Sample records for science joint genome
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Joint Genome Institute's Automation Approach and History
Energy Technology Data Exchange (ETDEWEB)
Roberts, Simon
2006-07-05
Department of Energy/Joint Genome Institute (DOE/JGI) collaborates with DOE national laboratories and community users, to advance genome science in support of the DOE missions of clean bio-energy, carbon cycling, and bioremediation.
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A Taste of Algal Genomes from the Joint Genome Institute
Energy Technology Data Exchange (ETDEWEB)
Kuo, Alan; Grigoriev, Igor
2012-06-17
Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.
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DOE Joint Genome Institute 2008 Progress Report
International Nuclear Information System (INIS)
Gilbert, David
2009-01-01
While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary-based sequencing process that
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DOE Joint Genome Institute 2008 Progress Report
Energy Technology Data Exchange (ETDEWEB)
Gilbert, David
2009-03-12
While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary
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A Blueprint for Genomic Nursing Science
Calzone, Kathleen A.; Jenkins, Jean; Bakos, Alexis D.; Cashion, Ann; Donaldson, Nancy; Feero, Greg; Feetham, Suzanne; Grady, Patricia A.; Hinshaw, Ada Sue; Knebel, Ann R.; Robinson, Nellie; Ropka, Mary E.; Seibert, Diane; Stevens, Kathleen R.; Tully, Lois A.; Webb, Jo Ann
2012-01-01
Purpose This article reports on recommendations arising from an invitational workshop series held at the National Institutes of Health for the purposes of identifying critical genomics problems important to the health of the public that can be addressed through nursing science. The overall purpose of the Genomic Nursing State of the Science Initiative is to establish a nursing research blueprint based on gaps in the evidence and expert evaluation of the current state of the science and through public comment. Organizing Constructs A Genomic Nursing State of the Science Advisory Panel was convened in 2012 to develop the nursing research blueprint. The Advisory Panel, which met via two webinars and two in-person meetings, considered existing evidence from evidence reviews, testimony from key stakeholder groups, presentations from experts in research synthesis, and public comment. Findings The genomic nursing science blueprint arising from the Genomic Nursing State of Science Advisory Panel focuses on biologic plausibility studies as well as interventions likely to improve a variety of outcomes (e.g., clinical, economic, environmental). It also includes all care settings and diverse populations. The focus is on (a) the client, defined as person, family, community, or population; (b) the context, targeting informatics support systems, capacity building, education, and environmental influences; and (c) cross-cutting themes. It was agreed that building capacity to measure the impact of nursing actions on costs, quality, and outcomes of patient care is a strategic and scientific priority if findings are to be synthesized and aggregated to inform practice and policy. Conclusions The genomic nursing science blueprint provides the framework for furthering genomic nursing science to improve health outcomes. This blueprint is an independent recommendation of the Advisory Panel with input from the public and is not a policy statement of the National Institutes of Health or the
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The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
Energy Technology Data Exchange (ETDEWEB)
Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
2013-11-12
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.
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Smith, David Roy
2017-05-01
Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.
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2012 U.S. Department of Energy: Joint Genome Institute: Progress Report
Energy Technology Data Exchange (ETDEWEB)
Gilbert, David [DOE JGI Public Affairs Manager
2013-01-01
The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.
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Frequently Asked Questions about Genetic and Genomic Science
... Genetic and Genomic Science and Research FAQ About Clinical Research FAQ About Genetic Research FAQ About Genetic and Genomic Science See Also: Talking Glossary of Genetic Terms Definitions for the genetic terms used on this page ...
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Directory of Open Access Journals (Sweden)
Chonglong Wang
Full Text Available Genomic selection has become a useful tool for animal and plant breeding. Currently, genomic evaluation is usually carried out using a single-trait model. However, a multi-trait model has the advantage of using information on the correlated traits, leading to more accurate genomic prediction. To date, joint genomic prediction for a continuous and a threshold trait using a multi-trait model is scarce and needs more attention. Based on the previously proposed methods BayesCπ for single continuous trait and BayesTCπ for single threshold trait, we developed a novel method based on a linear-threshold model, i.e., LT-BayesCπ, for joint genomic prediction of a continuous trait and a threshold trait. Computing procedures of LT-BayesCπ using Markov Chain Monte Carlo algorithm were derived. A simulation study was performed to investigate the advantages of LT-BayesCπ over BayesCπ and BayesTCπ with regard to the accuracy of genomic prediction on both traits. Factors affecting the performance of LT-BayesCπ were addressed. The results showed that, in all scenarios, the accuracy of genomic prediction obtained from LT-BayesCπ was significantly increased for the threshold trait compared to that from single trait prediction using BayesTCπ, while the accuracy for the continuous trait was comparable with that from single trait prediction using BayesCπ. The proposed LT-BayesCπ could be a method of choice for joint genomic prediction of one continuous and one threshold trait.
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Phytozome Comparative Plant Genomics Portal
Energy Technology Data Exchange (ETDEWEB)
Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel
2014-09-09
The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes
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Bridging the divide between genomic science and indigenous peoples.
Jacobs, Bette; Roffenbender, Jason; Collmann, Jeff; Cherry, Kate; Bitsói, LeManuel Lee; Bassett, Kim; Evans, Charles H
2010-01-01
The new science of genomics endeavors to chart the genomes of individuals around the world, with the dual goals of understanding the role genetic factors play in human health and solving problems of disease and disability. From the perspective of indigenous peoples and developing countries, the promises and perils of genomic science appear against a backdrop of global health disparity and political vulnerability. These conditions pose a dilemma for many communities when attempting to decide about participating in genomic research or any other biomedical research. Genomic research offers the possibility of improved technologies for managing the acute and chronic diseases that plague their members. Yet, the history of particularly biomedical research among people in indigenous and developing nations offers salient examples of unethical practice, misuse of data, and failed promises. This dilemma creates risks for communities who decide either to participate or not to participate in genomic science research. Some argue that the history of poor scientific practice justifies refusal to join genomic research projects. Others argue that disease poses such great threats to the well-being of people in indigenous communities and developing nations that not participating in genomic research risks irrevocable harm. Thus, some communities particularly among indigenous peoples have declined to participate as subjects in genomic research. At the same time, some communities have begun developing new guidelines, procedures, and practices for engaging with the scientific community that offer opportunities to bridge the gap between genomic science and indigenous and/or developing communities. Four new approaches warrant special attention and further support: consulting with local communities; negotiating the complexities of consent; training members of local communities in science and health care; and training scientists to work with indigenous communities. Implicit is a new
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Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum
Energy Technology Data Exchange (ETDEWEB)
Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.
2011-08-01
Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics
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Social and behavioral science priorities for genomic translation.
Koehly, Laura M; Persky, Susan; Spotts, Erica; Acca, Gillian
2018-01-29
This commentary highlights the essential role of the social and behavioral sciences for genomic translation, and discusses some priority research areas in this regard. The first area encompasses genetics of behavioral, social, and neurocognitive factors, and how integration of these relationships might impact the development of treatments and interventions. The second area includes the contributions that social and behavioral sciences make toward the informed translation of genomic developments. Further, there is a need for behavioral and social sciences to inform biomedical research for effective implementation. The third area speaks to the need for increased outreach and education efforts to improve the public's genomic literacy such that individuals and communities can make informed health-related and societal (e.g., in legal or consumer settings) decisions. Finally, there is a need to prioritize representation of diverse communities in genomics research and equity of access to genomic technologies. Examples from National Institutes of Health-based intramural and extramural research programs and initiatives are used to discuss these points. © Society of Behavioral Medicine 2018.
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75 FR 33613 - Notice of the Carbon Sequestration-Geothermal Energy-Science Joint Workshop
2010-06-14
... Energy, DOE. ACTION: Notice of the Carbon Sequestration--Geothermal Energy--Science Joint Workshop... Fossil Energy-Carbon Sequestration Program will be holding a joint workshop on Common Research Themes for...-- http://www.geothermal.energy.gov . DATES: The Carbon Sequestration--Geothermal Energy--Science Joint...
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The muon science facility at the JAERI/KEK joint project
International Nuclear Information System (INIS)
Miyake, Y.; Nishiyama, K.; Makimura, S.; Kawamura, N.; Shimomura, K.; Kadono, R.; Higemoto, W.; Fukuchi, K.; Beveridge, J.L.; Ishida, K.; Matsuzaki, T.; Watanabe, I.; Matsuda, Y.; Sakamoto, S.; Nakamura, S.N.; Nagamine, K.
2003-01-01
The Muon Science Facility is one of the experimental arenas of the JAERI/KEK Joint Project, which also includes neutron science, particle and nuclear physics, neutrino physics and nuclear transmutation science. Following the recommendations by the review committees, the Joint Project was finally approved for construction at the end of December, 2000. The approval is for Phase 1 of 1335 Oku Yen out of the total project cost of 1890 Oku Yen. It is planned to locate the muon science experimental area together with the neutron facility in an integrated building, as a facility for materials and life science studies. Because its construction will be started in April 2003, we are now working to complete the detailed design of the building structure, shielding, electrical services, cooling water, primary proton beam line, one muon target and secondary beam lines
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Opportunities in Africa for training in genome science | Masiga ...
African Journals Online (AJOL)
Genome science is a new type of biology that unites genetics, molecular biology, computational biology and bioinformatics. The availability of the human genome sequence, as well as the genome sequences of several other organisms relevant to health, agriculture and the environment in Africa necessitates the ...
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Joint Science Education Project: Learning about polar science in Greenland
Foshee Reed, Lynn
2014-05-01
The Joint Science Education Project (JSEP) is a successful summer science and culture opportunity in which students and teachers from the United States, Denmark, and Greenland come together to learn about the research conducted in Greenland and the logistics involved in supporting the research. They conduct experiments first-hand and participate in inquiry-based educational activities alongside scientists and graduate students at a variety of locations in and around Kangerlussuaq, Greenland, and on the top of the ice sheet at Summit Station. The Joint Committee, a high-level forum involving the Greenlandic, Danish and U.S. governments, established the Joint Science Education Project in 2007, as a collaborative diplomatic effort during the International Polar Year to: • Educate and inspire the next generation of polar scientists; • Build strong networks of students and teachers among the three countries; and • Provide an opportunity to practice language and communication skills Since its inception, JSEP has had 82 student and 22 teacher participants and has involved numerous scientists and field researchers. The JSEP format has evolved over the years into its current state, which consists of two field-based subprograms on site in Greenland: the Greenland-led Kangerlussuaq Science Field School and the U.S.-led Arctic Science Education Week. All travel, transportation, accommodations, and meals are provided to the participants at no cost. During the 2013 Kangerlussuaq Science Field School, students and teachers gathered data in a biodiversity study, created and set geo- and EarthCaches, calculated glacial discharge at a melt-water stream and river, examined microbes and tested for chemical differences in a variety of lakes, measured ablation at the edge of the Greenland Ice Sheet, and learned about fossils, plants, animals, minerals and rocks of Greenland. In addition, the students planned and led cultural nights, sharing food, games, stories, and traditions of
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Joint Genomic Prediction of Canine Hip Dysplasia in UK and US Labrador Retrievers
Directory of Open Access Journals (Sweden)
Stefan M. Edwards
2018-03-01
Full Text Available Canine hip dysplasia, a debilitating orthopedic disorder that leads to osteoarthritis and cartilage degeneration, is common in several large-sized dog breeds and shows moderate heritability suggesting that selection can reduce prevalence. Estimating genomic breeding values require large reference populations, which are expensive to genotype for development of genomic prediction tools. Combining datasets from different countries could be an option to help build larger reference datasets without incurring extra genotyping costs. Our objective was to evaluate genomic prediction based on a combination of UK and US datasets of genotyped dogs with records of Norberg angle scores, related to canine hip dysplasia. Prediction accuracies using a single population were 0.179 and 0.290 for 1,179 and 242 UK and US Labrador Retrievers, respectively. Prediction accuracies changed to 0.189 and 0.260, with an increased bias of genomic breeding values when using a joint training set (biased upwards for the US population and downwards for the UK population. Our results show that in this study of canine hip dysplasia, little or no benefit was gained from using a joint training set as compared to using a single population as training set. We attribute this to differences in the genetic background of the two populations as well as the small sample size of the US dataset.
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Holmes, Christina; Carlson, Siobhan M; McDonald, Fiona; Jones, Mavis; Graham, Janice
2016-01-02
Richard Lewontin proposed that the ability of a scientific field to create a narrative for public understanding garners it social relevance. This article applies Lewontin's conceptual framework of the functions of science (manipulatory and explanatory) to compare and explain the current differences in perceived societal relevance of genetics/genomics and proteomics. We provide three examples to illustrate the social relevance and strong cultural narrative of genetics/genomics for which no counterpart exists for proteomics. We argue that the major difference between genetics/genomics and proteomics is that genomics has a strong explanatory function, due to the strong cultural narrative of heredity. Based on qualitative interviews and observations of proteomics conferences, we suggest that the nature of proteins, lack of public understanding, and theoretical complexity exacerbates this difference for proteomics. Lewontin's framework suggests that social scientists may find that omics sciences affect social relations in different ways than past analyses of genetics.
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The Human Genome Project: big science transforms biology and medicine.
Hood, Leroy; Rowen, Lee
2013-01-01
The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called 'big science' - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and analytical tools, and how it brought the expertise of engineers, computer scientists and mathematicians together with biologists. It established an open approach to data sharing and open-source software, thereby making the data resulting from the project accessible to all. The genome sequences of microbes, plants and animals have revolutionized many fields of science, including microbiology, virology, infectious disease and plant biology. Moreover, deeper knowledge of human sequence variation has begun to alter the practice of medicine. The Human Genome Project has inspired subsequent large-scale data acquisition initiatives such as the International HapMap Project, 1000 Genomes, and The Cancer Genome Atlas, as well as the recently announced Human Brain Project and the emerging Human Proteome Project.
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INSA - AASAA joint workshop | Women in Science | Initiatives ...
Indian Academy of Sciences (India)
Presentations at the INSA-AASAA joint workshop on "Women in Science, Education and Research" ... Mon-Shu Ho, National ChungHsing University, Nepal ... Charusita Chakravarty, one of the stars of our community of women scientists, at a ...
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2013-05-14
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical Science Research and Development Services Scientific Merit Review Board; Notice of Meetings; Amendment The... Joint Biomedical Laboratory Research and Development and Clinical Science Research and Development...
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Genomic science provides new insights into the biology of forest trees
Andrew Groover
2015-01-01
Forest biology is undergoing a fundamental change fostered by the application of genomic science to longstanding questions surrounding the evolution, adaptive traits, development, and environmental interactions of tree species. Genomic science has made major technical leaps in recent years, most notably with the advent of 'next generation sequencing' but...
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Improving genomic prediction for Danish Jersey using a joint Danish-US reference population
DEFF Research Database (Denmark)
Su, Guosheng; Nielsen, Ulrik Sander; Wiggans, G
Accuracy of genomic prediction depends on the information in the reference population. Achieving an adequate sized reference population is a challenge for genomic prediction in small cattle populations. One way to increase the size of reference population is to combine reference data from different...... populations. The objective of this study was to assess the gain of genomic prediction accuracy when including US Jersey bulls in the Danish Jersey reference population. The data included 1,262 Danish progeny-tested bulls and 1,157 US progeny-tested bulls. Genomic breeding values (GEBV) were predicted using...... a GBLUP model from the Danish reference population and the joint Danish-US reference population. The traits in the analysis were milk yield, fat yield, protein yield, fertility, mastitis, longevity, body conformation, feet & legs, and longevity. Eight of the nine traits benefitted from the inclusion of US...
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2013-11-07
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical... the panels of the Joint Biomedical Laboratory Research and Development and Clinical Science Research..., behavioral, and clinical science research. The panel meetings will be open to the public for approximately...
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2013-04-16
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical... the panels of the Joint Biomedical Laboratory Research and Development and Clinical Science Research... biomedical, behavioral and clinical science research. The panel meetings will be open to the public for...
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2012-10-22
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical...) that the panels of the Joint Biomedical Laboratory Research and Development and Clinical Science... areas of biomedical, behavioral and clinical science research. The panel meetings will be open to the...
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Public attitudes to genomic science: an experiment in information provision.
Sturgis, Patrick; Brunton-Smith, Ian; Fife-Schaw, Chris
2010-03-01
We use an experimental panel study design to investigate the effect of providing "value-neutral" information about genomic science in the form of a short film to a random sample of the British public. We find little evidence of attitude change as a function of information provision. However, our results show that information provision significantly increased dropout from the study amongst less educated respondents. Our findings have implications both for our understanding of the knowledge-attitude relationship in public opinion toward genomic science and for science communication more generally.
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Learning about the Human Genome. Part 2: Resources for Science Educators. ERIC Digest.
Haury, David L.
This ERIC Digest identifies how the human genome project fits into the "National Science Education Standards" and lists Human Genome Project Web sites found on the World Wide Web. It is a resource companion to "Learning about the Human Genome. Part 1: Challenge to Science Educators" (Haury 2001). The Web resources and…
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2013 Progress Report -- DOE Joint Genome Institute
Energy Technology Data Exchange (ETDEWEB)
None
2013-11-01
In October 2012, we introduced a 10-Year Strategic Vision [http://bit.ly/JGI-Vision] for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the organism and ecosystem level. This involves the continued massive-scale generation of sequence data, complemented by orthogonal new capabilities to functionally annotate these large sequence data sets. Our Strategic Vision lays out a path to guide our decisions and ensure that the evolving set of experimental and computational capabilities available to DOE JGI users will continue to enable groundbreaking science.
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Roberts, Megan C; Clyne, Mindy; Kennedy, Amy E; Chambers, David A; Khoury, Muin J
2017-10-26
PurposeImplementation science offers methods to evaluate the translation of genomic medicine research into practice. The extent to which the National Institutes of Health (NIH) human genomics grant portfolio includes implementation science is unknown. This brief report's objective is to describe recently funded implementation science studies in genomic medicine in the NIH grant portfolio, and identify remaining gaps.MethodsWe identified investigator-initiated NIH research grants on implementation science in genomic medicine (funding initiated 2012-2016). A codebook was adapted from the literature, three authors coded grants, and descriptive statistics were calculated for each code.ResultsForty-two grants fit the inclusion criteria (~1.75% of investigator-initiated genomics grants). The majority of included grants proposed qualitative and/or quantitative methods with cross-sectional study designs, and described clinical settings and primarily white, non-Hispanic study populations. Most grants were in oncology and examined genetic testing for risk assessment. Finally, grants lacked the use of implementation science frameworks, and most examined uptake of genomic medicine and/or assessed patient-centeredness.ConclusionWe identified large gaps in implementation science studies in genomic medicine in the funded NIH portfolio over the past 5 years. To move the genomics field forward, investigator-initiated research grants should employ rigorous implementation science methods within diverse settings and populations.Genetics in Medicine advance online publication, 26 October 2017; doi:10.1038/gim.2017.180.
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Rehman, Maqsood; Hansen, Jennifer L; Mallory-Smith, Carol A; Zemetra, Robert S
2017-08-01
Wheat (Triticum aestivum) (ABD) and jointed goatgrass (Aegilops cylindrica) (CD) can cross and produce hybrids that can backcross to either parent. Such backcrosses can result in progeny with chromosomes and/or chromosome segments retained from wheat. Thus, a herbicide resistance gene could migrate from wheat to jointed goatgrass. In theory, the risk of gene migration from herbicide-resistant wheat to jointed goatgrass is more likely if the gene is located on the D genome and less likely if the gene is located on the A or B genome of wheat. BC 1 populations (jointed goatgrass as a recurrent parent) were analyzed for chromosome numbers and transgene transmission rates under sprayed and non-sprayed conditions. Transgene retention in the non-sprayed BC 1 generation for the A, B and D genomes was 84, 60 and 64% respectively. In the sprayed populations, the retention was 81, 59 and 74% respectively. The gene transmission rates were higher than the expected 50% or less under sprayed and non-sprayed conditions, possibly owing to meiotic chromosome restitution and/or chromosome non-disjunction. Such high transmission rates in the BC 1 generation negates the benefits of gene placement for reducing the potential of gene migration from wheat to jointed goatgrass. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.
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2010-09-22
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical... the panels of the Joint Biomedical Laboratory Research and Development and Clinical Science Research... Crowne Plaza Clinical Research Program December 3, 2010 *VA Central Office Mental Hlth & Behav Sci-A...
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2011-04-06
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical... the panels of the Joint Biomedical Laboratory Research and Development and Clinical Science Research.... Neurobiology-D June 10, 2011 Crowne Plaza DC/Silver Spring. Clinical Research Program June 13, 2011 VA Central...
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2010-05-04
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical... panels of the Joint Biomedical Laboratory Research and Development and Clinical Science Research and... & Behav Sci-A June 7, 2010 L'Enfant Plaza Hotel. Clinical Research Program June 9, 2010 *VA Central Office...
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Zhan, Qimin; Hu, Zhibin; He, Zhonghu; Jia, Weihua; Zhou, Yifeng; Yu, Kai; Shu, Xiao-Ou; Yuan, Jian-Min; Zheng, Wei; Zhao, Xue-Ke; Gao, She-Gan; Yuan, Zhi-Qing; Zhou, Fu-You; Fan, Zong-Min; Cui, Ji-Li; Lin, Hong-Li; Han, Xue-Na; Li, Bei; Chen, Xi; Dawsey, Sanford M.; Liao, Linda; Lee, Maxwell P.; Ding, Ti; Qiao, You-Lin; Liu, Zhihua; Liu, Yu; Yu, Dianke; Chang, Jiang; Wei, Lixuan; Gao, Yu-Tang; Koh, Woon-Puay; Xiang, Yong-Bing; Tang, Ze-Zhong; Fan, Jin-Hu; Han, Jing-Jing; Zhou, Sheng-Li; Zhang, Peng; Zhang, Dong-Yun; Yuan, Yuan; Huang, Ying; Liu, Chunling; Zhai, Kan; Qiao, Yan; Jin, Guangfu; Guo, Chuanhai; Fu, Jianhua; Miao, Xiaoping; Lu, Changdong; Yang, Haijun; Wang, Chaoyu; Wheeler, William A.; Gail, Mitchell; Yeager, Meredith; Yuenger, Jeff; Guo, Er-Tao; Li, Ai-Li; Zhang, Wei; Li, Xue-Min; Sun, Liang-Dan; Ma, Bao-Gen; Li, Yan; Tang, Sa; Peng, Xiu-Qing; Liu, Jing; Hutchinson, Amy; Jacobs, Kevin; Giffen, Carol; Burdette, Laurie; Fraumeni, Joseph F.; Shen, Hongbing; Ke, Yang; Zeng, Yixin; Wu, Tangchun; Kraft, Peter; Chung, Charles C.; Tucker, Margaret A.; Hou, Zhi-Chao; Liu, Ya-Li; Hu, Yan-Long; Liu, Yu; Wang, Li; Yuan, Guo; Chen, Li-Sha; Liu, Xiao; Ma, Teng; Meng, Hui; Sun, Li; Li, Xin-Min; Li, Xiu-Min; Ku, Jian-Wei; Zhou, Ying-Fa; Yang, Liu-Qin; Wang, Zhou; Li, Yin; Qige, Qirenwang; Yang, Wen-Jun; Lei, Guang-Yan; Chen, Long-Qi; Li, En-Min; Yuan, Ling; Yue, Wen-Bin; Wang, Ran; Wang, Lu-Wen; Fan, Xue-Ping; Zhu, Fang-Heng; Zhao, Wei-Xing; Mao, Yi-Min; Zhang, Mei; Xing, Guo-Lan; Li, Ji-Lin; Han, Min; Ren, Jing-Li; Liu, Bin; Ren, Shu-Wei; Kong, Qing-Peng; Li, Feng; Sheyhidin, Ilyar; Wei, Wu; Zhang, Yan-Rui; Feng, Chang-Wei; Wang, Jin; Yang, Yu-Hua; Hao, Hong-Zhang; Bao, Qi-De; Liu, Bao-Chi; Wu, Ai-Qun; Xie, Dong; Yang, Wan-Cai; Wang, Liang; Zhao, Xiao-Hang; Chen, Shu-Qing; Hong, Jun-Yan; Zhang, Xue-Jun; Freedman, Neal D; Goldstein, Alisa M.; Lin, Dongxin; Taylor, Philip R.; Wang, Li-Dong; Chanock, Stephen J.
2014-01-01
We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region. PMID:25129146
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2012-05-02
... DEPARTMENT OF VETERANS AFFAIRS Joint Biomedical Laboratory Research and Development and Clinical Science Research and Development Services Scientific Merit Review Board, Notice of Meeting Amendment The... Development and Clinical Science Research and Development Services Scientific Merit Review Board have changed...
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The Human Genome Project: big science transforms biology and medicine
Hood, Leroy; Rowen, Lee
2013-01-01
The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called ‘big science’ - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and a...
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Hyun, Jaehwan
2017-01-01
While gene doping and other technological means of sport enhancement have become a topic of ethical debate, a major outcome from genomic research in sports is often linked to the regulation of doping. In particular, researchers within the field of anti-doping science, a regulatory science that aims to develop scientific solutions for regulating doped athletes, have conducted genomic research on anabolic-androgenic steroids. Genomic knowledge on anabolic-androgenic steroids, a knowledge base that has been produced to improve doping regulation, has caused the ‘geneticization’ of cultural objects such as ethnic identities and dietary habits. Through examining how anti-doping genomic knowledge and its media representation unnecessarily reify cultural objects in terms of genomics, I argue that Ethical, Legal, and Social Implications (ELSI) research programs in human enhancement should include the social impacts of anti-doping science in their discussions. Furthermore, this article will propose that ELSI scholars begin their academic analysis on anti-doping science by engaging with the recent ELSI scholarship on genomics and race and consider the regulatory and political natures of anti-doping research. PMID:28536601
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Directory of Open Access Journals (Sweden)
Jaehwan Hyun
2017-05-01
Full Text Available While gene doping and other technological means of sport enhancement have become a topic of ethical debate, a major outcome from genomic research in sports is often linked to the regulation of doping. In particular, researchers within the field of anti-doping science, a regulatory science that aims to develop scientific solutions for regulating doped athletes, have conducted genomic research on anabolic-androgenic steroids. Genomic knowledge on anabolic-androgenic steroids, a knowledge base that has been produced to improve doping regulation, has caused the ‘geneticization’ of cultural objects such as ethnic identities and dietary habits. Through examining how anti-doping genomic knowledge and its media representation unnecessarily reify cultural objects in terms of genomics, I argue that Ethical, Legal, and Social Implications (ELSI research programs in human enhancement should include the social impacts of anti-doping science in their discussions. Furthermore, this article will propose that ELSI scholars begin their academic analysis on anti-doping science by engaging with the recent ELSI scholarship on genomics and race and consider the regulatory and political natures of anti-doping research.
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Hyun, Jaehwan
2017-01-01
While gene doping and other technological means of sport enhancement have become a topic of ethical debate, a major outcome from genomic research in sports is often linked to the regulation of doping. In particular, researchers within the field of anti-doping science, a regulatory science that aims to develop scientific solutions for regulating doped athletes, have conducted genomic research on anabolic-androgenic steroids. Genomic knowledge on anabolic-androgenic steroids, a knowledge base that has been produced to improve doping regulation, has caused the 'geneticization' of cultural objects such as ethnic identities and dietary habits. Through examining how anti-doping genomic knowledge and its media representation unnecessarily reify cultural objects in terms of genomics, I argue that Ethical, Legal, and Social Implications (ELSI) research programs in human enhancement should include the social impacts of anti-doping science in their discussions. Furthermore, this article will propose that ELSI scholars begin their academic analysis on anti-doping science by engaging with the recent ELSI scholarship on genomics and race and consider the regulatory and political natures of anti-doping research.
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Kano, Kei; Yahata, Saiko; Muroi, Kaori; Kawakami, Masahiro; Tomoda, Mari; Miyaki, Koichi; Nakayama, Takeo; Kosugi, Shinji; Kato, Kazuto
2008-01-01
Genome science, including topics such as gene recombination, cloning, genetic tests, and gene therapy, is now an established part of our daily lives; thus we need to learn genome science to better equip ourselves for the present day. Learning from topics directly related to the human has been suggested to be more effective than learning from…
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Joint sciences academies statement: global response to climate change
International Nuclear Information System (INIS)
2005-06-01
Taking into account that there is now strong evidence that significant global warming is occurring, the Joint Science Academies, urge, by this statement, all nations in the line with the UNFCCC principles, to take prompt action to reduce the causes of climate change, adapt to its impacts and ensure that the issue is included in all relevant national and international strategies. Some recommendations are also given. (A.L.B.)
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Energy Technology Data Exchange (ETDEWEB)
NONE
1995-09-01
The publication contains abstracts of the joint fifteenth biennial conference of the West African Science Association and the nineteenth biennial conference of the Ghana Science Association,held at the University of Cape Coast,Ghana in September 1995. The theme of the conference was enhancing regional economic integration through science and technology`. A total of 180 abstracts have been presented either in english or french. Subject areas covered are:science education, social sciences, policy research, botany, zoology, agriculture, chemistry, biochemistry, physics, mathematics, computer science, geology, earth and medical sciences.
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International Nuclear Information System (INIS)
1995-09-01
The publication contains abstracts of the joint fifteenth biennial conference of the West African Science Association and the nineteenth biennial conference of the Ghana Science Association,held at the University of Cape Coast,Ghana in September 1995. The theme of the conference was enhancing regional economic integration through science and technology'. A total of 180 abstracts have been presented either in english or french. Subject areas covered are:science education, social sciences, policy research, botany, zoology, agriculture, chemistry, biochemistry, physics, mathematics, computer science, geology, earth and medical sciences
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Directory of Open Access Journals (Sweden)
Singer Peter A
2005-01-01
Full Text Available Abstract Background While innovations in medicine, science and technology have resulted in improved health and quality of life for many people, the benefits of modern medicine continue to elude millions of people in many parts of the world. To assess the potential of genomics to address health needs in EMR, the World Health Organization's Eastern Mediterranean Regional Office and the University of Toronto Joint Centre for Bioethics jointly organized a Genomics and Public Health Policy Executive Course, held September 20th–23rd, 2003, in Muscat, Oman. The 4-day course was sponsored by WHO-EMRO with additional support from the Canadian Program in Genomics and Global Health. The overall objective of the course was to collectively explore how to best harness genomics to improve health in the region. This article presents the course findings and recommendations for genomics policy in EMR. Methods The course brought together senior representatives from academia, biotechnology companies, regulatory bodies, media, voluntary, and legal organizations to engage in discussion. Topics covered included scientific advances in genomics, followed by innovations in business models, public sector perspectives, ethics, legal issues and national innovation systems. Results A set of recommendations, summarized below, was formulated for the Regional Office, the Member States and for individuals. • Advocacy for genomics and biotechnology for political leadership; • Networking between member states to share information, expertise, training, and regional cooperation in biotechnology; coordination of national surveys for assessment of health biotechnology innovation systems, science capacity, government policies, legislation and regulations, intellectual property policies, private sector activity; • Creation in each member country of an effective National Body on genomics, biotechnology and health to: - formulate national biotechnology strategies - raise
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Quality of Kindergarten Teachers Training in regard to Science: a joint Nordic Approach
DEFF Research Database (Denmark)
Sortland, Merete; Tikkanen, Tarja Irene; Presthus Heggen, Marianne
2017-01-01
This article presents a new joint Nordic study module consisting of a theoretical framework, the kindergarten teacher students’ case study and a reflection talk, in natural science for the kindergarten teacher education. The module is developed through an interdisciplinary collaboration in the No......This article presents a new joint Nordic study module consisting of a theoretical framework, the kindergarten teacher students’ case study and a reflection talk, in natural science for the kindergarten teacher education. The module is developed through an interdisciplinary collaboration...... and competence are shortly discussed. It is followed by the module’s theoretical framework. Then the study module’s development process is described accompanied by reflections of the student’s case studies in relation to the theoretical framework. At the end, the work with the study module is summarised......, and the main conclusion is that the study module contributes positively to the students’ skills development, both in science and quality....
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Dheensa, Sandi; Carrieri, Daniele; Kelly, Susan; Clarke, Angus; Doheny, Shane; Turnpenny, Peter; Lucassen, Anneke
2017-07-01
Advances in genomics often lead healthcare professionals (HCPs) to learn new information, e.g., about reinterpreted variants that could have clinical significance for patients seen previously. A question arises of whether HCPs should recontact these former patients. We present some findings interrogating the views of patients (or parents of patients) with a rare or undiagnosed condition about how such recontacting might be organised ethically and practically. Forty-one interviews were analysed thematically. Participants suggested a 'joint venture' model in which efforts to recontact are shared with HCPs. Some proposed an ICT-approach involving an electronic health record that automatically alerts them to potentially relevant updates. The need for rigorous privacy controls and transparency about who could access their data was emphasised. Importantly, these findings highlight that the lack of clarity about recontacting is a symptom of a wider problem: the lack of necessary infrastructure to pool genomic data responsibly, to aggregate it with other health data, and to enable patients/parents to receive updates. We hope that our findings will instigate a debate about the way responsibilities for recontacting under any joint venture model could be allocated, as well as the limitations and normative implications of using ICT as a solution to this intractable problem. As a first step to delineating responsibilities in the clinical setting, we suggest HCPs should routinely discuss recontacting with patients/parents, including the new information that should trigger a HCP to initiate recontact, as part of the consent process for genetic testing. Copyright © 2017 The Authors. Published by Elsevier Masson SAS.. All rights reserved.
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Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences.
Kobeissy, Firas H; Gulbakan, Basri; Alawieh, Ali; Karam, Pierre; Zhang, Zhiqun; Guingab-Cagmat, Joy D; Mondello, Stefania; Tan, Weihong; Anagli, John; Wang, Kevin
2014-02-01
The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.
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The integrated microbial genome resource of analysis.
Checcucci, Alice; Mengoni, Alessio
2015-01-01
Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.
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Minari, Jusaku; Shirai, Tetsuya; Kato, Kazuto
2014-12-01
As evidenced by high-throughput sequencers, genomic technologies have recently undergone radical advances. These technologies enable comprehensive sequencing of personal genomes considerably more efficiently and less expensively than heretofore. These developments present a challenge to the conventional framework of biomedical ethics; under these changing circumstances, each research project has to develop a pragmatic research policy. Based on the experience with a new large-scale project-the Genome Science Project-this article presents a novel approach to conducting a specific policy for personal genome research in the Japanese context. In creating an original informed-consent form template for the project, we present a two-tiered process: making the draft of the template following an analysis of national and international policies; refining the draft template in conjunction with genome project researchers for practical application. Through practical use of the template, we have gained valuable experience in addressing challenges in the ethical review process, such as the importance of sharing details of the latest developments in genomics with members of research ethics committees. We discuss certain limitations of the conventional concept of informed consent and its governance system and suggest the potential of an alternative process using information technology.
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"Harnessing genomics to improve health in India" – an executive course to support genomics policy
Directory of Open Access Journals (Sweden)
Acharya Tara
2004-05-01
Full Text Available Abstract Background The benefits of scientific medicine have eluded millions in developing countries and the genomics revolution threatens to increase health inequities between North and South. India, as a developing yet also industrialized country, is uniquely positioned to pioneer science policy innovations to narrow the genomics divide. Recognizing this, the Indian Council of Medical Research and the University of Toronto Joint Centre for Bioethics conducted a Genomics Policy Executive Course in January 2003 in Kerala, India. The course provided a forum for stakeholders to discuss the relevance of genomics for health in India. This article presents the course findings and recommendations formulated by the participants for genomics policy in India. Methods The course goals were to familiarize participants with the implications of genomics for health in India; analyze and debate policy and ethical issues; and develop a multi-sectoral opinion leaders' network to share perspectives. To achieve these goals, the course brought together representatives of academic research centres, biotechnology companies, regulatory bodies, media, voluntary, and legal organizations to engage in discussion. Topics included scientific advances in genomics, followed by innovations in business models, public sector perspectives, ethics, legal issues and national innovation systems. Results Seven main recommendations emerged: increase funding for healthcare research with appropriate emphasis on genomics; leverage India's assets such as traditional knowledge and genomic diversity in consultation with knowledge-holders; prioritize strategic entry points for India; improve industry-academic interface with appropriate incentives to improve public health and the nation's wealth; develop independent, accountable, transparent regulatory systems to ensure that ethical, legal and social issues are addressed for a single entry, smart and effective system; engage the public and
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Moskowitz, Howard R
2012-11-05
The paper introduces the empirical science of 'mind genomics', whose objective is to understand the dimensions of ordinary, everyday experience, identify mind-set segments of people who value different aspects of that everyday experience, and then assign a new person to a mind-set by a statistically appropriate procedure. By studying different experiences using experimental design of ideas, 'mind genomics' constructs an empirical, inductive science of perception and experience, layer by layer. The ultimate objective of 'mind genomics' is a large-scale science of experience created using induction, with the science based upon emergent commonalities across many different types of daily experience. The particular topic investigated in the paper is the experience of healthful snacks, what makes a person 'want' them, and the dollar value of different sensory aspects of the healthful snack. Copyright © 2012 Elsevier Inc. All rights reserved.
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2009-01-01
From 1900 onwards, scientists and novelists have explored the contours of a future society based on the use of “anthropotechnologies” (techniques applicable to human beings for the purpose of performance enhancement ranging from training and education to genome-based biotechnologies). Gradually but steadily, the technologies involved migrated from (science) fiction into scholarly publications, and from “utopia” (or “dystopia”) into science. Building on seminal ideas borrowed from Nietzsche, Peter Sloterdijk has outlined the challenges inherent in this development. Since time immemorial, and at least since the days of Plato’s Academy, human beings have been interested in possibilities for (physical or mental) performance enhancement. We are constantly trying to improve ourselves, both collectively and individually, for better or for worse. At present, however, new genomics-based technologies are opening up new avenues for self-amelioration. Developments in research facilities using animal models may to a certain extent be seen as expeditions into our own future. Are we able to address the bioethical and biopolitical issues awaiting us? After analyzing and assessing Sloterdijk’s views, attention will shift to a concrete domain of application, namely sport genomics. For various reasons, top athletes are likely to play the role of genomics pioneers by using personalized genomics information to adjust diet, life-style, training schedules and doping intake to the strengths and weaknesses of their personalized genome information. Thus, sport genomics may be regarded as a test bed where the contours of genomics-based self-management are tried out. PMID:20234832
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The Evolution of Science in a Latin-American Country: Genetics and Genomics in Brazil.
Salzano, Francisco M
2018-03-01
This article begins with a brief overview of the history of Brazil and that of Brazilian science, from the European discovery of the country in 1500 up to the early 21st century. The history of the fields of genetics and genomics, from the 1930s, is then first examined from the focal point of the lives and publications of the three persons who are generally considered to be the founders of genetics in Brazil (C. A. Krug, F. G. Brieger, and A. Dreyfus), and then by 12 other researchers up to 1999. The area of molecular genetics and genomics from 2000 to present is then described. Despite the problems of underdevelopment and the periodical political and economic crises that have affected life in Brazil, the fields of genetics and genomics in Brazil can be regarded as having developed at an appropriate pace, and have contributed in several major ways to world science. Copyright © 2018 by the Genetics Society of America.
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York, A.; Blocksome, C.; Cheng, T.; Creighton, J.; Edwards, G.; Frederick, S.; Giardina, C. P.; Goebel, P. C.; Gucker, C.; Kobziar, L.; Lane, E.; Leis, S.; Long, A.; Maier, C.; Marschall, J.; McGowan-Stinski, J.; Mohr, H.; MontBlanc, E.; Pellant, M.; Pickett, E.; Seesholtz, D.; Skowronski, N.; Stambaugh, M. C.; Stephens, S.; Thode, A.; Trainor, S. F.; Waldrop, T.; Wolfson, B.; Wright, V.; Zedler, P.
2014-12-01
The Joint Fire Science Program's (JFSP) Fire Exchange Network is actively working to accelerate the awareness, understanding, and adoption of wildland fire science information by federal, tribal, state, local, and private stakeholders within ecologically similar regions. Our network of 15 regional exchanges provides timely, accurate, and regionally relevant science-based information to assist with fire management challenges. Regional activities, through which we engage fire and resource managers, scientists, and private landowners, include online newsletters and announcements, social media, regionally focused web-based clearinghouses of relevant science, field trips and demonstration sites, workshops and conferences, webinars and online training, and syntheses and fact sheets. Exchanges also help investigators design research that is relevant to regional management needs and assist with technology transfer to management audiences. This poster provides an introduction to and map of the regional exchanges.
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Application of micro-PIXE and imaging technology to life science (Joint research)
International Nuclear Information System (INIS)
Satoh, Takahiro; Ishii, Keizo
2011-03-01
The joint research on 'Application of micro-PIXE and imaging technology to life science' supported by the Inter-organizational Atomic Energy Research Program, had been performed for three years, from 2006FY to 2009FY. Aiming to apply in-air micro-PIXE analytical system to life science, the research was consisting of 7 collaborative themes related to beam engineering for micro-PIXE and applied technology of element mapping in biological/medical fields. The system, so-called micro-PIXE camera, to acquire spatial element mapping in living cells was originally developed by collaborative research between the JAEA and the department of engineering of Tohoku University. This review covers these research results. (author)
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Tanaka,Takeshi; Vutova,Katia
2014-01-01
The Department of Electronics and Computer Engineering, Hiroshima Institute of Technology (EC-HIT) started the international joint research with the Laboratory “Physical Problems of Electron Beam technologies” of the Institute of Electronics, Bulgarian Academy of Sciences (IE-BAS) from 1994. 20 papers, included a book chapter, were published by implementing the international joint research under 5 Agreements for Academic Cooperation and Exchange between HIT and IEBAS. Our international joint ...
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In Support of Access and Inclusion: Joint Professional Development for Science and Special Educators
Directory of Open Access Journals (Sweden)
Rita Brusca-Vega
2014-11-01
Full Text Available This article addresses the need for collaborative professional development of science and special educators to enhance access and inclusion for students with disabilities and improve science learning for all students. The purpose of the study was to examine changes in the teaching practices of science and special educators, grades 4 to 8, as they jointly completed an intense year-long professional development program designed to promote hands-on, inquiry-based science in their classrooms; expand their instructional repertoires to better serve students with disabilities and other learning problems; and facilitate communication between the groups. Quantitative and qualitative measures, including pre and post ratings of teacher classroom performance, action research projects, and teacher interviews, were used to determine changes in teacher instructional and collaborative practices.
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2011 Joint Science Education Project: Research Experience in Polar Science
Wilkening, J.; Ader, V.
2011-12-01
The Joint Science Education Project (JSEP), sponsored by the National Science Foundation, is a two-part program that brings together students and teachers from the United States, Greenland, and Denmark, for a unique cross-cultural, first-hand experience of the realities of polar science field research in Greenland. During JSEP, students experienced research being conducted on and near the Greenland ice sheet by attending researcher presentations, visiting NSF-funded field sites (including Summit and NEEM field stations, both located on the Greenland ice sheet), and designing and conducting research projects in international teams. The results of two of these projects will be highlighted. The atmospheric project investigated the differences in CO2, UVA, UVB, temperature, and albedo in different Arctic microenvironments, while also examining the interaction between the atmosphere and water present in the given environments. It was found that the carbon dioxide levels varied: glacial environments having the lowest levels, with an average concentration of 272.500 ppm, and non-vegetated, terrestrial environments having the highest, with an average concentration of 395.143 ppm. Following up on these results, it is planned to further investigate the interaction of the water and atmosphere, including water's role in the uptake of carbon dioxide. The ecology project investigated the occurrence of unusual large blooms of Nostoc cyanobacteria in Kangerlussuaq area lakes. The water chemistry of the lakes which contained the cyanobacteria and the lakes that did not were compared. The only noticeable difference was of the lakes' acidity, lakes containing the blooms had an average pH value of 8.58, whereas lakes without the blooms had an average pH value of 6.60. Further investigation of these results is needed to determine whether or not this was a cause or effect of the cyanobacteria blooms. As a next step, it is planned to attempt to grow the blooms to monitor their effects on
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Eijck, van M.W.
2010-01-01
Science education reform must anticipate the scientific literacy required by the next generation of citizens. Particularly, this counts for rapidly emerging and evolving scientific disciplines such as genomics. Taking this discipline as a case, such anticipation is becoming increasingly problematic
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Energy Technology Data Exchange (ETDEWEB)
Nichols, E.K.
2000-02-17
Advances in the biomedical sciences, especially in human genomics, will dramatically influence law, medicine, public health, and many other sectors of our society in the decades ahead. The public already senses the revolutionary nature of genomic knowledge. In the US and Europe, we have seen widespread discussions about genetic discrimination in health insurance; privacy issues raised by the proliferation of DNA data banks; the challenge of interpreting new DNA diagnostic tests; changing definitions of what it means to be healthy; and the science and ethics of cloning animals and human beings. The primary goal of the Whitehead/ASLME Policy Symposium was to provide a bridge between the research community and professionals, who were just beginning to grasp the potential impact of new genetic technologies on their fields. The ''Human Genome Project: Science, Law, and Social Change in the 21st Century'' initially was designed as a forum for 300-500 physicians, lawyers, consumers, ethicists, and scientists to explore the impact of new genetic technologies and prepare for the challenges ahead.
