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...

Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

Science.gov (United States)

Vincent, J.

2011-01-01

The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

Origins of the Human Genome Project

Science.gov (United States)

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.

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.

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

Science.gov (United States)

Holt, Carson; Yandell, Mark

2011-12-22

Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

Science.gov (United States)

Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

2013-04-10

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

A computational genomics pipeline for prokaryotic sequencing projects.

Science.gov (United States)

Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King

2010-08-01

New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

The Genome 10K Project: a way forward.

Science.gov (United States)

Koepfli, Klaus-Peter; Paten, Benedict; O'Brien, Stephen J

2015-01-01

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.

Genome projects and the functional-genomic era.

Science.gov (United States)

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

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

Human genome project: revolutionizing biology through leveraging technology

Science.gov (United States)

Dahl, Carol A.; Strausberg, Robert L.

1996-04-01

The Human Genome Project (HGP) is an international project to develop genetic, physical, and sequence-based maps of the human genome. Since the inception of the HGP it has been clear that substantially improved technology would be required to meet the scientific goals, particularly in order to acquire the complete sequence of the human genome, and that these technologies coupled with the information forthcoming from the project would have a dramatic effect on the way biomedical research is performed in the future. In this paper, we discuss the state-of-the-art for genomic DNA sequencing, technological challenges that remain, and the potential technological paths that could yield substantially improved genomic sequencing technology. The impact of the technology developed from the HGP is broad-reaching and a discussion of other research and medical applications that are leveraging HGP-derived DNA analysis technologies is included. The multidisciplinary approach to the development of new technologies that has been successful for the HGP provides a paradigm for facilitating new genomic approaches toward understanding the biological role of functional elements and systems within the cell, including those encoded within genomic DNA and their molecular products.

The African Genome Variation Project shapes medical genetics in Africa

Science.gov (United States)

Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

2014-01-01

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterisation of African genetic diversity is needed. The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across SSA. We identify new loci under selection, including for malaria and hypertension. We show that modern imputation panels can identify association signals at highly differentiated loci across populations in SSA. Using WGS, we show further improvement in imputation accuracy supporting efforts for large-scale sequencing of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa, showing for the first time that such designs are feasible. PMID:25470054

The Human Genome Project: big science transforms biology and medicine.

Science.gov (United States)

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.

All about the Human Genome Project (HGP)

Science.gov (United States)

... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

The Human Genome Project: how do we protect Australians?

Science.gov (United States)

Stott Despoja, N

It is the moon landing of the nineties: the ambitious Human Genome Project--identifying the up to 100,000 genes that make up human DNA and the sequences of the three billion base-pairs that comprise the human genome. However, unlike the moon landing, the effects of the genome project will have a fundamental impact on the way we see ourselves and each other.

A 1000 Arab genome project to study the Emirati population.

Science.gov (United States)

Al-Ali, Mariam; Osman, Wael; Tay, Guan K; AlSafar, Habiba S

2018-04-01

Discoveries from the human genome, HapMap, and 1000 genome projects have collectively contributed toward the creation of a catalog of human genetic variations that has improved our understanding of human diversity. Despite the collegial nature of many of these genome study consortiums, which has led to the cataloging of genetic variations of different ethnic groups from around the world, genome data on the Arab population remains overwhelmingly underrepresented. The National Arab Genome project in the United Arab Emirates (UAE) aims to address this deficiency by using Next Generation Sequencing (NGS) technology to provide data to improve our understanding of the Arab genome and catalog variants that are unique to the Arab population of the UAE. The project was conceived to shed light on the similarities and differences between the Arab genome and those of the other ethnic groups.

Attitudes towards the Human Genome Project.

Science.gov (United States)

Shahroudi, Julie; Shaw, Geraldine

Attitudes concerning the Human Genome Project were reported by faculty (N=40) and students (N=66) from a liberal arts college. Positive attitudes toward the project involved privacy, insurance and health, economic purposes, reproductive purposes, genetic counseling, religion and overall opinions. Negative attitudes were expressed regarding…

Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis; FINAL

International Nuclear Information System (INIS)

Simon, M. I.; Kim, U.-J.

2002-01-01

We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year

Comparative genomic data of the Avian Phylogenomics Project.

Science.gov (United States)

Zhang, Guojie; Li, Bo; Li, Cai; Gilbert, M Thomas P; Jarvis, Erich D; Wang, Jun

2014-01-01

genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.

Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

OpenAIRE

Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

2015-01-01

First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

Justice and the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Murphy, T.F.; Lappe, M. (eds.)

1992-01-01

Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

Justice and the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Murphy, T.F.; Lappe, M. [eds.

1992-12-31

Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

Final Project Report Project 10749-4.2.2.1 2007-2009

Energy Technology Data Exchange (ETDEWEB)

Zacher, Alan H.; Holladay, Johnathan E.; Frye, J. G.; Brown, Heather M.; Santosa, Daniel M.; Oberg, Aaron A.

2009-05-11

This is the final report for the DOE Project 10749-4.2.2.1 for the FY2007 - FY2009 period. This report is non-proprietary, and will be submitted to DOE as a final project report. The report covers activities under the DOE Project inside CRADA 269 (Project 53231) as well as project activites outside of that CRADA (Project 56662). This is the final report that is summarized from the non-proprietary quarterlies submitted to DOE over the past 2.5 years, which in turn are summaries from the proprietary technical reporting to UOP.

The Chlamydomonas genome project: a decade on

Science.gov (United States)

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

2014-01-01

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

The Qatar genome project: translation of whole-genome sequencing into clinical practice.

Science.gov (United States)

Zayed, Hatem

2016-10-01

Qatar Genome Project was launched in 2013 with the intent to sequence the genome of each Qatari citizen in an effort to protect Qataris from the high rate of indigenous genetic diseases by allowing the mapping of disease-causing variants/rare variants and establishing a Qatari reference genome. Indeed, this project is expected to have numerous global benefits because the elevated homogeneity of the Qatari population, that will make Qatar an excellent genetic laboratory that will generate a wealth of data that will allow us to make sense of the genotype-phenotype correlations of many diseases, especially the complex multifactorial diseases, and will pave the way for changing the traditional medical practice of looking first at the phenotype rather than the genotype. © 2016 John Wiley & Sons Ltd.

Harvard Personal Genome Project: lessons from participatory public research

Science.gov (United States)

2014-01-01

Background Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an ‘open consent’ framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Discussion Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project. Summary We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants. PMID:24713084

Harvard Personal Genome Project: lessons from participatory public research.

Science.gov (United States)

Ball, Madeleine P; Bobe, Jason R; Chou, Michael F; Clegg, Tom; Estep, Preston W; Lunshof, Jeantine E; Vandewege, Ward; Zaranek, Alexander; Church, George M

2014-02-28

Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an 'open consent' framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project. We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants.

Implications of the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Kitcher, P.

1998-11-01

The Human Genome Project (HGP), launched in 1991, aims to map and sequence the human genome by 2006. During the fifteen-year life of the project, it is projected that $3 billion in federal funds will be allocated to it. The ultimate aims of spending this money are to analyze the structure of human DNA, to identify all human genes, to recognize the functions of those genes, and to prepare for the biology and medicine of the twenty-first century. The following summary examines some of the implications of the program, concentrating on its scientific import and on the ethical and social problems that it raises. Its aim is to expose principles that might be used in applying the information which the HGP will generate. There is no attempt here to translate the principles into detailed proposals for legislation. Arguments and discussion can be found in the full report, but, like this summary, that report does not contain any legislative proposals.

Ethical considerations of research policy for personal genome analysis: the approach of the Genome Science Project in Japan.

Science.gov (United States)

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.

Los Alamos Science: The Human Genome Project. Number 20, 1992

Science.gov (United States)

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.

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.

The 1000 bull genome project

Science.gov (United States)

To meet growing global demands for high value protein from milk and meat, rates of genetic gain in domestic cattle must be accelerated. At the same time, animal health and welfare must be considered. The 1000 bull genomes project supports these goals by providing annotated sequence variants and ge...

Helminth genome projects: all or nothing

Czech Academy of Sciences Publication Activity Database

Lukeš, Julius; Horák, Aleš; Scholz, Tomáš

2005-01-01

Roč. 21, č. 6 (2005), s. 265-266 ISSN 1471-4922 Institutional research plan: CEZ:AV0Z60220518 Keywords : genome project * helminth * Dracunculus Subject RIV: EG - Zoology Impact factor: 4.526, year: 2005

The Human Genome Diversity Project

Energy Technology Data Exchange (ETDEWEB)

Cavalli-Sforza, L. [Stanford Univ., CA (United States)

1994-12-31

The Human Genome Diversity Project (HGD Project) is an international anthropology project that seeks to study the genetic richness of the entire human species. This kind of genetic information can add a unique thread to the tapestry knowledge of humanity. Culture, environment, history, and other factors are often more important, but humanity`s genetic heritage, when analyzed with recent technology, brings another type of evidence for understanding species` past and present. The Project will deepen the understanding of this genetic richness and show both humanity`s diversity and its deep and underlying unity. The HGD Project is still largely in its planning stages, seeking the best ways to reach its goals. The continuing discussions of the Project, throughout the world, should improve the plans for the Project and their implementation. The Project is as global as humanity itself; its implementation will require the kinds of partnerships among different nations and cultures that make the involvement of UNESCO and other international organizations particularly appropriate. The author will briefly discuss the Project`s history, describe the Project, set out the core principles of the Project, and demonstrate how the Project will help combat the scourge of racism.

The Human Genome Project (HGP): dividends and challenges: a ...

African Journals Online (AJOL)

The Human Genome Project (HGP): dividends and challenges: a review. ... Genomic studies have given profound insights into the genetic organization of ... with it will be an essential part of modern medicine and biology for years to come.

Final project report

Energy Technology Data Exchange (ETDEWEB)

Nitin S. Baliga and Leroy Hood

2008-11-12

The proposed overarching goal for this project was the following: Data integration, simulation and visualization will facilitate metabolic and regulatory network prediction, exploration, and formulation of hypotheses. We stated three specific aims to achieve the overarching goal of this project: (1) Integration of multiple levels of information such as mRNA and protein levels, predicted protein-protein interactions/associations and gene function will enable construction of models describing environmental response and dynamic behavior. (2) Flexible tools for network inference will accelerate our understanding of biological systems. (3) Flexible exploration and queries of model hypotheses will provide focus and reveal novel dependencies. The underlying philosophy of these proposed aims is that an iterative cycle of experiments, experimental design, and verification will lead to a comprehensive and predictive model that will shed light on systems level mechanisms involved in responses elicited by living systems upon sensing a change in their environment. In the previous years report we demonstrated considerable progress in development of data standards, regulatory network inference and data visualization and exploration. We are pleased to report that several manuscripts describing these procedures have been published in top international peer reviewed journals including Genome Biology, PNAS, and Cell. The abstracts of these manuscripts are given and they summarize our accomplishments in this project.

Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project.

Science.gov (United States)

Sliva, Anna; Yang, Huanming; Boeke, Jef D; Mathews, Debra J H

2015-08-01

First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) PROJECT is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with this field of research and operate under a common set of principles. In this commentary, we survey the current ethics and regulatory landscape of synthetic biology and present the Sc2.0 Statement of Ethics and Governance to which all members of the project adhere. This statement focuses on four aspects of the Sc2.0 PROJECT: societal benefit, intellectual property, safety, and self-governance. We propose that such project-level agreements are an important, valuable, and flexible model of self-regulation for similar global, large-scale synthetic biology projects in order to maximize the benefits and minimize potential harms. Copyright © 2015 by the Genetics Society of America.

Final Report: Bone Mass Inheritance: A Project to Identify the Genetic Regulation of Bone Mass; FINAL

International Nuclear Information System (INIS)

Recker, Robert R. M.D.

2002-01-01

This project was designed to find human chromosomal locations that contain genes regulating peak bone density. It is part of a whole genome search for those loci,each responsible for at least 15% of the variation in the peak adult bone density. We accomplished this with a sib pair design, combined with simultaneous examination of extended kindreds. This project gave partial support of the recruitment which has now been completed. The project will extend into 2003. During the remainder of the project, a whole genome scan will be performed from the entire cohort of 2226 persons who have DNA archived, followed by linkage analysis. This project will meet the scientific objective leading eventually to expanded options for treating the condition that leads to bone thinning osteoporosis, and potential fractures in aging populations

Public trust and 'ethics review' as a commodity: the case of Genomics England Limited and the UK's 100,000 genomes project.

Science.gov (United States)

Samuel, Gabrielle Natalie; Farsides, Bobbie

2018-06-01

The UK Chief Medical Officer's 2016 Annual Report, Generation Genome, focused on a vision to fully integrate genomics into all aspects of the UK's National Health Service (NHS). This process of integration, which has now already begun, raises a wide range of social and ethical concerns, many of which were discussed in the final Chapter of the report. This paper explores how the UK's 100,000 Genomes Project (100 kGP)-the catalyst for Generation Genome, and for bringing genomics into the NHS-is negotiating these ethical concerns. The UK's 100 kGP, promoted and delivered by Genomics England Limited (GEL), is an innovative venture aiming to sequence 100,000 genomes from NHS patients who have a rare disease, cancer, or an infectious disease. GEL has emphasised the importance of ethical governance and decision-making. However, some sociological critique argues that biomedical/technological organisations presenting themselves as 'ethical' entities do not necessarily reflect a space within which moral thinking occurs. Rather, the 'ethical work' conducted (and displayed) by organisations is more strategic, relating to the politics of the organisation and the need to build public confidence. We set out to explore whether GEL's ethical framework was reflective of this critique, and what this tells us more broadly about how genomics is being integrated into the NHS in response to the ethical and social concerns raised in Generation Genome. We do this by drawing on a series of 20 interviews with individuals associated with or working at GEL.

An overview of the human genome project

Energy Technology Data Exchange (ETDEWEB)

Batzer, M.A.

1994-01-01

The human genome project is one of the most ambitious scientific projects to date, with the ultimate goal being a nucleotide sequence for all four billion bases of human DNA. In the process of determining the nucleotide sequence for each base, the location, function, and regulatory regions from the estimated 100,000 human genes will be identified. The genome project itself relies upon maps of the human genetic code derived from several different levels of resolution. Genetic linkage analysis provides a low resolution genome map. The information for genetic linkage maps is derived from the analysis of chromosome specific markers such as Sequence Tagged Sites (STSs), Variable Number of Tandem Repeats (VNTRs) or other polymorphic (highly informative) loci in a number of different-families. Using this information the location of an unknown disease gene can be limited to a region comprised of one million base pairs of DNA or less. After this point, one must construct or have access to a physical map of the region of interest. Physical mapping involves the construction of an ordered overlapping (contiguous) set of recombinant DNA clones. These clones may be derived from a number of different vectors including cosmids, Bacterial Artificial Chromosomes (BACs), P1 derived Artificial Chromosomes (PACs), somatic cell hybrids, or Yeast Artificial Chromosomes (YACs). The ultimate goal for physical mapping is to establish a completely overlapping (contiguous) set of clones for the entire genome. After a gene or region of interest has been localized using physical mapping the nucleotide sequence is determined. The overlap between genetic mapping, physical mapping and DNA sequencing has proven to be a powerful tool for the isolation of disease genes through positional cloning.

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

Science.gov (United States)

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-04

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Human Genome Diversity (HGD) Project. Summary document

Energy Technology Data Exchange (ETDEWEB)

NONE

1993-12-31

In 1991 a group of human geneticists and molecular biologists proposed to the scientific community that a world wide survey be undertaken of variation in the human genome. To aid their considerations, the committee therefore decided to hold a small series of international workshops to explore the major scientific issues involved. The intention was to define a framework for the project which could provide a basis for much wider and more detailed discussion and planning--it was recognized that the successful implementation of the proposed project, which has come to be known as the Human Genome Diversity (HGD) Project, would not only involve scientists but also various national and international non-scientific groups all of which should contribute to the project`s development. The international HGD workshop held in Sardinia in September 1993 was the last in the initial series of planning workshops. As such it not only explored new ground but also pulled together into a more coherent form much of the formal and informal discussion that had taken place in the preceding two years. This report presents the deliberations of the Sardinia workshop within a consideration of the overall development of the HGD Project to date.

National human genome projects: an update and an agenda.

Science.gov (United States)

An, Joon Yong

2017-01-01

Population genetic and human genetic studies are being accelerated with genome technology and data sharing. Accordingly, in the past 10 years, several countries have initiated genetic research using genome technology and identified the genetic architecture of the ethnic groups living in the corresponding country or suggested the genetic foundation of a social phenomenon. Genetic research has been conducted from epidemiological studies that previously described the health or disease conditions in defined population. This perspective summarizes national genome projects conducted in the past 10 years and introduces case studies to utilize genomic data in genetic research.

Pac-Rim LNG project : final project report specifications

International Nuclear Information System (INIS)

1996-01-01

PAC-RIM LNG Inc. has submitted a proposal to the British Columbia Environmental Assessment Office, to develop a liquefied natural gas project which would purchase pipeline quality natural gas from sources in northeast British Columbia and Alberta and transport it via a dedicated pipeline system to a LNG processing plant on tidewater on the Pacific coast. The project would include storage and processing facilities and a marine loading terminal. This document sets out the final project report specifications prepared by the Project Committee on the basis of input received from the public, First Nations and federal, provincial and local governments

Mapping our genes: The genome projects: How big, how fast

Energy Technology Data Exchange (ETDEWEB)

none,

1988-04-01

For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.

Mapping Our Genes: The Genome Projects: How Big, How Fast

Science.gov (United States)

1988-04-01

For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for ?writing the rules? of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. The Office of Technology Assessment (OTA) prepared this report with the assistance of several hundred experts throughout the world.

The Human Genome Project: big science transforms biology and medicine

OpenAIRE

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...

Controlling our destinies: Historical, philosophical, social and ethical perspectives on the Human Genome Project: Final report, July 1, 1995-June 30, 1996

Energy Technology Data Exchange (ETDEWEB)

Sloan, P.R.

1996-09-25

This report briefly describes the efforts by the organizing committee in preparation for the conference entitled Controlling Our Destinies: Historical, Philosophical, Social, and Ethical Perspectives on the Human Genome Project. The conference was held October 5-8, 1995.

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

Science.gov (United States)

Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M.; Kyrpides, Nikos C.

2010-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/ PMID:19914934

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

Science.gov (United States)

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

Energy Technology Data Exchange (ETDEWEB)

Reddy, Tatiparthi B. K. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Thomas, Alex D. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Stamatis, Dimitri [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Bertsch, Jon [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Isbandi, Michelle [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Jansson, Jakob [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Mallajosyula, Jyothi [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Pagani, Ioanna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lobos, Elizabeth A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Kyrpides, Nikos C. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

2014-10-27

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

Gene disruptions using P transposable elements: an integral component of the Drosophila genome project.

OpenAIRE

Spradling, A C; Stern, D M; Kiss, I; Roote, J; Laverty, T; Rubin, G M

1995-01-01

Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome. DNA flanking the insertions is sequenced, thereby placing an extensive series of genetic markers on the physical genomic map and a...

The human Genome project and the future of oncology

International Nuclear Information System (INIS)

Collins, Francis S.

1996-01-01

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

Genomes to life project quarterly report June 2004.

Energy Technology Data Exchange (ETDEWEB)

Heffelfinger, Grant S.

2005-01-01

This SAND report provides the technical progress through June 2004 of the Sandia-led project, ''Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling'', funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO{sub 2} are important terms in the global environmental response to anthropogenic atmospheric inputs of CO{sub 2} and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes

nGASP - the nematode genome annotation assessment project

Energy Technology Data Exchange (ETDEWEB)

Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

2008-12-19

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C

Final Project Report for Award ER65581

Energy Technology Data Exchange (ETDEWEB)

Stoy, Paul C. [Montana State Univ., Bozeman, MT (United States)

2017-07-13

The attached final project report describes contributions of Montana State University (MSU) to the project "Bridging land-surface fluxes and aerosol concentrations to triggering convective rainfall" (PI: Fuentes).

The Human Genome Project and Biology Education.

Science.gov (United States)

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)

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter

NARCIS (Netherlands)

Archibald, A.L.; Bottema, C.D.; Brauning, R.; Burgess, S.C.; Burt, D.W.; Casas, E.; Cheng, H.H.; Clarke, L.; Couldrey, C.; Dalrymple, B.P.; Elsik, C.G.; Foissac, S.; Giuffra, E.; Groenen, M.A.M.; Hayes, B.J.; Huang, L.S.; Khatib, H.; Kijas, J.W.; Kim, H.; Lunney, J.K.; McCarthy, F.M.; McEwan, J.; Moore, S.; Nanduri, B.; Notredame, C.; Palti, Y.; Plastow, G.S.; Reecy, J.M.; Rohrer, G.; Sarropoulou, E.; Schmidt, C.J.; Silverstein, J.; Tellam, R.L.; Tixier-Boichard, M.; Tosser-klopp, G.; Tuggle, C.K.; Vilkki, J.; White, S.N.; Zhao, S.; Zhou, H.

2015-01-01

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

The 1000 Genomes Project: new opportunities for research and social challenges

Science.gov (United States)

2010-01-01

The 1000 Genomes Project, an international collaboration, is sequencing the whole genome of approximately 2,000 individuals from different worldwide populations. The central goal of this project is to describe most of the genetic variation that occurs at a population frequency greater than 1%. The results of this project will allow scientists to identify genetic variation at an unprecedented degree of resolution and will also help improve the imputation methods for determining unobserved genetic variants that are not represented on current genotyping arrays. By identifying novel or rare functional genetic variants, researchers will be able to pinpoint disease-causing genes in genomic regions initially identified by association studies. This level of detailed sequence information will also improve our knowledge of the evolutionary processes and the genomic patterns that have shaped the human species as we know it today. The new data will also lay the foundation for future clinical applications, such as prediction of disease susceptibility and drug response. However, the forthcoming availability of whole genome sequences at affordable prices will raise ethical concerns and pose potential threats to individual privacy. Nevertheless, we believe that these potential risks are outweighed by the benefits in terms of diagnosis and research, so long as rigorous safeguards are kept in place through legislation that prevents discrimination on the basis of the results of genetic testing. PMID:20193048

Final ITER CTA project board meeting

International Nuclear Information System (INIS)

Vlasenkov, V.

2003-01-01

The final ITER CTA Project Board Meeting (PB) took place in Barcelona, Spain on 8 December 2002. The PB took notes of the comments concerning the status of the International Team and the Participants Teams, including Dr. Aymar's report 'From ITER to a FUSION Power Reactor' and the assessment of the ITER project cost estimate

Sequencing of a new target genome: the Pediculus humanus humanus (Phthiraptera: Pediculidae) genome project.

Science.gov (United States)

Pittendrigh, B R; Clark, J M; Johnston, J S; Lee, S H; Romero-Severson, J; Dasch, G A

2006-11-01

The human body louse, Pediculus humanus humanus (L.), and the human head louse, Pediculus humanus capitis, belong to the hemimetabolous order Phthiraptera. The body louse is the primary vector that transmits the bacterial agents of louse-borne relapsing fever, trench fever, and epidemic typhus. The genomes of the bacterial causative agents of several of these aforementioned diseases have been sequenced. Thus, determining the body louse genome will enhance studies of host-vector-pathogen interactions. Although not important as a major disease vector, head lice are of major social concern. Resistance to traditional pesticides used to control head and body lice have developed. It is imperative that new molecular targets be discovered for the development of novel compounds to control these insects. No complete genome sequence exists for a hemimetabolous insect species primarily because hemimetabolous insects often have large (2000 Mb) to very large (up to 16,300 Mb) genomes. Fortuitously, we determined that the human body louse has one of the smallest genome sizes known in insects, suggesting it may be a suitable choice as a minimal hemimetabolous genome in which many genes have been eliminated during its adaptation to human parasitism. Because many louse species infest birds and mammals, the body louse genome-sequencing project will facilitate studies of their comparative genomics. A 6-8X coverage of the body louse genome, plus sequenced expressed sequence tags, should provide the entomological, evolutionary biology, medical, and public health communities with useful genetic information.

