologic type(90%-95%), while the incidence of esophageal adenocarcinoma(EAC) remains extremely low in China. Traditional epidemiological studies have revealed that environmental carcinogens are risk factors for EC. Molecular epidemiological studies revealed that susceptibility to EC is influenced by both environmental and genetic risk factors. Of all the risk factors for EC, some are associated with the risk of ESCC and others with the risk of EAC. However, the details and mechanisms of risk factors involved in the process for EC are unclear. The advanced methods and techniques used in human genome studies bring a great opportunity for researchers to explore and identify the details of those risk factors or susceptibility genes involved inthe process of EC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era to the era of genome wide association studies(GWAS). Here we review the epidemiological studies of EC(especially ESCC) in the era of GWAS, and provide an overview of the general risk factors and those genomic variants(genes, SNPs, miRNAs, proteins) involved in the process of ESCC.

  5. 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...

  6. 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

  7. Olive Tree in the Genomic Era: Focus on Plant Architecture

    Directory of Open Access Journals (Sweden)

    Juan José González Plaza

    2016-05-01

    Full Text Available For centuries olive tree is an important crop in many Mediterranean countries because it provides appreciated oil with healthy properties. The lack of genomic tools, such as molecular markers or sequence information, has hindered the development of new cultivars adapted to the challenges that this species faces due to the change in modern cultivation practices, such as the increase in the number of trees per hectare. This tree has an excessive vigour that can be a serious economic limitation for intensive or super-intensive orchards. These and other issues have been recently addressed by a number of scientific efforts. This review will give a broad view over the recent genomic developments in olive tree, and the plant architecture as a complex trait. Normal 0 21 false false false HR X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;}

  8. 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

    2016-11-28

    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.

  9. 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.

  10. 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.

  11. Progress in unraveling the genetic etiology of Parkinson disease in a genomic era.

    Science.gov (United States)

    Verstraeten, Aline; Theuns, Jessie; Van Broeckhoven, Christine

    2015-03-01

    Parkinson disease (PD) and Parkinson-plus syndromes are genetically heterogeneous neurological diseases. Initial studies into the genetic causes of PD relied on classical molecular genetic approaches in well-documented case families. More recently, these approaches have been combined with exome sequencing and together have identified 15 causal genes. Additionally, genome-wide association studies (GWASs) have discovered over 25 genetic risk factors. Elucidation of the genetic architecture of sporadic and familial parkinsonism, however, has lagged behind that of simple Mendelian conditions, suggesting the existence of features confounding genetic data interpretation. Here we discuss the successes and potential pitfalls of gene discovery in PD and related disorders in the post-genomic era. With an estimated 30% of trait variance currently unexplained, tackling current limitations will further expedite gene discovery and lead to increased application of these genetic insights in molecular diagnostics using gene panel and exome sequencing strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Functional genomics of tomato: Opportunities and challenges in post-genome NGS era

    Indian Academy of Sciences (India)

    Rahul Kumar; Ashima Khurana

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger’s and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-à-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other ‘omics’ tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  13. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    Science.gov (United States)

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  14. 毒性病理学家在基因组和后基因组时代的作用%Introduction of the Role of the Toxicologic Pathologist in the Genomic Era and Post-Genomic Era

    Institute of Scientific and Technical Information of China (English)

    吕建军; 霍桂桃; 林志; 屈哲; 杨艳伟; 张頔; 张硕; 李波

    2016-01-01

    Objective: To briefly introduce the role of the toxicologic pathologist in the genomic and post-genomic era, with the purpose to enhance the awareness of the importance of toxicity pathology in the ifeld of nonclinical safety evaluation of drugs and provide some references for toxicity pathologists in the genome era and the post-genomic era to master new technologies and develop fresh perspectives of China. Methods:Firstly, the paper brielfy introduced the method of dividing pre-genomic era, genomic era, and post-genomic era. Secondly, the papers reviewed the biomedical and tocicological events of each era. Finally, the paper also illustrated the role of the toxicologic pathologist during each era. Results:The pre-genomic era began around the year 1900 and ended in 1990. Genomc era started in the year 1990 and will end in 2050. Post-genomic era will begin in 2050. The biomedical and tocicological events of the pre-genomic era were two-year rodent cancer bioassay and its alternative approaches as well as short-term animal models. The biomedical and tocicological events of the genomic era were as follows:the cloning of the sheep, Dolly;completeness of the human genome project;sequencing of the human and the mouse genome;active research using stem cells;transgenic mouse bioassays;establishment of the International Conference on Harmonization (ICH);the“omics”technologies;high throughput screening of chemicals;and the building of predictive toxicology, etc. The biomedical and tocicological events of the post-genomic era will include entire genomes from multiple species, data from thousands of robotic high throughput chemical screenings as well as genetic toxicity and chemical structure-activity relationships in different databases and in silico predictive toxicology;conifrmation in intact mammalian animal models in vivo, etc. The pre-genomic era was a time when toxicologic pathologists played a major role in drug development. Toxicologic pathologists can combine

  15. Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

    Energy Technology Data Exchange (ETDEWEB)

    McCluskey, Kevin; Baker, Scott E.

    2017-02-17

    Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.

  16. 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.

  17. Behavioral Resilience In the Post-Genomic Era: Emerging Models Linking Genes With Environment

    Directory of Open Access Journals (Sweden)

    Richard eRende

    2012-03-01

    Full Text Available One of the most important deliverables of the post-genomic era has been a new and nuanced appreciation of how the environment shapes – and holds potential to alter – the expression of susceptibility genes for behavioral dimensions and disorders. This paper will consider three themes that have emerged from cutting-edge research studies that utilize newer molecular genetic approaches as well as tried-and-true genetic epidemiological methodologies, with particular reference to evolving perspectives on resilience and plasticity. These themes are: 1 evidence for replicable and robust shared environmental effects on a number of clinically relevant behaviors in childhood and adolescence; 2 evolving research on gene-environment interaction; and 3 a newer focus on differential susceptibility and plasticity. The net sum of these themes is that consideration of genetic effects on behavioral dimensions and disorders needs to be connected to thinking about the role of environment as a potent source for promoting resilience and change.

  18. [Genomics and metabolic engineering of filamentous fungi in the post-genomics era].

    Science.gov (United States)

    Chen, Xian-Zhong; Shen, Wei; Fan, You; Wang, Zheng-Xiang

    2011-10-01

    Filamentous fungi are used in a variety of industrial processes including the production of primary metabolites (e.g., organic acid, vitamins, and extracellular enzymes) and secondary metabolites (e.g., antibiotics, alkaloids, and gibberellins). Moreover, filamentous fungi have become preferred cell factories for production of foreign (heterologous) proteins in biotechnology in recent years. Compared to bacterial and yeast hosts, filamentous fungi showed predominant features such as the ability of growing on rather simple and inexpensive substrates, producing and secreting exceptionally large amounts of proteins, post-translational modifications, and GRAS (generally regarded as safe) approval. Therefore, the exploration of filamentous fungi has been attractive recently. This review summarizes the recent development in genomics, comparative genomics, transcriptomics, proteomics and metabolomics of filamentous fungi, and describes their applications and functions in reconstruction of metabolic network, discovery of novel proteins and genes, investigation of cell physiological and biochemical reactions, and strain breeding. This review also analyzes the bottlenecks of heterologous protein expression in filamentous fungi. Furthermore, special emphasis is given on the strategies for improving the protein production, including fusion expression of heterologous proteins, RNAi technology, manipulations of secretion pathways, codon optimization of foreign genes, and screening of protease mutants. Lastly, this review proposes the future direction of metabolic engineering of filamentous fungi.

  19. SHELTERING FROM AVALANCHES OF BIOLOGICAL DATA: A NEW RESEARCH DIMENSION IN THE POST-GENOMICS ERA

    Directory of Open Access Journals (Sweden)

    Neri Niccolai

    2013-12-01

    Full Text Available Biomedical research in the Post-genomic Era is characterized by huge amounts of data which cannot be manually analyzed soon after their collection, but only stored in data banks for further investigations. Thus, many data banks have been created to keep some order for results obtained from high throughput techniques applied to genomics or to other “omics” studies. Some order is also needed to browse fruitfully biological data among all the available databanks. National Center for Biotechnology Information of USA offers to researchers a powerful interface to achieve this effort, but in a way that is not suitable for the public perception. A Google Earth kind of software would help to sail safely within this data ocean to specific pieces of information, as required both by researchers and by just curious people. Bioinformatics, a new interdisciplinary field that develops and improves on methods for storing, retrieving, organizing and analyzing biological data, is emerging as a powerful tool to derive novel perspective of biological processes. In our laboratory, for instance, scanning the Protein Data Bank to analyze amino acids distribution inside protein structures, new scenarios appeared which can account for long distance protein-protein interactions.

  20. Birth defects registries in the genomics era: challenges and opportunities for developing countries.

    Science.gov (United States)

    Thong, Meow-Keong

    2014-01-01

    Birth defects or congenital anomalies are one of the major causes of disability in developed and developing countries. Data on birth defects from population-based studies originating from developing countries are lacking. Increasingly, there is a shift to genetic testing and genomics study of birth defects. However, the translation from bench findings to bedside medicine has been muted. There is a need to address this imbalance where congenital anomalies remained the top etiology for neonatal mortality in developing countries. To build capacity in low resource countries, there is a need for accurate collection and ascertainment of birth defects in developing countries. The systematic collection and analysis of data on major birth defects using birth defects registries (BDRs) are an integral part of all clinical genetic services. Healthcare planners in developing countries must be aware of the advantages and limitations of BDRs. Despite the advent of the genomics era, BDRs are essential to the planning and developing care and prevention services at local and national levels, particularly in low resource or developing countries.

  1. Comparison of GenomEra C. difficile and Xpert C. difficile as confirmatory tests in a multistep algorithm for diagnosis of Clostridium difficile infection.

    Science.gov (United States)

    Alcalá, Luis; Reigadas, Elena; Marín, Mercedes; Fernández-Chico, Antonia; Catalán, Pilar; Bouza, Emilio

    2015-01-01

    We compared two multistep diagnostic algorithms based on C. Diff Quik Chek Complete and, as confirmatory tests, GenomEra C. difficile and Xpert C. difficile. The sensitivity, specificity, positive predictive value, and negative predictive value were 87.2%, 99.7%, 97.1%, and 98.3%, respectively, for the GenomEra-based algorithm and 89.7%, 99.4%, 95.5%, and 98.6%, respectively, for the Xpert-based algorithm. GenomEra represents an alternative to Xpert as a confirmatory test of a multistep algorithm for Clostridium difficile infection (CDI) diagnosis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

    Science.gov (United States)

    Dhanapal, Arun Prabhu; Govindaraj, Mahalingam

    2015-01-01

    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.

  3. 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.

  4. Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks.

    Science.gov (United States)

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a whole entity in cancer functional studies. With the advances of genome sequencing and computational analysis, we are able to quantify and computationally dissect clones from tumors, and then conduct clone-based analysis. Emerging technologies such as single-cell genome sequencing and RNA-Seq could profile tumor clones. Thus, we should reconsider how to conduct cancer systems biology studies in the genome sequencing era. We will outline new directions for conducting cancer systems biology by considering that genome sequencing technology can be used for dissecting, quantifying and genetically characterizing clones from tumors. Topics discussed in Part 1 of this review include computationally quantifying of tumor subpopulations; clone-based network modeling, cancer hallmark-based networks and their high-order rewiring principles and the principles of cell survival networks of fast-growing clones. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  5. Aspergillus and Penicillium in the Post-genomic Era

    DEFF Research Database (Denmark)

    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...... in Penicillium and Aspergillus and a promise of many more things to come. An essential reference for everyone working with Aspergillus and Penicillium and other filamentous fungi and the book is also recommended reading for everyone with an interest in fungal genomics....... 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...

  6. 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.

  7. Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

    Science.gov (United States)

    2017-01-01

    A fundamental question in biology is how the extraordinary range of living organisms arose. In this theme issue, we celebrate how evolutionary studies on the origins of morphological diversity have changed over the past 350 years since the first publication of the Philosophical Transactions of The Royal Society. Current understanding of this topic is enriched by many disciplines, including anatomy, palaeontology, developmental biology, genetics and genomics. Development is central because it is the means by which genetic information of an organism is translated into morphology. The discovery of the genetic basis of development has revealed how changes in form can be inherited, leading to the emergence of the field known as evolutionary developmental biology (evo-devo). Recent approaches include imaging, quantitative morphometrics and, in particular, genomics, which brings a new dimension. Articles in this issue illustrate the contemporary evo-devo field by considering general principles emerging from genomics and how this and other approaches are applied to specific questions about the evolution of major transitions and innovations in morphology, diversification and modification of structures, intraspecific morphological variation and developmental plasticity. Current approaches enable a much broader range of organisms to be studied, thus building a better appreciation of the origins of morphological diversity. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994116

  8. The Future of Children’s Health in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Alan L. Schwartz

    2011-07-01

    Full Text Available The effects of genomic medicine on child health promise to be profound. Medical applications will eventually include characterizing patients’ genomes to detect predictive mutations for pre-symptomatic counseling where treatment exists; to search for causes of diseases of unknown etiology, and to detect carriers for prenatal counseling; to define cancer and other disease-based genomes to design individualized therapy; and to understand our microbiomes to modify these in health and disease. Rapid advances in technology and bioinformatics have reduced the cost and the time and increased the accuracy necessary to sequence whole genomes or whole exomes. However, complete understanding of disease will also require correlation of genomic information with high-quality phenotypic data. In addition, several critical ethical, psycho-social, and public policy issues will require clarity in the coming years. Ultimately these advances will improve the effectiveness of health care for children and for society.

  9. Using multilocus sequence typing to study bacterial variation: prospects in the genomic era.

    Science.gov (United States)

    Jolley, Keith A; Maiden, Martin C J

    2014-01-01

    Multilocus sequence typing (MLST) indexes the sequence variation present in a small number (usually seven) of housekeeping gene fragments located around the bacterial genome. Unique alleles at these loci are assigned arbitrary integer identifiers, which effectively summarizes the variation present in several thousand base pairs of genome sequence information as a series of numbers. Comparing bacterial isolates using allele-based methods efficiently corrects for the effects of lateral gene transfer present in many bacterial populations and is computationally efficient. This 'gene-by-gene' approach can be applied to larger collections of loci, such as the ribosomal protein genes used in ribosomal MLST (rMLST), up to and including the complete set of coding sequences present in a genome, whole-genome MLST (wgMLST), providing scalable, efficient and readily interpreted genome analysis.

  10. A New Era of Genome Integration-Simply Cut and Paste!

    Science.gov (United States)

    Liu, Zihe; Liang, Youyun; Ang, Ee Lui; Zhao, Huimin

    2017-01-24

    Genome integration is a powerful tool in both basic and applied biological research. However, traditional genome integration, which is typically mediated by homologous recombination, has been constrained by low efficiencies and limited host range. In recent years, the emergence of homing endonucleases and programmable nucleases has greatly enhanced integration efficiencies and allowed alternative integration mechanisms such as nonhomologous end joining and microhomology-mediated end joining, enabling integration in hosts deficient in homologous recombination. In this review, we will highlight recent advances and breakthroughs in genome integration methods made possible by programmable nucleases, and their new applications in synthetic biology and metabolic engineering.

  11. 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.

  12. Natural products discovery from micro-organisms in the post-genome era.

    Science.gov (United States)

    Ikeda, Haruo

    2017-01-01

    With the decision to award the Nobel Prize in Physiology or Medicine to Drs. S. Ōmura, W.C. Campbell, and Y. Tu, the importance and usefulness of natural drug discovery and development have been revalidated. Since the end of the twentieth century, many genome analyses of organisms have been conducted, and accordingly, numerous microbial genomes have been decoded. In particular, genomic studies of actinomycetes, micro-organisms that readily produce natural products, led to the discovery of biosynthetic gene clusters responsible for producing natural products. New explorations for natural products through a comprehensive approach combining genomic information with conventional methods show great promise for the discovery of new natural products and even systematic generation of unnaturally occurring compounds.

  13. 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...

  14. The Nobel Prize as a Reward Mechanism in the Genomics Era: Anonymous Researchers, Visible Managers and the Ethics of Excellence.

    Science.gov (United States)

    Zwart, Hub

    2010-09-01

    The Human Genome Project (HGP) is regarded by many as one of the major scientific achievements in recent science history, a large-scale endeavour that is changing the way in which biomedical research is done and expected, moreover, to yield considerable benefit for society. Thus, since the completion of the human genome sequencing effort, a debate has emerged over the question whether this effort merits to be awarded a Nobel Prize and if so, who should be the one(s) to receive it, as (according to current procedures) no more than three individuals can be selected. In this article, the HGP is taken as a case study to consider the ethical question to what extent it is still possible, in an era of big science, of large-scale consortia and global team work, to acknowledge and reward individual contributions to important breakthroughs in biomedical fields. Is it still viable to single out individuals for their decisive contributions in order to reward them in a fair and convincing way? Whereas the concept of the Nobel prize as such seems to reflect an archetypical view of scientists as solitary researchers who, at a certain point in their careers, make their one decisive discovery, this vision has proven to be problematic from the very outset. Already during the first decade of the Nobel era, Ivan Pavlov was denied the Prize several times before finally receiving it, on the basis of the argument that he had been active as a research manager (a designer and supervisor of research projects) rather than as a researcher himself. The question then is whether, in the case of the HGP, a research effort that involved the contributions of hundreds or even thousands of researchers worldwide, it is still possible to "individualise" the Prize? The "HGP Nobel Prize problem" is regarded as an exemplary issue in current research ethics, highlighting a number of quandaries and trends involved in contemporary life science research practices more broadly.

  15. 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.

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

    Directory of Open Access Journals (Sweden)

    Roy Michael Robins-Browne

    2016-11-01

    Full Text Available 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.

  17. Microbial taxonomy in the post-genomic era: rebuilding from scratch?

    Science.gov (United States)

    Thompson, Cristiane C; Amaral, Gilda R; Campeão, Mariana; Edwards, Robert A; Polz, Martin F; Dutilh, Bas E; Ussery, David W; Sawabe, Tomoo; Swings, Jean; Thompson, Fabiano L

    2015-04-01

    Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, 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.

  18. 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...... suitability for identifying the genetic determinants of a phenotypic trait of interest, whole genome sequencing is expected to be one of the major driving forces in industrial biotechnology in the coming years. We present some of the recent studies that have successfully applied high-throughput sequencing...

  19. 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...

  20. Parents' Experience with Pediatric Microarray: Transferrable Lessons in the Era of Genomic Counseling.

    Science.gov (United States)

    Hayeems, R Z; Babul-Hirji, R; Hoang, N; Weksberg, R; Shuman, C

    2016-04-01

    Advances in genome-based microarray and sequencing technologies hold tremendous promise for understanding, better-managing and/or preventing disease and disease-related risk. Chromosome microarray technology (array based comparative genomic hybridization [aCGH]) is widely utilized in pediatric care to inform diagnostic etiology and medical management. Less clear is how parents experience and perceive the value of this technology. This study explored parents' experiences with aCGH in the pediatric setting, focusing on how they make meaning of various types of test results. We conducted in-person or telephone-based semi-structured interviews with parents of 21 children who underwent aCGH testing in 2010. Transcripts were coded and analyzed thematically according to the principles of interpretive description. We learned that parents expect genomic tests to be of personal use; their experiences with aCGH results characterize this use as intrinsic in the test's ability to provide a much sought-after answer for their child's condition, and instrumental in its ability to guide care, access to services, and family planning. In addition, parents experience uncertainty regardless of whether aCGH results are of pathogenic, uncertain, or benign significance; this triggers frustration, fear, and hope. Findings reported herein better characterize the notion of personal utility and highlight the pervasive nature of uncertainty in the context of genomic testing. Empiric research that links pre-test counseling content and psychosocial outcomes is warranted to optimize patient care.

  1. 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 ...

  2. Updating the Model Definition of the Gene in the Modern Genomic Era with Implications for Instruction

    Science.gov (United States)

    Smith, Mike U.; Adkison, Linda R.

    2010-01-01

    Gericke and Hagberg (G & H, "Sci Educ" 16:849-881, 2007) recently published in this journal a thoughtful analysis of the historical progression of our understanding of the nature of the gene for use in instruction. This analysis, however, did not include the findings of the Human Genome Project (HGP), which must be included in any introductory…

  3. Mycoplasma haemocanis – the canine hemoplasma and its feline counterpart in the genomic era

    Directory of Open Access Journals (Sweden)

    do Nascimento Naíla C

    2012-09-01

    Full Text Available Abstract Mycoplasma haemocanis is a hemotrophic mycoplasma (hemoplasma, blood pathogen that may cause acute disease in immunosuppressed or splenectomized dogs. The genome of the strain Illinois, isolated from blood of a naturally infected dog, has been entirely sequenced and annotated to gain a better understanding of the biology of M. haemocanis. Its single circular chromosome has 919 992 bp and a low G + C content (35%, representing a typical mycoplasmal genome. A gene-by-gene comparison against its feline counterpart, M. haemofelis, reveals a very similar composition and architecture with most of the genes having conserved synteny extending over their entire chromosomes and differing only by a small set of unique protein coding sequences. As in M. haemofelis, M. haemocanis metabolic pathways are reduced and apparently rely heavily on the nutrients afforded by its host environment. The presence of a major percentage of its genome dedicated to paralogous genes (63.7% suggests that this bacterium might use antigenic variation as a mechanism to evade the host’s immune system as also observed in M. haemofelis genome. Phylogenomic comparisons based on average nucleotide identity (ANI and tetranucleotide signature suggest that these two pathogens are different species of mycoplasmas, with M. haemocanis infecting dogs and M. haemofelis infecting cats.

  4. Updating the Model Definition of the Gene in the Modern Genomic Era with Implications for Instruction

    Science.gov (United States)

    Smith, Mike U.; Adkison, Linda R.

    2010-01-01

    Gericke and Hagberg (G & H, "Sci Educ" 16:849-881, 2007) recently published in this journal a thoughtful analysis of the historical progression of our understanding of the nature of the gene for use in instruction. This analysis, however, did not include the findings of the Human Genome Project (HGP), which must be included in any introductory…

  5. 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.

  6. Population and clinical genetics of human transposable elements in the (post) genomic era

    Science.gov (United States)

    Rishishwar, Lavanya; Wang, Lu; Clayton, Evan A.; Mariño-Ramírez, Leonardo; McDonald, John F.; Jordan, I. King

    2017-01-01

    ABSTRACT Recent technological developments—in genomics, bioinformatics and high-throughput experimental techniques—are providing opportunities to study ongoing human transposable element (TE) activity at an unprecedented level of detail. It is now possible to characterize genome-wide collections of TE insertion sites for multiple human individuals, within and between populations, and for a variety of tissue types. Comparison of TE insertion site profiles between individuals captures the germline activity of TEs and reveals insertion site variants that segregate as polymorphisms among human populations, whereas comparison among tissue types ascertains somatic TE activity that generates cellular heterogeneity. In this review, we provide an overview of these new technologies and explore their implications for population and clinical genetic studies of human TEs. We cover both recent published results on human TE insertion activity as well as the prospects for future TE studies related to human evolution and health.

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

    Directory of Open Access Journals (Sweden)

    Markus Herrgård

    2012-10-01

    Full Text Available 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 suitability for identifying the genetic determinants of a phenotypic trait of interest, whole genome sequencing is expected to be one of the major driving forces in industrial biotechnology in the coming years. We present some of the recent studies that have successfully applied high-throughput sequencing 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 exploiting natural diversity in natural isolates or crosses between isolates, classical mutagenesis and evolutionary engineering.

  8. 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.

  9. Evolving Ideas on the Origin and Evolution of Flowers: New Perspectives in the Genomic Era.

    Science.gov (United States)

    Chanderbali, Andre S; Berger, Brent A; Howarth, Dianella G; Soltis, Pamela S; Soltis, Douglas E

    2016-04-01

    The origin of the flower was a key innovation in the history of complex organisms, dramatically altering Earth's biota. Advances in phylogenetics, developmental genetics, and genomics during the past 25 years have substantially advanced our understanding of the evolution of flowers, yet crucial aspects of floral evolution remain, such as the series of genetic and morphological changes that gave rise to the first flowers; the factors enabling the origin of the pentamerous eudicot flower, which characterizes ∼70% of all extant angiosperm species; and the role of gene and genome duplications in facilitating floral innovations. A key early concept was the ABC model of floral organ specification, developed by Elliott Meyerowitz and Enrico Coen and based on two model systems,Arabidopsis thalianaandAntirrhinum majus Yet it is now clear that these model systems are highly derived species, whose molecular genetic-developmental organization must be very different from that of ancestral, as well as early, angiosperms. In this article, we will discuss how new research approaches are illuminating the early events in floral evolution and the prospects for further progress. In particular, advancing the next generation of research in floral evolution will require the development of one or more functional model systems from among the basal angiosperms and basal eudicots. More broadly, we urge the development of "model clades" for genomic and evolutionary-developmental analyses, instead of the primary use of single "model organisms." We predict that new evolutionary models will soon emerge as genetic/genomic models, providing unprecedented new insights into floral evolution.

  10. 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. PMID:28265284

  11. 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.

  12. 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.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-05-01

    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.

  15. Surgical margins in the genomic era: The Hayes Martin Lecture, 2012.

    Science.gov (United States)

    Wolf, Gregory T

    2012-11-01

    One of the highest honors of one's career is to be asked to address colleagues, mentors, and students who represent the world's leading health professionals dedicated to reducing the morbidity and mortality associated with head and neck cancer. Hayes Martin would certainly share this feeling of honor and humility in having a lecture given in his name on the occasion of the Eighth International Conference on Head and Neck Cancer. I am so very pleased to share with you some thoughts on the assessment, adequacy, and application of surgical resection margins in an era in which personalized surgery and molecular medicine will have a major impact on patient outcomes. My thoughts about surgical margins have evolved over nearly 40 years of performing surgical resections for cancer. A discussion of margins may seem somewhat mundane to many of you; however, I hope to provide a futuristic and somewhat theoretical view of how surgical margin issues will relate to the personalization of modern head and neck cancer treatment and how the biology of the tumor microenvironment may be instructive in the application of our surgical approaches. This is particularly relevant because of the rapid expansion of functional surgical approaches utilizing minimally invasive endoscopic resections and robotic techniques that may not achieve the same wide oncologic margins that have been emphasized historically.(1,2) Proper selection of patients for such procedures is critical if we are to improve overall treatment results.

  16. The geometric increase in meta-analyses from China in the genomic era.

    Directory of Open Access Journals (Sweden)

    John P A Ioannidis

    Full Text Available Meta-analyses are increasingly popular. It is unknown whether this popularity is driven by specific countries and specific meta-analyses types. PubMed was used to identify meta-analyses since 1995 (last update 9/1/2012 and catalogue their types and country of origin. We focused more on meta-analyses from China (the current top producer of meta-analyses versus the USA (top producer until recently. The annual number of meta-analyses from China increased 40-fold between 2003 and 2011 versus 2.4-fold for the USA. The growth of Chinese meta-analyses was driven by genetics (110-fold increase in 2011 versus 2003. The HuGE Navigator identified 612 meta-analyses of genetic association studies published in 2012 from China versus only 109 from the USA. We compared in-depth 50 genetic association meta-analyses from China versus 50 from USA in 2012. Meta-analyses from China almost always used only literature-based data (92%, and focused on one or two genes (94% and variants (78% identified with candidate gene approaches (88%, while many USA meta-analyses used genome-wide approaches and raw data. Both groups usually concluded favorably for the presence of genetic associations (80% versus 74%, but nominal significance (P<0.05 typically sufficed in the China group. Meta-analyses from China typically neglected genome-wide data, and often included candidate gene studies published in Chinese-language journals. Overall, there is an impressive rise of meta-analyses from China, particularly on genetic associations. Since most claimed candidate gene associations are likely false-positives, there is an urgent global need to incorporate genome-wide data and state-of-the art statistical inferences to avoid a flood of false-positive genetic meta-analyses.