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DEFF Research Database (Denmark)
Li, Xiujin; Buitenhuis, Albert Johannes; Lund, Mogens Sandø
2015-01-01
is highly consistent between the Chinese and Danish Holstein populations, such that a joint genome-wide association study (GWAS) can be performed. In this study, a joint GWAS was performed for 16 milk FA traits based on data of 784 Chinese and 371 Danish Holstein cows genotyped by a high-density bovine...... different effects in the 2 populations. Ten FA were influenced by a quantitative trait loci (QTL) region including DGAT1. Both C14:1 and the C14 index were influenced by a QTL region including SCD1 in the combined population. Other QTL regions also showed significant associations with the studied FA....... A large region (14.9–24.9 Mbp) in BTA26 significantly influenced C14:1 and the C14 index in both populations, mostly likely due to the SNP in SCD1. A QTL region (69.97–73.69 Mbp) on BTA9 showed a significantly different effect on C18:0 between the 2 populations. Detection of these important SNP...
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Özdemir, Vural; Badr, Kamal F; Dove, Edward S; Endrenyi, Laszlo; Geraci, Christy Jo; Hotez, Peter J; Milius, Djims; Neves-Pereira, Maria; Pang, Tikki; Rotimi, Charles N; Sabra, Ramzi; Sarkissian, Christineh N; Srivastava, Sanjeeva; Tims, Hesther; Zgheib, Nathalie K; Kickbusch, Ilona
2013-04-01
Biomedical science in the 21(st) century is embedded in, and draws from, a digital commons and "Big Data" created by high-throughput Omics technologies such as genomics. Classic Edisonian metaphors of science and scientists (i.e., "the lone genius" or other narrow definitions of expertise) are ill equipped to harness the vast promises of the 21(st) century digital commons. Moreover, in medicine and life sciences, experts often under-appreciate the important contributions made by citizen scholars and lead users of innovations to design innovative products and co-create new knowledge. We believe there are a large number of users waiting to be mobilized so as to engage with Big Data as citizen scientists-only if some funding were available. Yet many of these scholars may not meet the meta-criteria used to judge expertise, such as a track record in obtaining large research grants or a traditional academic curriculum vitae. This innovation research article describes a novel idea and action framework: micro-grants, each worth $1000, for genomics and Big Data. Though a relatively small amount at first glance, this far exceeds the annual income of the "bottom one billion"-the 1.4 billion people living below the extreme poverty level defined by the World Bank ($1.25/day). We describe two types of micro-grants. Type 1 micro-grants can be awarded through established funding agencies and philanthropies that create micro-granting programs to fund a broad and highly diverse array of small artisan labs and citizen scholars to connect genomics and Big Data with new models of discovery such as open user innovation. Type 2 micro-grants can be funded by existing or new science observatories and citizen think tanks through crowd-funding mechanisms described herein. Type 2 micro-grants would also facilitate global health diplomacy by co-creating crowd-funded micro-granting programs across nation-states in regions facing political and financial instability, while sharing similar disease
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Enslow, Electra; Fricke, Suzanne; Vela, Kathryn
2017-01-01
The purpose of this organizational case study is to describe the complexities librarians face when serving a multi-campus institution that supports both a joint-use library and expanding health sciences academic partnerships. In a system without a centralized health science library administration, liaison librarians are identifying dispersed programs and user groups and collaborating to define their unique service and outreach needs within a larger land-grant university. Using a team-based approach, health sciences librarians are communicating to integrate research and teaching support, systems differences across dispersed campuses, and future needs of a new community-based medical program.
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"Harnessing genomics to improve health in Africa" – an executive course to support genomics policy
Directory of Open Access Journals (Sweden)
Singer Peter A
2005-01-01
Full Text Available Abstract Background Africa in the twenty-first century is faced with a heavy burden of disease, combined with ill-equipped medical systems and underdeveloped technological capacity. A major challenge for the international community is to bring scientific and technological advances like genomics to bear on the health priorities of poorer countries. The New Partnership for Africa's Development has identified science and technology as a key platform for Africa's renewal. Recognizing the timeliness of this issue, the African Centre for Technology Studies and the University of Toronto Joint Centre for Bioethics co-organized a course on Genomics and Public Health Policy in Nairobi, Kenya, the first of a series of similar courses to take place in the developing world. This article presents the findings and recommendations that emerged from this process, recommendations which suggest that a regional approach to developing sound science and technology policies is the key to harnessing genome-related biotechnology to improve health and contribute to human development in Africa. Methods The objectives of the course were to familiarize participants with the current status and implications of genomics for health in Africa; to provide frameworks for analyzing and debating the policy and ethical questions; and to begin developing a network across different sectors by sharing perspectives and building relationships. To achieve these goals the course brought together a diverse group of stakeholders from academic research centres, the media, non-governmental, voluntary and legal organizations to stimulate multi-sectoral debate around issues of policy. Topics included scientific advances in genomics innovation systems and business models, international regulatory frameworks, as well as ethical and legal issues. Results Seven main recommendations emerged: establish a network for sustained dialogue among participants; identify champions among politicians; use the
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The JOVE initiative - A NASA/university Joint Venture in space science
Six, F.; Chappell, R.
1990-01-01
The JOVE (NASA/university Joint Venture in space science) initiative is a point program between NASA and institutions of higher education whose aim is to bring about an extensive merger between these two communities. The project is discussed with emphasis on suggested contributions of partnership members, JOVE process timeline, and project schedules and costs. It is suggested that NASA provide a summer resident research associateship (one ten week stipend); scientific on-line data from space missions; an electronic network and work station, providing a link to the data base and to other scientists; matching student support, both undergraduate and graduate; matching summer salary for up to three faculty participants; and travel funds. The universities will be asked to provide research time for faculty participants, matching student support, matching summer salary for faculty participants, an instructional unit in space science, and an outreach program to pre-college students.
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Life Sciences Division and Center for Human Genome Studies 1994
Energy Technology Data Exchange (ETDEWEB)
Cram, L.S.; Stafford, C. [comp.
1995-09-01
This report summarizes the research and development activities of the Los Alamos National Laboratory`s Life Sciences Division and the biological aspects of the Center for Human Genome Studies for the calendar year 1994. The technical portion of the report is divided into two parts, (1) selected research highlights and (2) research projects and accomplishments. The research highlights provide a more detailed description of a select set of projects. A technical description of all projects is presented in sufficient detail so that the informed reader will be able to assess the scope and significance of each project. Summaries useful to the casual reader desiring general information have been prepared by the group leaders and appear in each group overview. Investigators on the staff of the Life Sciences Division will be pleased to provide further information.
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Serra, Reviewed By Martin J.
2000-01-01
Genomics is one of the most rapidly expanding areas of science. This book is an outgrowth of a series of lectures given by one of the former heads (CRC) of the Human Genome Initiative. The book is designed to reach a wide audience, from biologists with little chemical or physical science background through engineers, computer scientists, and physicists with little current exposure to the chemical or biological principles of genetics. The text starts with a basic review of the chemical and biological properties of DNA. However, without either a biochemistry background or a supplemental biochemistry text, this chapter and much of the rest of the text would be difficult to digest. The second chapter is designed to put DNA into the context of the larger chromosomal unit. Specialized chromosomal structures and sequences (centromeres, telomeres) are introduced, leading to a section on chromosome organization and purification. The next 4 chapters cover the physical (hybridization, electrophoresis), chemical (polymerase chain reaction), and biological (genetic) techniques that provide the backbone of genomic analysis. These chapters cover in significant detail the fundamental principles underlying each technique and provide a firm background for the remainder of the text. Chapters 79 consider the need and methods for the development of physical maps. Chapter 7 primarily discusses chromosomal localization techniques, including in situ hybridization, FISH, and chromosome paintings. The next two chapters focus on the development of libraries and clones. In particular, Chapter 9 considers the limitations of current mapping and clone production. The current state and future of DNA sequencing is covered in the next three chapters. The first considers the current methods of DNA sequencing - especially gel-based methods of analysis, although other possible approaches (mass spectrometry) are introduced. Much of the chapter addresses the limitations of current methods, including
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Zenan, Joan S
2003-04-01
The Association of Academic Health Sciences Libraries' (AAHSL's) involvement in national legislative activities and other advocacy initiatives has evolved and matured over the last twenty-five years. Some activities conducted by the Medical Library Association's (MLA's) Legislative Committee from 1976 to 1984 are highlighted to show the evolution of MLA's and AAHSL's interests in collaborating on national legislative issues, which resulted in an agreement to form a joint legislative task force. The history, work, challenges, and accomplishments of the Joint MLA/AAHSL Legislative Task Force, formed in 1985, are discussed.
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Learning about the Human Genome. Part 1: Challenge to Science Educators. ERIC Digest.
Haury, David L.
This digest explains how to inform high school students and their parents about the human genome project (HGP) and how the information from this milestone finding will affect future biological and medical research and challenge science educators. The sections include: (1) "The Emerging Legacy of the HGP"; (2) "Transforming How…
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Opportunities and challenges of big data for the social sciences: The case of genomic data.
Liu, Hexuan; Guo, Guang
2016-09-01
In this paper, we draw attention to one unique and valuable source of big data, genomic data, by demonstrating the opportunities they provide to social scientists. We discuss different types of large-scale genomic data and recent advances in statistical methods and computational infrastructure used to address challenges in managing and analyzing such data. We highlight how these data and methods can be used to benefit social science research. Copyright © 2016 Elsevier Inc. All rights reserved.
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Statistical Methods in Integrative Genomics
Richardson, Sylvia; Tseng, George C.; Sun, Wei
2016-01-01
Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531
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Energy Technology Data Exchange (ETDEWEB)
Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office
1998-01-04
The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.
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Badr, Kamal F.; Dove, Edward S.; Endrenyi, Laszlo; Geraci, Christy Jo; Hotez, Peter J.; Milius, Djims; Neves-Pereira, Maria; Pang, Tikki; Rotimi, Charles N.; Sabra, Ramzi; Sarkissian, Christineh N.; Srivastava, Sanjeeva; Tims, Hesther; Zgheib, Nathalie K.; Kickbusch, Ilona
2013-01-01
Abstract Biomedical science in the 21st century is embedded in, and draws from, a digital commons and “Big Data” created by high-throughput Omics technologies such as genomics. Classic Edisonian metaphors of science and scientists (i.e., “the lone genius” or other narrow definitions of expertise) are ill equipped to harness the vast promises of the 21st century digital commons. Moreover, in medicine and life sciences, experts often under-appreciate the important contributions made by citizen scholars and lead users of innovations to design innovative products and co-create new knowledge. We believe there are a large number of users waiting to be mobilized so as to engage with Big Data as citizen scientists—only if some funding were available. Yet many of these scholars may not meet the meta-criteria used to judge expertise, such as a track record in obtaining large research grants or a traditional academic curriculum vitae. This innovation research article describes a novel idea and action framework: micro-grants, each worth $1000, for genomics and Big Data. Though a relatively small amount at first glance, this far exceeds the annual income of the “bottom one billion”—the 1.4 billion people living below the extreme poverty level defined by the World Bank ($1.25/day). We describe two types of micro-grants. Type 1 micro-grants can be awarded through established funding agencies and philanthropies that create micro-granting programs to fund a broad and highly diverse array of small artisan labs and citizen scholars to connect genomics and Big Data with new models of discovery such as open user innovation. Type 2 micro-grants can be funded by existing or new science observatories and citizen think tanks through crowd-funding mechanisms described herein. Type 2 micro-grants would also facilitate global health diplomacy by co-creating crowd-funded micro-granting programs across nation-states in regions facing political and financial instability, while
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Large-Scale Sequencing: The Future of Genomic Sciences Colloquium
Energy Technology Data Exchange (ETDEWEB)
Margaret Riley; Merry Buckley
2009-01-01
by other experimental data, particularly transcriptomics and metabolomics data, all of which should be gathered and curated continuously. Systematic genomics efforts like the ones outlined in this document would significantly broaden our view of biological diversity and have major effects on science. This has to be backed up with examples. Considering these potential impacts and the need for acquiescence from both the public and scientists to get such projects funded and functioning, education and training will be crucial. New collaborations within the scientific community will also be necessary.
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Human Genome Project discoveries: Dialectics and rhetoric in the science of genetics
Robidoux, Charlotte A.
The Human Genome Project (HGP), a $437 million effort that began in 1990 to chart the chemical sequence of our three billion base pairs of DNA, was completed in 2003, marking the 50th anniversary that proved the definitive structure of the molecule. This study considered how dialectical and rhetorical arguments functioned in the science, political, and public forums over a 20-year period, from 1980 to 2000, to advance human genome research and to establish the official project. I argue that Aristotle's continuum of knowledge--which ranges from the probable on one end to certified or demonstrated knowledge on the other--provides useful distinctions for analyzing scientific reasoning. While contemporary scientific research seeks to discover certified knowledge, investigators generally employ the hypothetico-deductive or scientific method, which often yields probable rather than certain findings, making these dialectical in nature. Analysis of the discourse describing human genome research revealed the use of numerous rhetorical figures and topics. Persuasive and probable reasoning were necessary for scientists to characterize unknown genetic phenomena, to secure interest in and funding for large-scale human genome research, to solve scientific problems, to issue probable findings, to convince colleagues and government officials that the findings were sound and to disseminate information to the public. Both government and private venture scientists drew on these tools of reasoning to promote their methods of mapping and sequencing the genome. The debate over how to carry out sequencing was rooted in conflicting values. Scientists representing the academic tradition valued a more conservative method that would establish high quality results, and those supporting private industry valued an unconventional approach that would yield products and profits more quickly. Values in turn influenced political and public forum arguments. Agency representatives and investors sided
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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
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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.
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Energy Technology Data Exchange (ETDEWEB)
Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others
2002-06-01
Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)
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International Nuclear Information System (INIS)
Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu
2002-01-01
Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)
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Directory of Open Access Journals (Sweden)
Dana B Hancock
Full Text Available Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second (FEV(1, and its ratio to forced vital capacity (FEV(1/FVC. Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA of single nucleotide polymorphism (SNP and SNP-by-smoking (ever-smoking or pack-years associations on FEV(1 and FEV(1/FVC across 19 studies (total N = 50,047. We identified three novel loci not previously associated with pulmonary function. SNPs in or near DNER (smallest P(JMA = 5.00×10(-11, HLA-DQB1 and HLA-DQA2 (smallest P(JMA = 4.35×10(-9, and KCNJ2 and SOX9 (smallest P(JMA = 1.28×10(-8 were associated with FEV(1/FVC or FEV(1 in meta-analysis models including SNP main effects, smoking main effects, and SNP-by-smoking (ever-smoking or pack-years interaction. The HLA region has been widely implicated for autoimmune and lung phenotypes, unlike the other novel loci, which have not been widely implicated. We evaluated DNER, KCNJ2, and SOX9 and found them to be expressed in human lung tissue. DNER and SOX9 further showed evidence of differential expression in human airway epithelium in smokers compared to non-smokers. Our findings demonstrated that joint testing of SNP and SNP-by-environment interaction identified novel loci associated with complex traits that are missed when considering only the genetic main effects.
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Lehner, Thomas; Senthil, Geetha; Addington, Anjené M
2015-01-01
After many years of unfilled promise, psychiatric genetics has seen an unprecedented number of successes in recent years. We hypothesize that the field has reached an inflection point through a confluence of four key developments: advances in genomics; the orientation of the scientific community around large collaborative team science projects; the development of sample and data repositories; and a policy framework for sharing and accessing these resources. We discuss these domains and their effect on scientific progress and provide a perspective on why we think this is only the beginning of a new era in scientific discovery. Published by Elsevier Inc.
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Energy Technology Data Exchange (ETDEWEB)
NONE
2003-03-01
Joint meeting of the 6th Simulation Science Symposium and the NIFS Collaboration Research 'Large Scale Computer Simulation' was held on December 12-13, 2002 at National Institute for Fusion Science, with the aim of promoting interdisciplinary collaborations in various fields of computer simulations. The present meeting attended by more than 40 people consists of the 11 invited and 22 contributed papers, of which topics were extended not only to fusion science but also to related fields such as astrophysics, earth science, fluid dynamics, molecular dynamics, computer science etc. (author)
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Mapping and sequencing the human genome: Science, ethics, and public policy. Final report
Energy Technology Data Exchange (ETDEWEB)
McInerney, J.D.
1993-03-31
Development of Mapping and Sequencing the Human Genome: Science, Ethics, and Public Policy followed the standard process of curriculum development at the Biological Sciences Curriculum Study (BSCS), the process is described. The production of this module was a collaborative effort between BSCS and the American Medical Association (AMA). Appendix A contains a copy of the module. Copies of reports sent to the Department of Energy (DOE) during the development process are contained in Appendix B; all reports should be on file at DOE. Appendix B also contains copies of status reports submitted to the BSCS Board of Directors.
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How computer science can help in understanding the 3D genome architecture.
Shavit, Yoli; Merelli, Ivan; Milanesi, Luciano; Lio', Pietro
2016-09-01
Chromosome conformation capture techniques are producing a huge amount of data about the architecture of our genome. These data can provide us with a better understanding of the events that induce critical regulations of the cellular function from small changes in the three-dimensional genome architecture. Generating a unified view of spatial, temporal, genetic and epigenetic properties poses various challenges of data analysis, visualization, integration and mining, as well as of high performance computing and big data management. Here, we describe the critical issues of this new branch of bioinformatics, oriented at the comprehension of the three-dimensional genome architecture, which we call 'Nucleome Bioinformatics', looking beyond the currently available tools and methods, and highlight yet unaddressed challenges and the potential approaches that could be applied for tackling them. Our review provides a map for researchers interested in using computer science for studying 'Nucleome Bioinformatics', to achieve a better understanding of the biological processes that occur inside the nucleus. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.
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Modeling biological problems in computer science: a case study in genome assembly.
Medvedev, Paul
2018-01-30
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts. Please note this is not an introduction to how genome assembly algorithms work and, if treated as such, would be incomplete and unnecessarily long-winded. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Zhao, Feifei; Chen, Yan; Ge, Siqi; Yu, Xinwei; Shao, Shuang; Black, Michael; Wang, Youxin; Zhang, Jie; Song, Manshu; Wang, Wei
2014-04-01
Science journalism is a previously neglected but rapidly growing area of scholarship in postgenomics medicine and socio-technical studies of knowledge-based innovations. Science journalism can help evaluate the quantity and quality of information flux between traditional scientific expert communities and the broader public, for example, in personalized medicine education. Newspapers can play a crucial role in science and health communication, and more importantly, in framing public engagement. However, research on the role of newspaper coverage of genomics-related articles has not been readily available in resource-limited settings. As genomics is rapidly expanding worldwide, this gap in newspaper reportage in China is therefore an important issue. In order to bridge this gap, we investigated the coverage of genomics medicine in eight major Chinese national newspapers, using the China Core Newspapers Full-text Database (CCND) and articles in scientific journals in PubMed from 2000 to 2011. Coverage of genomics medicine in these eight official government Chinese newspapers has remained low, with only 12 articles published per newspaper per year between 2000 and 2011. Between 2000 and 2011, over a 40-fold difference was observed in the number of genomics medicine-related articles in PubMed, as compared to that in newspapers. The numbers of genomics-related articles among the eight major newspapers from 2000 to 2011 were significantly different (p=0.001). Commentary/mini reviews and articles about gene therapy for specific diseases were most frequently published in 2006 and 2011. In parallel, we observed that "cancer gene therapy," "new susceptibility gene locus," and "gene technology revolution" were the top three thematic strands addressed in the newspapers, even though their volume remained low. This study reports on the under-representation of newspaper coverage of genomics medicine in China, despite the vast growth of scientific articles in journals in this
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Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.
Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U
2008-08-01
Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.
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23 science societies issue joint call for more federal research dollars
Carlowicz, Michael
In an unprecedented demonstration of unity, the leaders of 23 American scientific societies and umbrella organizations gathered on March 4 in Washington, D.C., to press the U.S. federal government for increased funding for scientific research and to make an investment in the nation's future. In a “Joint Statement on Scientific Research” addressed to President Bill Clinton and the Congress, the presidents of learned societies representing more than one million scientists, mathematicians, and engineers asked the government “to renew the nation's historical commitment to scientific research and education,” and to reverse the decline of federal investment in science and engineering. The American Geophysical Union was one of the signatories of the statement.
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Proceedings of a joint US-Japan Seminar in the Environmental Sciences
Energy Technology Data Exchange (ETDEWEB)
DeAngelis, D.L. [ed.] [Oak Ridge National Lab., TN (United States); Teramoto, E. [ed.] [Ryukoku Univ., Otsu (Japan); Neergaard, D.A. [ed.] [Tennessee Univ., Knoxville, TN (United States)
1993-11-01
The Joint US-Japan Seminar in the Environmental Sciences was based on the premises that questions remain concerning the factors that control many of the regularities observed in ecological communities and that increased collaboration between researchers in the United States and Japan can contribute to answering these questions. The papers included in this report resulted from the Seminar. These papers as well as workshop discussions summarized here outline the main issues that face theoretical ecology today. The papers cover four different areas of theoretical ecology: (1) individual species adaptations, (2) ecological community-food web interactions, (3) food web theory, and (4) concepts related to the ecosystem. Individual projects are processed separately for the databases.
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Proceedings of a joint US-Japan Seminar in the Environmental Sciences
International Nuclear Information System (INIS)
DeAngelis, D.L.; Teramoto, E.; Neergaard, D.A.
1993-11-01
The Joint US-Japan Seminar in the Environmental Sciences was based on the premises that questions remain concerning the factors that control many of the regularities observed in ecological communities and that increased collaboration between researchers in the United States and Japan can contribute to answering these questions. The papers included in this report resulted from the Seminar. These papers as well as workshop discussions summarized here outline the main issues that face theoretical ecology today. The papers cover four different areas of theoretical ecology: (1) individual species adaptations, (2) ecological community-food web interactions, (3) food web theory, and (4) concepts related to the ecosystem. Individual projects are processed separately for the databases
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Energy Technology Data Exchange (ETDEWEB)
NONE
2005-06-01
Taking into account that there is now strong evidence that significant global warming is occurring, the Joint Science Academies, urge, by this statement, all nations in the line with the UNFCCC principles, to take prompt action to reduce the causes of climate change, adapt to its impacts and ensure that the issue is included in all relevant national and international strategies. Some recommendations are also given. (A.L.B.)
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Genomics Portals: integrative web-platform for mining genomics data.
Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario
2010-01-13
A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.
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The Art and Science of Thyroid Surgery in the Age of Genomics: 100 years after Theodor Kocher
Directory of Open Access Journals (Sweden)
Seza Gulec
2017-02-01
Full Text Available Cancer is a disorder of the genome. The thyroid cancer genome is being decoded. Recent studies have identified a mutation or a genetic alteration in 95% of thyroid cancers. The National Cancer Institute initiated the Cancer Genome Atlas project in 2006 to catalogue genetic mutations associated with cancer, using genome sequencing and bioinformatics. The project has expanded to carry out genomic characterization and sequence analysis of thyroid cancer. The concept of risk stratification based on traditional parameters will soon vacate their role for clear molecular markers of non-invasive/focal, invasive/metastatic and systemic stages/phases of neoplastic disorder. A refined classification scheme based on genomics and its phenotypic expressions will accurately reflect the biologic differences between the different morphologic definitions we use today. Tumor differentiation/de-differentiation, and clinical behavior of an individual cancer will be defined by molecular markers, in addition to standard morpho-pathology. Empiricism in science of medicine and surgery has acquired a new method for testing the appropriate treatment for individual patients; that is molecular pathology, governed by genomics. The technology is present and rapidly evolving. The surgeons will determine the extent of interventions with molecular evidence and guidance.
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Overview of the Joint NASA ISRO Imaging Spectroscopy Science Campaign in India
Green, R. O.; Bhattacharya, B. K.; Eastwood, M. L.; Saxena, M.; Thompson, D. R.; Sadasivarao, B.
2016-12-01
In the period from December 2015 to March 2016 the Airborne Visible-Infrared Imaging Spectrometer Next Generation (AVIRIS-NG) was deployed to India for a joint NASA ISRO science campaign. This campaign was conceived to provide first of their kind high fidelity imaging spectroscopy measurements of a diverse set of Asian environments for science and applications research. During this campaign measurements were acquired for 57 high priority sites that have objectives spanning: snow/ice of the Himalaya; coastal habitats and water quality; mangrove forests; soils; dry and humid forests; hydrocarbon alteration; mineralogy; agriculture; urban materials; atmospheric properties; and calibration/validation. Measurements from the campaign have been processed to at-instrument spectral radiance and atmospherically corrected surface reflectance. New AVIRIS-NG algorithms for retrieval of vegetation canopy water and for estimation of the fractions of photosynthetic, non-photosynthetic vegetation have been tested and evaluated on these measurements. An inflight calibration validation experiment was performed on the 11thof December 2015 in Hyderabad to assess the spectral and radiometric calibration of AVIRIS-NG in the flight environment. We present an overview of the campaign, calibration and validation results, and initial science analysis of a subset of these unique and diverse data sets.
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Post-genome integrative biology: so that's what they call clinical science.
Rees, J
2001-01-01
Medical science is increasingly dominated by slogans, a characteristic reflecting its growing bureaucratic and corporate structure. Chief amongst these slogans is the idea that genomics will transform the public health. I believe this view is mistaken. Using studies of the genetics of skin cancer and the genetics of skin pigmentation, I describe how recent discoveries have contributed to our understanding of these topics and of human evolution. I contrast these discoveries with insights gained from other approaches, particularly those based on clinical studies. The 'IKEA model of medical advance'--you just do the basic science in the laboratory and self-assemble in the clinic--is not only damaging to clinical advance, but reflects a widespread ignorance about the nature of disease and how clinical discovery arises. We need to think more about disease and less about genes; more in the clinic and less in the laboratory.
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Energy Technology Data Exchange (ETDEWEB)
NONE
2003-03-01
Joint meeting of the 6th Simulation Science Symposium and the NIFS Collaboration Research 'Large Scale Computer Simulation' was held on December 12-13, 2002 at National Institute for Fusion Science, with the aim of promoting interdisciplinary collaborations in various fields of computer simulations. The present meeting attended by more than 40 people consists of the 11 invited and 22 contributed papers, of which topics were extended not only to fusion science but also to related fields such as astrophysics, earth science, fluid dynamics, molecular dynamics, computer science etc. (author)
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Genomics Portals: integrative web-platform for mining genomics data
Directory of Open Access Journals (Sweden)
Ghosh Krishnendu
2010-01-01
Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.
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The joint project for high-intensity proton accelerators
Energy Technology Data Exchange (ETDEWEB)
NONE
1999-08-01
Japan Atomic Energy Research Institute (JAERI) and the High Energy Accelerator Research Organization (KEK) agreed to promote the joint project integrating both the Neutron Science Project (NSP) of JAERI and the Japan Hadron Facility Project (JHF) of KEK for comprehensive studies on basic science and technology using high-intensity proton accelerator. This document describes the joint proposal prepared by the Joint Project Team of JAERI and KEK to construct accelerators and research facilities necessary both for the NSP and the JHF at the site of JAERI Tokai Establishment. (author)
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On the Epistemological Crisis in Genomics
Dougherty, Edward R
2008-01-01
There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood. PMID:19440447
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Zenan, Joan S.
2003-01-01
The Association of Academic Health Sciences Libraries' (AAHSL's) involvement in national legislative activities and other advocacy initiatives has evolved and matured over the last twenty-five years. Some activities conducted by the Medical Library Association's (MLA's) Legislative Committee from 1976 to 1984 are highlighted to show the evolution of MLA's and AAHSL's interests in collaborating on national legislative issues, which resulted in an agreement to form a joint legislative task forc...
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2015-08-01
and organisational sciences; organisational psychology and behavioural psychology disciplines; and systems sciences and network centric warfare. From...Kernot and Tim McKay Joint and Operations Analysis Division Defence Science and Technology Organisation DST-Group-TN-1474 ABSTRACT In...dimensional space comprising: Coordination and Organisation ; Social Capital; and Optimisation of the Socio-technical Systems. Given the variability of the
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Energy Technology Data Exchange (ETDEWEB)
Arkin, Adam [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bader, David C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Coffey, Richard [Argonne National Lab. (ANL), Argonne, IL (United States); Antypas, Katie [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bard, Deborah [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Dart, Eli [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Esnet; Dosanjh, Sudip [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Gerber, Richard [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hack, James [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Monga, Inder [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Esnet; Papka, Michael E. [Argonne National Lab. (ANL), Argonne, IL (United States); Riley, Katherine [Argonne National Lab. (ANL), Argonne, IL (United States); Rotman, Lauren [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Esnet; Straatsma, Tjerk [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Wells, Jack [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Aluru, Srinivas [Georgia Inst. of Technology, Atlanta, GA (United States); Andersen, Amity [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Aprá, Edoardo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). EMSL; Azad, Ariful [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bates, Susan [National Center for Atmospheric Research, Boulder, CO (United States); Blaby, Ian [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaby-Haas, Crysten [Brookhaven National Lab. (BNL), Upton, NY (United States); Bonneau, Rich [New York Univ. (NYU), NY (United States); Bowen, Ben [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bradford, Mark A. [Yale Univ., New Haven, CT (United States); Brodie, Eoin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brown, James (Ben) [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Buluc, Aydin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bernholdt, David [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bylaska, Eric [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Calvin, Kate [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Cannon, Bill [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Chen, Xingyuan [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Cheng, Xiaolin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cheung, Margaret [Univ. of Houston, Houston, TX (United States); Chowdhary, Kenny [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Colella, Phillip [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Collins, Bill [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Compo, Gil [National Oceanic and Atmospheric Administration (NOAA), Boulder, CO (United States); Crowley, Mike [National Renewable Energy Lab. (NREL), Golden, CO (United States); Debusschere, Bert [Sandia National Lab. (SNL-CA), Livermore, CA (United States); D’Imperio, Nicholas [Brookhaven National Lab. (BNL), Upton, NY (United States); Dror, Ron [Stanford Univ., Stanford, CA (United States); Egan, Rob [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Evans, Katherine [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Friedberg, Iddo [Iowa State Univ., Ames, IA (United States); Fyke, Jeremy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Gao, Zheng [Stony Brook Univ., Stony Brook, NY (United States); Georganas, Evangelos [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Giraldo, Frank [Naval Postgraduate School, Monterey, CA (United States); Gnanakaran, Gnana [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Govind, Niri [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). EMSL; Grandy, Stuart [Univ. of New Hampshire, Durham, NH (United States); Gustafson, Bill [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hammond, Glenn [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hargrove, William [USDA Forest Service, Washington, D.C. (United States); Heroux, Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hoffman, Forrest [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hofmeyr, Steven [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hunke, Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jackson, Charles [Univ. of Texas-Austin, Austin, TX (United States); Jacob, Rob [Argonne National Lab. (ANL), Argonne, IL (United States); Jacobson, Dan [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Jacobson, Matt [Univ. of California, San Francisco, CA (United States); Jain, Chirag [Georgia Inst. of Technology, Atlanta, GA (United States); Johansen, Hans [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Johnson, Jeff [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jones, Andy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jones, Phil [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kalyanaraman, Ananth [Washington State Univ., Pullman, WA (United States); Kang, Senghwa [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); King, Eric [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Koanantakool, Penporn [Univ. of California, Berkeley, CA (United States); Kollias, Pavlos [Stony Brook Univ., Stony Brook, NY (United States); Kopera, Michal [Univ. of California, Santa Cruz, CA (United States); Kotamarthi, Rao [Argonne National Lab. (ANL), Argonne, IL (United States); Kowalski, Karol [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). EMSL; Kumar, Jitendra [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kyrpides, Nikos [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Leung, Ruby [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Li, Xiaolin [Stony Brook Univ., Stony Brook, NY (United States); Lin, Wuyin [Brookhaven National Lab. (BNL), Upton, NY (United States); Link, Robert [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Liu, Yangang [Brookhaven National Lab. (BNL), Upton, NY (United States); Loew, Leslie [Univ. of Connecticut, Storrs, CT (United States); Luke, Edward [Brookhaven National Lab. (BNL), Upton, NY (United States); Ma, Hsi -Yen [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mahadevan, Radhakrishnan [Univ. of Toronto, Toronto, ON (Canada); Maranas, Costas [Pennsylvania State Univ., University Park, PA (United States); Martin, Daniel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Maslowski, Wieslaw [Naval Postgraduate School, Monterey, CA (United States); McCue, Lee Ann [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McInnes, Lois Curfman [Argonne National Lab. (ANL), Argonne, IL (United States); Mills, Richard [Intel Corp., Santa Clara, CA (United States); Molins Rafa, Sergi [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Morozov, Dmitriy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Mostafavi, Sara [Center for Molecular Medicine and Therapeutics, Vancouver, BC (Canada); Moulton, David J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mourao, Zenaida [Univ. of Cambridge (United Kingdom); Najm, Habib [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Ng, Bernard [Center for Molecular Medicine and Therapeutics, Vancouver, BC (Canada); Ng, Esmond [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Norman, Matt [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Oh, Sang -Yun [Univ. of California, Santa Barbara, CA (United States); Oliker, Leonid [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Pan, Chongle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pass, Rebecca [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Pau, George S. H. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Petridis, Loukas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Prakash, Giri [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Price, Stephen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Randall, David [Colorado State Univ., Fort Collins, CO (United States); Renslow, Ryan [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Riihimaki, Laura [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Ringler, Todd [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Roberts, Andrew [Naval Postgraduate School, Monterey, CA (United States); Rokhsar, Dan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ruebel, Oliver [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Salinger, Andrew [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Scheibe, Tim [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Schulz, Roland [Intel, Mountain View, CA (United States); Sivaraman, Chitra [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Smith, Jeremy [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sreepathi, Sarat [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Steefel, Carl [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Talbot, Jenifer [Boston Univ., Boston, MA (United States); Tantillo, D. J. [Univ. of California, Davis, CA (United States); Tartakovsky, Alex [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Taylor, Mark [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Taylor, Ronald [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Trebotich, David [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Urban, Nathan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Valiev, Marat [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). EMSL; Wagner, Allon [Univ. of California, Berkeley, CA (United States); Wainwright, Haruko [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wieder, Will [NCAR/Univ. of Colorado, Boulder, CO (United States); Wiley, Steven [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Williams, Dean [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Worley, Pat [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Xie, Shaocheng [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Yelick, Kathy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Yoo, Shinjae [Brookhaven National Lab. (BNL), Upton, NY (United States); Yosef, Niri [Univ. of California, Berkeley, CA (United States); Zhang, Minghua [Stony Brook Univ., Stony Brook, NY (United States)
2016-03-31
Understanding the fundamentals of genomic systems or the processes governing impactful weather patterns are examples of the types of simulation and modeling performed on the most advanced computing resources in America. High-performance computing and computational science together provide a necessary platform for the mission science conducted by the Biological and Environmental Research (BER) office at the U.S. Department of Energy (DOE). This report reviews BER’s computing needs and their importance for solving some of the toughest problems in BER’s portfolio. BER’s impact on science has been transformative. Mapping the human genome, including the U.S.-supported international Human Genome Project that DOE began in 1987, initiated the era of modern biotechnology and genomics-based systems biology. And since the 1950s, BER has been a core contributor to atmospheric, environmental, and climate science research, beginning with atmospheric circulation studies that were the forerunners of modern Earth system models (ESMs) and by pioneering the implementation of climate codes onto high-performance computers. See http://exascaleage.org/ber/ for more information.
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Bubela, T
2006-11-01
This essay reports on the final session of a 2-day workshop entitled 'Genetic Diversity and Science Communication', hosted by the CIHR Institute of Genetics in Toronto, April 2006. The first speaker, Timothy Caulfield, introduced the intersecting communities that promulgate a 'cycle of hype' of the timelines and expected outcomes of the Human Genome Project (HGP): scientists, the media and the public. Other actors also contribute to the overall hype, the social science and humanities communities, industry and politicians. There currently appears to be an abatement of the overblown rhetoric of the HGP. As pointed out by the second speaker, Sharon Kardia, there is broad recognition that most phenotypic traits, including disease susceptibility are multi-factorial. That said, George Davey-Smith reminded us that some direct genotype-phenotype associations may be useful for public health issues. The Mendelian randomization approach hopes to revitalize the discipline of epidemiology by strengthening causal influences about environmentally modifiable risk factors. A more realistic informational environment paves the way for greater public engagement in science policy. Two such initiatives were presented by Kardia and Jason Robert, and Peter Finegold emphasized that science education and professional development for science teachers are important components of later public engagement in science issues. However, pressures on public research institutions to commercialize and seek industry funding may have negative impacts in both encouraging scientists to inappropriately hype research and on diminishing public trust in the scientific enterprise. The latter may have a significant effect on public engagement processes, such as those proposed by Robert and Kardia.
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Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach
Directory of Open Access Journals (Sweden)
Claudia Bartoli
2017-05-01
Full Text Available The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes. In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.
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Genome Variation Map: a data repository of genome variations in BIG Data Center
Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang
2017-01-01
Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...
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eGenomics: Cataloguing Our Complete Genome Collection III
Directory of Open Access Journals (Sweden)
Dawn Field
2007-01-01
Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.
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JAERI-KEK joint project on high intensity proton accelerators
International Nuclear Information System (INIS)
Nagamiya, Shoji
2000-01-01
Japan Atomic Energy Research Institute (JAERI) and the High Energy Accelerator Organization (KEK) are promoting the joint project integrating both the Neutron Science Project (NSP) of JAERI and the Japan Hadron Facility Project (JHF) of KEK for comprehensive studies on basic science and technology using high-intensity proton accelerator. This paper describes the joint project prepared by the Joint Project Team of JAERI and KEK to construct accelerators and research facilities necessary both for the NSP and the JHF at the site of JAERI Tokai Establishment. (author)
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Haplotype assembly in polyploid genomes and identical by descent shared tracts.
Aguiar, Derek; Istrail, Sorin
2013-07-01
Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the genome is vast and the population samples are growing so rapidly that algorithms processing high-throughput sequencing data must scale favorably in terms of both accuracy and computational efficiency. Furthermore, current models and methodologies for haplotype assembly (i) do not consider individuals sharing haplotypes jointly, which reduces the size and accuracy of assembled haplotypes, and (ii) are unable to model genomes having more than two sets of homologous chromosomes (polyploidy). Polyploid organisms are increasingly becoming the target of many research groups interested in the genomics of disease, phylogenetics, botany and evolution but there is an absence of theory and methods for polyploid haplotype reconstruction. In this work, we present a number of results, extensions and generalizations of compass graphs and our HapCompass framework. We prove the theoretical complexity of two haplotype assembly optimizations, thereby motivating the use of heuristics. Furthermore, we present graph theory-based algorithms for the problem of haplotype assembly using our previously developed HapCompass framework for (i) novel implementations of haplotype assembly optimizations (minimum error correction), (ii) assembly of a pair of individuals sharing a haplotype tract identical by descent and (iii) assembly of polyploid genomes. We evaluate our methods on 1000 Genomes Project, Pacific Biosciences and simulated sequence data. HapCompass is available for download at http://www.brown.edu/Research/Istrail_Lab/. Supplementary data are available at Bioinformatics online.
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The Chlamydomonas genome project: a decade on
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
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Martínez, Carlos Alberto; Khare, Kshitij; Banerjee, Arunava; Elzo, Mauricio A
2017-03-21
It is important to consider heterogeneity of marker effects and allelic frequencies in across population genome-wide prediction studies. Moreover, all regression models used in genome-wide prediction overlook randomness of genotypes. In this study, a family of hierarchical Bayesian models to perform across population genome-wide prediction modeling genotypes as random variables and allowing population-specific effects for each marker was developed. Models shared a common structure and differed in the priors used and the assumption about residual variances (homogeneous or heterogeneous). Randomness of genotypes was accounted for by deriving the joint probability mass function of marker genotypes conditional on allelic frequencies and pedigree information. As a consequence, these models incorporated kinship and genotypic information that not only permitted to account for heterogeneity of allelic frequencies, but also to include individuals with missing genotypes at some or all loci without the need for previous imputation. This was possible because the non-observed fraction of the design matrix was treated as an unknown model parameter. For each model, a simpler version ignoring population structure, but still accounting for randomness of genotypes was proposed. Implementation of these models and computation of some criteria for model comparison were illustrated using two simulated datasets. Theoretical and computational issues along with possible applications, extensions and refinements were discussed. Some features of the models developed in this study make them promising for genome-wide prediction, the use of information contained in the probability distribution of genotypes is perhaps the most appealing. Further studies to assess the performance of the models proposed here and also to compare them with conventional models used in genome-wide prediction are needed. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Middleton, A; Bragin, E; Parker, M
2014-10-01
This paper offers a description of how social media, traditional media and direct invitation were used as tools for the recruitment of 6,944 research participants for a social sciences study on genomics. The remit was to gather the views of various stakeholders towards sharing incidental findings from whole genome studies. This involved recruiting members of the public, genetic health professionals, genomic researchers and non-genetic health professionals. A novel survey was designed that contained ten integrated films; this was made available online and open for completion by anyone worldwide. The recruitment methods are described together with the convenience and snowballing sampling framework. The most successful strategy involved the utilisation of social media; Facebook, Blogging, Twitter, LinkedIn and Google Ads led to the ascertainment of over 75 % of the final sample. We conclude that the strategies used were successful in recruiting in eclectic mix of appropriate participants. Design of the survey and results from the study are presented separately.
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2007-04-01
Medical and Biotechnology Businesses in Proteomics , Genomics, Medicine, and Dentistry PRINCIPAL INVESTIGATOR: Mark S. Long Brian C...2007 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Incubation and Growth of Life Sciences, Medical and Biotechnology Businesses in Proteomics ...aflatoxins B1 and G1 from Aspergillus flavus. All toxins studied were purchased from Sigma Aldrich and used without further purification. Solutions
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Toward genome-enabled mycology.
Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W
2013-01-01
Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.
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Application of Genomic In Situ Hybridization in Horticultural Science
Directory of Open Access Journals (Sweden)
Fahad Ramzan
2017-01-01
Full Text Available Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH techniques in horticultural plants.
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Genome Improvement at JGI-HAGSC
Energy Technology Data Exchange (ETDEWEB)
Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.
2012-03-03
Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.
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Directory of Open Access Journals (Sweden)
Steven W Cole
2014-08-01
Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.
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Owolabi, Mayowa; Peprah, Emmanuel; Xu, Huichun; Akinyemi, Rufus; Tiwari, Hemant K; Irvin, Marguerite R; Wahab, Kolawole Wasiu; Arnett, Donna K; Ovbiagele, Bruce
2017-11-15
We systematically reviewed the genetic variants associated with stroke in genome-wide association studies (GWAS) and examined the emerging priorities and opportunities for rapidly advancing stroke research in the era of Trans-Omics science. Using the PRISMA guideline, we searched PubMed and NHGRI- EBI GWAS catalog for stroke studies from 2007 till May 2017. We included 31 studies. The major challenge is that the few validated variants could not account for the full genetic risk of stroke and have not been translated for clinical use. None of the studies included continental Africans. Genomic study of stroke among Africans presents a unique opportunity for the discovery, validation, functional annotation, Trans-Omics study and translation of genomic determinants of stroke with implications for global populations. This is because all humans originated from Africa, a continent with a unique genomic architecture and a distinctive epidemiology of stroke; as well as substantially higher heritability and resolution of fine mapping of stroke genes. Understanding the genomic determinants of stroke and the corresponding molecular mechanisms will revolutionize the development of a new set of precise biomarkers for stroke prediction, diagnosis and prognostic estimates as well as personalized interventions for reducing the global burden of stroke. Copyright © 2017 Elsevier B.V. All rights reserved.
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Fungal Genomics for Energy and Environment
Energy Technology Data Exchange (ETDEWEB)
Grigoriev, Igor V.
2013-03-11
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). One of its projects, 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) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 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.
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Predicting the Functional Roles of Knee Joint Muscles from Internal Joint Moments
DEFF Research Database (Denmark)
Flaxman, Teresa E; Alkjær, Tine; Simonsen, Erik B
2017-01-01
INTRODUCTION: Knee muscles are commonly labeled as flexors or extensors and aptly stabilize the knee against sagittal plane loads. However, how these muscles stabilize the knee against adduction-abduction and rotational loads remains unclear. Our study sought 1) to classify muscle roles as they r...... on its role in maintaining knee joint stability in the frontal and transverse loading planes. This is useful for delineating the roles of biarticular knee joint muscles and could have implications in robotics, musculoskeletal modeling, sports sciences, and rehabilitation....
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Shmulevich, Ilya
2007-01-01
Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema
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International Nuclear Information System (INIS)
Anon.
1989-01-01
An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base
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Organizational heterogeneity of vertebrate genomes.
Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham
2012-01-01
Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.
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Organizational heterogeneity of vertebrate genomes.
Directory of Open Access Journals (Sweden)
Svetlana Frenkel
Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.