Documenting genomics: Applying archival theory to preserving the records of the Human Genome Project.

Science.gov (United States)

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.

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

Science.gov (United States)

Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A.; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M.; Kyrpides, Nikos C.

2012-01-01

The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11 472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond. PMID:22135293

The human genome project and the future of medical practice ...

African Journals Online (AJOL)

Contrary to the scepticism that characterised the planning stages of the human genome project, the technology and sequence data resulting from the project are set to revolutionise medical practice for good. The expected benefits include: enhanced discovery of disease genes, which will lead to improved knowledge on the ...

The Human Genome Project: An Imperative for International Collaboration.

Science.gov (United States)

Allende, J. E.

1989-01-01

Discussed is the Human Genome Project which aims to decipher the totality of the human genetic information. The historical background, the objectives, international cooperation, ethical discussion, and the role of UNESCO are included. (KR)

Reconsidering democracy - History of the human genome project

NARCIS (Netherlands)

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

Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

OpenAIRE

Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R.; Turner, Gloria E.; Sachs, Matthew S.; Glass, N. Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E.; Birren, Bruce W.; Weiss, Richard L.; Townsend, Jeffrey P.; Loros, Jennifer J.; Nelson, Mary Anne; Lambreghts, Randy

2007-01-01

A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building fr...

Genome Writing: Current Progress and Related Applications

Directory of Open Access Journals (Sweden)

Yueqiang Wang

2018-02-01

Full Text Available The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafety

Reconsidering democracy. History of the Human Genome Project.

NARCIS (Netherlands)

Marli Huijer

2003-01-01

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

The Genome of the Netherlands: design, and project goals

Science.gov (United States)

Boomsma, Dorret I; Wijmenga, Cisca; Slagboom, Eline P; Swertz, Morris A; Karssen, Lennart C; Abdellaoui, Abdel; Ye, Kai; Guryev, Victor; Vermaat, Martijn; van Dijk, Freerk; Francioli, Laurent C; Hottenga, Jouke Jan; Laros, Jeroen F J; Li, Qibin; Li, Yingrui; Cao, Hongzhi; Chen, Ruoyan; Du, Yuanping; Li, Ning; Cao, Sujie; van Setten, Jessica; Menelaou, Androniki; Pulit, Sara L; Hehir-Kwa, Jayne Y; Beekman, Marian; Elbers, Clara C; Byelas, Heorhiy; de Craen, Anton J M; Deelen, Patrick; Dijkstra, Martijn; den Dunnen, Johan T; de Knijff, Peter; Houwing-Duistermaat, Jeanine; Koval, Vyacheslav; Estrada, Karol; Hofman, Albert; Kanterakis, Alexandros; Enckevort, David van; Mai, Hailiang; Kattenberg, Mathijs; van Leeuwen, Elisabeth M; Neerincx, Pieter B T; Oostra, Ben; Rivadeneira, Fernanodo; Suchiman, Eka H D; Uitterlinden, Andre G; Willemsen, Gonneke; Wolffenbuttel, Bruce H; Wang, Jun; de Bakker, Paul I W; van Ommen, Gert-Jan; van Duijn, Cornelia M

2014-01-01

Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent–offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910–1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14–15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project. PMID:23714750

Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels

Directory of Open Access Journals (Sweden)

Xiaoyi eGao

2012-06-01

Full Text Available Genotype imputation is a vital tool in genome-wide association studies (GWAS and meta-analyses of multiple GWAS results. Imputation enables researchers to increase genomic coverage and to pool data generated using different genotyping platforms. HapMap samples are often employed as the reference panel. More recently, the 1000 Genomes Project resource is becoming the primary source for reference panels. Multiple GWAS and meta-analyses are targeting Latinos, the most populous and fastest growing minority group in the US. However, genotype imputation resources for Latinos are rather limited compared to individuals of European ancestry at present, largely because of the lack of good reference data. One choice of reference panel for Latinos is one derived from the population of Mexican individuals in Los Angeles contained in the HapMap Phase 3 project and the 1000 Genomes Project. However, a detailed evaluation of the quality of the imputed genotypes derived from the public reference panels has not yet been reported. Using simulation studies, the Illumina OmniExpress GWAS data from the Los Angles Latino Eye Study and the MACH software package, we evaluated the accuracy of genotype imputation in Latinos. Our results show that the 1000 Genomes Project AMR+CEU+YRI reference panel provides the highest imputation accuracy for Latinos, and that also including Asian samples in the panel can reduce imputation accuracy. We also provide the imputation accuracy for each autosomal chromosome using the 1000 Genomes Project panel for Latinos. Our results serve as a guide to future imputation-based analysis in Latinos.

The Human Genome Project: applications in the diagnosis and treatment of neurologic disease.

Science.gov (United States)

Evans, G A

1998-10-01

The Human Genome Project (HGP), an international program to decode the entire DNA sequence of the human genome in 15 years, represents the largest biological experiment ever conducted. This set of information will contain the blueprint for the construction and operation of a human being. While the primary driving force behind the genome project is the potential to vastly expand the amount of genetic information available for biomedical research, the ramifications for other fields of study in biological research, the biotechnology and pharmaceutical industry, our understanding of evolution, effects on agriculture, and implications for bioethics are likely to be profound.

Earth BioGenome Project: Sequencing life for the future of life.

Science.gov (United States)

Lewin, Harris A; Robinson, Gene E; Kress, W John; Baker, William J; Coddington, Jonathan; Crandall, Keith A; Durbin, Richard; Edwards, Scott V; Forest, Félix; Gilbert, M Thomas P; Goldstein, Melissa M; Grigoriev, Igor V; Hackett, Kevin J; Haussler, David; Jarvis, Erich D; Johnson, Warren E; Patrinos, Aristides; Richards, Stephen; Castilla-Rubio, Juan Carlos; van Sluys, Marie-Anne; Soltis, Pamela S; Xu, Xun; Yang, Huanming; Zhang, Guojie

2018-04-24

Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

Genomes to Life Project Quartely Report October 2004.

Energy Technology Data Exchange (ETDEWEB)

Heffelfinger, Grant S.; Martino, Anthony; Rintoul, Mark Daniel; Geist, Al; Gorin, Andrey; Xu, Ying; Palenik, Brian

2005-02-01

a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these - 4 - pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort. More information about this project, including a copy of the original proposal, can be found at www.genomes

TcruziDB, an Integrated Database, and the WWW Information Server for the Trypanosoma cruzi Genome Project

Directory of Open Access Journals (Sweden)

Degrave Wim

1997-01-01

Full Text Available Data analysis, presentation and distribution is of utmost importance to a genome project. A public domain software, ACeDB, has been chosen as the common basis for parasite genome databases, and a first release of TcruziDB, the Trypanosoma cruzi genome database, is available by ftp from ftp://iris.dbbm.fiocruz.br/pub/genomedb/TcruziDB as well as versions of the software for different operating systems (ftp://iris.dbbm.fiocruz.br/pub/unixsoft/. Moreover, data originated from the project are available from the WWW server at http://www.dbbm.fiocruz.br. It contains biological and parasitological data on CL Brener, its karyotype, all available T. cruzi sequences from Genbank, data on the EST-sequencing project and on available libraries, a T. cruzi codon table and a listing of activities and participating groups in the genome project, as well as meeting reports. T. cruzi discussion lists (tcruzi-l@iris.dbbm.fiocruz.br and tcgenics@iris.dbbm.fiocruz.br are being maintained for communication and to promote collaboration in the genome project

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Science.gov (United States)

Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Kuehn, Michael S; Taylor, Christopher M; Neph, Shane; Koch, Christoph M; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A; Andrews, Robert M; Flicek, Paul; Boyle, Patrick J; Cao, Hua; Carter, Nigel P; Clelland, Gayle K; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C; Dorschner, Michael O; Fiegler, Heike; Giresi, Paul G; Goldy, Jeff; Hawrylycz, Michael; Haydock, Andrew; Humbert, Richard; James, Keith D; Johnson, Brett E; Johnson, Ericka M; Frum, Tristan T; Rosenzweig, Elizabeth R; Karnani, Neerja; Lee, Kirsten; Lefebvre, Gregory C; Navas, Patrick A; Neri, Fidencio; Parker, Stephen C J; Sabo, Peter J; Sandstrom, Richard; Shafer, Anthony; Vetrie, David; Weaver, Molly; Wilcox, Sarah; Yu, Man; Collins, Francis S; Dekker, Job; Lieb, Jason D; Tullius, Thomas D; Crawford, Gregory E; Sunyaev, Shamil; Noble, William S; Dunham, Ian; Denoeud, France; Reymond, Alexandre; Kapranov, Philipp; Rozowsky, Joel; Zheng, Deyou; Castelo, Robert; Frankish, Adam; Harrow, Jennifer; Ghosh, Srinka; Sandelin, Albin; Hofacker, Ivo L; Baertsch, Robert; Keefe, Damian; Dike, Sujit; Cheng, Jill; Hirsch, Heather A; Sekinger, Edward A; Lagarde, Julien; Abril, Josep F; Shahab, Atif; Flamm, Christoph; Fried, Claudia; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Tanzer, Andrea; Washietl, Stefan; Korbel, Jan; Emanuelsson, Olof; Pedersen, Jakob S; Holroyd, Nancy; Taylor, Ruth; Swarbreck, David; Matthews, Nicholas; Dickson, Mark C; Thomas, Daryl J; Weirauch, Matthew T; Gilbert, James; Drenkow, Jorg; Bell, Ian; Zhao, XiaoDong; Srinivasan, K G; Sung, Wing-Kin; Ooi, Hong Sain; Chiu, Kuo Ping; Foissac, Sylvain; Alioto, Tyler; Brent, Michael; Pachter, Lior; Tress, Michael L; Valencia, Alfonso; Choo, Siew Woh; Choo, Chiou Yu; Ucla, Catherine; Manzano, Caroline; Wyss, Carine; Cheung, Evelyn; Clark, Taane G; Brown, James B; Ganesh, Madhavan; Patel, Sandeep; Tammana, Hari; Chrast, Jacqueline; Henrichsen, Charlotte N; Kai, Chikatoshi; Kawai, Jun; Nagalakshmi, Ugrappa; Wu, Jiaqian; Lian, Zheng; Lian, Jin; Newburger, Peter; Zhang, Xueqing; Bickel, Peter; Mattick, John S; Carninci, Piero; Hayashizaki, Yoshihide; Weissman, Sherman; Hubbard, Tim; Myers, Richard M; Rogers, Jane; Stadler, Peter F; Lowe, Todd M; Wei, Chia-Lin; Ruan, Yijun; Struhl, Kevin; Gerstein, Mark; Antonarakis, Stylianos E; Fu, Yutao; Green, Eric D; Karaöz, Ulaş; Siepel, Adam; Taylor, James; Liefer, Laura A; Wetterstrand, Kris A; Good, Peter J; Feingold, Elise A; Guyer, Mark S; Cooper, Gregory M; Asimenos, George; Dewey, Colin N; Hou, Minmei; Nikolaev, Sergey; Montoya-Burgos, Juan I; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Huang, Haiyan; Zhang, Nancy R; Holmes, Ian; Mullikin, James C; Ureta-Vidal, Abel; Paten, Benedict; Seringhaus, Michael; Church, Deanna; Rosenbloom, Kate; Kent, W James; Stone, Eric A; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross C; Haussler, David; Miller, Webb; Sidow, Arend; Trinklein, Nathan D; Zhang, Zhengdong D; Barrera, Leah; Stuart, Rhona; King, David C; Ameur, Adam; Enroth, Stefan; Bieda, Mark C; Kim, Jonghwan; Bhinge, Akshay A; Jiang, Nan; Liu, Jun; Yao, Fei; Vega, Vinsensius B; Lee, Charlie W H; Ng, Patrick; Shahab, Atif; Yang, Annie; Moqtaderi, Zarmik; Zhu, Zhou; Xu, Xiaoqin; Squazzo, Sharon; Oberley, Matthew J; Inman, David; Singer, Michael A; Richmond, Todd A; Munn, Kyle J; Rada-Iglesias, Alvaro; Wallerman, Ola; Komorowski, Jan; Fowler, Joanna C; Couttet, Phillippe; Bruce, Alexander W; Dovey, Oliver M; Ellis, Peter D; Langford, Cordelia F; Nix, David A; Euskirchen, Ghia; Hartman, Stephen; Urban, Alexander E; Kraus, Peter; Van Calcar, Sara; Heintzman, Nate; Kim, Tae Hoon; Wang, Kun; Qu, Chunxu; Hon, Gary; Luna, Rosa; Glass, Christopher K; Rosenfeld, M Geoff; Aldred, Shelley Force; Cooper, Sara J; Halees, Anason; Lin, Jane M; Shulha, Hennady P; Zhang, Xiaoling; Xu, Mousheng; Haidar, Jaafar N S; Yu, Yong; Ruan, Yijun; Iyer, Vishwanath R; Green, Roland D; Wadelius, Claes; Farnham, Peggy J; Ren, Bing; Harte, Rachel A; Hinrichs, Angie S; Trumbower, Heather; Clawson, Hiram; Hillman-Jackson, Jennifer; Zweig, Ann S; Smith, Kayla; Thakkapallayil, Archana; Barber, Galt; Kuhn, Robert M; Karolchik, Donna; Armengol, Lluis; Bird, Christine P; de Bakker, Paul I W; Kern, Andrew D; Lopez-Bigas, Nuria; Martin, Joel D; Stranger, Barbara E; Woodroffe, Abigail; Davydov, Eugene; Dimas, Antigone; Eyras, Eduardo; Hallgrímsdóttir, Ingileif B; Huppert, Julian; Zody, Michael C; Abecasis, Gonçalo R; Estivill, Xavier; Bouffard, Gerard G; Guan, Xiaobin; Hansen, Nancy F; Idol, Jacquelyn R; Maduro, Valerie V B; Maskeri, Baishali; McDowell, Jennifer C; Park, Morgan; Thomas, Pamela J; Young, Alice C; Blakesley, Robert W; Muzny, Donna M; Sodergren, Erica; Wheeler, David A; Worley, Kim C; Jiang, Huaiyang; Weinstock, George M; Gibbs, Richard A; Graves, Tina; Fulton, Robert; Mardis, Elaine R; Wilson, Richard K; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B; Chang, Jean L; Lindblad-Toh, Kerstin; Lander, Eric S; Koriabine, Maxim; Nefedov, Mikhail; Osoegawa, Kazutoyo; Yoshinaga, Yuko; Zhu, Baoli; de Jong, Pieter J

2007-06-14

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Enhancing Biology Instruction with the Human Genome Project

Science.gov (United States)

Buxeda, Rosa J.; Moore-Russo, Deborah A.

2003-01-01

The Human Genome Project (HGP) is a recent scientific milestone that has received notable attention. This article shows how a biology course is using the HGP to enhance students' experiences by providing awareness of cutting edge research, with information on new emerging career options, and with opportunities to consider ethical questions raised…

The Human Genome Project: Biology, Computers, and Privacy.

Science.gov (United States)

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…

ROLL OUT THE TALENT : Final project report

OpenAIRE

Eerola, Tuomas; Tuominen, Pirjo; Hakkarainen, Riitta-Liisa; Laurikainen, Marja; Mero, Niina

2014-01-01

The ROLL OUT THE TALENT project was born out of the desire to recognise and support the strengths of vocational students and to develop new and innovative operating models. ROLL OUT THE TALENT promoted regional cooperation between institutes and companies. The project produced operating and study path models that take into consideration the individual strengths of vocational students and the principles of lifelong learning. This is the final report of the ROLL OUT THE TALENT project, and ...

The fracture zone project - final report

International Nuclear Information System (INIS)

Andersson, Peter

1993-09-01

This report summarizes the work and the experiences gained during the fracture zone project at the Finnsjoen study site. The project is probably the biggest effort, so far, to characterize a major fracture zone in crystalline bedrock. The project was running between 1984-1990 involving a large number of geological, geohydrological, geochemical, and geomechanical investigation. The methods used for identification and characterization are reviewed and discussed in terms of applicability and possible improvements for future investigations. The discussion is exemplified with results from the investigation within the project. Flow and transport properties of the zone determined from hydraulic tests and tracer tests are discussed. A large number of numerical modelling efforts performed within the fracture zone project, the INTRAVAL project, and the SKB91-study are summarized and reviewed. Finally, occurrence of similar zones and the relevance of major low angle fracture zones in connection to the siting of an underground repository is addressed

Genomics England's implementation of its public engagement strategy: Blurred boundaries between engagement for the United Kingdom's 100,000 Genomes project and the need for public support.

Science.gov (United States)

Samuel, Gabrielle Natalie; Farsides, Bobbie

2018-04-01

The United Kingdom's 100,000 Genomes Project has the aim of sequencing 100,000 genomes from National Health Service patients such that whole genome sequencing becomes routine clinical practice. It also has a research-focused goal to provide data for scientific discovery. Genomics England is the limited company established by the Department of Health to deliver the project. As an innovative scientific/clinical venture, it is interesting to consider how Genomics England positions itself in relation to public engagement activities. We set out to explore how individuals working at, or associated with, Genomics England enacted public engagement in practice. Our findings show that individuals offered a narrative in which public engagement performed more than one function. On one side, public engagement was seen as 'good practice'. On the other, public engagement was presented as core to the project's success - needed to encourage involvement and ultimately recruitment. We discuss the implications of this in this article.

Comparing genetic variants detected in the 1000 genomes project ...

Indian Academy of Sciences (India)

Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide ...

Enabling a community to dissect an organism: overview of the Neurospora functional genomics project.

Science.gov (United States)

Dunlap, Jay C; Borkovich, Katherine A; Henn, Matthew R; Turner, Gloria E; Sachs, Matthew S; Glass, N Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E; Birren, Bruce W; Weiss, Richard L; Townsend, Jeffrey P; Loros, Jennifer J; Nelson, Mary Anne; Lambreghts, Randy; Colot, Hildur V; Park, Gyungsoon; Collopy, Patrick; Ringelberg, Carol; Crew, Christopher; Litvinkova, Liubov; DeCaprio, Dave; Hood, Heather M; Curilla, Susan; Shi, Mi; Crawford, Matthew; Koerhsen, Michael; Montgomery, Phil; Larson, Lisa; Pearson, Matthew; Kasuga, Takao; Tian, Chaoguang; Baştürkmen, Meray; Altamirano, Lorena; Xu, Junhuan

2007-01-01

A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to accomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of non yeast fungi. Building from the completely sequenced 43-Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes. Oligonucleotide-based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.

78 FR 26063 - Central Utah Project Completion Act; East Hobble Creek Restoration Project Final Environmental...

Science.gov (United States)

2013-05-03

...-100-00-0-0, CUPCA00] Central Utah Project Completion Act; East Hobble Creek Restoration Project Final... Creek Restoration Project. These two agencies have determined that the proposed [[Page 26064

Advanced Air Transportation Technologies Project, Final Document Collection

Science.gov (United States)

Mogford, Richard H.; Wold, Sheryl (Editor)

2008-01-01

This CD ROM contains a compilation of the final documents of the Advanced Air Transportation Technologies (AAIT) project, which was an eight-year (1996 to 2004), $400M project managed by the Airspace Systems Program office, which was part of the Aeronautics Research Mission Directorate at NASA Headquarters. AAIT focused on developing advanced automation tools and air traffic management concepts that would help improve the efficiency of the National Airspace System, while maintaining or enhancing safety. The documents contained in the CD are final reports on AAIT tasks that serve to document the project's accomplishments over its eight-year term. Documents include information on: Advanced Air Transportation Technologies, Autonomous Operations Planner, Collaborative Arrival Planner, Distributed Air/Ground Traffic Management Concept Elements 5, 6, & 11, Direct-To, Direct-To Technology Transfer, Expedite Departure Path, En Route Data Exchange, Final Approach Spacing Tool - (Active and Passive), Multi-Center Traffic Management Advisor, Multi Center Traffic Management Advisor Technology Transfer, Surface Movement Advisor, Surface Management System, Surface Management System Technology Transfer and Traffic Flow Management Research & Development.

76 FR 57729 - Boundary Hydroelectric Project; Sullivan Creek Project; Notice of Availability of the Final...

Science.gov (United States)

2011-09-16

...-015] Boundary Hydroelectric Project; Sullivan Creek Project; Notice of Availability of the Final Environmental Impact Statement for the Relicensing of the Boundary Hydroelectric Project and the Surrender of... reviewed the applications for license for the Boundary Hydroelectric Project (FERC No. 2144-38), and the...

Prototypical Consolidation Demonstration Project: Final report

International Nuclear Information System (INIS)

Gili, J.A.; Poston, V.K.

1993-11-01

This is the final report of the Prototypical Consolidation Demonstration Project, which was funded by the US Department of Energy's Office of Civilian Radioactive Waste Management. The project had two objectives: (a) to develop and demonstrate a prototype of production-scale equipment for the dry, horizontal consolidation and packaging of spent nuclear fuel rods from commercial boiling water reactor and pressurized water reactor fuel assemblies, and (b) to report the development and demonstration results to the US Department of Energy, Idaho Operations Office. This report summarizes the activities and conclusions of the project management contractor, EG ampersand G Idaho, Inc., and the fabrication and testing contractor, NUS Corporation (NUS). The report also presents EG ampersand G Idaho's assessments of the equipment and procedures developed by NUS

Increasing Prediction the Original Final Year Project of Student Using Genetic Algorithm

Science.gov (United States)

Saragih, Rijois Iboy Erwin; Turnip, Mardi; Sitanggang, Delima; Aritonang, Mendarissan; Harianja, Eva

2018-04-01

Final year project is very important forgraduation study of a student. Unfortunately, many students are not seriouslydidtheir final projects. Many of studentsask for someone to do it for them. In this paper, an application of genetic algorithms to predict the original final year project of a studentis proposed. In the simulation, the data of the final project for the last 5 years is collected. The genetic algorithm has several operators namely population, selection, crossover, and mutation. The result suggest that genetic algorithm can do better prediction than other comparable model. Experimental results of predicting showed that 70% was more accurate than the previous researched.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Science.gov (United States)

Cai, Binghuang; Li, Biao; Kiga, Nikki; Thusberg, Janita; Bergquist, Timothy; Chen, Yun-Ching; Niknafs, Noushin; Carter, Hannah; Tokheim, Collin; Beleva-Guthrie, Violeta; Douville, Christopher; Bhattacharya, Rohit; Yeo, Hui Ting Grace; Fan, Jean; Sengupta, Sohini; Kim, Dewey; Cline, Melissa; Turner, Tychele; Diekhans, Mark; Zaucha, Jan; Pal, Lipika R; Cao, Chen; Yu, Chen-Hsin; Yin, Yizhou; Carraro, Marco; Giollo, Manuel; Ferrari, Carlo; Leonardi, Emanuela; Tosatto, Silvio C E; Bobe, Jason; Ball, Madeleine; Hoskins, Roger A; Repo, Susanna; Church, George; Brenner, Steven E; Moult, John; Gough, Julian; Stanke, Mario; Karchin, Rachel; Mooney, Sean D

2017-09-01

The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features. © 2017 Wiley Periodicals, Inc.