  17. The geometric increase in meta-analyses from China in the genomic era.

    Science.gov (United States)

    Ioannidis, John P A; Chang, Christine Q; Lam, Tram Kim; Schully, Sheri D; Khoury, Muin J

    2013-01-01

    Meta-analyses are increasingly popular. It is unknown whether this popularity is driven by specific countries and specific meta-analyses types. PubMed was used to identify meta-analyses since 1995 (last update 9/1/2012) and catalogue their types and country of origin. We focused more on meta-analyses from China (the current top producer of meta-analyses) versus the USA (top producer until recently). The annual number of meta-analyses from China increased 40-fold between 2003 and 2011 versus 2.4-fold for the USA. The growth of Chinese meta-analyses was driven by genetics (110-fold increase in 2011 versus 2003). The HuGE Navigator identified 612 meta-analyses of genetic association studies published in 2012 from China versus only 109 from the USA. We compared in-depth 50 genetic association meta-analyses from China versus 50 from USA in 2012. Meta-analyses from China almost always used only literature-based data (92%), and focused on one or two genes (94%) and variants (78%) identified with candidate gene approaches (88%), while many USA meta-analyses used genome-wide approaches and raw data. Both groups usually concluded favorably for the presence of genetic associations (80% versus 74%), but nominal significance (PChina group. Meta-analyses from China typically neglected genome-wide data, and often included candidate gene studies published in Chinese-language journals. Overall, there is an impressive rise of meta-analyses from China, particularly on genetic associations. Since most claimed candidate gene associations are likely false-positives, there is an urgent global need to incorporate genome-wide data and state-of-the art statistical inferences to avoid a flood of false-positive genetic meta-analyses.

  18. Current progress in the biology of members of the Sporothrix schenckii complex following the genomic era.

    Science.gov (United States)

    Mora-Montes, Héctor M; Dantas, Alessandra da Silva; Trujillo-Esquivel, Elías; de Souza Baptista, Andrea R; Lopes-Bezerra, Leila M

    2015-09-01

    Sporotrichosis has been attributed for more than a century to one single etiological agent, Sporothrix schencki. Only eight years ago, it was described that, in fact, the disease is caused by several pathogenic cryptic species. The present review will focus on recent advances to understand the biology and virulence of epidemiologically relevant pathogenic species of the S. schenckii complex. The main subjects covered are the new clinical and epidemiological aspects including diagnostic and therapeutic challenges, the development of molecular tools, the genome database and the perspectives for study of virulence of emerging Sporothrix species.

  19. Drug-target and disease networks: polypharmacology in the post-genomic era

    OpenAIRE

    Masoudi-Nejad, Ali; Mousavian, Zaynab; Bozorgmehr, Joseph H.

    2013-01-01

    With the growing understanding of complex diseases, the focus of drug discovery has shifted away from the well-accepted “one target, one drug” model, to a new “multi-target, multi-drug” model, aimed at systemically modulating multiple targets. Identification of the interaction between drugs and target proteins plays an important role in genomic drug discovery, in order to discover new drugs or novel targets for existing drugs. Due to the laborious and costly experimental process of drug-targe...

  20. Developments in obesity genetics in the era of genome-wide association studies.

    Science.gov (United States)

    Day, Felix R; Loos, Ruth J F

    2011-01-01

    Obesity is an important factor contributing to the global burden of morbidity and mortality. By identifying obesity susceptibility genes, scientists aim to elucidate some of its aetiology. Early studies used candidate gene and genome-wide linkage approaches to search for such genes with limited success. However, the advent of genome-wide association studies (GWAS) has dramatically increased the pace of gene discovery. So far, GWAS have identified at least 50 loci robustly associated with body mass index (BMI), waist-to-hip ratio, body fat percentage and extreme obesity. Some of these have been shown to replicate in non-white populations and in children and adolescents. Furthermore, for some loci interaction studies have shown that the BMI-increasing effect is attenuated in physically active individuals. Despite many successful discoveries, the effect sizes of the established loci are small, and combined they explain only a fraction of the inter-individual variation in BMI. The low predictive value means that their value in mainstream health care is limited. However, as most of these newly established loci were not previously linked to obesity, they may provide new insights into body weight regulation. Continued efforts in gene discovery, using a range of approaches, will be needed to increase our understanding of obesity. Copyright © 2011 S. Karger AG, Basel.

  1. Emerging technologies for amino acid nutrition research in the post-genome era.

    Science.gov (United States)

    Wang, Junjun; Wu, Guoyao; Zhou, Huaijun; Wang, Fenglai

    2009-05-01

    Amino acids (AA) are not only the building blocks of proteins but are also key regulators of metabolic pathways in cells. However, the mechanisms responsible for the effects of AA are largely unknown. With the completion of human and other mammalian genome projects, revolutionary technologies in life sciences characterized by high throughput, high efficiency, and rapid computation are now available for AA nutrition research. These advanced tools include genetics (the genomic variety), epigenetics (stable and heritable changes in gene expression or cellular phenotype that occurs without changes in DNA sequence), transcriptomics (alternative mRNA splicing, microRNAs, and gene transcription), proteomics (protein expression and interactions), metabolomics (metabolite profiles in cells and tissues), and bioinformatics (analysis of metabolic pathways using systems biology approach). These robust, powerful methods can be employed for the analysis of DNA, RNA, protein, and low-molecular-weight metabolites, whose expression and concentration are affected by the interaction between genes and dietary AA. With the omics and other advanced methodologies, we expect that the molecular actions of AA on target tissues can be defined and that optimal dietary recommendations for these nutrients can be devised for individual humans (personalized nutrition) and animals (targeted feeding) in response to changes in physiological and pathological conditions.

  2. Targeting the undruggable: immunotherapy meets personalized oncology in the genomic era.

    Science.gov (United States)

    Martin, S D; Coukos, G; Holt, R A; Nelson, B H

    2015-12-01

    Owing to recent advances in genomic technologies, personalized oncology is poised to fundamentally alter cancer therapy. In this paradigm, the mutational and transcriptional profiles of tumors are assessed, and personalized treatments are designed based on the specific molecular abnormalities relevant to each patient's cancer. To date, such approaches have yielded impressive clinical responses in some patients. However, a major limitation of this strategy has also been revealed: the vast majority of tumor mutations are not targetable by current pharmacological approaches. Immunotherapy offers a promising alternative to exploit tumor mutations as targets for clinical intervention. Mutated proteins can give rise to novel antigens (called neoantigens) that are recognized with high specificity by patient T cells. Indeed, neoantigen-specific T cells have been shown to underlie clinical responses to many standard treatments and immunotherapeutic interventions. Moreover, studies in mouse models targeting neoantigens, and early results from clinical trials, have established proof of concept for personalized immunotherapies targeting next-generation sequencing identified neoantigens. Here, we review basic immunological principles related to T-cell recognition of neoantigens, and we examine recent studies that use genomic data to design personalized immunotherapies. We discuss the opportunities and challenges that lie ahead on the road to improving patient outcomes by incorporating immunotherapy into the paradigm of personalized oncology.

  3. Current therapeutic leads for the treatment of melanoma: targeted immunotherapy in the post-genomic era.

    Science.gov (United States)

    Papanastasiou, Anastasios D; Sirinian, Chaido; Kalofonos, Haralabos P; Repanti, Maria

    2014-01-01

    Metastatic melanoma has a poor prognosis and until today most therapeutic approaches are ineffective. Advances in molecular pathology and genome analysis technologies have led to the identification of genetic events and immune regulatory checkpoints that provide novel targets for pharmaceutical intervention in melanoma. Development of selective mitogen-activated kinase (MAPK) pathway inhibitors was the first major achievement coming from genetic studies that identified a constitutively active MAP kinase pathway and BRAF activating mutations in melanoma. At the same time, the manipulation of immune system checkpoints through monoclonal antibodies changed clinical practice and led to further improvement of patient outcomes. In an effort to further develop melanoma targeted therapies that depend on the genetic profile of a given patient, high-throughput genome wide approaches (next-generation sequencing [NGS], gene arrays, etc) have been employed for the characterization of genetic alterations in the patient's tumor. In the near future, the combined information from the genetic and immune background of an individual will provide the basis for a personalized, highly targeted approach in the treatment of melanoma.

  4. The re-emergence of natural products for drug discovery in the genomics era.

    Science.gov (United States)

    Harvey, Alan L; Edrada-Ebel, RuAngelie; Quinn, Ronald J

    2015-02-01

    Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.

  5. Instrumenting the health care enterprise for discovery research in the genomic era.

    Science.gov (United States)

    Murphy, Shawn; Churchill, Susanne; Bry, Lynn; Chueh, Henry; Weiss, Scott; Lazarus, Ross; Zeng, Qing; Dubey, Anil; Gainer, Vivian; Mendis, Michael; Glaser, John; Kohane, Isaac

    2009-09-01

    Tens of thousands of subjects may be required to obtain reliable evidence relating disease characteristics to the weak effects typically reported from common genetic variants. The costs of assembling, phenotyping, and studying these large populations are substantial, recently estimated at three billion dollars for 500,000 individuals. They are also decade-long efforts. We hypothesized that automation and analytic tools can repurpose the informational byproducts of routine clinical care, bringing sample acquisition and phenotyping to the same high-throughput pace and commodity price-point as is currently true of genome-wide genotyping. Described here is a demonstration of the capability to acquire samples and data from densely phenotyped and genotyped individuals in the tens of thousands for common diseases (e.g., in a 1-yr period: N = 15,798 for rheumatoid arthritis; N = 42,238 for asthma; N = 34,535 for major depressive disorder) in one academic health center at an order of magnitude lower cost. Even for rare diseases caused by rare, highly penetrant mutations such as Huntington disease (N = 102) and autism (N = 756), these capabilities are also of interest.

  6. Advances in targeted and immunobased therapies for colorectal cancer in the genomic era

    Directory of Open Access Journals (Sweden)

    Seow HF

    2016-03-01

    Full Text Available Heng Fong Seow,1 Wai Kien Yip,1 Theodora Fifis2 1Immunology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia; 2Department of Surgery, University of Melbourne, Melbourne, Australia Abstract: Targeted therapies require information on specific defective signaling pathways or mutations. Advances in genomic technologies and cell biology have led to identification of new therapeutic targets associated with signal-transduction pathways. Survival times of patients with colorectal cancer (CRC can be extended with combinations of conventional cytotoxic agents and targeted therapies. Targeting EGFR- and VEGFR-signaling systems has been the major focus for treatment of metastatic CRC. However, there are still limitations in their clinical application, and new and better drug combinations are needed. This review provides information on EGFR and VEGF inhibitors, new therapeutic agents in the pipeline targeting EGFR and VEGFR pathways, and those targeting other signal-transduction pathways, such as MET, IGF1R, MEK, PI3K, Wnt, Notch, Hedgehog, and death-receptor signaling pathways for treatment of metastatic CRC. Additionally, multitargeted approaches in combination therapies targeting negative-feedback loops, compensatory networks, and cross talk between pathways are highlighted. Then, immunobased strategies to enhance antitumor immunity using specific monoclonal antibodies, such as the immune-checkpoint inhibitors anti-CTLA4 and anti-PD1, as well as the challenges that need to be overcome for increased efficacy of targeted therapies, including drug resistance, predictive markers of response, tumor subtypes, and cancer stem cells, are covered. The review concludes with a brief insight into the applications of next-generation sequencing, expression profiling for tumor subtyping, and the exciting progress made in in silico predictive analysis in the development of a prescription strategy for

  7. The significance of a nineteenth century definition in the era of genomics: linitis plastica.

    Science.gov (United States)

    Agnes, Annamaria; Estrella, Jeannelyn S; Badgwell, Brian

    2017-07-05

    Linitis plastica due to gastric adenocarcinoma is a condition with a long history, but still lacks a standardized definition and is commonly confused with Borrmann type IV, Lauren diffuse, and signet-cell type gastric cancer. The absence of a clear definition is a problem when investigating its biological characteristics and role as a possible independent factor for prognosis. Nevertheless, the biological behavior for linitis plastica, which is unique, may be valuable in risk stratification and have implications for treatment. A definition of linitis plastica based on molecular or genomic criteria could represent a useful starting point for investigating new targeted therapies. This literature review of linitis plastica will focus on the current classifications for gastric cancer, illustrating how the concept of linitis plastica relates to them in most cases and identifying a clear and reproducible definition. Moreover, the review will highlight the diagnostic challenges associated with linitis plastica, its prognostic implications, and the therapeutic options available. Future perspectives for its management are also addressed. Linitis plastica is a carcinoma with a scirrhous stroma, involving the submucosal and muscular layers of the stomach even in the absence of mucosal alteration. In most cases, the primary cancer cells are signet-ring cells or scattered cells in the context of a poorly differentiated carcinoma. Diagnosis is challenging. Staging should be thorough, including diagnostic laparoscopy in all cases due to the high incidence of peritoneal involvement. The prognostic significance of linitis plastica is still controversial. Curative-intent surgery, when feasible, should be performed, with a multimodality treatment approach. Cancer-stroma interactions are important features of this disease, and represent attaining potential target for future therapies. Future pathologic assessments of gastric cancer should report the stromal reaction in order to allow

  8. Improving the efficiency and relevance of evidence-based recommendations in the era of whole-genome sequencing: an EGAPP methods update.

    Science.gov (United States)

    Veenstra, David L; Piper, Margaret; Haddow, James E; Pauker, Stephen G; Klein, Roger; Richards, Carolyn Sue; Tunis, Sean R; Djulbegovic, Benjamin; Marrone, Michael; Lin, Jennifer S; Berg, Alfred O; Calonge, Ned

    2013-01-01

    To provide an update on recent revisions to Evaluation of Genomic Applications in Practice and Prevention (EGAPP) methods designed to improve efficiency, and an assessment of the implications of whole genome sequencing for evidence-based recommendation development. Improvements to the EGAPP approach include automated searches for horizon scanning, a quantitative ranking process for topic prioritization, and the development of a staged evidence review and evaluation process. The staged process entails (i) triaging tests with minimal evidence of clinical validity, (ii) using and updating existing reviews, (iii) evaluating clinical validity prior to analytic validity or clinical utility, (iv) using decision modeling to assess potential clinical utility when direct evidence is not available. EGAPP experience to date suggests the following approaches will be critical for the development of evidence based recommendations in the whole genome sequencing era: (i) use of triage approaches and frameworks to improve efficiency, (ii) development of evidence thresholds that consider the value of further research, (iii) incorporation of patient preferences, and (iv) engagement of diverse stakeholders. The rapid advances in genomics present a significant challenge to traditional evidence based medicine, but also an opportunity for innovative approaches to recommendation development.

  9. The role of epidemiology in the era of molecular epidemiology and genomics: Summary of the 2013 AJE-sponsored Society of Epidemiologic Research Symposium.

    Science.gov (United States)

    Kuller, Lewis H; Bracken, Michael B; Ogino, Shuji; Prentice, Ross L; Tracy, Russell P

    2013-11-01

    On June 20, 2013, the American Journal of Epidemiology sponsored a symposium at the Society for Epidemiologic Research's 46th Annual Meeting in Boston, Massachusetts, entitled, "What Is the Role of Epidemiology in the Era of Molecular Biology and Genomics?" The future of epidemiology depends on innovation in generating interesting and important testable hypotheses that are relevant to population health. These new strategies will depend on new technology, both in measurement of agents and environment and in the fields of pathophysiology and outcomes, such as cellular epidemiology and molecular pathology. The populations to be studied, sample sizes, and study designs should be selected based on the hypotheses to be tested and include case-control, cohort, and clinical trials. Developing large mega cohorts without attention to specific hypotheses is inefficient, will fail to address many associations with high-quality data, and may well produce spurious results.

  10. Introduction to the Post-Human Genome Project era, a target for interactions between polygenic and/or multiphenotypical components in cancer control in South America

    Directory of Open Access Journals (Sweden)

    Iscovich José

    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.

  11. Introduction to the Post-Human Genome Project era, a target for interactions between polygenic and/or multiphenotypical components in cancer control in South America

    Directory of Open Access Journals (Sweden)

    José Iscovich

    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.

  12. The Molecular Revolution in Cutaneous Biology: The Era of Genome-Wide Association Studies and Statistical, Big Data, and Computational Topics.

    Science.gov (United States)

    Anbunathan, Hima; Bowcock, Anne M

    2017-05-01

    The investigation of biological systems involving all organs of the body including the skin is in era of big data. This requires heavy-duty computational tools, and novel statistical methods. Microarrays have allowed the interrogation of thousands of common genetic markers in thousands of individuals from the same population (termed genome wide association studies or GWAS) to reveal common variation associated with disease or phenotype. These markers are usually single nucleotide polymorphisms (SNPs) that are relatively common in the population. In the case of dermatological diseases such as alopecia areata, vitiligo, psoriasis and atopic dermatitis, common variants have been identified that are associated with disease, and these provide insights into biological pathways and reveal possible novel drug targets. Other skin phenotypes such as acne, color and skin cancers are also being investigated with GWAS. Analyses of such large GWAS datasets require a consideration of a number of statistical issues including the testing of multiple markers, population substructure, and ultimately a requirement for replication. There are also issues regarding the missing heritability of disease that cannot be entirely explained with current GWAS approaches. Next generation sequencing technologies such as exome and genome sequencing of similar patient cohorts will reveal additional variants contributing to disease susceptibility. However, the data generated with these approaches will be orders of magnitude greater than that those generated with arrays, with concomitant challenges in the identification of disease causing variants. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  13. 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.

  14. 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.

  15. 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.

  16. Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era.

    Science.gov (United States)

    Teng, Jade L L; Tang, Ying; Huang, Yi; Guo, Feng-Biao; Wei, Wen; Chen, Jonathan H K; Wong, Samson S Y; Lau, Susanna K P; Woo, Patrick C Y

    2016-01-01

    Owing to the highly similar phenotypic profiles, protein spectra and 16S rRNA gene sequences observed between three pairs of Tsukamurella species (Tsukamurella pulmonis/Tsukamurella spongiae, Tsukamurella tyrosinosolvens/Tsukamurella carboxy-divorans, and Tsukamurella pseudospumae/Tsukamurella sunchonensis), we hypothesize that and the six Tsukamurella species may have been misclassified and that there may only be three Tsukamurella species. In this study, we characterized the type strains of these six Tsukamurella species by tradition DNA-DNA hybridization (DDH) and "digital DDH" after genome sequencing to determine their exact taxonomic positions. Traditional DDH showed 81.2 ± 0.6% to 99.7 ± 1.0% DNA-DNA relatedness between the two Tsukamurella species in each of the three pairs, which was above the threshold for same species designation. "Digital DDH" based on Genome-To-Genome Distance Calculator and Average Nucleotide Identity for the three pairs also showed similarity results in the range of 82.3-92.9 and 98.1-99.1%, respectively, in line with results of traditional DDH. Based on these evidence and according to Rules 23a and 42 of the Bacteriological Code, we propose that T. spongiae Olson et al. 2007, should be reclassified as a later heterotypic synonym of T. pulmonis Yassin et al. 1996, T. carboxydivorans Park et al. 2009, as a later heterotypic synonym of T. tyrosinosolvens Yassin et al. 1997, and T. sunchonensis Seong et al. 2008 as a later heterotypic synonym of T. pseudospumae Nam et al. 2004. With the advancement of genome sequencing technologies, classification of bacterial species can be readily achieved by "digital DDH" than traditional DDH.

  17. Molecular Marker Development in Post-genomic Era:Leveraging Multiple Resources for Marker Development in Cotton and Other Crops

    Institute of Scientific and Technical Information of China (English)

    KUMPATLA Siva P; SHAH Manali R; MUKHOPADHYAY Snehasis; THOMPSON Steven A; GREENE Thomas W

    2008-01-01

    @@ While the importance of molecular marker technology was realized more than two decades ago,high-throughput marker development came into vogue only after the availability of hundreds of thousands of sequences in public databases.Many examples now exist where markers are being used routinely in breeding programs for marker-assisted selection (MAS) of traits of interest or marker assisted recovery of genome of interest.

  18. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.

    Science.gov (United States)

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  19. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

    Science.gov (United States)

    Orlek, Alex; Stoesser, Nicole; Anjum, Muna F.; Doumith, Michel; Ellington, Matthew J.; Peto, Tim; Crook, Derrick; Woodford, Neil; Walker, A. Sarah; Phan, Hang; Sheppard, Anna E.

    2017-01-01

    Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of ‘accessory genes,’ such as antibiotic resistance genes, as well as ‘backbone’ loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made. PMID:28232822

  20. Molecular Marker Development in Post-genomic Era:Leveraging Multiple Resources for Marker Development in Cotton and Other Crops

    Institute of Scientific and Technical Information of China (English)

    KUMPATLA; Siva; P; SHAH; Manali; R; MUKHOPADHYAY; Snehasis; THOMPSON; Steven; A; GREENE; Thomas; W

    2008-01-01

    While the importance of molecular marker technology was realized more than two decades ago,high-throughput marker development came into vogue only after the availability of hundreds of thousands of sequences in public databases.Many examples now exist where markers are being used routinely in breeding programs for marker-assisted selection(MAS) of traits of interest or marker assisted recovery of genome of interest.Genetic analysis with thousands to tens of thousands of markers is now possible due to the...

  1. 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.

  2. Linkage analysis and the study of Mendelian disease in the era of whole exome and genome sequencing.

    Science.gov (United States)

    Teare, M Dawn; Santibañez Koref, Mauro F

    2014-09-01

    Whole exome and whole genome sequencing are now routinely used in the study of inherited disease, and some of their major successes have been the identification of genes involved in disease predisposition in pedigrees where disease seems to follow Mendelian inheritance patterns. These successes include scenarios where only a single individual was sequenced and raise the question whether linkage analysis has become superfluous. Linkage analysis requires genome-wide genotyping on family-based data, and traditionally the linkage analysis was performed before the targeting sequencing stage. However, methods are emerging that seek to exploit the capability of linkage analysis to integrate data both across individuals and across pedigrees. This ability has been exploited to select samples used for sequencing studies and to identify among the variants uncovered by sequencing those mapping to regions likely to contain the gene of interest and, more generally, to improve variant detection. So, although the formal isolated linkage analysis stage is less commonly seen, when uncovering the genetic basis of Mendelian disease, methods relying heavily on genetic linkage analysis principles are being integrated directly into the whole mapping process ranging from sample selection to variant calling and filtering. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  3. 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.

  4. 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.

  5. Targeting tyrosine kinases in cancer: the converging roles of cytopathology and molecular pathology in the era of genomic medicine.

    Science.gov (United States)

    Dumur, Catherine I; Idowu, Michael O; Powers, Celeste N

    2013-02-01

    Because of knowledge gained in the field of cancer biology, clinicians are currently witnessing an explosion of molecular tests as companion diagnostics to targeted therapies against growth factor receptors and their signaling pathways. Such tests are being applied increasingly to cytology specimens as essential components of genomic medicine, because less invasive diagnostic procedures are becoming the norm. The objective of this review was to present an overview of the current and future role of cytopathology in molecular diagnostics, including the adequacy of cytology specimens for such studies. The authors also discuss the critical methodologic aspects of the molecular assays used for the selection of tyrosine kinase treatment for oncology patients. Copyright © 2012 American Cancer Society.

  6. 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.

  7. Epidemiological studies in the information and genomics era: experience of the Clinical Genome of Cancer Project in São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Wünsch-Filho V.

    2006-01-01

    Full Text Available Genomics is expanding the horizons of epidemiology, providing a new dimension for classical epidemiological studies and inspiring the development of large-scale multicenter studies with the statistical power necessary for the assessment of gene-gene and gene-environment interactions in cancer etiology and prognosis. This paper describes the methodology of the Clinical Genome of Cancer Project in São Paulo, Brazil (CGCP, which includes patients with nine types of tumors and controls. Three major epidemiological designs were used to reach specific objectives: cross-sectional studies to examine gene expression, case-control studies to evaluate etiological factors, and follow-up studies to analyze genetic profiles in prognosis. The clinical groups included patients' data in the electronic database through the Internet. Two approaches were used for data quality control: continuous data evaluation and data entry consistency. A total of 1749 cases and 1509 controls were entered into the CGCP database from the first trimester of 2002 to the end of 2004. Continuous evaluation showed that, for all tumors taken together, only 0.5% of the general form fields still included potential inconsistencies by the end of 2004. Regarding data entry consistency, the highest percentage of errors (11.8% was observed for the follow-up form, followed by 6.7% for the clinical form, 4.0% for the general form, and only 1.1% for the pathology form. Good data quality is required for their transformation into useful information for clinical application and for preventive measures. The use of the Internet for communication among researchers and for data entry is perhaps the most innovative feature of the CGCP. The monitoring of patients' data guaranteed their quality.

  8. Sexual and apomictic plant reproduction in the genomics era: exploring the mechanisms potentially useful in crop plants.

    Science.gov (United States)

    Dwivedi, Sangam L; Perotti, Enrico; Upadhyaya, Hari D; Ortiz, Rodomiro

    2010-12-01

    Arabidopsis, Mimulus and tomato have emerged as model plants in researching genetic and molecular basis of differences in mating systems. Variations in floral traits and loss of self-incompatibility have been associated with mating system differences in crops. Genomics research has advanced considerably, both in model and crop plants, which may provide opportunities to modify breeding systems as evidenced in Arabidopsis and tomato. Mating system, however, not recombination per se, has greater effect on the level of polymorphism. Generating targeted recombination remains one of the most important factors for crop genetic enhancement. Asexual reproduction through seeds or apomixis, by producing maternal clones, presents a tremendous potential for agriculture. Although believed to be under simple genetic control, recent research has revealed that apomixis results as a consequence of the deregulation of the timing of sexual events rather than being the product of specific apomixis genes. Further, forward genetic studies in Arabidopsis have permitted the isolation of novel genes reported to control meiosis I and II entry. Mutations in these genes trigger the production of unreduced or apomeiotic megagametes and are an important step toward understanding and engineering apomixis.

  9. From dissection of disease pathogenesis to elucidation of mechanisms of targeted therapies: leukemia research in the genomic era

    Institute of Scientific and Technical Information of China (English)

    Guang-biao ZHOU; Guo LI; Sai-juan CHEW; Zhu CHEN

    2007-01-01

    Leukemia is a group of heterozygous diseases of hematopoietic stem/progenitor cells that involves dynamic change in the genome. Dissection of genetic abnor-malities critical to leukemia initiation provides insights into the elusive leukemogenesis, identifies distinct subsets of leukemia and predicts prognosisindividually, and can also provide rational therapeutic targets for curative approaches. The past three decades have seen tremendous advances in the analysis of genotype-phenotype connection of leukemia, and in the identifica-tion of molecular biomarkers for leukemia subtypes. Intriguingly, differentiation therapy, targeted therapy and chemotherapy have turned several subtypes of leukemia from highly fatal to highly curable. The use of all-trans retinoic acid and arsenic trioxide, which trigger degradation of PML-RARα, the causative fusion protein generated by t (15;17) translocation in acute promyelocytic leukemia (APL),has led to a dramatic improvement of APL clinical outcome. Imatinib mesylate/Gleevec/STI571, which inhibits the tyrosine kinase activity of BCR-ABL oncoprotein, has now become the new gold standard for the treatmtent of chronic myeloid leukemia. Optimal use of chemotherapeutic agents together with a strin-gent application of prognostic factors for risk-directed therapy in clinical trials has resulted in a steady improvement in the treatment outcome of acute lympho-blastic leukemia. Hence, the pace of progress extrapolates to a prediction of leukemia control in the twenty-first century.