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Golden, Aaron; McLellan, Andrew S; Dubin, Robert A; Jing, Qiang; O Broin, Pilib; Moskowitz, David; Zhang, Zhengdong; Suzuki, Masako; Hargitai, Joseph; Calder, R Brent; Greally, John M
2012-01-01
Massively-parallel sequencing (MPS) technologies and their diverse applications in genomics and epigenomics research have yielded enormous new insights into the physiology and pathophysiology of the human genome. The biggest hurdle remains the magnitude and diversity of the datasets generated, compromising our ability to manage, organize, process and ultimately analyse data. The Wiki-based Automated Sequence Processor (WASP), developed at the Albert Einstein College of Medicine (hereafter Einstein), uniquely manages to tightly couple the sequencing platform, the sequencing assay, sample metadata and the automated workflows deployed on a heterogeneous high performance computing cluster infrastructure that yield sequenced, quality-controlled and 'mapped' sequence data, all within the one operating environment accessible by a web-based GUI interface. WASP at Einstein processes 4-6 TB of data per week and since its production cycle commenced it has processed ~ 1 PB of data overall and has revolutionized user interactivity with these new genomic technologies, who remain blissfully unaware of the data storage, management and most importantly processing services they request. The abstraction of such computational complexity for the user in effect makes WASP an ideal middleware solution, and an appropriate basis for the development of a grid-enabled resource - the Einstein Genome Gateway - as part of the Extreme Science and Engineering Discovery Environment (XSEDE) program. In this paper we discuss the existing WASP system, its proposed middleware role, and its planned interaction with XSEDE to form the Einstein Genome Gateway.
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Pre-Medical Education in the Physical Sciences for Tomorrow's Physicians
Long, Sharon
2009-05-01
Medical knowledge is being transformed by instrumentation advances and by research results including genomic and population level studies; at the same time, though, the premedical curriculum is constrained by a relatively unchanging overall content in the MCAT examination, which inhibits innovation on undergraduate science education. A committee convened jointly by the Association of American Medical Colleges and the Howard Hughes Medical Institute has examined the science and mathematics competencies that the graduating physician will need, and has asked which of these should be achieved during undergraduate study. The recommendations emphasize competency -- what the learner should be able to ``do'' at the end of the learning experience -- rather than dictating specific courses. Because the scientific content of modern medical practice is evolving, new science competencies are desirable for the entering medical student. An example is statistics, an increasingly prominent foundation for database and genomic analysis but which is not yet uniformly recommended as preparation for medical school. On the other hand, the committee believes that the value of a broad liberal arts education is enduring, and science coursework should not totally consume a premedical student's time. Thus if we recommend new areas of science and mathematics competency for pre-meds, we must find other areas that can be trimmed or combined. Indeed, at present there are some science topics mandated for premedical study, which may not be essential. For these reasons, the committee aims to state premedical recommendations in ways that can be met either through traditional disciplinary courses, or through innovative and/or interdisciplinary courses. Finally, we acknowledge that practice of medicine requires grounding in scientific principles and knowledge and in the practice of critical inquiry. These principles may be learned and practiced in undergraduate study through work in the physical
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Genomic research perspectives in Kazakhstan
Directory of Open Access Journals (Sweden)
Ainur Akilzhanova
2014-01-01
Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well
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Genome Engineering for Personalized Arthritis Therapeutics.
Adkar, Shaunak S; Brunger, Jonathan M; Willard, Vincent P; Wu, Chia-Lung; Gersbach, Charles A; Guilak, Farshid
2017-10-01
Arthritis represents a family of complex joint pathologies responsible for the majority of musculoskeletal conditions. Nearly all diseases within this family, including osteoarthritis, rheumatoid arthritis, and juvenile idiopathic arthritis, are chronic conditions with few or no disease-modifying therapeutics available. Advances in genome engineering technology, most recently with CRISPR-Cas9, have revolutionized our ability to interrogate and validate genetic and epigenetic elements associated with chronic diseases such as arthritis. These technologies, together with cell reprogramming methods, including the use of induced pluripotent stem cells, provide a platform for human disease modeling. We summarize new evidence from genome-wide association studies and genomics that substantiates a genetic basis for arthritis pathogenesis. We also review the potential contributions of genome engineering in the development of new arthritis therapeutics. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Propionibacterium avidum as an Etiological Agent of Prosthetic Hip Joint Infection.
Directory of Open Access Journals (Sweden)
Peter Wildeman
Full Text Available Propionibacterium acnes is well-established as a possible etiologic agent of prosthetic joint infections (PJIs. Other Propionibacterium spp. have occasionally been described as a cause of PJIs, but this has not previously been the case for P. avidum despite its capacity to form biofilm. We describe two patients with prosthetic hip joint infections caused by P. avidum. Both patients were primarily operated with an anteriorly curved skin incision close to the skin crease of the groin, and both were obese. Initial treatment was performed according to the DAIR procedure (debridement, antibiotics, and implant retention. In case 1, the outcome was successful, but in case 2, a loosening of the cup was present 18 months post debridement. The P. avidum isolate from case 1 and two isolates from case 2 (obtained 18 months apart were selected for whole genome sequencing. The genome of P. avidum obtained from case 1 was approximately 60 kb larger than the genomes of the two isolates of case 2. These latter isolates were clonal with the exception of SNPs in the genome. All three strains possessed the gene cluster encoding exopolysaccharide synthesis. P. avidum has a pathogenic potential and the ability to cause clinically relevant infections, including abscess formation, in the presence of foreign bodies such as prosthetic joint components. Skin incision in close proximity to the groin or deep skin crease, such as the anteriorly curved skin incision approach, might pose a risk of PJIs by P. avidum, especially in obese patients.
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Efficient strategy for detecting gene × gene joint action and its application in schizophrenia
Won, Sungho; Kwon, Min-Seok; Mattheisen, Manuel; Park, Suyeon; Park, Changsoon; Kihara, Daisuke; Cichon, Sven; Ophoff, Roel; Nöthen, Markus M.; Rietschel, Marcella; Baur, Max; Uitterlinden, Andre G.; Hofmann, A.; Lange, Christoph; Kahn, René S.; Linszen, Don H.; van Os, Jim; Wiersma, Durk; Bruggeman, Richard; Cahn, Wiepke; de Haan, Lieuwe; Krabbendam, Lydia; Myin-Germeys, Inez
2014-01-01
We propose a new approach to detect gene × gene joint action in genome-wide association studies (GWASs) for case-control designs. This approach offers an exhaustive search for all two-way joint action (including, as a special case, single gene action) that is computationally feasible at the
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Web Apollo: a web-based genomic annotation editing platform.
Lee, Eduardo; Helt, Gregg A; Reese, Justin T; Munoz-Torres, Monica C; Childers, Chris P; Buels, Robert M; Stein, Lincoln; Holmes, Ian H; Elsik, Christine G; Lewis, Suzanna E
2013-08-30
Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.
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Enhancing fire science exchange: The Northern Rockies Fire Science Network [poster
Vita Wright
2011-01-01
The Joint Fire Science Program is developing a national network of knowledge exchange consortia comprised of interested management and science stakeholders working together to tailor and actively demonstrate existing fire science information to benefit management.
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Solder joint technology materials, properties, and reliability
Tu, King-Ning
2007-01-01
Solder joints are ubiquitous in electronic consumer products. The European Union has a directive to ban the use of Pb-based solders in these products on July 1st, 2006. There is an urgent need for an increase in the research and development of Pb-free solders in electronic manufacturing. For example, spontaneous Sn whisker growth and electromigration induced failure in solder joints are serious issues. These reliability issues are quite complicated due to the combined effect of electrical, mechanical, chemical, and thermal forces on solder joints. To improve solder joint reliability, the science of solder joint behavior under various driving forces must be understood. In this book, the advanced materials reliability issues related to copper-tin reaction and electromigration in solder joints are emphasized and methods to prevent these reliability problems are discussed.
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Clay, Alexis; Delord, Elric; Couture, Nadine; Domenger, Gaël
We describe the joint research that we conduct in gesture-based emotion recognition and virtual augmentation of a stage, bridging together the fields of computer science and dance. After establishing a common ground for dialogue, we could conduct a research process that equally benefits both fields. As computer scientists, dance is a perfect application case. Dancer's artistic creativity orient our research choices. As dancers, computer science provides new tools for creativity, and more importantly a new point of view that forces us to reconsider dance from its fundamentals. In this paper we hence describe our scientific work and its implications on dance. We provide an overview of our system to augment a ballet stage, taking a dancer's emotion into account. To illustrate our work in both fields, we describe three events that mixed dance, emotion recognition and augmented reality.
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2012-12-20
... Genome Initiative--What's Next? AGENCY: Office of Science, Office of Biological and Environmental... INFORMATION CONTACT: Dr. Catherine Ronning, U.S. Department of Energy, Office of Science, Office of Biological... 20585-1290. Phone 301-903-9549, fax (301) 903-5051, email: [email protected]science.doe.gov ; Dr. Jane...
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Caporale, Lynn Helena
2012-09-01
This overview of a special issue of Annals of the New York Academy of Sciences discusses uneven distribution of distinct types of variation across the genome, the dependence of specific types of variation upon distinct classes of DNA sequences and/or the induction of specific proteins, the circumstances in which distinct variation-generating systems are activated, and the implications of this work for our understanding of evolution and of cancer. Also discussed is the value of non text-based computational methods for analyzing information carried by DNA, early insights into organizational frameworks that affect genome behavior, and implications of this work for comparative genomics. © 2012 New York Academy of Sciences.
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Weber, K Scott; Jensen, Jamie L; Johnson, Steven M
2015-01-01
An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.
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A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes
Directory of Open Access Journals (Sweden)
Michael Strong
2009-12-01
Full Text Available As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the Escherichia coli genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.
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Comyn, John
1997-01-01
The use of adhesives is widespread and growing, and there are few modern artefacts, from the simple cereal packet, to the jumbo jet, that are without this means of joining. Adhesion Science provides an illuminating account of the science underlying the use of adhesives, a branch of chemical technology which is fundamental to the science of coatings and composite materials and to the performance of all types of bonded structures. This book guides the reader through the essential basic polymer science, and the chemistry of adhesives in use at present. It discusses surface preparation for adhesive bonding, and the use of primers and coupling agents. There is a detailed chapter on contact angles and what can be predicted from them. A simple guide on stress distribution joints and how this relates to testing is included. It also examines the interaction of adhesives and the environment, including an analysis of the resistance of joints to water, oxygen and ultra-violet light. Adhesion Science provides a comprehens...
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Indian Academy of Sciences (India)
Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:
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Elkins, James G; Hamilton-Brehm, Scott D; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren; Kyrpides, Nikos C; Ivanova, Natalia N; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W
2013-04-11
Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments.
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Zhou, L; Lund, M S; Wang, Y; Su, G
2014-08-01
This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G-matrices) across these two breeds. Single-trait genomic best linear unbiased prediction (GBLUP) model and two-trait GBLUP model were used for single-breed and two-breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedish Red and Finnish Ayrshire. The bulls were genotyped with 50 000 SNP chip. Using the two-breed predictions with a joint Nordic Holstein and Nordic Red reference population, accuracies increased slightly for all traits in Nordic Red, but only for some traits in Nordic Holstein. Among the three subpopulations of Nordic Red, accuracies increased more for Danish Red than for Swedish Red and Finnish Ayrshire. This is because closer genetic relationships exist between Danish Red and Nordic Holstein. Among Danish Red, individuals with higher genomic relationship coefficients with Nordic Holstein showed more increased accuracies in the two-breed predictions. Weighting the two-breed G-matrices by LD phase consistencies, marker effects or both did not further improve accuracies of the two-breed predictions. © 2014 Blackwell Verlag GmbH.
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A Euclid, LSST and WFIRST Joint Processing Study
Chary, Ranga-Ram; Joint Processing Working Group
2018-01-01
Euclid, LSST and WFIRST are the flagship cosmological projects of the next decade. By mapping several thousand square degrees of sky and covering the electromagnetic spectrum from the optical to the NIR with (sub-)arcsec resolution, these projects will provide exciting new constraints on the nature of dark energy and dark matter. The ultimate cosmological, astrophysical and time-domain science yield from these missions, which will detect several billions of sources, requires joint processing at the pixel-level. Three U.S. agencies (DOE, NASA and NSF) are supporting an 18-month study which aims to 1) assess the optimal techniques to combine these, and ancillary data sets at the pixel level; 2) investigate options for an interface that will enable community access to the joint data products; and 3) identify the computing and networking infrastructure to properly handle and manipulate these large datasets together. A Joint Processing Working Group (JPWG) is carrying out this study and consists of US-based members from the community and science/data processing centers of each of these projects. Coordination with European partners is envisioned in the future and European Euclid members are involved in the JPWG as observers. The JPWG will scope the effort and resources required to build up the capabilities to support scientific investigations using joint processing in time for the start of science surveys by LSST and Euclid.
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Energy Technology Data Exchange (ETDEWEB)
Mansfield, Betty Kay [ORNL; Martin, Sheryl A [ORNL
2006-02-01
Welcome to the 2006 joint meeting of the fourth Genomics:GTL Contractor-Grantee Workshop and the six Metabolic Engineering Working Group Inter-Agency Conference. The vision and scope of the Genomics:GTL program continue to expand and encompass research and technology issues from diverse scientific disciplines, attracting broad interest and support from researchers at universities, DOE national laboratories, and industry. Metabolic engineering's vision is the targeted and purposeful alteration of metabolic pathways to improve the understanding and use of cellular pathways for chemical transformation, energy transduction, and supramolecular assembly. These two programs have much complementarity in both vision and technological approaches, as reflected in this joint workshop. GLT's challenge to the scientific community remains the further development and use of a broad array of innovative technologies and computational tools to systematically leverage the knowledge and capabilities brought to us by DNA sequencing projects. The goal is to seek a broad and predictive understanding of the functioning and control of complex systems--individual microbes, microbial communities, and plants. GTL's prominent position at the interface of the physical, computational, and biological sciences is both a strength and challenge. Microbes remain GTL's principal biological focus. In the complex 'simplicity' of microbes, they find capabilities needed by DOE and the nation for clean and secure energy, cleanup of environmental contamination, and sequestration of atmospheric carbon dioxide that contributes to global warming. An ongoing challenge for the entire GTL community is to demonstrate that the fundamental science conducted in each of your research projects brings us a step closer to biology-based solutions for these important national energy and environmental needs.
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Genome projects and the functional-genomic era.
Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans
2005-12-01
The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.
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Hurle, Belen; Citrin, Toby; Jenkins, Jean F; Kaphingst, Kimberly A; Lamb, Neil; Roseman, Jo Ellen; Bonham, Vence L
2013-08-01
Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public's understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from kindergarten to grade 12 to adult education. The role of the media in disseminating scientific messages and in perpetuating or reducing misconceptions was also discussed. Workshop participants agreed that genomic literacy will be achieved only through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society.
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Energy Technology Data Exchange (ETDEWEB)
NONE
2005-07-01
This joint meeting of the Geological Association of Canada, the Mineralogical Association of Canada, the Canadian Society of Petroleum Geologists, and the Canadian Society of Soil Science addressed many topical issues dealing with geosciences, with particular reference to resource exploration. The 7 sessions within the general session were: (1) economic geology, (2) structural geology and tectonics, (3) mineralogy, crystallography and crystal chemistry, (4) igneous petrology, volcanology and metamorphic petrology, (5) sedimentology, paleontology and micropaleontology, (6) geophysics, and (7) soil science. In addition to the general session, the conference included exhibits, symposia, special courses, workshops, poster sessions, field trips and an outreach program. The conference featured approximately 80 presentations, of which 45 have been catalogued separately for inclusion in this database.
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International Nuclear Information System (INIS)
2005-01-01
This joint meeting of the Geological Association of Canada, the Mineralogical Association of Canada, the Canadian Society of Petroleum Geologists, and the Canadian Society of Soil Science addressed many topical issues dealing with geosciences, with particular reference to resource exploration. The 7 sessions within the general session were: (1) economic geology, (2) structural geology and tectonics, (3) mineralogy, crystallography and crystal chemistry, (4) igneous petrology, volcanology and metamorphic petrology, (5) sedimentology, paleontology and micropaleontology, (6) geophysics, and (7) soil science. In addition to the general session, the conference included exhibits, symposia, special courses, workshops, poster sessions, field trips and an outreach program. The conference featured approximately 80 presentations, of which 45 have been catalogued separately for inclusion in this database. (author)
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Hoch, Michael
2011-01-01
Signature of the Joint Declaration by the Minor Academy of Science of Ukraine and CERN concerning participation by Ukrainian teachers and students in educational programmes at CERN The signatories: Dr Rolf Landua Education Group Leader Professor Stanislav Dovgyi President of the Minor Academy of Science of Ukraine On the photos: Mick Storr, Marina Savino, Rolf Landua, Stanislav Dovgyi, Tetiana Hryn'Ova
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In the Beginning was the Genome: Genomics and the Bi-textuality of Human Existence.
Zwart, H A E Hub
2018-04-01
This paper addresses the cultural impact of genomics and the Human Genome Project (HGP) on human self-understanding. Notably, it addresses the claim made by Francis Collins (director of the HGP) that the genome is the language of God and the claim made by Max Delbrück (founding father of molecular life sciences research) that Aristotle must be credited with having predicted DNA as the soul that organises bio-matter. From a continental philosophical perspective I will argue that human existence results from a dialectical interaction between two types of texts: the language of molecular biology and the language of civilisation; the language of the genome and the language of our socio-cultural, symbolic ambiance. Whereas the former ultimately builds on the alphabets of genes and nucleotides, the latter is informed by primordial texts such as the Bible and the Quran. In applied bioethics deliberations on genomics, science is easily framed as liberating and progressive, religious world-views as conservative and restrictive (Zwart 1993). This paper focusses on the broader cultural ambiance of the debate to discern how the bi-textuality of human existence is currently undergoing a transition, as not only the physiological, but also the normative dimension is being reframed in biomolecular and terabyte terms.
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GAViT: Genome Assembly Visualization Tool for Short Read Data
Energy Technology Data Exchange (ETDEWEB)
Syed, Aijazuddin; Shapiro, Harris; Tu, Hank; Pangilinan, Jasmyn; Trong, Stephan
2008-03-14
It is a challenging job for genome analysts to accurately debug, troubleshoot, and validate genome assembly results. Genome analysts rely on visualization tools to help validate and troubleshoot assembly results, including such problems as mis-assemblies, low-quality regions, and repeats. Short read data adds further complexity and makes it extremely challenging for the visualization tools to scale and to view all needed assembly information. As a result, there is a need for a visualization tool that can scale to display assembly data from the new sequencing technologies. We present Genome Assembly Visualization Tool (GAViT), a highly scalable and interactive assembly visualization tool developed at the DOE Joint Genome Institute (JGI).
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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
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Naveed, Muhammad; Ayday, Erman; Clayton, Ellen W; Fellay, Jacques; Gunter, Carl A; Hubaux, Jean-Pierre; Malin, Bradley A; Wang, Xiaofeng
2015-09-01
Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.
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Design of artificial human joints & organs
Pal, Subrata
2013-01-01
This book covers the design science and methodology of artificial joints and organs. It presents the mechanical characterization of the hard and soft tissues as well as the viscoelastic properties of the tissue.
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Detection of genomic rearrangements in cucumber using genomecmp software
Kulawik, Maciej; Pawełkowicz, Magdalena Ewa; Wojcieszek, Michał; PlÄ der, Wojciech; Nowak, Robert M.
2017-08-01
Comparative genomic by increasing information about the genomes sequences available in the databases is a rapidly evolving science. A simple comparison of the general features of genomes such as genome size, number of genes, and chromosome number presents an entry point into comparative genomic analysis. Here we present the utility of the new tool genomecmp for finding rearrangements across the compared sequences and applications in plant comparative genomics.
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Computation of the Likelihood of Joint Site Frequency Spectra Using Orthogonal Polynomials
Directory of Open Access Journals (Sweden)
Claus Vogl
2016-02-01
Full Text Available In population genetics, information about evolutionary forces, e.g., mutation, selection and genetic drift, is often inferred from DNA sequence information. Generally, DNA consists of two long strands of nucleotides or sites that pair via the complementary bases cytosine and guanine (C and G, on the one hand, and adenine and thymine (A and T, on the other. With whole genome sequencing, most genomic information stored in the DNA has become available for multiple individuals of one or more populations, at least in humans and model species, such as fruit flies of the genus Drosophila. In a genome-wide sample of L sites for M (haploid individuals, the state of each site may be made binary, by binning the complementary bases, e.g., C with G to C/G, and contrasting C/G to A/T, to obtain a “site frequency spectrum” (SFS. Two such samples of either a single population from different time-points or two related populations from a single time-point are called joint site frequency spectra (joint SFS. While mathematical models describing the interplay of mutation, drift and selection have been available for more than 80 years, calculation of exact likelihoods from joint SFS is difficult. Sufficient statistics for inference of, e.g., mutation or selection parameters that would make use of all the information in the genomic data are rarely available. Hence, often suites of crude summary statistics are combined in simulation-based computational approaches. In this article, we use a bi-allelic boundary-mutation and drift population genetic model to compute the transition probabilities of joint SFS using orthogonal polynomials. This allows inference of population genetic parameters, such as the mutation rate (scaled by the population size and the time separating the two samples. We apply this inference method to a population dataset of neutrally-evolving short intronic sites from six DNA sequences of the fruit fly Drosophila melanogaster and the reference
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Directory of Open Access Journals (Sweden)
Arun Prabhu Dhanapal
2015-01-01
Full Text Available The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.
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Academic Training - Bioinformatics: Decoding the Genome
Chris Jones
2006-01-01
ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...
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International Nuclear Information System (INIS)
1999-08-01
The International Review Committee composed of twelve Japanese and foreign experts was set up under the Research Evaluation Committee of JAERI, and has reviewed the proposed joint project combining JAERI's Neutron Science Project and KEK's Japan Hadron Facility into one major facility. The review meeting took place on April 26-27, 1999, at JAERI Head quarters, Tokyo. According to the points of review given in advance, the review was implemented based on the joint project report submitted and presentations of both institutions. The Research Evaluation Committee received the review report and its explanations from the Review Committee on July 5. The Research Evaluation Committee has acknowledged appropriateness of the review results. This report describes the review results. (author)
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Genomics and bioinformatics resources for translational science in Rosaceae.
Jung, Sook; Main, Dorrie
2014-01-01
Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.
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Kuo, Wen-Hua
2011-10-01
This paper compares the development of genomics as a form of state project in Japan and Taiwan. Broadening the concepts of genomic sovereignty and bionationalism, I argue that the establishment and use of genomic databases vary according to techno-political context. While both Japan and Taiwan hold population-based databases to be necessary for scientific advance and competitiveness, they differ in how they have attempted to transform the information produced by databases into regulatory schemes for drug approval. The effectiveness of Taiwan's biobank is severely limited by the IRB reviewing process. By contrast, while updating its regulations for drug approval, Japan, is using pharmacogenomics to deal with matters relating to ethnic identity. By analysing genomic initiatives in the political context that nurtures them, this paper seeks to capture how global science and local societies interact and offers insight into the assessment of state-sponsored science in East Asia as they become transnational. Copyright © 2011 Elsevier Ltd. All rights reserved.
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Knee joint vibroarthrographic signal processing and analysis
Wu, Yunfeng
2015-01-01
This book presents the cutting-edge technologies of knee joint vibroarthrographic signal analysis for the screening and detection of knee joint injuries. It describes a number of effective computer-aided methods for analysis of the nonlinear and nonstationary biomedical signals generated by complex physiological mechanics. This book also introduces several popular machine learning and pattern recognition algorithms for biomedical signal classifications. The book is well-suited for all researchers looking to better understand knee joint biomechanics and the advanced technology for vibration arthrometry. Dr. Yunfeng Wu is an Associate Professor at the School of Information Science and Technology, Xiamen University, Xiamen, Fujian, China.
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2008-01-01
Heliophysical Explorers (HELEX) brings together and augments the unique capabilities of ESA's Solar Orbiter mission (near-Sun and out-of-ecliptic in-situ plus remote-sensing observations) with those of NASA's Inner Heliospheric Sentinels (in-situ observations from multiple platforms arrayed at varying radial distances and azimuthal locations in the near-ecliptic plane)to investigate, characterize, and understand how the Sun determines the environment of the inner solar system and, more broadly, generates the heliosphere itself. This joint ESA-NASA science program offers a unique opportunity for coordinated, correlative measurements, resulting in a combined observational capability and science return that far outweighs that of either mission alone. Building on the knowledge gained from missions like Helios and Ulysses, and STEREO, HELEX will bring to bear the power of multipoint, in-situ measurements using previously unavailable instrumental capabilities in combination with remote-sensing observations from a new, inner heliospheric perspective to answer fundamental questions about the Sun-heliosphere linkage.
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Anselmetti, Yoann; Duchemin, Wandrille; Tannier, Eric; Chauve, Cedric; Bérard, Sèverine
2018-05-09
Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. We demonstrate the method's ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.
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Efficient strategy for detecting gene × gene joint action and its application in schizophrenia.
Won, Sungho; Kwon, Min-Seok; Mattheisen, Manuel; Park, Suyeon; Park, Changsoon; Kihara, Daisuke; Cichon, Sven; Ophoff, Roel; Nöthen, Markus M; Rietschel, Marcella; Baur, Max; Uitterlinden, Andre G; Hofmann, A; Lange, Christoph
2014-01-01
We propose a new approach to detect gene × gene joint action in genome-wide association studies (GWASs) for case-control designs. This approach offers an exhaustive search for all two-way joint action (including, as a special case, single gene action) that is computationally feasible at the genome-wide level and has reasonable statistical power under most genetic models. We found that the presence of any gene × gene joint action may imply differences in three types of genetic components: the minor allele frequencies and the amounts of Hardy-Weinberg disequilibrium may differ between cases and controls, and between the two genetic loci the degree of linkage disequilibrium may differ between cases and controls. Using Fisher's method, it is possible to combine the different sources of genetic information in an overall test for detecting gene × gene joint action. The proposed statistical analysis is efficient and its simplicity makes it applicable to GWASs. In the current study, we applied the proposed approach to a GWAS on schizophrenia and found several potential gene × gene interactions. Our application illustrates the practical advantage of the proposed method. © 2013 WILEY PERIODICALS, INC.
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Genome Island: A Virtual Science Environment in Second Life
Clark, Mary Anne
2009-01-01
Mary Anne CLark describes the organization and uses of Genome Island, a virtual laboratory complex constructed in Second Life. Genome Island was created for teaching genetics to university undergraduates but also provides a public space where anyone interested in genetics can spend a few minutes, or a few hours, interacting with genetic…
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The Human Genome Project and Biology Education.
McInerney, Joseph D.
1996-01-01
Highlights the importance of the Human Genome Project in educating the public about genetics. Discusses four challenges that science educators must address: teaching for conceptual understanding, the nature of science, the personal and social impact of science and technology, and the principles of technology. Contains 45 references. (JRH)
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Epidemiology & Genomics Research Program
The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.
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Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
Wright, James C.; Sugden, Deana; Francis-McIntyre, Sue; Riba Garcia, Isabel; Gaskell, Simon J.; Grigoriev, Igor V.; Baker, Scott E.; Beynon, Robert J.; Hubbard, Simon J.
2009-01-01
Abstract Background Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were ac...
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A post-genomic surprise. The molecular reinscription of race in science, law and medicine.
Duster, Troy
2015-03-01
The completion of the first draft of the Human Genome Map in 2000 was widely heralded as the promise and future of genetics-based medicines and therapies - so much so that pundits began referring to the new century as 'The Century of Genetics'. Moreover, definitive assertions about the overwhelming similarities of all humans' DNA (99.9 per cent) by the leaders of the Human Genome Project were trumpeted as the end of racial thinking about racial taxonomies of human genetic differences. But the first decade of the new century brought unwelcomed surprises. First, gene therapies turned out to be far more complicated than any had anticipated - and instead the pharmaceutical industry turned to a focus on drugs that might be 'related' to population differences based upon genetic markers. While the language of 'personalized medicine' dominated this frame, research on racially and ethnically designated populations differential responsiveness to drugs dominated the empirical work in the field. Ancestry testing and 'admixture research' would play an important role in a new kind of molecular reification of racial categories. Moreover, the capacity of the super-computer to map differences reverberated into personal identification that would affect both the criminal justice system and forensic science, and generate new levels of concern about personal privacy. Social scientists in general, and sociologists in particular, have been caught short by these developments - relying mainly on assertions that racial categories are socially constructed, regionally and historically contingent, and politically arbitrary. While these assertions are true, the imprimatur of scientific legitimacy has shifted the burden, since now 'admixture research' can claim that its results get at the 'reality' of human differentiation, not the admittedly flawed social constructions of racial categories. Yet what was missing from this framing of the problem: 'admixture research' is itself based upon socially
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Guetterman, Timothy C; Fetters, Michael D; Creswell, John W
2015-11-01
Mixed methods research is becoming an important methodology to investigate complex health-related topics, yet the meaningful integration of qualitative and quantitative data remains elusive and needs further development. A promising innovation to facilitate integration is the use of visual joint displays that bring data together visually to draw out new insights. The purpose of this study was to identify exemplar joint displays by analyzing the various types of joint displays being used in published articles. We searched for empirical articles that included joint displays in 3 journals that publish state-of-the-art mixed methods research. We analyzed each of 19 identified joint displays to extract the type of display, mixed methods design, purpose, rationale, qualitative and quantitative data sources, integration approaches, and analytic strategies. Our analysis focused on what each display communicated and its representation of mixed methods analysis. The most prevalent types of joint displays were statistics-by-themes and side-by-side comparisons. Innovative joint displays connected findings to theoretical frameworks or recommendations. Researchers used joint displays for convergent, explanatory sequential, exploratory sequential, and intervention designs. We identified exemplars for each of these designs by analyzing the inferences gained through using the joint display. Exemplars represented mixed methods integration, presented integrated results, and yielded new insights. Joint displays appear to provide a structure to discuss the integrated analysis and assist both researchers and readers in understanding how mixed methods provides new insights. We encourage researchers to use joint displays to integrate and represent mixed methods analysis and discuss their value. © 2015 Annals of Family Medicine, Inc.
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Guetterman, Timothy C.; Fetters, Michael D.; Creswell, John W.
2015-01-01
PURPOSE Mixed methods research is becoming an important methodology to investigate complex health-related topics, yet the meaningful integration of qualitative and quantitative data remains elusive and needs further development. A promising innovation to facilitate integration is the use of visual joint displays that bring data together visually to draw out new insights. The purpose of this study was to identify exemplar joint displays by analyzing the various types of joint displays being used in published articles. METHODS We searched for empirical articles that included joint displays in 3 journals that publish state-of-the-art mixed methods research. We analyzed each of 19 identified joint displays to extract the type of display, mixed methods design, purpose, rationale, qualitative and quantitative data sources, integration approaches, and analytic strategies. Our analysis focused on what each display communicated and its representation of mixed methods analysis. RESULTS The most prevalent types of joint displays were statistics-by-themes and side-by-side comparisons. Innovative joint displays connected findings to theoretical frameworks or recommendations. Researchers used joint displays for convergent, explanatory sequential, exploratory sequential, and intervention designs. We identified exemplars for each of these designs by analyzing the inferences gained through using the joint display. Exemplars represented mixed methods integration, presented integrated results, and yielded new insights. CONCLUSIONS Joint displays appear to provide a structure to discuss the integrated analysis and assist both researchers and readers in understanding how mixed methods provides new insights. We encourage researchers to use joint displays to integrate and represent mixed methods analysis and discuss their value. PMID:26553895
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Genomics education for medical professionals - the current UK landscape.
Slade, Ingrid; Subramanian, Deepak N; Burton, Hilary
2016-08-01
Genomics education in the UK is at an early stage of development, and its pace of evolution has lagged behind that of the genomics research upon which it is based. As a result, knowledge of genomics and its applications remains limited among non-specialist clinicians. In this review article, we describe the complex landscape for genomics education within the UK, and highlight the large number and variety of organisations that can influence, direct and provide genomics training to medical professionals. Postgraduate genomics education is being shaped by the work of the Health Education England (HEE) Genomics Education Programme, working in conjunction with the Joint Committee on Genomics in Medicine. The success of their work will be greatly enhanced by the full cooperation and engagement of the many groups, societies and organisations involved with medical education and training (such as the royal colleges). Without this cooperation, there is a risk of poor coordination and unnecessary duplication of work. Leadership from an organisation such as the HEE Genomics Education Programme will have a key role in guiding the formulation and delivery of genomics education policy by various stakeholders among the different disciplines in medicine. © 2016 Royal College of Physicians.
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Lawler, Mark; Siu, Lillian L; Rehm, Heidi L; Chanock, Stephen J; Alterovitz, Gil; Burn, John; Calvo, Fabien; Lacombe, Denis; Teh, Bin Tean; North, Kathryn N; Sawyers, Charles L
2015-11-01
The recent explosion of genetic and clinical data generated from tumor genome analysis presents an unparalleled opportunity to enhance our understanding of cancer, but this opportunity is compromised by the reluctance of many in the scientific community to share datasets and the lack of interoperability between different data platforms. The Global Alliance for Genomics and Health is addressing these barriers and challenges through a cooperative framework that encourages "team science" and responsible data sharing, complemented by the development of a series of application program interfaces that link different data platforms, thus breaking down traditional silos and liberating the data to enable new discoveries and ultimately benefit patients. ©2015 American Association for Cancer Research.
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Bulletin of Materials Science | Indian Academy of Sciences
Indian Academy of Sciences (India)
Home; Journals; Bulletin of Materials Science. Zhang Lei. Articles written in Bulletin of Materials Science. Volume 34 Issue 1 February 2011 pp 161-167. Characterization on strength and toughness of welded joint for Q550 steel · Jiang Qinglei Li Yajiang Wang Juan Zhang Lei · More Details Abstract Fulltext PDF. Q550 high ...
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2015-05-20
Joint Oil Analysis Program Spectrometer Standards SCP Science (Conostan) Qualification Report For D19-0, D3-100, and D12- XXX Series Standards NF...Candidate Type D19-0 ICP-AES Results ..................................................................... 4 Table V. Candidate Type D12- XXX ...Physical Property Results .................................................. 5 Table VI. Candidate Type D12- XXX Rotrode-AES Results
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Energy Technology Data Exchange (ETDEWEB)
Stewart, Jeffrey S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-07-28
LLNL’s successful history of taking on big science projects spans beyond national security and has helped create billions of dollars per year in new economic activity. One example is LLNL’s role in helping sequence the human genome. Over $796 billion in new economic activity in over half a dozen fields has been documented since LLNL successfully completed this Grand Challenge.
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DOE and NASA joint Dark Energy mission
2003-01-01
"DOE and NASA announced their plan for a Joint Dark Energy Mission (JDEM) on October 23, 2003, at the NASA Office of Space Science Structure and Evolution of the Universe Subcommittee (SEUS) meeting" (1 paragraph).
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2000-01-25
were anesthetized with urethane (i.p. 20%, 7ml/kg). For Second Korea-US Joint Workshop on Brain Science single unit recording, craniotomy was done...information, see Lee, D. and J.G. Malpeli. J. Neurophysiol. 79: 922-926, 1998. Methods These experiments were performed on awake cats, trained to perform
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Fueling the Future with Fungal Genomes
Energy Technology Data Exchange (ETDEWEB)
Grigoriev, Igor V.
2014-10-27
Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 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 will lead 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.
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The science commons in health research: structure, function, and value.
Cook-Deegan, Robert
The "science commons," knowledge that is widely accessible at low or no cost, is a uniquely important input to scientific advance and cumulative technological innovation. It is primarily, although not exclusively, funded by government and nonprofit sources. Much of it is produced at academic research centers, although some academic science is proprietary and some privately funded R&D enters the science commons. Science in general aspires to Mertonian norms of openness, universality, objectivity, and critical inquiry. The science commons diverges from proprietary science primarily in being open and being very broadly available. These features make the science commons particularly valuable for advancing knowledge, for training innovators who will ultimately work in both public and private sectors, and in providing a common stock of knowledge upon which all players-both public and private-can draw readily. Open science plays two important roles that proprietary R&D cannot: it enables practical benefits even in the absence of profitable markets for goods and services, and its lays a shared foundation for subsequent private R&D. The history of genomics in the period 1992-2004, covering two periods when genomic startup firms attracted significant private R&D investment, illustrates these features of how a science commons contributes value. Commercial interest in genomics was intense during this period. Fierce competition between private sector and public sector genomics programs was highly visible. Seemingly anomalous behavior, such as private firms funding "open science," can be explained by unusual business dynamics between established firms wanting to preserve a robust science commons to prevent startup firms from limiting established firms' freedom to operate. Deliberate policies to create and protect a large science commons were pursued by nonprofit and government funders of genomics research, such as the Wellcome Trust and National Institutes of Health. These
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Get your high-quality low-cost genome sequence
Faino, L.; Thomma, B.P.H.J.
2014-01-01
The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model
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CRISPR Mediated Genome Engineering and its Application in Industry.
Kaboli, Saeed; Babazada, Hasan
2018-01-01
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) method has been dramatically changing the field of genome engineering. It is a rapid, highly efficient and versatile tool for precise modification of genome that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This novel RNA-guided genome-editing technique has become a revolutionary tool in biomedical science and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing tool, summarize the recent advances in CRISPR/Cas9 technology to engineer the genomes of a wide variety of organisms, and discuss their applications to treatment of fungal and viral disease. We also discuss advantageous of CRISPR/Cas9 technology to drug design, creation of animal model, and to food, agricultural and energy sciences. Adoption of the CRISPR/Cas9 technology in biomedical and biotechnological researches would create innovative applications of it not only for breeding of strains exhibiting desired traits for specific industrial and medical applications, but also for investigation of genome function.
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Energy Technology Data Exchange (ETDEWEB)
Crkvenjakov, R.; Drmanac, R.
1991-07-01
The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.
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Pang, T
2009-12-01
Scientific and technological advances derived from the genomics revolution have a central role to play in dealing with continuing infectious disease threats in the developing world caused by emerging and re-emerging pathogens. These techniques, coupled with increasing knowledge of host-pathogen interactions, can assist in the early identification and containment of outbreaks as well as in the development of preventive vaccination and therapeutic interventions, including the urgent need for new antibiotics. However, the effective application of genomics technologies faces key barriers and challenges which occur at three stages: from the research to the products, from the products to individual patients, and, finally, from patients to entire populations. There needs to be an emphasis on research in areas of greatest need, in facilitating the translation of research into interventions and, finally, the effective delivery of such interventions to those in greatest need. Ultimate success will depend on bringing together science, society and policy to develop effective public health implementation strategies to provide health security and health equity for all peoples.
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African Journals Online (AJOL)
The GHANA JOURNAL OF SCIENCE is published jointly by the Council for Scientific and Industrial Research of Ghana and the Ghana Science Association. It is open to all ... the authors belong. The topics need not be related to West Africa.
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Somayaji, R; Lynch, T; Powell, J N; Gregson, D
2016-11-04
Lactobacillus spp. are uncommon pathogens in immunocompetent hosts, and even rarer causes of prosthetic device infections. A case of chronic hip prosthetic joint infection (PJI) caused by L. animalis is described. This occurred 5 years after a transient bacteremia with the same organism. Whole genome sequencing of both isolates proved this PJI infection resulted from this remote bacteremia. We document that prosthetic joint infections may be a consequence of bacteremia as much as 3 years before the onset of symptoms.
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Boerwinkel, D.J.; Waarlo, A.J.
2011-01-01
Advances in genomics research and technology generate new personal and societal choices. As science education has the task of preparing students for decision-making on socio-scientific issues, research is needed to develop genomics education aimed at empowering students in the decision-making
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[Development of Plant Metabolomics and Medicinal Plant Genomics].
Saito, Kazuki
2018-01-01
A variety of chemicals produced by plants, often referred to as 'phytochemicals', have been used as medicines, food, fuels and industrial raw materials. Recent advances in the study of genomics and metabolomics in plant science have accelerated our understanding of the mechanisms, regulation and evolution of the biosynthesis of specialized plant products. We can now address such questions as how the metabolomic diversity of plants is originated at the levels of genome, and how we should apply this knowledge to drug discovery, industry and agriculture. Our research group has focused on metabolomics-based functional genomics over the last 15 years and we have developed a new research area called 'Phytochemical Genomics'. In this review, the development of a research platform for plant metabolomics is discussed first, to provide a better understanding of the chemical diversity of plants. Then, representative applications of metabolomics to functional genomics in a model plant, Arabidopsis thaliana, are described. The extension of integrated multi-omics analyses to non-model specialized plants, e.g., medicinal plants, is presented, including the identification of novel genes, metabolites and networks for the biosynthesis of flavonoids, alkaloids, sulfur-containing metabolites and terpenoids. Further, functional genomics studies on a variety of medicinal plants is presented. I also discuss future trends in pharmacognosy and related sciences.
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Multiscale modeling of three-dimensional genome
Zhang, Bin; Wolynes, Peter
The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.
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Bozinovic, Goran; Oleksiak, Marjorie F.
2010-01-01
Transcriptomics and population genomics are two complementary genomic approaches that can be used to gain insight into pollutant effects in natural populations. Transcriptomics identify altered gene expression pathways while population genomics approaches more directly target the causative genomic polymorphisms. Neither approach is restricted to a pre-determined set of genes or loci. Instead, both approaches allow a broad overview of genomic processes. Transcriptomics and population genomic approaches have been used to explore genomic responses in populations of fish from polluted environments and have identified sets of candidate genes and loci that appear biologically important in response to pollution. Often differences in gene expression or loci between polluted and reference populations are not conserved among polluted populations suggesting a biological complexity that we do not yet fully understand. As genomic approaches become less expensive with the advent of new sequencing and genotyping technologies, they will be more widely used in complimentary studies. However, while these genomic approaches are immensely powerful for identifying candidate gene and loci, the challenge of determining biological mechanisms that link genotypes and phenotypes remains. PMID:21072843
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Genome Variation Map: a data repository of genome variations in BIG Data Center.
Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang
2018-01-04
The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Genome Variation Map: a data repository of genome variations in BIG Data Center
Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang
2018-01-01
Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473
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Database Description - TMBETA-GENOME | LSDB Archive [Life Science Database Archive metadata
Lifescience Database Archive (English)
Full Text Available ENOME is a database for transmembrane β-barrel proteins in complete genomes. For each genome, calculations with machine learning algo...rithms and statistical methods have been perfumed and th
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Governance in genomics: a conceptual challenge for public health genomics law
Directory of Open Access Journals (Sweden)
Tobias Schulte in den Bäumen
2006-12-01
Full Text Available Increasing levels of genomic knowledge has led to awareness that new governance issues need to be taken into consideration. While some countries have created new statutory laws in the last 10 years, science supports the idea that genomic data should be treated like other medical data. In this article we discuss the three core models of governance in medical law on a conceptual level. The three models, the Medical, Public Health and Fundamental Rights Model stress different values, or in legal terms serve different principles. The Medical Model stands for expert knowledge and the standardisation of quality in healthcare. The Public Health Model fosters a social point of view as it advocates distribution justice in healthcare and an awareness of healthcare as a broader concept. The Fundamental Rights Model focuses on individual rights such as the right to privacy and autonomy. We argue that none of the models can be used in a purist fashion as governance in genomics should enable society and individuals to protect individual rights, to strive for a distribution justice and to ensure the quality of genomic services in one coherent process. Thus, genomic governance in genomics requires procedural law and a set of applicable principles. The principle which underlies all three models is the principle of medical beneficence. Therefore genomic governance should refer to it as a key principle when conflicting rights of individuals or communities need to be balanced.
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Indian Academy of Sciences (India)
2014-10-20
Oct 20, 2014 ... 1Repository of Tomato Genomics Resources, Department of Plant Sciences, School .... Due to its position at the crossroads of Sanger's sequencing .... replacement for the microarray-based expression profiling. .... during RNA fragmentation step prior to library construction, ...... tomato pollen as a test case.
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Experience of joint use NDA instruments between Japan and IAEA in inspection fields
International Nuclear Information System (INIS)
Yoshii, Hiroshi; Aoki, Minoru; Shimizu, Toku
1997-01-01
In order to implement more effective and efficient safeguards scheme in Japan, Japan and IAEA established joint use program of NDA instruments which was commenced in 1989 from LEU fuel fabrication facilities. The joint use program was proposed by Science and Technology Agency (STA) in the 10th (1989) Joint Japan and IAEA Committee, and it was agreed. Subsequently, Japan and IAEA established working group of the joint use program, whose prepared necessary joint use procedures. Currently, the joint use program has been expanding to almost facilities in domestic, and has been contributing reduce the facility operator's burden for the for inspection activities. (author)
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A bibliometric analysis of global research on genome sequencing ...
African Journals Online (AJOL)
The results show that disease and protein related researches were the leading research focuses, and comparative genomics and evolution related research had strong potential in the near future. Key words: Genome sequencing, research trend, scientometrics, science citation index expanded (SCI-Expanded), word cluster ...
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Jordan, Tuajuanda C; Burnett, Sandra H; Carson, Susan; Caruso, Steven M; Clase, Kari; DeJong, Randall J; Dennehy, John J; Denver, Dee R; Dunbar, David; Elgin, Sarah C R; Findley, Ann M; Gissendanner, Chris R; Golebiewska, Urszula P; Guild, Nancy; Hartzog, Grant A; Grillo, Wendy H; Hollowell, Gail P; Hughes, Lee E; Johnson, Allison; King, Rodney A; Lewis, Lynn O; Li, Wei; Rosenzweig, Frank; Rubin, Michael R; Saha, Margaret S; Sandoz, James; Shaffer, Christopher D; Taylor, Barbara; Temple, Louise; Vazquez, Edwin; Ware, Vassie C; Barker, Lucia P; Bradley, Kevin W; Jacobs-Sera, Deborah; Pope, Welkin H; Russell, Daniel A; Cresawn, Steven G; Lopatto, David; Bailey, Cheryl P; Hatfull, Graham F
2014-02-04
Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training. Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome
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Geomechanical Response of Jointed Caprock During CO2 Geological Sequestration
Newell, P.; Martinez, M. J.; Bishop, J. E.