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Science.gov (United States)

Lewis, Tony E; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L; Buchan, Daniel W A; Chothia, Cyrus; Cuff, Alison; Dana, Jose M; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T; Kelley, Lawrence A; Kleywegt, Gerard J; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G; Ochoa-Montaño, Bernardo; Rackham, Owen J L; Smith, James; Sternberg, Michael J E; Velankar, Sameer; Yeats, Corin; Orengo, Christine

2013-01-01

Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).

The Human Genome Project and the social contract: a law policy approach.

Science.gov (United States)

Byk, C

1992-08-01

For the first time in history, genetics will enable science to completely identify each human as genetically unique. Will this knowledge reinforce the trend for more individual liberties or will it create a 'brave new world'? A law policy approach to the problems raised by the human genome project shows how far our democratic institutions are from being the proper forum to discuss such issues. Because of the fears and anxiety raised in the population, and also because of its wide implications on the everyday life, the human genome analysis more than any other project needs to succeed in setting up such a social assessment.

Genome-wide analysis of wild-type Epstein-Barr virus genomes derived from healthy individuals of the 1,000 Genomes Project.

Science.gov (United States)

Santpere, Gabriel; Darre, Fleur; Blanco, Soledad; Alcami, Antonio; Villoslada, Pablo; Mar Albà, M; Navarro, Arcadi

2014-04-01

Most people in the world (∼90%) are infected by the Epstein-Barr virus (EBV), which establishes itself permanently in B cells. Infection by EBV is related to a number of diseases including infectious mononucleosis, multiple sclerosis, and different types of cancer. So far, only seven complete EBV strains have been described, all of them coming from donors presenting EBV-related diseases. To perform a detailed comparative genomic analysis of EBV including, for the first time, EBV strains derived from healthy individuals, we reconstructed EBV sequences infecting lymphoblastoid cell lines (LCLs) from the 1000 Genomes Project. As strain B95-8 was used to transform B cells to obtain LCLs, it is always present, but a specific deletion in its genome sets it apart from natural EBV strains. After studying hundreds of individuals, we determined the presence of natural EBV in at least 10 of them and obtained a set of variants specific to wild-type EBV. By mapping the natural EBV reads into the EBV reference genome (NC007605), we constructed nearly complete wild-type viral genomes from three individuals. Adding them to the five disease-derived EBV genomic sequences available in the literature, we performed an in-depth comparative genomic analysis. We found that latency genes harbor more nucleotide diversity than lytic genes and that six out of nine latency-related genes, as well as other genes involved in viral attachment and entry into host cells, packaging, and the capsid, present the molecular signature of accelerated protein evolution rates, suggesting rapid host-parasite coevolution.

Final Report of the Final Meeting of Project Coordinators

International Nuclear Information System (INIS)

Cordero Calderon, Carlos F.

1996-06-01

The Costa Rican Electricity Institute has always been worried of the verification of the good state of the works and thus to guarantee their operation. For that reason, it has established different sorts of auscultation of the Arenal's Dam. Some investigations have been done to find new methods to improve and to eliminate risks in different works or projects. The Arenal's Dam is one of the greatest engineering works in Costa Rica, it has the Arenal, Corobici and Sandillal Hydroelectric Plants. Furthermore, the irrigation system in the Tempisque River Valley, in the Guanacaste province. One special characteristic of the Site of the Dam, is the near location of the Arenal Volcano, in full activity and located at 6 Km. from the dam. This report has two goals, one is the traditional permanent measurements report for the project, and the other, is to present it as a final work of the Project Arcal XVIII, to the International Atomic Energy Agency. This report analyses the geo-hydraulic, structural and topographic auscultation, as well as the activities accomplished during the ARCAL XVIII /8/018, Application of Tracer Techniques for Leakage in Dams and Damming Project, based on information gathered through the geo-chemical auscultation, until June 1996. (author).30 ills., 80 charts, 35 tabs

Project Rio Blanco: site restoration. Final report

International Nuclear Information System (INIS)

1978-01-01

Project Rio Blanco was a joint Government-industry experiment using nuclear explosives to stimulate the flow of natural gas from low permeability formations which could not be economically produced through conventional methods. The project consisted of the simultaneous detonation of three nuclear explosives on May 17, 1973, in a 7,000 foot well in northwestern Colorado. Gas production testing and project evaluation continued through June 1976. The site cleanup and restoration planning phase began in December 1975 and was concluded with the issuance of an operational plan, Project Rio Blanco Site Cleanup and Restoration Plan, NVO-173, in May 1976. Actual site restoration activities were conducted during the period from July to November 1976. The activities throughout the restoration period are summarized and the final site status, including the disposition of all project facilities and the status of all project related wells after plug and abandonment and recompletion work are described

LYNX community advocacy & service engagement (CASE) project final report.

Science.gov (United States)

2009-05-14

This report is a final assessment of the Community Advocacy & Service Engagement (CASE) project, a LYNX-FTA research project designed : to study transit education and public engagement methods in Central Florida. In the Orlando area, as in other part...

Getting the Word Out on the Human Genome Project: A Course for Physicians

Energy Technology Data Exchange (ETDEWEB)

Sara L. Tobin

2004-09-29

Our project, ''Getting the Word Out on the Human Genome Project: A Course for Physicians,'' presented educational goals to convey the power and promise of the Human Genome Program to a variety of professional, educational, and public audiences. Our initial goal was to provide practicing physicians with a comprehensive multimedia tool to update their skills in the genomic era. We therefore created the multimedia courseware, ''The New Genetics: Courseware for Physicians. Molecular Concepts, Applications, and Ramifications.'' However, as the project moved forward, several unanticipated audiences found the courseware to be useful for instruction and for self-education, so an additional edition of the courseware ''The New Genetics: Medicine and the Human Genome. Molecular Concepts, Applications, and Ramifications'' was published simultaneously with the physician version. At the time that both versions of the courseware were being completed, Stanford's Office of Technology Licensing opted not to commercialize the courseware and offered a license-back agreement if the authors founded a commercial business. The authors thus became closely involved in marketing and sales, and several thousand copies of the courseware have been sold. Surprisingly, the non-physician version has turned out to be more in demand, and this has led us in several new directions, most of which involve undergraduate education. These are discussed in detail in the Report.

Primer on molecular genetics. DOE Human Genome Program

Energy Technology Data Exchange (ETDEWEB)

1992-04-01

This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

Admiralty Inlet Pilot Tidal Project Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Collar, Craig [Public Utility District No. 1 of Snohomish County, Everett, WA (United States)

2015-09-14

This document represents the final report for the Admiralty Inlet Pilot Tidal Project, located in Puget Sound, Washington, United States. The Project purpose was to license, permit, and install a grid-connected deep-water tidal turbine array (two turbines) to be used as a platform to gather operational and environmental data on tidal energy generation. The data could then be used to better inform the viability of commercial tidal energy generation from technical, economic, social, and environmental standpoints. This data would serve as a critical step towards the responsible advancement of commercial scale tidal energy in the United States and around the world. In late 2014, Project activities were discontinued due to escalating costs, and the DOE award was terminated in early 2015. Permitting, licensing, and engineering design activities were completed under this award. Final design, deployment, operation, and monitoring were not completed. This report discusses the results and accomplishments achieved under the subject award.

The modest beginnings of one genome project.

Science.gov (United States)

Kaback, David B

2013-06-01

One of the top things on a geneticist's wish list has to be a set of mutants for every gene in their particular organism. Such a set was produced for the yeast, Saccharomyces cerevisiae near the end of the 20th century by a consortium of yeast geneticists. However, the functional genomic analysis of one chromosome, its smallest, had already begun more than 25 years earlier as a project that was designed to define most or all of that chromosome's essential genes by temperature-sensitive lethal mutations. When far fewer than expected genes were uncovered, the relatively new field of molecular cloning enabled us and indeed, the entire community of yeast researchers to approach this problem more definitively. These studies ultimately led to cloning, genomic sequencing, and the production and phenotypic analysis of the entire set of knockout mutations for this model organism as well as a better concept of what defines an essential function, a wish fulfilled that enables this model eukaryote to continue at the forefront of research in modern biology.

The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants.

Science.gov (United States)

Reuter, Miriam S; Walker, Susan; Thiruvahindrapuram, Bhooma; Whitney, Joe; Cohn, Iris; Sondheimer, Neal; Yuen, Ryan K C; Trost, Brett; Paton, Tara A; Pereira, Sergio L; Herbrick, Jo-Anne; Wintle, Richard F; Merico, Daniele; Howe, Jennifer; MacDonald, Jeffrey R; Lu, Chao; Nalpathamkalam, Thomas; Sung, Wilson W L; Wang, Zhuozhi; Patel, Rohan V; Pellecchia, Giovanna; Wei, John; Strug, Lisa J; Bell, Sherilyn; Kellam, Barbara; Mahtani, Melanie M; Bassett, Anne S; Bombard, Yvonne; Weksberg, Rosanna; Shuman, Cheryl; Cohn, Ronald D; Stavropoulos, Dimitri J; Bowdin, Sarah; Hildebrandt, Matthew R; Wei, Wei; Romm, Asli; Pasceri, Peter; Ellis, James; Ray, Peter; Meyn, M Stephen; Monfared, Nasim; Hosseini, S Mohsen; Joseph-George, Ann M; Keeley, Fred W; Cook, Ryan A; Fiume, Marc; Lee, Hin C; Marshall, Christian R; Davies, Jill; Hazell, Allison; Buchanan, Janet A; Szego, Michael J; Scherer, Stephen W

2018-02-05

The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set ( n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care. © 2018 Joule Inc. or its licensors.

Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics.

Science.gov (United States)

Dong, Zirui; Wang, Huilin; Chen, Haixiao; Jiang, Hui; Yuan, Jianying; Yang, Zhenjun; Wang, Wen-Jing; Xu, Fengping; Guo, Xiaosen; Cao, Ye; Zhu, Zhenzhen; Geng, Chunyu; Cheung, Wan Chee; Kwok, Yvonne K; Yang, Huanming; Leung, Tak Yeung; Morton, Cynthia C; Cheung, Sau Wai; Choy, Kwong Wai

2017-11-02

PurposeRecent studies demonstrate that whole-genome sequencing enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in the 1000 Genomes Project without knowing which bands were affected.MethodsThe 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparent BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold).ResultsWith this approach, we detected four reciprocal balanced translocations and four inversions, ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and polymerase chain reaction studies. One of these DNAs has a subtle translocation that is not readily identified by chromosome analysis because of the similarity of the banding patterns and size of exchanged segments, and another results in disruption of all transcripts of an OMIM gene.ConclusionOur study demonstrates the extension of utilizing low-pass whole-genome sequencing for unbiased detection of BCAs including translocations and inversions previously unknown in the 1000 Genomes Project.GENETICS in MEDICINE advance online publication, 2 November 2017; doi:10.1038/gim.2017.170.

Competence development organizations in project management on the basis of genomic model methodologies

OpenAIRE

Бушуев, Сергей Дмитриевич; Рогозина, Виктория Борисовна; Ярошенко, Юрий Федерович

2013-01-01

The matrix technology for identification of organisational competencies in project management is presented in the article. Matrix elements are the components of organizational competence in the field of project management and project management methodology represented in the structure of the genome. The matrix model of competence in the framework of the adopted methodologies and scanning method for identifying organizational competences formalised. Proposed methods for building effective proj...

Understanding our genetic inheritance: The US Human Genome Project, The first five years FY 1991--1995

Energy Technology Data Exchange (ETDEWEB)

None

1990-04-01

The Human Genome Initiative is a worldwide research effort with the goal of analyzing the structure of human DNA and determining the location of the estimated 100,000 human genes. In parallel with this effort, the DNA of a set of model organisms will be studied to provide the comparative information necessary for understanding the functioning of the human genome. The information generated by the human genome project is expected to be the source book for biomedical science in the 21st century and will by of immense benefit to the field of medicine. It will help us to understand and eventually treat many of the more than 4000 genetic diseases that affect mankind, as well as the many multifactorial diseases in which genetic predisposition plays an important role. A centrally coordinated project focused on specific objectives is believed to be the most efficient and least expensive way of obtaining this information. The basic data produced will be collected in electronic databases that will make the information readily accessible on convenient form to all who need it. This report describes the plans for the U.S. human genome project and updates those originally prepared by the Office of Technology Assessment (OTA) and the National Research Council (NRC) in 1988. In the intervening two years, improvements in technology for almost every aspect of genomics research have taken place. As a result, more specific goals can now be set for the project.

MIT LMFBR blanket research project. Final summary report

International Nuclear Information System (INIS)

Driscoll, M.J.

1983-08-01

This is a final summary report on an experimental and analytical program for the investigation of LMFBR blanket characteristics carried out at MIT in the period 1969 to 1983. During this span of time, work was carried out on a wide range of subtasks, ranging from neutronic and photonic measurements in mockups of blankets using the Blanket Test Facility at the MIT Research Reactor, to analytic/numerical investigations of blanket design and economics. The main function of this report is to serve as a resource document which will permit ready reference to the more detailed topical reports and theses issued over the years on the various aspects of project activities. In addition, one aspect of work completed during the final year of the project, on doubly-heterogeneous blanket configurations, is documented for the record

U.S. LCI Database Project--Final Phase I Report

Energy Technology Data Exchange (ETDEWEB)

2003-08-01

This Phase I final report reviews the process and provides a plan for the execution of subsequent phases of the database project, including recommended data development priorities and a preliminary cost estimate. The ultimate goal of the project is to develop publicly available LCI Data modules for commonly used materials, products, and processes.

Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class.

Science.gov (United States)

Jarvis, Erich D

2016-01-01

The rapid pace of advances in genome technology, with concomitant reductions in cost, makes it feasible that one day in our lifetime we will have available extant genomes of entire classes of species, including vertebrates. I recently helped cocoordinate the large-scale Avian Phylogenomics Project, which collected and sequenced genomes of 48 bird species representing most currently classified orders to address a range of questions in phylogenomics and comparative genomics. The consortium was able to answer questions not previously possible with just a few genomes. This success spurred on the creation of a project to sequence the genomes of at least one individual of all extant ∼10,500 bird species. The initiation of this project has led us to consider what questions now impossible to answer could be answered with all genomes, and could drive new questions now unimaginable. These include the generation of a highly resolved family tree of extant species, genome-wide association studies across species to identify genetic substrates of many complex traits, redefinition of species and the species concept, reconstruction of the genomes of common ancestors, and generation of new computational tools to address these questions. Here I present visions for the future by posing and answering questions regarding what scientists could potentially do with available genomes of an entire vertebrate class.

Deep whole-genome sequencing of 90 Han Chinese genomes.

Science.gov (United States)

Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

2017-09-01

Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project.

Science.gov (United States)

Higgins, Anne W; Alkuraya, Fowzan S; Bosco, Amy F; Brown, Kerry K; Bruns, Gail A P; Donovan, Diana J; Eisenman, Robert; Fan, Yanli; Farra, Chantal G; Ferguson, Heather L; Gusella, James F; Harris, David J; Herrick, Steven R; Kelly, Chantal; Kim, Hyung-Goo; Kishikawa, Shotaro; Korf, Bruce R; Kulkarni, Shashikant; Lally, Eric; Leach, Natalia T; Lemyre, Emma; Lewis, Janine; Ligon, Azra H; Lu, Weining; Maas, Richard L; MacDonald, Marcy E; Moore, Steven D P; Peters, Roxanna E; Quade, Bradley J; Quintero-Rivera, Fabiola; Saadi, Irfan; Shen, Yiping; Shendure, Jay; Williamson, Robin E; Morton, Cynthia C

2008-03-01

Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.

Relationship between Deleterious Variation, Genomic Autozygosity, and Disease Risk: Insights from The 1000 Genomes Project.

Science.gov (United States)

Pemberton, Trevor J; Szpiech, Zachary A

2018-04-05

Genomic regions of autozygosity (ROAs) represent segments of individual genomes that are homozygous for haplotypes inherited identical-by-descent (IBD) from a common ancestor. ROAs are nonuniformly distributed across the genome, and increased ROA levels are a reported risk factor for numerous complex diseases. Previously, we hypothesized that long ROAs are enriched for deleterious homozygotes as a result of young haplotypes with recent deleterious mutations-relatively untouched by purifying selection-being paired IBD as a consequence of recent parental relatedness, a pattern supported by ROA and whole-exome sequence data on 27 individuals. Here, we significantly bolster support for our hypothesis and expand upon our original analyses using ROA and whole-genome sequence data on 2,436 individuals from The 1000 Genomes Project. Considering CADD deleteriousness scores, we reaffirm our previous observation that long ROAs are enriched for damaging homozygotes worldwide. We show that strongly damaging homozygotes experience greater enrichment than weaker damaging homozygotes, while overall enrichment varies appreciably among populations. Mendelian disease genes and those encoding FDA-approved drug targets have significantly increased rates of gain in damaging homozygotes with increasing ROA coverage relative to all other genes. In genes implicated in eight complex phenotypes for which ROA levels have been identified as a risk factor, rates of gain in damaging homozygotes vary across phenotypes and populations but frequently differ significantly from non-disease genes. These findings highlight the potential confounding effects of population background in the assessment of associations between ROA levels and complex disease risk, which might underlie reported inconsistencies in ROA-phenotype associations. Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Iowa Hill Pumped Storage Project Investigations - Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Hanson, David [Sacramento Municipal Unitlity District, Sacramento, CA (United States)

2016-07-01

This Final Technical Report is a summary of the activities and outcome of the Department of Energy (DOE) Assistance Agreement DE-EE0005414 with the Sacramento Municipal Utility District (SMUD). The Assistance Agreement was created in 2012 to support investigations into the Iowa Hill Pumped-storage Project (Project), a new development that would add an additional 400 MW of capacity to SMUD’s existing 688MW Upper American River Hydroelectric Project (UARP) in the Sierra Nevada mountains east of Sacramento, California.

FINAL REPORT FOR THE DIII-D RADIATIVE DIVERTOR PROJECT

International Nuclear Information System (INIS)

O'NEIL, RC; STAMBAUGH, RD

2002-01-01

OAK A271 FINAL REPORT FOR THE DIII-D RADIATIVE DIVERTOR PROJECT. The Radiative Divertor Project originated in 1993 when the DIII-D Five Year Plan for the period 1994--1998 was prepared. The Project Information Sheet described the objective of the project as ''to demonstrate dispersal of divertor power by a factor of then with sufficient diagnostics and modeling to extend the results to ITER and TPX''. Key divertor components identified were: (1) Carbon-carbon and graphite armor tiles; (2) The divertor structure providing a gas baffle and cooling; and (3) The divertor cryopumps to pump fuel and impurities

Final report for the 'Melt-Vessel Interactions' Project. European Union R and TD Program 4th Framework. MVI project final research report

International Nuclear Information System (INIS)

Sehgal, B.R.; Dinh, T.N.; Nourgaliev, R.R.; Bui, V.A.; Green, J.; Kolb, G.; Karbojian, A.; Theerthan, S.A.; Gubaidulline, A.; Bonnet, J.M.; Rouge, S.; Narcoux, M.; Liegeois, A.; Turland, B.D.; Dobson, G.P.; Siccama, A.; Ikonen, K.; Parozzi, F.; Kolev, N.; Caira, M.

1999-04-01

The Melt Vessel Interaction (MVI) project is concerned with the consequences of the interactions that a core melt, generated during a postulated severe accident in a light water reactor, may have with the pressure vessel. In particular, the issues concerned with the failure of the vessel bottom head are the focus of the research. The specific objectives of the project are to obtain data and develop validated models, which could be applied to prototypic plants, and accident conditions, for resolution of issues related to the melt vessel interactions. The project work has been performed by nine partners having varied responsibility. The work included a large number of experiments, with simulant materials, whose observations and results are employed, respectively, to understand the physical mechanisms and to develop validated models. Applications to the prototypic geometry and conditions have also been performed. This report is volume 1 of the Final Report for the Project, in which a summary of the progress achieved in the experimental program is provided. We have, however, included some aspects of the modeling activities. Volume 2 of the Final report describes the progress achieved in the modeling program. The progress achieved in the experimental and modeling parts of the Project has led to the resolution of some of the issues of melt vessel interaction. Considerable progress was also achieved towards resolution of the remaining issues

Northeast Oregon Hatchery Project final siting report. Final report

International Nuclear Information System (INIS)

1995-03-01

This report presents the results of site analysis for the Bonneville Power Administration Northeast Oregon Hatchery Project. The purpose of this project is to provide engineering services for the siting and conceptual design of hatchery facilities for the Bonneville Power Administration. The hatchery project consists of artificial production facilities for salmon and steelhead to enhance production in three adjacent tributaries to the Columbia River in northeast Oregon: the Grande Ronde, Walla Walla, and Imnaha River drainage basins. Facilities identified in the master plan include adult capture and holding facilities; spawning incubation, and early rearing facilities; full-term rearing facilities; and direct release or acclimation facilities. The evaluation includes consideration of a main production facility for one or more of the basins or several smaller satellite production facilities to be located within major subbasins. The historic and current distribution of spring and fall chinook salmon and steelhead was summarized for the Columbia River tributaries. Current and future production and release objectives were reviewed. Among the three tributaries, forty seven sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed

Cloning, production, and purification of proteins for a medium-scale structural genomics project.

Science.gov (United States)

Quevillon-Cheruel, Sophie; Collinet, Bruno; Trésaugues, Lionel; Minard, Philippe; Henckes, Gilles; Aufrère, Robert; Blondeau, Karine; Zhou, Cong-Zhao; Liger, Dominique; Bettache, Nabila; Poupon, Anne; Aboulfath, Ilham; Leulliot, Nicolas; Janin, Joël; van Tilbeurgh, Herman

2007-01-01

The South-Paris Yeast Structural Genomics Pilot Project (http://www.genomics.eu.org) aims at systematically expressing, purifying, and determining the three-dimensional structures of Saccharomyces cerevisiae proteins. We have already cloned 240 yeast open reading frames in the Escherichia coli pET system. Eighty-two percent of the targets can be expressed in E. coli, and 61% yield soluble protein. We have currently purified 58 proteins. Twelve X-ray structures have been solved, six are in progress, and six other proteins gave crystals. In this chapter, we present the general experimental flowchart applied for this project. One of the main difficulties encountered in this pilot project was the low solubility of a great number of target proteins. We have developed parallel strategies to recover these proteins from inclusion bodies, including refolding, coexpression with chaperones, and an in vitro expression system. A limited proteolysis protocol, developed to localize flexible regions in proteins that could hinder crystallization, is also described.

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

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

2009-03-01

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

Tritium research laboratory cleanup and transition project final report

International Nuclear Information System (INIS)

Johnson, A.J.

1997-02-01

This Tritium Research Laboratory Cleanup and Transition Project Final Report provides a high-level summary of this project's multidimensional accomplishments. Throughout this report references are provided for in-depth information concerning the various topical areas. Project related records also offer solutions to many of the technical and or administrative challenges that such a cleanup effort requires. These documents and the experience obtained during this effort are valuable resources to the DOE, which has more than 1200 other process contaminated facilities awaiting cleanup and reapplication or demolition

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Science.gov (United States)

Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

2015-04-01

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

Hunting for genes for hypertension: the Millennium Genome Project for Hypertension.

Science.gov (United States)

Tabara, Yasuharu; Kohara, Katsuhiko; Miki, Tetsuro

2012-06-01

The Millennium Genome Project for Hypertension was started in 2000 to identify genetic variants conferring susceptibility to hypertension, with the aim of furthering the understanding of the pathogenesis of this condition and realizing genome-based personalized medical care. Two different approaches were launched, genome-wide association analysis using single-nucleotide polymorphisms (SNPs) and microsatellite markers, and systematic candidate gene analysis, under the hypothesis that common variants have an important role in the etiology of common diseases. These multilateral approaches identified ATP2B1 as a gene responsible for hypertension in not only Japanese but also Caucasians. The high blood pressure susceptibility conferred by certain alleles of ATP2B1 has been widely replicated in various populations. Ex vivo mRNA expression analysis in umbilical artery smooth muscle cells indicated that reduced expression of this gene associated with the risk allele may be an underlying mechanism relating the ATP2B1 variant to hypertension. However, the effect size of a SNP was too small to clarify the entire picture of the genetic basis of hypertension. Further, dense genome analysis with accurate phenotype data may be required.