  10. 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

  11. 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

  12. 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...

  13. Nueva Era

    Directory of Open Access Journals (Sweden)

    Alma Mancilla

    2004-01-01

    Full Text Available El artículo aborda la problemática de la interpretación de las nuevas religiones a través del caso del estudio de la Nueva Era. Se aborda en principio la cuestión de la definición de la Nueva Era, y la necesidad de tomar en cuenta los diferentes puntos de vista por parte de los diversos actores que contribuyen a su construcción como objeto de análisis sociológico. Enseguida, se trata la problemática del análisis sobre el terreno con algunos puntos de particular interés para el análisis de la experiencia religiosa: la subjetividad y la reflexividad en el análisis etnográfico, la postura del ateísmo metodológico y la exclusión epistemológica con respecto a los informantes. Por último, se presentan algunos de los problemas a superar para la realización un análisis cuantitativo de la Nueva Era.

  14. Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing.

    Science.gov (United States)

    Xue, Yuan; Ankala, Arunkanth; Wilcox, William R; Hegde, Madhuri R

    2015-06-01

    Next-generation sequencing is changing the paradigm of clinical genetic testing. Today there are numerous molecular tests available, including single-gene tests, gene panels, and exome sequencing or genome sequencing. As a result, ordering physicians face the conundrum of selecting the best diagnostic tool for their patients with genetic conditions. Single-gene testing is often most appropriate for conditions with distinctive clinical features and minimal locus heterogeneity. Next-generation sequencing-based gene panel testing, which can be complemented with array comparative genomic hybridization and other ancillary methods, provides a comprehensive and feasible approach for heterogeneous disorders. Exome sequencing and genome sequencing have the advantage of being unbiased regarding what set of genes is analyzed, enabling parallel interrogation of most of the genes in the human genome. However, current limitations of next-generation sequencing technology and our variant interpretation capabilities caution us against offering exome sequencing or genome sequencing as either stand-alone or first-choice diagnostic approaches. A growing interest in personalized medicine calls for the application of genome sequencing in clinical diagnostics, but major challenges must be addressed before its full potential can be realized. Here, we propose a testing algorithm to help clinicians opt for the most appropriate molecular diagnostic tool for each scenario.

  15. Research Progress of Trangsgenic Mice in Post-genomic Era in Life Science%后基因组时代转基因小鼠在生命科学中的研究进展

    Institute of Scientific and Technical Information of China (English)

    马微; 赵伟; 李丹; 汪坤福

    2011-01-01

    Following arrival of the post-genomics era,transgenic animals have become the most effective novel experimental model, and the application field of Transgenic mice ( Tg mice ) is becoming more and more extensive. The study of the functional genomics using Tg mice is called post-genomics as well. The in vivo study of genome and it's regulatory role has overcome the limitations and one-sidedness in the field. The technical platform for preparation of genetically engineered mice has been formed scaled up and commercialized both at home and abroad. The article here is an overview of the application, development and the status and trend of Tg mice at home and oversea.%随着后基因组时代的到来,转基因动物已成为新兴的最有效的动物实验模型,转基因小鼠应用领域越来越广泛.利用转基因小鼠,从生物整体上研究基因组的功能学,又称为后基因组学.活体研究各基因及调控作用,克服了原来此领域研究的局限性和片面性.国内外基因工程小鼠的制备已经形成了技术平台,发展规模化、商业化.现就转基因小鼠的发展、应用及转基因小鼠国内外现状和发展趋势予以综述.

  16. The search for novel insecticide targets in the post-genomics era, with a specific focus on G-protein coupled receptors

    Directory of Open Access Journals (Sweden)

    Michelle Ngai

    Full Text Available Insects are considered pests globally, implicated in the destruction of agricultural fields and transmission of pathogens that cause deadly human diseases, such as dengue, Zika and malaria. The diversity of the insecticide arsenal has remained stagnant for decades, but the recent rise of insecticide resistance fueled the discovery of novel modes of action, and the power of genomics has reinvigorated this search. This review discusses the importance of comparative and functional insect genomics in the identification of potential gene targets for an insecticidal mode of action with low off-target toxicity. Due to the global participation in the sequencing and annotation of insect genomes, the targeting of specific genes with molecular tools like RNAi and CRISPR/Cas9 for genome engineering and consequent functional identification and validation has become more efficient. While there are multiple avenues to explore for insecticidal candidates, this review identifies G-protein coupled receptors as attractive targets, and hones in on the octopamine and dopamine receptors due to their potential.

  17. The search for novel insecticide targets in the post-genomics era, with a specific focus on G-protein coupled receptors

    Science.gov (United States)

    Ngai, Michelle; McDowell, Mary Ann

    2017-01-01

    Insects are considered pests globally, implicated in the destruction of agricultural fields and transmission of pathogens that cause deadly human diseases, such as dengue, Zika and malaria. The diversity of the insecticide arsenal has remained stagnant for decades, but the recent rise of insecticide resistance fueled the discovery of novel modes of action, and the power of genomics has reinvigorated this search. This review discusses the importance of comparative and functional insect genomics in the identification of potential gene targets for an insecticidal mode of action with low off-target toxicity. Due to the global participation in the sequencing and annotation of insect genomes, the targeting of specific genes with molecular tools like RNAi and CRISPR/Cas9 for genome engineering and consequent functional identification and validation has become more efficient. While there are multiple avenues to explore for insecticidal candidates, this review identifies G-protein coupled receptors as attractive targets, and hones in on the octopamine and dopamine receptors due to their potential. PMID:28076467

  18. Genomics era and complex disorders: Implications of GWAS with special reference to coronary artery disease, type 2 diabetes mellitus, and cancers

    Directory of Open Access Journals (Sweden)

    R Pranavchand

    2016-01-01

    Full Text Available The Human Genome Project (HGP has identified millions of single nucleotide polymorphisms (SNPs and their association with several diseases, apart from successfully characterizing the Mendelian/monogenic diseases. However, the dissection of precise etiology of complex genetic disorders still poses a challenge for human geneticists. This review outlines the landmark results of genome-wide association studies (GWAS with respect to major complex diseases - Coronary artery disease (CAD, type 2 diabetes mellitus (T2DM, and predominant cancers. A brief account on the current Indian scenario is also given. All the relevant publications till mid-2015 were accessed through web databases such as PubMed and Google. Several databases providing genetic information related to these diseases were tabulated and in particular, the list of the most significant SNPs identified through GWAS was made, which may be useful for designing studies in functional validation. Post-GWAS implications and emerging concepts such as epigenomics and pharmacogenomics were also discussed.

  19. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  20. 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

  1. G1P[8] species A rotavirus over 27 years--pre- and post-vaccination eras--in Brazil: full genomic constellation analysis and no evidence for selection pressure by Rotarix® vaccine.

    Science.gov (United States)

    Silva, Marcelle Figueira Marques da; Rose, Tatiana Lundgren; Gómez, Mariela Martínez; Carvalho-Costa, Filipe Anibal; Fialho, Alexandre Madi; Assis, Rosane Maria Santos de; Andrade, Juliana da Silva Ribeiro de; Volotão, Eduardo de Mello; Leite, José Paulo Gagliardi

    2015-03-01

    Epidemiological data on species A rotavirus (RVA) infections have demonstrated the genetic diversity of strains circulating worldwide. Many G and P genotype combinations have been described over the years, varying regionally and temporally, especially in developing countries. However, the most common G and P genotype combinations identified in RVA human strains worldwide are G1P[8], G2P[4], G3P[8], G4P[8] and G9P[8]. RVA genotype G1P[8] strains are responsible for more than 50% of child infections worldwide and component of the two vaccines (Rotarix® [RV1] and RotaTeq® [RV5]) licensed globally. For a better understanding of the evolutionary mechanisms of this genotype in Brazil, phylogenetic analyses based on the 11 RVA genome segments (genomic constellation) from 90 G1P[8] RVA strains collected in two eras - (i) pre-vaccination with RV1 (1996-February 2006); (ii) post-vaccination (March 2006-2013) - in different Brazilian states were performed. The results showed the Wa-like genomic constellation of the Brazilian G1P[8] strains with a I1-R1-C1-M1-A1-N1-T1-E1-H1 specificity, except for two strains (rj14055-07 and ba19030-10) that belong to a I1-R1-C1-M1-A1-N1-T3-E1-H1 genomic constellation, evidencing the occurrence of reassortment (Wa-like×AU-1-like) of the NSP3 gene. Reassortment events were also demonstrated between Brazilian G1P[8] strains and the RV1 vaccine strain in some genes in vaccinated and unvaccinated children. VP7 and VP8* antigenic site analysis showed that the amino acid substitutions observed in samples collected after the introduction of RV1 in Brazil were already detected in samples collected in the 1980s and 1990s, suggesting that mass Brazilian RV1 vaccination had no impact on the diversity observed inside antigenic sites for these two proteins.

  2. Toward 959 nematode genomes

    National Research Council Canada - National Science Library

    Kumar, Sujai; Koutsovoulos, Georgios; Kaur, Gaganjot; Blaxter, Mark

    2012-01-01

    The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism...

  3. 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

  4. Nutrição no pós-genoma: fundamentos e aplicações de ferramentas ômicas Nutrition in the post-genome era: 'omic' tools basics and applications

    Directory of Open Access Journals (Sweden)

    Eliane Fialho

    2008-12-01

    Full Text Available Após seqüenciamento do genoma humano, os estudos genômicos têm se voltado à elucidação das funções de todos os genes, bem como à caracterização de suas interações com fatores ambientais. A nutrigenômica surgiu no contexto do pós-genoma humano e é considerada área-chave para a nutrição nesta década. Seu foco de estudo baseia-se na interação gene-nutriente. Esta ciência recente tem como objetivo principal o estabelecimento de dietas personalizadas, com base no genótipo, para a promoção da saúde e a redução do risco de doenças crônicas não transmissíveis como as cardiovasculares, o câncer, o diabetes, entre outras. Nesse contexto, é fundamental a aplicação na área de nutrição das ferramentas de genômica funcional para análise do transcritoma (transcritômica, do proteoma (proteômica e do metaboloma (metabolômica. As aplicabilidades dessas metodologias em estudos nutricionais parecem ilimitadas, pois podem ser conduzidas em cultura de células, modelos de experimentação em animais, estudos pré-clinicos e clínicos. Tais técnicas apresentam potencial para identificar biomarcadores que respondem especificamente a um determinado nutriente ou composto bioativo dos alimentos e para estabelecer as melhores recomendações dietéticas individuais para redução do risco das doenças crônicas não transmissíveis e promoção da saúde.After sequencing the human genome, genomic studies have been focusing on elucidating the function of all genes, as well as characterizing their interactions with environmental factors. Nutrigenomics emerged in the pos-genome era and is considered a key-area for nutrition in the present decade. Its research focus is nutrient-gene interaction. The main objective of this recent science is to establish personalized genotype-based diets that promote health and reduce the risk of non-communicable chronic diseases such as cardiovascular diseases, cancer, diabetes and others. In this

  5. Primate molecular phylogenetics in a genomic era.

    Science.gov (United States)

    Ting, Nelson; Sterner, Kirstin N

    2013-02-01

    A primary objective of molecular phylogenetics is to use molecular data to elucidate the evolutionary history of living organisms. Dr. Morris Goodman founded the journal Molecular Phylogenetics and Evolution as a forum where scientists could further our knowledge about the tree of life, and he recognized that the inference of species trees is a first and fundamental step to addressing many important evolutionary questions. In particular, Dr. Goodman was interested in obtaining a complete picture of the primate species tree in order to provide an evolutionary context for the study of human adaptations. A number of recent studies use multi-locus datasets to infer well-resolved and well-supported primate phylogenetic trees using consensus approaches (e.g., supermatrices). It is therefore tempting to assume that we have a complete picture of the primate tree, especially above the species level. However, recent theoretical and empirical work in the field of molecular phylogenetics demonstrates that consensus methods might provide a false sense of support at certain nodes. In this brief review we discuss the current state of primate molecular phylogenetics and highlight the importance of exploring the use of coalescent-based analyses that have the potential to better utilize information contained in multi-locus data.

  6. Enabling functional genomics with genome engineering.

    Science.gov (United States)

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.

  7. Ecological recovery in ERA

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... ecological recovery for any assessed products, and invasive alien species that are harmful for plant health. This framework proposes an integrative approach based on well-defined specific protection goals, scientific knowledge derived by means of experimentation, modelling and monitoring, and the selection...... 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...

  8. Research progress in Shigella in the postgenomic era

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Gram-negative,facultative intracellular anaerobes of the genus Shigella,the principal etiologic agents of shigellosis,continue to pose a threat to public health. Shigellosis causes 1.1 million deaths with over 164 million annual cases. The Shigella spp. can be divided into four serogroups:Shigella dysenteriae,Shigella flexneri, Shigella boydii and Shigella sonnei. The completion of seven Shigella genome sequences of representative strains from each of the Shigella species has introduced an era of whole-genome study.This paper reviews contemporary understanding of genomics,transcriptomics,proteomics and the structural biology of Shigella.

  9. Second Nuclear Era

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. 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.

  11. Nasionalisme di Era Internet

    Directory of Open Access Journals (Sweden)

    Danu Widhyatmoko

    2015-07-01

    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.

  12. Ancient genomics.

    Science.gov (United States)

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence 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, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  13. Nano-Biodevice for Genomic Medicine and Systems Biology%纳米生物装置在基因药物和系统生物学研究中的应用

    Institute of Scientific and Technical Information of China (English)

    BABA Yoshinobu

    2004-01-01

    Since human genome sequencing has been almost completed, human genome project will quickly move on to the post genome sequencing era, including single nucleotide polymorphism (SNP) analysis, functional genomics, mutation analysis, transeriptome analysis, proteome analy-

  14. Three eras of planetary exploration

    Science.gov (United States)

    Ingersoll, Andrew P.

    2017-01-01

    The number of known exoplanets rose from zero to one in the mid-1990s, and has been doubling approximately every two years ever since. Although this can justifiably be called the beginning of an era, an earlier era began in the 1960s when humankind began exploring the Solar System with spacecraft. Even earlier than that, the era of modern scientific study of the Solar System began with Copernicus, Galileo, Brahe, Kepler and Newton. These eras overlap in time, and many individuals have worked across all three. This Review explores what the past can tell us about the future and what the exploration of the Solar System can teach us about exoplanets, and vice versa. We consider two primary examples: the history of water on Venus and Mars; and the study of Jupiter, including its water, with the Juno spacecraft.

  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. 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.

  17. Prospects for the management of insect pests in the genomic era%基因组学时代害虫治理的研究进展及前景

    Institute of Scientific and Technical Information of China (English)

    彭露; 何玮毅; 夏晓峰; 谢苗; 柯富士; 尤士骏; 黄宇萍; 尤民生

    2015-01-01

    随着 DNA 测序技术的不断更新和生物信息学的快速发展,昆虫基因组学的研究与日俱增,提高了人们对种群遗传学和进化生态学的理解和认识,促进了对重要农业害虫的适应性和致害机理的研究,为安全、有效、可持续地开展害虫综合治理提供了新思路和新手段。近两年来,全球发布的昆虫基因组数量每年可达30个。在遗传学、生态学和进化论等生命科学基本原理和方法的指导下,基因组学的研究为揭示害虫遗传变异的内在机制、生态适应性策略和种群变动规律提供了重要的数据和信息资源,同时催生了一系列害虫治理新技术和新方法的研发与应用。为了进一步促进和加强基因组时代的害虫治理研究,拓展该领域研究的广度与深度,本文就昆虫基因组的研究,昆虫与植物协同进化模式及其互作机理,昆虫免疫和抗药性分子机制,以及害虫防治新技术等方面进行了综述,旨在为了解基因组时代害虫治理的研究进展及前景提供参考,对进一步改进害虫生态控制的策略和措施也具有指导意义。%The rapid development of DNA sequencing technology and bioinformatics has resulted in an increase in genomic studies of insects. Better knowledge of population genetics and evolutionary ecology has allowed better understanding of the local/global adaptation and infestation mechanisms of key agricultural pests, thereby providing novel strategies and approaches for the implementation of integrated pest management (IMP) in a safe, cost-effective and sustainable manner. Genome information has been released for approximately 30 insect species annually over the past two years. Genomic-related studies of agricultural insect herbivores generate a great deal of important data, and reveal the mechanisms underlying the genetic variation, strategic adaptation, and the population dynamics, of these pests. Such

  18. 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.

  19. 后基因组时代的丝状真菌基因组学与代谢工程%Genomics and metabolic engineering of filamentous fungi in the postgenomics era

    Institute of Scientific and Technical Information of China (English)

    陈献忠; 沈微; 樊游; 王正祥

    2011-01-01

    Filamentous fungi are used in a variety of industrial processes including the production of primary metabolites (e.g., organic acid, vitamins, and extracellular enzymes) and secondary metabolites (e.g., antibiotics, alkaloids, and gibberellins). Moreover, filamentous fungi have become preferred cell factories for production of foreign (heterologous) proteins in biotechnology in recent years. Compared to bacterial and yeast hosts, filamentous fungi showed predominant features such as the ability of growing on rather simple and inexpensive substrates, producing and secreting exceptionally large amounts of proteins, post-translational modifications, and GRAS (generally regarded as safe) approval. Therefore, the exploration of filamentous fungi has been attractive recently. This review summarizes the recent development in genomics, comparative genomics, transcriptomics, proteomics and metabolomics of filamentous fungi, and describes their applications and functions in reconstruction of metabolic network, discovery of novel proteins and genes, investigation of cell physiological and biochemical reactions, and strain breeding. This review also analyzes the bottlenecks of heterologous proteinexpression in filamentous fungi. Furthermore, special emphasis is given on the strategies for improving the protein production, including fusion expression of heterologous proteins, RNAi technology, manipulations of secretion pathways, codon optimization of foreign genes, and screening of protease mutants. Lastly, this review proposes the future direction of metabolic engineering of filamentous fungi.%丝状真菌不仅是传统发酵工业中抗生素、酶制剂和有机酸的主要生产者,而且也是代谢工程育种中异源蛋白表达的重要细胞工厂.丝状真菌的遗传修饰和代谢工程研究是现代工业生物技术领域最具活力的研究方向之一.特别是与细菌和酵母相比,丝状真菌在细胞生长、营养需求、环境适应性、翻译后

  20. 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

  1. Data on Vietnam Era Veterans.

    Science.gov (United States)

    Veterans Administration, Washington, DC. Office of the Controller.

    Statistical data are presented on Vietnam era veterans for the following topics: employment status, medical status, compensation and pension, education, housing assistance, expenditures, and demographic information. The estimated number and age of veterans in civil life, categorized by sex and state, and the educational attainment of veterans at…

  2. Microbial genomics: from sequence to function.

    OpenAIRE

    Schwartz, I

    2000-01-01

    The era of genomics (the study of genes and their function) began a scant dozen years ago with a suggestion by James Watson that the complete DNA sequence of the human genome be determined. Since that time, the human genome project has attracted a great deal of attention in the scientific world and the general media; the scope of the sequencing effort, and the extraordinary value that it will provide, has served to mask the enormous progress in sequencing other genomes. Microbial genome seque...

  3. Manajemen Pendidikan dalam Era Reformasi

    Directory of Open Access Journals (Sweden)

    Willem Mantja

    2016-02-01

    Full Text Available Planning, Organizing, actuating, and controlling are the functions of educational management of all kinds of fields of management. The differences between educational management and others are in the components of its substances. Educational management components include instructional, personnel, student, facilitation, financial, include and school public relation management. The educational managers in the reform era require a competence and managerial skills to perform their jobs as professional managers

  4. The Era of Super Capitalism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The world has entered the "super capitalism" era when one third of its economic activities are controlled by less than 3 percent of global financial capital. This year,a global economic recession,triggered by the U.S. subprime mortgage crisis,seems unavoidable. To tackle international financial problems,Tao Dong,Chief Economist for Asia at Credit Suisse First Boston in Hong Kong,shared his insights with China Business Journal. Excerpts follow.

  5. 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

  6. Quality Assessment of Domesticated Animal Genome Assemblies.

    Science.gov (United States)

    Seemann, Stefan E; Anthon, Christian; Palasca, Oana; Gorodkin, Jan

    2015-01-01

    The era of high-throughput sequencing has made it relatively simple to sequence genomes and transcriptomes of individuals from many species. In order to analyze the resulting sequencing data, high-quality reference genome assemblies are required. However, this is still a major challenge, and many domesticated animal genomes still need to be sequenced deeper in order to produce high-quality assemblies. In the meanwhile, ironically, the extent to which RNAseq and other next-generation data is produced frequently far exceeds that of the genomic sequence. Furthermore, basic comparative analysis is often affected by the lack of genomic sequence. Herein, we quantify the quality of the genome assemblies of 20 domesticated animals and related species by assessing a range of measurable parameters, and we show that there is a positive correlation between the fraction of mappable reads from RNAseq data and genome assembly quality. We rank the genomes by their assembly quality and discuss the implications for genotype analyses.

  7. Imaging genomics of Glioblastoma: state of the art bridge between genomics and neuroradiology.

    Science.gov (United States)

    ElBanan, Mohamed G; Amer, Ahmed M; Zinn, Pascal O; Colen, Rivka R

    2015-02-01

    Glioblastoma (GBM) is the most common and most aggressive primary malignant tumor of the central nervous system. Recently, researchers concluded that the "one-size-fits-all" approach for treatment of GBM is no longer valid and research should be directed toward more personalized and patient-tailored treatment protocols. Identification of the molecular and genomic pathways underlying GBM is essential for achieving this personalized and targeted therapeutic approach. Imaging genomics represents a new era as a noninvasive surrogate for genomic and molecular profile identification. This article discusses the basics of imaging genomics of GBM, its role in treatment decision-making, and its future potential in noninvasive genomic identification.

  8. The bacterial species definition in the genomic era

    National Research Council Canada - National Science Library

    Konstantinos T Konstantinidis; Alban Ramette; James M Tiedje

    2006-01-01

    .... Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations...

  9. Understanding cardiac electrical phenotypes in the genomic era

    NARCIS (Netherlands)

    A. Milano

    2015-01-01

    Sudden cardiac death (SCD) is defined as unexpected death due to a cardiac cause. It most often results from life-threatening ventricular fibrillation (VF) and ranks among the most common causes of death worldwide, with an incidence in the community varying between 0.6 and >1.4 per 1,000 individuals

  10. Starch-binding domains in the post-genome era.

    Science.gov (United States)

    Machovic, M; Janecek, S

    2006-12-01

    Starch belongs to the most abundant biopolymers on Earth. As a source of energy, starch is degraded by a large number of various amylolytic enzymes. However, only about 10% of them are capable of binding and degrading raw starch. These enzymes usually possess a distinct sequence-structural module, the so-called starchbinding domain (SBD). In general, all carbohydrate-binding modules (CBMs) have been classified into the CBM families. In this sequence-based classification the individual types of SBDs have been placed into seven CBM families: CBM20, CBM21, CBM25, CBM26, CBM34, CBM41 and CBM45. The family CBM20, known also as a classical C-terminal SBD of microbial amylases, is the most thoroughly studied. The three-dimensional structures have already been determined by X-ray crystallography or nuclear magnetic resonance for SBDs from five CBM families (20, 25, 26, 34 and 41), and the structure of the CBM21 has been modelled. Despite differences among the amino acid sequences, the fold of a distorted beta-barrel seems to be conserved together with a similar way of substrate binding (mainly stacking interactions between aromatic residues and glucose rings). SBDs have recently been discovered in many non-amylolytic proteins. These may, for example, have regulatory functions in starch metabolism in plants or glycogen metabolism in mammals. SBDs have also found practical uses.

  11. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications

    OpenAIRE

    Imam, Jahangir; Singh, Puneet K.; Shukla, Pratyoosh

    2016-01-01

    Deciphering plant–microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in ...

  12. Proteomics or Genomics: A New Era in Periodontics

    Directory of Open Access Journals (Sweden)

    Sharmila Khopade

    2013-01-01

    Full Text Available Proteins are the building blocks for both microorganisms and periodontium. Periodontitis is the result of complex interrelationship between infectious agents and host factors. The onset, progression and severity of periodontal disease are mainly mediated by various protein molecules. The study of proteins as biomarkers in periodontal diseases has increased attention during the last few years. The proteins involved in pathogenesis of periodontal disease can be used as biomarkers. The knowledge of various proteins involved in periodontal disease pathogenesis can be used in the diagnosis, prevention and treatment of periodontal diseases.

  13. Bringing the fathead minnow into the genomic era

    Science.gov (United States)

    The fathead minnow is a well-established ecotoxicological model organism that has been widely used for regulatory ecotoxicity testing and research for over a half century. While a large amount of molecular information has been gathered on the fathead minnow over the years, the la...

  14. Dissecting complex behaviours in the post-genomic era

    NARCIS (Netherlands)

    Kas, Martien J H; Van Ree, Jan M

    2004-01-01

    Identifying gene functions in behaviours has so far relied mainly on achievements in the field of molecular genetics. Further progress can be made by developing new approaches that allow refinement of behavioural phenotypes. The current availability of several thousand different mutant mice challeng

  15. 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.

  16. Galactoseismology in the GAIA Era

    CERN Document Server

    Chakrabarti, Sukanya

    2016-01-01

    The GAIA satellite will provide unprecedented phase-space information for our Galaxy and enable a new era of Galactic dynamics. We may soon see successful realizations of Galactoseismology, i.e., inferring the characteristics of the Galactic potential and sub-structure from a dynamical analysis of observed perturbations in the gas or stellar disk of the Milky Way. Here, we argue that to maximally take advantage of the GAIA data and other complementary surveys, it is necessary to build comprehensive models for both the stars and the gas. We outline several key morphological puzzles of the Galactic disk and proposed solutions that may soon be tested.

  17. Genome evolution in Reptilia, the sister group of mammals.

    Science.gov (United States)

    Janes, Daniel E; Organ, Christopher L; Fujita, Matthew K; Shedlock, Andrew M; Edwards, Scott V

    2010-01-01

    The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.

  18. Phototroph genomics ten years on.

    Science.gov (United States)

    Raymond, Jason; Swingley, Wesley D

    2008-07-01

    The onset of the genome era means different things to different people, but it is clear that this new age brings with it paradigm shifts that will forever affect biological research. Less clear is just how these shifts are changing the scope and scale of research. Are gigabases of raw data more useful than a single well-understood gene? Do we really need a full genome to understand the physiology of a single organism? The photosynthetic field is poised at the periphery of the bulk of genome sequencing work--understandably skewed toward health-related disciplines--and, as such, is subject to different motivations, limitations, and primary focus for each new genome. To understand some of these differences, we focus here on various indicators of the impact that genomics has had on the photosynthetic community, now a full decade since the publication of the first photosynthetic genome. Many useful indicators are indexed in public databases, providing pre- and post-genome sequence snapshots of changes in factors such as publication rate, number of proteins characterized, and sequenced genome coverage versus known diversity. As more genomes are sequenced and metagenomic projects begin to pour out billions of bases, it becomes crucial to understand how to harness this data in order to accumulate possible benefits and avoid possible pitfalls, especially as resources become increasingly directed toward natural environments governed by photosynthetic activity, ranging from hot springs to tropical forest ecosystems to the open ocean.