2014-12-01
Geological sequestration of CO2 refers to the injection of supercritical CO2 into deep reservoirs trapped beneath a low-permeability caprock formation. Maintaining caprock integrity during the injection process is the most important factor for a successful injection. In this work we evaluate the potential for jointed caprock during injection scenarios using coupled three-dimensional multiphase flow and geomechanics modeling. Evaluation of jointed/fractured caprock systems is of particular concern to CO2 sequestration because creation or reactivation of joints (mechanical damage) can lead to enhanced pathways for leakage. In this work, we use an equivalent continuum approach to account for the joints within the caprock. Joint's aperture and non-linear stiffness of the caprock will be updated dynamically based on the effective normal stress. Effective permeability field will be updated based on the joints' aperture creating an anisotropic permeability field throughout the caprock. This feature would add another coupling between the solid and fluid in addition to basic Terzaghi's effective stress concept. In this study, we evaluate the impact of the joint's orientation and geometry of caprock and reservoir layers on geomechanical response of the CO2 geological systems. This work is supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
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Frontotemporal dementia and its subtypes: a genome-wide association study.
Ferrari, Raffaele; Hernandez, Dena G; Nalls, Michael A; Rohrer, Jonathan D; Ramasamy, Adaikalavan; Kwok, John B J; Dobson-Stone, Carol; Brooks, William S; Schofield, Peter R; Halliday, Glenda M; Hodges, John R; Piguet, Olivier; Bartley, Lauren; Thompson, Elizabeth; Haan, Eric; Hernández, Isabel; Ruiz, Agustín; Boada, Mercè; Borroni, Barbara; Padovani, Alessandro; Cruchaga, Carlos; Cairns, Nigel J; Benussi, Luisa; Binetti, Giuliano; Ghidoni, Roberta; Forloni, Gianluigi; Galimberti, Daniela; Fenoglio, Chiara; Serpente, Maria; Scarpini, Elio; Clarimón, Jordi; Lleó, Alberto; Blesa, Rafael; Waldö, Maria Landqvist; Nilsson, Karin; Nilsson, Christer; Mackenzie, Ian R A; Hsiung, Ging-Yuek R; Mann, David M A; Grafman, Jordan; Morris, Christopher M; Attems, Johannes; Griffiths, Timothy D; McKeith, Ian G; Thomas, Alan J; Pietrini, P; Huey, Edward D; Wassermann, Eric M; Baborie, Atik; Jaros, Evelyn; Tierney, Michael C; Pastor, Pau; Razquin, Cristina; Ortega-Cubero, Sara; Alonso, Elena; Perneczky, Robert; Diehl-Schmid, Janine; Alexopoulos, Panagiotis; Kurz, Alexander; Rainero, Innocenzo; Rubino, Elisa; Pinessi, Lorenzo; Rogaeva, Ekaterina; St George-Hyslop, Peter; Rossi, Giacomina; Tagliavini, Fabrizio; Giaccone, Giorgio; Rowe, James B; Schlachetzki, Johannes C M; Uphill, James; Collinge, John; Mead, Simon; Danek, Adrian; Van Deerlin, Vivianna M; Grossman, Murray; Trojanowski, John Q; van der Zee, Julie; Deschamps, William; Van Langenhove, Tim; Cruts, Marc; Van Broeckhoven, Christine; Cappa, Stefano F; Le Ber, Isabelle; Hannequin, Didier; Golfier, Véronique; Vercelletto, Martine; Brice, Alexis; Nacmias, Benedetta; Sorbi, Sandro; Bagnoli, Silvia; Piaceri, Irene; Nielsen, Jørgen E; Hjermind, Lena E; Riemenschneider, Matthias; Mayhaus, Manuel; Ibach, Bernd; Gasparoni, Gilles; Pichler, Sabrina; Gu, Wei; Rossor, Martin N; Fox, Nick C; Warren, Jason D; Spillantini, Maria Grazia; Morris, Huw R; Rizzu, Patrizia; Heutink, Peter; Snowden, Julie S; Rollinson, Sara; Richardson, Anna; Gerhard, Alexander; Bruni, Amalia C; Maletta, Raffaele; Frangipane, Francesca; Cupidi, Chiara; Bernardi, Livia; Anfossi, Maria; Gallo, Maura; Conidi, Maria Elena; Smirne, Nicoletta; Rademakers, Rosa; Baker, Matt; Dickson, Dennis W; Graff-Radford, Neill R; Petersen, Ronald C; Knopman, David; Josephs, Keith A; Boeve, Bradley F; Parisi, Joseph E; Seeley, William W; Miller, Bruce L; Karydas, Anna M; Rosen, Howard; van Swieten, John C; Dopper, Elise G P; Seelaar, Harro; Pijnenburg, Yolande A L; Scheltens, Philip; Logroscino, Giancarlo; Capozzo, Rosa; Novelli, Valeria; Puca, Annibale A; Franceschi, Massimo; Postiglione, Alfredo; Milan, Graziella; Sorrentino, Paolo; Kristiansen, Mark; Chiang, Huei-Hsin; Graff, Caroline; Pasquier, Florence; Rollin, Adeline; Deramecourt, Vincent; Lebert, Florence; Kapogiannis, Dimitrios; Ferrucci, Luigi; Pickering-Brown, Stuart; Singleton, Andrew B; Hardy, John; Momeni, Parastoo
2014-07-01
Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes-MAPT, GRN, and C9orf72--have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder. We did a two-stage genome-wide association study on clinical FTD, analysing samples from 3526 patients with FTD and 9402 healthy controls. To reduce genetic heterogeneity, all participants were of European ancestry. In the discovery phase (samples from 2154 patients with FTD and 4308 controls), we did separate association analyses for each FTD subtype (behavioural variant FTD, semantic dementia, progressive non-fluent aphasia, and FTD overlapping with motor neuron disease [FTD-MND]), followed by a meta-analysis of the entire dataset. We carried forward replication of the novel suggestive loci in an independent sample series (samples from 1372 patients and 5094 controls) and then did joint phase and brain expression and methylation quantitative trait loci analyses for the associated (p<5 × 10(-8)) single-nucleotide polymorphisms. We identified novel associations exceeding the genome-wide significance threshold (p<5 × 10(-8)). Combined (joint) analyses of discovery and replication phases showed genome-wide significant association at 6p21.3, HLA locus (immune system), for rs9268877 (p=1·05 × 10(-8); odds ratio=1·204 [95% CI 1·11-1·30]), rs9268856 (p=5·51 × 10(-9); 0·809 [0·76-0·86]) and rs1980493 (p value=1·57 × 10(-8), 0·775 [0·69-0·86]) in the entire cohort. We also identified a potential novel locus at 11q14, encompassing RAB38/CTSC (the transcripts of which are related to lysosomal biology), for the behavioural FTD subtype for which joint analyses showed suggestive association for rs302668 (p=2·44 × 10(-7); 0·814 [0·71-0·92]). Analysis of expression and methylation quantitative trait loci data
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Office Staff | About IASc | Indian Academy of Sciences
Indian Academy of Sciences (India)
Administration; Editorial Staff - Academy; Editorial Staff - Current Science ... Coordinator, Summer Research Fellowship Programme (Science Education Panel), .... Joint Statement by the Three Science Academies of India on the teaching of the ...
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Biomolecular Sciences: uniting Biology and Chemistry
Vrieling, Engel
2017-01-01
Biomolecular Sciences: uniting Biology and Chemistry www.rug.nl/research/gbb The scientific discoveries in biomolecular sciences have benefitted enormously from technological innovations. At the Groningen Biomolecular Science and Biotechnology Institute (GBB) we now sequence a genome in days,
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Directory of Open Access Journals (Sweden)
R. Somayaji
2016-11-01
Full Text Available Abstract Background Lactobacillus spp. are uncommon pathogens in immunocompetent hosts, and even rarer causes of prosthetic device infections. Case presentation A case of chronic hip prosthetic joint infection (PJI caused by L. animalis is described. This occurred 5 years after a transient bacteremia with the same organism. Whole genome sequencing of both isolates proved this PJI infection resulted from this remote bacteremia. Conclusions We document that prosthetic joint infections may be a consequence of bacteremia as much as 3 years before the onset of symptoms.
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Moses, J. F.; Jain, P.; Johnson, J.; Doiron, J. A.
2017-12-01
New Earth observation instruments are planned to enable advancements in Earth science research over the next decade. Diversity of Earth observing instruments and their observing platforms will continue to increase as new instrument technologies emerge and are deployed as part of National programs such as Joint Polar Satellite System (JPSS), Geostationary Operational Environmental Satellite system (GOES), Landsat as well as the potential for many CubeSat and aircraft missions. The practical use and value of these observational data often extends well beyond their original purpose. The practicing community needs intuitive and standardized tools to enable quick unfettered development of tailored products for specific applications and decision support systems. However, the associated data processing system can take years to develop and requires inherent knowledge and the ability to integrate increasingly diverse data types from multiple sources. This paper describes the adaptation of a large-scale data processing system built for supporting JPSS algorithm calibration and validation (Cal/Val) node to a simplified science data system for rapid application. The new configurable data system reuses scalable JAVA technologies built for the JPSS Government Resource for Algorithm Verification, Independent Test, and Evaluation (GRAVITE) system to run within a laptop environment and support product generation and data processing of AURA Ozone Monitoring Instrument (OMI) science products. Of particular interest are the root requirements necessary for integrating experimental algorithms and Hierarchical Data Format (HDF) data access libraries into a science data production system. This study demonstrates the ability to reuse existing Ground System technologies to support future missions with minimal changes.
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Almli, Lynn M; Duncan, Richard; Feng, Hao; Ghosh, Debashis; Binder, Elisabeth B; Bradley, Bekh; Ressler, Kerry J; Conneely, Karen N; Epstein, Michael P
2014-12-01
Genetic association studies of psychiatric outcomes often consider interactions with environmental exposures and, in particular, apply tests that jointly consider gene and gene-environment interaction effects for analysis. Using a genome-wide association study (GWAS) of posttraumatic stress disorder (PTSD), we report that heteroscedasticity (defined as variability in outcome that differs by the value of the environmental exposure) can invalidate traditional joint tests of gene and gene-environment interaction. To identify the cause of bias in traditional joint tests of gene and gene-environment interaction in a PTSD GWAS and determine whether proposed robust joint tests are insensitive to this problem. The PTSD GWAS data set consisted of 3359 individuals (978 men and 2381 women) from the Grady Trauma Project (GTP), a cohort study from Atlanta, Georgia. The GTP performed genome-wide genotyping of participants and collected environmental exposures using the Childhood Trauma Questionnaire and Trauma Experiences Inventory. We performed joint interaction testing of the Beck Depression Inventory and modified PTSD Symptom Scale in the GTP GWAS. We assessed systematic bias in our interaction analyses using quantile-quantile plots and genome-wide inflation factors. Application of the traditional joint interaction test to the GTP GWAS yielded systematic inflation across different outcomes and environmental exposures (inflation-factor estimates ranging from 1.07 to 1.21), whereas application of the robust joint test to the same data set yielded no such inflation (inflation-factor estimates ranging from 1.01 to 1.02). Simulated data further revealed that the robust joint test is valid in different heteroscedasticity models, whereas the traditional joint test is invalid. The robust joint test also has power similar to the traditional joint test when heteroscedasticity is not an issue. We believe the robust joint test should be used in candidate-gene studies and GWASs of
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A Collection of Algal Genomes from the JGI
Energy Technology Data Exchange (ETDEWEB)
Kuo, Alan; Grigoriev, Igor
2012-03-19
Algae, defined as photosynthetic eukaryotes other than plants, constitute a major component of fundamental eukaryotic diversity. Acquisition of the ability to conduct oxygenic photosynthesis through endosymbiotic events has been a principal driver of eukaryotic evolution, and today algae continue to underpin aquatic food chains as primary producers. Algae play profound roles in the carbon cycle, can impose health and economic costs through toxic blooms, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE?s Joint Genome Institute (JGI). A collection of algal projects ongoing at JGI contributes to each of these areas and illustrates analyses employed in their genome exploration.
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'Science summit' sets ambitious agenda
Dickson, D
1998-01-01
The World Conference on Science for the 21st Century will be held in Budapest next June, organised jointly by UNESCO and ICSU. It may be the most important international meeting on the relationship between science and politics for 20 years.
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Insights from 20 years of bacterial genome sequencing
DEFF Research Database (Denmark)
Land, Miriam; Hauser, Loren; Jun, Se-Ran
2015-01-01
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along...... the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative...... genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling...
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Results of the joint ESARDA/INMM workshop on science and modern technology for safeguards
International Nuclear Information System (INIS)
Stein, G.; Dupree, S.; Sonnier, C.
1997-01-01
The Joint ESARDA/INMM Workshop on Science and Modem Technology for Safeguards was held in Arona, Italy, October 28-31, 1996. It was attended by some 120 participants, consisting principally of scientists from various disciplines and safeguards experts from the inspectorates. The Workshop provided a full discussion on the near and far term scientific technologies that may be applied to safeguards. In addition, there were extended discussions on the social and political aspects surrounding the areas of Nonproliferation, International Safeguards, and Regional Safeguards. The general opinion was that the Workshop met and exceeded its goals, setting the stage for future workshops of this type. One of the outstanding characteristics of this Workshop was the ample amount of time allowed for full discussion of each presentation, both for technical issues and social/political issues. This procedure was substantially different from the usual ESARDA and INMM meetings. This paper will discuss the organization and conduct of the Workshop, as well as the results as reported by the four Working Group Chairs and the Workshop Co-chairs
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Ishiyama, Izumi; Tanzawa, Tetsuro; Watanabe, Maiko; Maeda, Tadahiko; Muto, Kaori; Tamakoshi, Akiko; Nagai, Akiko; Yamagata, Zentaro
2012-05-01
This study aimed to assess public attitudes in Japan to the promotion of genomic selection in crop studies and to examine associated factors. We analysed data from a nationwide opinion survey. A total of 4,000 people were selected from the Japanese general population by a stratified two-phase sampling method, and 2,171 people participated by post; this survey asked about the pros and cons of crop-related genomic studies promotion, examined people's scientific literacy in genomics, and investigated factors thought to be related to genomic literacy and attitude. The relationships were examined using logistic regression models stratified by gender. Survey results showed that 50.0% of respondents approved of the promotion of crop-related genomic studies, while 6.7% disapproved. No correlation was found between literacy and attitude towards promotion. Trust in experts, belief in science, an interest in genomic studies and willingness to purchase new products correlated with a positive attitude towards crop-related genomic studies.
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Next-Generation Genomics Facility at C-CAMP: Accelerating Genomic Research in India
S, Chandana; Russiachand, Heikham; H, Pradeep; S, Shilpa; M, Ashwini; S, Sahana; B, Jayanth; Atla, Goutham; Jain, Smita; Arunkumar, Nandini; Gowda, Malali
2014-01-01
Next-Generation Sequencing (NGS; http://www.genome.gov/12513162) is a recent life-sciences technological revolution that allows scientists to decode genomes or transcriptomes at a much faster rate with a lower cost. Genomic-based studies are in a relatively slow pace in India due to the non-availability of genomics experts, trained personnel and dedicated service providers. Using NGS there is a lot of potential to study India's national diversity (of all kinds). We at the Centre for Cellular and Molecular Platforms (C-CAMP) have launched the Next Generation Genomics Facility (NGGF) to provide genomics service to scientists, to train researchers and also work on national and international genomic projects. We have HiSeq1000 from Illumina and GS-FLX Plus from Roche454. The long reads from GS FLX Plus, and high sequence depth from HiSeq1000, are the best and ideal hybrid approaches for de novo and re-sequencing of genomes and transcriptomes. At our facility, we have sequenced around 70 different organisms comprising of more than 388 genomes and 615 transcriptomes – prokaryotes and eukaryotes (fungi, plants and animals). In addition we have optimized other unique applications such as small RNA (miRNA, siRNA etc), long Mate-pair sequencing (2 to 20 Kb), Coding sequences (Exome), Methylome (ChIP-Seq), Restriction Mapping (RAD-Seq), Human Leukocyte Antigen (HLA) typing, mixed genomes (metagenomes) and target amplicons, etc. Translating DNA sequence data from NGS sequencer into meaningful information is an important exercise. Under NGGF, we have bioinformatics experts and high-end computing resources to dissect NGS data such as genome assembly and annotation, gene expression, target enrichment, variant calling (SSR or SNP), comparative analysis etc. Our services (sequencing and bioinformatics) have been utilized by more than 45 organizations (academia and industry) both within India and outside, resulting several publications in peer-reviewed journals and several genomic
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Genomics, transcriptomics and proteomics to elucidate the pathogenesis of rheumatoid arthritis.
Song, Xinqiang; Lin, Qingsong
2017-08-01
Rheumatoid arthritis is an autoimmune disease that affects several organs and tissues, predominantly the synovial joints. The pathogenesis of this disease is not completely understood, which maybe involved in the genomic variations, gene expression, protein translation and post-translational modifications. These system variations in genomics, transcriptomics and proteomics are dynamic in nature and their crosstalk is overwhelmingly complex, thus analyzing them separately may not be very informative. However, various '-omics' techniques developed in recent years have opened up new possibilities for clarifying disease pathways and thereby facilitating early diagnosis and specific therapies. This review examines how recent advances in the fields of genomics, transcriptomics and proteomics have contributed to our understanding of rheumatoid arthritis.
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US congressman boycotts science meeting with China
Dalton, R B
1999-01-01
Congressman Sensenbrenner, chairman of the House Science Committee, withdrew from the first Sino-US Joint Science Policy Seminar citing allegations of Chinese spying and illegal technology uses (1/2 page).
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Innovations in Undergraduate Science Education: Going Viral
Hatfull, Graham F.
2015-01-01
Bacteriophage discovery and genomics provides a powerful and effective platform for integrating missions in research and education. Implementation of the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program facilitates a broad impact by including a diverse array of schools, faculty, and students. The program generates new insights into the diversity and evolution of the bacteriophage population and presents a model for introducing first-yea...
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Pang, T
2013-01-01
Genome-wide association studies and biobanks are at the forefront of genomics research and possess unprecedented potential to improve public health. However, for public health genomics to ultimately fulfill its potential, technological and scientific advances alone are insufficient. Scientists, ethicists, policy makers, and regulators must work closely together with research participants and communities in order to craft an equitable and just ethical framework, and a sustainable environment for effective policies. Such a framework should be a 'hybrid' form which balances equity and solidarity with entrepreneurship and scientific advances. A good balance between research and policy on one hand, and privacy, protection and trust on the other is the key for public health improvement based on advances in genomics science. Copyright © 2013 S. Karger AG, Basel.
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2016-01-26
reduction efforts that need to be led by the Joint Services include One Way Luminescence, where the improvement in hit goes up for the follow on shots...new technology would enable spectral segment defeat, ranging from ultraviolet ( UV ), visible, Infrared (IR), radar, and radio and any combinations...program of work as directed via the Land Armaments Management Plan ( LAMP ) and advise the NAAG on systems and equipment aspects of dismounted operations
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Journal of Biosciences | Indian Academy of Sciences
Indian Academy of Sciences (India)
2007-08-06
Aug 6, 2007 ... Author Affiliations. Pawan K Dhar1. Synthetic Genomics, Systems Biology Group, E209, RIKEN Genomic Sciences Centre, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan ...
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Los Alamos Science: The Human Genome Project. Number 20, 1992
Cooper, N. G.; Shea, N. eds.
1992-01-01
This document provides a broad overview of the Human Genome Project, with particular emphasis on work being done at Los Alamos. It tries to emphasize the scientific aspects of the project, compared to the more speculative information presented in the popular press. There is a brief introduction to modern genetics, including a review of classic work. There is a broad overview of the Genome Project, describing what the project is, what are some of its major five-year goals, what are major technological challenges ahead of the project, and what can the field of biology, as well as society expect to see as benefits from this project. Specific results on the efforts directed at mapping chromosomes 16 and 5 are discussed. A brief introduction to DNA libraries is presented, bearing in mind that Los Alamos has housed such libraries for many years prior to the Genome Project. Information on efforts to do applied computational work related to the project are discussed, as well as experimental efforts to do rapid DNA sequencing by means of single-molecule detection using applied spectroscopic methods. The article introduces the Los Alamos staff which are working on the Genome Project, and concludes with brief discussions on ethical, legal, and social implications of this work; a brief glimpse of genetics as it may be practiced in the next century; and a glossary of relevant terms.
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Los Alamos Science: The Human Genome Project. Number 20, 1992
Energy Technology Data Exchange (ETDEWEB)
Cooper, N G; Shea, N [eds.
1992-01-01
This article provides a broad overview of the Human Genome Project, with particular emphasis on work being done at Los Alamos. It tries to emphasize the scientific aspects of the project, compared to the more speculative information presented in the popular press. There is a brief introduction to modern genetics, including a review of classic work. There is a broad overview of the Genome Project, describing what the project is, what are some of its major five-year goals, what are major technological challenges ahead of the project, and what can the field of biology, as well as society expect to see as benefits from this project. Specific results on the efforts directed at mapping chromosomes 16 and 5 are discussed. A brief introduction to DNA libraries is presented, bearing in mind that Los Alamos has housed such libraries for many years prior to the Genome Project. Information on efforts to do applied computational work related to the project are discussed, as well as experimental efforts to do rapid DNA sequencing by means of single-molecule detection using applied spectroscopic methods. The article introduces the Los Alamos staff which are working on the Genome Project, and concludes with brief discussions on ethical, legal, and social implications of this work; a brief glimpse of genetics as it may be practiced in the next century; and a glossary of relevant terms.
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Electronic Health Record for Temporomandibular Joint Disorders – Support in Therapeutic Process
Czech Academy of Sciences Publication Activity Database
Hippmann, R.; Nagy, Miroslav; Dostálová, T.; Zvárová, Jana; Seydlová, M.; Feltlová, E.
2010-01-01
Roč. 6, č. 1 (2010), s. 27-32 ISSN 1801-5603 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : electronic health record * automatic speech recognition * dental cross * temporomandibular joint * temporomandibular joint disorders * structured data entry * dentistry * data model * text-to-speech system * Research Diagnostic Criteria for TMD Subject RIV: IN - Informatics, Computer Science http://www.ejbi.org/en/ejbi/article/25-en- electronic - health - record -for-temporomandibular-joint-disorders-support-in-therapeutic-process.html
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[Advances on biomechanics and kinematics of sprain of ankle joint].
Zhao, Yong; Wang, Gang
2015-04-01
Ankle sprains are orthopedic clinical common disease, accounting for joint ligament sprain of the first place. If treatment is not timely or appropriate, the joint pain and instability maybe develop, and even bone arthritis maybe develop. The mechanism of injury of ankle joint, anatomical basis has been fully study at present, and the diagnostic problem is very clear. Along with the development of science and technology, biological modeling and three-dimensional finite element, three-dimensional motion capture system,digital technology study, electromyographic signal study were used for the basic research of sprain of ankle. Biomechanical and kinematic study of ankle sprain has received adequate attention, combined with the mechanism research of ankle sprain,and to explore the the biomechanics and kinematics research progress of the sprain of ankle joint.
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Ten years of maintaining and expanding a microbial genome and metagenome analysis system.
Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C
2015-11-01
Launched in March 2005, the Integrated Microbial Genomes (IMG) system is a comprehensive data management system that supports multidimensional comparative analysis of genomic data. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets sequenced at the Joint Genome Institute or provided by scientific users, as well as public genome datasets available at the National Center for Biotechnology Information Genbank sequence data archive. Genomes and metagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing pipelines and are integrated into the data warehouse using IMG's data integration toolkits. Microbial genome and metagenome application specific data marts and user interfaces provide access to different subsets of IMG's data and analysis toolkits. This review article revisits IMG's original aims, highlights key milestones reached by the system during the past 10 years, and discusses the main challenges faced by a rapidly expanding system, in particular the complexity of maintaining such a system in an academic setting with limited budgets and computing and data management infrastructure. Copyright © 2015 Elsevier Ltd. All rights reserved.
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BioCreative Workshops for DOE Genome Sciences: Text Mining for Metagenomics
Energy Technology Data Exchange (ETDEWEB)
Wu, Cathy H. [Univ. of Delaware, Newark, DE (United States). Center for Bioinformatics and Computational Biology; Hirschman, Lynette [The MITRE Corporation, Bedford, MA (United States)
2016-10-29
The objective of this project was to host BioCreative workshops to define and develop text mining tasks to meet the needs of the Genome Sciences community, focusing on metadata information extraction in metagenomics. Following the successful introduction of metagenomics at the BioCreative IV workshop, members of the metagenomics community and BioCreative communities continued discussion to identify candidate topics for a BioCreative metagenomics track for BioCreative V. Of particular interest was the capture of environmental and isolation source information from text. The outcome was to form a “community of interest” around work on the interactive EXTRACT system, which supported interactive tagging of environmental and species data. This experiment is included in the BioCreative V virtual issue of Database. In addition, there was broad participation by members of the metagenomics community in the panels held at BioCreative V, leading to valuable exchanges between the text mining developers and members of the metagenomics research community. These exchanges are reflected in a number of the overview and perspective pieces also being captured in the BioCreative V virtual issue. Overall, this conversation has exposed the metagenomics researchers to the possibilities of text mining, and educated the text mining developers to the specific needs of the metagenomics community.
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Report of joint utilization results in fiscal year 1994
International Nuclear Information System (INIS)
1995-01-01
Joint utilization seems to aim at the effective use of limited funds by concentrating facilities. There is a demerit that for doing experiment, it is necessary to take a trouble of going to the place. However by utilizing jointly one facility, there is the possibility of the occurrence of sympathizing phenomena directly connected to new ideas among researchers, and it is just the state joint utilization should be in. In fiscal year 1994, the Yayoi and the linac were put to joint utilization as expected, and many results of researches were obtained by the users. In this book, in addition to the report of the results of joint utilization, the report of the Yayoi research meetings held in fiscal year 1994 is included. Eight lectures on fast neutron science, the reports of joint utilization results of 15 Yayoi on-pile studies, 9 Yayoi off-pile studies and 16 linac studies, and the reports of 11 Yayoi research meetings are included in this book. The list of the events held in the Nuclear Engineering Research Laboratory, University of Tokyo, in fiscal year 1994, the list of the names of various committee members, and the list of the names of the persons in charge of joint utilization experiments are attached. (K.I.)
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Genomic Data-Sharing: What will be our legacy?
Directory of Open Access Journals (Sweden)
Shawneequa eCallier
2014-03-01
Full Text Available Prior to 1974, the Tuskegee Syphilis experiments, expansive use of the HeLa cells, and other blatant instances of research abuse pervaded the medical research field. Discussion today about these challenges have caused the general public to develop a reluctance and distrust for medical research. This has significant implications for the advancement of genomic science, and the public's perception of genomic research.
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The Human Genome Project: Biology, Computers, and Privacy.
Cutter, Mary Ann G.; Drexler, Edward; Gottesman, Kay S.; Goulding, Philip G.; McCullough, Laurence B.; McInerney, Joseph D.; Micikas, Lynda B.; Mural, Richard J.; Murray, Jeffrey C.; Zola, John
This module, for high school teachers, is the second of two modules about the Human Genome Project (HGP) produced by the Biological Sciences Curriculum Study (BSCS). The first section of this module provides background information for teachers about the structure and objectives of the HGP, aspects of the science and technology that underlie the…
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Passage relevance models for genomics search
Directory of Open Access Journals (Sweden)
Frieder Ophir
2009-03-01
Full Text Available Abstract We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and document are represented as potential functions within a Markov Random Field. The probability of a passage being relevant to a biologist's information need is represented as the joint distribution across all potential functions. Relevance model feedback of top ranked passages is used to improve distributional estimates of query concepts and topics in context, and a dimensional indexing strategy is used for efficient aggregation of concept and term statistics. By integrating multiple sources of evidence including dependencies between topics, concepts, and terms, we seek to improve genomics literature passage retrieval precision. Using this model, we are able to demonstrate statistically significant improvements in retrieval precision using a large genomics literature corpus.
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Energy Technology Data Exchange (ETDEWEB)
John C. Meeks
2001-12-31
Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.
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Re-examining the Gene in Personalized Genomics
Bartol, Jordan
2013-10-01
Personalized genomics companies (PG; also called `direct-to-consumer genetics') are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept presented to customers and the relation between the information given and the science behind PG. Two quite different gene concepts are present in company rhetoric, but only one features in the science. To explain this, we must appreciate the delicate tension between PG, academic science, public expectation, and market forces.
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WFIRST Project Science Activities
Gehrels, Neil
2012-01-01
The WFIRST Project is a joint effort between GSFC and JPL. The project scientists and engineers are working with the community Science Definition Team to define the requirements and initial design of the mission. The objective is to design an observatory that meets the WFIRST science goals of the Astr02010 Decadal Survey for minimum cost. This talk will be a report of recent project activities including requirements flowdown, detector array development, science simulations, mission costing and science outreach. Details of the interim mission design relevant to scientific capabilities will be presented.
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Integrated Genome-Based Studies of Shewanella Ecophysiology
Energy Technology Data Exchange (ETDEWEB)
Andrei L. Osterman, Ph.D.
2012-12-17
Integration of bioinformatics and experimental techniques was applied to mapping and characterization of the key components (pathways, enzymes, transporters, regulators) of the core metabolic machinery in Shewanella oneidensis and related species with main focus was on metabolic and regulatory pathways involved in utilization of various carbon and energy sources. Among the main accomplishments reflected in ten joint publications with other participants of Shewanella Federation are: (i) A systems-level reconstruction of carbohydrate utilization pathways in the genus of Shewanella (19 species). This analysis yielded reconstruction of 18 sugar utilization pathways including 10 novel pathway variants and prediction of > 60 novel protein families of enzymes, transporters and regulators involved in these pathways. Selected functional predictions were verified by focused biochemical and genetic experiments. Observed growth phenotypes were consistent with bioinformatic predictions providing strong validation of the technology and (ii) Global genomic reconstruction of transcriptional regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors, 8 riboswitches and 6 translational attenuators. Of those, 45 regulons were inferred directly from the genome context analysis, whereas others were propagated from previously characterized regulons in other species. Selected regulatory predictions were experimentally tested. Integration of this analysis with microarray data revealed overall consistency and provided additional layer of interactions between regulons. All the results were captured in the new database RegPrecise, which is a joint development with the LBNL team. A more detailed analysis of the individual subsystems, pathways and regulons in Shewanella spp included bioinfiormatics-based prediction and experimental characterization of: (i) N-Acetylglucosamine catabolic pathway; (ii)Lactate utilization machinery; (iii) Novel Nrt
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Lifescience Database Archive (English)
Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Genome analysis... methods Data detail Data name Genome analysis methods DOI 10.18908/lsdba.nbdc01194-01-005 De...scription of data contents The current status and related information of the genomic analysis about each org...anism (March, 2014). In the case of organisms carried out genomic analysis, the d...e File name: pgdbj_dna_marker_linkage_map_genome_analysis_methods_en.zip File URL: ftp://ftp.biosciencedbc.j
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Czech Academy of Sciences Publication Activity Database
Krahulcová, Anna; Trávníček, Pavel; Krahulec, František; Rejmánek, M.
2017-01-01
Roč. 119, č. 6 (2017), s. 957-964 ISSN 0305-7364 Institutional support: RVO:67985939 Keywords : Aesculus * chromosome number * genome size * phylogeny * seed mass Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 4.041, year: 2016
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Concept of Operations for the Establishment of the Joint Pathology Center
2008-12-19
the Joint Task Force National Capital Region Medical (JTF CapMed ) in collaboration with the Uniformed Services University of Health Sciences (USUHS...Medical Examiner (OAFME). The Board deems the identification of appropriate support for the OAFME as critical , since with the disestablishment of...the DoD. The establishment of the JPC within JTF CapMed is a logical choice to the extent that JTF Cap Med is a joint medical organization and can
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Exploring Girls' Science Affinities Through an Informal Science Education Program
Todd, Brandy; Zvoch, Keith
2017-10-01
This study examines science interests, efficacy, attitudes, and identity—referred to as affinities, in the context of an informal science outreach program for girls. A mixed methods design was used to explore girls' science affinities before, during, and after participation in a cohort-based summer science camp. Multivariate analysis of survey data revealed that girls' science affinities varied as a function of the joint relationship between family background and number of years in the program, with girls from more affluent families predicted to increase affinities over time and girls from lower income families to experience initial gains in affinities that diminish over time. Qualitative examination of girls' perspectives on gender and science efficacy, attitudes toward science, and elements of science identities revealed a complex interplay of gendered stereotypes of science and girls' personal desires to prove themselves knowledgeable and competent scientists. Implications for the best practice in fostering science engagement and identities in middle school-aged girls are discussed.
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The Functional Genomics Initiative at Oak Ridge National Laboratory
Energy Technology Data Exchange (ETDEWEB)
Johnson, Dabney; Justice, Monica; Beattle, Ken; Buchanan, Michelle; Ramsey, Michael; Ramsey, Rose; Paulus, Michael; Ericson, Nance; Allison, David; Kress, Reid; Mural, Richard; Uberbacher, Ed; Mann, Reinhold
1997-12-31
The Functional Genomics Initiative at the Oak Ridge National Laboratory integrates outstanding capabilities in mouse genetics, bioinformatics, and instrumentation. The 50 year investment by the DOE in mouse genetics/mutagenesis has created a one-of-a-kind resource for generating mutations and understanding their biological consequences. It is generally accepted that, through the mouse as a surrogate for human biology, we will come to understand the function of human genes. In addition to this world class program in mammalian genetics, ORNL has also been a world leader in developing bioinformatics tools for the analysis, management and visualization of genomic data. Combining this expertise with new instrumentation technologies will provide a unique capability to understand the consequences of mutations in the mouse at both the organism and molecular levels. The goal of the Functional Genomics Initiative is to develop the technology and methodology necessary to understand gene function on a genomic scale and apply these technologies to megabase regions of the human genome. The effort is scoped so as to create an effective and powerful resource for functional genomics. ORNL is partnering with the Joint Genome Institute and other large scale sequencing centers to sequence several multimegabase regions of both human and mouse genomic DNA, to identify all the genes in these regions, and to conduct fundamental surveys to examine gene function at the molecular and organism level. The Initiative is designed to be a pilot for larger scale deployment in the post-genome era. Technologies will be applied to the examination of gene expression and regulation, metabolism, gene networks, physiology and development.
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Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.
Dunn, Joshua G; Weissman, Jonathan S
2016-11-22
Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis. Many assay-specific pipelines exist for this purpose, but there remains a need for user-friendly, generalized, nucleotide-resolution tools that are not limited to specific experimental regimes or analytical workflows. Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data. As such, Plastid is designed to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such arrays. Plastid also includes numerous tools to manipulate even discontinuous genomic features, such as spliced transcripts, with nucleotide precision. Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, freeing users of burdensome accounting. Finally, Plastid's data models use consistent and familiar biological idioms, enabling even beginners to develop sophisticated analytical workflows with minimal effort. Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily
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Journal of Genetics | Indian Academy of Sciences
Indian Academy of Sciences (India)
Joint Laboratory of the Hungarian Academy of Sciences and the Semmelweis University Budapest, Szentkirályi u. 46., H-1085 Budapest, Hungary; Department of Histology and Embryology, University School of Medicine, ul. Chalubińskiego 6a, 50-356 Wroclaw, Poland; Joint Research Laboratory for Pediatrics and ...
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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.
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[Review of: K.-S. Taussig Ordinary genomes: science, citizenship, and genetic identities
Kato, M.
2010-01-01
Ordinary Genomes is an ethnography of clinical genetics practice in the Netherlands, written by US anthropologist Karen-Sue Taussig. By looking at the case of the Netherlands, this book aims to illuminate the way specific scientific knowledge - in this case genomics - which is generally presumed to
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Genomics and the Ark: an ecocentric perspective on human history.
Zwart, Hub; Penders, Bart
2011-01-01
Views of ourselves in relationship to the rest of the biosphere are changing. Theocentric and anthropocentric perspectives are giving way to more ecocentric views on the history, present, and future of humankind. Novel sciences, such as genomics, have deepened and broadened our understanding of the process of anthropogenesis, the coming into being of humans. Genomics suggests that early human history must be regarded as a complex narrative of evolving ecosystems, in which human evolution both influenced and was influenced by the evolution of companion species. During the agricultural revolution, human beings designed small-scale artificial ecosystems or evolutionary "Arks," in which networks of plants, animals, and microorganisms coevolved. Currently, our attitude towards this process seems subject to a paradoxical reversal. The boundaries of the Ark have dramatically broadened, and genomics is not only being used to increase our understanding of our ecological past, but may also help us to conserve, reconstruct, or even revivify species and ecosystems to whose degradation or (near) extinction we have contributed. This article explores the role of genomics in the elaboration of a more ecocentric view of ourselves with the help of two examples, namely the renaissance of Paleolithic diets and of Pleistocene parks. It argues that an understanding of the world in ecocentric terms requires new partnerships and mutually beneficial forms of collaboration and convergence between life sciences, social sciences, and the humanities.
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Noone, K. J.; Manderscheid, P.; Monfray, P.
2017-12-01
It is becoming increasingly apparent that the separation between science and the rest of society is not helping us find solutions to "wicked" problems like climate change or achieving the Sustainable Development Goals. It is clear that a broader approach to research is necessary - one that includes stakeholders in the research process itself. What is unclear is how best to do this. The Transdisciplinary Advisory Board (TAB) of the European Joint Programming Initiative on Climate (JPI Climate) is an example of scientists and stakeholders working together to frame climate research and move the results of scientific research into decision support. JPI Climate is a consortium of 12 European countries (with partners from nine more countries) and is a major funding channel and forum for climate research in Europe. The TAB has an equal number of stakeholders and researchers from 10 different European countries, has an even gender balance, and its members have widely differing backgrounds. The TAB provides input and advice to the governing board of JPI Climate, and influences both the strategic planning for this funding initiative as well as specific calls for proposals issued through the consortium. In addition to its advisory role, the TAB explores the transdisciplinary process itself, expanding the boundaries of how stakeholders and science can interact positively. The TAB is a two-way mechanism through which stakeholders can help improve research and science can help improve society. We will give examples of the spectrum of how the TAB provides mutual influence between stakeholders and science - from helping to draft 10-year research strategies to helping advance the uptake of climate research into the private and policy sectors.
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Genome edited animals: Learning from GM crops?
Bruce, Ann
2017-06-01
Genome editing of livestock is poised to become commercial reality, yet questions remain as to appropriate regulation, potential impact on the industry sector and public acceptability of products. This paper looks at how genome editing of livestock has attempted to learn some of the lessons from commercialisation of GM crops, and takes a systemic approach to explore some of the complexity and ambiguity in incorporating genome edited animals in a food production system. Current applications of genome editing are considered, viewed from the perspective of past technological applications. The question of what is genome editing, and can it be considered natural is examined. The implications of regulation on development of different sectors of livestock production systems are studied, with a particular focus on the veterinary sector. From an EU perspective, regulation of genome edited animals, although not necessarily the same as for GM crops, is advocated from a number of different perspectives. This paper aims to open up new avenues of research on genome edited animals, extending from the current primary focus on science and regulation, to engage with a wider-range of food system actors.
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Energy Technology Data Exchange (ETDEWEB)
NONE
1997-03-01
For wide use of genome information in the industrial field, the required R and D was surveyed from the standpoints of biology and information science. To clarify the present state and issues of the international research on genome analysis, the genome map as well as sequence and function information are first surveyed. The current analysis/use technologies of genome information are analyzed, and the following are summarized: prediction and identification of gene regions in genome sequences, techniques for searching and selecting useful genes, and techniques for predicting the expression of gene functions and the gene-product structure and functions. It is recommended that R and D and data collection/interpretation necessary to clarify inter-gene interactions and information networks should be promoted by integrating Japanese advanced know-how and technologies. As examples of the impact of the research results on industry and society, the present state and future expected effect are summarized for medicines, diagnosis/analysis instruments, chemicals, foods, agriculture, fishery, animal husbandry, electronics, environment and information. 278 refs., 42 figs., 5 tabs.
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Joint Force Quarterly. Issue 77, 2nd Quarter 2015
2015-04-01
photonics, nanomaterials, nanocrystals Biotechnology Synthetic biology, genomics Biological sciences, DNA gene-sequencing Information technology Cyber...The New York Times, December 11, 2013, sec. Magazine , available at <www.nytimes.com/2013/12/15/ magazine / googles-plan-for-global-domination-dont
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Bonnema, A.B.; Lin, Zhai; Qu, Liang; Jacobsen, E.
2006-01-01
Scientific co-operation between the Chinese Academy of Agricultural Sciences (CAAS) and Wageningen University (WU) has been underway since 1990, especially in the field of plant sciences. In 2001, CAAS and WU initiated a formal joint PhD training programme to further structure their co-operation. The goals of this co-operation are to: (1) initiate long-term institutional collaboration through capacity building; (2) jointly establish a modern laboratory; (3) jointly develop a cross-cultural sc...
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Genome interplay in the grain transcriptome of hexaploid bread wheat.
Pfeifer, Matthias; Kugler, Karl G; Sandve, Simen R; Zhan, Bujie; Rudi, Heidi; Hvidsten, Torgeir R; Mayer, Klaus F X; Olsen, Odd-Arne
2014-07-18
Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome. Copyright © 2014, American Association for the Advancement of Science.
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Genomic Approaches in Marine Biodiversity and Aquaculture
Directory of Open Access Journals (Sweden)
Jorge A Huete-Pérez
2013-01-01
Full Text Available Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes, mollusks and crustaceans, to mention a few, has provided a better understanding of phenotypic variability and functional genomics. The past few years have also seen advances in applications relevant to marine aquaculture and fisheries. In this review we introduce several examples of recent discoveries and progress made towards engendering genomic resources aimed at enhancing our understanding of marine biodiversity and promoting the development of aquaculture. Finally, we discuss the need for auspicious science policies to address challenges confronting smaller nations in the appropriate oversight of this growing domain as they strive to guarantee food security and conservation of their natural resources.
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Czech Academy of Sciences Publication Activity Database
Hippmann, R.; Nagy, Miroslav; Dostálová, T.; Zvárová, Jana; Seydlová, M.
2011-01-01
Roč. 7, č. 1 (2011), s. 11-16 ISSN 1801-5603 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : temporomandibular joint * temporomandibular joint disorders * DentCross * electronic health record * AAOP classification Subject RIV: IN - Informatics, Computer Science http://www.ejbi.eu/images/2011-1/Hippmann_en.pdf
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An analysis of a joint shear model for jointed media with orthogonal joint sets
International Nuclear Information System (INIS)
Koteras, J.R.
1991-10-01
This report describes a joint shear model used in conjunction with a computational model for jointed media with orthogonal joint sets. The joint shear model allows nonlinear behavior for both joint sets. Because nonlinear behavior is allowed for both joint sets, a great many cases must be considered to fully describe the joint shear behavior of the jointed medium. An extensive set of equations is required to describe the joint shear stress and slip displacements that can occur for all the various cases. This report examines possible methods for simplifying this set of equations so that the model can be implemented efficiently form a computational standpoint. The shear model must be examined carefully to obtain a computationally efficient implementation that does not lead to numerical problems. The application to fractures in rock is discussed. 5 refs., 4 figs
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Temporomandibular joint formation requires two distinct hedgehog-dependent steps.
Purcell, Patricia; Joo, Brian W; Hu, Jimmy K; Tran, Pamela V; Calicchio, Monica L; O'Connell, Daniel J; Maas, Richard L; Tabin, Clifford J
2009-10-27
We conducted a genetic analysis of the developing temporo-mandibular or temporomandi-bular joint (TMJ), a highly specialized synovial joint that permits movement and function of the mammalian jaw. First, we used laser capture microdissection to perform a genome-wide expression analysis of each of its developing components. The expression patterns of genes identified in this screen were examined in the TMJ and compared with those of other synovial joints, including the shoulder and the hip joints. Striking differences were noted, indicating that the TMJ forms via a distinct molecular program. Several components of the hedgehog (Hh) signaling pathway are among the genes identified in the screen, including Gli2, which is expressed specifically in the condyle and in the disk of the developing TMJ. We found that mice deficient in Gli2 display aberrant TMJ development such that the condyle loses its growth-plate-like cellular organization and no disk is formed. In addition, we used a conditional strategy to remove Smo, a positive effector of the Hh signaling pathway, from chondrocyte progenitors. This cell autonomous loss of Hh signaling allows for disk formation, but the resulting structure fails to separate from the condyle. Thus, these experiments establish that Hh signaling acts at two distinct steps in disk morphogenesis, condyle initiation, and disk-condyle separation and provide a molecular framework for future studies of the TMJ.
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Energy Technology Data Exchange (ETDEWEB)
Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabian; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.
2013-03-05
The class of Dothideomycetes is one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops that are grown for biofuel, food or feed. Most Dothideomycetes have only a single host plant, and related species can have very diverse hosts. Eighteen genomes of Dothideomycetes have currently been sequenced by the Joint Genome Institute and other sequencing centers. Here we describe the results of comparative analyses of the fungi in this group.
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Journal of Earth System Science | Indian Academy of Sciences
Indian Academy of Sciences (India)
SELENE (Selenological and Engineering Explorer) project started as a joint mission of the former ISAS (Institute of Space and Astronautical Science) and the former NASDA (National Space Development Agency: the two organizations were merged into JAXA in 2002) of Japan in 1998. The launch target is rescheduled for ...