Final environmental impact statement, Beaufort Sea oil and gas development/Northstar Project. Appendix A: BP Exploration (Alaska) Inc. Final project description - Revision 1, March 27, 1997

International Nuclear Information System (INIS)

1999-02-01

BP Exploration (Alaska) Inc. (BPXA) submitted a permit application to the US Army Engineer District, Alaska to initiate the review process for BPXA's plans to develop and produce oil and gas from the Northstar Unit. This report contains Appendix A of an Environmental Impact Statement which was undertaken to identify and evaluate the potential effects the proposed project may have on the environment. This document is the Northstar Development Project, Final Project Description, Revision 1 for BPXA Northstar Project

From Mendel to the Human Genome Project: The Implications for Nurse Education.

Science.gov (United States)

Burton, Hilary; Stewart, Alison

2003-01-01

The Human Genome Project is brining new opportunities to predict and prevent diseases. Although pediatric nurses are the closest to these developments, most nurses will encounter genetic aspects of practice and must understand the basic science and its ethical, legal, and social dimensions. (Includes commentary by Peter Birchenall.) (SK)

MORE: Management of Requirements in NPP Modernisation Projects, final report

International Nuclear Information System (INIS)

Fredriksen, R.; Katta, V.; Raspotnig, C.; Valkonen, J.

2008-09-01

This report documents the work and related activities of the MORE (Management of Requirements in NPP Modernisation Projects) (NKS-R project number NKS-R-2005-47) project. This report also provides a summary of the project activities and deliverables, and discusses possible application areas. The project has aimed at the industrial utilisation of the results from the TACO: (Traceability and Communication of Requirements in Digital I and C Systems Development) (NKS-R project number NKS-R-2002-16, completed June, 2005) project, and practical application of improved approaches and methods for requirements engineering and change management. Finally, the report provides a brief description of the extended industrial network and disseminations of the results in Nordic and NKS related events such as seminars and workshops. (au)

MORE: Management of Requirements in NPP Modernisation Projects, final report

Energy Technology Data Exchange (ETDEWEB)

Fredriksen, R.; Katta, V.; Raspotnig, C. (Inst. for energiteknikk (IFE) (Norway)); Valkonen, J. (Technical Research Centre of Finland (VTT) (Finland))

2008-09-15

This report documents the work and related activities of the MORE (Management of Requirements in NPP Modernisation Projects) (NKS-R project number NKS-R-2005-47) project. This report also provides a summary of the project activities and deliverables, and discusses possible application areas. The project has aimed at the industrial utilisation of the results from the TACO: (Traceability and Communication of Requirements in Digital I and C Systems Development) (NKS-R project number NKS-R-2002-16, completed June, 2005) project, and practical application of improved approaches and methods for requirements engineering and change management. Finally, the report provides a brief description of the extended industrial network and disseminations of the results in Nordic and NKS related events such as seminars and workshops. (author)

The RadGenomics project. Prediction for radio-susceptibility of individuals with genetic predisposition

International Nuclear Information System (INIS)

Imai, Takashi

2003-01-01

The ultimate goal of our project, named RadGenomics, is to elucidate the heterogeneity of the response to ionizing radiation arising from genetic variation among individuals, for the purpose of developing personalized radiation therapy regimens for cancer patients. Cancer patients exhibit patient-to-patient variability in normal tissue reactions after radiotherapy. Several observations support the hypothesis that the radiosensitivity of normal tissue is influenced by genetic factors. The rapid progression of human genome sequencing and the recent development of new technologies in molecular biology are providing new opportunities for elucidating the genetic basis of individual differences in susceptibility to radiation exposure. The development of a sufficiently robust, predictive assay enabling individual dose adjustment would improve the outcome of radiation therapy in patients. Our strategy for identification of DNA polymorphisms that contribute to the individual radiosensitivity is as follows. First, we have been categorizing DNA samples obtained from cancer patients, who have been kindly introduced to us through many collaborators, according to their clinical characteristics including the method and effect of treatment and side effects as scored by toxicity criteria, and also the result of an in vitro radiosensitivity assay, e.g., the micronuclei assay of their lymphocytes. Second, we have identified candidate genes for genotyping mainly by using our custom-designed oligonucleotide array with RNA samples, in which the probes were obtained from more than 40 cancer and 3 fibroblast cell lines whose radiosensitivity level was quite heterogeneous. We have also been studying the modification of proteins after irradiation of cells which may be caused by mainly phosphorylation or dephosphorylation, using mass spectrometry. Genes encoding the modified proteins and/or other proteins with which they interact such as specific protein kinases and phosphatases are also

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

Science.gov (United States)

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

Final Design Report for the RH LLW Disposal Facility (RDF) Project, Revision 3

International Nuclear Information System (INIS)

Austad, Stephanie Lee

2015-01-01

The RH LLW Disposal Facility (RDF) Project was designed by AREVA Federal Services (AFS) and the design process was managed by Battelle Energy Alliance (BEA) for the Department of Energy (DOE). The final design report for the RH LLW Disposal Facility Project is a compilation of the documents and deliverables included in the facility final design.

Decontamination and dismantlement of the JANUS Reactor at Argonne National Laboratory-East. Project final report

International Nuclear Information System (INIS)

Fellhauer, C.R.; Clark, F.R.

1997-10-01

The decontamination and dismantlement of the JANUS Reactor at Argonne National Laboratory-East (ANL-E) was completed in October 1997. Descriptions and evaluations of the activities performed and analyses of the results obtained during the JANUS D and D Project are provided in this Final Report. The following information is included: objective of the JANUS D and D Project; history of the JANUS Reactor facility; description of the ANL-E site and the JANUS Reactor facility; overview of the D and D activities performed; description of the project planning and engineering; description of the D and D operations; summary of the final status of the JANUS Reactor facility based upon the final survey results; description of the health and safety aspects of the project, including personnel exposure and OSHA reporting; summary of the waste minimization techniques utilized and total waste generated by the project; and summary of the final cost and schedule for the JANUS D and D Project

Final report for the 'Melt-Vessel Interactions' Project. European Union R and TD Program 4th Framework. MVI project final research report

Energy Technology Data Exchange (ETDEWEB)

Sehgal, B.R.; Dinh, T.N.; Nourgaliev, R.R.; Bui, V.A.; Green, J.; Kolb, G.; Karbojian, A.; Theerthan, S.A.; Gubaidulline, A. [Royal Inst. of Tech., Stockholm (Sweden). Div. of Nuclear Power Safety; Helle, M.; Kymaelaeinen, O.; Tuomisto, H. [IVO Power Engineering Ltd., Vantaa (Finland); Bonnet, J.M.; Rouge, S.; Narcoux, M.; Liegeois, A. [CEA - Grenoble (France); Turland, B.D.; Dobson, G.P. [AEA Technology plc, Dorchester (United Kingdom); Siccama, A. [ECN Nuclear Research, Petten (Netherlands); Ikonen, K. [VTT Energy, Helsinki (Finland); Parozzi, F. [ENEL - SRI/PAM/GRA, Segrate, MI (Italy); Kolev, N. [Siemens AG, Erlangen (Germany); Caira, M. [Univ. of Roma (Italy)

1999-04-01

The Melt Vessel Interaction (MVI) project is concerned with the consequences of the interactions that a core melt, generated during a postulated severe accident in a light water reactor, may have with the pressure vessel. In particular, the issues concerned with the failure of the vessel bottom head are the focus of the research. The specific objectives of the project are to obtain data and develop validated models, which could be applied to prototypic plants, and accident conditions, for resolution of issues related to the melt vessel interactions. The project work has been performed by nine partners having varied responsibility. The work included a large number of experiments, with simulant materials, whose observations and results are employed, respectively, to understand the physical mechanisms and to develop validated models. Applications to the prototypic geometry and conditions have also been performed. This report is volume 1 of the Final Report for the Project, in which a summary of the progress achieved in the experimental program is provided. We have, however, included some aspects of the modeling activities. Volume 2 of the Final report describes the progress achieved in the modeling program. The progress achieved in the experimental and modeling parts of the Project has led to the resolution of some of the issues of melt vessel interaction. Considerable progress was also achieved towards resolution of the remaining issues.

Field of genes: the politics of science and identity in the Estonian Genome Project.

Science.gov (United States)

Fletcher, Amy L

2004-04-01

This case study of the Estonian Genome Project (EGP) analyses the Estonian policy decision to construct a national human gene bank. Drawing upon qualitative data from newspaper articles and public policy documents, it focuses on how proponents use discourse to link the EGP to the broader political goal of securing Estonia's position within the Western/European scientific and cultural space. This dominant narrative is then situated within the analytical notion of the "brand state", which raises potentially negative political consequences for this type of market-driven genomic research. Considered against the increasing number of countries engaging in gene bank and/or gene database projects, this analysis of Estonia elucidates issues that cross national boundaries, while also illuminating factors specific to this small, post-Soviet state as it enters the global biocybernetic economy.

The GenABEL Project for statistical genomics.

Science.gov (United States)

Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

Understanding the Human Genome Project — A Fact Sheet | NIH MedlinePlus the Magazine

Science.gov (United States)

... The Human Genome Project spurred a revolution in biotechnology innovation around the world and played a key ... the U.S. the global leader in the new biotechnology sector. In April 2003, researchers successfully completed the ...

Social implications of the Human Genome Project: Policy roundtable series and journals. Final progress report, March 15, 2001 - March 15, 2002

Energy Technology Data Exchange (ETDEWEB)

Seiguer, Erica

2002-12-30

This report reflects the activities of the Harvard Health Caucus at Harvard Medical School that were supported, in part, by the Department of Energy. The following policy roundtables and panels were held: Spring 2001 Policy Roundtable Series: The social implications of the Human Genome Project; Spring 2002 Policy Roundtable Series: Managing globalization to improve health; 13 February 2002 Keynote Address: The globalization of health; 25 February 2002 Healthier or Wealthier: Which comes first in the new global era?; 28 February 2002 The crisis of neglected diseases: Creating R&D incentives for diseases of developing countries; 7 March 2002 Health care education in the developing world: Bridging global and local health care practices; 20 March 2002 Building a legal framework for global health: How can the US and UN work to reduce global disparities?; 25 April 2002 The role of mass media and tobacco control efforts. Caucus organizational information is also included.

Evolution of small prokaryotic genomes

Directory of Open Access Journals (Sweden)

David José Martínez-Cano

2015-01-01

Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

Leven estuary project. Fisheries Department final report

OpenAIRE

Bayliss, B.D.

1997-01-01

This is the report on the Leven estuary project: Fisheries Department final report produced by the Environment Agency North West in 1997. This report contains information about Leven estuary, river Leven catchment, river Crake catchment and the Ulverston Discharges. The Leven estuary is characterised by being very shallow, and shares the extremely variable tides and currents that characterize the whole of Morecambe Bay. There was little detailed knowledge of the impact on the Leven estuary, a...

Analysis of final year DVM research projects submitted to the Faculty ...

African Journals Online (AJOL)

This study analyzed the intellectual output of the undergraduate final year students. research projects submitted to the Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, from 1994 to 2004. The findings of the study show that a total of 194 research projects were produced within the period under study.

77 FR 62256 - Notice of Availability of the Final Environmental Impact Statement for the Mount Hope Project...

Science.gov (United States)

2012-10-12

... of the Final Environmental Impact Statement for the Mount Hope Project, Eureka County, NE AGENCY... prepared a Final Environmental Impact Statement (EIS) for the Mount Hope Project and by this notice is... Register. ADDRESSES: Copies of the Mount Hope Project Final EIS are available at the Battle Mountain...

Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

Science.gov (United States)

Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

2014-01-01

Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

Directory of Open Access Journals (Sweden)

Magness Charles L

2007-01-01

Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine.

Science.gov (United States)

Vassy, Jason L; Lautenbach, Denise M; McLaughlin, Heather M; Kong, Sek Won; Christensen, Kurt D; Krier, Joel; Kohane, Isaac S; Feuerman, Lindsay Z; Blumenthal-Barby, Jennifer; Roberts, J Scott; Lehmann, Lisa Soleymani; Ho, Carolyn Y; Ubel, Peter A; MacRae, Calum A; Seidman, Christine E; Murray, Michael F; McGuire, Amy L; Rehm, Heidi L; Green, Robert C

2014-03-20

Whole genome sequencing (WGS) is already being used in certain clinical and research settings, but its impact on patient well-being, health-care utilization, and clinical decision-making remains largely unstudied. It is also unknown how best to communicate sequencing results to physicians and patients to improve health. We describe the design of the MedSeq Project: the first randomized trials of WGS in clinical care. This pair of randomized controlled trials compares WGS to standard of care in two clinical contexts: (a) disease-specific genomic medicine in a cardiomyopathy clinic and (b) general genomic medicine in primary care. We are recruiting 8 to 12 cardiologists, 8 to 12 primary care physicians, and approximately 200 of their patients. Patient participants in both the cardiology and primary care trials are randomly assigned to receive a family history assessment with or without WGS. Our laboratory delivers a genome report to physician participants that balances the needs to enhance understandability of genomic information and to convey its complexity. We provide an educational curriculum for physician participants and offer them a hotline to genetics professionals for guidance in interpreting and managing their patients' genome reports. Using varied data sources, including surveys, semi-structured interviews, and review of clinical data, we measure the attitudes, behaviors and outcomes of physician and patient participants at multiple time points before and after the disclosure of these results. The impact of emerging sequencing technologies on patient care is unclear. We have designed a process of interpreting WGS results and delivering them to physicians in a way that anticipates how we envision genomic medicine will evolve in the near future. That is, our WGS report provides clinically relevant information while communicating the complexity and uncertainty of WGS results to physicians and, through physicians, to their patients. This project will not only

The LiveWire Project final report

Energy Technology Data Exchange (ETDEWEB)

Brown, C.D.; Nelson, T.T. [Enova Technology, San Diego, CA (United States); Kelly, J.C.; Dominguez, H.A. [Paragon Consulting Services, La Verne, CA (United States)

1997-10-01

Utilities across the US have begun pilot testing a variety of hardware and software products to develop a two-way communications system between themselves and their customers. Their purpose is to reduce utility operating costs and to provide new and improved services for customers in light of pending changes in the electric industry being brought about by deregulation. A consortium including utilities, national labs, consultants, and contractors, with the support of the Department of Energy (DOE) and the Electric Power Research Institute (EPRI), initiated a project that utilized a hybrid fiber-coax (HFC) wide-area network integrated with a CEBus based local area network within the customers home. The system combined energy consumption data taken within the home, and home automation features to provide a suite of energy management services for residential customers. The information was transferred via the Internet through the HFC network, and presented to the customer on their personal computer. This final project report discusses the design, prototype testing, and system deployment planning of the energy management system.

El Paso County Geothermal Project at Fort Bliss. Final Project Report

Energy Technology Data Exchange (ETDEWEB)

Lear, Jon [Ruby Mountain Inc., Salt Lake City, UT (United State); Bennett, Carlon [Ruby Mountain Inc., Salt Lake City, UT (United State); Lear, Dan [Ruby Mountain Inc., Salt Lake City, UT (United State); Jones, Phil L. [Ruby Mountain Inc., Salt Lake City, UT (United State); Burdge, Mark [Evergreen Clean Energy Management, Provo, UT (United States); Barker, Ben [Evergreen Clean Energy Management, Provo, UT (United States); Segall, Marylin [Univ. of Utah, Salt Lake City, UT (United States). Energy and Geoscience Inst.; Moore, Joseph [Univ. of Utah, Salt Lake City, UT (United States). Energy and Geoscience Inst.; Nash, Gregory [Univ. of Utah, Salt Lake City, UT (United States). Energy and Geoscience Inst.; Jones, Clay [Univ. of Utah, Salt Lake City, UT (United States). Energy and Geoscience Inst.; Simmons, Stuart [Univ. of Utah, Salt Lake City, UT (United States). Energy and Geoscience Inst.; Taylor, Nancy [Univ. of Utah, Salt Lake City, UT (United States). Energy and Geoscience Inst.

2016-02-01

The El Paso County Geothermal Project at Fort Bliss was an effort to determine the scale and scope of geothermal resources previously identified on Fort Bliss’ McGregor Range in southern Otero County, New Mexico. The project was funded with a $5,000,000 grant to El Paso County from the U.S. Department of Energy (DOE) as part of the American Recovery and Reinvestment Act of 2009 and a $4,812,500 match provided by private sector partners. The project was administered through the DOE Golden Field Office to awardee El Paso County. The primary subcontractor to El Paso County and project Principal Investigator - Ruby Mountain Inc. (RMI) of Salt Lake City, Utah - assembled the project team consisting of Evergreen Clean Energy Management (ECEM) of Provo, Utah, and the Energy & Geoscience Institute at the University of Utah (EGI) in Salt Lake City, UT to complete the final phases of the project. The project formally began in May of 2010 and consisted of two preliminary phases of data collection and evaluation which culminated in the identification of a drilling site for a Resource Confirmation Well on McGregor Range. Well RMI 56-5 was drilled May and June 2013 to a depth of 3,030 ft. below ground level. A string of slotted 7 inch casing was set in 8.75 inch hole on bottom fill at 3,017 ft. to complete the well. The well was drilled using a technique called flooded reverse circulation, which is most common in mineral exploration. This technique produced an exceptionally large and complete cuttings record. An exciting development at the conclusion of drilling was the suspected discovery of a formation that has proven to be of exceptionally high permeability in three desalinization wells six miles to the south. Following drilling and preliminary testing and analysis, the project team has determined that the McGregor Range thermal anomaly is large and can probably support development in the tens of megawatts.

Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999; FINAL

International Nuclear Information System (INIS)

Harger, Carol A.

1999-01-01

Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence.[The annual report for June 1996 to August 1997 is included as an attachment to this final report.

Prototypical consolidation demonstration project - Final fuel recommendation report

International Nuclear Information System (INIS)

Piscitella, R.R.; Paskey, W.R.

1987-01-01

The Prototypical Consolidation Demonstration (PCD) Project will, in its final phase, conduct a demonstration of the equipment's ability to consolidate actual spent commercial fuel. Since budget and schedule limitations do not allow this demonstration to include all types of fuel assemblies, a selection process was utilized to identify the fuel types that would represent predominate fuel inventories and that would demonstrate the equipment's abilities. The Pressurized Water Reactor (PWR) fuel assemblies that were suggested for use in the PCD Project Hot Demonstration were Babcock and Wilcox (B and W) 15 x 15's, and Westinghouse (WE) 15 x 15's. The Boiling Water Reactor (BWR) fuel suggested was the General Electric (GE) 8 x 8

Energy final consumption projection - 1985/2005 - basic scenery - Minas Gerais State

International Nuclear Information System (INIS)

1989-03-01

A projection of the final energy consumption study for the Minas Gerais State until 2005 year is presented. The conclusion of this projection shows a increasing of 108,8% for the total energy. The industries will be response for 62,0% and the transport sector will use 20,7% of the total energy in 2005. (L.J.C.)

76 FR 64085 - Post-2014 Resource Pool-Loveland Area Projects, Final Power Allocation

Science.gov (United States)

2011-10-17

... Resource Pool; Loveland Area Projects, General Eligibility Criteria. The resource pool for capacity and... transmission in Kansas. Final allocation of the Post-2014 Resource Pool; Loveland Area Projects, is contingent...

Final report on the maintenance asset management project : phase II.

Science.gov (United States)

2013-07-01

Iowa Department of Transportation (IA DOT) is finalizing research to streamline field inventory/inspection of culverts by Maintenance and Construction staff while maximizing the use of tablet technologies. The project began in 2011 to develop some ne...

Human Genome Project discoveries: Dialectics and rhetoric in the science of genetics

Science.gov (United States)

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

Final report: 'Rhodopseudomonas palustris' genome workshop to be held in Spring of 2001; FINAL

International Nuclear Information System (INIS)

Harwood, Caroline S.

2002-01-01

The 'Rhodopseudomonas palustris' genome workshop took place in Iowa City on April 6-8, 2001. The purpose of the meeting was to instruct members of the annotation working group in approaches to accomplishing the 'human' phase of the 'R. palustris' genome annotation. A partial draft of a paper describing the 'Rhodopseudomonas palustris' genome has been written and a full version of the paper should be ready for submission by the end of the summer 2002

Ethical challenges and innovations in the dissemination of genomic data: the experience of the PERSPECTIVE project

Directory of Open Access Journals (Sweden)

Lévesque E

2015-08-01

Full Text Available Emmanuelle Lévesque,1 Bartha Maria Knoppers,1 Jacques Simard,2 1Department of Human Genetics, Centre for Genomics and Policy, McGill University, Montréal, 2Genomics Centre, CHU de Québec Research Center, Department of Molecular Medicine, Laval University, Québec City, QC, Canada Abstract: The importance of making genomic data available for future research is now widely recognized among the scientific community and policymakers. In this era of shared responsibility for data dissemination, improved patient care through research depends on the development of powerful and secure data-sharing systems. As part of the concerted effort to share research resources, the project entitled Personalized Risk Stratification for Prevention and Early Detection of Breast Cancer (PERSPECTIVE makes effective data sharing through the development of a data-sharing framework, one of its goals. The secondary uses of data from PERSPECTIVE for future research promise to enhance our knowledge of breast cancer etiologies without duplicating data-gathering efforts. Despite its benefit for research, we recognize the ethical challenges of data sharing on the local, national, and international levels. The effective management of ethical approvals for projects spanning across jurisdictions, the return of results to research participants, and research incentives and recognition for data production, are but a few pressing issues that need to be properly addressed. We discuss how we managed these issues and suggest how ongoing innovations might help to facilitate data sharing in future genomic research projects. Keywords: data sharing, research ethics, cancer

Project No. 8 - Final decommissioning plan

International Nuclear Information System (INIS)

2000-01-01

Ignalina NPP should prepare the final Ignalina NPP unit 1 decommissioning plan by march 31, 2002. This plan should include the following : description of Ignalina NPP and the Ignalina NPP boundary that could be influenced by decommissioning process; decommissioning strategy selected and a logical substantiation for this selection; description of the decommissioning actions suggested and a time schedule for the actions to be performed; conceptual safety and environmental impact assessment covering ionizing radiation and other man and environment impact; description of the environmental monitoring program proposed during decommissioning process; description of the waste management proposed; assessment of decommissioning expenses including waste management, accumulated funds and other sources. Estimated project cost - 0.75 M EURO

N Area Final Project Program Plan

International Nuclear Information System (INIS)

Day, R.S.; Duncan, G.M; Trent, S.J.

1998-07-01

The N Area Final Project Program Plan is issued for information and use by the U.S. Department of Energy (DOE), the Environmental Restoration Contractor (ERC) for the Hanford Site, and other parties that require workscope knowledge for the deactivation of N Reactor facilities and remediation of the 100-N Area. This revision to the program plan contains the updated critical path schedule to deactivate N Reactor and its supporting facilities, cleanout of the N Reactor Fuel Storage Basin (105-N Basin), and remediate the 100-N Area. This document reflects notable changes in the deactivation plan for N Reactor, including changes in deactivation status, the N Basin cleanout task, and 100-N Area remediation

The fishes of Genome 10K

KAUST Repository

Bernardi, Giacomo

2012-09-01

The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

The fishes of Genome 10K

KAUST Repository

Bernardi, Giacomo; Wiley, Edward O.; Mansour, Hicham; Miller, Michael R.; Ortí , Guillermo; Haussler, David H.; O'Brien, Stephen J O; Ryder, Oliver A.; Venkatesh, Byrappa

2012-01-01

The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

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.