  19. 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

  20. 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

  1. 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)

  2. 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.

  3. ERA [Material gráfico

    OpenAIRE

    Fundación para la Etnografía y el Desarrollo de la Artesanía Canaria

    1990-01-01

    ALTERACIONES NATURALES A CAUSA DE LA COLONIZACION VEGETAL EN EL INTERIOR DE LA ERA. PRESENTA AUSENCIA DE ALGUNAS LAJAS. ASCENDEMOS POR LA CARRETERA QUE DISCURRE POR EL FONDO DEL BARRANCO HASTA LLEGAR A LA ZONA DENOMINADA CUEVA BERMEJA, JUNTO AL RESTAURANTE "EL CENTRO" Y LA ERMITA. LA ERA SE ENCUENTRAL LADO DEL COLEGIO. Antiguedad: SIGLO XX Calificación del suelo: RÚSTICO DE PROTECCIÓN DE ENTORNOS Clasificación del suelo: RÚSTICO Declaración BIC:No ERA DE PLANTA CIRCULAR RODE...

  4. 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.

  5. A new era of thromboelastometry.

    Science.gov (United States)

    Crochemore, Tomaz; Piza, Felipe Maia de Toledo; Rodrigues, Roseny Dos Reis; Guerra, João Carlos de Campos; Ferraz, Leonardo José Rolim; Corrêa, Thiago Domingos

    2017-06-12

    Severe hemorrhage with necessity of allogeneic blood transfusion is common complication in intensive care unit and is associated with increased morbidity and mortality. Prompt recognition and treatment of bleeding causes becomes essential for the effective control of hemorrhage, rationalizing the use of allogeneic blood components, and in this way, preventing an occurrence of their potential adverse effects. Conventional coagulation tests such as prothrombin time and activated partial thromboplastin time present limitations in predicting bleeding and guiding transfusion therapy in critically ill patients. Viscoelastic tests such as thromboelastography and rotational thromboelastometry allow rapid detection of coagulopathy and goal-directed therapy with specific hemostatic drugs. The new era of thromboelastometry relies on its efficacy, practicality, reproducibility and cost-effectiveness to establish itself as the main diagnostic tool and transfusion guide in patients with severe active bleeding. RESUMO A hemorragia grave com necessidade de transfusão de sangue e componentes é uma complicação frequente na unidade de terapia intensiva e está associada ao aumento da morbidade e da mortalidade. A identificação adequada e o tratamento precoce da causa específica da coagulopatia tornam-se fundamentais para o controle efetivo da hemorragia, racionalizando a utilização de sangue e componentes, e desta forma, prevenindo a ocorrência de efeitos adversos. Testes convencionais da coagulação (tempo de ativação de protrombina e tempo de tromboplastina parcial ativada) apresentam limitações para prever sangramento e guiar a terapia transfusional em pacientes graves. Testes viscoelásticos como a tromboelastografia e tromboelastometria rotacional permitem a rápida detecção da coagulopatia e orientam a terapia de forma individualizada, alvo dirigida com drogas hemostáticas específicas. A nova era da tromboelastometria confia na sua eficácia, praticidade

  6. Genetics and genomics: impact on perinatal nursing.

    Science.gov (United States)

    Lewis, Judith A

    2011-01-01

    In 1953, Watson and Crick first described the structure of the DNA molecule, an event that led to a new understanding of the nature of heredity. Just 50 years later, a conference was held in Bethesda, Maryland to announce the completion of the sequencing of the human genome. The era of genomic healthcare has begun, and it has profound implications for nursing education, nursing practice, and nursing research. This article will highlight some important areas in perinatal and neonatal nursing that have been affected by genetics and genomics, as well as some emerging areas of research that will be relevant to perinatal and neonatal nursing.

  7. Functional genomics of intracellular bacteria.

    Science.gov (United States)

    de Barsy, Marie; Greub, Gilbert

    2013-07-01

    During the genomic era, a large amount of whole-genome sequences accumulated, which identified many hypothetical proteins of unknown function. Rapidly, functional genomics, which is the research domain that assign a function to a given gene product, has thus been developed. Functional genomics of intracellular pathogenic bacteria exhibit specific peculiarities due to the fastidious growth of most of these intracellular micro-organisms, due to the close interaction with the host cell, due to the risk of contamination of experiments with host cell proteins and, for some strict intracellular bacteria such as Chlamydia, due to the absence of simple genetic system to manipulate the bacterial genome. To identify virulence factors of intracellular pathogenic bacteria, functional genomics often rely on bioinformatic analyses compared with model organisms such as Escherichia coli and Bacillus subtilis. The use of heterologous expression is another common approach. Given the intracellular lifestyle and the many effectors that are used by the intracellular bacteria to corrupt host cell functions, functional genomics is also often targeting the identification of new effectors such as those of the T4SS of Brucella and Legionella.

  8. 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.

  9. Paleogenomic data suggest mammal-like genome size in the ancestral amniote and derived large genome size in amphibians.

    Science.gov (United States)

    Organ, C L; Canoville, A; Reisz, R R; Laurin, M

    2011-02-01

    An unsolved question in evolutionary genomics is whether amniote genomes have been expanding or contracting since the common ancestor of this diverse group. Here, we report on the polarity of amniote genome size evolution using genome size estimates for 14 extinct tetrapod genera from the Paleozoic and early Mesozoic Eras using osteocyte lacunae size as a correlate. We find substantial support for a phylogenetically controlled regression model relating genome size to osteocyte lacunae size (P of slopes amphibians, contractions along the diapsid lineage, and no directional change within the synapsid lineage leading to mammals.

  10. 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.

  11. Pancreas Transplantation in the Modern Era.

    Science.gov (United States)

    Redfield, Robert R; Rickels, Michael R; Naji, Ali; Odorico, Jon S

    2016-03-01

    The field of pancreas transplantation has evolved from an experimental procedure in the 1980s to become a routine transplant in the modern era. With short- and long-term outcomes continuing to improve and the significant mortality, quality-of-life, and end-organ disease benefits, pancreas transplantation should be offered to more patients. In this article, we review current indications, patient selection, surgical considerations, complications, and outcomes in the modern era of pancreas transplantation.

  12. A New Era of Intelligence Research

    Directory of Open Access Journals (Sweden)

    Andrew R. A. Conway

    2014-04-01

    Full Text Available A consensus definition of intelligence remains elusive but there are many reasons to believe that the field of intelligence is entering a new era of significant progress. The convergence of recent advances in psychometrics, cognitive psychology, and neuroscience has set the stage for the development of stronger theories and more sophisticated models. The establishment of a new open access journal as an outlet for new intelligence research is evidence that the new era has begun.

  13. A New Era of Intelligence Research

    OpenAIRE

    Conway, Andrew R. A.

    2014-01-01

    A consensus definition of intelligence remains elusive but there are many reasons to believe that the field of intelligence is entering a new era of significant progress. The convergence of recent advances in psychometrics, cognitive psychology, and neuroscience has set the stage for the development of stronger theories and more sophisticated models. The establishment of a new open access journal as an outlet for new intelligence research is evidence that the new era has begun.

  14. TANTANGAN DAKWAH DI ERA GLOBALISASI

    Directory of Open Access Journals (Sweden)

    Istina Rakhmawati

    2015-11-01

    Full Text Available Potret dakwah yang berkembang selama ini memiliki kecenderungan doktrinasi, di mana masyarakat diibaratkan seperti sebuah celengan yang harus diisi dengan perangkat keyakinan serta nilai moral dan praktek kehidupan agar disimpan dan pada saat dibutuhkan juga dikeluarkan. Salah satu persoalan krusial sebagai dampak proses globalisasi yang terkait dengan kehidupan keagamaan adalah makin menipisnya ruang religiositas dalam konteks kehidupan manusia. Pada sisi yang sama, kita bisa saksikan sebagian umat muslim yang lain justru cenderung menerima apa yang datang dari timur dan barat tanpa reserve. Selain itu, fenomena globalisasi yang perlu menjadi bahan kajian terpenting saat ini adalah penyebaran cara pandang seputar hubungan keluarga, kerukunan umat, social, terutama yang berkembang di negara maju yang notabene merupakan pemeran utama globalisasi. Untuk itu, perkembangan arus globalisasi menuntut para dai-dai untuk lebih mampu menyesuaikan dengan perkembangan zaman. Kata Kunci: Tantangan Dakwah, Globalisasi. THECHALLENGEOFDAWAINTHEGLOBALIZATION ERA. The portrait of dawa that developed during this time has a tendency of doctrinisation. In this term, the society are likened such a piggy bank which must be filled with believe and moral values and practices of life in order to be saved and in times of need is also issued. One of the crucial issues as the impact of globalization processes related to the religious life is the more depletion of religiosity space in contexts of human life. On the same side, we can see some of the other muslims thus tend to accept what is coming from the East and West without reserve. In addition, the phenomenon of globalization that need to be the most important study materials at the moment is the dissemination of viewpoints regarding family relationships, people harmony, social, especially which are developed in the developing countries that in fact is the main character of the globalization. Therefore, the development

  15. Implementing genomic medicine in pathology.

    Science.gov (United States)

    Williams, Eli S; Hegde, Madhuri

    2013-07-01

    The finished sequence of the Human Genome Project, published 50 years after Watson and Crick's seminal paper on the structure of DNA, pushed human genetics into the public eye and ushered in the genomic era. A significant, if overlooked, aspect of the race to complete the genome was the technology that propelled scientists to the finish line. DNA sequencing technologies have become more standardized, automated, and capable of higher throughput. This technology has continued to grow at an astounding rate in the decade since the Human Genome Project was completed. Today, massively parallel sequencing, or next-generation sequencing (NGS), allows the detection of genetic variants across the entire genome. This ability has led to the identification of new causes of disease and is changing the way we categorize, treat, and manage disease. NGS approaches such as whole-exome sequencing and whole-genome sequencing are rapidly becoming an affordable genetic testing strategy for the clinical laboratory. One test can now provide vast amounts of health information pertaining not only to the disease of interest, but information that may also predict adult-onset disease, reveal carrier status for a rare disease and predict drug responsiveness. The issue of what to do with these incidental findings, along with questions pertaining to NGS testing strategies, data interpretation and storage, and applying genetic testing results into patient care, remains without a clear answer. This review will explore these issues and others relevant to the implementation of NGS in the clinical laboratory.

  16. 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...

  17. 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

  18. Different People, Different Views on Era

    Institute of Scientific and Technical Information of China (English)

    Qiu Yuanlun; He Nan

    2010-01-01

    History can be divided into various segments based on the various .developing stages. We call these segments eras. The era issue has been raised to discuss time and time again, which is often associated with the major transition of political system, economic system and ideology in world life, and sometimes also linked with a number of far-reaching historical events. In the recent 15-20 years, we have many important issues that prompt people to rethink of the era issues, like the East and West economic restructuring, the collapse of the former Soviet Union, the war in Iraq and the former Yugoslavia, the "9 -11" event and the war in Afghanistan and Iraq, as well as all aspects of major global changes resulting from the process of globalization. It should be pointed out that in the West's political, academic and business circle, there are very few articles totally devoted to the clef'tuition of era; most of people only mention the word "era" or such kind of expression here and there in their political speeches or writings.

  19. Ecmwf Global Reanalysis Project, Era-40

    Science.gov (United States)

    Uppala, S.; Kållberg, P.; Simmons, A.; Fiorino, M.; Hernandez, A.; Li, Xu; Onogi, K.; Saarinen, S.; Sokka, N.

    ECMWF is currently performing the ERA-40 reanalysis of the global atmosphere for the period 1957-2001, with support from the European Union and several other or- ganizations. The ERA-40 analyses will complement the existing reanalysis datasets from NCEP (1947-2000) and ECMWF (ERA-15, 1979-1993). Reanalyses in general seek to achieve as great a time consistency as possible within the limitations of the data-assimilation scheme and the available observing systems. The historical ground- based WWW observations and observations from special experiments such as GATE, FGGE and ALPEX have been made available to the project, mainly by NCAR/NCEP, ECMWF, JMA and USNAVY. In addition, and to a much larger extent than in ERA- 15, ERA-40 makes use of multichannel satellite radiances through a T159L60/ 3D- variational assimilation starting with data from the first VTPR sounding instrument in 1972 and continuing up to the present SSM/I, TOVS and ATOVS instruments. Cloud Motion Winds are used from 1979 onwards and EUMETSAT has undertaken to repro- cess Meteosat winds for 1983-1988. The length of the period allows studies relating to climate change, long term trends and fluctuations such as El Nino and the QBO. The presentation will describe the project, including its status, the assimilation system and the characteristics of the observing systems through the period, with indications of their performance and impact on medium-range weather forecasts.

  20. 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.

  1. Chlamydia genomics: providing novel insights into chlamydial biology.

    Science.gov (United States)

    Bachmann, Nathan L; Polkinghorne, Adam; Timms, Peter

    2014-08-01

    Chlamydiaceae are obligate intracellular pathogens that have successfully evolved to colonize a diverse range of hosts. There are currently 11 described species of Chlamydia, most of which have a significant impact on the health of humans or animals. Expanding chlamydial genome sequence information has revolutionized our understanding of chlamydial biology, including aspects of their unique lifecycle, host-pathogen interactions, and genetic differences between Chlamydia strains associated with different host and tissue tropisms. This review summarizes the major highlights of chlamydial genomics and reflects on the considerable impact these have had on understanding the biology of chlamydial pathogens and the changing nature of genomics tools in the 'post-genomics' era.

  2. 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

  3. Globalization Era vs. International Order Transformation

    Institute of Scientific and Technical Information of China (English)

    Cui Liru; Ma Zongshi

    2009-01-01

    @@ The world has entered a globalization era in the true sense of the expression. In the words of Thomas Friedman, author of the best seller The World Is Flat, though the globalization process began in as early back as 1492 when Christopher Columbus's first voyage to the Americas opened up wade between the old and the new world, yet only now are we ushering in "an entirely new era of globalization 3.0." Unlike its two predecessors of globalizations 1.0 and 2.0,the current one, driven increasingly by non-white, non-western institutions, is a truly worldwide process, a matter of crucial significance.

  4. ERA [Material gráfico

    OpenAIRE

    Fundación para la Etnografía y el Desarrollo de la Artesanía Canaria

    1990-01-01

    Antiguedad: SIGLO XX Calificación del suelo: RÚSTICO DE PROTECCIÓN PAISAJÍSTICA Clasificación del suelo: RÚSTICO Declaración BIC:No EN EL CRUCE ENTRE FAGAGESTO-MOYA Y CAIDEROS TOMAMOS HACIA FAGAGESTO Y ENTRAMOS POR LA CERCANA 1° ENTRADA A LA IZQUIERDA RECORRIENDO 1200M. TOMANDO PRIMERO A LA DERECHA Y A LA IZQUIERDA EN LOS CRUCES RESTANTES, HASTA EL FINAL. SUBIMOS POR LA LADERA 85M. EN DIRECCIÓN SURESTE HASTA LA ERA. ERA DE TIERRA, DE PLANTA CIRCULAR, SIN MURO, CON PIEDRAS EMPEN...

  5. Obesity: Interactions of Genome and Nutrients Intake

    OpenAIRE

    Doo, Miae; Kim, Yangha

    2015-01-01

    Obesity has become one of the major public health problems all over the world. Recent novel eras of research are opening for the effective management of obesity though gene and nutrient intake interactions because the causes of obesity are complex and multifactorial. Through GWASs (genome-wide association studies) and genetic variations (SNPs, single nucleotide polymorphisms), as the genetic factors are likely to determine individuals’ obesity predisposition. The understanding of genetic appr...

  6. Three-Dimensional Genome Organization and Function in Drosophila.

    Science.gov (United States)

    Schwartz, Yuri B; Cavalli, Giacomo

    2017-01-01

    Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques. Copyright © 2017 Schwartz and Cavalli.

  7. Three-Dimensional Genome Organization and Function in Drosophila

    Science.gov (United States)

    Schwartz, Yuri B.; Cavalli, Giacomo

    2017-01-01

    Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques. PMID:28049701

  8. Dinosaur dynamics in the Jurassic Era

    Science.gov (United States)

    Lee, Scott

    2010-04-01

    Dinosaurs were fascinating animals and elicit much excitement in the classroom. Analysis of fossilized dinosaur trackways permits one to estimate the locomotion speeds and accelerations of these extinct beasts. Such analysis allows one to apply Newton's laws of motion to examples from the Jurassic Era.

  9. 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…

  10. 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…

  11. Women Reformers in the Progressive Era.

    Science.gov (United States)

    McDonough, Judith

    1999-01-01

    Presents an overview of women in the Progressive Era, providing a glimpse at how women attempted to reform society and simultaneously change ideas about the role of women at the turn of the 20th century. Reviews the various roles of these women, such as suffragettes, individual freedom activists, and labor organizers. (CMK)

  12. Green Era Should Herald Smarter Buildings

    Science.gov (United States)

    Carlson, Scott

    2008-01-01

    In the past two decades, the most elite and ambitious colleges have commissioned buildings by "starchitects" for notoriety. However, people live in a green era now and there is a need for a new kind of star architecture to go with it, one in which the building is a star for its efficiency as well as its elegance. The new star architecture would…

  13. A New Era of Open Access?

    Science.gov (United States)

    Mercieca, Paul; Macauley, Peter

    2008-01-01

    There has been a push for open access journals for more than a decade in a higher education and research environment in which the "publish or perish" syndrome is as dominant as ever. This article examines the success, or otherwise, of open access schemes in light of the Excellence in Research for Australia (ERA) initiative. It compares…

  14. The new era for geo-information

    Institute of Scientific and Technical Information of China (English)

    LI DeRen; SHAO ZhenFeng

    2009-01-01

    Along with the forthcoming of Google Earth, Virtual Earth, the next generation of Internet, Web 2.0, grid computing and smart sensor web, comes the new era for geo-information. In this paper, main features of new geo-information era are discussed. This new era is characterized by these features: serviced users are extended from professionals to all public users, the users are data and information providers as well, geospatial data provided are no longer measurement-by-specification but measurement-on-demand through smart sensor web, and services are transferred from being data-driven to application-driven. Such problems as out-of-order issues in geographic data collection and information proliferation, quality issues in geographic information updating, security issues in geographic information services, privacy issues in sharing geographic information and property issues in sharing geographic information, which are brought about by new geo-information era, especially those confronted in geo-information science and geo-spatial information industry, are analyzed. Then strategies concerning standards, planning, laws, technology and applications are proposed.

  15. Libraries in the post-scarcity era

    NARCIS (Netherlands)

    Bodó, B.; Porsdam, H.

    2015-01-01

    In the digital era where, thanks to the ubiquity of electronic copies, the book is no longer a scarce resource, libraries find themselves in an extremely competitive environment. Several different actors are now in a position to provide low cost access to knowledge. One of these competitors are

  16. Libraries in the post-scarcity era

    NARCIS (Netherlands)

    B. Bodó

    2015-01-01

    In the digital era where, thanks to the ubiquity of electronic copies, the book is no longer a scarce resource, libraries find themselves in an extremely competitive environment. Several different actors are now in a position to provide low cost access to knowledge. One of these competitors are shad

  17. 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…

  18. A New Era of Open Access?

    Science.gov (United States)

    Mercieca, Paul; Macauley, Peter

    2008-01-01

    There has been a push for open access journals for more than a decade in a higher education and research environment in which the "publish or perish" syndrome is as dominant as ever. This article examines the success, or otherwise, of open access schemes in light of the Excellence in Research for Australia (ERA) initiative. It compares…

  19. 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.

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

    NARCIS (Netherlands)

    S. Brul; W. Kallemeijn; G. Smits

    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

  1. The European Union's Normative Power in a more Global Era

    DEFF Research Database (Denmark)

    Manners, Ian James

    2013-01-01

    The globalising, multilateralising and multipolarising era requires a reconsideration of the nature of European Union (EU) power and actorness in a more global era. The article does this by first looking at the study of the EU in a more global era. Second, the normative power approach will be exa...

  2. The genome revolution and its role in understanding complex diseases

    NARCIS (Netherlands)

    Hofker, Marten H.; Fu, Jingyuan; Wijmenga, Cisca

    2014-01-01

    The completion of the human genome sequence in 2003 clearly marked the beginning of a new era for biomedical research. It spurred technological progress that was unprecedented in the life sciences, including the development of high-throughput technologies to detect genetic variation and gene express

  3. Genomic counseling: next generation counseling.

    Science.gov (United States)

    Mills, Rachel; Haga, Susanne B

    2014-08-01

    Personalized medicine continues to expand with the development and increasing use of genome-based testing. While these advances present new opportunities for diagnosis and risk assessment, they also present challenges to clinical delivery. Genetic counselors will play an important role in ushering in this new era of testing; however, it will warrant a shift from traditional genetic counseling to "genomic counseling." This shift will be marked by a move from reactive genetic testing for diagnosis of primarily single-gene diseases to proactive genome-based testing for multiple complex diseases for the purpose of disease prevention. It will also require discussion of risk information for a number of diseases, some of which may have low relative risks or weak associations, and thus, may not substantially impact clinical care. Additionally, genomic counselors will expand their roles, particularly in the area of health promotion to reduce disease risk. This additional role will require a style of counseling that is more directive than traditional counseling and require greater knowledge about risk reducing behaviors and disease screening.

  4. 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.

  5. Cosmology with a stiff matter era

    Science.gov (United States)

    Chavanis, Pierre-Henri

    2015-11-01

    We consider the possibility that the Universe is made of a dark fluid described by a quadratic equation of state P =K ρ2 , where ρ is the rest-mass density and K is a constant. The energy density ɛ =ρ c2+K ρ2 is the sum of two terms: a rest-mass term ρ c2 that mimics "dark matter" (P =0 ) and an internal energy term u =K ρ2=P that mimics a "stiff fluid" (P =ɛ ) in which the speed of sound is equal to the speed of light. In the early universe, the internal energy dominates and the dark fluid behaves as a stiff fluid (P ˜ɛ , ɛ ∝a-6). In the late universe, the rest-mass energy dominates and the dark fluid behaves as pressureless dark matter (P ≃0 , ɛ ∝a-3). We provide a simple analytical solution of the Friedmann equations for a universe undergoing a stiff matter era, a dark matter era, and a dark energy era due to the cosmological constant. This analytical solution generalizes the Einstein-de Sitter solution describing the dark matter era, and the Λ CDM model describing the dark matter era and the dark energy era. Historically, the possibility of a primordial stiff matter era first appeared in the cosmological model of Zel'dovich where the primordial universe is assumed to be made of a cold gas of baryons. A primordial stiff matter era also occurs in recent cosmological models where dark matter is made of relativistic self-gravitating Bose-Einstein condensates (BECs). When the internal energy of the dark fluid mimicking stiff matter is positive, the primordial universe is singular like in the standard big bang theory. It expands from an initial state with a vanishing scale factor and an infinite density. We consider the possibility that the internal energy of the dark fluid is negative (while, of course, its total energy density is positive), so that it mimics anti-stiff matter. This happens, for example, when the BECs have an attractive self-interaction with a negative scattering length. In that case, the primordial universe is nonsingular and

  6. Past Eras In Cyclic Cosmological Models

    CERN Document Server

    Frampton, Paul H

    2009-01-01

    In infinitely cyclic cosmology past eras are discussed using set theory and transfinite numbers. One consistent scenario, already in the literature, is where there is always a countably infinite number, $\\aleph_0$, of universes and no big bang. I describe here an alternative where the present number of universes is $\\aleph_0$ and in the infinite past there was only a finite number of universes. In this alternative model it is also possible that there was no big bang.

  7. China's Cheap-Labor Era Is Ending

    Institute of Scientific and Technical Information of China (English)

    International Finance News

    2010-01-01

    @@ This year,salary has increased in eastern China's enterprises;governments in central and western China have raised minimum-wage standards…signals for higher labor cost emerge from time to time.This rising economic phenomenon poses a series of problems-is China's economy stepping out of the cheap-labor era? What opportunities and challenges may lie ahead in this important course of transition?

  8. ERA [Material gráfico

    OpenAIRE

    Fundación para la Etnografía y el Desarrollo de la Artesanía Canaria

    1990-01-01

    Antiguedad: SIGLO XIX Calificación del suelo: RÚSTICO DE PROTECCIÓN DE ENTORNOS Clasificación del suelo: RÚSTICO DE FORMA CASI CIRCULAR, CON PIEDRAS EMPENICADAS EN LOS BORDES, EMPEDRADO SIN DIBUJO APARENTE Y CON GRANDES LOSAS EN SU INTERIOR. MIXTA, EMPEDRADO Y LOSAS. Declaración BIC:No HAY BASTANTE BASURA EN EL INTERIOR Y ALREDEDOR DE LA ERA. LA VEGETACION HA LOGRADO INTRODUCIRSE ENTREEL EMPEDRADO, (ALGUNA ZONA HA PERDIDO EL ...

  9. Belydenisgebondenheid in ’n postmoderne era

    OpenAIRE

    C.F.C. Coetzee

    2010-01-01

    The binding to confessions in a postmodern era We are experiencing a paradigm shift between Modernism and Postmodernism in almost every sphere of life, and also in the sphere of church and theology. This paradigm shift has far-reaching consequences, especially for churches in the reformed tradition and the practice of reformed theology as far as the binding to the confessions is concerned. From the viewpoint of Postmodernism, there is no absolute truth. This applies also to Scripture. ...

  10. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  11. On the limits of computational functional genomics for bacterial lifestyle prediction

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Röttger, Richard; Hauschild, Anne-Christin

    2014-01-01

    We review the level of genomic specificity regarding actinobacterial pathogenicity. As they occupy various niches in diverse habitats, one may assume the existence of lifestyle-specific genomic features. We include 240 actinobacteria classified into four pathogenicity classes: human pathogens (HP...... in the post-genome era and despite next-generation sequencing technology, our ability to efficiently deduce real-world conclusions, such as pathogenicity classification, remains quite limited....

  12. Humorous "Era" stories from the Arilje region

    Directory of Open Access Journals (Sweden)

    Nikolić Desanka P.

    2004-01-01

    Full Text Available This paper discusses humorous stories collected in the village of Brekovo near Arilje; the stories were created in the first half of the 20th century and noted down by Momčilo Jovanović, a villager from Brekovo. Later on, in the 1980's, the stories were passed down to the author of this paper. These narrations are mostly short stories and anecdotes; in a very realistic fashion, the stories depict life and culture of the Dinaric race from old Vlah - Zlatibor cultural area, namely, the type of person also known as "Era", well-known for its wittiness, smartness and wisdom. Based on the analysis of seven Era-stories, the author identified the social and cultural values highlighted in the stories (such as attitudes toward authorities intergenerational relationship, status of women, power relations between townsmen and peasants, propensity toward justice and truth. In summary, the stories document the mutual influence between traditional culture and the Era personality in this particular rural region; therefore, they could contribute to studies on character traits of the inhabitants in a given area of western Serbia.

  13. Nanotechnology: A new era for photodetection?

    Science.gov (United States)

    Ambrosio, M.; Ambrosio, A.; Ambrosone, G.; Campajola, L.; Cantele, G.; Carillo, V.; Coscia, U.; Iadonisi, G.; Ninno, D.; Maddalena, P.; Perillo, E.; Raulo, A.; Russo, P.; Trani, F.; Esposito, E.; Grossi, V.; Passacantando, M.; Santucci, S.; Allegrini, M.; Gucciardi, P. G.; Patanè, S.; Bobba, F.; Di Bartolomeo, A.; Giubileo, F.; Iemmo, L.; Scarfato, A.; Cucolo, A. M.