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BIOLOGIC JOINT RECONSTRUCTION: ALTERNATIVES TO ARTHROPLASTY
Directory of Open Access Journals (Sweden)
Brian J. Cole
2009-06-01
Full Text Available A comprehensive source of information in the management of cartilage lesions of major joints using nonoperative or surgical techniques other than total joint replacement. The text also includes chapters in basic sciences, imaging and rehabilitation.The editors are aiming to provide a reference about the latest concepts and techniques in the treatment of cartilage lesions including future aspects by a comprehensive approach to the alternative joint restoration procedures such as biological, pharmacological and surgical techniques of cartilage repairing and partial resurfacing etc.Orthopedic surgeons in sports medicine, orthopedic surgeons performing joint replacements, orthopedic resident and fellows will be the main audiences.The text is 349 pages, divided into 34 chapters in 7 sections. Section I is "Background-articular cartilage and allograft processing" including chapters about pathology, patient evaluation, imaging and allograft processing. Section II is "Nonoperative treatment" including chapters about neutraceuticals, pharmacological treatment and rehabilitation. Section III is "Operative treatment-knee" including chapters about arthroscopic debridment, microfracture, osteochondral autograft transplantation, mosaicplasty, osteochondral autograft transfer, osteochondral allografts, autologous chondrocyte implantation, existing cell-based technologies, minimally invasive second-generation autologous chondrocyte implantation, future development in cartilage repair, meniscus transplantation, management of OCD, patellafemoral chondral disease, proximal tibial and distal femoral osteotomies, unicompartmental arthritis current techniques, unicompartmental knee replacement. Section IV is "Operative treatment-Hip" including chapters about hip arthroscopy and arthroscopic partial resurfacing, related osteotomies. Section V is "operative treatment-shoulder" including chapters about arthroscopic debridment and release, biologic resurfacing and
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Development and application of Human Genome Epidemiology
Xu, Jingwen
2017-12-01
Epidemiology is a science that studies distribution of diseases and health in population and its influencing factors, it also studies how to prevent and cure disease and promote health strategies and measures. Epidemiology has developed rapidly in recent years and it is an intercross subject with various other disciplines to form a series of branch disciplines such as Genetic epidemiology, molecular epidemiology, drug epidemiology and tumor epidemiology. With the implementation and completion of Human Genome Project (HGP), Human Genome Epidemiology (HuGE) has emerged at this historic moment. In this review, the development of Human Genome Epidemiology, research content, the construction and structure of relevant network, research standards, as well as the existing results and problems are briefly outlined.
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COGNITIVE SCIENCE: FROM MULTIDISCIPLINARITY TO INTERDISCIPLINARITY
Directory of Open Access Journals (Sweden)
Marina Bogdanova
2017-12-01
Full Text Available Cognitive science is a network of interrelated scientific disciplines engaged in researching human cognition and its brain mechanisms. The birth of cognitive science has been the result of numerous integrated processes. Cognitive science is made up of experimental psychology cognition, philosophy consciousness, neuroscience, cognitive anthropology, linguistics, computer science and artificial intelligence. In recent years, a number of other research areas have been added to the body of cognitive science. Among researchers there have been discussions about whether cognitive science is a separate research area or it consists of a series of specialized areas. In fact, the point at issue is whether cognitive science is still a multidisciplinary project or already an interdisciplinary one. P. Thagard believes that cognitive science has reached the level of interdisciplinarity and explains the advances in this area through the metaphor of “trading zones”. The success elements of cognitive science are: fruitful unification of scientific interests of cognitive science founders; organizational structure of the scientific community – universities, where a special interdisciplinary intellectual environment has been created; a large number of joint research projects supported by governments and business; integrated use of scientific methods and fundamental ideas. D. Sperber and J. Miller prefer to talk not about a unified cognitive science but cognitive sciences, i.e., the commonwealth of sciences working together on the study of a single object - human cognition, however, the extent of their interactive communication is still small. Thus, we should speak about multidisciplinarity rather than genuine interdisciplinarity of the joint research of separate sciences.
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Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes
Energy Technology Data Exchange (ETDEWEB)
Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor; Kohler, Annegret; Martin, Francis
2013-03-08
Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze dozens of mycorrhizal genomes of all Basidiomycota and Ascomycota orders and multiple ecological types (ericoid, orchid, and ectomycorrhizal). JGI has developed and deployed high-throughput sequencing techniques, and Assembly, RNASeq, and Annotation Pipelines. In 2012 alone we sequenced, assembled, and annotated 12 draft or improved genomes of mycorrhizae, and predicted ~;;232831 genes and ~;;15011 multigene families, All of this data is publicly available on JGI MycoCosm (http://jgi.doe.gov/fungi/), which provides access to both the genome data and tools with which to analyze the data. Preliminary comparisons of the current total of 14 public mycorrhizal genomes suggest that 1) short secreted proteins potentially involved in symbiosis are more enriched in some orders than in others amongst the mycorrhizal Agaricomycetes, 2) there are wide ranges of numbers of genes involved in certain functional categories, such as signal transduction and post-translational modification, and 3) novel gene families are specific to some ecological types.
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Dheensa, Sandi; Carrieri, Daniele; Kelly, Susan; Clarke, Angus; Doheny, Shane; Turnpenny, Peter; Lucassen, Anneke
Advances in genomics often lead healthcare professionals (HCPs) to learn new information, e.g., about reinterpreted variants that could have clinical significance for patients seen previously. A question arises of whether HCPs should recontact these former patients. We present some findings
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Exploration of Metagenome Assemblies with an Interactive Visualization Tool
Energy Technology Data Exchange (ETDEWEB)
Cantor, Michael; Nordberg, Henrik; Smirnova, Tatyana; Andersen, Evan; Tringe, Susannah; Hess, Matthias; Dubchak, Inna
2014-07-09
Metagenomics, one of the fastest growing areas of modern genomic science, is the genetic profiling of the entire community of microbial organisms present in an environmental sample. Elviz is a web-based tool for the interactive exploration of metagenome assemblies. Elviz can be used with publicly available data sets from the Joint Genome Institute or with custom user-loaded assemblies. Elviz is available at genome.jgi.doe.gov/viz
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Nuclear-like Seq in mt Genome - RMG | LSDB Archive [Life Science Database Archive metadata
Lifescience Database Archive (English)
Full Text Available ar-like Seq in mt Genome Data detail Data name Nuclear-like Seq in mt Genome DOI 10...e Site Policy | Contact Us Nuclear-like Seq in mt Genome - RMG | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us RMG Nucle
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Weird Animals, Sex, and Genome Evolution.
Graves, Jennifer A Marshall
2018-02-15
Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide stunning examples of epigenetic control and break all the evolutionary rules that we currently understand. Here I describe some of those amazing animals and the insights on genome structure, function, and evolution they have afforded us. I also describe my sometimes-random walk in science and the factors and people who influenced my direction. Being a woman in science is still not easy, and I hope others will find encouragement and empathy in my story.
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Analysis of TCRAD gene recombination: radio-induct rearrangement and signal joint structure
International Nuclear Information System (INIS)
Touvrey, C.
2005-09-01
We have shown that irradiation of pre-TCR-deficient CD3ε -/- mice restores thymocyte differentiation, by a p53-dependent and by a p53-independent pathway. Events normally associated during normal thymocyte development are dissociated in response to radiation exposure. Both of these pathways require LAT expression. Therefore, radiation exposure activates pre-TCR-like signals. TCRA gene rearrangement is induced following radiation exposure. The signal joints resulting from TCRA gene rearrangement have the same structure than those found in wild type mice. All signal joint analyzed in un-manipulated wild type mice do exhibit junctional diversity. This diversity results mainly from TdT activity. We present evidences that proteins involved in DNA repair and genomic stability participated in SJ formation. We propose that signal joint diversity is not an aberrant process but is a key feature of V(D)J recombination. All our work increases our understanding of molecular events associated with V(D)J recombination. (author)
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Genomics and advances towards precision medicine for head and neck squamous cell carcinoma.
Van Waes, Carter; Musbahi, Omar
2017-10-01
To provide a review of emerging knowledge from genomics and related basic science, preclinical, and clinical precision medicine studies in head and neck squamous cell carcinoma (HNSCC). The Cancer Genome Atlas Network (TCGA) publications, PubMed-based literature review, and ClinicalTrials.gov. TCGA publications, PubMed, and ClinicalTrials.gov were queried for genomics and related basic science, preclinical, and developmental clinical precision medicine studies in HNSCC. TCGA reported comprehensive genomic analyses of 279 HNSCC, defining the landscape and frequency of chromosomal copy number alterations, mutations, and expressed genes that contribute to pathogenesis, prognosis, and resistance to therapy. This provides a road map for basic science and preclinical studies to identify key pathways in cancer and cells of the tumor microenvironment affected by these alterations, and candidate targets for new small molecule and biologic therapies. Recurrent chromosomal abnormalities, mutations, and expression of genes affecting HNSCC subsets are associated with differences in prognosis, and define molecules, pathways, and deregulated immune responses as candidates for therapy. Activity of molecularly targeted agents appears to be enhanced by rational combinations of these agents and standard therapies targeting the complex alterations that affect multiple pathways and mechanisms in HNSCC. NA.
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Life sciences: Lawrence Berkeley Laboratory, 1988
International Nuclear Information System (INIS)
1989-07-01
Life Sciences Research at LBL has both a long history and a new visibility. The physics technologies pioneered in the days of Ernest O. Lawrence found almost immediate application in the medical research conducted by Ernest's brother, John Lawrence. And the tradition of nuclear medicine continues today, largely uninterrupted for more than 50 years. Until recently, though, life sciences research has been a secondary force at the Lawrence Berkeley Laboratory (LBL). Today, a true multi-program laboratory has emerged, in which the life sciences participate as a full partner. The LBL Human Genome Center is a contribution to the growing international effort to map the human genome. Its achievements represent LBL divisions, including Engineering, Materials and Chemical Sciences, and Information and Computing Sciences, along with Cell and Molecular Biology and Chemical Biodynamics. The Advanced Light Source Life Sciences Center will comprise not only beamlines and experimental end stations, but also supporting laboratories and office space for scientists from across the US. This effort reflects a confluence of scientific disciplines --- this time represented by individuals from the life sciences divisions and by engineers and physicists associated with the Advanced Light Source project. And finally, this report itself, the first summarizing the efforts of all four life sciences divisions, suggests a new spirit of cooperation. 30 figs
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Complete genome sequence of Rhodospirillum rubrum type strain (S1).
Munk, A Christine; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Barry, Kerrie; Detter, John C; Hammon, Nancy; Israni, Sanjay; Pitluck, Sam; Brettin, Thomas; Bruce, David; Han, Cliff; Tapia, Roxanne; Gilna, Paul; Schmutz, Jeremy; Larimer, Frank; Land, Miriam; Kyrpides, Nikos C; Mavromatis, Konstantinos; Richardson, Paul; Rohde, Manfred; Göker, Markus; Klenk, Hans-Peter; Zhang, Yaoping; Roberts, Gary P; Reslewic, Susan; Schwartz, David C
2011-07-01
Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.
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International Nuclear Information System (INIS)
Kazumata, Yukio
1993-01-01
The joint seminar on Solid State Physics, Atomic and Molecular Physics and Materials Science in the Energy Region of Tandem Acceleration was held at Tokai Research Establishment of JAERI, for two days from January 22 to 23, 1991. About 60 physicists and material scientists participated and 18 papers were presented in this seminar. The topics presented in this seminar included lattice defects in semiconductors, ion-solid collisions, atomic collisions by high energy particles, radiation effects on high T c superconducting materials and FCC metals, radiation effects on materials of space and fusion reactors, uranium compounds and superlattice. (J.P.N.)
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Second-year dental students' perceptions about a joint basic ...
African Journals Online (AJOL)
Reports from the USA and Australia, however, show that it may be problematic because joint basic science curricula are mostly tailored around the needs of the medical students only, which may lead to prejudice and marginalisation of dental students. There are no local studies to inform decision-making in this regard.
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MR diagnosis of temporomandibular joint. A study of joint effusion
International Nuclear Information System (INIS)
Kaneda, Takashi; Yamashiro, Mitsuaki; Ozawa, Kaoru; Suzuki, Hiromi; Okada, Hiroyuki; Yamamoto, Hirotsugu
1998-01-01
The purposes of this study were to evaluate the relationship between correlation of MR joint effusion of the temporomandibular joint and disk position, to evaluate the relationship between joint effusion and aging, and to assess the frequency of MR joint effusion of bilateral temporomandibular joints. The temporomandibular joints of 192 patients with clinical symptoms of temporomandibular joint disorders were imaged bilaterally using high field, surface-coil MR imaging. Oblique sagittal and coronal proton density-weighted and T2-weighted images were obtained. Imaging findings of joint effusion were correlated with disk position, aging, and bilateral temporomandibular joints. MR showed effusion in 4% of the joints with normal superior disk position, 36% of the joints with disk displacement with reduction, and 45% of the joints with disk displacement without reduction. There were significant differences in the incidence of joint effusion between normal disk position and anterior disk displacement with or without reduction. Younger patients less than 40 years were significant higher the incidence of joint effusion than those of older patients. A significant association was seen between joint effusion and aging. MR showed effusion in 17% of the unilateral temporomandibular joint, 24% of the bilateral temporomandibular joints. There was no significant difference between unilateral and bilateral case. These results indicated that joint effusion using MR imaging was associated with varied temporomandibular joint pathologic states. (author)
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Energy Technology Data Exchange (ETDEWEB)
Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabien; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.
2012-03-13
The class of Dothideomycetes is one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related species can have very diverse host plants. Eighteen genomes of Dothideomycetes have currently been sequenced by the Joint Genome Institute and other sequencing centers. Here we describe the results of comparative analyses of the fungi in this group.
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McBride, Colleen M; Birmingham, Wendy C; Kinney, Anita Y
2015-01-01
The past decade has witnessed rapid advances in human genome sequencing technology and in the understanding of the role of genetic and epigenetic alterations in cancer development. These advances have raised hopes that such knowledge could lead to improvements in behavioral risk reduction interventions, tailored screening recommendations, and treatment matching that together could accelerate the war on cancer. Despite this optimism, translation of genomic discovery for clinical and public health applications has moved relatively slowly. To date, health psychologists and the behavioral sciences generally have played a very limited role in translation research. In this report we discuss what we mean by genomic translational research and consider the social forces that have slowed translational research, including normative assumptions that translation research must occur downstream of basic science, thus relegating health psychology and other behavioral sciences to a distal role. We then outline two broad priority areas in cancer prevention, detection, and treatment where evidence will be needed to guide evaluation and implementation of personalized genomics: (a) effective communication, to broaden dissemination of genomic discovery, including patient-provider communication and familial communication, and (b) the need to improve the motivational impact of behavior change interventions, including those aimed at altering lifestyle choices and those focusing on decision making regarding targeted cancer treatments and chemopreventive adherence. We further discuss the role that health psychologists can play in interdisciplinary teams to shape translational research priorities and to evaluate the utility of emerging genomic discoveries for cancer prevention and control. PsycINFO Database Record (c) 2015 APA, all rights reserved.
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Joint Institute for Nuclear Research Exhibition Science Bringing Nations Together
2000-01-01
The JOINT INSTITUTE FOR NUCLEAR RESEARCH, JINR, was established by its founding countries in 1956 with the purpose of joining together the scientific and material potential of Member States in studies of the fundamental properties of matter. JINR is an international inter-governmental scientific research organization, whose activities are based on the principles of openness for participation to all interested states and of their equal, mutually beneficial collaboration.
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Joint Institute for Nuclear Research Exhibition Science Bringing Nations Together
1999-01-01
The JOINT INSTITUTE FOR NUCLEAR RESEARCH, JINR, was established by its founding countries in 1956 with the purpose of joining together the scientific and material potential of Member States in studies of the fundamental properties of matter. JINR is an international inter-governmental scientific research organization, the activities of which are based on the principles of openness for participation to all interested states of their equal, mutually beneficial collaboration.
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Virtual Welded-Joint Design Integrating Advanced Materials and Processing Technologies
Energy Technology Data Exchange (ETDEWEB)
Yang, Z.; Dong, P.; Liu, S.; Babu, S.; Olson, G.; DebRoy, T.
2005-04-15
The primary goal of this project is to increase the fatigue life of a welded-joint by 10 times and to reduce energy use by 25% through product performance and productivity improvements using an integrated modeling approach. The fatigue strength of a welded-joint is currently the bottleneck to design high performance and lightweight welded structures using advanced materials such as high strength steels. In order to achieve high fatigue strength in a welded-joint it is necessary to manage the weld bead shape for lower stress concentration, produce preferable residual stress distribution, and obtain the desired microstructure for improved material toughness and strength. This is a systems challenge that requires the optimization of the welding process, the welding consumable, the base material, as well as the structure design. The concept of virtual welded-joint design has been proposed and established in this project. The goal of virtual welded-joint design is to develop a thorough procedure to predict the relationship of welding process, microstructure, property, residual stress, and the ultimate weld fatigue strength by a systematic modeling approach. The systematic approach combines five sub-models: weld thermal-fluid model, weld microstructure model, weld material property model, weld residual stress model, and weld fatigue model. The systematic approach is thus based on interdisciplinary applied sciences including heat transfer, computational fluid dynamics, materials science, engineering mechanics, and material fracture mechanics. The sub-models are based on existing models with further development. The results from modeling have been validated with critical experiments. The systematic modeling approach has been used to design high fatigue resistant welds considering the combined effects of weld bead geometry, residual stress, microstructure, and material property. In particular, a special welding wire has been developed in this project to introduce
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Genomics and the making of yeast biodiversity.
Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan; Boekhout, Teun; Gonçalves, Paula; Jeffries, Thomas W; Kominek, Jacek; Lachance, Marc-André; Libkind, Diego; Rosa, Carlos A; Sampaio, José Paulo; Kurtzman, Cletus P
2015-12-01
Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Fellowship | Indian Academy of Sciences
Indian Academy of Sciences (India)
Specialization: DNA Double-Strand Break Repair, Genomic Instability, Cancer ... Address: Indian Institute of Science Education & Research, Dr Homi Bhabha Road, .... Inflammatory Bowel Disease, Gastrointestinal Microbiome Stem Cells
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Fellowship | Indian Academy of Sciences
Indian Academy of Sciences (India)
Specialization: Medical Biostatistics, Medical Research Methodology, Medical ... Address: Centre for Advanced Research & Development, SBM Jain College of ... Joint Statement by the Three Science Academies of India on the teaching of the ...
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Energy Technology Data Exchange (ETDEWEB)
Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian
2013-01-24
The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
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International Nuclear Information System (INIS)
1975-01-01
The results of research works by universities with Rikkyo University's joint-use reactor and RCNST's (Research Center for Nuclear Science and Technology) instruments for fiscal 1974 are described. Comprising the areas of activation analysis (in such as earth science, biology and environmental science), hot atom chemistry, etc., the results are presented in individual summaries. (Mori, K.)
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Evolving approaches to the ethical management of genomic data.
McEwen, Jean E; Boyer, Joy T; Sun, Kathie Y
2013-06-01
The ethical landscape in the field of genomics is rapidly shifting. Plummeting sequencing costs, along with ongoing advances in bioinformatics, now make it possible to generate an enormous volume of genomic data about vast numbers of people. The informational richness, complexity, and frequently uncertain meaning of these data, coupled with evolving norms surrounding the sharing of data and samples and persistent privacy concerns, have generated a range of approaches to the ethical management of genomic information. As calls increase for the expanded use of broad or even open consent, and as controversy grows about how best to handle incidental genomic findings, these approaches, informed by normative analysis and empirical data, will continue to evolve alongside the science. Published by Elsevier Ltd.
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Life sciences and environmental sciences
Energy Technology Data Exchange (ETDEWEB)
1992-02-01
The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER's mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.
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Life sciences and environmental sciences
Energy Technology Data Exchange (ETDEWEB)
1992-02-01
The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER`s mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment, applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.
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Voice-supported Electronic Health Record for Temporomandibular Joint Disorders
Czech Academy of Sciences Publication Activity Database
Hippmann, R.; Dostálová, T.; Zvárová, Jana; Nagy, Miroslav; Seydlová, M.; Hanzlíček, Petr; Kříž, P.; Šmídl, L.; Trmal, J.
2010-01-01
Roč. 49, č. 2 (2010), s. 168-172 ISSN 0026-1270 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : electronic health record * structured data entry * dentistry * temporomandibular joint disorder Subject RIV: IN - Informatics, Computer Science Impact factor: 1.472, year: 2010
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Ardley, Julie; Tian, Rui; Howieson, John; Yates, Ron; Bräu, Lambert; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Chen, Amy; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos; Reeve, Wayne
2014-01-01
Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing microsymbionts of species of the African crotalarioid genus Listia. Strain WSM2598 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated in 2002 from a Listia bainesii root nodule collected at Estcourt Research Station in South Africa. Here we describe the features of Methylobacterium sp. WSM2598, together with information and annotation of a high-quality draft genome sequence. The 7,669,765 bp draft genome is arranged in 5 scaffolds of 83 contigs, contains 7,236 protein-coding genes and 18 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 G enomic E ncyclopedia for B acteria and A rchaea- R oot N odule B acteria (GEBA-RNB) project.
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Open science versus commercialization: a modern research conflict?
Caulfield, Timothy; Harmon, Shawn He; Joly, Yann
2012-02-27
Efforts to improve research outcomes have resulted in genomic researchers being confronted with complex and seemingly contradictory instructions about how to perform their tasks. Over the past decade, there has been increasing pressure on university researchers to commercialize their work. Concurrently, they are encouraged to collaborate, share data and disseminate new knowledge quickly (that is, to adopt an open science model) in order to foster scientific progress, meet humanitarian goals, and to maximize the impact of their research. We present selected guidelines from three countries (Canada, United States, and United Kingdom) situated at the forefront of genomics to illustrate this potential policy conflict. Examining the innovation ecosystem and the messages conveyed by the different policies surveyed, we further investigate the inconsistencies between open science and commercialization policies. Commercialization and open science are not necessarily irreconcilable and could instead be envisioned as complementary elements of a more holistic innovation framework. Given the exploratory nature of our study, we wish to point out the need to gather additional evidence on the coexistence of open science and commercialization policies and on its impact, both positive and negative, on genomics academic research.
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Breithaupt, Lauren; Hubel, Christopher; Bulik, Cynthia M
2018-02-22
Heterogeneity, frequent diagnostic fluctuation across presentations, and global concerns with the absence of effective treatments all encourage science that moves the field toward individualized or precision medicine in eating disorders. We review recent advances in psychiatric genetics focusing on genome-wide association studies (GWAS) in eating disorders and enumerate the prospects and challenges of a genomics-driven approach towards personalized intervention. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
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A chromosome conformation capture ordered sequence of the barley genome
Czech Academy of Sciences Publication Activity Database
Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S. O.; Wicker, T.; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, S.; Munoz-Amatrian, M.; Houben, A.; Doležel, Jaroslav; Ayling, S.; Lonardi, S.; Mayer, K.F.X.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh, R.; Stein, N.
2017-01-01
Roč. 544, č. 7651 (2017), s. 427-433 ISSN 0028-0836 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : bacterial artificial chromosomes * inverted-repeat elements * complex-plant genomes * hi-c * environmental adaptation * ltr retrotransposons * structural variation * maize genome * software * database Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 40.137, year: 2016
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H.E. Mr. Ronaldo Mota Sardenberg, Minister for Science, Technology and Innovation, Brazil
Maximilien Brice
2002-01-01
Photo 01: Signature of the joint statement by H.E. Mr Ronaldo Mota Sardenberg, Minister for Science, Technology and Innovation, Brazil (centre) with CERN Director-General, L. Maiani (right) and C. Melo. Photo 02: Signature of the joint statement by H.E. Mr Ronaldo Mota Sardenberg, Minister for Science, Technology and Innovation, Brazil (left) and CERN Director-General, L. Maiani. Photo 03: H.E. Mr Ronaldo Mota Sardenberg, Minister for Science, Technology and Innovation, Brazil and CERN Director-General, L. Maiani.
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Journal of Biosciences | Indian Academy of Sciences
Indian Academy of Sciences (India)
Author Affiliations. Rahul Kumar1 Ashima Khurana2. Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India; Zakir Husain Delhi College, Botany Department, University of Delhi, New Delhi 110 002, India ...
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Some certainties among the many questions of the last 10 years about the primate genome
International Nuclear Information System (INIS)
Nieves, Mariela; Mudry, Marta Dolores
2011-01-01
In 2000 the first draft of the human genome, what became known as our book of life, was presented. It generated high expectations for its potential applications to the benefit of the biological sciences. What happened 10 years later? We know how many genes we have in our genome and analyzed the function of some of them. Nowadays, we know the sequences of 3 mammalians genomes: M. musculus, P. troglodytes y S. scrofa and the genomes or borradores from other eucaryotes (other animals, plants, fungi and protists) and procaryotes (Archea and Bacterias). However, the study of the genome is not merely a description of the sequences that compose it. The answers provided will have very different approaches from evolution and conservation of biodiversity to gene therapy and malignant transformation, where the study of individual and population particularities requires sources of information both past and present on these genomes under survey. Thus, advances in science are always provisional and therefore liable to be continued, completed and even reinterpreted as we advance in knowledge, new questions arise.
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Opinion piece: genomics and crop plant science in Europe.
Hughes, Steve
2006-01-01
Recent report reviews and funding initiatives in the field of plant genomic research are considered in the context of their translation into practical and economic value via plant breeding. It is concluded that there is a deficit in investment and that a change in working styles towards knowledge sharing and connectivity is required.
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Advances in welding science - a perspective
International Nuclear Information System (INIS)
David, S.A.; Vitek, J.M.; Babu, S.S.; DebRoy, T.
1995-01-01
The ultimate goal of welding technology is to improve the joint integrity and increase productivity. Over the years, welding has been more of an art than a science, but in the last few decades major advances have taken place in welding science and technology. With the development of new methodologies at the crossroads of basic and applied sciences, enormous opportunities and potential exist to develop a science-based tailoring of composition, structure, and properties of welds with intelligent control and automation of the welding processes
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New trends in networking, computing, e-learning, systems sciences, and engineering
Sobh, Tarek
2015-01-01
This book includes a set of rigorously reviewed world-class manuscripts addressing and detailing state-of-the-art research projects in the areas of Computer Science, Informatics, and Systems Sciences, and Engineering. It includes selected papers form the conference proceedings of the Ninth International Joint Conferences on Computer, Information, and Systems Sciences, and Engineering (CISSE 2013). Coverage includes topics in: Industrial Electronics, Technology & Automation, Telecommunications and Networking, Systems, Computing Sciences and Software Engineering, Engineering Education, Instructional Technology, Assessment, and E-learning. • Provides the latest in a series of books growing out of the International Joint Conferences on Computer, Information, and Systems Sciences, and Engineering; • Includes chapters in the most advanced areas of Computing, Informatics, Systems Sciences, and Engineering; • Accessible to a wide range of readership, including professors, researchers, practitioners and...
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Mind the gap; seven reasons to close fragmented genome assemblies.
Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi
2016-05-01
Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.
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Closing the gap between knowledge and clinical application: challenges for genomic translation.
Burke, Wylie; Korngiebel, Diane M
2015-01-01
Despite early predictions and rapid progress in research, the introduction of personal genomics into clinical practice has been slow. Several factors contribute to this translational gap between knowledge and clinical application. The evidence available to support genetic test use is often limited, and implementation of new testing programs can be challenging. In addition, the heterogeneity of genomic risk information points to the need for strategies to select and deliver the information most appropriate for particular clinical needs. Accomplishing these tasks also requires recognition that some expectations for personal genomics are unrealistic, notably expectations concerning the clinical utility of genomic risk assessment for common complex diseases. Efforts are needed to improve the body of evidence addressing clinical outcomes for genomics, apply implementation science to personal genomics, and develop realistic goals for genomic risk assessment. In addition, translational research should emphasize the broader benefits of genomic knowledge, including applications of genomic research that provide clinical benefit outside the context of personal genomic risk.
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Education through fiction: acquiring opinion-forming skills in the context of genomics
Knippels, M.C.P.J.; Severiens, S.E.; Klop, T.
2009-01-01
The present study examined the outcomes of a newly designed four-lesson science module on opinion-forming in the context of genomics in upper secondary education. The lesson plan aims to foster 16-year-old students’ opinion-forming skills in the context of genomics and to test the effect of the use
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Genomes-based phylogeny of the genus Xanthomonas
Directory of Open Access Journals (Sweden)
Rodriguez-R Luis M
2012-03-01
Full Text Available Abstract Background The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. Results Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. Conclusions Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.
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Life sciences: Lawrence Berkeley Laboratory, 1988
Energy Technology Data Exchange (ETDEWEB)
1989-07-01
Life Sciences Research at LBL has both a long history and a new visibility. The physics technologies pioneered in the days of Ernest O. Lawrence found almost immediate application in the medical research conducted by Ernest's brother, John Lawrence. And the tradition of nuclear medicine continues today, largely uninterrupted for more than 50 years. Until recently, though, life sciences research has been a secondary force at the Lawrence Berkeley Laboratory (LBL). Today, a true multi-program laboratory has emerged, in which the life sciences participate as a full partner. The LBL Human Genome Center is a contribution to the growing international effort to map the human genome. Its achievements represent LBL divisions, including Engineering, Materials and Chemical Sciences, and Information and Computing Sciences, along with Cell and Molecular Biology and Chemical Biodynamics. The Advanced Light Source Life Sciences Center will comprise not only beamlines and experimental end stations, but also supporting laboratories and office space for scientists from across the US. This effort reflects a confluence of scientific disciplines --- this time represented by individuals from the life sciences divisions and by engineers and physicists associated with the Advanced Light Source project. And finally, this report itself, the first summarizing the efforts of all four life sciences divisions, suggests a new spirit of cooperation. 30 figs.
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SNU-KAERI Degree and Research Center for Radiation Convergence Sciences
International Nuclear Information System (INIS)
Jo, Sungkee; Kim, S. U.; Roh, C. H
2011-12-01
In this study, we tried to establish and perform the demonstrative operation of the 'Degree and Research Center for Radiation Convergence Sciences' to raise the Korea's technology competitiveness. As results of this project we got the successful accomplishment as below: 1. Operation of Degree and Research Center for Radiation Convergence Sciences and establishment of expert researcher training system Ο Presentation of an efficient model for expert researcher training program through the operation of university-institute collaboration courses by combining of Graduate course and DRC system. Ο Radiation Convergence Sciences major is scheduled to be established in 2013 at SNU Graduate School of Convergence Science and Technology Ο A big project for research, education, and training of radiation convergence science is under planning 2. Establishment and conduction of joint research by organization of radiation convergence research consortium · Joint research was conducted in close connection with the research projects of researchers participating in this DRC project (44 articles published in journals, 6 patents applied, 88 papers presented in conferences) · The resources of the two organization (SNU and KAERI), such as research infrastructure (hightech equipment and etc), manpower (professor/researcher), and original technology and know how were utilized to conduct the joint research and to establish the collaboration system of the two organizations
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Joint Institute for Nanoscience Annual Report 2003
Energy Technology Data Exchange (ETDEWEB)
Baer, Donald R.; Campbell, Charles
2004-02-01
The Joint Institute for Nanoscience (JIN) is a cooperative venture of the University of Washington and Pacific Northwest National Laboratory to encourage and enhance high-impact and high-quality nanoscience and nanotechnology of all types. This first annual report for the JIN summarizes activities beginning in 2001 and ending at the close of fiscal year 2003 and therefore represents somewhat less than two years of activities. Major portions of the JIN resources are dedicated to funding graduate students and postdoctoral research associates to perform research in collaborations jointly directed by Pacific Northwest National Laboratory (PNNL) staff scientists and University of Washington (UW) professors. These fellowships were awarded on the basis of applications that included research proposals. JIN co-sponsors an annual Nanoscale Science and Technology Workshop held in Seattle. In addition to involving PNNL staff in various UW nanoscience courses and seminars, a National Science Foundation grant Development of UW-PNL Collaborative Curriculums in Nano-Science and Technology has allowed the development of three intensive short courses that are taught by UW faculty, PNNL staff, and faculty from other institutions, including Washington State University, the University of Idaho, Stanford University, and the University of Alaska. The initial JIN agreement recognized that expansion of cooperation beyond UW and PNNL would be highly valuable. Starting in early 2003, efforts were initiated to form a regional communication link called the Northwest Nanoscience and Nanotechnology Network (N₄). In concept, N₄ is a tool to encourage communication and help identify regional resources and nanoscience and technology activities.
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The plant ontology as a tool for comparative plant anatomy and genomic analyses
Plant science is now a major player in the fields of genomics, gene expression analysis, phenomics and metabolomics. Recent advances in sequencing technologies have led to a windfall of data, with new species being added rapidly to the list of species whose genomes have been decoded. The Plant Ontol...
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Genetic counselors: translating genomic science into clinical practice
Bennett, Robin L.; Hampel, Heather L.; Mandell, Jessica B.; Marks, Joan H.
2003-01-01
In a time of emerging genetic tests and technologies, genetic counselors are faced with the challenge of translating complex genomic data into information that will aid their client’s ability to learn about, understand, make, and cope with decisions relating to genetic diagnoses. The first of two companion articles in this issue examines the role of the genetic counselor, particularly in counseling individuals at risk for or diagnosed with breast cancer, in an era of high-tech health care and...
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DEFF Research Database (Denmark)
Edwards, Stefan McKinnon
externally founded information, such as KEGG pathways, Gene Ontology gene sets, or genomic features, and estimate the joint contribution of the genetic variants within these sets to complex trait phenotypes. The analysis of complex trait phenotypes is hampered by the myriad of genes that control the trait...
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Heldmann, J. L.; Lim, D.S.S.; Hughes, S.; Nawotniak, S. Kobs; Garry, B.; Sears, D.; Neish, C.; Osinski, G. R.; Hodges, K.; Downs, M.;
2016-01-01
NASA's FINESSE (Field Investigations to Enable Solar System Science and Exploration) project was selected as a research team by NASA's Solar System Exploration Research Virtual Institute (SSERVI). SSERVI is a joint Institute supported by NASA's Science Mission Directorate (SMD) and Human Exploration and Operations Mission Directorate (HEOMD). As such, FINESSE is focused on a science and exploration field-based research program to generate strategic knowledge in preparation for human and robotic exploration of other planetary bodies including our Moon, Mars moons Phobos and Deimos, and near-Earth asteroids. FINESSE embodies the philosophy that "science enables exploration and exploration enables science".
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Complete Genome Sequence of the Probiotic Lactic Acid Bacterium Lactobacillus Rhamnosus
Directory of Open Access Journals (Sweden)
Samat Kozhakhmetov
2014-01-01
Full Text Available Introduction: Lactobacilli are a bacteria commonly found in the gastrointestinal tract. Some species of this genus have probiotic properties. The most common of these is Lactobacillus rhamnosus, a microoganism, generally regarded as safe (GRAS. It is also a homofermentative L-(+-lactic acid producer. The genus Lactobacillus is characterized by an extraordinary degree of the phenotypic and genotypic diversity. However, the studies of the genus were conducted mostly with the unequally distributed, non-random choice of species for sequencing; thus, there is only one representative genome from the Lactobacillus rhamnosus clade available to date. The aim of this study was to characterize the genome sequencing of selected strains of Lactobacilli. Methods: 109 samples were isolated from national domestic dairy products in the laboratory of Center for life sciences. After screaning isolates for probiotic properties, a highly active Lactobacillus spp strain was chosen. Genomic DNA was extracted according to the manufacturing protocol (Wizard® Genomic DNA Purification Kit. The Lactobacillus rhamnosus strain was identified as the highly active Lactobacillus strain accoridng to its morphological, cultural, physiological, and biochemical properties, and a genotypic analysis. Results: The genome of Lactobacillus rhamnosus was sequenced using the Roche 454 GS FLX (454 GS FLX platforms. The initial draft assembly was prepared from 14 large contigs (20 all contigs by the Newbler gsAssembler 2.3 (454 Life Sciences, Branford, CT. Conclusion: A full genome-sequencing of selected strains of lactic acid bacteria was made during the study.
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Report on the Human Genome Initiative
Energy Technology Data Exchange (ETDEWEB)
Tinoco, I.; Cahill, G.; Cantor, C.; Caskey, T.; Dulbecco, R.; Engelhardt, D. L.; Hood, L.; Lerman, L. S.; Mendelsohn, M. L.; Sinsheimer, R. L.; Smith, T.; Soll, D.; Stormo, G.; White, R. L.
1987-04-01
The report urges DOE and the Nation to commit to a large. multi-year. multidisciplinary. technological undertaking to order and sequence the human genome. This effort will first require significant innovation in general capability to manipulate DNA. major new analytical methods for ordering and sequencing. theoretical developments in computer science and mathematical biology, and great expansions in our ability to store and manipulate the information and to interface it with other large and diverse genetic databases. The actual ordering and sequencing involves the coordinated processing of some 3 billion bases from a reference human genome. Science is poised on the rudimentary edge of being able to read and understand human genes. A concerted. broadly based. scientific effort to provide new methods of sufficient power and scale should transform this activity from an inefficient one-gene-at-a-time. single laboratory effort into a coordinated. worldwide. comprehensive reading of "the book of man". The effort will be extraordinary in scope and magnitude. but so will be the benefit to biological understanding. new technology and the diagnosis and treatment of human disease.
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Sjoberg, W.; McWilliams, G.
2017-12-01
This presentation will focus on the continuity of the NOAA Joint Polar Satellite System (JPSS) Program's Proving Ground and Risk Reduction (PGRR) and key activities of the PGRR Initiatives. The PGRR Program was established in 2012, following the launch of the Suomi National Polar Partnership (SNPP) satellite. The JPSS Program Office has used two PGRR Project Proposals to establish an effective approach to managing its science and algorithm teams in order to focus on key NOAA missions. The presenter will provide details of the Initiatives and the processes used by the initiatives that have proven so successful. Details of the new 2017 PGRR Call-for-Proposals and the status of project selections will be discussed.
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Chen, Hao; Capellini, Terence D; Schoor, Michael; Mortlock, Doug P; Reddi, A Hari; Kingsley, David M
2016-11-01
Synovial joints are crucial for support and locomotion in vertebrates, and are the frequent site of serious skeletal defects and degenerative diseases in humans. Growth and differentiation factor 5 (Gdf5) is one of the earliest markers of joint formation, is required for normal joint development in both mice and humans, and has been genetically linked to risk of common osteoarthritis in Eurasian populations. Here, we systematically survey the mouse Gdf5 gene for regulatory elements controlling expression in synovial joints. We identify separate regions of the locus that control expression in axial tissues, in proximal versus distal joints in the limbs, and in remarkably specific sub-sets of composite joints like the elbow. Predicted transcription factor binding sites within Gdf5 regulatory enhancers are required for expression in particular joints. The multiple enhancers that control Gdf5 expression in different joints are distributed over a hundred kilobases of DNA, including regions both upstream and downstream of Gdf5 coding exons. Functional rescue tests in mice confirm that the large flanking regions are required to restore normal joint formation and patterning. Orthologs of these enhancers are located throughout the large genomic region previously associated with common osteoarthritis risk in humans. The large array of modular enhancers for Gdf5 provide a new foundation for studying the spatial specificity of joint patterning in vertebrates, as well as new candidates for regulatory regions that may also influence osteoarthritis risk in human populations.
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Innovations and advances in computing, informatics, systems sciences, networking and engineering
Elleithy, Khaled
2015-01-01
Innovations and Advances in Computing, Informatics, Systems Sciences, Networking and Engineering This book includes a set of rigorously reviewed world-class manuscripts addressing and detailing state-of-the-art research projects in the areas of Computer Science, Informatics, and Systems Sciences, and Engineering. It includes selected papers from the conference proceedings of the Eighth and some selected papers of the Ninth International Joint Conferences on Computer, Information, and Systems Sciences, and Engineering (CISSE 2012 & CISSE 2013). Coverage includes topics in: Industrial Electronics, Technology & Automation, Telecommunications and Networking, Systems, Computing Sciences and Software Engineering, Engineering Education, Instructional Technology, Assessment, and E-learning. · Provides the latest in a series of books growing out of the International Joint Conferences on Computer, Information, and Systems Sciences, and Engineering; · Includes chapters in the most a...
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Pre-Service Science Teacher Preparation in China: Challenges and Promises
Liu, Enshan; Liu, Cheng; Wang, Jian
2015-01-01
The purpose of this article was to present an overview of pre-service science teacher preparation in China, which is heavily influenced by Chinese tradition, Confucianism, and rapid social and economic development. The policies, science teacher education systems and related programs jointly contribute to producing enough science teachers for…
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Re-Examining the Gene in Personalized Genomics
Bartol, Jordan
2013-01-01
Personalized genomics companies (PG; also called "direct-to-consumer genetics") are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept…
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NUCLEONICA: a nuclear science portal
International Nuclear Information System (INIS)
Magill, J.; Galy, J.; Dreher, R.; Hamilton, D.; Tufan, M.; Normand, C.; Schwenk-Ferrero, A.; Wiese, H.W.
2008-01-01
NUCLEONICA is a new nuclear science web portal from the European Commission's Joint Research Centre. The portal provides a customizable, integrated environment and collaboration platform for the nuclear sciences using the latest 'Web 2.0' dynamic technology. NUCLEONICA is aimed at professionals, academics and students working with radionuclides in fields as diverse as the life sciences (e.g., biology, medicine, agriculture), the earth sciences (geology, meteorology, environmental science) and the more traditional disciplines such as nuclear power, health physics and radiation protection, nuclear and radio-chemistry, and astrophysics. It is also used as a knowledge management tool to preserve nuclear knowledge built up over many decades by creating modern web-based versions of so-called legacy computer codes. (authors)
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Human genes and genomes: science, health, society
National Research Council Canada - National Science Library
Rosenberg, Leon E; Rosenberg, Diane Drobnis
2012-01-01
"In the nearly 60 years since Watson and Crick proposed the double helical structure of DNA, the molecule of heredity, waves of discoveries have made genetics the most thrilling field in the sciences...
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The Informatics (R) Evolution in Biology: The Case of Genomics
International Nuclear Information System (INIS)
Michan Aguirre, Layla; Alvarez, Eduardo; Montoya Perez, Laura Elizabeth
2011-01-01
Biology has been revolutionized by the introduction of new disciplines, such is the case of genomics that introduced in the 80s has turned unlikely to modern science, the discipline refers to the study not only of genes but their roles, relations among themselves and with the environment. Arises, with the consolidation of the human genome project and introduces us to a period of transition in which specific genetic knowledge becomes critical. Differs from other approaches in the type of information provided, the prospects for technical and intellectual improvements in the collection and use of data from the whole genome, (Murray, 2000). This work aims to investigate the recent biology, in particular, to show the history of genomics, through literature search and bibliometric analysis.
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Genome Editing Redefines Precision Medicine in the Cardiovascular Field
Directory of Open Access Journals (Sweden)
Elda Dzilic
2018-01-01
Full Text Available Genome editing is a powerful tool to study the function of specific genes and proteins important for development or disease. Recent technologies, especially CRISPR/Cas9 which is characterized by convenient handling and high precision, revolutionized the field of genome editing. Such tools have enormous potential for basic science as well as for regenerative medicine. Nevertheless, there are still several hurdles that have to be overcome, but patient-tailored therapies, termed precision medicine, seem to be within reach. In this review, we focus on the achievements and limitations of genome editing in the cardiovascular field. We explore different areas of cardiac research and highlight the most important developments: (1 the potential of genome editing in human pluripotent stem cells in basic research for disease modelling, drug screening, or reprogramming approaches and (2 the potential and remaining challenges of genome editing for regenerative therapies. Finally, we discuss social and ethical implications of these new technologies.
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How life changes itself: the Read-Write (RW) genome.
Shapiro, James A
2013-09-01
The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. © 2013 Elsevier B.V. All rights reserved.
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Primer to analysis of genomic data using R
Gondro, Cedric
2015-01-01
Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for advanced undergraduate and graduate classes in bioinformatics, genomics and statistical genetics or for use in lab sessions. This book is also designed to be used by students in computer science and statistics who want to learn the practical aspects of genomic analysis without delving into algorithmic details. The datasets used throughout the book may be downloaded from the publisher’s website. Chapters show how to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R. A wide range of R packages useful for working with genomic data are illustrated with practical examples. In recent years R has b...
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Nuclear science and engineering workshop for secondary science teachers
International Nuclear Information System (INIS)
Miller, W.H.; Neumeyer, G.M.; Langhorst, S.M.