Decontamination and decommissioning of the Experimental Boiling Water Reactor (EBWR): Project final report, Argonne National Laboratory

International Nuclear Information System (INIS)

Fellhauer, C.R.; Boing, L.E.; Aldana, J.

1997-03-01

The Final Report for the Decontamination and Decommissioning (D ampersand D) of the Argonne National Laboratory - East (ANL-E) Experimental Boiling Water Reactor (EBWR) facility contains the descriptions and evaluations of the activities and the results of the EBWR D ampersand D project. It provides the following information: (1) An overall description of the ANL-E site and EBWR facility. (2) The history of the EBWR facility. (3) A description of the D ampersand D activities conducted during the EBWR project. (4) A summary of the final status of the facility, including the final and confirmation surveys. (5) A summary of the final cost, schedule, and personnel exposure associated with the project, including a summary of the total waste generated. This project report covers the entire EBWR D ampersand D project, from the initiation of Phase I activities to final project closeout. After the confirmation survey, the EBWR facility was released as a open-quotes Radiologically Controlled Area,close quotes noting residual elevated activity remains in inaccessible areas. However, exposure levels in accessible areas are at background levels. Personnel working in accessible areas do not need Radiation Work Permits, radiation monitors, or other radiological controls. Planned use for the containment structure is as an interim transuranic waste storage facility (after conversion)

Poplar Interactome: Project Final Report

Energy Technology Data Exchange (ETDEWEB)

Jaiswal, Pankaj [Oregon State Univ., Corvallis, OR (United States)

2018-03-21

The feedstock plant Poplar has many advantages over traditional crop plants. Not only Poplar needs low energy input and off season storage as compared to feedstocks such as corn, in the winter season Poplar biomass is stored on the stem/trunk, and Poplar plantations serve as large carbon sink. A key constraint to the expansion of cellulosic bioenergy sources such as in Poplar however, is the negative consequence of converting land use from food crops to energy crops. Therefore in order for Poplar to become a viable energy crop it needs to be grown mostly on marginal land unsuitable agricultural crops. For this we need a better understanding of abiotic stress and adaptation response in poplar. In the process we expected to find new and existing poplar genes and their function that respond to sustain abiotic stress. We carried out an extensive gene expression study on the control untreated and stress (drought, salinity, cold and heat) treated poplar plants. The samples were collected from the stem, leaf and root tissues. The RNA of protein coding genes and regulatory smallRNA genes were sequenced generating more than a billion reads. This is the first such known study in Poplar plants. These were used for quantification and genomic analysis to identify stress responsive genes in poplar. Based on the quantification and genomic analysis, a select set of genes were studied for gene-gene interactions to find their association to stress response. The data was also used to find novel stress responsive genes in poplar that were previously not identified in the Poplar reference genome. The data is made available to the public through the national and international genomic data archives.

Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project

Directory of Open Access Journals (Sweden)

McDonagh Paul D

2003-06-01

Full Text Available Abstract Background Seattle Biomedical Research Institute (SBRI as part of the Leishmania Genome Network (LGN is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces. Results Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODONUSAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence. Conclusion An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation.

78 FR 45268 - Notice of Availability of the San Diego Gas & Electric Ocotillo Sol Solar Project Final...

Science.gov (United States)

2013-07-26

...] Notice of Availability of the San Diego Gas & Electric Ocotillo Sol Solar Project Final Environmental...) Ocotillo Sol Solar Project in Imperial County, California, and by this notice is announcing its... Ocotillo Sol Solar Project Final EIS/Proposed CDCA Plan Amendment have been sent to affected Federal, State...

The Human Genome Project and Eugenics: Identifying the Impact on Individuals with Mental Retardation.

Science.gov (United States)

Kuna, Jason

2001-01-01

This article explores the impact of the mapping work of the Human Genome Project on individuals with mental retardation and the negative effects of genetic testing. The potential to identify disabilities and the concept of eugenics are discussed, along with ethical issues surrounding potential genetic therapies. (Contains references.) (CR)

The Elder Abuse Prevention Project, Phase Two, Three and Four. Final Report.

Science.gov (United States)

Regina Univ. (Saskatchewan). Univ. Extension. Seniors Education Centre.

This document presents the final report from an educational and community development program designed to raise awareness about the abuse and neglect of the elderly. The Elder Abuse Prevention Project is briefly described in terms of project goals, objectives, the model used, the target groups served, and the evaluation processes employed. It is…

Functional food ingredients against colorectal cancer. An example project integrating functional genomics, nutrition and health

NARCIS (Netherlands)

Stierum, R.; Burgemeister, R.; Helvoort, van A.; Peijnenburg, A.; Schütze, K.; Seidelin, M.; Vang, O.; Ommen, van B.

2001-01-01

Functional Food Ingredients Against Colorectal Cancer is one of the first European Union funded Research Projects at the cross-road of functional genomics [comprising transcriptomics, the measurement of the expression of all messengers RNA (mRNAs) and proteomics, the measurement of expression/state

Commentary: The Materials Project: A materials genome approach to accelerating materials innovation

Directory of Open Access Journals (Sweden)

Anubhav Jain

2013-07-01

Full Text Available Accelerating the discovery of advanced materials is essential for human welfare and sustainable, clean energy. In this paper, we introduce the Materials Project (www.materialsproject.org, a core program of the Materials Genome Initiative that uses high-throughput computing to uncover the properties of all known inorganic materials. This open dataset can be accessed through multiple channels for both interactive exploration and data mining. The Materials Project also seeks to create open-source platforms for developing robust, sophisticated materials analyses. Future efforts will enable users to perform ‘‘rapid-prototyping’’ of new materials in silico, and provide researchers with new avenues for cost-effective, data-driven materials design.

Hellsgate Winter Range : Wildlife Mitigation Project. Final Environmental Assessment.

Energy Technology Data Exchange (ETDEWEB)

United States. Bonneville Power Administration.

1995-03-01

Bonneville Power Administration (BPA) proposes to fund the Hellsgate Winter Range Wildlife Mitigation Project (Project) in a cooperative effort with the Colville Confederated Tribes and the Bureau of Indian Affairs (BIA). The proposed action would allow the sponsors to secure property and conduct wildlife management activities within the boundaries of the Colville Indian Reservation. This Final Environmental Assessment (EA) examines the potential environmental effects of acquiring and managing property for wildlife and wildlife habitat within a large project area. This area consists of several separated land parcels, of which 2,000 hectares (4,943 acres) have been purchased by BPA and an additional 4,640 hectares (11,466 acres) have been identified by the Colville Confederated Tribes for inclusion in the Project. Four proposed activities (habitat protection, habitat enhancement, operation and maintenance, and monitoring and evaluation) are analyzed. The proposed action is intended to meet the need for mitigation of wildlife and wildlife habitat that was adversely affected by the construction of Grand Coulee and Chief Joseph Dams and their reservoirs.

Hellsgate Winter Range: Wildlife mitigation project. Final environmental assessment

International Nuclear Information System (INIS)

1995-03-01

Bonneville Power Administration (BPA) proposes to fund the Hellsgate Winter Range Wildlife Mitigation Project (Project) in a cooperative effort with the Colville Confederated Tribes and the Bureau of Indian Affairs (BIA). The proposed action would allow the sponsors to secure property and conduct wildlife management activities within the boundaries of the Colville Indian Reservation. This Final Environmental Assessment (EA) examines the potential environmental effects of acquiring and managing property for wildlife and wildlife habitat within a large project area. This area consists of several separated land parcels, of which 2,000 hectares (4,943 acres) have been purchased by BPA and an additional 4,640 hectares (11,466 acres) have been identified by the Colville Confederated Tribes for inclusion in the Project. Four proposed activities (habitat protection, habitat enhancement, operation and maintenance, and monitoring and evaluation) are analyzed. The proposed action is intended to meet the need for mitigation of wildlife and wildlife habitat that was adversely affected by the construction of Grand Coulee and Chief Joseph Dams and their reservoirs

The Epilepsy Phenome/Genome Project (EPGP) informatics platform.

Science.gov (United States)

Nesbitt, Gerry; McKenna, Kevin; Mays, Vickie; Carpenter, Alan; Miller, Kevin; Williams, Michael

2013-04-01

The Epilepsy Phenome/Genome Project (EPGP) is a large-scale, multi-institutional, collaborative network of 27 epilepsy centers throughout the U.S., Australia, and Argentina, with the objective of collecting detailed phenotypic and genetic data on a large number of epilepsy participants. The goals of EPGP are (1) to perform detailed phenotyping on 3750 participants with specific forms of non-acquired epilepsy and 1500 parents without epilepsy, (2) to obtain DNA samples on these individuals, and (3) to ultimately genotype the samples in order to discover novel genes that cause epilepsy. To carry out the project, a reliable and robust informatics platform was needed for standardized electronic data collection and storage, data quality review, and phenotypic analysis involving cases from multiple sites. EPGP developed its own suite of web-based informatics applications for participant tracking, electronic data collection (using electronic case report forms/surveys), data management, phenotypic data review and validation, specimen tracking, electroencephalograph and neuroimaging storage, and issue tracking. We implemented procedures to train and support end-users at each clinical site. Thus far, 3780 study participants have been enrolled and 20,957 web-based study activities have been completed using this informatics platform. Over 95% of respondents to an end-user satisfaction survey felt that the informatics platform was successful almost always or most of the time. The EPGP informatics platform has successfully and effectively allowed study management and efficient and reliable collection of phenotypic data. Our novel informatics platform met the requirements of a large, multicenter research project. The platform has had a high level of end-user acceptance by principal investigators and study coordinators, and can serve as a model for new tools to support future large scale, collaborative research projects collecting extensive phenotypic data. Copyright © 2012

Zachary-Fort Lauderdale pipeline construction and conversion project: final supplement to final environmental impact statement. Docket No. CP74-192

Energy Technology Data Exchange (ETDEWEB)

None

1980-05-01

This Final Supplement to the Final Environmental Impact Statement (Final Supplement) evaluates the economic, engineering, and environmental aspects of newly developed alternatives to an abandonment/conversion project proposed by Florida Gas Transmission Company (Florida Gas). It also updates the staff's previous FEIS and studies revisions to the original proposal. Wherever possible, the staff has adopted portions of its previous FEIS in lieu of reprinting portions of that analysis which require no change. 60 references, 8 figures, 35 tables.

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Science.gov (United States)

Swain, Martin T; Tsai, Isheng J; Assefa, Samual A; Newbold, Chris; Berriman, Matthew; Otto, Thomas D

2012-06-07

Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.

Northeast Oregon Hatchery Project, Final Siting Report.

Energy Technology Data Exchange (ETDEWEB)

Watson, Montgomery

1995-03-01

This report presents the results of site analysis for the Bonneville Power Administration Northeast Oregon Hatchery Project. The purpose of this project is to provide engineering services for the siting and conceptual design of hatchery facilities for the Bonneville Power Administration. The hatchery project consists of artificial production facilities for salmon and steelhead to enhance production in three adjacent tributaries to the Columbia River in northeast Oregon: the Grande Ronde, Walla Walla, and Imnaha River drainage basins. Facilities identified in the master plan include adult capture and holding facilities; spawning incubation, and early rearing facilities; full-term rearing facilities; and direct release or acclimation facilities. The evaluation includes consideration of a main production facility for one or more of the basins or several smaller satellite production facilities to be located within major subbasins. The historic and current distribution of spring and fall chinook salmon and steelhead was summarized for the Columbia River tributaries. Current and future production and release objectives were reviewed. Among the three tributaries, forty seven sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.

District heating demonstration project. Swiecie, Poland. Final report

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-06-01

In January 1997 the district heating company in Swiecie, Poland, was donated DKK 1.3 Mio. as a part of the environmental related energy sector programme by the Danish government for a demonstration project. The Danish consultancy company Carl Bro a/s was appointed to conduct the work. The project was finished in January 1999. The present final report outlines the activities of the demonstration project. The activities of the project were several. Carl Bro a/s elaborated tender documents and procured 79 heat meters for all the substrations in the city in order to prepare for the new energy law and a changed tariff system which was introduced in January 1999. Carl Bro a/s further supported ZEC Swiecie in the development of their new tariff system through information from Danish district heating companies. The demonstration project was designed in the first phase of the project. During the design period one engineer from Swiecie participated in a study tour to Denmark to learn about technical solutions to present problems in Poland. The training course focused on preparation of hot tap water. The site for the demonstation project was in the centre of Swiecie in a housing society located in Wojska Polskiego. The blocks 75 and 75A were selected for modernisation of the substations, and block no. 73 was appointed as a reference block in which only a heat meter was installed. Further, block 75A was equipped with thermostatic valves at all the radiators in the flats. The registered savings during the monitoring period were between 7% and 14%, and an increased comfort in the flats was observed. The housing society`s board of directors were so pleased with the project that by their initiative block no. 77 was refurbished in the same way as the blocks covered by the demonstration project. However, the activities were extended with individual heat meters and the introduction of a new tariff system for the block. The energy savings from this project were substantial, and today

The AGP-Project conceptual design for a Spanish HLW final disposal facility

International Nuclear Information System (INIS)

Biurrun, E.; Engelmann, H.-J.; Huertas, F.; Ulibarri, A.

1992-01-01

Within the framework of the AGP Project a Conceptual Design for a HLW Final Disposal Facility to be eventually built in an underground salt formation in Spain has been developed. The AGP Project has the character of a system analysis. In the current project phase I several alternatives has been considered for different subsystems and/or components of the repository. The system variants, developed to such extent as to allow a comparison of their advantages and disadvantages, will allow the selection of a reference concept, which will be further developed to technical maturity in subsequent project phases. (author)

The human genome project: Information management, access, and regulation. Technical progress report, 1 April--31 August 1993

Energy Technology Data Exchange (ETDEWEB)

McInerney, J.D.; Micikas, L.B.

1993-09-10

Efforts are described to prepare educational materials including computer based as well as conventional type teaching materials for training interested high school and elementary students in aspects of Human Genome Project.

HGVA: the Human Genome Variation Archive

OpenAIRE

Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gr?f, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

2017-01-01

Abstract High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic...

76 FR 12096 - McCloud-Pit Project; Notice of Availability of the Final Environmental Impact Statement for the...

Science.gov (United States)

2011-03-04

... Project; Notice of Availability of the Final Environmental Impact Statement for the Mccloud-Pit... Pit Rivers in Shasta County, California and has prepared a final environmental impact statement (EIS... and the alternatives for relicensing the McCloud-Pit Project. The final EIS documents the views of...

HGVA: the Human Genome Variation Archive.

Science.gov (United States)

Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

2017-07-03

High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterization of the radon source in North-Central Florida. Final report part 1 -- Final project report; Final report part 2 -- Technical report

International Nuclear Information System (INIS)

1997-01-01

This report contains two separate parts: Characterization of the Radon Source in North-Central Florida (final report part 1 -- final project report); and Characterization of the Radon Source in North-Central Florida (technical report). The objectives were to characterize the radon 222 source in a region having a demonstrated elevated indoor radon potential and having geology, lithology, and climate that are different from those in other regions of the U.S. where radon is being studied. Radon availability and transport in this region were described. Approaches for predicting the radon potential of lands in this region were developed

Griffith energy project final environmental impact statement

International Nuclear Information System (INIS)

1999-03-01

Griffith Energy Limited Liability Corporation (Griffith) proposes to construct and operate the Griffith Energy Project (Project), a natural gas-fired, combined cycle power plant, on private lands south of Kingman, Arizona. The Project would be a merchant plant which means that it is not owned by a utility and there is currently no long-term commitment or obligation by any utility to purchase the capacity and energy generated by the power plant. Griffith applied to interconnect its proposed power plant with the Western Area Power Administration's (Western) Pacific Northwest-Pacific Southwest Intertie and Parker-Davis transmission systems. Western, as a major transmission system owner, needs to provide access to its transmission system when it is requested by an eligible organization per existing policies, regulations and laws. The proposed interconnection would integrate the power generated by the Project into the regional transmission grid and would allow Griffith to supply its power to the competitive electric wholesale market. Based on the application, Western's proposed action is to enter into an interconnection and construction agreement with Griffith for the requested interconnections. The proposed action includes the power plant, water wells and transmission line, natural gas pipelines, new electrical transmission lines and a substation, upgrade of an existing transmission line, and access road to the power plant. Construction of segments of the transmission lines and a proposed natural gas pipeline also require a grant of right-of-way across Federal lands administered by the Bureau of Land Management. Public comments on the Draft EIS are addressed in the Final EIS, including addenda and modifications made as a result of the comments and/or new information

Griffith Energy Project Final Environmental Impact Statement

Energy Technology Data Exchange (ETDEWEB)

N/A

1999-04-02

Griffith Energy Limited Liability Corporation (Griffith) proposes to construct and operate the Griffith Energy Project (Project), a natural gas-fuel, combined cycle power plant, on private lands south of Kingman, Ariz. The Project would be a ''merchant plant'' which means that it is not owned by a utility and there is currently no long-term commitment or obligation by any utility to purchase the capacity and energy generated by the power plant. Griffith applied to interconnect its proposed power plant with the Western Area Power Administration's (Western) Pacific Northwest-Pacific Southwest Intertie and Parker-Davis transmission systems. Western, as a major transmission system owner, needs to provide access to its transmission system when it is requested by an eligible organization per existing policies, regulations and laws. The proposed interconnection would integrate the power generated by the Project into the regional transmission grid and would allow Griffith to supply its power to the competitive electric wholesale market. Based on the application, Western's proposed action is to enter into an interconnection and construction agreement with Griffith for the requested interconnections. The proposed action includes the power plant, water wells and transmission line, natural gas pipelines, new electrical transmission lines and a substation, upgrade of an existing transmission line, and access road to the power plant. Construction of segments of the transmission lines and a proposed natural gas pipeline also require a grant of right-of-way across Federal lands administered by the Bureau of Land Management. Public comments on the Draft EIS are addressed in the Final EIS, including addenda and modifications made as a result of the comments and/or new information.

Identifying Problems in Students’ Final Projects Based on Scientific Writing Guidelines

Directory of Open Access Journals (Sweden)

Endang Ernawati

2010-11-01

Full Text Available Article analyzed student’s difficulties and abilities in writing their final projects, which were undergraduate theses and undergraduate paper conducted by some students at the English Department, Bina Nusantara University. This was a preliminary study to support an appropriate student guideline in writing their final project. The study was conducted by applying qualitative methods that was by analyzing the four theses and one paper in terms of their format: titles, introduction, theoretical background, analysis, conclusion, bibliography, and paper rubric to analyze the contents. It can be concluded that generally, students, guided by their mentor/lecturer, understand the final paper guidelines and they are able to apply it in their thesis and paper. But, there are still lack of clarity and relevancy in expressing their ideas properly, and their ability in writing in both English and Bahasa Indonesia must be improved. These problems can be overcome by socializing the writing guidelines to both students and lecturers, providing them with critical thinking skills, cooperation with library that will guide them in information literacy skills, and language center that will improve their writing skills. 

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

Science.gov (United States)

Mao, Qing; Ciotlos, Serban; Zhang, Rebecca Yu; Ball, Madeleine P; Chin, Robert; Carnevali, Paolo; Barua, Nina; Nguyen, Staci; Agarwal, Misha R; Clegg, Tom; Connelly, Abram; Vandewege, Ward; Zaranek, Alexander Wait; Estep, Preston W; Church, George M; Drmanac, Radoje; Peters, Brock A

2016-10-11

Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

Energy Technology Data Exchange (ETDEWEB)

Nakhleh, Luay

2014-03-12

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

Exploring Other Genomes: Bacteria.

Science.gov (United States)

Flannery, Maura C.

2001-01-01

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

Human Genome Program

Energy Technology Data Exchange (ETDEWEB)

1993-01-01

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

76 FR 67178 - Wells Hydroelectric Project; Notice of Availability of the Final Environmental Impact Statement...

Science.gov (United States)

2011-10-31

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Project No. 2149-152] Wells Hydroelectric Project; Notice of Availability of the Final Environmental Impact Statement for the Wells... application for license for the Wells Hydroelectric Project (FERC No. 2149), located on the Columbia River in...

Staff Helping Attain Relevant Education (Project SHARE): Final Evaluation Report, 1992-93. OREA Report.

Science.gov (United States)

Ranadive, Jyoti

Project SHARE (Staff Helping Attain Relevant Education), a project funded by Title VII of the Elementary and Secondary Education Act, was in its third and final year of operation in 1992-93, in eight primary schools in the Bronx, Brooklyn, and Manhattan (New York). The project served 141 limited English proficient students from low-income families…

District Heating Demonstration project. Bydgoszcz, Poland, Final report

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-06-01

The project was finished in January 1999. The present final report outlines the activities of the pilot project. The activities of the project were: Development of a general model or a design strategy for the modernisation of group substations; Training of selected staff in updated design and latest technologies; Comparing experiences from the reconstructed heat exchanger station with alternative solutions; Investigation of potential sources of financing for the modernisation of the district heating system based on a revised feasibility study. The development of a general model for the future design of the heat exchanger station and the substations resulted in a design guideline which was used for the design of the heat exchanger station. KPEC selected the heat exchanger station CC02, located in area B1, as the object for the heat exchanger reconstruction. The station supplies 42 substations in 20 dwelling houses with a total heat demand of 11 MW. The design of the reconstruction began in the autumn of 1996. The equipment was procured during the spring of 1997 and the bulk of the installation work was finished by October 1997. The appointed design engineer participated in two study tours to Denmark. During the implementation the project was enlarged with an addendum. The addendum consisted of a modernisation of twelve building substations. The monitoring programme was enlarged accordingly and the efficiency of the two solutions were compared and evaluated through the monitoring programme. Even though some of the data are rather limited, the monitoring programme reveals a tendency towards the substation modernisation being twice as efficient as the heat exchanger modernisation. The reconstruction of the heat exchanger station has indicated a heat saving potential of 10% whereas the substation project has indicated a heat saving potential of 20%. The project further shows a huge potential for power savings in the main pumps due to the automatic control. (EHS)

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko

2018-02-14

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

Genome Sequences of Oryza Species

KAUST Repository

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

2018-01-01

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

The human genome project and the Catholic Church (1)

Science.gov (United States)

Moraczewski, Albert S

1991-12-01

The Cathlic Church has not made any formal statements about the Human Genome Project as such. But the present Pope, John Paul II, has commented, albeit very briefly, on various aspects of genetic manipulation. Genetic interventions which are therapeutic (e.g. gene therapy), namely, directed to the correction or amelioration of a disorder are acceptable, in principle, provided they promote the personal well being of the individual being so treated. Genetic interventions which are not therapeutic for the specific individual involved but are experimental and directed primarily to improving humans as biological entities are of dubious moral probity, but are not necessarily to be totally rejected out of hand. To be morally acceptable such genetic intervention should meet certain conditions which include due respect for the given psychological nature of each individual human being. In addition, no harm should be inflicted on the process of human generation, and its fundamental design should not be altered. Any genetic manipulation which results in, or tends to, the creation of groups with different qualities such that there would result a fresh marginalization of these people must be avoided. It has been also suggested by a few that because the Son of God took on a human nature in Jesus Christ, one may not so alter the human genome that a new distinct species would be created....

Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1).