    2009-10-01

    Nowadays we live in the so-called "Silicon Era", in which devices based on the silicon technology permeate all aspects of our daily life. One can simply think how much silicon is in the everyday household objects, gadgets and appliances. The impact of silicon technology has been very relevant in photodetection as well. It enables designing large or very large-scale integration devices, in particular microchips and pixelled detectors like the Silicon Photo Multiplier made of micrometric channels grouped in mm 2 pixels. However, on the horizon, the recent development of nanotechnologies is opening a new direction in the design of sub-micron photodevices, owing to the capability to deal with individual molecules of compounds or to chemically grow various kinds of materials. Among them, carbon compounds appear to be the most promising materials being chemically very similar to silicon, abundant and easy to handle. In particular, carbon nanotubes (CNT) are a very intriguing new form of material, whose properties are being studied worldwide providing important results. The photoelectric effects observed on carbon nanotubes indicate the possibility to build photodetectors based on CNTs inducing many people to claim that we are at the beginning of a Post Silicon Era or of the Carbon Era. In this paper, we report on the most important achievements obtained on the application of nanotechnologies to photodetection and medical imaging, as well as to the development of radiation detectors for astro-particle physics experiments.

  14. Nanotechnology: A new era for photodetection?

    Energy Technology Data Exchange (ETDEWEB)

    Ambrosio, M. [INFN Sezione di Napoli, Via Cintia 2, 80125 Napoli (Italy)], E-mail: ambrosio@na.infn.it; Ambrosio, A.; Ambrosone, G.; Campajola, L.; Cantele, G.; Carillo, V.; Coscia, U.; Iadonisi, G.; Ninno, D.; Maddalena, P.; Perillo, E.; Raulo, A.; Russo, P.; Trani, F. [INFN Sezione di Napoli, Via Cintia 2, 80125 Napoli (Italy); Dipartimento di Fisica, Universita ' Federico II' di Napoli (Italy); Esposito, E. [INFN Sezione di Napoli, Via Cintia 2, 80125 Napoli (Italy); Istituto di Cibernetica ' E. Caianiello' (Italy); Grossi, V.; Passacantando, M.; Santucci, S. [INFN Sezione di Napoli, Via Cintia 2, 80125 Napoli (Italy); Dipartimento di Fisica, Universita dell' Aquila (Italy); Allegrini, M. [INFN Sezione di Napoli, Via Cintia 2, 80125 Napoli (Italy); Dipartimento di Fisica, Universia di Pisa (Italy); Gucciardi, P.G. [INFN Sezione di Napoli, Via Cintia 2, 80125 Napoli (Italy); CNR-IPCF Sezione di Messina (Italy)] (and others)

    2009-10-21

    Nowadays we live in the so-called 'Silicon Era', in which devices based on the silicon technology permeate all aspects of our daily life. One can simply think how much silicon is in the everyday household objects, gadgets and appliances. The impact of silicon technology has been very relevant in photodetection as well. It enables designing large or very large-scale integration devices, in particular microchips and pixelled detectors like the Silicon Photo Multiplier made of micrometric channels grouped in mm{sup 2} pixels. However, on the horizon, the recent development of nanotechnologies is opening a new direction in the design of sub-micron photodevices, owing to the capability to deal with individual molecules of compounds or to chemically grow various kinds of materials. Among them, carbon compounds appear to be the most promising materials being chemically very similar to silicon, abundant and easy to handle. In particular, carbon nanotubes (CNT) are a very intriguing new form of material, whose properties are being studied worldwide providing important results. The photoelectric effects observed on carbon nanotubes indicate the possibility to build photodetectors based on CNTs inducing many people to claim that we are at the beginning of a Post Silicon Era or of the Carbon Era. In this paper, we report on the most important achievements obtained on the application of nanotechnologies to photodetection and medical imaging, as well as to the development of radiation detectors for astro-particle physics experiments.

  15. Philosophical Pragmatism in the Digital Era

    Directory of Open Access Journals (Sweden)

    Marius Constantin CUCU

    2014-03-01

    Full Text Available The view of the philosophic pragmatism warns against the growing danger of the technological modernization of the human being in the mechanization era, which is gradually transforming and approaching a digital era. Authors such as R. Rorty believe that only the return to the paradigm of the human reality separated from metaphysical ideals could keep us away from exacerbations of ideas and the dehumanizing automatisms of technology. In the view of pragmatic philosophy, the human being is not a mechanic, operational construction; on the contrary, he has a consciousness that opts for free actions, which may prove, in the end, to be genuine or not, thanks to the success or due to the failure in the concrete reality. The aim of this article is to underline that the digital era must be perceived as a product of human ingenuity and its applicative potentialities and should not be seen as the domination of techne, but only as a stage of the developments in the technologies that must assist our life. Classification-JEL: A23

  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. 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...

  18. A call for an international network of genomic observatories (GOs).

    Science.gov (United States)

    Davies, Neil; Meyer, Chris; Gilbert, Jack A; Amaral-Zettler, Linda; Deck, John; Bicak, Mesude; Rocca-Serra, Philippe; Assunta-Sansone, Susanna; Willis, Kathy; Field, Dawn

    2012-07-12

    We are entering a new era in genomics-that of large-scale, place-based, highly contextualized genomic research. Here we review this emerging paradigm shift and suggest that sites of utmost scientific importance be expanded into 'Genomic Observatories' (GOs). Investment in GOs should focus on the digital characterization of whole ecosystems, from all-taxa biotic inventories to time-series 'omics studies. The foundational layer of biodiversity-genetic variation-would thus be mainstreamed into Earth Observation systems enabling predictive modelling of biodiversity dynamics and resultant impacts on ecosystem services.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    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.......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 metabolic...

  20. ERA-MIN: The European network (ERA-NET) on non-energy raw materials

    Science.gov (United States)

    vidal, o.; christmann, p.; Bol, d.; Goffé, b.; Groth, m.; Kohler, e.; Persson Nelson, k.; Schumacher, k.

    2012-04-01

    Non-energy raw materials are vital for the EU's economy, and for the development of environmentally friendly technologies. The EU is the world's largest consumers of non-energy minerals, but it remains dependent on the importation of many metals, as its domestic production is limited to about 3% of world production. We will present the project ERA-MIN, which is an ERA-NET on the Industrial Handling of Raw Materials for European industries, financially supported by the European Commission. The main objectives of ERA-MIN are: 1) Mapping and Networking: interconnecting the members of the currently fragmented European mineral resources research area, to the aim of fostering convergence of public research programs, industry, research institutes, academia and the European Commission, 2) Coordinating: establishing a permanent mechanism for planning and coordination of the European non-energy mineral raw materials research community (ENERC). 3) Roadmapping: defining the most important scientific and technological challenges that should be supported by the EU and its state members, 4) Programming: designing a Joint European Research Programme model and implementating it into a call for proposals open to academic and industrial research. The topics of interest in ERA-MIN are the primary continental and marine resources, the secondary resources and their related technologies, substitution and material efficiency, along with transversal topics such as environmental impact, public policy support, mineral intelligence, and public education and teaching. Public scientific research is very central in the scope of the ERA-MIN activity, whose consortium is indeed lead by a public organisation of fundamental research. Thus, universities and public research organisations are warmly invited to play an active role in defining the scientific questions and challenges that shall determine the European Raw Materials Roadmap and should be addressed by joint programming at the European scale

  1. Human evolution: a tale from ancient genomes.

    Science.gov (United States)

    Llamas, Bastien; Willerslev, Eske; Orlando, Ludovic

    2017-02-05

    The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

  2. 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...

  3. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  4. GENÉTICA MOLECULAR Y BIOGERONTOLOGÍA EN LA ERA POSTGENÓMICA

    Directory of Open Access Journals (Sweden)

    Michán Aguirre Shaday

    2011-12-01

    chromosomes up to the knowledge of DNA structure. This last event lead the development of recombinant DNA technology and the massive and automated sequencing, which allowed later to determine the anatomy of genomes. All of these discoveries have pushed the evolution of biomedicine towards the genomic and postgenomic eras, in which the use of reverse genetics prevails over the basic or direct one. Furthermore, it emerges the molecular genetics, the functional genomics and the diverse omic technologies that together pretend to understand in an integrative way the function of all of the genome components and its products. Biogerontology, discipline that studies the biological mechanisms of aging, is one of the fields that has developed notoriously in the last 15 years and reflects the scientific advances of the postgenomic era. Currently, there have been identified several gerontogenes and molecular pathways that modify and regulate age-related processes and diseases. Among these genes are the sirtuins, an evolutionarily preserved family of genes, which codify for proteins with NAD+ dependent deacetylase activity and that play an important role on aging. Here we review different reverse genetics approaches that have been used in order to identify some of the functions of these genes in mammals. Key words: molecular genetics, biogerontology, aging, postgenomic era, gerontogenes.

  5. La era de la cibercultura publicitaria

    Directory of Open Access Journals (Sweden)

    Dra. Rocío Jiménez

    2001-01-01

    Full Text Available La autora hace un recorrido hacia una dimensión ciberpublicitaria y se detiene en aspectos como el cibernauta, la fuerza de la interacción, la belleza y funcionalidad, el concepto de originar un producto para cada cibernauta, la voz del cibernauta y la vuelta al trueque. Insiste en algunos aspectos relevantes sobre la ciberpublidad: pull, cibercasting y banners publicitarios, para acabar su trabajo con el análisis de ideas como la era de la cibercultura publicitaria, la creación de comunidades y la retroalimentación de contenidos.

  6. PERGESERAN MITOLOGI PESANTREN DI ERA MODERN

    Directory of Open Access Journals (Sweden)

    Arif Junaidi

    2011-12-01

    Masalah utama dari kajian ini adalah mencari akar, pola, dan fungsi keyakinan mengenai karamah kiai pesantren Futuhiyah Mranggen Demak dan sejauh mana pergeseran mitologi yang terjadi di kalangan masyarakat sejalan dengan perubahan masyarakat di era modern ini. Kajian ini merupakan kajian lapangan. Paradigma yang digunakan adalah kualitatif karena kajian ini berupaya menemukan makna. Adapun penemuan dari kajian ini adalah bahwa kehidupan kiai di pesantren Futuhiyah Mranggen juga diliputi mitos kiai, dalam makna keyakinan bahwa kiai memiliki karamah.

  7. Spectroscopy in the Era of LSST

    CERN Document Server

    Matheson, Thomas; Green, Richard; McConnachie, Alan; Newman, Jeff; Olsen, Knut; Szkody, Paula; Wood-Vasey, W Michael

    2013-01-01

    This report summarizes the results of the 'Spectroscopy in the Era of LSST' workshop held April 11-12, 2013 in Tucson, Arizona. At the workshop, there were breakout sessions covering four broad science topics. These were: time domain science, Galactic structure and stellar populations, galaxies and AGN, and dark energy and cosmology. We present the science cases discussed in these breakout sessions and provide a synthesis of highly desired capabilities that meet needs across all four broad topics. We also present a table that will be useful to characterize the needs of specific science cases in a format that provides a general framework for discussion of future spectroscopic capabilities.

  8. ERA [Material gráfico

    OpenAIRE

    Fundación para la Etnografía y el Desarrollo de la Artesanía Canaria

    1990-01-01

    Antiguedad: SIGLO XX BASTANTE VEGETACION EN SU INTERIOR. Clasificación del suelo: RÚSTICO Declaración BIC:No ENTIDAD CON FORMA SEMICIRCULAR, ENLOSADA EN ALGUNOS SECTORES. NO PRESENTA PIEDRAS EN EL BORDE. Nivel de protección: 0 POR LA CARRETERA QUE VA DESDE EL ASERRADOR A CARRIZAL DE TEJEDA, LA PRIMERA PISTA A LA IZQUIERDA, LA ERA ESTA A LA DERECHA DENTRO DE ESTA PISTA. Propiedad: PRIVADA RESALTAR LAS GRANDES LOSAS DE SU INTERIOR, LAS LOSAS ESTAN CUBIERTAS DE TIERRA Y V...

  9. ERA [Material gráfico

    OpenAIRE

    Fundación para la Etnografía y el Desarrollo de la Artesanía Canaria

    1990-01-01

    Antiguedad: SIGLO XX Construcción circular realizada con grandes losas que la cubren en su totalidad. No presenta borde de piedras. Declaración BIC:No En muy buen estado. Cubierta de vegetación que ha crecido entre las losas. Nivel de protección: 0 Pasados los Lomos de Pedro Afonso hacia Cercados de Araña hay un cruce de pistas. Tomamos la de la derecha y a unos 350 metros está la era, bajo la carretera. Por los alrededores hay restos de antiguos bancales. Propiedad: PRIV...

  10. ERA ROJITA [Material gráfico

    OpenAIRE

    Fundación para la Etnografía y el Desarrollo de la Artesanía Canaria

    1990-01-01

    Antiguedad: SIGLO XIX Calificación del suelo: RÚSTICO DE PROTECCIÓN DE ENTORNOS Clasificación del suelo: RÚSTICO DE PLANTA CIRCULAR EMPEDRADA CON GRANDES LAJAS POR CASI TODA SU SUPERFICIE Y CON OTRAS PIEDRAS DE TAMAÑO DECIMETRICO. ESTA DELIMITADA POR UN LADO CON GRANDES PIEDRAS Y POR EL OTRO EL MURO ESTA SOBRE UN MURO DE PIEDRAS MUY ANCHO Y CASI NO SALVA PENDIENTE. SITUADA EN UN LOMITILLO MUY CERCA DEL CAUCE DEL BARRANQUILLO PERO EXPUESTA A LOS VIENTOS. DESDE LA ERA SE DOMINA PART...

  11. Transforming healthcare in the Internet Era.

    Science.gov (United States)

    Detmer, D E

    2001-01-01

    Healthcare services will be transformed in the Internet Era by developments in biotechnology, bioinformatics, health informatics, assimilation of modern business processes, and changing policy expectations. Discoveries in biology and communications technology offer the potential for improvements in health status of individuals and populations. Improved access to information about health and disease will typify early progress. Care in hospitals will shift toward palliation and end-of-life care; curing and prevention will increase in outpatient settings and/or within the home or workplace. Barriers include resistance to change and a lack of a global health information infrastructure that includes financing, standards, and coherent policy.

  12. Studying Stepfamilies: Four Eras of Family Scholarship.

    Science.gov (United States)

    Ganong, Lawrence; Coleman, Marilyn

    2017-07-23

    Historically, there have always been stepfamilies, but until the early 1970s, they remained largely unnoticed by social scientists. Research interest in stepfamilies followed shortly after divorce became the primary precursor to stepfamily formation. Because stepfamilies are structurally diverse and much more complex than nuclear families, they have created considerable challenges for both researchers and clinicians. This article examines four eras of stepfamily scholarship, tracing the development of research questions, study designs and methods, and conceptual frameworks from the mid-1970s to the present and drawing implications for the current state of the field. © 2017 Family Process Institute.

  13. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; 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...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  14. 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...

  15. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  16. Teachers as Cultural Mediators: A Comparison of the Accountability Era to the Assimilation Era

    Science.gov (United States)

    Eick, Caroline; Valli, Linda

    2010-01-01

    This article examines teachers' relationships with foreign students during eras marked by large waves of immigration to the United States and by policies that shifted from cultural assimilation (1900-1920) to present-day accountability. We compare teachers' understandings of and instructional practices regarding foreign-born English language…

  17. 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...

  18. PEMBELAJARAN BAHASA ARAB DI ERA POSMETODE

    Directory of Open Access Journals (Sweden)

    Muhbib Abdul Wahab

    2015-06-01

    Full Text Available This article is aimed to answer two essential problems; (1 development map of Arabic learning method from 1990s until today which has been formulated unclearly, and (2 developing Arabic learning in posmethod era by optimilizing teacher’s strategic role in the process of Arabic learning. This article used bibliographic sources from some books and articles in scientific journal about linguistic and Arabic learning. The interpretation data of academician thought and Arabic linguistic experts was done by using historical-critical approach and content analysis for substancial interpretation. B. Kumaravadivelu concept in Beyond Methods: Macrostrategies for Language Teaching (2003 which requires teacher to play three essential roles; pasif technician, reflective practician, and transformative intelectual is very inportant in Arabic learning in posmethod era. The principle of at-tharîqatu ahammu min al-mâddah (method is more important than content can be developed to be main principle “spirit, profesionality and strategic role of language educator is more important in teaching Arabic than the method itself”, since basically there is no most appropriate and ideal method for any goals and situation of Arabic learning.

  19. Aplikasi Citizen Journalism di Era Konvergensi Media

    Directory of Open Access Journals (Sweden)

    Rahmat Edi Irawan

    2014-10-01

    Full Text Available Citizen journalist has now become one of the concepts most developed television programs. If initially the concept is more widely used in radio and online media, this time with technology coverage and delivery of images that are easier and cheaper, it is a concept that provides a place for people to become amateur journalists also can be applied with ease in the medium of television. Application of citizen journalism in the television media is also increasingly facilitated by the start of the television is now the era of media convergence, different recent media, such as television media with print media , radio and internet media . The era of media convergence, making the concept of citizen journalism can be more developed , because of the platform or distribution media is also increasingly diverse television for the amateur journalists . However, the system equipment must be provided, human resources must be owned , as well as huge capital to be owned, make not many television stations that opened a lot of platforms to provide space for amateur journalists in citizen journalism

  20. 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...

  1. Recent advances in genome-based polyketide discovery.

    Science.gov (United States)

    Helfrich, Eric J N; Reiter, Silke; Piel, Jörn

    2014-10-01

    Polyketides are extraordinarily diverse secondary metabolites of great pharmacological value and with interesting ecological functions. The post-genomics era has led to fundamental changes in natural product research by inverting the workflow of secondary metabolite discovery. As opposed to traditional bioactivity-guided screenings, genome mining is an in silico method to screen and analyze sequenced genomes for natural product biosynthetic gene clusters. Since genes for known compounds can be recognized at the early computational stage, genome mining presents an opportunity for dereplication. This review highlights recent progress in bioinformatics, pathway engineering and chemical analytics to extract the biosynthetic secrets hidden in the genome of both well-known natural product sources as well as previously neglected bacteria.

  2. 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.

  3. Tracking genome engineering outcome at individual DNA breakpoints.

    Science.gov (United States)

    Certo, Michael T; Ryu, Byoung Y; Annis, James E; Garibov, Mikhail; Jarjour, Jordan; Rawlings, David J; Scharenberg, Andrew M

    2011-07-10

    Site-specific genome engineering technologies are increasingly important tools in the postgenomic era, where biotechnological objectives often require organisms with precisely modified genomes. Rare-cutting endonucleases, through their capacity to create a targeted DNA strand break, are one of the most promising of these technologies. However, realizing the full potential of nuclease-induced genome engineering requires a detailed understanding of the variables that influence resolution of nuclease-induced DNA breaks. Here we present a genome engineering reporter system, designated 'traffic light', that supports rapid flow-cytometric analysis of repair pathway choice at individual DNA breaks, quantitative tracking of nuclease expression and donor template delivery, and high-throughput screens for factors that bias the engineering outcome. We applied the traffic light system to evaluate the efficiency and outcome of nuclease-induced genome engineering in human cell lines and identified strategies to facilitate isolation of cells in which a desired engineering outcome has occurred.

  4. 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 (Austri...

  5. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...

  6. Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

    Directory of Open Access Journals (Sweden)

    Bishop-Lilly Kimberly A

    2010-04-01

    Full Text Available Abstract While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.

  7. Comparative study between ERA-20C and ERA INTERIM reanalysis datasets

    Science.gov (United States)

    Krisztina Balázs, Zita; Ihász, István

    2016-04-01

    The continuous development of the 20th century had a positive effect on the meteorological forecasts as well. Thanks to that the numerical models and their forecasts became more precise by the end of the century. Therefore in the 1990s scientists required to verify the results of previous numerical models with the available new technologies. In this way now it is possible to get a more accurate picture of the atmosphere's past. To meet this need reanalyses were improved. Reanalyses not only help to represent the conditions of the atmosphere more precisely, but they also help to recognize the errors of the numerical models. All these progresses are the basics of making trustworthy forecasts, and getting precise results of global climate models as well. Thanks to the innovation of data-assimilated methods and further technical developments several reanalysis projects were improved in the last decades. In our current studies we are making a proper, comparative study between the two most modern ECMWF reanalysis datasets (ERA INTERIM, ERA-20C). In the first step we assigned three periods of ERA-20C (1901-2000, 1901-1950 and 1951-2000) where we examine several selected parameters. We also assigned a collective period from both ERA INTERIM and ERA-20C (1981-2010). Four different meteorological parameters - 500 hPa height, 850 hPa temperature, mean sea level pressure, and ice coverage in the Arctic- Circle regions were investigated in our study. Emphasis is also placed on extreme weather situations. Firstly we are monitoring the detectability and the changes in frequencies of rapid cyclones in the period 1981-2010 collectively in both reanalysis datasets. Besides we examine some selected cyclones' frequency and spatial location in three periods of ERA-20C (1901-2000, 1901-1950 and 1951-2000). By the results we can recognize the strengths and weaknesses of the two reanalyses. It is a great benefit for all the reanalysis users, such as climate researchers, and the developers

  8. Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era.

    Science.gov (United States)

    Cheng, Feixiong; Hong, Huixiao; Yang, Shengyong; Wei, Yuquan

    2016-06-12

    Advances in next-generation sequencing technologies have generated the data supporting a large volume of somatic alterations in several national and international cancer genome projects, such as The Cancer Genome Atlas and the International Cancer Genome Consortium. These cancer genomics data have facilitated the revolution of a novel oncology drug discovery paradigm from candidate target or gene studies toward targeting clinically relevant driver mutations or molecular features for precision cancer therapy. This focuses on identifying the most appropriately targeted therapy to an individual patient harboring a particularly genetic profile or molecular feature. However, traditional experimental approaches that are used to develop new chemical entities for targeting the clinically relevant driver mutations are costly and high-risk. Drug repositioning, also known as drug repurposing, re-tasking or re-profiling, has been demonstrated as a promising strategy for drug discovery and development. Recently, computational techniques and methods have been proposed for oncology drug repositioning and identifying pharmacogenomics biomarkers, but overall progress remains to be seen. In this review, we focus on introducing new developments and advances of the individualized network-based drug repositioning approaches by targeting the clinically relevant driver events or molecular features derived from cancer panomics data for the development of precision oncology drug therapies (e.g. one-person trials) to fully realize the promise of precision medicine. We discuss several potential challenges (e.g. tumor heterogeneity and cancer subclones) for precision oncology. Finally, we highlight several new directions for the precision oncology drug discovery via biotherapies (e.g. gene therapy and immunotherapy) that target the 'undruggable' cancer genome in the functional genomics era.

  9. Association Claims in the Sequencing Era

    Directory of Open Access Journals (Sweden)

    Sara L. Pulit

    2014-03-01

    Full Text Available Since the completion of the Human Genome Project, the field of human genetics has been in great flux, largely due to technological advances in studying DNA sequence variation. Although community-wide adoption of statistical standards was key to the success of genome-wide association studies, similar standards have not yet been globally applied to the processing and interpretation of sequencing data. It has proven particularly challenging to pinpoint unequivocally disease variants in sequencing studies of polygenic traits. Here, we comment on a number of factors that may contribute to irreproducible claims of association in scientific literature and discuss possible steps that we can take towards cultural change.

  10. G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures

    OpenAIRE

    Solomon, Oz; Kunik, Vered; Simon, Amos; Kol, Nitzan; Barel, Ortal; Lev, Atar; Amariglio, Ninette; Somech, Raz; Rechavi, Gidi; Eyal, Eran

    2016-01-01

    Background Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates...

  11. 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.

  12. 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.

  13. Introductory overview : a new era of asteroseismology

    Science.gov (United States)

    Christensen-Dalsgaard, J.

    2006-08-01

    In the last few years, asteroseismology of solar-like stars has been converted from a dream to a solid reality. New observational facilities, particularly very stable spectrographs, have allowed the detection and study of oscillations in a number of stars on, and just after, the main sequence, placing increasingly strong constraints on the modelling of stellar interiors. Further great advances are expected in the coming years, from continued ground- based efforts and from space missions. Particularly interesting will be the results from CoRoT, to be launched later this year; on a slightly longer time scale the NASA Kepler mission is expected to provide asteroseismic data for a large number of stars. The interpretation of these data will certainly start a new era of realistic stellar modelling with a strong observational base.

  14. Big data era in meteor science

    Science.gov (United States)

    Vinković, D.; Gritsevich, M.; Srećković, V.; Pečnik, B.; Szabó, G.; Debattista, V.; Škoda, P.; Mahabal, A.; Peltoniemi, J.; Mönkölä, S.; Mickaelian, A.; Turunen, E.; Kákona, J.; Koskinen, J.; Grokhovsky, V.

    2016-01-01

    Over the last couple of decades technological advancements in observational techniques in meteor science have yielded drastic improvements in the quality, quantity and diversity of meteor data, while even more ambitious instruments are about to become operational. This empowers meteor science to boost its experimental and theoretical horizons and seek more advanced science goals. We review some of the developments that push meteor science into the big data era that requires more complex methodological approaches through interdisciplinary collaborations with other branches of physics and computer science. We argue that meteor science should become an integral part of large surveys in astronomy, aeronomy and space physics, and tackle the complexity of micro-physics of meteor plasma and its interaction with the atmosphere.

  15. Gauss-Bonnet Cosmology Unifying Late and Early-time Acceleration Eras with Intermediate Eras

    CERN Document Server

    Oikonomou, V K

    2016-01-01

    In this paper we demonstrate that with vacuum $F(G)$ gravity it is possible to describe the unification of late and early-time acceleration eras with the radiation and matter domination era. The Hubble rate of the unified evolution contains two mild singularities, so called Type IV singularities, and the evolution itself has some appealing features, such as the existence of a deceleration-acceleration transition at late times. We also address quantitatively a fundamental question related to modified gravity models description of cosmological evolution: Is it possible for all modified gravity descriptions of our Universe evolution, to produce a nearly scale invariant spectrum of primordial curvature perturbations? As we demonstrate, the answer for the $F(G)$ description is no, since the resulting power spectrum is not scale invariant, in contrast to the $F(R)$ description studied in the literature. Therefore, although the cosmological evolution can be realized in the context of vacuum $F(G)$ gravity, the evolu...

  16. 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.