1992-01-01
A 2-week workshop has been held for the past 10 yr at the University of Missouri-Columbia for secondary science teachers to increase their knowledge of nuclear science and its applications. It is sponsored jointly by Union Electric Company (St. Louis, Missouri), the University of Missouri-Columbia, the American Nuclear Society (ANS) student branch at the University of Missouri-Columbia, and the Central/Eastern Section of the ANS. The workshop focuses on two principal educational areas: basic nuclear science and its applications and nuclear energy systems. The philosophy of the workshop is to provide factual information without emphasis on the political issues of the use of nuclear without emphasis on the political issues of the use of nuclear science in the modern society, allowing the participants to form their own perceptions of the risks and benefits of nuclear technology. The paper describes the workshop organization, curriculum, and evaluation
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Jiang, Wen-kai; Liu, Yun-long; Xia, En-hua; Gao, Li-zhi
2013-01-01
The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs. PMID:23396833
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Energy Technology Data Exchange (ETDEWEB)
NONE
1998-03-01
The paper clarified the whole image of cell functions by elucidating the function and manifestation control mechanism of genes existing in genomes, and the network of their interactions, and surveyed applicability of the useful functions obtained of cells and proteins to the industrial field. The survey was made from a viewpoint of the fields of both biology and information science. Especially, based on the function-known DNA base sequence database, the following technologies were surveyed: technology to predict the function of the function-unknown DNA base sequence, search/separation technology to acquire the genes to be functionally elucidated in a state of being suitable for manifestation, technology to get perfect proteins by effectively manifesting the genes to be functionally elucidated, and technology to analyze the function of the proteins obtained by manifestation of genes. Further, the International Symposium was held which is titled `Genome Research Opens a New World to Bioindustry (New Developments in Genome Informatics Technologies). With the future progress of technology to decipher and use genome information, the construction of much newer genome industry is anticipated. 165 refs., 44 figs., 10 tabs.
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The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
DEFF Research Database (Denmark)
Xu, Xun; Pan, Shengkai; Liu, Xin
2011-01-01
Chinese hamster ovary (CHO)-derived cell lines are the preferred host cells for the production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45 Gb of genomic sequence, with 24,383 predicted genes. We associate most....... Homologs of most human glycosylation-associated genes are present in the CHO-K1 genome, although 141 of these homologs are not expressed under exponential growth conditions. Many important viral entry genes are also present in the genome but not expressed, which may explain the unusual viral resistance...... property of CHO cell lines. We discuss how the availability of this genome sequence may facilitate genome-scale science for the optimization of biopharmaceutical protein production....
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Towards A Regional Science Academy: A Manifesto
Directory of Open Access Journals (Sweden)
Karima Kourtit
2016-04-01
Full Text Available This Manifesto provides a joint proposal to create a Regional Science Academy as a think-tank support platform for a strategic development of the spatial sciences. The Regional Science Academy is a strategic spatial knowledge catalyst: it acts as a global intellectual powerhouse for new knowledge network initiatives and scholarly views on regions and cities as vital centrepieces of interconnected spatial systems. This contribution highlights its role and presents various activity plans.
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Joint Institute for Nanoscience Annual Report 2004
Energy Technology Data Exchange (ETDEWEB)
Baer, Donald R.; Campbell, Charles
2005-02-01
Due to the inherently interdisciplinary nature of nanoscience and nanotechnology, research in this arena is often significantly enhanced through creative cooperative activities. The Joint Institute for Nanoscience (JIN) is a venture of the University of Washington (UW) and Pacific Northwest National Laboratory (PNNL) to encourage and enhance high impact and high quality nanoscience and nanotechnology research that leverages the strengths and capabilities of both institutions, and to facilitate education in these areas. This report summarizes JIN award activities that took place during fiscal year 2004 and provides a historical list of JIN awardees, their resulting publications, and JIN-related meetings. Major portions of the JIN efforts and resources are dedicated to funding graduate students and postdoctoral research associates to perform research in collaborations jointly directed by PNNL staff scientists and UW professors. JIN fellowships are awarded on the basis of applications that include research proposals. They have been very successful in expanding collaborations between PNNL and UW, which have led to many excellent joint publications and presentations and enhanced the competitiveness of both institutions for external grant funding. JIN-based interactions are playing a significant role in creating new research directions and reshaping existing research programs at both the UW and PNNL. The JIN also co-sponsors workshops on Nanoscale Science and Technology, four of which have been held in Seattle and one in Richland. In addition to involving PNNL staff in various UW nanoscience courses and seminars, a National Science Foundation grant, Development of UW-PNL Collaborative Curriculums in Nano-Science and Technology, has allowed the development of three intensive short courses that are taught by UW faculty, PNNL staff, and faculty from other institutions, including Washington State University, the University of Idaho, Stanford University, and the University of
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Recent developments in life sciences research: Role of bioinformatics
African Journals Online (AJOL)
Life sciences research and development has opened up new challenges and opportunities for bioinformatics. The contribution of bioinformatics advances made possible the mapping of the entire human genome and genomes of many other organisms in just over a decade. These discoveries, along with current efforts to ...
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Shaw, Jennifer
2016-02-01
The Human Genome Archive Project (HGAP) aimed to preserve the documentary heritage of the UK's contribution to the Human Genome Project (HGP) by using archival theory to develop a suitable methodology for capturing the results of modern, collaborative science. After assessing past projects and different archival theories, the HGAP used an approach based on the theory of documentation strategy to try to capture the records of a scientific project that had an influence beyond the purely scientific sphere. The HGAP was an archival survey that ran for two years. It led to ninety scientists being contacted and has, so far, led to six collections being deposited in the Wellcome Library, with additional collections being deposited in other UK repositories. In applying documentation strategy the HGAP was attempting to move away from traditional archival approaches to science, which have generally focused on retired Nobel Prize winners. It has been partially successful in this aim, having managed to secure collections from people who are not 'big names', but who made an important contribution to the HGP. However, the attempt to redress the gender imbalance in scientific collections and to improve record-keeping in scientific organisations has continued to be difficult to achieve. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.
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Determination of Parachute Joint Factors using Seam and Joint Testing
Mollmann, Catherine
2015-01-01
This paper details the methodology for determining the joint factor for all parachute components. This method has been successfully implemented on the Capsule Parachute Assembly System (CPAS) for the NASA Orion crew module for use in determining the margin of safety for each component under peak loads. Also discussed are concepts behind the joint factor and what drives the loss of material strength at joints. The joint factor is defined as a "loss in joint strength...relative to the basic material strength" that occurs when "textiles are connected to each other or to metals." During the CPAS engineering development phase, a conservative joint factor of 0.80 was assumed for each parachute component. In order to refine this factor and eliminate excess conservatism, a seam and joint testing program was implemented as part of the structural validation. This method split each of the parachute structural joints into discrete tensile tests designed to duplicate the loading of each joint. Breaking strength data collected from destructive pull testing was then used to calculate the joint factor in the form of an efficiency. Joint efficiency is the percentage of the base material strength that remains after degradation due to sewing or interaction with other components; it is used interchangeably with joint factor in this paper. Parachute materials vary in type-mainly cord, tape, webbing, and cloth -which require different test fixtures and joint sample construction methods. This paper defines guidelines for designing and testing samples based on materials and test goals. Using the test methodology and analysis approach detailed in this paper, the minimum joint factor for each parachute component can be formulated. The joint factors can then be used to calculate the design factor and margin of safety for that component, a critical part of the design verification process.
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Smeraglia, Francesco; Mariconda, Massimo; Balato, Giovanni; Di Donato, Sigismondo Luca; Criscuolo, Giovanni; Maffulli, Nicola
2018-04-06
Trapeziometacarpal arthritis is a common and disabling condition. There is no evidence in the literature of superiority of one surgical procedure over others. Several prosthetic implants have been introduced to preserve joint mobility. We searched the on Medline (PubMed), Web of Science and Scopus databases using the combined keywords 'artelon', 'thumb', 'carpometacarpal', 'trapeziometacarpal' and 'rhizoarthrosis'; 11 studies were identified. The use of Artelon implant is not recommended because of its high revision rate and worse outcomes compared to conventional techniques. Inert materials subjected to compressive and shearing forces could produce debris and subsequent inflammatory response. There is debate in the published scientific literature regarding the role of preoperative antibiotic profilaxis and post-surgery inflammatory response. Standard techniques such as trapeziectomy alone or combined with interposition or suspensionplasty offer effective treatment for thumb basal joint arthritis. Several prosthetic implants show promising results in terms of pain relief and functional request, but there is a need of long-term randomized controlled trials to demonstrate their equivalence, and eventually superiority, compared to standard techniques.
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Human genes and genomes: science, health, society
National Research Council Canada - National Science Library
Rosenberg, Leon E; Rosenberg, Diane Drobnis
2012-01-01
.... With the use of core concepts and the integration of extensive references, this book provides students and professionals alike with the most in-depth view of the current state of the science and its relevance across disciplines."--Publisher's website.
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Mitropoulos, Konstantinos; Cooper, David N; Mitropoulou, Christina; Agathos, Spiros; Reichardt, Jürgen K V; Al-Maskari, Fatima; Chantratita, Wasun; Wonkam, Ambroise; Dandara, Collet; Katsila, Theodora; Lopez-Correa, Catalina; Ali, Bassam R; Patrinos, George P
2017-11-01
Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized. This begs a timely, difficult but crucial question: How should developing countries, and the resource-limited regions of developed countries, invest in genomic medicine? Although a full-scale investment in infrastructure from discovery to the translational implementation of genomic science is ideal, this may not always be feasible in all countries at all times. A simple "transplantation of genomics" from developed to developing countries is unlikely to be feasible. Nor should developing countries be seen as simple recipients and beneficiaries of genomic medicine developed elsewhere because important advances in genomic medicine have materialized in developing countries as well. There are several noteworthy examples of genomic medicine success stories involving resource-limited settings that are contextualized and described in this global genomic medicine innovation analysis. In addition, we outline here a new long-term development strategy for global genomic medicine in a way that recognizes the individual country's pressing public health priorities and disease burdens. We term this approach the "Fast-Second Winner" model of innovation that supports innovation commencing not only "upstream" of discovery science but also "mid-stream," building on emerging highly promising biomarker and diagnostic candidates from the global science discovery pipeline, based on the unique needs of each country. A mid-stream entry into innovation can enhance collective
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CRISPR-Cas9; an efficient tool for precise plant genome editing.
Islam, Waqar
2018-04-03
Efficient plant genome editing is dependent upon induction of double stranded DNA breaks (DSBs) through site specified nucleases. These DSBs initiate the process of DNA repair which can either base upon homologous recombination (HR) or non-homologous end jointing (NHEJ). Recently, CRISPR-Cas9 mechanism got highlighted as revolutionizing genetic tool due to its simpler frame work along with the broad range of adaptability and applications. So, in this review, I have tried to sum up the application of this biotechnological tool in plant genome editing. Furthermore, I have tried to explain successful adaptation of CRISPR in various plant species where it is used for the successful generation of stable mutations in a steadily growing number of species through NHEJ. The review also sheds light upon other biotechnological approaches relying upon single DNA lesion induction such as genomic deletion or pair wise nickases for evasion of offsite effects. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Energy Technology Data Exchange (ETDEWEB)
Tringe, Susannah
2011-10-12
Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.
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Origins of the Human Genome Project
Cook-Deegan, Robert (Affiliation: Institute of Medicine, National Academy of Sciences)
1993-07-01
The human genome project was borne of technology, grew into a science bureaucracy in the United States and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.
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Origins of the Human Genome Project
Energy Technology Data Exchange (ETDEWEB)
Cook-Deegan, Robert
1993-07-01
The human genome project was borne of technology, grew into a science bureaucracy in the US and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.
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Temporomandibular joint space in children without joint disease
International Nuclear Information System (INIS)
Larheim, T.A.
1981-01-01
Bilateral assessment of the temporomandibular joint space in children without joint disease is reported. Twenty-eight children were examined with conventional radiography and 23 with tomography. High prevalence of asymmetric joint spaces with both techniques indicated that great care should be taken when using narrowing or widening of the joint space as a diagnostic criterion in children with juvenile rheumatoid arthritis. Other signs, such as restricted translation of the mandibular head, and clinical symptoms should be evaluated. (Auth.)
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H3Africa and the African life sciences ecosystem: building sustainable innovation.
Dandara, Collet; Huzair, Farah; Borda-Rodriguez, Alexander; Chirikure, Shadreck; Okpechi, Ikechi; Warnich, Louise; Masimirembwa, Collen
2014-12-01
Interest in genomics research in African populations is experiencing exponential growth. This enthusiasm stems in part from the recognition that the genomic diversity of African populations is a window of opportunity for innovations in postgenomics medicine, ecology, and evolutionary biology. The recently launched H3Africa initiative, for example, captures the energy and momentum of this interest. This interdisciplinary socio-technical analysis highlights the challenges that have beset previous genomics research activities in Africa, and looking ahead, suggests constructive ways H3Africa and similar large scale science efforts could usefully chart a new era of genomics and life sciences research in Africa that is locally productive and globally competitive. As independent African scholars and social scientists, we propose that any serious global omics science effort, including H3Africa, aiming to build genomics research capacity and capability in Africa, needs to fund the establishment of biobanks and the genomic analyses platforms within Africa. Equally they need to prioritize community engagement and bioinformatics capability and the training of African scientists on these platforms. Historically, the financial, technological, and skills imbalance between Africa and developed countries has created exploitative frameworks of collaboration where African researchers have become merely facilitators of Western funded and conceived research agendas involving offshore expatriation of samples. Not surprisingly, very little funding was allocated to infrastructure and human capital development in the past. Moving forward, capacity building should materialize throughout the entire knowledge co-production trajectory: idea generation (e.g., brainstorming workshops for innovative hypotheses development by African scientists), data generation (e.g., genome sequencing), and high-throughput data analysis and contextualization. Additionally, building skills for political science
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transPLANT Resources for Triticeae Genomic Data
Directory of Open Access Journals (Sweden)
Manuel Spannagl
2016-03-01
Full Text Available The genome sequences of many important Triticeae species, including bread wheat ( L. and barley ( L., remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT ( is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.
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International Nuclear Information System (INIS)
DAVENPORT, J.
2006-01-01
Computational Science is an integral component of Brookhaven's multi science mission, and is a reflection of the increased role of computation across all of science. Brookhaven currently has major efforts in data storage and analysis for the Relativistic Heavy Ion Collider (RHIC) and the ATLAS detector at CERN, and in quantum chromodynamics. The Laboratory is host for the QCDOC machines (quantum chromodynamics on a chip), 10 teraflop/s computers which boast 12,288 processors each. There are two here, one for the Riken/BNL Research Center and the other supported by DOE for the US Lattice Gauge Community and other scientific users. A 100 teraflop/s supercomputer will be installed at Brookhaven in the coming year, managed jointly by Brookhaven and Stony Brook, and funded by a grant from New York State. This machine will be used for computational science across Brookhaven's entire research program, and also by researchers at Stony Brook and across New York State. With Stony Brook, Brookhaven has formed the New York Center for Computational Science (NYCCS) as a focal point for interdisciplinary computational science, which is closely linked to Brookhaven's Computational Science Center (CSC). The CSC has established a strong program in computational science, with an emphasis on nanoscale electronic structure and molecular dynamics, accelerator design, computational fluid dynamics, medical imaging, parallel computing and numerical algorithms. We have been an active participant in DOES SciDAC program (Scientific Discovery through Advanced Computing). We are also planning a major expansion in computational biology in keeping with Laboratory initiatives. Additional laboratory initiatives with a dependence on a high level of computation include the development of hydrodynamics models for the interpretation of RHIC data, computational models for the atmospheric transport of aerosols, and models for combustion and for energy utilization. The CSC was formed to bring together
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The Power and Potential of Genomics in Weed Biology and Management.
Ravet, Karl; Patterson, Eric L; Krähmer, Hansjörg; Hamouzová, Kateřina; Fan, Longjiang; Jasieniuk, Marie; Lawton-Rauh, Amy; Malone, Jenna M; Scott McElroy, J; Merotto, Aldo; Westra, Philip; Preston, Christopher; Vila-Aiub, Martin M; Busi, Roberto; Tranel, Patrick J; Reinhardt, Carl; Saski, Christopher; Beffa, Roland; Neve, Paul; Gaines, Todd A
2018-04-24
There have been previous calls for, and efforts focused on, realizing the power and potential of weed genomics for better understanding of weeds. Sustained advances in genome sequencing and assembly technologies now make it possible for individual research groups to generate reference genomes for multiple weed species at reasonable costs. Here, we present the outcomes from several meetings, discussions, and workshops focused on establishing an International Weed Genomics Consortium (IWGC) for a coordinated international effort in weed genomics. We review the 'state of the art' in genomics and weed genomics, including technologies, applications, and on-going weed genome projects. We also report the outcomes from a workshop and a global survey of the weed science community to identify priority species, key biological questions, and weed management applications that can be addressed through greater availability of, and access to, genomic resources. Major focus areas include the evolution of herbicide resistance and weedy traits, the development of molecular diagnostics, and the identification of novel targets and approaches for weed management. There is increasing interest in, and need for, weed genomics, and the establishment of the IWGC will provide the necessary global platform for communication and coordination of weed genomics research. This article is protected by copyright. All rights reserved.
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What stories can the Frankia genomes start to tell us?
Indian Academy of Sciences (India)
2013-10-01
Oct 1, 2013 ... 1Department of Molecular, Cellular, and Biomedical Sciences, ... of the first three complete genome sequences, which suggested a correlation between ..... 2008 The implication of life style on codon usage patterns and.
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Private and Efficient Query Processing on Outsourced Genomic Databases.
Ghasemi, Reza; Al Aziz, Md Momin; Mohammed, Noman; Dehkordi, Massoud Hadian; Jiang, Xiaoqian
2017-09-01
Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a time consuming and expensive process. Second, it requires large-scale computation and storage systems to process genomic sequences. Third, genomic databases are often owned by different organizations, and thus, not available for public usage. Cloud computing paradigm can be leveraged to facilitate the creation and sharing of big genomic databases for these applications. Genomic data owners can outsource their databases in a centralized cloud server to ease the access of their databases. However, data owners are reluctant to adopt this model, as it requires outsourcing the data to an untrusted cloud service provider that may cause data breaches. In this paper, we propose a privacy-preserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases. Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently. Experimental results demonstrate that a count and a top-k query over 40 Single Nucleotide Polymorphisms (SNPs) in a database of 20 000 records takes around 100 and 150 s, respectively.
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Desai, Aarti; Marwah, Veer Singh; Yadav, Akshay; Jha, Vineet; Dhaygude, Kishor; Bangar, Ujwala; Kulkarni, Vivek; Jere, Abhay
2013-01-01
Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.
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CoGI: Towards Compressing Genomes as an Image.
Xie, Xiaojing; Zhou, Shuigeng; Guan, Jihong
2015-01-01
Genomic science is now facing an explosive increase of data thanks to the fast development of sequencing technology. This situation poses serious challenges to genomic data storage and transferring. It is desirable to compress data to reduce storage and transferring cost, and thus to boost data distribution and utilization efficiency. Up to now, a number of algorithms / tools have been developed for compressing genomic sequences. Unlike the existing algorithms, most of which treat genomes as one-dimensional text strings and compress them based on dictionaries or probability models, this paper proposes a novel approach called CoGI (the abbreviation of Compressing Genomes as an Image) for genome compression, which transforms the genomic sequences to a two-dimensional binary image (or bitmap), then applies a rectangular partition coding algorithm to compress the binary image. CoGI can be used as either a reference-based compressor or a reference-free compressor. For the former, we develop two entropy-based algorithms to select a proper reference genome. Performance evaluation is conducted on various genomes. Experimental results show that the reference-based CoGI significantly outperforms two state-of-the-art reference-based genome compressors GReEn and RLZ-opt in both compression ratio and compression efficiency. It also achieves comparable compression ratio but two orders of magnitude higher compression efficiency in comparison with XM--one state-of-the-art reference-free genome compressor. Furthermore, our approach performs much better than Gzip--a general-purpose and widely-used compressor, in both compression speed and compression ratio. So, CoGI can serve as an effective and practical genome compressor. The source code and other related documents of CoGI are available at: http://admis.fudan.edu.cn/projects/cogi.htm.
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Reconsidering democracy - History of the human genome project
Huijer, M
What options are open for people-citizens, politicians, and other nonscientists-to become actively involved in and anticipate new directions in the life sciences? In addressing this question, this article focuses on the start of the Human Genome Project (1985-1990). By contrasting various models of
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Bioinformatics: future of life sciences
International Nuclear Information System (INIS)
Arif, R.; Ghafoor, M.; Saleem, M.; Baig, S.J.; Hassan, S.W.
2004-01-01
The vital part of our life or the basic unit of life is the cell. The cellular biomolecules function in a conjugate manner and this system provide us with the necessary elements of life, and the sciences that deals with nature function of the cell and it's molecular components are defined as life sciences. Vital subjects involved in maintaining the identity and functioning of cells are genomics and proteomics. (author)
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DEFF Research Database (Denmark)
Athanasiadis, Georgios; Jorgensen, Frank G.; Cheng, Jade Y.
2016-01-01
Scientific outreach delivers science to the people. But it can also deliver people to the science. In this work, we report our experience from a large-scale public engagement project promoting genomic literacy among Danish high school students with the additional benefit of collecting data...... for studying the genetic makeup of the Danish population. Not only did we confirm that students have a great interest in their genetic past, but we were also gratified to see that, with the right motivation, adolescents can provide high-quality data for genetic studies....
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International Nuclear Information System (INIS)
Feinendegen, L.E.
1997-01-01
The US Department of Energy (DOE) and the National Institutes of Health (NIH) conducted a workshop on Isotope-Based Medical Research in the Post Genome Era at NIH, Bethesda, Maryland, November 12--14, 1997. The workshop aimed at identifying the role of stable and radioisotopes for advanced diagnosis and therapy of a wide range of illnesses using the new information that comes from the human genome program. In this sense, the agenda addressed the challenge of functional genomics in humans. The workshop addressed: functional genomics in clinical medicine; new diagnostic potentials; new therapy potentials; challenge to tracer- and effector-pharmaceutical chemistry; and project plans for joint ventures
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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.
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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
Ellrott, Kyle; Bailey, Matthew H.; Saksena, Gordon; Covington, Kyle R.; Kandoth, Cyriac; Stewart, Chip; Hess, Julian; Ma, Singer; Chiotti, Kami E.; McLellan, Michael; Sofia, Heidi J.; Hutter, Carolyn M.; Getz, Gad; Wheeler, David A.; Ding, Li; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David A.; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Angulo Gonzalez, Ana Maria; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, Jonathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Mora Pinero, Edna M.; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz
2018-01-01
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a
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Analysis of radiation-induced genome alterations in Vigna unguiculata
Directory of Open Access Journals (Sweden)
van der Vyver C
2011-09-01
Full Text Available Christell van der Vyver1, B Juan Vorster2, Karl J Kunert3, Christopher A Cullis41Institute for Plant Biotechnology, Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa; 2Department of Plant Production and Soil Science, and 3Department of Plant Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa; 4Case Western Reserve University, Department of Biology, Cleveland, OH, USAAbstract: Seeds from an inbred Vigna unguiculata (cowpea cultivar were gamma-irradiated with a dose of 180 Gy in order to identify and characterize possible mutations. Three techniques, ie, random amplified polymorphic DNA, microsatellites, and representational difference analysis, were used to characterize possible DNA variation among the mutants and nonirradiated control plants both immediately after irradiation and in subsequent generations. A large portion of putative radiation-induced genome changes had significant similarities to chloroplast sequences. The frequency of mutation at three of these isolated polymorphic regions with chloroplast similarity was further determined by polymerase chain reaction screening using a large number of individual parental, M1, and M2 plants. Analysis of these sequences indicated that the rate at which various regions of the genome is mutated in irradiation experiments differs significantly and also that mutations have variable “repair” rates. Furthermore, regions of the nuclear DNA derived from the chloroplast genome are highly susceptible to modification by radiation treatment. Overall, data have provided detailed information on the effects of gamma irradiation on the cowpea genome and about the ability of the plant to repair these genome changes in subsequent plant generations.Keywords: mutation breeding, gamma radiation, genetic mutations, cowpea, representational difference analysis
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Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.
Avni, Raz; Nave, Moran; Barad, Omer; Baruch, Kobi; Twardziok, Sven O; Gundlach, Heidrun; Hale, Iago; Mascher, Martin; Spannagl, Manuel; Wiebe, Krystalee; Jordan, Katherine W; Golan, Guy; Deek, Jasline; Ben-Zvi, Batsheva; Ben-Zvi, Gil; Himmelbach, Axel; MacLachlan, Ron P; Sharpe, Andrew G; Fritz, Allan; Ben-David, Roi; Budak, Hikmet; Fahima, Tzion; Korol, Abraham; Faris, Justin D; Hernandez, Alvaro; Mikel, Mark A; Levy, Avraham A; Steffenson, Brian; Maccaferri, Marco; Tuberosa, Roberto; Cattivelli, Luigi; Faccioli, Primetta; Ceriotti, Aldo; Kashkush, Khalil; Pourkheirandish, Mohammad; Komatsuda, Takao; Eilam, Tamar; Sela, Hanan; Sharon, Amir; Ohad, Nir; Chamovitz, Daniel A; Mayer, Klaus F X; Stein, Nils; Ronen, Gil; Peleg, Zvi; Pozniak, Curtis J; Akhunov, Eduard D; Distelfeld, Assaf
2017-07-07
Wheat ( Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer ( T. turgidum ssp. dicoccoides ). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 ( TtBtr1 ) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties. Copyright © 2017, American Association for the Advancement of Science.
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Science communication in European projects
International Nuclear Information System (INIS)
Vachev, Boyko; Stamenov, Jordan
2009-01-01
Science communication in several resent successful projects of Institute for Nuclear Research and Nuclear Energy, Bulgarian Academy of Sciences (INRNE, BAS) from the 5th and 6th Framework Programmes of EC is presented: the joint INRNE, BAS project with JRC of EC (FP5 NUSES) and two subsequent Centre of Excellence projects (FP5 HIMONTONET and FP6 BEOBAL) are considered. Innovations and traditional forms development and application are discussed. An overview of presentation and communication of INRNE, BAS contribution to Bulgarian European Project is made. Good practices have been derived. Keywords: Science communication, European projects, Innovations
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Genomic cloud computing: legal and ethical points to consider.
Dove, Edward S; Joly, Yann; Tassé, Anne-Marie; Knoppers, Bartha M
2015-10-01
The biggest challenge in twenty-first century data-intensive genomic science, is developing vast computer infrastructure and advanced software tools to perform comprehensive analyses of genomic data sets for biomedical research and clinical practice. Researchers are increasingly turning to cloud computing both as a solution to integrate data from genomics, systems biology and biomedical data mining and as an approach to analyze data to solve biomedical problems. Although cloud computing provides several benefits such as lower costs and greater efficiency, it also raises legal and ethical issues. In this article, we discuss three key 'points to consider' (data control; data security, confidentiality and transfer; and accountability) based on a preliminary review of several publicly available cloud service providers' Terms of Service. These 'points to consider' should be borne in mind by genomic research organizations when negotiating legal arrangements to store genomic data on a large commercial cloud service provider's servers. Diligent genomic cloud computing means leveraging security standards and evaluation processes as a means to protect data and entails many of the same good practices that researchers should always consider in securing their local infrastructure.
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Building Repository Networks with DRIVER: Joint Explorations with the IR Grid in China
Horstmann, Wolfram; Rosemann, Uwe
2009-01-01
Scenarios of collaboration for supporting Open Access to research results through institutional repository networks have been explored between the IR Grid of the National Science Library of the Chinese Academy of Sciences and the European DRIVER-Initiative through its German partners Bielefeld University Library as well as the State and University Library Göttingen. The activities included a joint analysis of the DRIVER infrastructure software D-NET and also resulted in the registration of ch...
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Joint Replacement (Finger and Wrist Joints)
... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is a Hand Surgeon? What is a Hand Therapist? Media Find a Hand Surgeon Home Anatomy Joint Replacement Email to a friend * required fields ...
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National Research Council Canada - National Science Library
2006-01-01
.... It sets forth joint doctrine to govern the joint operation planning activities and performance of the Armed Forces of the United States in joint operations, and provides the joint doctrinal basis...
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Jointness for the Rest of Us: Reforming Joint Professional Development
2016-06-10
transferred to the Joint Staff. 13 DOD’s instinct to “overly centralize planning, organization, and management.”20 The authors contend that this...2. 3 John F. Schank and others, Who is Joint? Reevaluating the Joint Duty Assignment List : A Study Prepared for the Joint Staff, by the RAND...and code those billets as such. Once identified, DOD must expand the Joint Duty Assignment List (JDAL) to include billets that offer enlisted personnel
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Reconsidering democracy. History of the Human Genome Project.
Marli Huijer
2003-01-01
What options are open for peoplecitizens, politicians, and other nonscientiststo become actively involved in and anticipate new directions in the life sciences? In addressing this question, this article focuses on the start of the Human Genome Project (1985-1990). By contrasting various models of
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Joint thesaurus Part I (A-L) + II (M-Z)
International Nuclear Information System (INIS)
2007-01-01
This is the second revision of the ETDE/INIS Joint Thesaurus, including all updates up to September 2006. It contains 21 147 valid descriptors and 9 114 forbidden terms. The Joint Thesaurus contains the controlled terminology for indexing all information within the subject scopes of the International Nuclear Information System (INIS) and the Energy Technology Data Exchange (ETDE). The terminology is intended for use in subject descriptions for input or retrieval of information in these systems. The thesaurus is a terminological control device used in translating from the natural language of documents, indexers or users into a more constrained system language It is also a controlled and dynamic vocabulary of semantically and generically related terms which covers a specific domain of knowledge. The basic terminology in this thesaurus goes back to the 1969 edition of the EURATOM Thesaurus. The structure subsequently given to that terminology was the result of a systematic study performed by INIS subject specialists. Further expansion of the thesaurus terminology was done by ETDE to incorporate information on all forms of energy. The ETDE/INIS Joint Thesaurus is the result of continued editing, carried out in parallel to the processing of the INIS and ETDE databases. The domain of knowledge covered by the Joint Thesaurus includes physics (in particular, plasma physics, atomic and molecular physics, and especially nuclear and high-energy physics), chemistry, materials science, earth sciences, radiation biology, radioisotope effects and kinetics, applied life sciences, radiology and nuclear medicine, isotope and radiation source technology, radiation protection, radiation applications, engineering, instrumentation, fossil fuels, synthetic fuels, renewable energy sources, advanced energy systems, fission and fusion reactor technology, safeguards and inspection, waste management, environmental aspects of the production and consumption of energy from nuclear and non
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A theoretical framework for understanding neuromuscular response to lower extremity joint injury.
Pietrosimone, Brian G; McLeod, Michelle M; Lepley, Adam S
2012-01-01
Neuromuscular alterations are common following lower extremity joint injury and often lead to decreased function and disability. These neuromuscular alterations manifest in inhibition or abnormal facilitation of the uninjured musculature surrounding an injured joint. Unfortunately, these neural alterations are poorly understood, which may affect clinical recognition and treatment of these injuries. Understanding how these neural alterations affect physical function may be important for proper clinical management of lower extremity joint injuries. Pertinent articles focusing on neuromuscular consequences and treatment of knee and ankle injuries were collected from peer-reviewed sources available on the Web of Science and Medline databases from 1975 through 2010. A theoretical model to illustrate potential relationships between neural alterations and clinical impairments was constructed from the current literature. Lower extremity joint injury affects upstream cortical and spinal reflexive excitability pathways as well as downstream muscle function and overall physical performance. Treatment targeting the central nervous system provides an alternate means of treating joint injury that may be effective for patients with neuromuscular alterations. Disability is common following joint injury. There is mounting evidence that alterations in the central nervous system may relate to clinical changes in biomechanics that may predispose patients to further injury, and novel clinical interventions that target neural alterations may improve therapeutic outcomes.
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KAIKObase: An integrated silkworm genome database and data mining tool
Directory of Open Access Journals (Sweden)
Nagaraju Javaregowda
2009-10-01
Full Text Available Abstract Background The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, B. mori has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for B. mori were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups. Description Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size among the sequenced insect genomes and provided a high degree of nucleotide coverage (88% of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from two-dimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a Bombyx trap database was constructed for documenting insertion positions and expression data of transposon insertion lines. Conclusion For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the
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Periprosthetic joint infection: are patients with multiple prosthetic joints at risk?
Jafari, S Mehdi; Casper, David S; Restrepo, Camilo; Zmistowski, Benjamin; Parvizi, Javad; Sharkey, Peter F
2012-06-01
Patients who present with a periprosthetic joint infection in a single joint may have multiple prosthetic joints. The risk of these patients developing a subsequent infection in another prosthetic joint is unknown. Our purposes were (1) to identify the risk of developing a subsequent infection in another prosthetic joint and (2) to describe the time span and organism profile to the second prosthetic infection. We retrospectively identified 55 patients with periprosthetic joint infection who had another prosthetic joint in place at the time of presentation. Of the 55 patients, 11 (20%) developed a periprosthetic joint infection in a second joint. The type of organism was the same as the first infection in 4 (36%) of 11 patients. The time to developing a second infection averaged 2.0 years (range, 0-6.9 years). Copyright © 2012 Elsevier Inc. All rights reserved.
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Kelly Ivors; Matteo Garbelotto; Ineke De Vries; Peter Bonants
2006-01-01
Investigating the population genetics of Phytophthora ramorum, the causal agent of sudden oak death (SOD), is critical to understanding the biology and epidemiology of this important phytopathogen. Raw sequence data (445,000 reads) of P. ramorum was provided by the Joint Genome Institute. Our objective was to develop and utilize...
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Data analysis in the post-genome-wide association study era
Directory of Open Access Journals (Sweden)
Qiao-Ling Wang
2016-12-01
Full Text Available Since the first report of a genome-wide association study (GWAS on human age-related macular degeneration, GWAS has successfully been used to discover genetic variants for a variety of complex human diseases and/or traits, and thousands of associated loci have been identified. However, the underlying mechanisms for these loci remain largely unknown. To make these GWAS findings more useful, it is necessary to perform in-depth data mining. The data analysis in the post-GWAS era will include the following aspects: fine-mapping of susceptibility regions to identify susceptibility genes for elucidating the biological mechanism of action; joint analysis of susceptibility genes in different diseases; integration of GWAS, transcriptome, and epigenetic data to analyze expression and methylation quantitative trait loci at the whole-genome level, and find single-nucleotide polymorphisms that influence gene expression and DNA methylation; genome-wide association analysis of disease-related DNA copy number variations. Applying these strategies and methods will serve to strengthen GWAS data to enhance the utility and significance of GWAS in improving understanding of the genetics of complex diseases or traits and translate these findings for clinical applications. Keywords: Genome-wide association study, Data mining, Integrative data analysis, Polymorphism, Copy number variation
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Rare and common regulatory variation in population-scale sequenced human genomes.
Directory of Open Access Journals (Sweden)
Stephen B Montgomery
2011-07-01
Full Text Available Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.
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An evaluation of the carrying angle of the elbow joint in adolescents
African Journals Online (AJOL)
McRoy
Department of Anatomy and Orthopedics, Sri Lakshmi Narayana Institute of Medical Sciences,. Pondicherry - 605 502 ... forearm deviates laterally from the long axis of the humerus, with the arm extended and the palm ... for elbow reconstruction. Key words: Carrying angle, elbow joint, adolescent, forearm, humerus, ulna ...
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Energy Technology Data Exchange (ETDEWEB)
Kim, Kun Sang; Park, Chan Il; Ahn, Jae Doo; Lim, Chong Won [Seoul National University College of Medicine, Seoul (Korea, Republic of)
1970-10-15
The coracoclvicular joint, a rear abnormality which may be the cause of pain in the shoulder and limitation of motion of the shoulder joint, is discussed. A case of coracoclvicular joint with shoulder pain was observed in 65 yrs old Korean male.
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Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
Directory of Open Access Journals (Sweden)
Grigoriev Igor V
2009-02-01
Full Text Available Abstract Background Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR. Results 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6% of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. Conclusion This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.
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Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger.
Wright, James C; Sugden, Deana; Francis-McIntyre, Sue; Riba-Garcia, Isabel; Gaskell, Simon J; Grigoriev, Igor V; Baker, Scott E; Beynon, Robert J; Hubbard, Simon J
2009-02-04
Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR). 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.
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Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A.
Kelly, Simon; Sullivan, John; Ronson, Clive; Tian, Rui; Bräu, Lambert; Munk, Christine; Goodwin, Lynne; Han, Cliff; Woyke, Tanja; Reddy, Tatiparthi; Huntemann, Marcel; Pati, Amrita; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne
2014-01-01
Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a Lotus corniculatus root nodule and is a reisolate of the inoculant strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative, non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or ICEMlSym(R7A). M. loti is the microsymbiont of the model legume Lotus japonicus and strain R7A has been used extensively in studies of the plant-microbe interaction. This report reveals that the genome of M. loti strain R7A does not harbor any plasmids and contains a single scaffold of size 6,529,530 bp which encodes 6,323 protein-coding genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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Lu, Qiongshi; Hu, Yiming; Sun, Jiehuan; Cheng, Yuwei; Cheung, Kei-Hoi; Zhao, Hongyu
2015-05-27
Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu.
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Somatic DNA recombination yielding circular DNA and deletion of a genomic region in embryonic brain
International Nuclear Information System (INIS)
Maeda, Toyoki; Chijiiwa, Yoshiharu; Tsuji, Hideo; Sakoda, Saburo; Tani, Kenzaburo; Suzuki, Tomokazu
2004-01-01
In this study, a mouse genomic region is identified that undergoes DNA rearrangement and yields circular DNA in brain during embryogenesis. External region-directed inverse polymerase chain reaction on circular DNA extracted from late embryonic brain tissue repeatedly detected DNA of this region containing recombination joints. Wide-range genomic PCR and digestion-circularization PCR analysis showed this region underwent recombination accompanied with deletion of intervening sequences, including the circularized regions. This region was mapped by fluorescence in situ hybridization to C1 on mouse chromosome 16, where no gene and no physiological DNA rearrangement had been identified. DNA sequence in the region has segmental homology to an orthologous region on human chromosome 3q.13. These observations demonstrated somatic DNA recombination yielding genomic deletions in brain during embryogenesis
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International Nuclear Information System (INIS)
Westesson, P.L.; Hatala, M.; Tallents, R.H.; Katzberg, R.W.; Musgrave, M.; Levitt, S.
1990-01-01
This paper determines the frequency of MR signs of abnormal temporomandibular joints (TMJs) in asymptomatic volunteers. Forty-two volunteers with 84 clinically normal TMJs were imaged in the sagittal and coronal planes with surface coil MR imaging. Sagittal closed and open and coronal closed views were obtained bilaterally in all volunteers. The images were classified as normal (superior disk position) or abnormal (disk displacement of degenerative joint disease). Eighteen joints in 11 volunteers were abnormal; 12 had disk displacement with reduction and six had disk displacement without reduction, with associated degenerative joint disease in three of the six. Asymptomatic internal derangement and degenerative joint disease occur in about one-fourth of asymptomatic volunteers
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The OME Framework for genome-scale systems biology
Energy Technology Data Exchange (ETDEWEB)
Palsson, Bernhard O. [Univ. of California, San Diego, CA (United States); Ebrahim, Ali [Univ. of California, San Diego, CA (United States); Federowicz, Steve [Univ. of California, San Diego, CA (United States)
2014-12-19
The life sciences are undergoing continuous and accelerating integration with computational and engineering sciences. The biology that many in the field have been trained on may be hardly recognizable in ten to twenty years. One of the major drivers for this transformation is the blistering pace of advancements in DNA sequencing and synthesis. These advances have resulted in unprecedented amounts of new data, information, and knowledge. Many software tools have been developed to deal with aspects of this transformation and each is sorely needed [1-3]. However, few of these tools have been forced to deal with the full complexity of genome-scale models along with high throughput genome- scale data. This particular situation represents a unique challenge, as it is simultaneously necessary to deal with the vast breadth of genome-scale models and the dizzying depth of high-throughput datasets. It has been observed time and again that as the pace of data generation continues to accelerate, the pace of analysis significantly lags behind [4]. It is also evident that, given the plethora of databases and software efforts [5-12], it is still a significant challenge to work with genome-scale metabolic models, let alone next-generation whole cell models [13-15]. We work at the forefront of model creation and systems scale data generation [16-18]. The OME Framework was borne out of a practical need to enable genome-scale modeling and data analysis under a unified framework to drive the next generation of genome-scale biological models. Here we present the OME Framework. It exists as a set of Python classes. However, we want to emphasize the importance of the underlying design as an addition to the discussions on specifications of a digital cell. A great deal of work and valuable progress has been made by a number of communities [13, 19-24] towards interchange formats and implementations designed to achieve similar goals. While many software tools exist for handling genome
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Genome-wide association study identifies five new schizophrenia loci.
LENUS (Irish Health Repository)
Ripke, Stephan
2011-10-01
We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 × 10(-11)) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 × 10(-9)), ANK3 (rs10994359, P = 2.5 × 10(-8)) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 × 10(-9)).
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Technical note: Rapid calculation of genomic evaluations for new animals.
Wiggans, G R; VanRaden, P M; Cooper, T A
2015-03-01
A method was developed to calculate preliminary genomic evaluations daily or weekly before the release of official monthly evaluations by processing only newly genotyped animals using estimates of single nucleotide polymorphism effects from the previous official evaluation. To minimize computing time, reliabilities and genomic inbreeding are not calculated, and fixed weights are used to combine genomic and traditional information. Correlations of preliminary and September official monthly evaluations for animals with genotypes that became usable after the extraction of genotypes for August 2014 evaluations were >0.99 for most Holstein traits. Correlations were lower for breeds with smaller population size. Earlier access to genomic evaluations benefits producers by enabling earlier culling decisions and genotyping laboratories by making workloads more uniform across the month. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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Canine urothelial carcinoma: genomically aberrant and comparatively relevant.
Shapiro, S G; Raghunath, S; Williams, C; Motsinger-Reif, A A; Cullen, J M; Liu, T; Albertson, D; Ruvolo, M; Bergstrom Lucas, A; Jin, J; Knapp, D W; Schiffman, J D; Breen, M
2015-06-01
Urothelial carcinoma (UC), also referred to as transitional cell carcinoma (TCC), is the most common bladder malignancy in both human and canine populations. In human UC, numerous studies have demonstrated the prevalence of chromosomal imbalances. Although the histopathology of the disease is similar in both species, studies evaluating the genomic profile of canine UC are lacking, limiting the discovery of key comparative molecular markers associated with driving UC pathogenesis. In the present study, we evaluated 31 primary canine UC biopsies by oligonucleotide array comparative genomic hybridization (oaCGH). Results highlighted the presence of three highly recurrent numerical aberrations: gain of dog chromosome (CFA) 13 and 36 and loss of CFA 19. Regional gains of CFA 13 and 36 were present in 97 % and 84 % of cases, respectively, and losses on CFA 19 were present in 77 % of cases. Fluorescence in situ hybridization (FISH), using targeted bacterial artificial chromosome (BAC) clones and custom Agilent SureFISH probes, was performed to detect and quantify these regions in paraffin-embedded biopsy sections and urine-derived urothelial cells. The data indicate that these three aberrations are potentially diagnostic of UC. Comparison of our canine oaCGH data with that of 285 human cases identified a series of shared copy number aberrations. Using an informatics approach to interrogate the frequency of copy number aberrations across both species, we identified those that had the highest joint probability of association with UC. The most significant joint region contained the gene PABPC1, which should be considered further for its role in UC progression. In addition, cross-species filtering of genome-wide copy number data highlighted several genes as high-profile candidates for further analysis, including CDKN2A, S100A8/9, and LRP1B. We propose that these common aberrations are indicative of an evolutionarily conserved mechanism of pathogenesis and harbor genes
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Journal of Earth System Science
Indian Academy of Sciences (India)
YouTube; Twitter; Facebook; Blog. Academy News. IAS Logo. Theory Of Evolution. Posted on 23 January 2018. Joint Statement by the Three Science Academies of India on the teaching of the theory of evolution more... ACADEMY PUBLIC LECTURE: Animal Sex Determination by Genes, Chromosomes and Environment.
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Baumler, David J.; Banta, Lois M.; Hung, Kai F.; Schwarz, Jodi A.; Cabot, Eric L.; Glasner, Jeremy D.; Perna, Nicole T.
2012-01-01
Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples…
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DEFF Research Database (Denmark)
Bertelsen, Rasmus Gjedssø; Du, Xiangyun; Søndergaard, Morten Karnøe
2016-01-01
Genetics is observed as a particularly active field of Sino-Danish science collaboration, brain circulation and funding. Explaining the level of activity of this scientific field is therefore valuable for understanding the conditions allowing such activity. This paper identifies Danish scientific...... excellence as a necessary, but insufficient, condition. This condition becomes sufficient together with another necessary, but insufficient, condition, which is Sino-Danish transnational science guanxi, or networks and acquaintanceship. This guanxi is based on the previous graduate studies of Chinese...... in Denmark, or brain circulation. The paper finds that brain circulation in the form of graduate students can have revolutionary long-term effects on Sino-Danish science collaboration and investments, exemplified in the location of Beijing Genomics Institute Europe in Copenhagen....
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Joint resistance measurements of pancake and terminal joints for JT-60SA EF coils
Energy Technology Data Exchange (ETDEWEB)
Obana, Tetsuhiro, E-mail: obana.tetsuhiro@LHD.nifs.ac.jp [National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292 (Japan); Takahata, Kazuya; Hamaguchi, Shinji; Mito, Toshiyuki; Imagawa, Shinsaku [National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292 (Japan); Kizu, Kaname; Murakami, Haruyuki; Yoshida, Kiyoshi [Japan Atomic Energy Agency, 801-1 Mukoyama, Naka, Ibaraki 311-0193 (Japan)
2013-11-15
Highlights: • To evaluate the joint fabrication technology for the JT-60SA EF coils, joint resistance measurements were conducted with a joint sample. • The joint sample was composed of pancake and terminal joints. • The measurements demonstrated that both joints fulfilled the design requirement. • Considering the measurements, the characteristics of both joints were investigated using an analytical model that represents the joints. -- Abstract: To evaluate the joint fabrication technology for the JT-60SA EF coils, joint resistance measurements were conducted using a sample consisting of pancake and terminal joints. Both joints are shake-hands lap joints composed of cable-in-conduit conductors and a pure copper saddle-shaped spacer. The measurements demonstrated that both joints fulfilled the design requirement. Considering these measurements, the characteristics of both joints were investigated using analytical models that represent the joints. The analyses indicated that the characteristics of the conductors used in the joints affect the characteristics of the joints.