Science.gov (United States)

Kiss, Hajnalka; Cleland, David; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Lu, Megan; Brettin, Thomas; Detter, John C; Göker, Markus; Tindall, Brian J; Beck, Brian; McDermott, Timothy R; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Cheng, Jan-Fang

2010-10-27

'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

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

Science.gov (United States)

2011-01-01

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

Lawrence Livermore National Laboratory- Completing the Human Genome Project and Triggering Nearly $1 Trillion in U.S. Economic Activity

Energy Technology Data Exchange (ETDEWEB)

Stewart, Jeffrey S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-07-28

The success of the Human Genome project is already nearing $1 Trillion dollars of U.S. economic activity. Lawrence Livermore National Laboratory (LLNL) was a co-leader in one of the biggest biological research effort in history, sequencing the Human Genome Project. This ambitious research effort set out to sequence the approximately 3 billion nucleotides in the human genome, an effort many thought was nearly impossible. Deoxyribonucleic acid (DNA) was discovered in 1869, and by 1943 came the discovery that DNA was a molecule that encodes the genetic instructions used in the development and functioning of living organisms and many viruses. To make full use of the information, scientists needed to first sequence the billions of nucleotides to begin linking them to genetic traits and illnesses, and eventually more effective treatments. New medical discoveries and improved agriculture productivity were some of the expected benefits. While the potential benefits were vast, the timeline (over a decade) and cost ($3.8 Billion) exceeded what the private sector would normally attempt, especially when this would only be the first phase toward the path to new discoveries and market opportunities. The Department of Energy believed its best research laboratories could meet this Grand Challenge and soon convinced the National Institute of Health to formally propose the Human Genome project to the federal government. The U.S. government accepted the risk and challenge to potentially create new healthcare and food discoveries that could benefit the world and the U.S. Industry.

The UK Human Genome Mapping Project online computing service.

Science.gov (United States)

Rysavy, F R; Bishop, M J; Gibbs, G P; Williams, G W

1992-04-01

This paper presents an overview of computing and networking facilities developed by the Medical Research Council to provide online computing support to the Human Genome Mapping Project (HGMP) in the UK. The facility is connected to a number of other computing facilities in various centres of genetics and molecular biology research excellence, either directly via high-speed links or through national and international wide-area networks. The paper describes the design and implementation of the current system, a 'client/server' network of Sun, IBM, DEC and Apple servers, gateways and workstations. A short outline of online computing services currently delivered by this system to the UK human genetics research community is also provided. More information about the services and their availability could be obtained by a direct approach to the UK HGMP-RC.

Ferrocyanide safety project ferrocyanide aging studies. Final report

International Nuclear Information System (INIS)

Lilga, M.A.; Hallen, R.T.; Alderson, E.V.

1996-06-01

This final report gives the results of the work conducted by Pacific Northwest National Laboratory (PNNL) from FY 1992 to FY 1996 on the Ferrocyanide Aging Studies, part of the Ferrocyanide Safety Project. The Ferrocyanide Safety Project was initiated as a result of concern raised about the safe storage of ferrocyanide waste intermixed with oxidants, such as nitrate and nitrite salts, in Hanford Site single-shell tanks (SSTs). In the laboratory, such mixtures can be made to undergo uncontrolled or explosive reactions by heating dry reagents to over 200 degrees C. In 1987, an Environmental Impact Statement (EIS), published by the U.S. Department of Energy (DOE), Final Environmental Impact Statement, Disposal of Hanford Defense High-Level Transuranic and Tank Waste, Hanford Site, Richland, Washington, included an environmental impact analysis of potential explosions involving ferrocyanide-nitrate mixtures. The EIS postulated that an explosion could occur during mechanical retrieval of saltcake or sludge from a ferrocyanide waste tank, and concluded that this worst-case accident could create enough energy to release radioactive material to the atmosphere through ventilation openings, exposing persons offsite to a short-term radiation dose of approximately 200 mrem. Later, in a separate study (1990), the General Accounting Office postulated a worst-case accident of one to two orders of magnitude greater than that postulated in the DOE EIS. The uncertainties regarding the safety envelope of the Hanford Site ferrocyanide waste tanks led to the declaration of the Ferrocyanide Unreviewed Safety Question (USQ) in October 1990

Final Project Report

DEFF Research Database (Denmark)

Workspace

2003-01-01

of the Disappearing Computer to be that of  “Augmenting reality”, where “Augmented reality” meant:  •  Augmented user – positioning, visualising. •  Augmented environment, Panels, tables and site-pack •  Augmented Artifacts - RFID , tagging, tracking •  Augmented communications – efficient exchange and integration......The primary focus of the WORKSPACE project was to augment the working  environment through the development of spatial computing components, initially for  members of the design professions, but with wider applicability to a range of work  domains.     The project interpreted the requirements...... of the above.    The philosophy was to make the computer disappear by both making it large and  embedding it into the environment (e.g. furniture).  The project has successfully achieved its objectives, and has developed a range of  demonstrator prototypes, some of which is in daily use by practitioners within...

The lawful uses of knowledge from the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Grad, F.P.

1994-04-15

Part I of this study deals with the right to know or not to know personal genetic information, and examines available legal protections of the right of privacy and the adverse effect of the disclosure of genetic information both on employment and insurance interests and on self esteem and protection of personal integrity. The study examines the rationale for the legal protection of privacy as the protection of a public interest. It examines the very limited protections currently available for privacy interests, including genetic privacy interests, and concludes that there is a need for broader, more far-reaching legal protections. The second part of the study is based on the assumption that as major a project as the Human Genome Project, spending billions of dollars on science which is health related, will indeed be applied for preventive and therapeutic public health purposes, as it has been in the past. It also addresses the recurring fear that public health initiatives in the genetic area must evolve a new eugenic agenda, that we must not repeat the miserable discriminatory experiences of the past.

Lessons learned in demonstration projects regarding operational safety during final disposal of vitrified waste and spent fuel

International Nuclear Information System (INIS)

Filbert, Wolfgang; Herold, Philipp

2015-01-01

The paper summarizes the lessons learned in demonstration projects regarding operational safety during the final disposal of vitrified waste and spent fuel. The three demonstration projects for the direct disposal of vitrified waste and spent fuel are described. The first two demonstration projects concern the shaft transport of heavy payloads of up to 85 t and the emplacement operations in the mine. The third demonstration project concerns the borehole emplacement operation. Finally, open issues for the next steps up to licensing of the emplacement and disposal systems are summarized.

Programmable SAW development :Sandia/NASA project final report.

Energy Technology Data Exchange (ETDEWEB)

Brocato, Robert Wesley

2004-10-01

This report describes a project to develop both fixed and programmable surface acoustic wave (SAW) correlators for use in a low power space communication network. This work was funded by NASA at Sandia National Laboratories for fiscal years 2004, 2003, and the final part of 2002. The role of Sandia was to develop the SAW correlator component, although additional work pertaining to use of the component in a system and system optimization was also done at Sandia. The potential of SAW correlator-based communication systems, the design and fabrication of SAW correlators, and general system utilization of those correlators are discussed here.

Final Technical Report, Wind Generator Project (Ann Arbor)

Energy Technology Data Exchange (ETDEWEB)

Geisler, Nathan [City of Ann Arbor, MI (United States)

2017-03-20

A Final Technical Report (57 pages) describing educational exhibits and devices focused on wind energy, and related outreach activities and programs. Project partnership includes the City of Ann Arbor, MI and the Ann Arbor Hands-on Museum, along with additional sub-recipients, and U.S. Department of Energy/Office of Energy Efficiency and Renewable Energy (EERE). Report relays key milestones and sub-tasks as well as numerous graphics and images of five (5) transportable wind energy demonstration devices and five (5) wind energy exhibits designed and constructed between 2014 and 2016 for transport and use by the Ann Arbor Hands-on Museum.

GENRE ANALYSIS OF THE ENGLISH FINAL PROJECT ABSTRACTS WRITTEN BY THE STUDENTS OF ENGLISH EDUCATION DEPARTMENT OF IKIP PGRI SEMARANG

Directory of Open Access Journals (Sweden)

Wiyaka Wiyaka

2010-12-01

Full Text Available This study is specifically focused on the student final project abstract based on genre analysis which covers the study of the generic structure and the linguistic features. The statements of the study are: (1. How do the students of English Education Department of IKIP PGRI Semarang realize the generic structure in their final project abstracts (2. How do they realize the linguistic features in their final project abstracts, and (3. What is the contribution of the result of the study to the English Education Program of IKIP PGRI Semarang. The main purpose of this study is to find out the generic structure and linguistic features of the final project abstracts and analyze the contribution of this study to the English Department. This study applies the descriptive qualitative method. The object of this study is the final project abstracts written by English Education Department students of ‘IKIP PGRI Semarang’. The total of 10 final projects formed the data of this study. The data of the study were analyzed using the genre analysis approach. The first step of data analysis was identifying the Moves which was done by using Linguistic evidence and understanding the texts. The finding shows that only some of the final project abstracts made by the students of IKIP PGRI applied the five Moves. It is found that two Moves are applied in all abstracts, they are Purpose and Method Moves (100%. Situating the research is used in five abstracts (50%. Meanwhile the third move that is the Result Move used in eight abstracts (80%. The Conclusion Move found in five abstracts (50%. The result of the analysis showed that two personal pronouns were found in the final project abstracts. Personal pronouns such as ‘the writer’ and ‘the researcher’ were found in all of the abstracts. Personal pronoun ‘she’ was found in one abstract. Finally, there are only five expressions of hedges that are used in the final project abstracts, they

Nuclear emergency preparedness. Final report of the Nordic Nuclear Safety Research Project BOK-1

DEFF Research Database (Denmark)

Lauritzen, B.

2002-01-01

Final report of the Nordic Nuclear Safety Research project BOK-1. The BOK-1 project, “Nuclear Emergency Preparedness”, was carried out in 1998-2001 with participants from the Nordic and Baltic Sea regions. The project consists of six sub-projects:Laboratory measurements and quality assurance (BOK-1.......1); Mobile measurements and measurement strategies (BOK-1.2); Field measurements and data assimilation (BOK-1.3); Countermeasures in agriculture and forestry (BOK-1.4); Emergency monitoring in theNordic and Baltic Sea countries (BOK-1.5); and Nuclear exercises (BOK-1.6). For each sub-project, the project...

The analysis of APOL1 genetic variation and haplotype diversity provided by 1000 Genomes project.

Science.gov (United States)

Peng, Ting; Wang, Li; Li, Guisen

2017-08-11

The APOL1 gene variants has been shown to be associated with an increased risk of multiple kinds of diseases, particularly in African Americans, but not in Caucasians and Asians. In this study, we explored the single nucleotide polymorphism (SNP) and haplotype diversity of APOL1 gene in different races provided by 1000 Genomes project. Variants of APOL1 gene in 1000 Genome Project were obtained and SNPs located in the regulatory region or coding region were selected for genetic variation analysis. Total 2504 individuals from 26 populations were classified as four groups that included Africa, Europe, Asia and Admixed populations. Tag SNPs were selected to evaluate the haplotype diversities in the four populations by HaploStats software. APOL1 gene was surrounded by some of the most polymorphic genes in the human genome, variation of APOL1 gene was common, with up to 613 SNP (1000 Genome Project reported) and 99 of them (16.2%) with MAF ≥ 1%. There were 79 SNPs in the URR and 92 SNPs in 3'UTR. Total 12 SNPs in URR and 24 SNPs in 3'UTR were considered as common variants with MAF ≥ 1%. It is worth noting that URR-1 was presents lower frequencies in European populations, while other three haplotypes taken an opposite pattern; 3'UTR presents several high-frequency variation sites in a short segment, and the differences of its haplotypes among different population were significant (P < 0.01), UTR-1 and UTR-5 presented much higher frequency in African population, while UTR-2, UTR-3 and UTR-4 were much lower. APOL1 coding region showed that two SNP of G1 with higher frequency are actually pull down the haplotype H-1 frequency when considering all populations pooled together, and the diversity among the four populations be widen by the G1 two mutation (P 1  = 3.33E-4 vs P 2  = 3.61E-30). The distributions of APOL1 gene variants and haplotypes were significantly different among the different populations, in either regulatory or coding regions. It could provide

Final design review report for K basin dose reduction project

International Nuclear Information System (INIS)

Blackburn, L.D.

1996-01-01

The strategy for reducing radiation dose originating from radionuclides absorbed in the K East Basin concrete is to raise the pool water level to provide additional shielding. This report documents a final design review for cleaning/coating basin walls and modifying other basin components where appropriate. The conclusion of this review was that the documents developed constitute an acceptable design for the Dose Reduction Project

Reflections on Mental Retardation and Eugenics, Old and New: Mensa and the Human Genome Project.

Science.gov (United States)

Smith, J. David

1994-01-01

This article addresses the moral and ethical issues of mental retardation and a continuing legacy of belief in eugenics. It discusses the involuntary sterilization of Carrie Buck in 1927, support for legalized killing of subnormal infants by 47% of respondents to a Mensa survey, and implications of the Human Genome Project for the field of mental…

Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project.

Science.gov (United States)

Biesecker, Leslie G

2012-04-01

The debate surrounding the return of results from high-throughput genomic interrogation encompasses many important issues including ethics, law, economics, and social policy. As well, the debate is also informed by the molecular, genetic, and clinical foundations of the emerging field of clinical genomics, which is based on this new technology. This article outlines the main biomedical considerations of sequencing technologies and demonstrates some of the early clinical experiences with the technology to enable the debate to stay focused on real-world practicalities. These experiences are based on early data from the ClinSeq project, which is a project to pilot the use of massively parallel sequencing in a clinical research context with a major aim to develop modes of returning results to individual subjects. The study has enrolled >900 subjects and generated exome sequence data on 572 subjects. These data are beginning to be interpreted and returned to the subjects, which provides examples of the potential usefulness and pitfalls of clinical genomics. There are numerous genetic results that can be readily derived from a genome including rare, high-penetrance traits, and carrier states. However, much work needs to be done to develop the tools and resources for genomic interpretation. The main lesson learned is that a genome sequence may be better considered as a health-care resource, rather than a test, one that can be interpreted and used over the lifetime of the patient.

Energy Storage and Distributed Energy Generation Project, Final Project Report

Energy Technology Data Exchange (ETDEWEB)

Schwank, Johannes; Mader, Jerry; Chen, Xiaoyin; Mi, Chris; Linic, Suljo; Sastry, Ann Marie; Stefanopoulou, Anna; Thompson, Levi; Varde, Keshav

2008-03-31

This report serves as a Final Report under the “Energy Storage and Distribution Energy Generation Project” carried out by the Transportation Energy Center (TEC) at the University of Michigan (UM). An interdisciplinary research team has been working on fundamental and applied research on: -distributed power generation and microgrids, -power electronics, and -advanced energy storage. The long-term objective of the project was to provide a framework for identifying fundamental research solutions to technology challenges of transmission and distribution, with special emphasis on distributed power generation, energy storage, control methodologies, and power electronics for microgrids, and to develop enabling technologies for novel energy storage and harvesting concepts that can be simulated, tested, and scaled up to provide relief for both underserved and overstressed portions of the Nation’s grid. TEC’s research is closely associated with Sections 5.0 and 6.0 of the DOE "Five-year Program Plan for FY2008 to FY2012 for Electric Transmission and Distribution Programs, August 2006.”

Ensembl Genomes 2013: scaling up access to genome-wide data.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

The promise of insect genomics

DEFF Research Database (Denmark)

Grimmelikhuijzen, Cornelis J P; Cazzamali, Giuseppe; Williamson, Michael

2007-01-01

Insects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state-of-the-art of these genome projects and the impacts...

Nuclear emergency preparedness. Final report of the Nordic nuclear safety research project BOK-1

Energy Technology Data Exchange (ETDEWEB)

Lauritzen, Bent [Risoe National Lab., Roskilde (Denmark)

2002-02-01

Final report of the Nordic Nuclear Safety Research project BOK-1. The BOK-1 project, 'Nuclear Emergency Preparedness', was carried out in 1998-2001 with participants from the Nordic and Baltic Sea regions. The project consists of six sub-projects: Laboratory measurements and quality assurance (BOK-1.1); Mobile measurements and measurement strategies (BOK-1.2); Field measurement and data assimilation (BOK-1.3); Countermeasures in agriculture and forestry (BOK-1.4); Emergency monitoring in the Nordic and Baltic Sea countries (BOK-1.5); and Nuclear exercises (BOK-1.6). For each sub-project, the project outline, objectives and organization are described and main results presented. (au)

Nuclear emergency preparedness. Final report of the Nordic nuclear safety research project BOK-1

International Nuclear Information System (INIS)

Lauritzen, Bent

2002-02-01

Final report of the Nordic Nuclear Safety Research project BOK-1. The BOK-1 project, 'Nuclear Emergency Preparedness', was carried out in 1998-2001 with participants from the Nordic and Baltic Sea regions. The project consists of six sub-projects: Laboratory measurements and quality assurance (BOK-1.1); Mobile measurements and measurement strategies (BOK-1.2); Field measurement and data assimilation (BOK-1.3); Countermeasures in agriculture and forestry (BOK-1.4); Emergency monitoring in the Nordic and Baltic Sea countries (BOK-1.5); and Nuclear exercises (BOK-1.6). For each sub-project, the project outline, objectives and organization are described and main results presented. (au)

Ensembl Genomes 2016: more genomes, more complexity.

Science.gov (United States)

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

2016-01-04

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

Consortium biology in immunology: the perspective from the Immunological Genome Project.

Science.gov (United States)

Benoist, Christophe; Lanier, Lewis; Merad, Miriam; Mathis, Diane

2012-10-01

Although the field has a long collaborative tradition, immunology has made less use than genetics of 'consortium biology', wherein groups of investigators together tackle large integrated questions or problems. However, immunology is naturally suited to large-scale integrative and systems-level approaches, owing to the multicellular and adaptive nature of the cells it encompasses. Here, we discuss the value and drawbacks of this organization of research, in the context of the long-running 'big science' debate, and consider the opportunities that may exist for the immunology community. We position this analysis in light of our own experience, both positive and negative, as participants of the Immunological Genome Project.

SPEAR 3 Upgrade Project: The Final Year

International Nuclear Information System (INIS)

Hettel, R

2004-01-01

During April, 2003, the SPEAR 2 storage ring, which served the high energy physics community from 1972 to 1987, and the synchrotron radiation community for an additional 15 years, was removed from its shielding tunnel in order to install the new 3-GeV, 500-mA SPEAR 3 light source. From May to November, SSRL will excavate the tunnel floor and pour a new concrete floor, and then install pre-assembled girders holding magnets, copper vacuum chambers, PEP-II-style rf cavities, and beam line front end components. At the same time, power supply, instrumentation and control, and other ancillary systems will be configured, leading to a commissioning period beginning in November 2003. The progress of accelerator component implementation and installation during the final year of the project will be reviewed

The pig genome project has plenty to squeal about.

Science.gov (United States)

Fan, B; Gorbach, D M; Rothschild, M F

2011-01-01

Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future 'systems biology' that integrates and optimizes the information from all research levels can enhance the pig community's understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed. Copyright © 2011 S. Karger AG, Basel.

A novel genome-information content-based statistic for genome-wide association analysis designed for next-generation sequencing data.

Science.gov (United States)

Luo, Li; Zhu, Yun; Xiong, Momiao

2012-06-01

The genome-wide association studies (GWAS) designed for next-generation sequencing data involve testing association of genomic variants, including common, low frequency, and rare variants. The current strategies for association studies are well developed for identifying association of common variants with the common diseases, but may be ill-suited when large amounts of allelic heterogeneity are present in sequence data. Recently, group tests that analyze their collective frequency differences between cases and controls shift the current variant-by-variant analysis paradigm for GWAS of common variants to the collective test of multiple variants in the association analysis of rare variants. However, group tests ignore differences in genetic effects among SNPs at different genomic locations. As an alternative to group tests, we developed a novel genome-information content-based statistics for testing association of the entire allele frequency spectrum of genomic variation with the diseases. To evaluate the performance of the proposed statistics, we use large-scale simulations based on whole genome low coverage pilot data in the 1000 Genomes Project to calculate the type 1 error rates and power of seven alternative statistics: a genome-information content-based statistic, the generalized T(2), collapsing method, multivariate and collapsing (CMC) method, individual χ(2) test, weighted-sum statistic, and variable threshold statistic. Finally, we apply the seven statistics to published resequencing dataset from ANGPTL3, ANGPTL4, ANGPTL5, and ANGPTL6 genes in the Dallas Heart Study. We report that the genome-information content-based statistic has significantly improved type 1 error rates and higher power than the other six statistics in both simulated and empirical datasets.

Rhipicephalus (Boophilus) microplus strain Deutsch, whole genome shotgun sequencing project first submission of genome sequence

Science.gov (United States)

The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence difficult. Cot filtration/selection techniques were used to reduce the repetitive fraction of the tick genome and enrich for the fraction of DNA with gene-containing regions. The Cot-selected ...

Final project report: TA-35 Los Alamos Power Reactor Experiment No. II (LAPRE II) decommissioning project

International Nuclear Information System (INIS)

Montoya, G.M.

1993-02-01

This final report addresses the decommissioning of the LAPRE II Reactor, safety enclosure, fuel reservoir tanks, emergency fuel recovery system, primary pump pit, secondary loop, associated piping, and the post-remediation activities. Post-remedial action measurements are also included. The cost of the project including, Phase I assessment and Phase II remediation was approximately $496K. The decommissioning operation produced 533 M 3 of mixed waste

Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

Science.gov (United States)

Konkel, Miriam K; Walker, Jerilyn A; Hotard, Ashley B; Ranck, Megan C; Fontenot, Catherine C; Storer, Jessica; Stewart, Chip; Marth, Gabor T; Batzer, Mark A

2015-08-29

The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Democratizing Human Genome Project Information: A Model Program for Education, Information and Debate in Public Libraries.

Science.gov (United States)

Pollack, Miriam

The "Mapping the Human Genome" project demonstrated that librarians can help whomever they serve in accessing information resources in the areas of biological and health information, whether it is the scientists who are developing the information or a member of the public who is using the information. Public libraries can guide library…

Analysis of final year DVM research projects submitted to the Faculty ...

African Journals Online (AJOL)

Central Research Laboratory

in the library. The essence of this study is to guide prospective final year students and researchers in the choice of research topics as this will help in saving their time. It will also ... and Undergraduate projects of the same department in 2002. Obajemu (1999) also .... majority of the rural people. The distribution by animal ...

WormBase 2016: expanding to enable helminth genomic research.

Science.gov (United States)

Howe, Kevin L; Bolt, Bruce J; Cain, Scott; Chan, Juancarlos; Chen, Wen J; Davis, Paul; Done, James; Down, Thomas; Gao, Sibyl; Grove, Christian; Harris, Todd W; Kishore, Ranjana; Lee, Raymond; Lomax, Jane; Li, Yuling; Muller, Hans-Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, Michael; Raciti, Daniela; Schindelman, Gary; Stanley, Eleanor; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Williams, Gary; Wright, Adam; Yook, Karen; Berriman, Matthew; Kersey, Paul; Schedl, Tim; Stein, Lincoln; Sternberg, Paul W

2016-01-04

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Bat biology, genomes, and the Bat1K project

DEFF Research Database (Denmark)

Teeling, Emma C; Vernes, Sonja C; Dávalos, Liliana M

2018-01-01

and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any...