  17. PROFIL STRATEGI PEMASARAN INTERNASIONAL DI ERA GLOBAL

    Directory of Open Access Journals (Sweden)

    Moh Munir

    2006-01-01

    Full Text Available Memasuki era tahun 2006 sebagai era pemulihan struktur kehidupan ekonomi setelah sekian tahun dilanda krisis ekonomi dan adanya kenaikan BBM.  Namun kenyataan yang ada asumsi pertumbuhan ekonomi sebesar 6 % tampaknya masih terlalu berat. Sumber pendapatan negara dari sektor non pajak masih kecil, kita lebih pas sebagai negara pengimpor dari pada pengekspor. Kita lebih banyak bertindak sebagai tujuan pasar dari pada produsen atau suplier barang. Kenyataan ini tidak bisa kita pungkiri sebagai akibat dari berlakunya pasar global. Kita lebih banyak terlena dan terlalu puas dengan kondisi produk yang dihasilkan, tanpa berpikir panjang bahwa sautu saat nanti ada produk barang yang sama bahkan lebih bagus dengan harga lebih murah. Kondisi inilah yang memaksa kita untuk mereviu kembali strategi pemasaran internasional kita, apakah sudah menyesuaikan dan menjawab tantangan global. Tampaknya masih banyak kebijakan-kebijakan yang harus diambil dalam hal ini terutama bagaimana kita mempunyai daya saing tinggi dengan mempunyai produk unggulan dimasing-masing otonomi daerah. Salah satu bentuk riilnya yaitu dengan menelusuri tiga macam strategic resources . Pertama kita harus membenahi aspek tangible resources yang meliputi : karyawan atau SDM, pelanggan, kapasitas, dana dan produk. Kedua menyangkut tentang intangible resources yang meliputi : ketrampilan karyawan, mutu pelanggan, efisiensi biaya produksi dan mutu produk. Ketiga aspek very intangible resources yang meliputi : moral karywan, reputasi dimata pelanggan dan reputasi dimata investor. Selain cara ini bisa juga dengan model  “Satu Kabupaten Satu Kompetensi Inti” (Saka-Sakti dimana model ini sejalan dengan kebijakan otonomi daerah, saka yang berarti tiang atau tonggak dan sakti yang berarti keampuhan, kekuatan atau ilmu. Jadi tonggak keampuhan atau tonggak kekuatan andalan yang dimiliki oleh setiap kabupaten di Indonesia guna membangun kompetensi inti agar bisa bersaing di pasar global.

  18. 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.

  19. Genome editing. The new frontier of genome engineering with CRISPR-Cas9.

    Science.gov (United States)

    Doudna, Jennifer A; Charpentier, Emmanuelle

    2014-11-28

    The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.

  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 My

  1. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  2. Genomics-based plant germplasm research (GPGR

    Directory of Open Access Journals (Sweden)

    Jizeng Jia

    2017-04-01

    Full Text Available 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.

  3. Modern Era Retrospective-Analysis for Research and Applications

    Science.gov (United States)

    Bosilovich, Michael G.; Robertson, Franklin R.; Chen, Junye

    2009-01-01

    The Modern Era Retrospective-analysis for Research and Applications (MERRA) reanalyses has produced several years of data, on the way to a. completing the 1979-present modern satellite era. Here, we present a preliminary evaluation of those years currently available, including comparisons with the existing long reanalyses (ERA40, JPA25 and NCEP I and II) as well as with global data sets for the water and energy cycle. Time series shows that the MERRA budgets can change with some of the variations in observing systems. We will present all terms of the budgets in MERRA including the time rates of change and analysis increments (tendency due to the analysis of observations).

  4. ALPENDRE Y ERA [Material gráfico

    OpenAIRE

    Fundación para la Etnografía y el Desarrollo de la Artesanía Canaria

    1990-01-01

    Antiguedad: SIGLO XIX Antrópicas: construcción de un camino que atraviesa la era. En el alpendre se encuentran basuras y planchas metálicas. Naturales: colonización vegetal. Clasificación del suelo: RÚSTICO Conjunto de era y alpendre. La era es de planta circular, de tierra y conjunto de piedras, localizándose en un lomo. El alpendre está excavado en la roca, a modo de cuatro compartimentos de diferentes tamaños en donde se amaraban los anima-les a una serie de palos horizontales q...

  5. A call for an international network of genomic observatories (GOs

    Directory of Open Access Journals (Sweden)

    Davies Neil

    2012-07-01

    Full Text Available Abstract We are entering a new era in genomics–that of large-scale, place-based, highly contextualized genomic research. Here we review this emerging paradigm shift and suggest that sites of utmost scientific importance be expanded into ‘Genomic Observatories’ (GOs. Investment in GOs should focus on the digital characterization of whole ecosystems, from all-taxa biotic inventories to time-series ’omics studies. The foundational layer of biodiversity–genetic variation–would thus be mainstreamed into Earth Observation systems enabling predictive modelling of biodiversity dynamics and resultant impacts on ecosystem services.

  6. 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.

  7. Databases and Web Tools for Cancer Genomics Study

    Institute of Scientific and Technical Information of China (English)

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

    2015-01-01

    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 com-prehensiveness, 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.

  8. Key Exoplanets in the Era of JWST

    Science.gov (United States)

    Batalha, Natasha; Mandell, Avi; Lewis, Nikole K.; Pontoppidan, Klaus

    2017-01-01

    In 2018, exoplanet science will enter a new era with the launch of the James Webb Space Telescope (JWST). With JWST's observing power, several studies have sought to characterize how the instruments will perform and what atmospheric spectral features could theoretically be detected using transmission spectroscopy. With just two years left until launch, it is imperative that the exoplanet community begins to digest and integrate these studies into their observing plans and strategies. In order to encourage this and to allow all members of the community access to JWST simulations, we present here an open source tool for creating observation simulations of all observatory-supported time-series spectroscopy modes. We describe our tool, PandExo and use it to calculate the expected signal-to-noise ratio (SNR) for every confirmed planetary system with Jhours are needed to attain a SNR of 5 on key molecular absorption bands of H2O, CH4, and CO. We end by determining the number of planets (hot Jupiters, warm Neptunes, super-Earths, etc.) that are currently attainable with JWST.

  9. 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...

  10. 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...

  11. 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...

  12. Modelling Viking ERA Water Ice Clouds

    Science.gov (United States)

    Tamppari, L. K.; Wilson, R. J.; Zurek, R. W.; Paige, D. A.

    1999-09-01

    Water ice clouds in the Martian atmosphere are increasingly becoming recognized as a potentially important aspect of the water cycle and potentially potent mechanism for climte change. In particular, it has been suggested that water ice cloud formation can control the extent of the water column (Kahn, 1990). Further, water ice cloud formation may scavenge dust out of the atmosphere and may prevent cross-equatorial water transport, especially in the northern summer (Clancy, 1996). To address these questions, a combintion of modelling and data analysis can be used. The Viking era water ice clouds were identified (Tamppari et al., 1998) from the IRTM data set. Following that, Tamppari et al. (1999) attempted to identify the cloud opacity and temperature using a 1D, 2-layer ice and dust cloud model. However, data fits were sensitive to the surface temperature, dust opacity and temperature, and ice particle mode radius value, as well as the water ice cloud temperature and opacity. This resulted in an underconstrained problem. A Mars GCM will be employed to provide realistic atmospheric conditions as a function of season, latitude, and longitude. The non-unit surface emissivities (Christensen, 1998) will be added and synthetic IRTM brightness temperatures will be calculated. Results of the comparison of the synthetic and measured brightness temperatures will be presented.

  13. Belydenisgebondenheid in ’n postmoderne era

    Directory of Open Access Journals (Sweden)

    C.F.C. Coetzee

    2010-07-01

    Full Text Available The binding to confessions in a postmodern era We are experiencing a paradigm shift between Modernism and Postmodernism in almost every sphere of life, and also in the sphere of church and theology. This paradigm shift has far-reaching consequences, especially for churches in the reformed tradition and the practice of reformed theology as far as the binding to the confessions is concerned. From the viewpoint of Postmodernism, there is no absolute truth. This applies also to Scripture. As far as their hermeneutics is concerned, they adhere to the principles of deduction as formulated by Derrida. According to these principles, a text has no intrinsic meaning but rather creates meaning. There is nothing outside the text. This leads to radical relativism. Over against the postmodern view, reformed hermeneutics maintain that Scripture is the infallible Word of God and proclaims everlasting truth. In the confessions this truth is formulated. Confessions belong to the very essence of the church. The binding to the confessions therefore applies to every member as well as all office-bearers and also professors in theology. In this regard there can be no compromise with Postmodernism.

  14. 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.

  15. Multi-omic data integration and analysis using systems genomics approaches

    DEFF Research Database (Denmark)

    Suravajhala, Prashanth; Kogelman, Lisette; Kadarmideen, Haja

    2016-01-01

    In the past years, there has been a remarkable development of high-throughput omics (HTO) technologies such as genomics, epigenomics, transcriptomics, proteomics and metabolomics across all facets of biology. This has spearheaded the progress of the systems biology era, including applications on ...

  16. 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 an

  17. 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).

  18. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

    DEFF Research Database (Denmark)

    Martin, Michael David; Cappellini, Enrico; Samaniego Castruita, Jose Alfredo;

    2013-01-01

    Responsible for the Irish potato famine of 1845-49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era str...

  19. Genome sequence analysis with MonetDB: a case study on Ebola virus diversity

    NARCIS (Netherlands)

    Cijvat, C.P.; Manegold, S.; Kersten, M.L.; Klau, G.W.; Schoenhuth, 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 results in terabytes of data to be stored and analysed. Biologists are often exposed to excessively time consuming and error-prone data management an

  20. 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 t

  1. 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…

  2. 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…

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

    NARCIS (Netherlands)

    Cijvat, C.P.; Manegold, S.; Kersten, M.L.; Klau, G.W.; Schoenhuth, 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 a

  4. 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.

  5. 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...

  6. 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

  7. Genome sequence analysis with MonetDB: a case study on Ebola virus diversity

    NARCIS (Netherlands)

    C.P. Cijvat (Robin); S. Manegold (Stefan); M.L. Kersten (Martin); G.W. Klau (Gunnar); A. Schönhuth (Alexander); T. Marschall (Tobias); Y. Zhang (Ying)

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    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 t

  9. Beijing New Era Architectural Design Co.,Ltd.

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Beijing New Era Architectural Design Co.,Ltd., an A-Class design enterprise approved by the Ministry of Construction, provides services of industrial and civil architectural design, interior decoration, consultation for real estate development,

  10. 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.

  11. 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

  12. Dragon paves the way for new spaceflight era

    Science.gov (United States)

    Gwynne, Peter

    2012-07-01

    The success of the first private mission to the International Space Station (ISS) has opened up a new era in commercial spaceflight after SpaceX's Dragon capsule splashed down safely in the Pacific Ocean on 31 May.

  13. 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

  14. Planning for the Future of Epidemiology in the Era of Big Data and Precision Medicine.

    Science.gov (United States)

    Khoury, Muin J

    2015-12-15

    We live in the era of genomics and big data. Evaluating the impact on health of large-scale biological, social, and environmental data is an emerging challenge in the field of epidemiology. In the past 3 years, major discussions and plans for the future of epidemiology, including with several recommendations for actions to transform the field, have been launched by 2 institutes within the National Institutes of Health. In the present commentary, I briefly explore the themes of these recommendations and their effects on leadership, resources, cohort infrastructure, and training. Ongoing engagement within the epidemiology community is needed to determine how to shape the evolution of the field and what truly matters for changing population health. We also need to assess how to leverage existing epidemiology resources and develop new studies to improve human health. Readers are invited to examine these recommendations, consider others that might be important, and join in the conversation about the future of epidemiology.

  15. 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.

  16. 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...

  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.

  18. 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.

  19. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. 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.

  1. [Prolactinoma treatment status in the cabergoline era].

    Science.gov (United States)

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

    2011-11-01

    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.

  2. 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.

  3. 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

  4. Plant Genome Duplication Database.

    Science.gov (United States)

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  5. 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. falciparu

  6. 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.

  7. Insights from genomics into bacterial pathogen populations.

    Directory of Open Access Journals (Sweden)

    Daniel J Wilson

    2012-09-01

    Full Text Available Bacterial pathogens impose a heavy burden of disease on human populations worldwide. The gravest threats are posed by highly virulent respiratory pathogens, enteric pathogens, and HIV-associated infections. Tuberculosis alone is responsible for the deaths of 1.5 million people annually. Treatment options for bacterial pathogens are being steadily eroded by the evolution and spread of drug resistance. However, population-level whole genome sequencing offers new hope in the fight against pathogenic bacteria. By providing insights into bacterial evolution and disease etiology, these approaches pave the way for novel interventions and therapeutic targets. Sequencing populations of bacteria across the whole genome provides unprecedented resolution to investigate (i within-host evolution, (ii transmission history, and (iii population structure. Moreover, advances in rapid benchtop sequencing herald a new era of real-time genomics in which sequencing and analysis can be deployed within hours in response to rapidly changing public health emergencies. The purpose of this review is to highlight the transformative effect of population genomics on bacteriology, and to consider the prospects for answering abiding questions such as why bacteria cause disease.

  8. Role of genomics in eliminating health disparities

    Directory of Open Access Journals (Sweden)

    Meghana V Kashyap

    2015-01-01

    Full Text Available The Texas Center for Health Disparities, a National Institute on Minority Health and Health Disparities Center of Excellence, presents an annual conference to discuss prevention, awareness education, and ongoing research about health disparities both in Texas and among the national population. The 2014 Annual Texas Conference on Health Disparities brought together experts in research, patient care, and community outreach on the "Role of Genomics in Eliminating Health Disparities." Rapid advances in genomics and pharmacogenomics are leading the field of medicine to use genetics and genetic risk to build personalized or individualized medicine strategies. We are at a critical juncture of ensuring such rapid advances benefit diverse populations. Relatively few forums have been organized around the theme of the role of genomics in eliminating health disparities. The conference consisted of three sessions addressing "Gene-Environment Interactions and Health Disparities," "Personalized Medicine and Elimination of Health Disparities," and "Ethics and Public Policy in the Genomic Era." This article summarizes the basic science, clinical correlates, and public health data presented by the speakers.

  9. Coastal Cover Change Analysis Program (C-CAP) Great Lakes 1996-era and 2001-era land cover change analysis (NODC Accession 0042437)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains the 1996-era and 2001-era classifications of Great lakes and can be used to analyze change. This imagery was collected as part of the...

  10. 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...

  11. 大肠杆菌YggG与结合蛋白Era的相互作用研究%Interaction between YggG and Era in Escherichia coli

    Institute of Scientific and Technical Information of China (English)

    黄勇; 陈苏民; 黄庆生; 梅其炳

    2009-01-01

    Era是细菌生长必须的一高度保守的GTPase.yggG是从大肠杆菌全基因组文库中钓取并克隆的Era结合蛋白基因,进一步的研究表明该基因在大肠杆菌中的表达与环境应激相关,提示yggG基因产物参与细菌的应激调控.为了阐明YggG蛋白与Era蛋白间的相互关系,利用所构建的双启动子表达载体pDH2-YggG-Ptac-Era在同一细胞中同时表达YggG与Era蛋白,并通过免疫共沉淀实验检测细菌裂解产物YggG与Era蛋白间的相互作用;在此基础上,构建并表达纯化了GST融合的Era蛋白氨基端截短肽和Era羧基端截短肽,通过GsT Pull-down检测了Era不同功能区域与YggG蛋白间的相互作用.结果显示,Era/YggG复合物仅存在于同时过表达Era和YggG蛋白的细菌细胞内,不诱导Era或者不诱导YggG蛋白过表达,均检测不到Era/YggG复合物存在;纯化的GST不能Pull-down YggG蛋白,而纯化的GST融合的Era蛋白、Era氨基端截短肽及Era羧基端截短肽均可以Pull-dowrl YggG蛋白;GST融合Era氨基端截短肽和GST融合的Era蛋白对YggG蛋白结合作用明显高于GST融合的Era蛋白羧基端截短肽.上述结果说明,YggG是一大肠杆菌Era结合蛋白,YggG与Era的氨基端和羧基端的结合活性存在差异.%Era is a highly conserved GTPase essential for bacterial growth. yggG gene was identified to encod a Era-binding protein when using a digoxigenin-labeled Era protein to screen a phage expression library of Escherichia coli genomic DNA. Subsequent study showed the regulation of yggG gene was associated with environment stress, indicating yggG expression products involved in the stress regulation of bacteria responding to environment changes. To confirm the interactions between Era and YggG proteins when overexpressed, E. coli cells were exposed to a double promoter plasmid, pDH2-YggG-Ptac-Era that was induced to express the Era and YggG proteins by different induction methods. Immunoprecipitation of cell

  12. Biodiversity analysis in the digital era.

    Science.gov (United States)

    La Salle, John; Williams, Kristen J; Moritz, Craig

    2016-09-05

    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'.

  13. 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

  14. 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,

  15. Genome Mapping in Plant Comparative Genomics.

    Science.gov (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  16. Ontology for Genome Comparison and Genomic Rearrangements

    Directory of Open Access Journals (Sweden)

    Anil Wipat

    2006-04-01

    Full Text Available We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

  17. 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)

  18. Human Genomics in China——Ten Years Endeavor: From Planning to Implementation

    Institute of Scientific and Technical Information of China (English)

    CHEN Zhu; ZHAO Guo-Ping

    2009-01-01

    @@ Ten years ago, the Chinese National Human Genome Center at Shanghai (South Center, hereafter) was es-tablished in the Zhangjiang HiTech Park of Pudong District in Shanghai. To commemorate this important event, which marks the beginning of the Genomics Era in China, we specially organize a series of mini-reviews for this special issue. We hope that this effort may draw the attention of the Chinese life science research workers to collectively recall the short but fruitful history of human genome project and coordinately explore the trend and goal of the future development of this academic discipline in China.

  19. 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.

  20. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  1. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  2. Functional Genetics in the Post-genomics Era: Building a Better Roadmap in Drosophila

    OpenAIRE

    Kulathinal, Rob J.

    2013-01-01

    In this commentary, Rob Kulathinal describes two papers from the Perrimon laboratory, each describing a new online resource that can assist geneticists with the design of their RNAi experiments. Hu et al.’s “UP-TORR: online tool for accurate and up-to-date annotation of RNAi reagents” and “FlyPrimerBank: An online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents” are published, respectively, in this month’s issue of GENETICS and G3: Genes...

  3. Studying stress responses in the post-genomic era: its ecological and evolutionary role

    Indian Academy of Sciences (India)

    Jesper G Sørensen; Volker Loeschcke

    2007-04-01

    Most investigations on the effects of and responses to stress exposures have been performed on a limited number of model organisms in the laboratory. Here much progress has been made in terms of identifying and describing beneficial and detrimental effects of stress, responses to stress and the mechanisms behind stress tolerance. However, to gain further understanding of which genes are involved in stress resistance and how the responses are regulated from an ecological and evolutionary perspective there is a need to combine studies on multiple levels of biological organization from DNA to phenotypes. Furthermore, we emphasize the importance of studying ecologically relevant traits and natural or semi-natural conditions to verify whether the results obtained are representative of the ecological and evolutionary processes in the field. Here, we will review what we currently know about thermal adaptation and the role of different stress responses to thermal challenges in insects, particularly Drosophila. Furthermore, we address some key questions that require future attention.

  4. Challenges in phenotype definition in the whole-genome era: multivariate models of memory and intelligence.

    Science.gov (United States)

    Sabb, F W; Burggren, A C; Higier, R G; Fox, J; He, J; Parker, D S; Poldrack, R A; Chu, W; Cannon, T D; Freimer, N B; Bilder, R M

    2009-11-24

    Refining phenotypes for the study of neuropsychiatric disorders is of paramount importance in neuroscience. Poor phenotype definition provides the greatest obstacle for making progress in disorders like schizophrenia, bipolar disorder, Attention Deficit/Hyperactivity Disorder (ADHD), and autism. Using freely available informatics tools developed by the Consortium for Neuropsychiatric Phenomics (CNP), we provide a framework for defining and refining latent constructs used in neuroscience research and then apply this strategy to review known genetic contributions to memory and intelligence in healthy individuals. This approach can help us begin to build multi-level phenotype models that express the interactions between constructs necessary to understand complex neuropsychiatric diseases. These results are available online through the http://www.phenowiki.org database. Further work needs to be done in order to provide consensus-building applications for the broadly defined constructs used in neuroscience research.

  5. Suberin research in the genomics era--new interest for an old polymer.

    Science.gov (United States)

    Ranathunge, Kosala; Schreiber, Lukas; Franke, Rochus

    2011-03-01

    Suberin is an apoplastic biopolymer with tissue-specific deposition in the cell walls of the endo- and exodermis of roots, of periderms including wound periderm and other border tissues. Suberised cell walls contain both polyaliphatic and polyaromatic domains which are supposedly cross-linked. The predominant aliphatic components are ω-hydroxyacids, α,ω-diacids, fatty acids and primary alcohols, whereas hydroxycinnamic acids, especially ferulic acid, are the main components of the polyaromatic domain. Although the monomeric composition of suberin has been known for decades, its biosynthesis and deposition has mainly been a subject of speculation. Only recently, significant progress elucidating suberin biosynthesis has been achieved using molecular genetic approaches, especially in the model species Arabidopsis. In parallel, the long-standing hypothesis that suberin functions as an apoplastic barrier has been corroborated by sophisticated, quantitative physiological studies in the past decade. These studies demonstrated that suberised cell walls could act as barriers, minimising the movement of water and nutrients, restricting pathogen invasion and impeding toxic gas diffusion. In addition, suberised cell walls provide a barrier to radial oxygen loss from roots to the anaerobic root substrate in wetland plants. The recent onset of multidisciplinary approaches combining genetic, analytical and physiological studies has begun to deliver further insights into the physiological importance of suberin depositions in plants.

  6. New Challenges Facing Integrative Biological Science in the Post-Genomic Era

    Energy Technology Data Exchange (ETDEWEB)

    Oehmen, Chris S.; Straatsma, TP; Anderson, Gordon A.; Orr, Galya; Webb-Robertson, Bobbie-Jo M.; Taylor, Ronald C.; Mooney, Ryan W.; Baxter, Douglas J.; Jones, Donald R.; Dixon, David A.

    2006-06-01

    The future of biology will be increasingly driven by the fundamental paradigm shift from hypothesis-driven research to data-driven discovery research employing the massive amounts of available biological data. We identify key technological developments needed to enable this paradigm shift involving (1) the ability to store and manage extremely large datasets which are dispersed over a wide geographical area, (2) development of novel analysis and visualization tools which are capable of operating on enormous data resources without overwhelming researchers with unusable information, and (3) formalisms for integrating mathematical models of biosystems from the molecular level to the organism population level. This will require the development of tools which efficiently utilize high-performance compute power, large storage infrastructures and large aggregate memory architectures. The end result will be the ability of a researcher to integrate complex data from many different sources with simulations to analyze a given system at a wide range of temporal and spatial scales in a single conceptual model.

  7. 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...

  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 c...

  9. Bayesian molecular clock dating of species divergences in the genomics era.

    Science.gov (United States)

    dos Reis, Mario; Donoghue, Philip C J; Yang, Ziheng

    2016-02-01

    Five decades have passed since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species. This hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events. With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics and studying the macroevolutionary process of speciation and extinction to estimating a timescale for life on Earth.

  10. Between Two Fern Genomes

    OpenAIRE

    Sessa, Emily B.; Banks, Jo; Michael S Barker; Der, Joshua P; Duffy, Aaron M; Graham, Sean W.; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D; Kathleen M. Pryer; Rothfels, Carl J.; Roux, Stanley J.; Salmi, Mari L; Sigel, Erin M.

    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 divers...

  11. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  12. 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.

  13. 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

    2013-01-01

    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. PMID:23748955

  14. 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

    2017-03-09

    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).

  15. The role of protein structural analysis in the next generation sequencing era.

    Science.gov (United States)

    Yue, Wyatt W; Froese, D Sean; Brennan, Paul E

    2014-01-01

    Proteins are macromolecules that serve a cell's myriad processes and functions in all living organisms via dynamic interactions with other proteins, small molecules and cellular components. Genetic variations in the protein-encoding regions of the human genome account for >85% of all known Mendelian diseases, and play an influential role in shaping complex polygenic diseases. Proteins also serve as the predominant target class for the design of small molecule drugs to modulate their activity. Knowledge of the shape and form of proteins, by means of their three-dimensional structures, is therefore instrumental to understanding their roles in disease and their potentials for drug development. In this chapter we outline, with the wide readership of non-structural biologists in mind, the various experimental and computational methods available for protein structure determination. We summarize how the wealth of structure information, contributed to a large extent by the technological advances in structure determination to date, serves as a useful tool to decipher the molecular basis of genetic variations for disease characterization and diagnosis, particularly in the emerging era of genomic medicine, and becomes an integral component in the modern day approach towards rational drug development.

  16. Cardiovascular pharmacogenetics in the SNP era.

    Science.gov (United States)

    Mooser, V; Waterworth, D M; Isenhour, T; Middleton, L

    2003-07-01

    In the past pharmacological agents have contributed to a significant reduction in age-adjusted incidence of cardiovascular events. However, not all patients treated with these agents respond favorably, and some individuals may develop side-effects. With aging of the population and the growing prevalence of cardiovascular risk factors worldwide, it is expected that the demand for cardiovascular drugs will increase in the future. Accordingly, there is a growing need to identify the 'good' responders as well as the persons at risk for developing adverse events. Evidence is accumulating to indicate that responses to drugs are at least partly under genetic control. As such, pharmacogenetics - the study of variability in drug responses attributed to hereditary factors in different populations - may significantly assist in providing answers toward meeting this challenge. Pharmacogenetics mostly relies on associations between a specific genetic marker like single nucleotide polymorphisms (SNPs), either alone or arranged in a specific linear order on a certain chromosomal region (haplotypes), and a particular response to drugs. Numerous associations have been reported between selected genotypes and specific responses to cardiovascular drugs. Recently, for instance, associations have been reported between specific alleles of the apoE gene and the lipid-lowering response to statins, or the lipid-elevating effect of isotretinoin. Thus far, these types of studies have been mostly limited to a priori selected candidate genes due to restricted genotyping and analytical capacities. Thanks to the large number of SNPs now available in the public domain through the SNP Consortium and the newly developed technologies (high throughput genotyping, bioinformatics software), it is now possible to interrogate more than 200,000 SNPs distributed over the entire human genome. One pharmacogenetic study using this approach has been launched by GlaxoSmithKline to identify the approximately 4% of

  17. 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.

  18. Tensor Modes Damping in Matter and Vacuum Dominated Era

    CERN Document Server

    Khodagholizadeh, Jafar; Asgari, Ali A

    2016-01-01

    The present paper has developed an integro-differential equation to propagate cosmological gravitation waves in matter-dominated era in accounting for the presence of free streaming neutrinos as a traceless transverse tensor part of the anisotropic stress tensor. Its focus is on short and long wavelengths of GWs that enter the horizon in matter-dominated era. Results show that the anisotropic stress reduces the squared amplitude by $ 0.03\\%$ for wavelengths, entering the horizon during matter-dominated phase. This reduction is less for those wavelengths that enter the horizon at $ \\Lambda $ dominated era in flat spacetime. All of the calculations have been done in closed spacetime and the results have been compared with the radiation-dominated case for both flat and closed spacetimes. Finally the paper investigates the effect of closed background on the amplitude of the gravitational waves.

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

    DEFF Research Database (Denmark)

    2017-01-01

    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...... 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......, Kanstrup, Huybrechts, et al. 2016). The five papers in this special issue demonstrate how different perspectives on participation can be used and reconfigured in diverse contemporary contexts. The rich cases show how participatory design’s democratic and political values and ideals continue to be applied...

  20. %ERA: A SAS Macro for Extended Redundancy Analysis

    Directory of Open Access Journals (Sweden)

    Pietro Giorgio Lovaglio

    2016-10-01

    Full Text Available A new approach to structural equation modeling based on so-called extended redundancy analysis has been recently proposed in the literature, enhanced with the added characteristic of generalizing redundancy analysis and reduced-rank regression models for more than two blocks. In this approach, the relationships between the observed exogenous variables and the observed endogenous variables are moderated by the presence of unobservable composites that were estimated as linear combinations of exogenous variables, permitting a great flexibility to specify and fit a variety of structural relationships. In this paper, we propose the SAS macro %ERA to specify and fit structural relationships in the extended redundancy analysis (ERA framework. Two examples (simulation and real data are provided in order to reproduce results appearing in the original article where ERA was proposed.