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Genome resource banking of biomedically important laboratory animals.
Agca, Yuksel
2012-11-01
Genome resource banking is the systematic collection, storage, and redistribution of biomaterials in an organized, logistical, and secure manner. Genome cryobanks usually contain biomaterials and associated genomic information essential for progression of biomedicine, human health, and research. In that regard, appropriate genome cryobanks could provide essential biomaterials for both current and future research projects in the form of various cell types and tissues, including sperm, oocytes, embryos, embryonic or adult stem cells, induced pluripotent stem cells, and gonadal tissues. In addition to cryobanked germplasm, cryobanking of DNA, serum, blood products, and tissues from scientifically, economically, and ecologically important species has become a common practice. For revitalization of the whole organism, cryopreserved germplasm in conjunction with assisted reproductive technologies, offer a powerful approach for research model management, as well as assisting in animal production for agriculture, conservation, and human reproductive medicine. Recently, many developed and developing countries have allocated substantial resources to establish genome resources banks which are responsible for safeguarding scientifically, economically, and ecologically important wild type, mutant, and transgenic plants, fish, and local livestock breeds, as well as wildlife species. This review is dedicated to the memory of Dr. John K. Critser, who has made profound contributions to the science of cryobiology and establishment of genome research and resources centers for mice, rats, and swine. Emphasis will be given to application of genome resource banks to species with substantial contributions to the advancement of biomedicine and human health. Copyright © 2012 Elsevier Inc. All rights reserved.
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Joint Identification of Genetic Variants for Physical Activity in Korean Population
Directory of Open Access Journals (Sweden)
Jayoun Kim
2014-07-01
Full Text Available There has been limited research on genome-wide association with physical activity (PA. This study ascertained genetic associations between PA and 344,893 single nucleotide polymorphism (SNP markers in 8842 Korean samples. PA data were obtained from a validated questionnaire that included information on PA intensity and duration. Metabolic equivalent of tasks were calculated to estimate the total daily PA level for each individual. In addition to single- and multiple-SNP association tests, a pathway enrichment analysis was performed to identify the biological significance of SNP markers. Although no significant SNP was found at genome-wide significance level via single-SNP association tests, 59 genetic variants mapped to 76 genes were identified via a multiple SNP approach using a bootstrap selection stability measure. Pathway analysis for these 59 variants showed that maturity onset diabetes of the young (MODY was enriched. Joint identification of SNPs could enable the identification of multiple SNPs with good predictive power for PA and a pathway enriched for PA.
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Joint instability and osteoarthritis.
Blalock, Darryl; Miller, Andrew; Tilley, Michael; Wang, Jinxi
2015-01-01
Joint instability creates a clinical and economic burden in the health care system. Injuries and disorders that directly damage the joint structure or lead to joint instability are highly associated with osteoarthritis (OA). Thus, understanding the physiology of joint stability and the mechanisms of joint instability-induced OA is of clinical significance. The first section of this review discusses the structure and function of major joint tissues, including periarticular muscles, which play a significant role in joint stability. Because the knee, ankle, and shoulder joints demonstrate a high incidence of ligament injury and joint instability, the second section summarizes the mechanisms of ligament injury-associated joint instability of these joints. The final section highlights the recent advances in the understanding of the mechanical and biological mechanisms of joint instability-induced OA. These advances may lead to new opportunities for clinical intervention in the prevention and early treatment of OA.
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A digital beamforming processor for the joint DoD/NASA space based radar mission
Fischman, Mark A.; Le, Charles; Rosen, Paul A.
2004-01-01
The Space Based Radar (SBR) program includes a joint technology demonstration between NASA and the Air Force to design a low-earth orbiting, 2x50 m L-band radar system for both Earth science and intelligence related observations.
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Complete genome sequence of Tolumonas auensis type strain (TA 4T)
Energy Technology Data Exchange (ETDEWEB)
Chertkov, Olga; Copeland, Alex; Lucas1, Susa; Lapidus, Alla; Berry, KerrieW.; Detter, JohnC.; Glavina Del Rio, Tijana; Hammon, Nancy; Dalin, Eileen; Tice, Hope; Pitluck, Sam; Richardson, Paul; Bruce, David; Goodwin, Lynne; Han, Cliff; Tapia, Roxanne; Saunders, Elizabeth; Schmutz, Jeremy; Brettin, Thomas; Larimer, Frank; Land, Miriam; Hauser, Loren; Spring, Stefan; Rohde, Manfred; Kyrpides, NikosC.; Ivanova, Natalia; G& #246; ker, Markus; Beller, HarryR.; Klenk, Hans-Peter; Woyke, Tanja
2011-10-04
Tolumonas auensis (Fischer-Romero et al. 1996) is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292-bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.
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Complete genome sequence of Tolumonas auensis type strain (TA 4T)
Energy Technology Data Exchange (ETDEWEB)
Chertkov, Olga [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Berry, Alison M [California Institute of Technology, University of California, Davis; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Beller, Harry R. [Lawrence Berkeley National Laboratory (LBNL); Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute
2011-01-01
Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Oth- er than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.
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LENUS (Irish Health Repository)
Jia, Peilin
2012-02-01
After the recent successes of genome-wide association studies (GWAS), one key challenge is to identify genetic variants that might have a significant joint effect on complex diseases but have failed to be identified individually due to weak to moderate marginal effect. One popular and effective approach is gene set based analysis, which investigates the joint effect of multiple functionally related genes (eg, pathways). However, a typical gene set analysis method is biased towards long genes, a problem that is especially severe in psychiatric diseases.
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Fellowship | Indian Academy of Sciences
Indian Academy of Sciences (India)
Elected: 2010 Section: Plant Sciences. Khurana, Prof. Paramjit Ph.D. (Delhi), FNASc, FNA, FNAAS, FTWAS. Date of birth: 15 August 1956. Specialization: Plant Biotechnology, Plant Genomics, Plant Developmental Biology Address: Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez ...
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Highlights of recent articles on data mining in genomics & proteomics
This editorial elaborates on investigations consisting of different “OMICS” technologies and their application to biological sciences. In addition, advantages and recent development of the proteomic, genomic and data mining technologies are discussed. This information will be useful to scientists ...
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Joint Instability and Osteoarthritis
Directory of Open Access Journals (Sweden)
Darryl Blalock
2015-01-01
Full Text Available Joint instability creates a clinical and economic burden in the health care system. Injuries and disorders that directly damage the joint structure or lead to joint instability are highly associated with osteoarthritis (OA. Thus, understanding the physiology of joint stability and the mechanisms of joint instability-induced OA is of clinical significance. The first section of this review discusses the structure and function of major joint tissues, including periarticular muscles, which play a significant role in joint stability. Because the knee, ankle, and shoulder joints demonstrate a high incidence of ligament injury and joint instability, the second section summarizes the mechanisms of ligament injury-associated joint instability of these joints. The final section highlights the recent advances in the understanding of the mechanical and biological mechanisms of joint instability-induced OA. These advances may lead to new opportunities for clinical intervention in the prevention and early treatment of OA.
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DEFF Research Database (Denmark)
Sørensen, Karsten Engsig
2001-01-01
The article analysis problems connected with corporate joint ventures. Among others the possible conflicts between the joint venture agreement and the statutes of the companies is examined, as well as certain problems connected to the fact that the joint venture partners have created commen control...... over their joint company....
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Rapid and accurate pyrosequencing of angiosperm plastid genomes
Moore, Michael J; Dhingra, Amit; Soltis, Pamela S; Shaw, Regina; Farmerie, William G; Folta, Kevin M; Soltis, Douglas E
2006-01-01
Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20) System (454 Life Sciences Corporation), to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae) and Platanus occidentalis (Platanaceae). Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy observed in the GS 20 plastid
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Rapid and accurate pyrosequencing of angiosperm plastid genomes
Directory of Open Access Journals (Sweden)
Farmerie William G
2006-08-01
Full Text Available Abstract Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic increase in the number of completely sequenced plastid genomes, fuelled largely by advances in conventional Sanger sequencing technology. Here we report a further significant reduction in time and cost for plastid genome sequencing through the successful use of a newly available pyrosequencing platform, the Genome Sequencer 20 (GS 20 System (454 Life Sciences Corporation, to rapidly and accurately sequence the whole plastid genomes of the basal eudicot angiosperms Nandina domestica (Berberidaceae and Platanus occidentalis (Platanaceae. Results More than 99.75% of each plastid genome was simultaneously obtained during two GS 20 sequence runs, to an average depth of coverage of 24.6× in Nandina and 17.3× in Platanus. The Nandina and Platanus plastid genomes shared essentially identical gene complements and possessed the typical angiosperm plastid structure and gene arrangement. To assess the accuracy of the GS 20 sequence, over 45 kilobases of sequence were generated for each genome using conventional sequencing. Overall error rates of 0.043% and 0.031% were observed in GS 20 sequence for Nandina and Platanus, respectively. More than 97% of all observed errors were associated with homopolymer runs, with ~60% of all errors associated with homopolymer runs of 5 or more nucleotides and ~50% of all errors associated with regions of extensive homopolymer runs. No substitution errors were present in either genome. Error rates were generally higher in the single-copy and noncoding regions of both plastid genomes relative to the inverted repeat and coding regions. Conclusion Highly accurate and essentially complete sequence information was obtained for the Nandina and Platanus plastid genomes using the GS 20 System. More importantly, the high accuracy
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Energy Technology Data Exchange (ETDEWEB)
DAVENPORT, J.
2006-11-01
Computational Science is an integral component of Brookhaven's multi science mission, and is a reflection of the increased role of computation across all of science. Brookhaven currently has major efforts in data storage and analysis for the Relativistic Heavy Ion Collider (RHIC) and the ATLAS detector at CERN, and in quantum chromodynamics. The Laboratory is host for the QCDOC machines (quantum chromodynamics on a chip), 10 teraflop/s computers which boast 12,288 processors each. There are two here, one for the Riken/BNL Research Center and the other supported by DOE for the US Lattice Gauge Community and other scientific users. A 100 teraflop/s supercomputer will be installed at Brookhaven in the coming year, managed jointly by Brookhaven and Stony Brook, and funded by a grant from New York State. This machine will be used for computational science across Brookhaven's entire research program, and also by researchers at Stony Brook and across New York State. With Stony Brook, Brookhaven has formed the New York Center for Computational Science (NYCCS) as a focal point for interdisciplinary computational science, which is closely linked to Brookhaven's Computational Science Center (CSC). The CSC has established a strong program in computational science, with an emphasis on nanoscale electronic structure and molecular dynamics, accelerator design, computational fluid dynamics, medical imaging, parallel computing and numerical algorithms. We have been an active participant in DOES SciDAC program (Scientific Discovery through Advanced Computing). We are also planning a major expansion in computational biology in keeping with Laboratory initiatives. Additional laboratory initiatives with a dependence on a high level of computation include the development of hydrodynamics models for the interpretation of RHIC data, computational models for the atmospheric transport of aerosols, and models for combustion and for energy utilization. The CSC was formed to
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Journals | Indian Academy of Sciences
Indian Academy of Sciences (India)
Theory Of Evolution. Posted on 23 January 2018. Joint Statement by the Three Science Academies of India on the teaching of the theory of evolution more. ... Posted on 21 December 2017. ASTROPHYSICS: An Observational View of the Universe. Math Art and Design: MAD about Math, Math Education and Outreach.
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Associateship | Indian Academy of Sciences
Indian Academy of Sciences (India)
Theory Of Evolution. Posted on 23 January 2018. Joint Statement by the Three Science Academies of India on the teaching of the theory of evolution more. ... Posted on 21 December 2017. ASTROPHYSICS: An Observational View of the Universe. Math Art and Design: MAD about Math, Math Education and Outreach.
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Scherag, André; Dina, Christian; Hinney, Anke; Vatin, Vincent; Scherag, Susann; Vogel, Carla I. G.; Müller, Timo D.; Grallert, Harald; Wichmann, H.-Erich; Balkau, Beverley; Heude, Barbara; Jarvelin, Marjo-Riitta; Hartikainen, Anna-Liisa; Levy-Marchal, Claire; Weill, Jacques; Delplanque, Jérôme; Körner, Antje; Kiess, Wieland; Kovacs, Peter; Rayner, Nigel W.; Prokopenko, Inga; McCarthy, Mark I.; Schäfer, Helmut; Jarick, Ivonne; Boeing, Heiner; Fisher, Eva; Reinehr, Thomas; Heinrich, Joachim; Rzehak, Peter; Berdel, Dietrich; Borte, Michael; Biebermann, Heike; Krude, Heiko; Rosskopf, Dieter; Rimmbach, Christian; Rief, Winfried; Fromme, Tobias; Klingenspor, Martin; Schürmann, Annette; Schulz, Nadja; Nöthen, Markus M.; Mühleisen, Thomas W.; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; Boes, Tanja; Illig, Thomas; Froguel, Philippe; Hebebrand, Johannes; Meyre, David
2010-01-01
Meta-analyses of population-based genome-wide association studies (GWAS) in adults have recently led to the detection of new genetic loci for obesity. Here we aimed to discover additional obesity loci in extremely obese children and adolescents. We also investigated if these results generalize by estimating the effects of these obesity loci in adults and in population-based samples including both children and adults. We jointly analysed two GWAS of 2,258 individuals and followed-up the best, according to lowest p-values, 44 single nucleotide polymorphisms (SNP) from 21 genomic regions in 3,141 individuals. After this DISCOVERY step, we explored if the findings derived from the extremely obese children and adolescents (10 SNPs from 5 genomic regions) generalized to (i) the population level and (ii) to adults by genotyping another 31,182 individuals (GENERALIZATION step). Apart from previously identified FTO, MC4R, and TMEM18, we detected two new loci for obesity: one in SDCCAG8 (serologically defined colon cancer antigen 8 gene; p = 1.85×10−8 in the DISCOVERY step) and one between TNKS (tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase gene) and MSRA (methionine sulfoxide reductase A gene; p = 4.84×10−7), the latter finding being limited to children and adolescents as demonstrated in the GENERALIZATION step. The odds ratios for early-onset obesity were estimated at ∼1.10 per risk allele for both loci. Interestingly, the TNKS/MSRA locus has recently been found to be associated with adult waist circumference. In summary, we have completed a meta-analysis of two GWAS which both focus on extremely obese children and adolescents and replicated our findings in a large followed-up data set. We observed that genetic variants in or near FTO, MC4R, TMEM18, SDCCAG8, and TNKS/MSRA were robustly associated with early-onset obesity. We conclude that the currently known major common variants related to obesity overlap to a substantial degree between
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Directory of Open Access Journals (Sweden)
André Scherag
2010-04-01
Full Text Available Meta-analyses of population-based genome-wide association studies (GWAS in adults have recently led to the detection of new genetic loci for obesity. Here we aimed to discover additional obesity loci in extremely obese children and adolescents. We also investigated if these results generalize by estimating the effects of these obesity loci in adults and in population-based samples including both children and adults. We jointly analysed two GWAS of 2,258 individuals and followed-up the best, according to lowest p-values, 44 single nucleotide polymorphisms (SNP from 21 genomic regions in 3,141 individuals. After this DISCOVERY step, we explored if the findings derived from the extremely obese children and adolescents (10 SNPs from 5 genomic regions generalized to (i the population level and (ii to adults by genotyping another 31,182 individuals (GENERALIZATION step. Apart from previously identified FTO, MC4R, and TMEM18, we detected two new loci for obesity: one in SDCCAG8 (serologically defined colon cancer antigen 8 gene; p = 1.85x10(-8 in the DISCOVERY step and one between TNKS (tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase gene and MSRA (methionine sulfoxide reductase A gene; p = 4.84x10(-7, the latter finding being limited to children and adolescents as demonstrated in the GENERALIZATION step. The odds ratios for early-onset obesity were estimated at approximately 1.10 per risk allele for both loci. Interestingly, the TNKS/MSRA locus has recently been found to be associated with adult waist circumference. In summary, we have completed a meta-analysis of two GWAS which both focus on extremely obese children and adolescents and replicated our findings in a large followed-up data set. We observed that genetic variants in or near FTO, MC4R, TMEM18, SDCCAG8, and TNKS/MSRA were robustly associated with early-onset obesity. We conclude that the currently known major common variants related to obesity overlap to a substantial
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Journal of Genetics | Indian Academy of Sciences
Indian Academy of Sciences (India)
/jgen/088/01/0001-0007. Keywords. Down syndrome; trisomy 21; meiosis; Penrose; parental age; nondisjunction; human genetics. Author Affiliations. Santhosh Girirajan1. Department of Genome Sciences, University of Washington, Seattle, ...
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Science Academies' Summer Research Fellowship Programme for ...
Indian Academy of Sciences (India)
Applications are invited from interested students and teachers from all universities and colleges affiliated to ... forwarded by the teacher in the case of student applicants. The last date for receipt of ... Chairman, Joint Science Education Panel.
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Joint Chiefs of Staff > About > The Joint Staff > Senior Enlisted Advisor
Skip to main content (Press Enter). Toggle navigation Joint Chiefs of Staff Joint Chiefs of Staff Joint Chiefs of Staff Facebook Twitter YouTube Flickr Blog Instagram Search JCS: Search Search Search JCS: Search Home Media News Photos Videos Publications About The Joint Staff Chairman Vice Chairman
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A joint-constraint model for human joints using signed distance-fields
DEFF Research Database (Denmark)
Engell-Nørregård, Morten Pol; Abel, Sarah Maria Niebe; Erleben, Kenny
2012-01-01
We present a local joint-constraint model for a single joint which is based on distance fields. Our model is fast, general, and well suited for modeling human joints. In this work, we take a geometric approach and model the geometry of the boundary of the feasible region, i.e., the boundary of all...... allowed poses. A region of feasible poses can be built by embedding motion captured data points in a signed distance field. The only assumption is that the feasible poses form a single connected set of angular values. We show how signed distance fields can be used to generate fast and general joint......-joint dependencies, or joints with more than three degrees of freedom. The resolution of the joint-constraints can be tweaked individually for each degree of freedom, which can be used to optimize memory usage. We perform a comparative study of the key-properties of various joint-constraint models, as well...
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Energy Technology Data Exchange (ETDEWEB)
Jain, B. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Spergel, D. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Connolly, A. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Dell' antonio, I. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Frieman, J. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Gawiser, E. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Gehrels, N. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Gladney, L. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Heitmann, K. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Helou, G. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Hirata, C. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Ho, S. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Ivezic, Z. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Jarvis, M. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Kahn, S. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Kalirai, J. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Kim, A. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Lupton, R. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Mandelbaum, R. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Marshall, P. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Newman, J. A. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Postman, M. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Rhodes, J. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Strauss, M. A. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Tyson, J. A. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Wood-Vesey, W. M. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States)
2015-02-02
The scientific opportunity offered by the combination of data from LSST, WFIRST and Euclid goes well beyond the science enabled by any one of the data sets alone. The range in wavelength, angular resolution and redshift coverage that these missions jointly span is remarkable. With major investments in LSST and WFIRST, and partnership with ESA in Euclid, the US has an outstanding scientific opportunity to carry out a combined analysis of these data sets. It is imperative for us to seize it and, together with our European colleagues, prepare for the defining cosmological pursuit of the 21st century. The main argument for conducting a single, high-quality reference co-analysis exercise and carefully documenting the results is the complexity and subtlety of systematics that define this co-analysis. Falling back on many small efforts by different teams in selected fields and for narrow goals will be inefficient, leading to significant duplication of effort.
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Silkworm: A Promising Model Organism in Life Science.
Meng, Xu; Zhu, Feifei; Chen, Keping
2017-09-01
As an important economic insect, silkworm Bombyx mori (L.) (Lepidoptera: Bombycidae) has numerous advantages in life science, such as low breeding cost, large progeny size, short generation time, and clear genetic background. Additionally, there are rich genetic resources associated with silkworms. The completion of the silkworm genome has further accelerated it to be a modern model organism in life science. Genomic studies showed that some silkworm genes are highly homologous to certain genes related to human hereditary disease and, therefore, are a candidate model for studying human disease. In this article, we provided a review of silkworm as an important model in various research areas, including human disease, screening of antimicrobial agents, environmental safety monitoring, and antitumor studies. In addition, the application potentiality of silkworm model in life sciences was discussed. © The Author 2017. Published by Oxford University Press on behalf of Entomological Society of America.
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Temporomandibular joint dislocation due to acute propranolol intoxication
Directory of Open Access Journals (Sweden)
Abbas Aghabiklooei
2010-07-01
Full Text Available Abbas Aghabiklooei1, Homan Elahi2, Babak Mostafazadeh31Department of Medical Toxicology and Forensic Medicine, Iran University of Medical Sciences, Tehran, Iran; 2Firouzgar Hospital, Department of ENT, Tehran, Iran; 3Department of Medical Toxicology and Forensic Medicine, Shaheed Beheshty University of Medical Sciences, Tehran, IranAbstract: Temporomandibular joint (TMJ dislocation has not previously been reported as a complication of beta-blocker toxicity. We are reporting two cases of TMJ dislocation resulted from acute severe intoxication with pure propranolol (PPL for the first time. Bilateral TMJ dislocation happened in two patients who were admitted to intensive care unit with diagnosis of severe acute PPL toxicity. Clinical diagnosis of TMJ dislocation was obtained by physical examination. Successful reduction was performed for both patients without subsequent recurrence in two weeks following hospital discharge. Both of our subjects had no previous history of lower jaw dislocation. There was not any risk factor for dislocation such as convulsion during admission period, recent face trauma, or oral manipulation by the medical team. This study showed that TMJ dislocation may occur after severe acute PPL toxicity probably due to spastic contraction of the lateral pterygoid muscle. This is against previously mentioned hypothesis that stated masseteric muscles contraction as the main cause of a bilateral dislocated TMJ.Keywords: propranolol, toxicity, temporomandibular joint dislocation
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Estimation of Joint types and Joint Limits from Motion capture data
DEFF Research Database (Denmark)
Engell-Nørregård, Morten Pol; Erleben, Kenny
2009-01-01
It is time-consuming for an animator to explicitly model joint types and joint limits of articulated figures. In this paper we describe a simple and fast approach to automated joint estimation from motion capture data of articulated figures. Our method will make the joint modeling more efficient ...
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Technical note: Equivalent genomic models with a residual polygenic effect.
Liu, Z; Goddard, M E; Hayes, B J; Reinhardt, F; Reents, R
2016-03-01
Routine genomic evaluations in animal breeding are usually based on either a BLUP with genomic relationship matrix (GBLUP) or single nucleotide polymorphism (SNP) BLUP model. For a multi-step genomic evaluation, these 2 alternative genomic models were proven to give equivalent predictions for genomic reference animals. The model equivalence was verified also for young genotyped animals without phenotypes. Due to incomplete linkage disequilibrium of SNP markers to genes or causal mutations responsible for genetic inheritance of quantitative traits, SNP markers cannot explain all the genetic variance. A residual polygenic effect is normally fitted in the genomic model to account for the incomplete linkage disequilibrium. In this study, we start by showing the proof that the multi-step GBLUP and SNP BLUP models are equivalent for the reference animals, when they have a residual polygenic effect included. Second, the equivalence of both multi-step genomic models with a residual polygenic effect was also verified for young genotyped animals without phenotypes. Additionally, we derived formulas to convert genomic estimated breeding values of the GBLUP model to its components, direct genomic values and residual polygenic effect. Third, we made a proof that the equivalence of these 2 genomic models with a residual polygenic effect holds also for single-step genomic evaluation. Both the single-step GBLUP and SNP BLUP models lead to equal prediction for genotyped animals with phenotypes (e.g., reference animals), as well as for (young) genotyped animals without phenotypes. Finally, these 2 single-step genomic models with a residual polygenic effect were proven to be equivalent for estimation of SNP effects, too. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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Factors influencing success of clinical genome sequencing across a broad spectrum of disorders
Taylor, Jenny C; Martin, Hilary C; Lise, Stefano; Broxholme, John; Cazier, Jean-Baptiste; Rimmer, Andy; Kanapin, Alexander; Lunter, Gerton; Fiddy, Simon; Allan, Chris; Aricescu, A. Radu; Attar, Moustafa; Babbs, Christian; Becq, Jennifer; Beeson, David
2015-01-01
To assess factors influencing the success of whole genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases across a broad spectrum of disorders in whom prior screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritisation. We found that jointly calling variants across samples, filtering against both local and e...
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Czech Academy of Sciences Publication Activity Database
Kopecký, David; Šimoníková, Denisa; Ghesquière, M.; Doležel, Jaroslav
2017-01-01
Roč. 151, č. 2 (2017), s. 106-114 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Festulolium * Genome composition * Genomic in situ hybridization * Grass hybrids * Homoeologous recombination * Lolium × Festuca Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 1.354, year: 2016
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Ensembl Genomes 2016: more genomes, more complexity.
Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M
2016-01-04
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Genome-Based Microbial Taxonomy Coming of Age.
Hugenholtz, Philip; Skarshewski, Adam; Parks, Donovan H
2016-06-01
Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.
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Nowrousian, Minou; Würtz, Christian; Pöggeler, Stefanie; Kück, Ulrich
2004-03-01
One of the most challenging parts of large scale sequencing projects is the identification of functional elements encoded in a genome. Recently, studies of genomes of up to six different Saccharomyces species have demonstrated that a comparative analysis of genome sequences from closely related species is a powerful approach to identify open reading frames and other functional regions within genomes [Science 301 (2003) 71, Nature 423 (2003) 241]. Here, we present a comparison of selected sequences from Sordaria macrospora to their corresponding Neurospora crassa orthologous regions. Our analysis indicates that due to the high degree of sequence similarity and conservation of overall genomic organization, S. macrospora sequence information can be used to simplify the annotation of the N. crassa genome.
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Materials science symposium 'materials science using accelerators'
International Nuclear Information System (INIS)
Ishii, Tetsuro; Asai, Masato; Chimi, Yasuhiro
2005-07-01
The facility of the JAERI-Tokai tandem accelerator and its booster has been contributing to advancing heavy-ion sciences in the fields of nuclear physics, nuclear chemistry, atomic and solid-state physics and materials science, taking advantage of its prominent performance of heavy-ion acceleration. This facility was recently upgraded by changing the acceleration tubes and installing an ECR ion-source at the terminal. The radioactive nuclear beam facility (Tokai Radioactive Ion Accelerator Complex, TRIAC) was also installed by the JAERI-KEK joint project. On this occasion, this meeting was held in order to provide a new step for the advancement of heavy-ion science, and to exchange information on recent activities and future plans using the tandem facility as well as on promising new experimental techniques. This meeting was held at Tokai site of JAERI on January 6th and 7th in 2005, having 24 oral presentations, and was successfully carried out with as many as 90 participants and lively discussions among scientists from all the fields of heavy-ion science, including solid-sate physics, nuclear physics and chemistry, and accelerator physics. This summary is the proceedings of this meeting. We would like to thank all the staffs of the accelerators section, participants and office workers in the Department of Materials Science for their support. The 24 of the presented papers are indexed individually. (J.P.N.)
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Big data, open science and the brain: lessons learned from genomics
Directory of Open Access Journals (Sweden)
Suparna eChoudhury
2014-05-01
Full Text Available The BRAIN Initiative aims to break new ground in the scale and speed of data collection in neuroscience, requiring tools to handle data in the magnitude of yottabytes (1024. The scale, investment and organization of it are being compared to the Human Genome Project (HGP, which has exemplified ‘big science’ for biology. In line with the trend towards Big Data in genomic research, the promise of the BRAIN Initiative, as well as the European Human Brain Project, rests on the possibility to amass vast quantities of data to model the complex interactions between the brain and behaviour and inform the diagnosis and prevention of neurological disorders and psychiatric disease. Advocates of this ‘data driven’ paradigm in neuroscience argue that harnessing the large quantities of data generated across laboratories worldwide has numerous methodological, ethical and economic advantages, but it requires the neuroscience community to adopt a culture of data sharing and open access to benefit from them. In this article, we examine the rationale for data sharing among advocates and briefly exemplify these in terms of new ‘open neuroscience’ projects. Then, drawing on the frequently invoked model of data sharing in genomics, we go on to demonstrate the complexities of data sharing, shedding light on the sociological and ethical challenges within the realms of institutions, researchers and participants, namely dilemmas around public/private interests in data, (lack of motivation to share in the academic community, and potential loss of participant anonymity. Our paper serves to highlight some foreseeable tensions around data sharing relevant to the emergent ‘open neuroscience’ movement.
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phiGENOME: an integrative navigation throughout bacteriophage genomes.
Stano, Matej; Klucar, Lubos
2011-11-01
phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.
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DEFF Research Database (Denmark)
Sørensen, John Dalsgaard; Thoft-Christensen, Palle
In this paper the preliminary results obtained by tests on tubular joints are presented. The joints are T-joints and the loading is static. It is the intention in continuation of these tests to perform tests on other types of joints (e.g. Y-joints) and also with dynamic loading. The purpose...... of the test is partly to obtain empirical data for the ultimate load-carrying capacity of tubular T-joints and partly to obtain some experience in performing tests with tubular joints. It is well known that tubular joints are usually designed in offshore engineering on the basis of empirical formulas obtained...... by experimental test results. Therefore, there is a need for performing experimental tests in this area....
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Sensevy, Gérard; Gruson, Brigitte; Forest, Dominique
2015-01-01
In this paper, we first sketch the joint action theory paradigm from a general viewpoint in sciences of culture. Then we specify this generic description by focusing on the joint action theory in didactics (JATD). We elaborate on three currently developed elements of the theory: the reticence-expression dialectics; the contract-milieu dialectics,…
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[Culpability and the problem of the human genome. Between being and having to be].
Donna, Edgardo
2011-01-01
In a liberal-democratic system, there is no possibility of a criminal liability charge without a minimum of freedom. Nevertheless, since a long time ago and, nowadays, with the advancement of science in the human genome, understanding it as a closed system--farm theory--is intended to demonstrate that the genome is a destination, thus criminal liability will be void, giving rise to security measures.
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U.S, Department of Energy's Bioenergy Research Centers An Overview of the Science
Energy Technology Data Exchange (ETDEWEB)
None
2009-07-01
. This program is bringing together scientists in diverse fields to understand the complex biology underlying solutions to DOE missions in energy production, environmental remediation, and climate change science. New interdisciplinary research communities are emerging, as are knowledgebases and scientific and computational resources critical to advancing large-scale, genome-based biology. To focus the most advanced biotechnology-based resources on the biological challenges of biofuel production, DOE established three Bioenergy Research Centers (BRCs) in September 2007. Each center is pursuing the basic research underlying a range of high-risk, high-return biological solutions for bioenergy applications. Advances resulting from the BRCs will provide the knowledge needed to develop new biobased products, methods, and tools that the emerging biofuel industry can use. The scientific rationale for these centers and for other fundamental genomic research critical to the biofuel industry was established at a DOE workshop involving members of the research community (see sidebar, Biofuel Research Plan, below). The DOE BRCs have developed automated, high-throughput analysis pipelines that will accelerate scientific discovery for biology-based biofuel research. The three centers, which were selected through a scientific peer-review process, are based in geographically diverse locations--the Southeast, the Midwest, and the West Coast--with partners across the nation. DOE's Oak Ridge National Laboratory leads the BioEnergy Science Center (BESC) in Tennessee; the University of Wisconsin-Madison leads the Great Lakes Bioenergy Research Center (GLBRC); and DOE's Lawrence Berkeley National Laboratory leads the DOE Joint BioEnergy Institute (JBEI) in California. Each center represents a multidisciplinary partnership with expertise spanning the physical and biological sciences, including genomics, microbial and plant biology, analytical chemistry, computational biology and
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A high-coverage Neandertal genome from Vindija Cave in Croatia.
Prüfer, Kay; de Filippo, Cesare; Grote, Steffi; Mafessoni, Fabrizio; Korlević, Petra; Hajdinjak, Mateja; Vernot, Benjamin; Skov, Laurits; Hsieh, Pinghsun; Peyrégne, Stéphane; Reher, David; Hopfe, Charlotte; Nagel, Sarah; Maricic, Tomislav; Fu, Qiaomei; Theunert, Christoph; Rogers, Rebekah; Skoglund, Pontus; Chintalapati, Manjusha; Dannemann, Michael; Nelson, Bradley J; Key, Felix M; Rudan, Pavao; Kućan, Željko; Gušić, Ivan; Golovanova, Liubov V; Doronichev, Vladimir B; Patterson, Nick; Reich, David; Eichler, Evan E; Slatkin, Montgomery; Schierup, Mikkel H; Andrés, Aida M; Kelso, Janet; Meyer, Matthias; Pääbo, Svante
2017-11-03
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
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Directory of Open Access Journals (Sweden)
Paulino Pérez
2010-09-01
Full Text Available The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO in a unified framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed.
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Jenkinson, Garrett; Abante, Jordi; Feinberg, Andrew P; Goutsias, John
2018-03-07
DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior. However, the performance of most currently available methods for methylation analysis is hampered by their inability to directly account for statistical dependencies between neighboring methylation sites, thus ignoring significant information available in WGBS reads. We present a powerful information-theoretic approach for genome-wide modeling and analysis of WGBS data based on the 1D Ising model of statistical physics. This approach takes into account correlations in methylation by utilizing a joint probability model that encapsulates all information available in WGBS methylation reads and produces accurate results even when applied on single WGBS samples with low coverage. Using the Shannon entropy, our approach provides a rigorous quantification of methylation stochasticity in individual WGBS samples genome-wide. Furthermore, it utilizes the Jensen-Shannon distance to evaluate differences in methylation distributions between a test and a reference sample. Differential performance assessment using simulated and real human lung normal/cancer data demonstrate a clear superiority of our approach over DSS, a recently proposed method for WGBS data analysis. Critically, these results demonstrate that marginal methods become statistically invalid when correlations are present in the data. This contribution demonstrates clear benefits and the necessity of modeling joint probability distributions of methylation using the 1D Ising model of statistical physics and of
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Genome Maps, a new generation genome browser.
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.
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ReMixT: clone-specific genomic structure estimation in cancer.
McPherson, Andrew W; Roth, Andrew; Ha, Gavin; Chauve, Cedric; Steif, Adi; de Souza, Camila P E; Eirew, Peter; Bouchard-Côté, Alexandre; Aparicio, Sam; Sahinalp, S Cenk; Shah, Sohrab P
2017-07-27
Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints. ReMixT is free, open-source software and is available at http://bitbucket.org/dranew/remixt .
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Human Genome Teacher Networking Project, Final Report, April 1, 1992 - March 31, 1998
Energy Technology Data Exchange (ETDEWEB)
Collins, Debra
1999-10-01
Project to provide education regarding ethical legal and social implications of Human Genome Project to high school science teachers through two consecutive summer workshops, in class activities, and peer teaching workshops.
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Protecting genomic data analytics in the cloud: state of the art and opportunities.
Tang, Haixu; Jiang, Xiaoqian; Wang, Xiaofeng; Wang, Shuang; Sofia, Heidi; Fox, Dov; Lauter, Kristin; Malin, Bradley; Telenti, Amalio; Xiong, Li; Ohno-Machado, Lucila
2016-10-13
The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies. To systematically investigate these issues, the NIH-funded National Center for Biomedical Computing iDASH (integrating Data for Analysis, 'anonymization' and SHaring) hosted the second Critical Assessment of Data Privacy and Protection competition to assess the capacity of cryptographic technologies for protecting computation over human genomes in the cloud and promoting cross-institutional collaboration. Data scientists were challenged to design and engineer practical algorithms for secure outsourcing of genome computation tasks in working software, whereby analyses are performed only on encrypted data. They were also challenged to develop approaches to enable secure collaboration on data from genomic studies generated by multiple organizations (e.g., medical centers) to jointly compute aggregate statistics without sharing individual-level records. The results of the competition indicated that secure computation techniques can enable comparative analysis of human genomes, but greater efficiency (in terms of compute time and memory utilization) are needed before they are sufficiently practical for real world environments.
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Efficient Server-Aided Secure Two-Party Function Evaluation with Applications to Genomic Computation
Directory of Open Access Journals (Sweden)
Blanton Marina
2016-10-01
Full Text Available Computation based on genomic data is becoming increasingly popular today, be it for medical or other purposes. Non-medical uses of genomic data in a computation often take place in a server-mediated setting where the server offers the ability for joint genomic testing between the users. Undeniably, genomic data is highly sensitive, which in contrast to other biometry types, discloses a plethora of information not only about the data owner, but also about his or her relatives. Thus, there is an urgent need to protect genomic data. This is particularly true when the data is used in computation for what we call recreational non-health-related purposes. Towards this goal, in this work we put forward a framework for server-aided secure two-party computation with the security model motivated by genomic applications. One particular security setting that we treat in this work provides stronger security guarantees with respect to malicious users than the traditional malicious model. In particular, we incorporate certified inputs into secure computation based on garbled circuit evaluation to guarantee that a malicious user is unable to modify her inputs in order to learn unauthorized information about the other user’s data. Our solutions are general in the sense that they can be used to securely evaluate arbitrary functions and offer attractive performance compared to the state of the art. We apply the general constructions to three specific types of genomic tests: paternity, genetic compatibility, and ancestry testing and implement the constructions. The results show that all such private tests can be executed within a matter of seconds or less despite the large size of one’s genomic data.
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The mitochondrial genome of the quiet-calling katydids, Xizicus ...
Indian Academy of Sciences (India)
College of Life Sciences, Hebei University, Baoding 071002, People's Republic of China. Abstract. To help determine whether the typical arthropod .... In the same way, the cycle was repeated to 'walk' around the rest of the genome. ..... Life Web Project (http://tolweb.org/). Hall T. A. 1999 BioEdit: a user-friendly biological ...
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Journal of Biosciences | Indian Academy of Sciences
Indian Academy of Sciences (India)
Home; Journals; Journal of Biosciences; Volume 30; Issue 5 ... A genomic library was generated using HindIII and the positive clones were sequenced and ... People's Republic of China; School of Agricultural Science and Technology, Suzhou ...
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García-Sancho, Miguel
2016-02-01
In this paper, I propose a strategy for navigating newly available archives in the study of late-twentieth century genomics. I demonstrate that the alleged 'explosion of data' characteristic of genomics-and of contemporary science in general-is not a new problem and that historians of earlier periods have dealt with information overload by relying on the 'perspective of time': the filtering effect the passage of time naturally exerts on both sources and memories. I argue that this reliance on the selective capacity of time results in inheriting archives curated by others and, consequently, poses the risk of reifying ahistorical scientific discourses. Through a preliminary examination of archives documenting early attempts at mapping and sequencing the human genome, I propose an alternative approach, in which historians proactively problematize and improve available sources. This approach provides historians with a voice in the socio-political management of scientific heritage and advances methodological innovations in the use of oral histories. It also provides a narrative framework in which to address big science initiatives by following second order administrators, rather than individual scientists. The new genomic archives thus represent an opportunity for historians to take an active role in current debates concerning 'big data' and critically embed the humanities in pressing global problems. Copyright © 2015 Elsevier Ltd. All rights reserved.
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74th Annual Meeting | Annual Meetings | Events | Indian Academy of ...
Indian Academy of Sciences (India)
The making of a flowering stem: lessons from molecular genetic analysis of flowering in model plants. 13.00 .... Genomics in cancer classification, prognostication and treatment ... Gamete formation without meiosis in plants ... Joint Statement by the Three Science Academies of India on the teaching of the theory of evolution
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Carver, Rebecca Bruu; Castéra, Jérémy; Gericke, Niklas; Evangelista, Neima Alice Menezes; El-Hani, Charbel N
2017-01-01
In this paper we present the development and validation a comprehensive questionnaire to assess college students' knowledge about modern genetics and genomics, their belief in genetic determinism, and their attitudes towards applications of modern genetics and genomic-based technologies. Written in everyday language with minimal jargon, the Public Understanding and Attitudes towards Genetics and Genomics (PUGGS) questionnaire is intended for use in research on science education and public understanding of science, as a means to investigate relationships between knowledge, determinism and attitudes about modern genetics, which are to date little understood. We developed a set of core ideas and initial items from reviewing the scientific literature on genetics and previous studies on public and student knowledge and attitudes about genetics. Seventeen international experts from different fields (e.g., genetics, education, philosophy of science) reviewed the initial items and their feedback was used to revise the questionnaire. We validated the questionnaire in two pilot tests with samples of university freshmen students. The final questionnaire contains 45 items, including both multiple choice and Likert scale response formats. Cronbach alpha showed good reliability for each section of the questionnaire. In conclusion, the PUGGS questionnaire is a reliable tool for investigating public understanding and attitudes towards modern genetics and genomic-based technologies.
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Carver, Rebecca Bruu; Castéra, Jérémy; Gericke, Niklas; Evangelista, Neima Alice Menezes
2017-01-01
In this paper we present the development and validation a comprehensive questionnaire to assess college students’ knowledge about modern genetics and genomics, their belief in genetic determinism, and their attitudes towards applications of modern genetics and genomic-based technologies. Written in everyday language with minimal jargon, the Public Understanding and Attitudes towards Genetics and Genomics (PUGGS) questionnaire is intended for use in research on science education and public understanding of science, as a means to investigate relationships between knowledge, determinism and attitudes about modern genetics, which are to date little understood. We developed a set of core ideas and initial items from reviewing the scientific literature on genetics and previous studies on public and student knowledge and attitudes about genetics. Seventeen international experts from different fields (e.g., genetics, education, philosophy of science) reviewed the initial items and their feedback was used to revise the questionnaire. We validated the questionnaire in two pilot tests with samples of university freshmen students. The final questionnaire contains 45 items, including both multiple choice and Likert scale response formats. Cronbach alpha showed good reliability for each section of the questionnaire. In conclusion, the PUGGS questionnaire is a reliable tool for investigating public understanding and attitudes towards modern genetics and genomic-based technologies. PMID:28114357
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Journal of the Ghana Science Association: Submissions
African Journals Online (AJOL)
Unless otherwise stated, the first named author of a joint publication will be taken as ... be sent to The Editor, Journal of Ghana Science Association, P.O. Box 7, Legon. ... Copyright for articles published in this journal is retained by the journal.
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tendernotices | office | Indian Academy of Sciences
Indian Academy of Sciences (India)
Theory Of Evolution. Posted on 23 January 2018. Joint Statement by the Three Science Academies of India on the teaching of the theory of evolution more. ... Posted on 21 December 2017. ASTROPHYSICS: An Observational View of the Universe. Math Art and Design: MAD about Math, Math Education and Outreach.
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CRISPR-Cas9: tool for qualitative and quantitative plant genome editing
Directory of Open Access Journals (Sweden)
Ali Noman
2016-11-01
Full Text Available Genome editing advancements have made many unachievable ideas practical. Increased adoption of genome editing has been geared by swiftly developing CRISPR-Cas9 technology. This technique is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR mediated genome editing is being used for rapid, easy and efficient alteration of indigenous genes among diverse plant species. With approximate completion of conceptual work about CRISPR/Cas9, plant scientists are applying this genome editing tool for crop attributes enhancement. The capability of CRISPR-Cas9 systems for performing targeted and efficient modifications in genome sequence as well as gene expression will certainly spur novel developments not only in model plants but also in crop plants. Additionally, due to non-involvement of foreign DNA, this technique may help alleviating regulatory issues associated with GM Plants. We expect that prevailing challenges in plant science like genomic region manipulation, crop specific vectors etc. will be addressed along with sustained growth of this genome editing tool. In this review, recent progress of CRISPR/Cas9 technology in plants has been summarized and discussed. We review potential of CRISPR/Cas9 for different aspects of plant life. It also covers strengths of this technique in comparison with other genome editing techniques e.g. ZFNs and TALENs and potential challenges in coming decades have been described.
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2011-02-15
... OFFICE OF SCIENCE AND TECHNOLOGY POLICY National Nanotechnology Coordination Office; Bridging NanoEHS Research Efforts: A Joint US-EU Workshop: Public Meeting AGENCY: National Nanotechnology Coordination Office, STPO. ACTION: Notice of public meeting. SUMMARY: The National Nanotechnology Coordination...
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Positioning genomics in biology education: content mapping of undergraduate biology textbooks.
Wernick, Naomi L B; Ndung'u, Eric; Haughton, Dominique; Ledley, Fred D
2014-12-01
Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.
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Genomics using the Assembly of the Mink Genome
DEFF Research Database (Denmark)
Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam
2018-01-01
The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...
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Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda
Energy Technology Data Exchange (ETDEWEB)
Houghton, John [Dept. of Energy (DOE), Washington DC (United States); Weatherwax, Sharlene [Dept. of Energy (DOE), Washington DC (United States); Ferrell, John [Dept. of Energy (DOE), Washington DC (United States)
2006-06-07
The Biomass to Biofuels Workshop, held December 7–9, 2005, was convened by the Department of Energy’s Office of Biological and Environmental Research in the Office of Science; and the Office of the Biomass Program in the Office of Energy Efficiency and Renewable Energy. The purpose was to define barriers and challenges to a rapid expansion of cellulosic-ethanol production and determine ways to speed solutions through concerted application of modern biology tools as part of a joint research agenda. Although the focus was ethanol, the science applies to additional fuels that include biodiesel and other bioproducts or coproducts having critical roles in any deployment scheme.