Wabash River Coal Gasification Repowering Project: A DOE Assessment; FINAL

International Nuclear Information System (INIS)

National Energy Technology Laboratory

2002-01-01

The goal of the U.S. Department of Energy (DOE) Clean Coal Technology Program (CCT) is to furnish the energy marketplace with a number of advanced, more efficient, and environmentally responsible coal utilization technologies through demonstration projects. These projects seek to establish the commercial feasibility of the most promising advanced coal technologies that have developed beyond the proof-of-concept stage. This document serves as a DOE post-project assessment (PPA) of a project selected in CCT Round IV, the Wabash River Coal Gasification Repowering (WRCGR) Project, as described in a Report to Congress (U.S. Department of Energy 1992). Repowering consists of replacing an existing coal-fired boiler with one or more clean coal technologies to achieve significantly improved environmental performance. The desire to demonstrate utility repowering with a two-stage, pressurized, oxygen-blown, entrained-flow, integrated gasification combined-cycle (IGCC) system prompted Destec Energy, Inc., and PSI Energy, Inc., to form a joint venture and submit a proposal for this project. In July 1992, the Wabash River Coal Gasification Repowering Project Joint Venture (WRCGRPJV, the Participant) entered into a cooperative agreement with DOE to conduct this project. The project was sited at PSI Energy's Wabash River Generating Station, located in West Terre Haute, Indiana. The purpose of this CCT project was to demonstrate IGCC repowering using a Destec gasifier and to assess long-term reliability, availability, and maintainability of the system at a fully commercial scale. DOE provided 50 percent of the total project funding (for capital and operating costs during the demonstration period) of$438 million. Construction for the demonstration project was started in July 1993. Pre-operational tests were initiated in August 1995, and construction was completed in November 1995. Commercial operation began in November 1995, and the demonstration period was completed in December

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

Science.gov (United States)

Kersey, Paul J; Staines, Daniel M; Lawson, Daniel; Kulesha, Eugene; Derwent, Paul; Humphrey, Jay C; Hughes, Daniel S T; Keenan, Stephan; Kerhornou, Arnaud; Koscielny, Gautier; Langridge, Nicholas; McDowall, Mark D; Megy, Karine; Maheswari, Uma; Nuhn, Michael; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Wilson, Derek; Yates, Andrew; Birney, Ewan

2012-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.

Public data and open source tools for multi-assay genomic investigation of disease.

Science.gov (United States)

Kannan, Lavanya; Ramos, Marcel; Re, Angela; El-Hachem, Nehme; Safikhani, Zhaleh; Gendoo, Deena M A; Davis, Sean; Gomez-Cabrero, David; Castelo, Robert; Hansen, Kasper D; Carey, Vincent J; Morgan, Martin; Culhane, Aedín C; Haibe-Kains, Benjamin; Waldron, Levi

2016-07-01

Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods. © The Author 2015. Published by Oxford University Press.

MIPS plant genome information resources.

Science.gov (United States)

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

2007-01-01

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

The genome of Arabidopsis thaliana.

OpenAIRE

Goodman, H M; Ecker, J R; Dean, C

1995-01-01

Arabidopsis thaliana is a small flowering plant that is a member of the family cruciferae. It has many characteristics--diploid genetics, rapid growth cycle, relatively low repetitive DNA content, and small genome size--that recommend it as the model for a plant genome project. The current status of the genetic and physical maps, as well as efforts to sequence the genome, are presented. Examples are given of genes isolated by using map-based cloning. The importance of the Arabidopsis project ...

Enewetak radiological support project. Final report

International Nuclear Information System (INIS)

Friesen, B.

1982-09-01

From 1972 through 1980, the Department of Energy acted in an advisory role to the Defense Nuclear Agency during planning for and execution of the cleanup of Enewetak Atoll. The Nevada Operations Office of the Department of Energy was responsible for the radiological characterization of the atoll and for certification of radiological condition of each island upon completion of the project. In-situ measurements of gamma rays emitted by americium-241 were utilized along with wet chemistry separation of plutonium from soil samples to identify and delineate surface areas requiring removal of soil. Military forces removed over 100,000 cubic yards of soil from the surface of five islands and deposited this material in a crater remaining from the nuclear testing period. Subsurface soil was excavated and removed from several locations where measurements indicated the presence of radionuclides above predetermined criteria. The methodologies of data acquisition, analysis and interpretation are described and detailed results are provided in text, figures and microfiche. The final radiological condition of each of 43 islets is reported

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

DEFF Research Database (Denmark)

Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya

2007-01-01

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses...

Final disposal of radioactive wastes in Switzerland: concept and overview of Project Guarantee 1985

International Nuclear Information System (INIS)

Anon.

1985-01-01

The validity of the operational licences of the existing Swiss nuclear power plants (NPP) Beznau I and II, Muehleberg, Goesgen and Leibstadt after 31st. December 1985 is, because of official requirements, dependent on the demonstration of permanent, safe management and final disposal of radioactive waste. For this purpose, the NPP companies have to prepare a so-called guarantee project and present this to the Bundesrat for review. The appropriate investigations and research have been carried out by Nagra (National Cooperative for the Storage of Radioactive Waste). The 1985 Project Gewaehr (Guarantee) is described in an eight volume report NGB 85-01 to 85-08 and individual research projects are reported on in separate NTB-series reference reports. The present volume NGB 85-01 takes the form of a self-contained project overview in which the concepts for nuclear waste management are described, the contents of the remaining volumes NGB 85-02 to 85-08 are summarized and Project conclusions are drawn from Project Gewaehr 1985. Project Gewaehr 1985 covers two repository types: Type C repository for high-level and certain alpha-containing intermediate-level waste, and Type B repository for all remaining intermediate- and low-level waste. The Project shows in detail that technical feasibility of final disposal can be assumed given presently available methods, that the technical safety barriers show a high level of efficiency and that suitable geological options are available to ensure long-term safety in Switzerland as the concept is defined by official requirements. The Project safety analyses show that the chosen disposal concepts assure the protection of mankind and the environment under all realistically anticipated conditions

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.

Final Technical Report - Kotzebue Wind Power Project - Volume II

Energy Technology Data Exchange (ETDEWEB)

Rana Zucchi, Global Energy Concepts, LLC; Brad Reeve, Kotzebue Electric Association; DOE Project Officer - Doug Hooker

2007-10-31

The Kotzebue Wind Power Project is a joint undertaking of the U.S. Department of Energy (DOE); Kotzebue Electric Association (KEA); and the Alaska Energy Authority (AEA). The goal of the project is to develop, construct, and operate a wind power plant interconnected to a small isolated utility grid in an arctic climate in Northwest Alaska. The primary objective of KEA’s wind energy program is to bring more affordable electricity and jobs to remote Alaskan communities. DOE funding has allowed KEA to develop a multi-faceted approach to meet these objectives that includes wind project planning and development, technology transfer, and community outreach. The first wind turbines were installed in the summer of 1997 and the newest turbines were installed in the spring of 2007. The total installed capacity of the KEA wind power project is 1.16 MW with a total of 17 turbines rated between 65 kW and 100 kW. The operation of the wind power plant has resulted in a wind penetration on the utility system in excess of 35% during periods of low loads. This document and referenced attachments are presented as the final technical report for the U.S. Department of Energy (DOE) grant agreement DE-FG36-97GO10199. Interim deliverables previously submitted are also referenced within this document and where reasonable to do so, specific sections are incorporated in the report or attached as appendices.

Final Project Report

Energy Technology Data Exchange (ETDEWEB)

Small, R. Justin [Woods Hole Oceanographic Institution, MA (United States); Bryan, Frank [Woods Hole Oceanographic Institution, MA (United States); Tribbia, Joseph [Woods Hole Oceanographic Institution, MA (United States); Park, Sungsu [Woods Hole Oceanographic Institution, MA (United States); Dennis, John [Woods Hole Oceanographic Institution, MA (United States); Saravanan, R. [Woods Hole Oceanographic Institution, MA (United States); Schneider, Niklas [Woods Hole Oceanographic Institution, MA (United States); Kwon, Young-Oh [Woods Hole Oceanographic Institution, MA (United States)

2015-06-01

Most climate models are currently run with grid spacings of around 100km, which, with today’s computing power, allows for long (up to 1000 year) simulations, or ensembles of simulations to explore climate change and variability. However this grid spacing does not resolve important components of the weather/climate system such as atmospheric fronts and mesoscale systems, and ocean boundary currents and eddies. The overall aim of this project has been to look at the effect of these small-scale features on the weather/climate system using a suite of high and low resolution climate models, idealized models and observations. This project was only possible due to the highly scalable aspect of the CAM Spectral Element dynamical core, and the significant resources allocated at Yellowstone and NERSC for which we are grateful.

Blue Creek Winter Range: Wildlife Mitigation Project. Final environmental assessment

International Nuclear Information System (INIS)

1994-11-01

Bonneville Power Administration (BPA) proposes to fund that portion of the Washington Wildlife Agreement pertaining to the Blue Creek Winter Range Wildlife Mitigation Project (Project) in a cooperative effort with the Spokane Tribe, Upper Columbia United Tribes, and the Bureau of Indian Affairs (BIA). If fully implemented, the proposed action would allow the sponsors to protect and enhance 2,631 habitat units of big game winter range and riparian shrub habitat on 2,185 hectares (5,400 acres) of Spokane Tribal trust lands, and to conduct long term wildlife management activities within the Spokane Indian Reservation project area. This Final Environmental Assessment (EA) examines the potential environmental effects of securing land and conducting wildlife habitat enhancement and long term management activities within the boundaries of the Spokane Indian Reservation. Four proposed activities (habitat protection, habitat enhancement, operation and maintenance, and monitoring and evaluation) are analyzed. The proposed action is intended to meet the need for mitigation of wildlife and wildlife habitat adversely affected by the construction of Grand Coulee Dam and its reservoir

Ensembl 2002: accommodating comparative genomics.

Science.gov (United States)

Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

2003-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

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.

Genome Maps, a new generation genome browser.

Science.gov (United States)

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

2013-07-01

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

Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project - Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Saurwein, John

2011-07-15

This report is the Final Technical Report for the Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project conducted by a team led by General Atomics under DOE Award DE-NE0000245. The primary overall objective of the project was to develop and document a conceptual design for the Steam Cycle Modular Helium Reactor (SC-MHR), which is the reactor concept proposed by General Atomics for the NGNP Demonstration Plant. The report summarizes the project activities over the entire funding period, compares the accomplishments with the goals and objectives of the project, and discusses the benefits of the work. The report provides complete listings of the products developed under the award and the key documents delivered to the DOE.

Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project - Final Technical Report

International Nuclear Information System (INIS)

Saurwein, J.

2011-01-01

This report is the Final Technical Report for the Next Generation Nuclear Plant (NGNP) Prismatic HTGR Conceptual Design Project conducted by a team led by General Atomics under DOE Award DE-NE0000245. The primary overall objective of the project was to develop and document a conceptual design for the Steam Cycle Modular Helium Reactor (SC-MHR), which is the reactor concept proposed by General Atomics for the NGNP Demonstration Plant. The report summarizes the project activities over the entire funding period, compares the accomplishments with the goals and objectives of the project, and discusses the benefits of the work. The report provides complete listings of the products developed under the award and the key documents delivered to the DOE.

O admirável Projeto Genoma Humano The brave New Human Genome Project

Directory of Open Access Journals (Sweden)

Marilena V. Corrêa

2002-12-01

Full Text Available Este artigo apresenta um panorama das implicações sociais, éticas e legais do Projeto Genoma Humano. Os benefícios desse megaprojeto, traduzidos em promessas de uma revolução terapêutica na medicina, não se realizarão sem conflitos. O processo de inovação tecnológica na genética traz problemas de ordens diversas: por um lado, pesquisas em consórcio, patenteamento de genes e produtos da genômica apontam interesses comerciais e dificuldades de gerenciamento dos resultados dessas pesquisas. Esses problemas colocam desafios em termos de uma possível desigualdade no acesso aos benefícios das pesquisas. Por outro lado, temos a questão da informação genética e da proteção de dados individuais sobre riscos e suscetibilidades a doenças e atributos humanos. O problema da definição de homens e mulheres em função de traços genéticos traz uma ameaça discriminatória clara, e se torna agudo em função do reducionismo genético que a mídia ajuda a propagar. As respostas a esses problemas não podem ser esperadas apenas da bioética. A abordagem bioética deve poder combinar-se a análises políticas da reprodução, da sexualidade, da saúde e da medicina. Um vastíssimo espectro de problemas como estes não pode ser discutido em profundidade em um artigo. Optou-se por mapeá-los no sentido de enfatizar em que medida, na reflexão sobre o projeto genoma, a genômica e a pós-genômica, enfrenta-se o desafio de articular aspectos tão diferenciados.This article presents an overview of the social, ethical, and legal implications of the Human Genome Project. The benefits of this mega-project, expressed as promises of a therapeutic revolution in medicine, will not be achieved without conflict. The process of technological innovation in genetics poses problems of various orders: on the one hand, consortium-based research, gene patenting, and genomic products tend to feature commercial interests and management of the results of such

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.

Final report on Paradox Basin/Gulf Interior: Regulatory project management

International Nuclear Information System (INIS)

1986-12-01

This final report on the Regulatory Project Manager (RPM) program begins with a discussion of the key products produced during the 9-year effort and then focuses on the work performed in the major disciplines. The report then discusses the management of the work effort and the Quality Assurance (QA) program. It concludes with a brief discussion of the records turned over to the Office of Nuclear Waste Isolation (ONWI) at the conclusion of the work. 14 figs., 14 tabs

The impact of project marketing on the projects finality

Directory of Open Access Journals (Sweden)

Oxana SAVCIUC

2015-06-01

Full Text Available In the last years we assist at the level of the Republic of Moldova and also at international level at a trend to offer financial support with a special focus on project-based funding. Once with the appearance and development of the project concept, other related concepts are being developed such as project management or newly, we can also speak about the projects marketing. Until recently, the product marketing was intensely discussed; concepts such as services marketing appeared afterwards, but also the specific marketing for various branches, such as agromarketing, political marketing, etc. Given that fact that the projects are a product / service itself, at the moment, more and more often projects marketing is discussed.

Short communication: Genomic selection in a crossbred cattle population using data from the Dairy Genetics East Africa Project.

Science.gov (United States)

Brown, A; Ojango, J; Gibson, J; Coffey, M; Okeyo, M; Mrode, R

2016-09-01

Due to the absence of accurate pedigree information, it has not been possible to implement genetic evaluations for crossbred cattle in African small-holder systems. Genomic selection techniques that do not rely on pedigree information could, therefore, be a useful alternative. The objective of this study was to examine the feasibility of using genomic selection techniques in a crossbred cattle population using data from Kenya provided by the Dairy Genetics East Africa Project. Genomic estimated breeding values for milk yield were estimated using 2 prediction methods, GBLUP and BayesC, and accuracies were calculated as the correlation between yield deviations and genomic breeding values included in the estimation process, mimicking the situation for young bulls. The accuracy of evaluation ranged from 0.28 to 0.41, depending on the validation population and prediction method used. No significant differences were found in accuracy between the 2 prediction methods. The results suggest that there is potential for implementing genomic selection for young bulls in crossbred small-holder cattle populations, and targeted genotyping and phenotyping should be pursued to facilitate this. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

Science.gov (United States)

Behura, Susanta K; Severson, David W

2013-02-01

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Automated metadata--final project report

International Nuclear Information System (INIS)

Schissel, David

2016-01-01

This report summarizes the work of the Automated Metadata, Provenance Cataloging, and Navigable Interfaces: Ensuring the Usefulness of Extreme-Scale Data Project (MPO Project) funded by the United States Department of Energy (DOE), Offices of Advanced Scientific Computing Research and Fusion Energy Sciences. Initially funded for three years starting in 2012, it was extended for 6 months with additional funding. The project was a collaboration between scientists at General Atomics, Lawrence Berkley National Laboratory (LBNL), and Massachusetts Institute of Technology (MIT). The group leveraged existing computer science technology where possible, and extended or created new capabilities where required. The MPO project was able to successfully create a suite of software tools that can be used by a scientific community to automatically document their scientific workflows. These tools were integrated into workflows for fusion energy and climate research illustrating the general applicability of the project's toolkit. Feedback was very positive on the project's toolkit and the value of such automatic workflow documentation to the scientific endeavor.

Final project report, TA-35 Los Alamos Power Reactor Experiment No. II (LAPRE II) decommissioning project

International Nuclear Information System (INIS)

Montoya, G.M.

1992-01-01

This final report addresses the decommissioning of the LAPRE II Reactor, safety enclosure, fuel reservoir tanks, emergency fuel recovery system, primary pump pit, secondary loop, associated piping, and the post-remediation activities. Post-remedial action measurements are also included. The cost of the project, including Phase I assessment and Phase II remediation was approximately $496K. The decommissioning operation produced 533 m 3 of low-level solid radioactive waste and 5 m 3 of mixed waste

Description of the supporting factors of final project in Mathematics and Natural Sciences Faculty of Syiah Kuala University with multiple correspondence analysis

Science.gov (United States)

Rusyana, Asep; Nurhasanah; Maulizasari

2018-05-01

Syiah Kuala University (Unsyiah) is hoped to have graduates who are qualified for working or creating a field of work. A final project course implementation process must be effective. This research uses data from the evaluation conducted by Mathematics and Natural Sciences Faculty (FMIPA) of Unsyiah. Some of the factors that support the completion of the final project are duration, guidance, the final project seminars, facility, public impact, and quality. This research aims to know the factors that have a relationship with the completion of the final project and identify similarities among variables. The factors that support the completion of the final project at every study program in FMIPA are (1) duration, (2) guidance and (3) facilities. These factors are examined for the correlations by chi-square test. After that, the variables are analyzed with multiple correspondence analysis. Based on the plot of correspondence, the activities of the guidance and facilities in Informatics Study Program are included in the fair category, while the guidance and facilities in the Chemistry are included in the best category. Besides that, students in Physics can finish the final project with the fastest completion duration, while students in Pharmacy finish for the longest time.

ELSI Bibliography: Ethical legal and social implications of the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Yesley, M.S. [comp.

1993-11-01

This second edition of the ELSI Bibliography provides a current and comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. Since the first edition of the ELSI Bibliography was printed last year, new publications and earlier ones identified by additional searching have doubled our computer database of ELSI publications to over 5600 entries. The second edition of the ELSI Bibliography reflects this growth of the underlying computer database. Researchers should note that an extensive collection of publications in the database is available for public use at the General Law Library of Los Alamos National Laboratory (LANL).

MIPS: a database for genomes and protein sequences.

Science.gov (United States)

Mewes, H W; Frishman, D; Güldener, U; Mannhaupt, G; Mayer, K; Mokrejs, M; Morgenstern, B; Münsterkötter, M; Rudd, S; Weil, B

2002-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

Puget Sound Tidal Energy In-Water Testing and Development Project Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Collar, Craig W

2012-11-16

others. All required permit and license applications were completed and submitted under this award, including a Final License Application for a pilot hydrokinetic license from the Federal Energy Regulatory Commission. The tasks described above have brought the project through all necessary requirements to construct a tidal pilot project in Admiralty Inlet with the exception of final permit and license approvals, and the selection of a general contractor to perform project construction.

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.

'Advancement of KHPS to DOE TRL 7/8' Project - Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Adonizio, Mary Ann [Verdant Power Inc., New York, NY (United States); Corren, Dean [Verdant Power Inc., New York, NY (United States); Smith, Ron [Verdant Power Inc., New York, NY (United States); Colby, Jonathan [Verdant Power Inc., New York, NY (United States); Hernandez, Aaron [Verdant Power Inc., New York, NY (United States)

2016-04-08

Final Report describing activities performed under the 'Advancement of the KHPS to DOE TRL 7/8' project, including the development of critical component test protocols, testing and analysis of the Gen5 KHPS main shaft seal, and continuing compliance work on approved operational environmental monitoring plans in anticipation of KHPS turbine installation at Verdant Power's Roosevelt Island Tidal Energy (RITE) Project site in New York, NY.

Final Report for NIREC Renewable Energy Research & Development Project

Energy Technology Data Exchange (ETDEWEB)

Borland, Walt [Nevada Institute for Renewable Energy Commercialization (NIREC), Las Vegas, NV (United States)

2017-05-02

This report is a compilation of progress reports and presentations submitted by NIREC to the DOE’s Solar Energy Technologies Office for award number DE-FG36-08GO88161. This compilation has been uploaded to OSTI by DOE as a substitute for the required Final Technical Report, which was not submitted to DOE by NIREC or received by DOE. Project Objective: The primary goal of NIREC is to advance the transformation of the scientific innovation of the institutional partner’s research in renewable energy into a proof of the scientific concept eventually leading to viable businesses with cost effective solutions to accelerate the widespread adoption of renewable energy. NIREC will a) select research projects that are determined to have significant commercialization potential as a result of vetting by the Technology and commercialization Advisory Board, b) assign an experienced Entrepreneur-in-Residence (EIR) to each manage the scientific commercialization-preparedness process, and c) facilitate connectivity with venture capital and other private-sector capital sources to fund the rollout, scaling and growth of the resultant renewable energy business.

Northeast Oregon Hatchery Project, Conceptual Design Report, Final Report.

Energy Technology Data Exchange (ETDEWEB)

Watson, Montgomery (Montgomery Watson, Bellevue, WA)

1995-03-01

This report presents the results of site analysis for the Bonneville Power Administration Northeast Oregon Hatchery Project. The purpose of this project is to provide engineering services for the siting and conceptual design of hatchery facilities for the Bonneville Power Administration. The hatchery project consists of artificial production facilities for salmon and steelhead to enhance production in three adjacent tributaries to the Columbia River in northeast Oregon: the Grande Ronde, Walla Walla, and Imnaha River drainage basins. Facilities identified in the master plan include adult capture and holding facilities; spawning incubation, and early rearing facilities; full-term rearing facilities; and direct release or acclimation facilities. The evaluation includes consideration of a main production facility for one or more of the basins or several smaller satellite production facilities to be located within major subbasins. The historic and current distribution of spring and fall chinook salmon and steelhead was summarized for the Columbia River tributaries. Current and future production and release objectives were reviewed. Among the three tributaries, forty seven sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.

Northeast Oregon Hatchery Project conceptual design report. Final report

International Nuclear Information System (INIS)

1995-03-01

This report presents the results of site analysis for the Bonneville Power Administration Northeast Oregon Hatchery Project. The purpose of this project is to provide engineering services for the siting and conceptual design of hatchery facilities for the Bonneville Power Administration. The hatchery project consists of artificial production facilities for salmon and steelhead to enhance production in three adjacent tributaries to the Columbia River in northeast Oregon: the Grande Ronde, Walla Walla, and Imnaha River drainage basins. Facilities identified in the master plan include adult capture and holding facilities; spawning incubation, and early rearing facilities; full-term rearing facilities; and direct release or acclimation facilities. The evaluation includes consideration of a main production facility for one or more of the basins or several smaller satellite production facilities to be located within major subbasins. The historic and current distribution of spring and fall chinook salmon and steelhead was summarized for the Columbia River tributaries. Current and future production and release objectives were reviewed. Among the three tributaries, forty seven sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed

Manitoba Motor Dealers Association pilot project : final report

International Nuclear Information System (INIS)

2006-08-01

This report described a 3-month pilot project conducted by EnerGuide for Vehicles in collaboration with the Manitoba Motor Dealers Association (MMDA) to increase dealership and consumer awareness of vehicle impacts on climate change. The project also aimed to engage MMDA's members in helping to promote and distribute information on fuel efficient vehicles and fuel efficient driving habits. Program tools in both the dealership showroom as well as service areas were used. Objectives of the project also included gaining public opinion research (POR) information regarding the impact of program tools; gaining feedback from new car dealers regarding the success of the project; gauging customer perceptions of the importance of fuel efficiency when selecting a new vehicle; determining whether or not drivers verify tire pressure on their vehicles; determining whether or not drivers incorporate energy efficient driving habits; and gauging customer perceptions regarding the importance of incorporating behaviours to improve fuel efficiency. The study used a mixed methodology of online and telephone surveys. A total of 41 dealerships participated in the project. The final sample of surveys consisted of 1926 customer records. The total overall number of completed interviews was 463. Results indicated that most dealers believed the campaign was a success, and that staff and customers learned about energy efficiency as a result of the campaign. Seventy-five per cent of dealers agreed that they would participate in future energy efficiency programs. Campaign materials and customer incentives were widely viewed as successful in raising awareness. Seven in 10 dealership customers recalled at least 1 of the promotional endeavours, and a large majority of customers indicated the information they saw at the dealership encouraged them to consider fuel efficiency when buying or maintaining a vehicle in the future. The majority of new customers considered fuel consumption to be the second

Terahertz spectral signatures :measurement and detection LDRD project 86361 final report.