  1. The reheating era leptogenesis in models with seesaw mechanism

    CERN Document Server

    Hamada, Yuta; Yasuhara, Daiki

    2016-01-01

    Observed baryon asymmetry can be achieved not only by the decay of right-handed neutrinos but also by the scattering processes in the reheating era. In the latter scenario, new physics in high energy scale does not need to be specified, but only two types of the higher dimensional operator of the standard model particles are assumed in the previous work. In this paper, we examine the origin of the higher dimensional operators assuming models with a certain seesaw mechanism at the high energy scale. The seesaw mechanism seems to be a simple realization of the reheating era leptogenesis because the lepton number violating interaction is included. We show that the effective interaction giving CP violating phases is provided in the several types of models and also the reheating era leptogenesis actually works in such models. Additionally, we discuss a possibility for lowering the reheating temperature in the radiative seesaw models, where the large Yukawa coupling is naturally realized.

  2. Biomedical innovation in the era of health care spending constraints.

    Science.gov (United States)

    Robinson, James C

    2015-02-01

    Insurers, hospitals, physicians, and consumers are increasingly weighing price against performance in their decisions to purchase and use new drugs, devices, and other medical technologies. This approach will tend to affect biomedical innovation adversely by reducing the revenues available for research and development. However, a more constrained funding environment may also have positive impacts. The passing era of largely cost-unconscious demand fostered the development of incremental innovations priced at premium levels. The new constrained-funding era will require medical technology firms to design their products with the features most valued by payers and patients, price them at levels justified by clinical performance, and manage distribution through organizations rather than to individual physicians. The emerging era has the potential to increase the social value of innovation by focusing industry on design, pricing, and distribution principles that are more closely aligned with the preferences-and pocketbooks-of its customers. Project HOPE—The People-to-People Health Foundation, Inc.

  3. 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

  4. DNA sequencing leads to genomics progress in China

    Institute of Scientific and Technical Information of China (English)

    WU JiaYan; XIAO JingFa; ZHANG RuoSi; YU Jun

    2011-01-01

    1 Science in the large-scale sequencing era Ten years ago,the first draft sequence assembly of the human genome was completed [1],bringing biomedical research one-step closer toward the goal of revolutionizing diagnosis,prevention,and treatment of human diseases.Recently,journalists from the journal Nature surveyed more than 1000 life scientists regarding this laudable aim [2],obtaining substantially negative responses [3].However,almost all of those surveyed had been influenced,in one way or another,by the availability of the human genome sequence,and they also agreed with the notion that the "sequence is the start." The complexity of genome biology and almost every aspect of human biology is far greater than previously thought [4].

  5. RNAi and functional genomics in plant parasitic nematodes.

    Science.gov (United States)

    Rosso, M N; Jones, J T; Abad, P

    2009-01-01

    Plant nematology is currently undergoing a revolution with the availability of the first genome sequences as well as comprehensive expressed sequence tag (EST) libraries from a range of nematode species. Several strategies are being used to exploit this wealth of information. Comparative genomics is being used to explore the acquisition of novel genes associated with parasitic lifestyles. Functional analyses of nematode genes are moving toward larger scale studies including global transcriptome profiling. RNA interference (RNAi) has been shown to reduce expression of a range of plant parasitic nematode genes and is a powerful tool for functional analysis of nematode genes. RNAi-mediated suppression of genes essential for nematode development, survival, or parasitism is revealing new targets for nematode control. Plant nematology in the genomics era is now facing the challenge to develop RNAi screens adequate for high-throughput functional analyses.

  6. Antidepressant drug discovery in the postgenomic era.

    Science.gov (United States)

    Holsboer, F

    2001-10-01

    The progress made in genome research raises the question whether the new knowledge bases that have emerged may also lead to better antidepressants. The past has seen many remarkable improvements over traditional drugs, but not a real breakthrough. More recently hypothesis-driven research in depression has focussed upon stress-hormone regulation as a possible target, but validation of new drugs is not yet in sight. In parallel, we see an upsurge of systematic unbiased research in a biotechnology-driven drug discovery effort. This research can only lead to results if clinical research adapts to these new demands by phenotyping depressed patients not only according to psychopathological characteristics but also by utilising functional (e.g. neuroendocrine, neuropsychological, neurophysiological, neuroimaging and clinical drug response) data that are to be correlated with data from genotyping. To achieve the goal of genotype/phenotype-based differential therapy, large-scale efforts with regards to both patient samples and genotyping capacities are needed. In the long term, increasingly detailed patient information, if translated into specific pharmacological treatments, will lead to customized drugs and thus to a partial fragmentation of the antidepressant market. Concurrently, the improved genotyping/phenotyping efforts will also lead to more widely applicable drugs that promise to avoid side effects and refractoriness and also to hasten the time to onset of action. Once these goals are achieved notorious undertreatment of depression may come to an end.

  7. La era de la información

    OpenAIRE

    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...

  8. Teaching in a Chaotic Era: A Complexity Pedagogy Manifesto

    OpenAIRE

    Brailas, Alexios

    2016-01-01

    We live in an era of constant changes and destabilization, in the era of liquid reality. Modern students are daily confronted with an enormous volume of information to cope with, without being disorganized and exhausted at the end of the day. A simple Google search results in million entries, each one pointing to many other web objects. The human brain, the brain of the caveman, is not prepared to handle such a vast information volume. How to teach this skill? Who will be the teacher for this...

  9. Gamma-Ray Bursts in the Swift Era

    Institute of Scientific and Technical Information of China (English)

    Bing Zhang

    2007-01-01

    Since the successful launch of NASA's dedicated gamma-ray burst (GRB) mission,Swift, the study of cosmological GRBs has entered a new era. Here I review the rapid observational and theoretical progress in this dynamical research field during the first two-year of the Swift mission, focusing on how observational breakthroughs have revolutionized our understanding of the physical origins of GRBs. Besides summarizing how Swift helps to solve some pre-Swift mysteries, I also list some outstanding problems raised by the Swift observations. An outlook of GRB science in the future, especially in the GLAST era, is briefly discussed.

  10. Gamma-Ray Bursts in the Swift Era

    CERN Document Server

    Zhang, B

    2007-01-01

    Since the successful launch of NASA's dedicated gamma-ray burst (GRB) mission, Swift, the study of cosmological GRBs has entered a new era. Here I review the rapid observational and theoretical progress in this dynamical research field during the first two-year of the Swift mission, focusing on how observational breakthroughs have revolutionized our understanding of the physical origins of GRBs. Besides summarizing how Swift helps to solve some pre-Swift mysteries, I also list some outstanding problems raised by the Swift observations. An outlook of GRB science in the future, especially in the GLAST era, is briefly discussed.

  11. 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.

  12. 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

  13. Survival strategies in the era of managed care.

    Science.gov (United States)

    Rudomin, M L; Spirakes, A S

    1996-02-01

    The era of managed care has forced an unprecedented restructuring of the health care environment. As hospitals downsize in response, materiel managers should consider adopting strategies that may help ensure their survival, including innovative approaches to supply management and the development of individual responses that will best position them to succeed in this new reality.

  14. Using Stephen Crane's "Maggie" To Teach the Progressive Era.

    Science.gov (United States)

    Gerwin, David; Manolios, Vassilios; Popodopoulos, Lia

    1999-01-01

    Outlines a lesson plan designed for an eleventh-grade U.S. history class in which the students learn about the Progressive Era by reading Stephen Crane's "Maggie: A Girl of the Streets." Explains that students analyze point of view, role play a talk show, write an essay, and complete a long-term research project. (CMK)

  15. 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.

  16. The 2006 ERA-EDTA Registry annual report: a precis

    NARCIS (Netherlands)

    V.S. Stel; A. Kramer; C. Zoccali; K.J. Jager

    2009-01-01

    Introduction: This paper provides a summary of the 2006 European Renal Association-European Dialysis and Transplant Association (ERA-EDTA) Registry report. Methods: Data on renal replacement therapy (RRT) were available from 50 national and regional registries in 28 countries in Europe and bordering

  17. 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…

  18. Music Teacher Stress in the Era of Accountability

    Science.gov (United States)

    Shaw, Ryan D.

    2016-01-01

    While there is an established body of literature on teacher stress and on the factors that may make music teaching uniquely stressful, there has been little or no research on how the recent era of accountability influences music teacher stress. In this article, I review the literature on music teacher stress and on how accountability reforms may…

  19. Academic knowledge in the digital era: top 5 podcasts

    OpenAIRE

    Mollett, Amy

    2011-01-01

    Academic research and debate seems to be finding a new home online, visible in the growth of academic blogging, tweeting, and the use of open access archives. LSE Impact Blog editor Amy Mollett recommends 5 podcasts and videocasts on the subject of academic knowledge in the digital era.

  20. Rethinking Themes for Teaching the Era of the Cold War.

    Science.gov (United States)

    Rosenberg, Norman L.; Rosenberg, Emily S.

    1994-01-01

    Maintains that the "tried and true" strategies for teaching about the early Cold War years highlight the U.S. response to Soviet expansionism. Identifies four other focus themes: (1) debates over mass culture and youth culture; (2) gender and sexuality; (3) the civil rights era; and (4) rethinking the cold war itself. (CFR)

  1. Radiation dominated era and the power of general relativity

    CERN Document Server

    Corda, Christian

    2012-01-01

    An analysis in the framework of the radiation dominated era permits to put bounds on the weak modification of general relativity which arises from the Lagrangian R^{1+epsilon}. Such a theory has been recently discussed in various papers in the literature. The new bounds together with previous ones in the literature rule out this theory in an ultimate way.

  2. 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…

  3. La era de la información

    Directory of Open Access Journals (Sweden)

    Mauro Florez Calderón

    2011-01-01

    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. 

  4. 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

  5. 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

  6. 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. Usi

  7. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2003-01-01

    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. Usi

  8. Directed genome engineering for genome optimization.

    Science.gov (United States)

    D'Halluin, Kathleen; Ruiter, Rene

    2013-01-01

    The ability to develop nucleases with tailor-made activities for targeted DNA double-strand break induction at will at any desired position in the genome has been a major breakthrough to make targeted genome optimization feasible in plants. The development of site specific nucleases for precise genome modification has expanded the repertoire of tools for the development and optimization of traits, already including mutation breeding, molecular breeding and transgenesis.Through directed genome engineering technology, the huge amount of information provided by genomics and systems biology can now more effectively be used for the creation of plants with improved or new traits, and for the dissection of gene functions. Although still in an early phase of deployment, its utility has been demonstrated for engineering disease resistance, herbicide tolerance, altered metabolite profiles, and for molecular trait stacking to allow linked transmission of transgenes. In this article, we will briefly review the different approaches for directed genome engineering with the emphasis on double strand break (DSB)-mediated engineering to-wards genome optimization for crop improvement and towards the acceleration of functional genomics.

  9. Genomic Data Commons | Office of Cancer Genomics

    Science.gov (United States)

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  10. 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,...

  11. 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.

  12. 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.

  13. 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.

  14. Genomics of Sorghum

    OpenAIRE

    PATERSON, ANDREW H

    2008-01-01

    Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relatin...

  15. National Human Genome Research Institute

    Science.gov (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... Landscape Social Media Videos Image Gallery Fact Sheets Human Genome Project Clinical Studies Genomic Careers DNA Day Calendar ...

  16. Eraõiguse normid avaliku korra osana / Illimar Pärnamägi

    Index Scriptorium Estoniae

    Pärnamägi, Illimar

    2016-01-01

    Avaliku korra mõistest, eraõiguslikud suhted avaliku korra osana. Avaliku korra osaks olevast korrakaitseseadusest. Korrakaitseorganite pädevusest ja volitustest, era- ja avaliku õiguse eristamisest ohutõrjeõiguslikus kontekstis. Politseilikult kaitstavatest eraõiguslikest suhetest avaliku korra osana

  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. Chicken's Genome Decoded

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ After completing the work on mapping chicken genome sequence and chicken genome variation in early March, 2004, two international research consortiums have made significant progress in reading the maps, shedding new light on the studies into the first bird as well as the first agricultural animal that has its genome sequenced and analyzed in the world.

  19. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  20. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  1. 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

  2. [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.

  3. [Genomics and functional genomics in microbiology].

    Science.gov (United States)

    Encarnación-Guevara, Sergio

    2006-01-01

    Functional genomics is changing our understanding of biology and changing our approach to biological research. It brings about concerted, high-throughput genetics with analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome-sequencing projects: what is the biological function of each and every gene? Functional genomics is stimulating a change in the research paradigm away from the analysis of single genes, proteins, or metabolites towards the analysis of each of these parameters on a global scale. By identifying and measuring several, if not the entire, molecular group of actors that take part in a given biological process, functional genomics offers the panorama of obtaining a truly holistic representation of life. Functional genomics methods are defined by high-throughput methods which are, not necessarily hypothesis-dependent. They offer insights into mRNA expression, protein expression, protein localization, and protein interactions and may cast light on the flow of information within signaling pathways. At its beginning, biology involved observing nature and experimenting on its isolated parts. Genomic research now generates new types of complex observational data derived from nature. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline on microbiology research.

  4. Comparison of clinical characteristics and survival on patients with idiopathic pulmonary arterial hypertension and familial pulmonary arterial hypertension during conventional therapy era and targeted therapy era

    Institute of Scientific and Technical Information of China (English)

    徐希奇

    2014-01-01

    Objective To compare the clinical characteristics and survival on Chinese patients with idiopathic pulmonary arterial hypertension(IPAH)and familiar pulmonary arterial hypertension(FPAH)during conventional therapy era and targeted therapy era.Methods IPAH and FPAH patients who were referred between Jan 1999and Oct 2004 in Fuwai Hospital were defined as conventional therapy era group(before 2005 no PAH-specific drug was available in China).All patients in this group

  5. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    . 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...

  6. Microbial genomic taxonomy.

    Science.gov (United States)

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-12-23

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.

  7. UCSC genome browser tutorial.

    Science.gov (United States)

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/.

  8. Whole-exome/genome sequencing and genomics.

    Science.gov (United States)

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

    2013-12-01

    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  9. GENÉTICA MOLECULAR Y BIOGERONTOLOGÍA EN LA ERA POSGENÓMICA:: UN ENFOQUE EN LAS SIRTUINAS Molecular Genetics of Aging in the Postgenomic Era:: A Focus on Sirtuins

    Directory of Open Access Journals (Sweden)

    SHADAY MICHÁN

    and automated sequencing, which allowed later to determine the anatomy of genomes. All of these discoveries have pushed the evolution of biomedicine towards the genomic and postgenomic eras, in which the use of reverse genetics prevails over the basic or direct one. Furthermore, it emerges the molecular genetics, the functional genomics and the diverse -omics- technologies that together pretend to understand, in an integrative way, the function of all of the genome components and its products. Biogerontology, discipline that studies the biological mechanisms of aging, is one of the fields that has developed notoriously in the last 15 years and reflects the scientific advances of the postgenomic era. Currently, there have been identified several gerontogenes and molecular pathways that modify and regulate age-related processes and diseases. Among these genes are the sirtuins, an evolutionarily preserved family of genes, which codify for proteins with NAD+ dependent deacetylase activity and that play an important role on aging. In this work, we review different reverse genetics approaches that have been used in order to identify some of the functions of these genes in mammals.

  10. 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

    2017-01-25

    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.

  11. Eras of Web Mapping Developments: Past, Present and Future

    Science.gov (United States)

    Veenendaal, Bert

    2016-06-01

    Developments in web mapping and web based geographic information systems (GIS) have evolved rapidly over the past two decades. What began as online map images available to a small group of geospatial experts and professionals has developed to a comprehensive and interactive web map based on integrated information from multiple sources and manipulated by masses of users globally. This paper introduces a framework that outlines the eras of web mapping and significant developments among those eras. From this framework, some of the influences and trends can be determined, particularly those in relation to the development of technologies and their relation to the growth in the number and diversity of users and applications that utilise web mapping and geospatial information online.

  12. Current and Future Treatment of Hypertension in the SPRINT Era.

    Science.gov (United States)

    Phillips, Robert A

    2015-01-01

    Based on the SPRINT trial, it is highly likely that new SPRINT-era guidelines will establish a blood pressure (BP) goal of SPRINT demonstrated that assignment to an intensive-treatment systolic BP (SBP) goal of SPRINT-era guidelines in the elderly, African Americans, and patients with uncomplicated essential hypertension, diabetes, chronic kidney disease, cardiovascular disease, and coronary artery disease. Specific attention is paid to BP goals and preferred pharmacological antihypertensive therapy in these populations, and an algorithm that incorporates the SPRINT trial results is presented. Inhibitors of the renin-angiotensin-aldosterone system as well as calcium channel blockers are universally accepted as first-line therapy in uncomplicated hypertension, but controversy exists over the role of thiazide diuretics and beta blockers. This review also discusses a physiologically and outcomes-based approach to combination therapy for treatment of hypertension.

  13. 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.

  14. Inherently safe reactors and a second nuclear era.

    Science.gov (United States)

    Weinberg, A M; Spiewak, I

    1984-06-29

    The Swedish PIUS reactor and the German-American small modular high-temperature gas-cooled reactor are inherently safe-that is, their safety relies not upon intervention of humans or of electromechanical devices but on immutable principles of physics and chemistry. A second nuclear era may require commercialization and deployment of such inherently safe reactors, even though existing light-water reactors appear to be as safe as other well-accepted sources of central electricity, particularly hydroelectric dams.

  15. 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...

  16. Reintegration of the Iraqi Military in Post-Conflict Era

    Science.gov (United States)

    2005-03-01

    NAVAL POSTGRADUATE SCHOOL THESIS Approved for public release; distribution is unlimited REINTEGRATION OF THE IRAQI MILITARY IN POST...DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE: Reintegration of the Iraqi Military in Post-Conflict Era. 6. AUTHOR(S) Ertürk, Sait 5...process of the United States led coalition is to be successful . The fulcrum of power in Iraq has always been the internecine ethnic, religious, and

  17. The impact of technological era in human resource management

    OpenAIRE

    2016-01-01

    The Impact of the Technological Era in Human Resource Management This work project is a literature review, which covers current studies (theoretical and empirical) on electronic Human Resource Management, human resources analytics and telework, and discusses some implications of the adoption of technology in human resource management processes. The Work Project presents and discusses different and contradictory perspectives between empirical and theoretical studies, demonstrating that t...

  18. A new era of catalysis: efficiency, value, and sustainability.

    Science.gov (United States)

    Cheng, Soofin; Lin, Shawn D

    2014-06-01

    Value proposition: Global warming and climate change urge the chemical industry to develop new processes, in which sustainability is a necessity and requirement. Catalysis is recognized to be one of the key technologies in enabling sustainability. This special issue, assembled by guest editors Soofing Chen and Shawn D. Lin, highlights some of the best work presented at "The 6th Asia-Pacific Congress on Catalysis (APCAT-6)", with as major theme "New Era of Catalysis: Efficiency, Value, and Sustainability".

  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. 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

  1. Language Policy in the KMT and DPP eras

    OpenAIRE

    Klöter, Henning

    2008-01-01

    The revival of the Taiwanese language (Taiyu) in the past two decades is a significant about-face, after the restrictive measures that the government has adopted for local languages in the past. This article compares the treatment of Taiyu by official language planning agencies during the Kuomintang) KMT and Democratic Progressive Party (DPP) eras. It focuses on the debates on the creation of a written norm for Taiyu. Attention is also given to the activities of non-governmental language revi...

  2. Stability analysis of the Martian obliquity during the Noachian era

    OpenAIRE

    2011-01-01

    Abstract We performed numerical simulations of the obliquity evolution of Mars during the Noachian era, at which time the giant planets were on drastically different orbits than today. For the preferred primordial configuration of the planets we find that there are two large zones where the Martian obliquity is stable and oscillates with an amplitude lower than 20?. These zones occur at obliquities below 30?and above 60?; intermediate values show either resonant or chaotic behaviou...

  3. ERA's: A New Approach to Small Sample Theory

    OpenAIRE

    1982-01-01

    This article proposes a new approach to small sample theory that achieves a meaningful integration of earlier directions of research in this field. The approach centers on the constructive technique of approximating distributions developed recently by the author in [10]. This technique utilizes extended rational approximants (ERA's) which methods (such as those based on asymptotic expansions) and which simultaneously blend information from diverse analytic, numerical and experimental sources....

  4. The impact of technological era in human resource management

    OpenAIRE

    Ritter, Andrea Fernandes Rodrigues

    2016-01-01

    The Impact of the Technological Era in Human Resource Management This work project is a literature review, which covers current studies (theoretical and empirical) on electronic Human Resource Management, human resources analytics and telework, and discusses some implications of the adoption of technology in human resource management processes. The Work Project presents and discusses different and contradictory perspectives between empirical and theoretical studies, demonstrating that t...

  5. 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.

  6. Hepatitis C virus in the new era: perspectives in epidemiology, prevention, diagnostics and predictors of response to therapy.

    Science.gov (United States)

    Ansaldi, Filippo; Orsi, Andrea; Sticchi, Laura; Bruzzone, Bianca; Icardi, Giancarlo

    2014-08-07

    Despite the great successes achieved in the fields of virology and diagnostics, several difficulties affect improvements in hepatitis C virus (HCV) infection control and eradication in the new era. New HCV infections still occur, especially in some of the poorest regions of the world, where HCV is endemic and long-term sequelae have a growing economic and health burden. An HCV vaccine is still no available, despite years of researches and discoveries about the natural history of infection and host-virus interactions: several HCV vaccine candidates have been developed in the last years, targeting different HCV antigens or using alternative delivery systems, but viral variability and adaption ability constitute major challenges for vaccine development. Many new antiviral drugs for HCV therapy are in preclinical or early clinical development, but different limitations affect treatment validity. Treatment predictors are important tools, as they provide some guidance for the management of therapy in patients with chronic HCV infection: in particular, the role of host genomics in HCV infection outcomes in the new era of direct-acting antivirals may evolve for new therapeutic targets, representing a chance for modulated and personalized treatment management, when also very potent therapies will be available. In the present review we discuss the most recent data about HCV epidemiology, the new perspectives for the prevention of HCV infection and the most recent evidence regarding HCV diagnosis, therapy and predictors of response to it.

  7. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu

    2014-01-01

    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  8. Genome-Editing Technologies for Enhancing Plant Disease Resistance

    Science.gov (United States)

    Andolfo, Giuseppe; Iovieno, Paolo; Frusciante, Luigi; Ercolano, Maria R.

    2016-01-01

    One of the greatest challenges for agricultural science in the 21st century is to improve yield stability through the progressive development of superior cultivars. The increasing numbers of infectious plant diseases that are caused by plant-pathogens make it ever more necessary to develop new strategies for plant disease resistance breeding. Targeted genome engineering allows the introduction of precise modifications directly into a commercial variety, offering a viable alternative to traditional breeding methods. Genome editing is a powerful tool for modifying crucial players in the plant immunity system. In this work, we propose and discuss genome-editing strategies and targets for improving resistance to phytopathogens. First of all, we present the opportunities to rewrite the effector-target sequence for avoiding effector-target molecular interaction and also to modify effector-target promoters for increasing the expression of target genes involved in the resistance process. In addition, we describe potential approaches for obtaining synthetic R-genes through genome-editing technologies (GETs). Finally, we illustrate a genome editing flowchart to modify the pathogen recognition sites and engineer an R-gene that mounts resistance to some phylogenetically divergent pathogens. GETs potentially mark the beginning of a new era, in which synthetic biology affords a basis for obtaining a reinforced plant defense system. Nowadays it is conceivable that by modulating the function of the major plant immunity players, we will be able to improve crop performance for a sustainable agriculture. PMID:27990151

  9. Shifting the genomic gold standard for the prokaryotic species definition.

    Science.gov (United States)

    Richter, Michael; Rosselló-Móra, Ramon

    2009-11-10

    DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. However, now, in the era of genomics, DDH appears to be an outdated method for classification that needs to be substituted. The average nucleotide identity (ANI) between two genomes seems the most promising method since it mirrors DDH closely. Here we examine the work package JSpecies as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons. The results agreed with the use of ANI to substitute DDH, with a narrowed boundary that could be set at approximately 95-96%. In addition, the JSpecies package implemented the tetranucleotide signature correlation index, an alignment-free parameter that generally correlates with ANI and that can be of help in deciding when a given pair of organisms should be classified in the same species. Moreover, for taxonomic purposes, the analyses can be produced by simply randomly sequencing at least 20% of the genome of the query strains rather than obtaining their full sequence.

  10. 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

  11. 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.

  12. Strangelove ocean at era boundaries, terrestrial or extraterrestrial cause

    Science.gov (United States)

    Hsue, Kenneth J.

    1988-01-01

    Negative perturbations in carbon-isotope value of calcite in pelagic sediments were found at times of biotic crisis, marking horizons which are, or were proposed as era boundaries: Cretaceous/Tertiary (K/T), Permian/Triassic (P/T), and Precambrian/Cambrian (PreC/C). The anomaly was also found at several other mass-extinction horizons, such as terminal Ordovician, Frasnian-Famenian, etc. Studies of K/T boundary indicate that only the planktic fraction of the sediments has the negative isotope anomaly, whereas the benthic fraction has the same value across the boundary. This geochemical signal is thus considered a record of strangelove ocean, or an ocean where isotope fractionation of dissolved carbonate ions in surface waters (by biotic function of planktic organisms) has been significantly reduced because of the drastic reduction of the biomass in the oceans. The reduction of marine biomass at each of the era boundaries was related to chemical pollution of the oceans as a consequence of a catastrophic event; a pH decrease of 0.5 could inhibit the fertility of planktons. Studies of earthquakes, volcanic eruptions, and meteorite-impact occurrences have indicated a linearly inverse log/log relationship between the magnitude and frequency of events. The frequency of era boundaries in geologic history supports the postulate that the rare events causing those biotic crises were large bolide-impacts.

  13. 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.

  14. [Okuda wooden human skeleton made in Edo era, Japan].

    Science.gov (United States)

    Baba, Hisao

    2006-03-01

    Probably in 1820 (late Edo era), a human skeleton for medical education was carved from cypress wood, based on a criminal's skeleton under the supervision of a medical doctor, Banri Okuda in Osaka City. The skeleton is called "Okuda wooden skeleton" and is now housed in the National Science Museum, Tokyo. The bones can be assembled into a skeleton by metal pivots or bamboo sticks. The thorax and pelvis were made of several pieces of wood and combined together, respectively. By and large, the wooden skeleton shows morphological characteristics usually seen in early middle-aged females of the Edo era. But the claviculae, distal ends of the femora, and the patellae are exceptionally larger than those of a female, implying that these bones of the original skeleton had already been lost or were deformed before the wooden skeleton was made. Actually the wooden skeleton might not have been used for medical education but rather for the promotion of European medicine, which was gradually developing in the Edo era.

  15. 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.

  16. 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.

  17. 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.

  18. 76 FR 37804 - NextEra Energy Resources, LLC, Peetz Logan Interconnect, LLC, PWEC, LLC; Notice of Petition for...

    Science.gov (United States)

    2011-06-28

    ... Energy Regulatory Commission NextEra Energy Resources, LLC, Peetz Logan Interconnect, LLC, PWEC, LLC...Era Energy Resources, LLC (NextEra) and two of its indirect subsidiaries, Peetz Logan Interconnect... convenience in this petition, all of NextEra's Logan County, Colorado projects collectively are...