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U.S. Department of Energy's Bioenergy Research Centers An Overview of the Science
Energy Technology Data Exchange (ETDEWEB)
None
2010-07-01
challenges of biofuel production, DOE established three Bioenergy Research Centers (BRCs) in September 2007. Each center is pursuing the basic research underlying a range of high-risk, high-return biological solutions for bioenergy applications. Advances resulting from the BRCs are providing the knowledge needed to develop new biobased products, methods, and tools that the emerging biofuel industry can use (see sidebar, Bridging the Gap from Fundamental Biology to Industrial Innovation for Bioenergy, p. 6). The DOE BRCs have developed automated, high-throughput analysis pipelines that will accelerate scientific discovery for biology-based biofuel research. The three centers, which were selected through a scientific peer-review process, are based in geographically diverse locations - the Southeast, the Midwest, and the West Coast - with partners across the nation (see U.S. map, DOE Bioenergy Research Centers and Partners, on back cover). DOE's Lawrence Berkeley National Laboratory leads the DOE Joint BioEnergy Institute (JBEI) in California; DOE's Oak Ridge National Laboratory leads the BioEnergy Science Center (BESC) in Tennessee; and the University of Wisconsin-Madison leads the Great Lakes Bioenergy Research Center (GLBRC). Each center represents a multidisciplinary partnership with expertise spanning the physical and biological sciences, including genomics, microbial and plant biology, analytical chemistry, computational biology and bioinformatics, and engineering. Institutional partners include DOE national laboratories, universities, private companies, and nonprofit organizations.
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BER Science Network Requirements Workshop -- July 26-27,2007
Energy Technology Data Exchange (ETDEWEB)
Tierney, Brian L.; Dart, Eli
2008-02-01
The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the US Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States of America. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In July 2007, ESnet and the Biological and Environmental Research (BER) Program Office of the DOE Office of Science organized a workshop to characterize the networking requirements of the science programs funded by the BER Program Office. These included several large programs and facilities, including Atmospheric Radiation Measurement (ARM) Program and the ARM Climate Research Facility (ACRF), Bioinformatics and Life Sciences Programs, Climate Sciences Programs, the Environmental Molecular Sciences Laboratory at PNNL, the Joint Genome Institute (JGI). National Center for Atmospheric Research (NCAR) also participated in the workshop and contributed a section to this report due to the fact that a large distributed data repository for climate data will be established at NERSC, ORNL and NCAR, and this will have an effect on ESnet. Workshop participants were asked to codify their requirements in a 'case study' format, which summarizes the instruments and facilities necessary for the science and the process by which the science is done, with emphasis on the network services needed and the way in which the network is used. Participants were asked to consider three time scales in their case studies--the near term (immediately and up to 12 months in the future), the medium term (3-5 years in the future), and the long term (greater than 5 years in the future). In addition to achieving its goal of collecting and
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Genomic dissection and prioritizing of candidate genes of QTL for ...
Indian Academy of Sciences (India)
of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA. 5Mudanjiang ..... Fragile X mental retardation gene 1,. −2.1 ... stimulus/stress and signalling associated with acute-phase response were .... This work was supported by the Center of Genomics and Bioinfor- matics and ...
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GeNemo: a search engine for web-based functional genomic data.
Zhang, Yongqing; Cao, Xiaoyi; Zhong, Sheng
2016-07-08
A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Visualization for genomics: the Microbial Genome Viewer.
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
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Does generalized joint hypermobility predict joint injury in sport? A review.
LENUS (Irish Health Repository)
Donaldson, Peter R
2012-02-01
OBJECTIVE: To determine whether persons with generalized joint hypermobility have an increased risk of lower limb joint injury during sport. DATA SOURCES: PubMed, CINAHL, EMBASE, and SportDiscus were searched through February 2009, without language restrictions, using terms related to risk; hip, ankle, and knee injuries; and joint instability. Reference lists of included studies and relevant reviews were searched by hand. STUDY SELECTION: Selection criteria were peer-reviewed studies with a prospective design that used an objective scale to measure generalized joint hypermobility; the participants were engaged in sport activity, and the injury data were quantitative and based on diagnosis by a health professional, were self-reported, or resulted in time lost to athletic participation. The studies were screened by 1 researcher and checked by a second. Study methods were independently assessed by 2 investigators using the 6-point scale for prognostic studies developed by Pengel. Disagreements were resolved through discussion. Of 4841 studies identified, 18 met inclusion criteria. Of these, 8 were included in random-effects meta-analyses. DATA EXTRACTION: The data extracted by 2 reviewers included participant and sport characteristics and details of joint hypermobility and injury measurements. More detailed data for 4 investigations were obtained from the study authors. Where possible, hypermobility was defined as >\\/=4 of 9 points on the British Society of Rheumatology Scale (BSRS). MAIN RESULTS: Lower limb joint injuries (3 studies, 1047 participants) occurred in 14% of participants. Using the BSRS of joint hypermobility, any lower limb injury was not associated with hypermobility [odds ratio (OR), 1.43; 95% confidence interval (CI), 0.56-3.67]. Using the original authors\\' definitions, hypermobility was associated with risk of knee joint injuries (OR, 2.62; 95% CI, 1.04-6.58) in 5 studies. In 4 studies in which the BSRS could be used (1167 participants; incidence
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Journal of Genetics | Indian Academy of Sciences
Indian Academy of Sciences (India)
... Oryza sativa; indica rice; cDNA libraries; rice genome; drought tolerance. ... Putative functions were assigned at a stringency E value of 10-6 in BLASTN and ... School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India ...
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Bunting, Alison
2003-04-01
The founders of the Association of Academic Health Sciences Libraries (AAHSL) envisioned the development of a professional organization that would provide a greater voice for academic health sciences libraries, facilitate cooperation and communication with the Association of American Medical Colleges, and create a forum for identifying problems and solutions that are common to academic health sciences libraries. This article focuses on the fulfillment of the "greater voice" vision by describing action and leadership by AAHSL and its members on issues that directly influenced the role of academic health sciences libraries. These include AAHSL's participation in the work that led to the publication of the landmark report, Academic Information in the Academic Health Sciences Center: Roles for the Library in Information Management; its contributions to the recommendations of the Physicians for the Twenty-first Century: The GPEP Report; and the joint publication with the Medical Library Association of Challenge to Action: Planning and Evaluation Guidelines for Academic Health Sciences Libraries.
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Hill, William G
2014-01-01
Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives' performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher's infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with "genomic selection" is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas.
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Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization
Liu, Jin; Huang, Jian; Ma, Shuangge
2012-01-01
Genome-wide association studies have been extensively conducted, searching for markers for biologically meaningful outcomes and phenotypes. Penalization methods have been adopted in the analysis of the joint effects of a large number of SNPs (single nucleotide polymorphisms) and marker identification. This study is partly motivated by the analysis of heterogeneous stock mice dataset, in which multiple correlated phenotypes and a large number of SNPs are available. Existing penalization methods designed to analyze a single response variable cannot accommodate the correlation among multiple response variables. With multiple response variables sharing the same set of markers, joint modeling is first employed to accommodate the correlation. The group Lasso approach is adopted to select markers associated with all the outcome variables. An efficient computational algorithm is developed. Simulation study and analysis of the heterogeneous stock mice dataset show that the proposed method can outperform existing penalization methods. PMID:23272092
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A computational model for three-dimensional jointed media with a single joint set
International Nuclear Information System (INIS)
Koteras, J.R.
1994-02-01
This report describes a three-dimensional model for jointed rock or other media with a single set of joints. The joint set consists of evenly spaced joint planes. The normal joint response is nonlinear elastic and is based on a rational polynomial. Joint shear stress is treated as being linear elastic in the shear stress versus slip displacement before attaining a critical stress level governed by a Mohr-Coulomb faction criterion. The three-dimensional model represents an extension of a two-dimensional, multi-joint model that has been in use for several years. Although most of the concepts in the two-dimensional model translate in a straightforward manner to three dimensions, the concept of slip on the joint planes becomes more complex in three dimensions. While slip in two dimensions can be treated as a scalar quantity, it must be treated as a vector in the joint plane in three dimensions. For the three-dimensional model proposed here, the slip direction is assumed to be the direction of maximum principal strain in the joint plane. Five test problems are presented to verify the correctness of the computational implementation of the model
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Dittrich, Kerstin; Bossert, Marie-Luise; Rothe-Wulf, Annelie; Klauer, Karl Christoph
2017-09-01
Previous studies observed compatibility effects in different interference paradigms such as the Simon and flanker task even when the task was distributed across two co-actors. In both Simon and flanker tasks, performance is improved in compatible trials relative to incompatible trials if one actor works on the task alone as well as if two co-actors share the task. These findings have been taken to indicate that actors automatically co-represent their co-actor's task. However, recent research on the joint Simon and joint flanker effect suggests alternative non-social interpretations. To which degree both joint effects are driven by the same underlying processes is the question of the present study, and it was scrutinized by manipulating the visibility of the co-actor. While the joint Simon effect was not affected by the visibility of the co-actor, the joint flanker effect was reduced when participants did not see their co-actors but knew where the co-actors were seated. These findings provide further evidence for a spatial interpretation of the joint Simon effect. In contrast to recent claims, however, we propose a new explanation of the joint flanker effect that attributes the effect to an impairment in the focusing of spatial attention contingent on the visibility of the co-actor.
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A Modelling Method of Bolt Joints Based on Basic Characteristic Parameters of Joint Surfaces
Yuansheng, Li; Guangpeng, Zhang; Zhen, Zhang; Ping, Wang
2018-02-01
Bolt joints are common in machine tools and have a direct impact on the overall performance of the tools. Therefore, the understanding of bolt joint characteristics is essential for improving machine design and assembly. Firstly, According to the experimental data obtained from the experiment, the stiffness curve formula was fitted. Secondly, a finite element model of unit bolt joints such as bolt flange joints, bolt head joints, and thread joints was constructed, and lastly the stiffness parameters of joint surfaces were implemented in the model by the secondary development of ABAQUS. The finite element model of the bolt joint established by this method can simulate the contact state very well.
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Proceedings of the joint Nordic spring meeting '92
International Nuclear Information System (INIS)
Lindgaard, P.-A.
1992-05-01
Proceedings in the form of extended abstracts of the Joint Nordic Spring Meeting '92 including the 3rd Nordic Conference on Surface Science, the 6th Nordic Symposium on Computer Simulation, and 3rd Nordic Symposium on Superconductivity. In addition there are contributions from workshops on the Physics of Small Cluster, on Soft Condensed Matter Physics and from an Electronic Properties Workshop. The proceedings constrain over 300 contributions on the mentioned subjects. Further, there are several contributions on general solid state subjects, magnetism, semiconductors etc. (au) (4 tabs., 187 ills., 931 refs.)
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Energy Technology Data Exchange (ETDEWEB)
Copeland, A [U.S. Department of Energy, Joint Genome Institute; O' Connor, Kathleen [Purdue University; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Berry, Kerrie W. [United States Department of Energy Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Vargas, Carmen [University of Seville; Nieto, Joaquin J. [University of Seville; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Csonka, Laszlo N. [Purdue University; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute
2011-01-01
Chromohalobacter salexigens is one of nine currently known species of the genus Chromoha- lobacter in the family Halomonadaceae. It is the most halotolerant of the so-called mod- erately halophilic bacteria currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11T and Halomonas elongata are the first and the second members of the family Halomonada- ceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.
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DEFF Research Database (Denmark)
Sørensen, Karsten Engsig
Afhandlingen analysere de konkurrenceretlige og selskabsretlige regler som er bestemmende for hvordan et joint venture samarbejde er struktureret......Afhandlingen analysere de konkurrenceretlige og selskabsretlige regler som er bestemmende for hvordan et joint venture samarbejde er struktureret...
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First fungal genome sequence from Africa: A preliminary analysis
Directory of Open Access Journals (Sweden)
Rene Sutherland
2012-01-01
Full Text Available Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists
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FWP executive summaries, Basic Energy Sciences Materials Sciences Programs (SNL/NM)
Energy Technology Data Exchange (ETDEWEB)
Samara, G.A.
1997-05-01
The BES Materials Sciences Program has the central theme of Scientifically Tailored Materials. The major objective of this program is to combine Sandia`s expertise and capabilities in the areas of solid state sciences, advanced atomic-level diagnostics and materials synthesis and processing science to produce new classes of tailored materials as well as to enhance the properties of existing materials for US energy applications and for critical defense needs. Current core research in this program includes the physics and chemistry of ceramics synthesis and processing, the use of energetic particles for the synthesis and study of materials, tailored surfaces and interfaces for materials applications, chemical vapor deposition sciences, artificially-structured semiconductor materials science, advanced growth techniques for improved semiconductor structures, transport in unconventional solids, atomic-level science of interfacial adhesion, high-temperature superconductors, and the synthesis and processing of nano-size clusters for energy applications. In addition, the program includes the following three smaller efforts initiated in the past two years: (1) Wetting and Flow of Liquid Metals and Amorphous Ceramics at Solid Interfaces, (2) Field-Structured Anisotropic Composites, and (3) Composition-Modulated Semiconductor Structures for Photovoltaic and Optical Technologies. The latter is a joint effort with the National Renewable Energy Laboratory. Separate summaries are given of individual research areas.
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Innovations and Advances in Computer, Information, Systems Sciences, and Engineering
Sobh, Tarek
2013-01-01
Innovations and Advances in Computer, Information, Systems Sciences, and Engineering includes the proceedings of the International Joint Conferences on Computer, Information, and Systems Sciences, and Engineering (CISSE 2011). The contents of this book are a set of rigorously reviewed, world-class manuscripts addressing and detailing state-of-the-art research projects in the areas of Industrial Electronics, Technology and Automation, Telecommunications and Networking, Systems, Computing Sciences and Software Engineering, Engineering Education, Instructional Technology, Assessment, and E-learning.
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International cooperation for promotion of nuclear science and engineering research
International Nuclear Information System (INIS)
Shibata, Toshikazu; Sugiyama, Kazusuke; Nakazawa, Masaharu; Katoh, Toshio; Kimura, Itsuro.
1993-01-01
For promotion of nuclear science and engineering research, examinations were made on the possibilities and necessary measures to extend joint research at international level. The present article is a summary of the reports of investigations performed during FY 1986 through 1991 by the Special Committee of the AESJ for Feasibility Study on International Cooperation for Promotion of Nuclear Science and Engineering Research, under contract with Science and Technology Agency of Japan. Background information was collected on the present status of scientific research facilities in US, European and Asian countries on one hand, and on the expectations and prospects of Japanese scientists on the other hand. Based on the analysis of these data, some measures necessary to expand the international cooperation were proposed. It was emphasized that international joint research on a reciprocal basis would be effective in order to strengthen the technological basis of peaceful uses of nuclear energy. Problems to be solved for the new development were also discussed. (author)
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A New Method for Determination of Joint Roughness Coefficient of Rock Joints
Directory of Open Access Journals (Sweden)
Shigui Du
2015-01-01
Full Text Available The joint roughness coefficient (JRC of rock joints has the characteristic of scale effect. JRC measured on small-size exposed rock joints should be evaluated by JRC scale effect in order to obtain the JRC of actual-scale rock joints, since field rock joints are hardly fully exposed or well saved. Based on the validity analysis of JRC scale effect, concepts of rate of JRC scale effect and effective length of JRC scale effect were proposed. Then, a graphic method for determination of the effective length of JRC scale effect was established. Study results show that the JRC of actual-scale rock joints can be obtained through a fractal model of JRC scale effect according to the statistically measured results of the JRC of small-size partial exposed rock joints and by the selection of fractal dimension of JRC scale effect and the determination of effective length of JRC scale effect.
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Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno
2013-02-01
Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.
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The CERN-JINR Joint Physics Schools Exhibition Science Bringing Nations Together
1997-01-01
Since 1970, CERN and JINR have been holding joint Schools of Physics attended by young scientists from many countries of the world. Here they not only learn the latest ideas in elementary particle physics but also become involved in a process that leads to better mutual understanding and rapprochement of people from different countries. Such schools may seem natural natural now, but long before the Berlin Wall and the Iron Curtain collapsed, they provided a unique opportunity for contact between young people from countries with different political systems. This long-standing co-operation between CERN and JINR helps to bridge the gap between East and West and stabilize the political situation.
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The CERN-JINR Joint Physics Schools Exhibition Science Bringing Nations Together
1999-01-01
Since 1970, CERN and JINR have been holding joint Schools of Physics attended by young scientists from many countries of the world. Here they not only learn the latest ideas in elementary particle physics but also become involved in a process that leads to better mutual understanding and rapprochement of people from different countries. Such schools may seem natural now, but long before the Berlin Wall and the Iron Curtain collapsed, they provided a unique opportunity for contact between young people from countries with different political systems. This long-standing co-operation between CERN and JINR helps to bridge the gap between East and West and stabilize the political situation.
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Joint Institute for Nuclear Research as an example of socialist integration in science
International Nuclear Information System (INIS)
Bogolyubov, N.N.
1979-01-01
History of establishing, main directions of works and some results of investigations which have been carried out in the Joint Institute of Nuclear Research according to the program of the JINR member-states are stated as well as directions of the JINR co-operation with other countries are given. In detail, main works are stated in the field of high energy physics, theoretical nuclear physics, investigation of interactions of elementary particles, nuclear spectroscopy of nuclides. Examples are given of joint researches which have been conducted by scientists from the JINR together with scientists from other scientific research centers of the JINR member-states and other countries. Content is stated of works in the field of synthesis of ultraheavy elements and development of methods of study as their chemical properties. Composition of the JINR computer center is given as well as the list of problems which are solved at this center. Some results are given of works conducted in the JINR in the field of development of equipment for nuclear-physical researches and improvement of accelerators. Some results are presented of the JINR activity and plans for future [ru
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Frontotemporal dementia and its subtypes: a genome-wide association study
Ferrari, Raffaele; Hernandez, Dena G; Nalls, Michael A; Rohrer, Jonathan D; Ramasamy, Adaikalavan; Kwok, John B J; Dobson-Stone, Carol; Brooks, William S; Schofield, Peter R; Halliday, Glenda M; Hodges, John R; Piguet, Olivier; Bartley, Lauren; Thompson, Elizabeth; Haan, Eric; Hernández, Isabel; Ruiz, Agustín; Boada, Mercè; Borroni, Barbara; Padovani, Alessandro; Cruchaga, Carlos; Cairns, Nigel J; Benussi, Luisa; Binetti, Giuliano; Ghidoni, Roberta; Forloni, Gianluigi; Galimberti, Daniela; Fenoglio, Chiara; Serpente, Maria; Scarpini, Elio; Clarimón, Jordi; Lleó, Alberto; Blesa, Rafael; Waldö, Maria Landqvist; Nilsson, Karin; Nilsson, Christer; Mackenzie, Ian R A; Hsiung, Ging-Yuek R; Mann, David M A; Grafman, Jordan; Morris, Christopher M; Attems, Johannes; Griffiths, Timothy D; McKeith, Ian G; Thomas, Alan J; Pietrini, P; Huey, Edward D; Wassermann, Eric M; Baborie, Atik; Jaros, Evelyn; Tierney, Michael C; Pastor, Pau; Razquin, Cristina; Ortega-Cubero, Sara; Alonso, Elena; Perneczky, Robert; Diehl-Schmid, Janine; Alexopoulos, Panagiotis; Kurz, Alexander; Rainero, Innocenzo; Rubino, Elisa; Pinessi, Lorenzo; Rogaeva, Ekaterina; George-Hyslop, Peter St; Rossi, Giacomina; Tagliavini, Fabrizio; Giaccone, Giorgio; Rowe, James B; Schlachetzki, J C M; Uphill, James; Collinge, John; Mead, S; Danek, Adrian; Van Deerlin, Vivianna M; Grossman, Murray; Trojanowsk, John Q; van der Zee, Julie; Deschamps, William; Van Langenhove, Tim; Cruts, Marc; Van Broeckhoven, Christine; Cappa, Stefano F; Le Ber, Isabelle; Hannequin, Didier; Golfier, Véronique; Vercelletto, Martine; Brice, Alexis; Nacmias, Benedetta; Sorbi, Sandro; Bagnoli, Silvia; Piaceri, Irene; Nielsen, Jørgen E; Hjermind, Lena E; Riemenschneider, Matthias; Mayhaus, Manuel; Ibach, Bernd; Gasparoni, Gilles; Pichler, Sabrina; Gu, Wei; Rossor, Martin N; Fox, Nick C; Warren, Jason D; Spillantini, Maria Grazia; Morris, Huw R; Rizzu, Patrizia; Heutink, Peter; Snowden, Julie S; Rollinson, Sara; Richardson, Anna; Gerhard, Alexander; Bruni, Amalia C; Maletta, Raffaele; Frangipane, Francesca; Cupidi, Chiara; Bernardi, Livia; Anfossi, Maria; Gallo, Maura; Conidi, Maria Elena; Smirne, Nicoletta; Rademakers, Rosa; Baker, Matt; Dickson, Dennis W; Graff-Radford, Neill R; Petersen, Ronald C; Knopman, David; Josephs, Keith A; Boeve, Bradley F; Parisi, Joseph E; Seeley, William W; Miller, Bruce L; Karydas, Anna M; Rosen, Howard; van Swieten, John C; Dopper, Elise G P; Seelaar, Harro; Pijnenburg, Yolande AL; Scheltens, Philip; Logroscino, Giancarlo; Capozzo, Rosa; Novelli, Valeria; Puca, Annibale A; Franceschi, M; Postiglione, Alfredo; Milan, Graziella; Sorrentino, Paolo; Kristiansen, Mark; Chiang, Huei-Hsin; Graff, Caroline; Pasquier, Florence; Rollin, Adeline; Deramecourt, Vincent; Lebert, Florence; Kapogiannis, Dimitrios; Ferrucci, Luigi; Pickering-Brown, Stuart; Singleton, Andrew B; Hardy, John; Momeni, Parastoo
2014-01-01
Summary Background Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes—MAPT, GRN, and C9orf72—have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder. Methods We did a two-stage genome-wide association study on clinical FTD, analysing samples from 3526 patients with FTD and 9402 healthy controls. All participants had European ancestry. In the discovery phase (samples from 2154 patients with FTD and 4308 controls), we did separate association analyses for each FTD subtype (behavioural variant FTD, semantic dementia, progressive non-fluent aphasia, and FTD overlapping with motor neuron disease [FTD-MND]), followed by a meta-analysis of the entire dataset. We carried forward replication of the novel suggestive loci in an independent sample series (samples from 1372 patients and 5094 controls) and then did joint phase and brain expression and methylation quantitative trait loci analyses for the associated (p<5 × 10−8) and suggestive single-nucleotide polymorphisms. Findings We identified novel associations exceeding the genome-wide significance threshold (p<5 × 10−8) that encompassed the HLA locus at 6p21.3 in the entire cohort. We also identified a potential novel locus at 11q14, encompassing RAB38/CTSC, for the behavioural FTD subtype. Analysis of expression and methylation quantitative trait loci data suggested that these loci might affect expression and methylation incis. Interpretation Our findings suggest that immune system processes (link to 6p21.3) and possibly lysosomal and autophagy pathways (link to 11q14) are potentially involved in FTD. Our findings need to be replicated to better define the association of the newly identified loci with disease and possibly to shed light on the pathomechanisms contributing to FTD. Funding The National Institute of
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Outline and Evaluation of a Joint European and Canadian Virtual Mobility: e-Learning Project
Hilliard, Alan
2006-01-01
The "virtual mobility" project was created as part of a joint Canadian and European Commission funded project to explore cross-cultural clinical curricular developments in the radiation sciences. The aim of the project was to facilitate student learning of the cross-cultural differences in the delivery of healthcare within the…
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Protection for the U.S. Automobile Industry: A Joint Class Simulation in Trade Policy.
Hess, Peter N.; Ortmayer, Louis M.
A description of a joint class simulation in trade policy undertaken by an international economics class and a political science class at Davidson College (Pennsylvania) is presented in three sections. Section I describes the structure of the simulation. Students were divided into groups of United States auto manufacturers, the United Auto…
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Family genome browser: visualizing genomes with pedigree information.
Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong
2015-07-15
Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Protecting genomic data analytics in the cloud: state of the art and opportunities
Directory of Open Access Journals (Sweden)
Haixu Tang
2016-10-01
Full Text Available Abstract The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies. To systematically investigate these issues, the NIH-funded National Center for Biomedical Computing iDASH (integrating Data for Analysis, ‘anonymization’ and SHaring hosted the second Critical Assessment of Data Privacy and Protection competition to assess the capacity of cryptographic technologies for protecting computation over human genomes in the cloud and promoting cross-institutional collaboration. Data scientists were challenged to design and engineer practical algorithms for secure outsourcing of genome computation tasks in working software, whereby analyses are performed only on encrypted data. They were also challenged to develop approaches to enable secure collaboration on data from genomic studies generated by multiple organizations (e.g., medical centers to jointly compute aggregate statistics without sharing individual-level records. The results of the competition indicated that secure computation techniques can enable comparative analysis of human genomes, but greater efficiency (in terms of compute time and memory utilization are needed before they are sufficiently practical for real world environments.
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Applied linguistics - a science of culture?
Directory of Open Access Journals (Sweden)
Benke, Gertraud
2003-01-01
Full Text Available In this article, the status of applied linguistics as discipline is questioned and problems of establishing it - and other newly formed scientific enterprises like cultural science - as disciplines are discussed. This discussion is contextualized using the author's own experience as applied linguist working in (the institutional structure of Austria. Secondly, applied linguistics is presented as complementing cultural science, with both exploring at times the same phenomena albeit under different perspectives and focussing on different levels of experience. Two examples of research involving such a joint interest with different foci are discussed.
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Laboratory characterization of rock joints
International Nuclear Information System (INIS)
Hsiung, S.M.; Kana, D.D.; Ahola, M.P.; Chowdhury, A.H.; Ghosh, A.
1994-05-01
A laboratory characterization of the Apache Leap tuff joints under cyclic pseudostatic and dynamic loads has been undertaken to obtain a better understanding of dynamic joint shear behavior and to generate a complete data set that can be used for validation of existing rock-joint models. Study has indicated that available methods for determining joint roughness coefficient (JRC) significantly underestimate the roughness coefficient of the Apache Leap tuff joints, that will lead to an underestimation of the joint shear strength. The results of the direct shear tests have indicated that both under cyclic pseudostatic and dynamic loadings the joint resistance upon reverse shearing is smaller than that of forward shearing and the joint dilation resulting from forward shearing recovers during reverse shearing. Within the range of variation of shearing velocity used in these tests, the shearing velocity effect on rock-joint behavior seems to be minor, and no noticeable effect on the peak joint shear strength and the joint shear strength for the reverse shearing is observed
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.pdf | Volumes | public | Indian Academy of Sciences
Indian Academy of Sciences (India)
Joint Statement by the Three Science Academies of India on the teaching of the theory of evolution more... Introducing: Summer Schools. Posted on 21 December 2017. ASTROPHYSICS: An Observational View of the ... Academy Public Lecture. Posted on 19 January 2018. Seasonal and Pandemic Influenza by Prof.
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THE RELATIONSHIP BETWEEN TEMPOROMANDIBULAR-JOINT MOBILITY AND PERIPHERAL JOINT MOBILITY RECONSIDERED
Dijkstra, P.U.; DEBONT, L.G.M.; VANDERWEELE, L.T.; Boering, G.
The purpose of this paper was to study the relationship between temporomandibular joint (TMJ) mobility and mobility of joints and to study the general character of joint mobility in 83 subjects, 55 females and 28 males (mean age 26.7, range 13-46 years). The subjects were recruited from the
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Energy Technology Data Exchange (ETDEWEB)
Choi, Hyung Sik; Chang, Duk Soo; Lee, Kyung Soo; Kim, Woo Sun; Sung, Jung Ho; Jun, Young Hwan [Capital Armed Forces General Hospital, Seoul (Korea, Republic of)
1989-02-15
The temporomandibular joint(TMJ) is really a complex of two synovial space separated by fibrocartilaginous disc. Single inferior joint space arthrography is commonly performed for evaluation of TMJ disorders, which is known to be superior in demonstrating joint dynamics. But it reveals only the inferior surface of the disc. Therefore, dual space arthrography is superior to demonstrate the soft tissue anatomic feature of the joint such as disc position and shape. Authors performed 83 TMJ arthrograms in TMJ problems. Initially, the inferior joint space was done and then the superior space was sequentially contrasted. The follow results were noted: 1. In all cases, dual space arthrography revealed accurate disc shape and positions. 2. Concordant findings between the two techniques: 68 cases (82%). Discordance between the two techniques: 15 cases (18%) 3. Possible causes of discordance between inferior and dual space arthrography. a) Normal varians of anterior recess: 3 cases b) Posterior disc displacement: 4 cases c) Influence of the patient's head position change :4 cases d) False perforation: 2 cases e) Reduction change: 2 cases 4. In 5 cases with anterior displacement, dual space arthrography gave additional findings such as adhesion within the superior space, which could not be evaluated by single inferior space.
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Materials science symposium 'heavy ion science in tandem energy region'
International Nuclear Information System (INIS)
Ikezoe, Hiroshi; Yoshida, Tadashi; Takeuchi, Suehiro
2003-10-01
The facility of the JAERI tandem accelerator and its booster has been contributing to advancing heavy ion science researches in the fields of nuclear physics, nuclear chemistry, atomic and solid state physics and materials science, taking advantage of its prominent performances in providing various heavy ions. This meeting, as well as the previous ones held twice, offered scientists from the fields of heavy ion science, including nuclear physics, solid-state physics and cross-field physics, an opportunity to have active discussions among them, as well as to review their research accomplishments in the last two years. Oral presentations were selected from a wider scope of prospective fields, expecting a new step of advancing in heavy ion science. Main topics of the meeting were the status of the JAERI-KEK joint project of developing a radioactive nuclear beam (RNB) facility and research programs related to the RNB. This meeting was held at Advanced Science Research Center in JAERI-Tokai on January 8th and 9th in 2003, and successfully carried out with as many as 190 participants and a lot of sincere discussions. The proceedings are presented in this report. The 51 of the presented papers are indexed individually. (J.P.N.)
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Kulynych, Jennifer; Greely, Henry T
2017-04-01
Widespread use of medical records for research, without consent, attracts little scrutiny compared to biospecimen research, where concerns about genomic privacy prompted recent federal proposals to mandate consent. This paper explores an important consequence of the proliferation of electronic health records (EHRs) in this permissive atmosphere: with the advent of clinical gene sequencing, EHR-based secondary research poses genetic privacy risks akin to those of biospecimen research, yet regulators still permit researchers to call gene sequence data 'de-identified', removing such data from the protection of the federal Privacy Rule and federal human subjects regulations. Medical centers and other providers seeking to offer genomic 'personalized medicine' now confront the problem of governing the secondary use of clinical genomic data as privacy risks escalate. We argue that regulators should no longer permit HIPAA-covered entities to treat dense genomic data as de-identified health information. Even with this step, the Privacy Rule would still permit disclosure of clinical genomic data for research, without consent, under a data use agreement, so we also urge that providers give patients specific notice before disclosing clinical genomic data for research, permitting (where possible) some degree of choice and control. To aid providers who offer clinical gene sequencing, we suggest both general approaches and specific actions to reconcile patients' rights and interests with genomic research.
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Greely, Henry T.
2017-01-01
Abstract Widespread use of medical records for research, without consent, attracts little scrutiny compared to biospecimen research, where concerns about genomic privacy prompted recent federal proposals to mandate consent. This paper explores an important consequence of the proliferation of electronic health records (EHRs) in this permissive atmosphere: with the advent of clinical gene sequencing, EHR-based secondary research poses genetic privacy risks akin to those of biospecimen research, yet regulators still permit researchers to call gene sequence data ‘de-identified’, removing such data from the protection of the federal Privacy Rule and federal human subjects regulations. Medical centers and other providers seeking to offer genomic ‘personalized medicine’ now confront the problem of governing the secondary use of clinical genomic data as privacy risks escalate. We argue that regulators should no longer permit HIPAA-covered entities to treat dense genomic data as de-identified health information. Even with this step, the Privacy Rule would still permit disclosure of clinical genomic data for research, without consent, under a data use agreement, so we also urge that providers give patients specific notice before disclosing clinical genomic data for research, permitting (where possible) some degree of choice and control. To aid providers who offer clinical gene sequencing, we suggest both general approaches and specific actions to reconcile patients’ rights and interests with genomic research. PMID:28852559
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Lapped scarf joint with inclined faces and wooden dowels: Experimental and numerical analysis
Czech Academy of Sciences Publication Activity Database
Arciszewska-Kędzior, Anna; Kunecký, Jiří; Hasníková, Hana; Sebera, V.
2015-01-01
Roč. 94, July (2015), s. 1-8 ISSN 0141-0296 R&D Projects: GA MK(CZ) DF12P01OVV004 Keywords : timber joint * wooden-dowels * full-scale experiments * FEM * failure criterion Subject RIV: AL - Art, Architecture, Cultural Heritage Impact factor: 1.893, year: 2015 http://www.sciencedirect.com/science/article/pii/S0141029615001807
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Single-Lap-Joint Screening of Hysol EA 9309NA Epoxy Adhesive
2017-05-01
Acknowledgments This research was supported in part by the US Army Education Outreach Programs (Science and Engineering Apprentice Program and College...useful for estimating downstream logistical phase- out risk based on current and pending environmental regulations . Second-tier testing consists of...was used to ensure that the breaking load of single-lap-joint samples fell between 15% and 85% of the cell’s full-scale capacity. A crosshead speed
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Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project
DEFF Research Database (Denmark)
Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D
Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...
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2011-12-21
... Science Research and Development Services Scientific Merit Review Board Panel for Eligibility, Notice of... and Clinical Science Research and Development Services Scientific Merit Review Board will meet on... medical specialties within the general areas of biomedical, behavioral, and clinical science research. The...
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Joint Electromagnetic Spectrum Management Operations
2012-03-20
promulgate command-specific policy and guidance for EMS use, the joint restricted frequency list (JRFL) process, the joint communications–electronics...joint communications–electronics operating instructions (JCEOI) and joint restricted frequency list (JRFL). Examples of FM include providing the...joint restricted frequency list Figure III-4. Joint Frequency Management Office Spectrum Management Process Chapter III III-10 JP 6-01 assignments
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Directory of Open Access Journals (Sweden)
David G Covell
Full Text Available Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE and Sanger Cancer Genome Project (CGP. The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a evaluate drug responses of compounds with similar mechanism of action (MOA, b examine measures of gene expression (GE, copy number (CN and mutation status (MUT biomarkers, combined with gene set enrichment analysis (GSEA, for hypothesizing biological processes important for drug response, c conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.
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Encyclopedia of Complexity and Systems Science
Meyers, Robert A
2009-01-01
Encyclopedia of Complexity and Systems Science provides an authoritative single source for understanding and applying the concepts of complexity theory together with the tools and measures for analyzing complex systems in all fields of science and engineering. The science and tools of complexity and systems science include theories of self-organization, complex systems, synergetics, dynamical systems, turbulence, catastrophes, instabilities, nonlinearity, stochastic processes, chaos, neural networks, cellular automata, adaptive systems, and genetic algorithms. Examples of near-term problems and major unknowns that can be approached through complexity and systems science include: The structure, history and future of the universe; the biological basis of consciousness; the integration of genomics, proteomics and bioinformatics as systems biology; human longevity limits; the limits of computing; sustainability of life on earth; predictability, dynamics and extent of earthquakes, hurricanes, tsunamis, and other n...
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Perceived barriers to online education by radiologic science educators.
Kowalczyk, Nina K
2014-01-01
Radiologic science programs continue to adopt the use of blended online education in their curricula, with an increase in the use of online courses since 2009. However, perceived barriers to the use of online education formats persist in the radiologic science education community. An electronic survey was conducted to explore the current status of online education in the radiologic sciences and to identify barriers to providing online courses. A random sample of 373 educators from radiography, radiation therapy, and nuclear medicine technology educational programs accredited by the Joint Review Committee on Education in Radiologic Technology and Joint Review Committee on Educational Programs in Nuclear Medicine Technology was chosen to participate in this study. A qualitative analysis of self-identified barriers to online teaching was conducted. Three common themes emerged: information technology (IT) training and support barriers, student-related barriers, and institutional barriers. Online education is not prevalent in the radiologic sciences, in part because of the need for the clinical application of radiologic science course content, but online course activity has increased substantially in radiologic science education, and blended or hybrid course designs can effectively provide opportunities for student-centered learning. Further development is needed to increase faculty IT self-efficacy and to educate faculty regarding pedagogical methods appropriate for online course delivery. To create an excellent online learning environment, educators must move beyond technology issues and focus on providing quality educational experiences for students.
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Bonnema, A.B.; Lin, Z.; Qu, L.; Jacobsen, E.
2006-01-01
Scientific co-operation between the Chinese Academy of Agricultural Sciences (CAAS) and Wageningen University (WU) has been underway since 1990, especially in the field of plant sciences. In 2001, CAAS and WU initiated a formal joint PhD training programme to further structure their co-operation.
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2011-05-03
... Science Research and Development Services Scientific Merit Review Board; Notice of Meeting Amendment The... and Clinical Science Research and Development Services Scientific Merit Review Board have been..., behavioral and clinical science research. The panel meetings will be open to the public for approximately one...
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International Nuclear Information System (INIS)
Weissman, S.D.
1989-01-01
The authors discuss how x-ray examination is essential in the diagnosis and evaluation of the arthritides. Most arthritides are first suspected by the clinician, and x-ray evaluation of these entities along with laboratory testing is important for confirmation of the clinical diagnosis and in staging of the disease process. Several arthritides are often diagnosed first by the podiatrist on x-ray evaluation, including pseudogout, ankylosing spondylitis, early rheumatoid arthritis, degenerative joint disease, and tuberculosis of bone. The joint responds to insult in only a limited number of ways that become apparent on x-ray. The soft tissues surrounding the joint, the articulating bones, and alignment of the joint space may all be involved by the arthritic process. On roentgenographic examination, the soft tissues must be examined for edema, masses, calcifications, and atrophy. The articulating bones must be examined for demineralization, erosions, osteophytes, periosteal reaction, cysts and sclerosis
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Barclay, John W.
2010-01-01
Advances in the genome sciences are leading to the development of new healthcare innovations relevant to the principles of personalized medicine. Genome BC, a non-profit research organization, invests in projects that will help facilitate the integration of these innovations into the delivery of healthcare. This analysis assesses the strategic positioning of private healthcare firms in BC to be early users of such innovations. The analysis assesses the suitability of investment from Genome BC...
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Journal of Genetics | Indian Academy of Sciences
Indian Academy of Sciences (India)
population stratification; ancestry informative markers (AIMs); race; ethnicity; genetic epidemiology; forensic genetics; Hispanics. ... Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029 ...
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Yeast Genomics for Bread, Beer, Biology, Bucks and Breath
Sakharkar, Kishore R.; Sakharkar, Meena K.
The rapid advances and scale up of projects in DNA sequencing dur ing the past two decades have produced complete genome sequences of several eukaryotic species. The versatile genetic malleability of the yeast, and the high degree of conservation between its cellular processes and those of human cells have made it a model of choice for pioneering research in molecular and cell biology. The complete sequence of yeast genome has proven to be extremely useful as a reference towards the sequences of human and for providing systems to explore key gene functions. Yeast has been a ‘legendary model’ for new technologies and gaining new biological insights into basic biological sciences and biotechnology. This chapter describes the awesome power of yeast genetics, genomics and proteomics in understanding of biological function. The applications of yeast as a screening tool to the field of drug discovery and development are highlighted and the traditional importance of yeast for bakers and brewers is discussed.
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77 FR 43237 - Genome in a Bottle Consortium-Work Plan Review Workshop
2012-07-24
... in human whole genome variant calls. A principal motivation for this consortium is to enable... standards and quantitative performance metrics are needed to achieve the confidence in measurement results... principal motivation for this consortium is to enable science-based regulatory oversight of clinical...
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Directory of Open Access Journals (Sweden)
Claire eBertelli
2015-02-01
Full Text Available With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by embedded bioinformaticians, i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the Sequence a genome class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2,233 putative proteins. Estrella also possesses a 9,136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.
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Directory of Open Access Journals (Sweden)
Martin eKussmann
2011-05-01
Full Text Available Comprehensive investigation of nutritional health effects at molecular level requires understanding the interplay between three genomes, the food, the gut microbial and the human host genome. Food genomes are researched for exploitation of macro- and micronutrients as well as bioactives, with the genes coding for bioactive proteins and peptides being of central interest. The human gut microbiota encompasses a complex intestinal ecosystem with profound impact on host metabolism. It is studied at genomic, proteomic and metabolomic level. Humans are characterized at the level of: genetic predisposition and variability in terms of dietary response and direction of health trajectories; epigenetic, metabolic programming at certain life stages with health consequences later in life and for subsequent generations; and acute genomic expression as a holistic response to diet, monitored at gene transcript, protein and metabolite level.Modern nutrition science explores health aspects of bioactive food components, thereby promoting health, preventing or delaying the onset of disease, optimizing performance and assessing benefits and risks. Personalized nutrition means adapting food to individual needs, depending on the human host’s life stage, -style and -situation. Traditionally, nutrigenomics and nutri(epigenetics have been seen as the key sciences to understand human variability in preferences and requirements for diet as well as responses to nutrition. This article puts the three nutrition and health-relevant genomes into perspective, i.e. the food, the gut microbial and the human host’s genome, and calls for an extended nutrigenomics approach to build the future tools for personalized nutrition, health maintenance and disease prevention. We discuss examples of these genomes, proteomes, transcriptomes and metabolomes under the overarching term genomics that covers all Omics rather than the sole study of DNA and RNA.
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2012-01-01
The nuclear plant accident at Fukushima in the wake of the Great East Japan Earthquake and tsunami has had a major impact on the energy strategy of Japan and the world. From a global perspective, approach to energy is of greater and greater consequence. The Global Center of Excellence (COE) Program of the Ministry of Education, Culture, Sports, Science and Technology of Japan, with the support of university faculty members, has established an international education and research platform to foster educators, researchers, and policy makers who can develop technologies and propose policies for establishing a CO2 zero-emission society no longer dependent on fossil fuels by the year 2100. Since 2008, a program called “Energy Science in the Age of Global Warming—Toward a CO2 Zero-Emission Energy System” has been in progress at Kyoto University. A third international symposium, titled “Zero-Carbon Energy, Kyoto 2011,” was held jointly with Ajou University, Korea, in August 2011, and this book is a compila...
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Zeng, Cong; Thomas, Leighton J; Kelly, Michelle; Gardner, Jonathan P A
2016-05-01
The complete mitochondrial genome of a New Zealand specimen of the deep-sea sponge Poecillastra laminaris (Sollas, 1886) (Astrophorida, Vulcanellidae), from the Colville Ridge, New Zealand, was sequenced using the 454 Life Science pyrosequencing system. To identify homologous mitochondrial sequences, the 454 reads were mapped to the complete mitochondrial genome sequence of Geodia neptuni (GeneBank No. NC_006990). The P. laminaris genome is 18,413 bp in length and includes 14 protein-coding genes, 24 transfer RNA genes and 2 ribosomal RNA genes. Gene order resembled that of other demosponges. The base composition of the genome is A (29.1%), T (35.2%), C (14.0%) and G (21.7%). This is the second published mitogenome for a sponge of the order Astrophorida and will be useful in future phylogenetic analysis of deep-sea sponges.
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Imaging findings of charcot joint
International Nuclear Information System (INIS)
Meng Quanfei; Zhou Chunxiang; Chen Yingming; Jiang Bo
2003-01-01
Objective: To analyze the MRI characters of Charcot joint, and to evaluate the diagnostic value of X-ray, CT, and MRI on Charcot joint. Methods: Eight patients with 8 Charcot joints underwent X-ray, CT, and MR examinations. 6 of them had syringomyelia, 1 patient had injury of the spinal cord, and 1 case had diabetes. All 8 patients had sensory reduction or deficit in the sick extremities. Results: There were two types of Charcot joint, hypertrophic and atrophic. Radiographic and CT features of hypertrophic joint (n=3) showed hyperostotic osteosclerosis and mammoth osteophytes in the sick bones, periarticular ossification, and articular disorganization. Radiographic and CT features of atrophic joint (n=5) showed extensive bone resorption (destruction), periarticular debris, and articular disorganization. Main MRI features of Charcot joint included hydrarthrosis within joint capsule, thickened, loose, and elongated joint capsule with para-joint, peri-diaphysis, and inter-muscular extension in a pseudopodia pattern. The irregular joint capsule wall was presented as mild hypointensity on T 1 WI, slight hyper-intensity on T 2 WI, and was markedly enhanced after Gd-DTPA was administrated, which was considered as a characteristic manifestation of the lesion. Soft tissue mass containing hypo-intense stripes on both T 1 WI and T 2 WI was commonly noted adjacent to the involved joint. Conclusion: X-rays plain film is the first choice for the diagnosis of Charcot joint, and MRI is pretty useful in the diagnosis of Charcot joint