  19. Toward high-resolution population genomics using archaeological samples

    Science.gov (United States)

    Morozova, Irina; Flegontov, Pavel; Mikheyev, Alexander S.; Bruskin, Sergey; Asgharian, Hosseinali; Ponomarenko, Petr; Klyuchnikov, Vladimir; ArunKumar, GaneshPrasad; Prokhortchouk, Egor; Gankin, Yuriy; Rogaev, Evgeny; Nikolsky, Yuri; Baranova, Ancha; Elhaik, Eran; Tatarinova, Tatiana V.

    2016-01-01

    The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research. PMID:27436340

  20. Viral taxonomy needs a spring clean; its exploration era is over.

    Science.gov (United States)

    Gibbs, Adrian J

    2013-08-09

    The International Committee on Taxonomy of Viruses has recently changed its approved definition of a viral species, and also discontinued work on its database of virus descriptions. These events indicate that the exploration era of viral taxonomy has ended; over the past century the principles of viral taxonomy have been established, the tools for phylogenetic inference invented, and the ultimate discriminatory data required for taxonomy, namely gene sequences, are now readily available. Further changes would make viral taxonomy more informative. First, the status of a 'taxonomic species' with an italicized name should only be given to viruses that are specifically linked with a single 'type genomic sequence' like those in the NCBI Reference Sequence Database. Secondly all approved taxa should be predominately monophyletic, and uninformative higher taxa disendorsed. These are 'quality assurance' measures and would improve the value of viral nomenclature to its users. The ICTV should also promote the use of a public database, such as Wikipedia, to replace the ICTV database as a store of the primary metadata of individual viruses, and should publish abstracts of the ICTV Reports in that database, so that they are 'Open Access'.

  1. Bioinformatics decoding the genome

    CERN Document Server

    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. Genomics of oral bacteria.

    Science.gov (United States)

    Duncan, Margaret J

    2003-01-01

    Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

  3. State of cat genomics.

    Science.gov (United States)

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn

    2008-06-01

    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

  4. Reference Based Genome Compression

    CERN Document Server

    Chern, Bobbie; Manolakos, Alexandros; No, Albert; Venkat, Kartik; Weissman, Tsachy

    2012-01-01

    DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target genome, and then compresses this mapping with an entropy coder. As an illustration of the performance: applying our algorithm to James Watson's genome with hg18 as a reference, we are able to reduce the 2991 megabyte (MB) genome down to 6.99 MB, while Gzip compresses it to 834.8 MB.

  5. Causes of genome instability

    DEFF Research Database (Denmark)

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

    2015-01-01

    , genome instability can be defined as an enhanced tendency for the genome to acquire mutations; ranging from changes to the nucleotide sequence to chromosomal gain, rearrangements or loss. This review raises the hypothesis that in addition to known human carcinogens, exposure to low dose of other...... scientists aware of the increasing need to unravel the underlying mechanisms via which chemicals at low doses can induce genome instability and thus promote carcinogenesis.......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...

  6. Biological data sciences in genome research.

    Science.gov (United States)

    Schatz, Michael C

    2015-10-01

    The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world.

  7. Querying genomic databases

    Energy Technology Data Exchange (ETDEWEB)

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  8. Reference Based Genome Compression

    OpenAIRE

    Chern, Bobbie; Ochoa, Idoia; Manolakos, Alexandros; No, Albert; Venkat, Kartik; Weissman, Tsachy

    2012-01-01

    DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target gen...

  9. Genome-based bioprospecting of microbes for new therapeutics.

    Science.gov (United States)

    Zotchev, Sergey B; Sekurova, Olga N; Katz, Leonard

    2012-12-01

    Bioprospecting of natural sources for new medicines has a long and successful history, exemplified by the fact that over 50% of all drugs currently on the market are either derived from or inspired by natural products. However, development of new natural product-based therapeutics has been on the decline over the past 20 years, mainly owing to frequent re-discovery of already known compounds coupled with high costs for screening, characterization and development. With the onset of the genomic era allowing rapid sequencing and analysis of bacterial and fungal genomes, it became evident that these organisms possess 'hidden treasures' in the form of gene clusters potentially governing biosynthesis of novel biologically active compounds. This review highlights current progress in mining for and expression of these gene clusters, which may revolutionize the drug discovery pipelines in the near future.

  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. 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...

  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. 51. Brazilian congress on genetics. From biostatistics to bioinformatics. Genomic era. Abstracts; 51. Congresso brasileiro de genetica. Da bioestatistica a bioinformatica. A era da genomica. Resumos

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    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.

  14. Genomic Database Searching.

    Science.gov (United States)

    Hutchins, James R A

    2017-01-01

    The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE.This chapter provides a broad overview of the major genomic databases and browsers, and describes various approaches and the latest resources for searching them. Methods are provided for identifying genomic locus and sequence information using gene names or codes, identifiers for DNA and RNA molecules and proteins; also from karyotype bands, chromosomal coordinates, sequences, motifs, and matrix-based patterns. Approaches are also described for batch retrieval of genomic information, performing more complex queries, and analyzing larger sets of experimental data, for example from next-generation sequencing projects.

  15. 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.

  16. Between two fern genomes.

    Science.gov (United States)

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    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.

  17. [Landscape and ecological genomics].

    Science.gov (United States)

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment.

  18. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... 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...

  19. Genomics of Clostridium tetani.

    Science.gov (United States)

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies.

  20. Verification of the new ECMWF ERA-Interim reanalysis over France

    Directory of Open Access Journals (Sweden)

    C. Szczypta

    2010-09-01

    Full Text Available An evaluation of the global ECMWF atmospheric reanalysis ERA-Interim (with a 0.5° grid is performed over France, based on the high resolution (8 km SAFRAN atmospheric reanalysis. The ERA-Interim precipitation, Incoming Solar Radiation (ISR, air temperature, air humidity, and wind speed, are compared with their SAFRAN counterparts. Also, interpolated in situ ISR observations are used in order to consolidate the evaluation of this variable. The daily precipitation estimates produced by ERA-Interim over France correlate very well with SAFRAN. However, the values are underestimated by 26%. A GPCP-corrected version of ERA-Interim is less biased (10–15%. The ERA-Interim estimates of ISR correlate very well with SAFRAN and with in situ observations on a daily basis. Whereas SAFRAN underestimates the ISR by 6–8 W m−2, ERA-Interim overestimates the ISR by 9–10 W m−2. In order to assess the impact of the ERA-Interim errors, simulations of the ISBA-A-gs land surface model are performed over the SMOSREX grassland site in southwestern France using ERA-Interim (with and without GPCP rescaling and SAFRAN. Latent and sensible heat fluxes are simulated, together with carbon dioxide fluxes. The rescaled ERA-Interim performs better than the original ERA-Interim and permits to achieve flux scores similar to those obtained with SAFRAN.

  1. Verification of the new ECMWF ERA-Interim reanalysis over France

    Science.gov (United States)

    Szczypta, C.; Calvet, J.-C.; Albergel, C.; Balsamo, G.; Boussetta, S.; Carrer, D.; Lafont, S.; Meurey, C.

    2011-02-01

    An evaluation of the global ECMWF atmospheric reanalysis ERA-Interim (with a 0.5° grid) is performed over France, based on the high resolution (8 km) SAFRAN atmospheric reanalysis. The ERA-Interim precipitation, Incoming Solar Radiation (ISR), air temperature, air humidity, and wind speed, are compared with their SAFRAN counterparts. Also, interpolated in situ ISR observations are used in order to consolidate the evaluation of this variable. The daily precipitation estimates produced by ERA-Interim over France correlate very well with SAFRAN. However, the values are underestimated by 27%. A GPCP-corrected version of ERA-Interim is less biased (13%). The ERA-Interim estimates of ISR correlate very well with SAFRAN and with in situ observations on a daily basis. Whereas SAFRAN underestimates the ISR by 6 Wm-2, ERA-Interim overestimates the ISR by 10 Wm-2. In order to assess the impact of the ERA-Interim errors, simulations of the ISBA-A-gs land surface model are performed over the SMOSREX grassland site in southwestern France using ERA-Interim (with and without GPCP rescaling) and SAFRAN. Latent and sensible heat fluxes are simulated, together with carbon dioxide fluxes. The rescaled ERA-Interim performs better than the original ERA-Interim and permits to achieve flux scores similar to those obtained with SAFRAN.

  2. 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.

  3. 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....

  4. An International Framework for Data Sharing: Moving Forward with the Global Alliance for Genomics and Health.

    Science.gov (United States)

    Rahimzadeh, Vasiliki; Dyke, Stephanie O M; Knoppers, Bartha M

    2016-06-01

    The Global Alliance for Genomics and Health is marshaling expertise in biomedical research and data sharing policy to propel bench-to-bedside translation of genomics in parallel with many of the BioSHaRE-EU initiatives described at length in this Issue. Worldwide representation of institutions, funders, researchers, and patient advocacy groups at the Global Alliance is testament to a shared ideal that sees maximizing the public good as a chief priority of genomic innovation in health. The Global Alliance has made a critical stride in this regard with the development of its Framework for Responsible Sharing of Genomic and Health-related Data.(1) This article first discusses the human rights pillars that underlie the Framework and mission of the Global Alliance. Second, it outlines the Global Alliance's use of data governance policies through a number of demonstration projects. Finally, the authors describe how the Global Alliance envisions international data sharing moving forward in the postgenomic era.

  5. [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.

  6. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... Breve guía de genómica A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is ... genetic basis for health and disease. Implications of Genomics for Medical Science Virtually every human ailment has ...

  7. Ensembl Genomes 2013

    DEFF Research Database (Denmark)

    Kersey, Paul Julian; Allen, James E; Christensen, Mikkel

    2014-01-01

    genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely...

  8. Estimation of genome length

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.

  9. Genetics and Genomics

    Science.gov (United States)

    Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

  10. Breeding-assisted genomics.

    Science.gov (United States)

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  11. 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 DNA...

  12. Genome-Scale Models

    DEFF Research Database (Denmark)

    Bergdahl, Basti; Sonnenschein, Nikolaus; Machado, Daniel

    2016-01-01

    An introduction to genome-scale models, how to build and use them, will be given in this chapter. Genome-scale models have become an important part of systems biology and metabolic engineering, and are increasingly used in research, both in academica and in industry, both for modeling chemical pr...

  13. Unlocking the bovine genome

    Directory of Open Access Journals (Sweden)

    Worley Kim C

    2009-04-01

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

  14. Genomic understanding of dinoflagellates.

    Science.gov (United States)

    Lin, Senjie

    2011-01-01

    The phylum of dinoflagellates is characterized by many unusual and interesting genomic and physiological features, the imprint of which, in its immense genome, remains elusive. Much novel understanding has been achieved in the last decade on various aspects of dinoflagellate biology, but most remarkably about the structure, expression pattern and epigenetic modification of protein-coding genes in the nuclear and organellar genomes. Major findings include: 1) the great diversity of dinoflagellates, especially at the base of the dinoflagellate tree of life; 2) mini-circularization of the genomes of typical dinoflagellate plastids (with three membranes, chlorophylls a, c1 and c2, and carotenoid peridinin), the scrambled mitochondrial genome and the extensive mRNA editing occurring in both systems; 3) ubiquitous spliced leader trans-splicing of nuclear-encoded mRNA and demonstrated potential as a novel tool for studying dinoflagellate transcriptomes in mixed cultures and natural assemblages; 4) existence and expression of histones and other nucleosomal proteins; 5) a ribosomal protein set expected of typical eukaryotes; 6) genetic potential of non-photosynthetic solar energy utilization via proton-pump rhodopsin; 7) gene candidates in the toxin synthesis pathways; and 8) evidence of a highly redundant, high gene number and highly recombined genome. Despite this progress, much more work awaits genome-wide transcriptome and whole genome sequencing in order to unfold the molecular mechanisms underlying the numerous mysterious attributes of dinoflagellates.

  15. The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004.

    Science.gov (United States)

    Wiechers, Ilse R; Perin, Noah C; Cook-Deegan, Robert

    2013-01-01

    Development of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble. A database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database. A biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents. These data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004.

  16. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation

    Science.gov (United States)

    Stepanov, Victor G.; Tirumalai, Madhan R.; Montazari, Saied; Checinska, Aleksandra; Venkateswaran, Kasthuri

    2016-01-01

    Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains. PMID:27351589

  17. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation.

    Directory of Open Access Journals (Sweden)

    Victor G Stepanov

    Full Text Available Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.

  18. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation.

    Science.gov (United States)

    Stepanov, Victor G; Tirumalai, Madhan R; Montazari, Saied; Checinska, Aleksandra; Venkateswaran, Kasthuri; Fox, George E

    2016-01-01

    Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.

  19. SISTEM BANK SOAL DAERAH TERKALIBRASI UNTUK MENYONGSONG ERA DESENTRALISASI

    Directory of Open Access Journals (Sweden)

    Heri Retnawati

    2015-08-01

    Full Text Available Abstract: Calibrated Local Governmental Test Item Bank in the Face of Decentralization. The purpose of this study is to develop a caliberated test item bank to face the era of decentralization. The data in the research and development (R & D project were collected through a delphi study, documen­tation, observations, and interviews. The project resulted in caliberated test item bank system, supple­mented with a guide book that has undergone limited try-out, revision, wide-scale try-out, and dissemi­nation. This system was then enriched with the addition of new items for mathematics and English. The system is presented on a website uny.ac.id under the Centre for Policy Studies and Testing System in Research and Community Service Institution of Yogyakarta State University. Keywords: test item bank, decentralisation, calibration, local government Abstrak: Sistem Bank Soal Daerah Terkalibrasi untuk Menyongsong Era Desentralisasi. Tujuan penelitian ini adalah mengembangkan sistem bank soal daerah terkalibrasi untuk menyongsong era de­sentralisasi. Penelitian ini menggunakan pendekatan penelitian dan pengembangan (research and de­velopment. Data penelitian dikumpulkan melalui delphi, dokumentasi, observasi dan wawancara. Analisis data dilakukan secara kuantitatif maupun kualitatif. Hasil penelitian yaitu telah dikembangkannya sis­tem bank soal daerah yang telah terkalibrasi, beserta buku panduan pemanfaatannya yang telah melalui ujicoba terbatas, revisi, ujicoba skala luas, dan desiminasi. Sistem Bank soal ini kemudian diperkaya dengan penambahan butir baru untuk matapelajaran matematika dan bahasa Inggris. Sistem bank soal ini disajikan pada laman uny.ac.id dibawah Pusat Studi Kebijakan dan Sistem Pengujian Lembaga Penelitian dan Pengabdian pada Masyarakat (LPPM Universitas Negeri Yogyakarta. Kata kunci: sistem bank soal, desentralisasi

  20. The era of star formation in galaxy clusters

    Energy Technology Data Exchange (ETDEWEB)

    Brodwin, M. [Department of Physics and Astronomy, University of Missouri, 5110 Rockhill Road, Kansas City, MO 64110 (United States); Stanford, S. A. [University of California, Davis, CA 95616 (United States); Gonzalez, Anthony H.; Mancone, C. L.; Gettings, D. P. [Department of Astronomy, University of Florida, Gainesville, FL 32611 (United States); Zeimann, G. R. [Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States); Snyder, G. F.; Ashby, M. L. N. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Pope, A.; Alberts, S. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Eisenhardt, P. R.; Stern, D.; Moustakas, L. A. [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 (United States); Brown, M. J. I. [School of Physics, Monash University, Clayton, Victoria 3800 (Australia); Chary, R.-R. [Spitzer Science Center, MC 220-6, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Dey, Arjun [National Optical Astronomy Observatory, 950 N. Cherry Avenue, Tucson, AZ 85719 (United States); Galametz, A. [INAF—Osservatorio di Roma, Via Frascati 33, I-00040 Monteporzio (Italy); Jannuzi, B. T. [Steward Observatory, University of Arizona, 933 N. Cherry Avenue, Tucson, AZ 85121 (United States); Miller, E. D. [Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Moustakas, J. [Department of Physics and Astronomy, Siena College, 515 Loudon Road, Loudonville, NY 12211 (United States)

    2013-12-20

    We analyze the star formation properties of 16 infrared-selected, spectroscopically confirmed galaxy clusters at 1 < z < 1.5 from the Spitzer/IRAC Shallow Cluster Survey (ISCS). We present new spectroscopic confirmation for six of these high-redshift clusters, five of which are at z > 1.35. Using infrared luminosities measured with deep Spitzer/Multiband Imaging Photometer for Spitzer observations at 24 μm, along with robust optical + IRAC photometric redshifts and spectral-energy-distribution-fitted stellar masses, we present the dust-obscured star-forming fractions, star formation rates, and specific star formation rates in these clusters as functions of redshift and projected clustercentric radius. We find that z ∼ 1.4 represents a transition redshift for the ISCS sample, with clear evidence of an unquenched era of cluster star formation at earlier times. Beyond this redshift, the fraction of star-forming cluster members increases monotonically toward the cluster centers. Indeed, the specific star formation rate in the cores of these distant clusters is consistent with field values at similar redshifts, indicating that at z > 1.4 environment-dependent quenching had not yet been established in ISCS clusters. By combining these observations with complementary studies showing a rapid increase in the active galactic nucleus (AGN) fraction, a stochastic star formation history, and a major merging episode at the same epoch in this cluster sample, we suggest that the starburst activity is likely merger-driven and that the subsequent quenching is due to feedback from merger-fueled AGNs. The totality of the evidence suggests we are witnessing the final quenching period that brings an end to the era of star formation in galaxy clusters and initiates the era of passive evolution.

  1. UNDERSTANDING “GEOPOLITICS” IN AN ERA OF GLOBALIZATION

    Directory of Open Access Journals (Sweden)

    John Agnew

    2016-01-01

    Full Text Available An older European-Enlightenment geopolitical imagination was lost in the late nineteenth century with the rise of naturalized understandings of inter-state and imperial relations that saw states and empires in terms of biological competition conditioned by relative location on the earth’s surface. The word “geopolitics” emerged in that context and since that time the term has had to contend with this original sin. Arguably, however, Montesquieu and Voltaire in their references to Alexander the Great had a somewhat different conception of geopolitics in mind: one in which reciprocity and exchange between places as well as the redistribution of resources from colonies to homeland are at work. It is this broader sense of the word that has been revived over the past fifty years in the course of attempts at linking the global political structure of states, empires, and other political authorities to what can be called the “globalization era.” The broader understanding of geopolitics is by no means restricted to this era, as the reference to the Enlightenment period should make clear. But it has become an increasingly attractive alternative. I discuss four aspects of the connection between geopolitics construed in the broader meaning and the globalization that the world economy has experienced over the past fifty years. The first is to challenge the idea that geopolitics in the broad sense is “opposed” to globalization. I then turn to what I see are the three dimensions of geopolitics in an era of globalization: the geopolitics of globalization, the geopolitics of development, and the geopolitics of global regulation. From this perspective, Montesquieu and Voltaire offer a much better inspiration for understanding world politics than do the geopolitical writers of the early twentieth century such as Kjellen and Mackinder.

  2. Combined use of genetic and genomics resources to understand virus resistance and fruit quality traits in melon.

    Science.gov (United States)

    Argyris, Jason M; Pujol, Marta; Martín-Hernández, Ana Montserrat; Garcia-Mas, Jordi

    2015-09-01

    The availability of the genome sequence of many crop species during the past few years has opened a new era in plant biology, allowing for the performance of massive genomic studies in plant species other than the classical models Arabidopsis and rice. One of these crop species is melon (Cucumis melo), a cucurbit of high economic value that has become an interesting model for the study of biological processes such as fruit ripening, sex determination and phloem transport. The recent availability of the melon genome sequence, together with a number of genetic and genomic resources, provides powerful tools that can be used to assist in the main melon breeding targets, namely disease resistance and fruit quality. In this review, we will describe recent data obtained combining the use of a melon near isogenic line (NIL) population and genomic resources to gain insight into agronomically important traits as fruit ripening, resistance to Cucumber Mosaic virus (CMV) and the accumulation of sugars in fruits.

  3. 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

  4. Revenue generation in the information era: Opportunities and challenges

    Directory of Open Access Journals (Sweden)

    Sreelata Jonnalagedda

    2011-03-01

    Full Text Available In an information economy, innovative revenue generating models are as critical for the sustenance of a firm as is bringing cutting edge technology to the market. In its first part, this article surveys the characteristics of the information goods market and identifies the opportunities and challenges that the information era presents. Further, it surveys the existing business models for information goods and maps them to the market characteristics to arrive at the viability of these models. The second part of the article presents the views and experiences of a panel of practitioners who face these challenges in the field of information goods.

  5. Rethinking vaccine policy making in an era of vaccine hesitancy

    Science.gov (United States)

    Opel, Douglas J; Marcuse, Edgar K

    2013-01-01

    Recently in this journal, David Ropeik argued for imposing additional burdens upon individuals who refused vaccines for themselves or for their children. Specifically, Ropeik advocated for policies that would decrease the ease of claiming vaccine exemptions and restricting unvaccinated children participation in social activities. We argue that, in order to derive the optimal societal benefit from modern vaccinology in an era of vaccine hesitancy, we need to consider doing more than conventional remodeling of current policies. We may need to fundamentally redesign and rebuild. PMID:24084386

  6. 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

  7. Origins of American Social Policies: the Progressive Era

    Directory of Open Access Journals (Sweden)

    Valentin FILIP

    2015-09-01

    Full Text Available This paper examines the evolution of social policy concerns, debates and reforms in the United States, especially starting with the Gilded Age and through the Progressive Era. It capitalizes on policy analysis literature in order to strengthen the argument of exploring context in order to understand social policy. It also delves into the social climate that gave birth to the Progressives and shaped their perceptions with regard to social change. Finally, it attempts to offer a new perspective on the distinctive social welfare track undertaken by the Americans, when compared to the European traditional model.

  8. Recombination era magnetic fields from axion dark matter

    Science.gov (United States)

    Banik, Nilanjan; Christopherson, Adam J.

    2016-02-01

    We introduce a new mechanism for generating magnetic fields in the recombination era. This Harrison-like mechanism utilizes vorticity in baryons that is sourced through the Bose-Einstein condensate of axions via gravitational interactions. The magnetic fields generated are on galactic scales ˜10 kpc and have a magnitude of the order of B ˜1 0-23G today. The field has a greater magnitude than those generated from other mechanisms relying on second-order perturbation theory, and is sufficient to provide a seed for battery mechanisms.

  9. Corpos e Corporeidade no Universo da Nova Era no Brasil

    OpenAIRE

    Amurabi Oliveira

    2012-01-01

    O presente trabalho busca explorar a dimensão corpórea enquanto central para a compreensão do fenômeno religioso, em especial do universo Nova Era – NE, em nossa interpretação o corpo apresenta-se enquanto estrutura estruturada estruturante que possibilita aos sujeitos vivenciar e interpretar o mundo, neste sentido, a experiência de imersão e de vivência das práticas da NE são, essencialmente, experiências corpóreas. No decorrer deste trabalho buscaremos dar destaque aos aspect...

  10. Seoul: Public policies to walk through a low carbon era

    Directory of Open Access Journals (Sweden)

    Silvia Guadalupe Figueroa González

    2013-06-01

    Full Text Available The economic and demographic growth that Seoul has experienced in recent decades has led to an increase in demand and energy consumption at the expense of the environment. In accordance with national green growth vision, Seoul is implementing a number of strategies that involve various actors for the transition to a low carbon era. The paper addresses Korea’s vision for green growth, analyzes presidential leadership to articulate policies in the domestic and international level and the actions executed locally by the Seoul Metropolitan Government.

  11. The Multi-Core Era - Trends and Challenges

    CERN Document Server

    Tröger, Peter

    2008-01-01

    Since the very beginning of hardware development, computer processors were invented with ever-increasing clock frequencies and sophisticated in-build optimization strategies. Due to physical limitations, this 'free lunch' of speedup has come to an end. The following article gives a summary and bibliography for recent trends and challenges in CMP architectures. It discusses how 40 years of parallel computing research need to be considered in the upcoming multi-core era. We argue that future research must be driven from two sides - a better expression of hardware structures, and a domain-specific understanding of software parallelism.

  12. 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.

  13. [German colonial plans for Africa in the Nazi era].

    Science.gov (United States)

    Linne, Karsten

    2003-12-01

    The German colonial plans concerning Africa in the era of National Socialism ascribed a central role the sciences. Scientists of all possible fields launched into activities. Especially subjects which were directly related to the practice of colonial policies, e.g. African languages, ethnology, law, economic sciences, and medicine, were developed. There were colonial ambitions at nearly every German university, but there was one which designated to become the centre of colonial sciences: the university of Hamburg. It has to be realized that working in this field of studies protected scientists from being drafted by the army for a long time.

  14. Recombination era magnetic fields from axion dark matter

    CERN Document Server

    Banik, Nilanjan

    2015-01-01

    We introduce a new mechanism for generating magnetic fields in the recombination era. This Harrison-like mechanism utilizes vorticity in baryons that is sourced through the Bose-Einstein condensate of axions via gravitational interactions. The magnetic fields generated are on the galactic scales $\\sim 10\\,{\\rm kpc}$ and have a magnitude of the order of $B\\sim10^{-23}\\,{\\rm G}$ today. The field has a greater magnitude than those generated from other mechanisms relying on second order perturbation theory, and is sufficient to provide a seed for battery mechanisms.

  15. The Development of modern Chinese Culture in Information Era

    Institute of Scientific and Technical Information of China (English)

    潘丽欣

    2016-01-01

    With the coming of the information era, new science and technology develops rapidly and the Internet gets further application. At present, the Internet becomes an indispensable tool in our daily life. What's more, Internet has deep influence on the development of modern Chinese culture. The Chinese civilization, extensive and profound, and with a long history behind it, has contributed tremendously to the progress of human civilization. Internet, an important medium for cultural activities, becomes one of the main influencing factors on the development of Chinese culture.

  16. 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].

  17. 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.

  18. Online Reputation Systems in Web 2.0 Era

    Science.gov (United States)

    Zheng, Weijun; Jin, Leigh

    Web 2.0 has transformed how reputation systems are designed and used by the Web. Based on a thorough review of the existing online reputation systems and their challenges in use, this paper studied a case of Amazon’s reputation system for the impacts of Web 2.0. Through our case study, several distinguished features of new generation reputation systems are noted including multimedia feedbacks, reviewer centered, folksonomy, community contribution, comprehensive reputation, dynamic and interactive system etc. These new developments move towards a relatively trustworthy and reliable online reputation system in the Web 2.0 era.

  19. Cosmology Era of Anania Shirakatsi in the Context of Civilization

    Science.gov (United States)

    Mirumyan, Karlen

    2015-07-01

    The article is devoted to the justification of the scientific status of cosmology and the problem of its relations with the Christian doctrine, which was important in given the historical and cultural period in the doctrine of the greatest Armenian scholar of the 7th century - Anania Shirakatsi. This was the era when the achievements and standards of ancient science was pushed into the background both in the West and the East. In such adverse conditions of the history of science the Armenian scientist not only continued, but also creatively developed a number of ancient astronomical concepts.

  20. COOPERATION AND EDUCATION FOR SUSTAINABLE DEVELOPMENT IN GLOBALIZATION ERA

    Directory of Open Access Journals (Sweden)

    NEDELCU ELENA

    2013-05-01

    Full Text Available The present paper aims to approach a relatively new topic: international cooperation for sustainable development. The first part of this paper is a theoretical construct which deals with the connection that exists between its main variables: globalization, democratization and development. This part of the paper also brings into evidence the necessity and importance of international cooperation for sustainable development (SD during the globalization era. The second part of the paper aims to briefly analyse the importance and practice of education for sustainable development (ESD in our contemporary society: the case of Romania. Conclusions represent the object of the last part of the paper.