Energy Technology Data Exchange (ETDEWEB)

Wanke, Michael Clement; Brener, Igal; Lee, Mark

2005-11-01

LDRD Project 86361 provided support to upgrade the chemical and material spectral signature measurement and detection capabilities of Sandia National Laboratories using the terahertz (THz) portion of the electromagnetic spectrum, which includes frequencies between 0.1 to 10 THz. Under this project, a THz time-domain spectrometer was completed. This instrument measures sample absorption spectra coherently, obtaining both magnitude and phase of the absorption signal, and has shown an operating signal-to-noise ratio of 10{sub 4}. Additionally, various gas cells and a reflectometer were added to an existing high-resolution THz Fourier transform spectrometer, which greatly extend the functionality of this spectrometer. Finally, preliminary efforts to design an integrated THz transceiver based on a quantum cascade laser were begun.

Human genome. 1993 Program report

Energy Technology Data Exchange (ETDEWEB)

1994-03-01

The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

Final Project Report

DEFF Research Database (Denmark)

Duer, Karsten

1997-01-01

The report summarizes the work that has been carried out within the project "B1 AEROGELS" as a part of the IEA SH&CP Task 18 "Advanced Glazing and Associated Materials For SolarAnd Building Applications". By providing at the same time thermal insulation and transparency the silica aerogel is a very...

Final environmental impact statement Kenetech/PacifiCorp Windpower Project Carbon County, Wyoming

International Nuclear Information System (INIS)

1995-08-01

The Draft and Final Environmental Impact Statements (DEIS and FEIS) assess the environmental consequences of a proposed windpower energy development in Carbon County, Wyoming. This abbreviated FEIS revises and supplements the DEIS for the project and addresses comments expressed for the DEIS. The proposed project entails the erection of approximately 1,390 wind turbine generators and associated facilities (e.g., roads, substations, distribution and communications lines) by KENETECH Windpower, Inc. A 230-kV transmission line would be built by PacifiCorp, Inc. to connect a proposed substation on Foote Creek Rim near Arlington to the Miner's substation near Hanna. The proposed project would use standard procedures as currently employed by other right-of-way projects, plus additional project-specific and site-specific mitigation measures to ensure that project impacts are minimized on all important resources. Impacts to most resources would be negligible to moderate during the life-of-project. Potentially significant impacts from the project include avian mortality; declining avian populations; threatened, endangered, candidate, and/or state sensitive species mortality and/or habitat loss; disturbance to nearby residents due to noise; changes in visual resources; disturbance of important Native American traditional sites; changes in plant community species composition due to snow redistribution; displacement of big game due to windfarm operation; and loss of sage grouse nesting habitat. The proposed project could also have numerous beneficial impacts including increased revenues generated by taxes, increased employment, and benefits derived from using a nonpolluting resource for electric power generation

Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Schuur, Edward [Northern Arizona Univ., Flagstaff, AZ (United States); Luo, Yiqi [Univ. of Oklahoma, Norman, OK (United States)

2016-12-01

This final grant report is a continuation of the final grant report submitted for DE-SC0006982 as the Principle Investigator (Schuur) relocated from the University of Florida to Northern Arizona University. This report summarizes the original project goals, as well as includes new project activities that were completed in the final period of the project.

Illuminating the Druggable Genome (IDG)

Data.gov (United States)

Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

Resource Contingency Program - Oregon : Final Environmental Impact Statement, Hermiston Power Project.

Energy Technology Data Exchange (ETDEWEB)

United States. Bonneville Power Administration.

1995-09-01

The Bonneville Power Administration (BPA) has statutory responsibilities to supply electrical power to its utility, industrial, and other customers in the Pacific Northwest. In 1990, to cover the outer range of potential load growth with new resources, BPA embarked upon the Resource Contingency Program (RCP). Instead of buying or building generating plants now, BPA has purchased options to acquire power later, if and when it is needed. The decision to acquire any of these option energy projects to fulfill statutory supply obligations will be influenced by Federal system load growth, the outcome of BPA`s Business Plan, required operational changes in Columbia-Snake River Hydroelectric facilities, and the loss of major generating resources. In September 1993, three option development agreements were signed with three proposed natural gas-fired, combined cycle combustion turbine CT projects near Chehalis and Satsop, Washington, and near Hermiston, Oregon. Together these three projects could supply BPA with 1,090 average megawatts (aMW) of power. Under these agreements, sponsors are obtaining permits and conducting project design work, and BPA is completing this EIS process. In September 1993, BPA published a Notice of Intent to prepare an environmental impact statement (EIS) on these three proposed gas-fired combustion turbine projects and held public scoping meetings in October 1993 at each site. In February 1994, BPA released an Implementation Plan on the proposed scope of the EIS. A draft EIS on the three proposed projects was published in February 1995. The impacts of the Chehalis and Satsop projects located in Washington State will be covered in one EIS document, while the impacts of the Hermiston project located in Oregon are covered in this final EIS document. It is BPA`s intent to continue to base the analysis of impacts on the assumption that all three projects may be constructed at some point in the future.

Resource contingency program - Oregon. Final environmental impact statement, Hermiston power project

International Nuclear Information System (INIS)

1995-09-01

The Bonneville Power Administration (BPA) has statutory responsibilities to supply electrical power to its utility, industrial, and other customers in the Pacific Northwest. In 1990, to cover the outer range of potential load growth with new resources, BPA embarked upon the Resource Contingency Program (RCP). Instead of buying or building generating plants now, BPA has purchased options to acquire power later, if and when it is needed. The decision to acquire any of these option energy projects to fulfill statutory supply obligations will be influenced by Federal system load growth, the outcome of BPA's Business Plan, required operational changes in Columbia-Snake River Hydroelectric facilities, and the loss of major generating resources. In September 1993, three option development agreements were signed with three proposed natural gas-fired, combined cycle combustion turbine CT projects near Chehalis and Satsop, Washington, and near Hermiston, Oregon. Together these three projects could supply BPA with 1,090 average megawatts (aMW) of power. Under these agreements, sponsors are obtaining permits and conducting project design work, and BPA is completing this EIS process. In September 1993, BPA published a Notice of Intent to prepare an environmental impact statement (EIS) on these three proposed gas-fired combustion turbine projects and held public scoping meetings in October 1993 at each site. In February 1994, BPA released an Implementation Plan on the proposed scope of the EIS. A draft EIS on the three proposed projects was published in February 1995. The impacts of the Chehalis and Satsop projects located in Washington State will be covered in one EIS document, while the impacts of the Hermiston project located in Oregon are covered in this final EIS document. It is BPA's intent to continue to base the analysis of impacts on the assumption that all three projects may be constructed at some point in the future

The impact of the human genome project on risk assessment

International Nuclear Information System (INIS)

Katarzyna Doerffer; Paul Unrau.

1996-01-01

The radiation protection approach to risk assessment assumes that cancer induction following radiation exposure is purely random. Present risk assessment methods derive risk from cancer incidence frequencies in exposed populations and associate disease outcomes totally with the level of exposure to ionizing red aeon. Exposure defines a risk factor that affects the probability of the disease outcome. But cancer risk can be affected by other risk factors such as underlying genetic factors (predisposition) of the exposed organism. These genetic risk factors are now becoming available for incorporation into ionizing radiation risk assessment Progress in the Human Genome Project (HOP) will lead to direct assays to measure the effects of genetic risk determinants in disease outcomes. When all genetic risk determinants are known and incorporated into risk assessment it will be possible to reevaluate the role of ionizing radiation in the causation of cancer. (author)

Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network.

Science.gov (United States)

Sperber, Nina R; Carpenter, Janet S; Cavallari, Larisa H; J Damschroder, Laura; Cooper-DeHoff, Rhonda M; Denny, Joshua C; Ginsburg, Geoffrey S; Guan, Yue; Horowitz, Carol R; Levy, Kenneth D; Levy, Mia A; Madden, Ebony B; Matheny, Michael E; Pollin, Toni I; Pratt, Victoria M; Rosenman, Marc; Voils, Corrine I; W Weitzel, Kristen; Wilke, Russell A; Ryanne Wu, R; Orlando, Lori A

2017-05-22

To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthesize data on challenges identified by six diverse projects that are part of a National Human Genome Research Institute (NHGRI)-funded network focused on implementing genomics into practice and strategies to overcome these challenges. We used a multiple-case study approach with each project considered as a case and qualitative methods to elicit and describe themes related to implementation challenges and strategies. We describe challenges and strategies in an implementation framework and typology to enable consistent definitions and cross-case comparisons. Strategies were linked to challenges based on expert review and shared themes. Three challenges were identified by all six projects, and strategies to address these challenges varied across the projects. One common challenge was to increase the relative priority of integrating genomics within the health system electronic health record (EHR). Four projects used data warehousing techniques to accomplish the integration. The second common challenge was to strengthen clinicians' knowledge and beliefs about genomic medicine. To overcome this challenge, all projects developed educational materials and conducted meetings and outreach focused on genomic education for clinicians. The third challenge was engaging patients in the genomic medicine projects. Strategies to overcome this challenge included use of mass media to spread the word, actively involving patients in implementation (e.g., a patient advisory board), and preparing patients to be active participants in their healthcare decisions. This is the first collaborative evaluation focusing on the description of genomic medicine innovations implemented in multiple real-world clinical settings. Findings suggest that strategies to facilitate integration of genomic

National Human Genome Research Institute

Science.gov (United States)

... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based imputation.

Science.gov (United States)

Wood, Andrew R; Perry, John R B; Tanaka, Toshiko; Hernandez, Dena G; Zheng, Hou-Feng; Melzer, David; Gibbs, J Raphael; Nalls, Michael A; Weedon, Michael N; Spector, Tim D; Richards, J Brent; Bandinelli, Stefania; Ferrucci, Luigi; Singleton, Andrew B; Frayling, Timothy M

2013-01-01

Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P1000 Genomes imputed data and one was nominally more strongly associated in HapMap imputed data. We also detected an association between a low frequency variant and phenotype that was previously missed by HapMap based imputation approaches. An association between rs112635299 and alpha-1 globulin near the SERPINA gene represented the known association between rs28929474 (MAF = 0.007) and alpha1-antitrypsin that predisposes to emphysema (P = 2.5×10(-12)). Our data provide important proof of principle that 1000 Genomes imputation will detect novel, low frequency-large effect associations.

JGI Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2011-03-14

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

Genomic Encyclopedia of Fungi

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-08-10

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

Herbarium genomics

DEFF Research Database (Denmark)

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

2016-01-01

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

Genomics: The Science and Technology Behind the Human Genome Project (by Charles R. Cantor and Cassandra L. Smith)

Science.gov (United States)

Serra, Reviewed By Martin J.

2000-01-01

analysis of error in sequencing and current bottlenecks in the sequencing effort. The next chapter describes the steps necessary to scale current technologies for the sequencing of entire genomes. Chapter 12 examines alternate methods for DNA sequencing. Initially, methods of single-molecule sequencing and sequencing by microscopy are introduced; the majority of the chapter is devoted to the development of DNA sequencing methods using chip microarrays and hybridization. The remaining chapters (13-15) consider the uses and analysis of DNA sequence information. The initial focus is on the identification of genes. Several examples are given of the use of DNA sequence information for diagnosis of inherited or infectious diseases. The sequence-specific manipulation of DNA is discussed in Chapter 14. The final chapter deals with the implications of large-scale sequencing, including methods for identifying genes and finding errors in DNA sequences, to the development of computer algorithms for the interpretation of DNA sequence information. The text figures are black and white line drawings that, although clearly done, seem a bit primitive for 1999. While I appreciated the simplicity of the drawings, many students accustomed to more colorful presentations will find them wanting. The four color figures in the center of the text seem an afterthought and add little to the text's clarity. Each chapter has a set of additional reading sources, mostly primary sources. Often, specialized topics are offset into boxes that provide clarification and amplification without cluttering the text. An appendix includes a list of the Web-based database resources. As an undergraduate instructor who has previously taught biochemistry, molecular biology, and a course on the human genome, I found many interesting tidbits and amplifications throughout the text. I would recommend this book as a text for an advanced undergraduate or beginning graduate course in genomics. Although the text works though

Molluscan Evolutionary Genomics

Energy Technology Data Exchange (ETDEWEB)

Simison, W. Brian; Boore, Jeffrey L.

2005-12-01

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

DE-NE0000735 - FINAL REPORT ON THORIUM FUEL CYCLE NEUP PROJECT

Energy Technology Data Exchange (ETDEWEB)

Krahn, Steven [Vanderbilt Univ., Nashville, TN (United States); Ault, Timothy [Vanderbilt Univ., Nashville, TN (United States); Worrall, Andrew [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-09-30

The report is broken into six chapters, including this executive summary chapter. Following an introduction, this report discusses each of the project’s three major components (Fuel Cycle Data Package (FCDP) Development, Thorium Fuel Cycle Literature Analysis and Database Development, and the Thorium Fuel Cycle Technical Track and Proceedings). A final chapter is devoted to summarization. Various outcomes, publications, etc. originating from this project can be found in the Appendices at the end of the document.

The human genome project and novel aspects of cytochrome P450 research

International Nuclear Information System (INIS)

Ingelman-Sundberg, Magnus

2005-01-01

Currently, 57 active cytochrome P450 (CYP) genes and 58 pseudogenes are known to be present in the human genome. Among the genes discovered by initiatives in the human genome project are CYP2R1, CYP2W1, CYP2S1, CYP2U1 and CYP3A43, the latter apparently encoding a pseudoenzyme. The function, polymorphism and regulation of these genes are still to be discovered to a great extent. The polymorphism of drug metabolizing CYPs is extensive and influences the outcome of drug therapy causing lack of response or adverse drug reactions. The basis for the differences in the global distribution of the polymorphic variants is inactivating gene mutations and subsequent genetic drift. However, polymorphic alleles carrying multiple active gene copies also exist and are suggested in case of CYP2D6 to be caused by positive selection due to development of alkaloid resistance in North East Africa about 10,000-5000 BC. The knowledge about the CYP genes and their polymorphisms is of fundamental importance for effective drug therapy and for drug development as well as for understanding metabolic activation of carcinogens and other xenobiotics. Here, a short review of the current knowledge is given

Final Technical Report for Award # ER64999

Energy Technology Data Exchange (ETDEWEB)

Metcalf, William W. [University of Illinois

2014-10-08

This report provides a summary of activities for Award # ER64999, a Genomes to Life Project funded by the Office of Science, Basic Energy Research. The project was entitled "Methanogenic archaea and the global carbon cycle: a systems biology approach to the study of Methanosarcina species". The long-term goal of this multi-investigator project was the creation of integrated, multiscale models that accurately and quantitatively predict the role of Methanosarcina species in the global carbon cycle under dynamic environmental conditions. To achieve these goals we pursed four specific aims: (1) genome sequencing of numerous members of the Order Methanosarcinales, (2) identification of genomic sources of phenotypic variation through in silico comparative genomics, (3) elucidation of the transcriptional networks of two Methanosarcina species, and (4) development of comprehensive metabolic network models for characterized strains to address the question of how metabolic models scale with genetic distance.

ISS-NIH Collaborative Programme: final report of the projects

International Nuclear Information System (INIS)

2009-01-01

In July 2003, the National Institutes of Health (NIH) of the United States of America and the Istituto Superiore di Sanita (ISS) of Italy signed an agreement aimed at strengthening the ongoing research cooperation between USA and Italy. Over the years, the programme was able to create new partnerships and to foster the establishment of innovative synergies, the exchange of young researcher, and the merging of the best available skills, talents and know-how in different fields of biomedical sciences. This book contains the final report of the projects of the scientific cooperation between the two Countries. The report consists of two parts (in Italian and English) divided into four sections: Cancer, Neuroscience, Cardiovascular diseases, Infectious diseases [it

Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-03-12

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

Pilot project Uljabuouda. Final report; Pilotprojekt Uljabuouda. Slutrapport

Energy Technology Data Exchange (ETDEWEB)

2011-07-01

During the period of 2007-2010 Skellefteaa Kraft AB erected a wind farm comprising 10 3 MW wind turbines on the mountain Uljabuouda in the municipality of Arjeplog. The turbines are of the type WWD-3 with a hub height of 80 meters and a rotor diameter of 90 meters. The Uljabuouda wind farm is one of the first erected above the treeline in the Swedish mountains. The wind turbines are adapted to cold climate equipped with an ice prevention system for the blades. The process of obtaining the necessary permits for the erection of the wind farm was lengthy and lasted during the period of 2000 to 2008. Also the procurement process took longer than expected. During the period of 2006-2008 when the procurement was performed it was difficult to find a supplier who could offer wind turbines equipped with a deicing system. In December 2006 the Uljabuouda project was granted a subsidy from the Swedish Energy Agency, the maximum of 35 million Swedish crowns. The final investment costs of the project will be higher than previously estimated. The main reason for this was the prevailing market conditions during the procurement period. The Uljabuouda wind farm is in full operation since the winter of 2010/2011 and so far our experiences are that the ice prevention system is working well even at harsh icing conditions

GDC 2: Compression of large collections of genomes.

Science.gov (United States)

Deorowicz, Sebastian; Danek, Agnieszka; Niemiec, Marcin

2015-06-25

The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about.

WP1 – Final project report

NARCIS (Netherlands)

Drachsler, Hendrik; Scheffel, Maren; Orrego, Carola; Stieger, Lina; Hartkopf, Kathleen; Henn, Patrick; Hynes, Helen; Przibilla, Monika; Geiger, Uschi; Schroeder, Hanna; Sopka, Sasa

2015-01-01

This report contains the complete project reporting of the PATIENT project from October 2012 until end of March 2015. It provides a summary of all project activities and achievements that are based on the previous WP deliverables such as the project progress reports from WP1 (D1.01) and the quality

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

OpenAIRE

Pfeifer, Bastian; Wittelsbürger, Ulrich; Ramos-Onsins, Sebastian E.; Lercher, Martin J.

2014-01-01

Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches. Here, we present PopGenome, a populati...

77 FR 5566 - Notice of Availability of the Final EIS for the HB In-Situ Solution Mine Project, Eddy County...

Science.gov (United States)

2012-02-03

...] Notice of Availability of the Final EIS for the HB In-Situ Solution Mine Project, Eddy County, New Mexico... Statement (Final EIS) for the HB In-Situ Solution Mine Project, and by this notice is announcing its... the Federal Register. ADDRESSES: Copies of the HB In-Situ Solution Mining EIS are available for public...

Phase V storage (Project W-112) Central Waste Complex operational readiness review, final report

International Nuclear Information System (INIS)

Wight, R.H.

1997-01-01

This document is the final report for the RFSH conducted, Contractor Operational Readiness Review (ORR) for the Central Waste Complex (CWC) Project W-112 and Interim Safety Basis implementation. As appendices, all findings, observations, lines of inquiry and the implementation plan are included

Phase 5 storage (Project W-112) Central Waste Complex operational readiness review, final report

Energy Technology Data Exchange (ETDEWEB)

Wight, R.H.

1997-05-30

This document is the final report for the RFSH conducted, Contractor Operational Readiness Review (ORR) for the Central Waste Complex (CWC) Project W-112 and Interim Safety Basis implementation. As appendices, all findings, observations, lines of inquiry and the implementation plan are included.

Human genome I

International Nuclear Information System (INIS)

Anon.

1989-01-01

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

Automated metadata--final project report

Energy Technology Data Exchange (ETDEWEB)

Schissel, David [General Atomics, San Diego, CA (United States)

2016-04-01

This report summarizes the work of the Automated Metadata, Provenance Cataloging, and Navigable Interfaces: Ensuring the Usefulness of Extreme-Scale Data Project (MPO Project) funded by the United States Department of Energy (DOE), Offices of Advanced Scientific Computing Research and Fusion Energy Sciences. Initially funded for three years starting in 2012, it was extended for 6 months with additional funding. The project was a collaboration between scientists at General Atomics, Lawrence Berkley National Laboratory (LBNL), and Massachusetts Institute of Technology (MIT). The group leveraged existing computer science technology where possible, and extended or created new capabilities where required. The MPO project was able to successfully create a suite of software tools that can be used by a scientific community to automatically document their scientific workflows. These tools were integrated into workflows for fusion energy and climate research illustrating the general applicability of the project’s toolkit. Feedback was very positive on the project’s toolkit and the value of such automatic workflow documentation to the scientific endeavor.

Genome-derived vaccines.

Science.gov (United States)

De Groot, Anne S; Rappuoli, Rino

2004-02-01

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

Genomic sequencing in clinical trials

OpenAIRE

Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

2011-01-01

Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

[The human variome project and its progress].

Science.gov (United States)

Gao, Shan; Zhang, Ning; Zhang, Lei; Duan, Guang-You; Zhang, Tao

2010-11-01

The main goal of post genomics is to explain how the genome, the map of which has been constructed in the Human Genome Project, affacts activities of life. This leads to generate multiple "omics": structural genomics, functional genomics, proteomics, metabonomics, et al. In Jun. 2006, Melbourne, Australia, Human Genome Variation Society (HGVS) initiated the Human Variome Project (HVP) to collect all the sequence variation and polymorphism data worldwidely. HVP is to search and determine those mutations related with human diseases by association study between genetype and phenotype on the scale of genome level and other methods. Those results will be translated into clinical application. Considering the potential effects of this project on human health, this paper introduced its origin and main content in detail and discussed its meaning and prospect.

The Genomic Code: Genome Evolution and Potential Applications

KAUST Repository

Bernardi, Giorgio

2016-01-25

The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

Whitehead Policy Symposium. The Human Genome Project: Science, law, and social change in the 21st century

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.

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

Final Report for the ADMX Phase 2a Project at the University of Washington

International Nuclear Information System (INIS)

Rosenberg, Leslie J.

2015-01-01

This is a final report of the ADMX (Axion Dark Matter eXperiment) Phase 2a program. This program is a project allowing for a sensitive axion dark-matter search at higher axion masses. The Phase 2a program also prepares the project for lower temperature anticipated in later operations. The Phase 2a program includes sensitive data-taking operations at two cavity modes, TM010 and TM020, allowing for faster data-taking operations and extending the search to higher and plausible dark-matter axion masses.

Reactor vessel decommissioning project. Final report

International Nuclear Information System (INIS)

Schoonen, D.H.

1984-09-01

This report describes a reactor vessel decommissioning project; it documents and explains the project objectives, scope, performance results, and sodium removal process. The project was successfully completed in FY-1983, within budget and without significant problems or adverse impact on the environment. Waste generated by the operation included the reactor vessel, drained sodium, and liquid, solid, and gaseous wastes which were significantly less than project estimates. Personnel radiation exposures were minimized, such that the project total was one-half the predicted exposure level. Except for the sodium removed, the material remaining in the reactor vessel is essentially the same as when the vessel arrived for processing

Parent Attitudes Toward the Virginia Beach Year-Round School Pilot Project. Final Report.

Science.gov (United States)

Schlechty, Phillip C.

Part of the Virginia Beach year-round school program evaluation, this final report contains a detailed analysis of parental attitudes, beliefs, and perceptions. The data leads to the following conclusions: a majority (53.3 percent) of parents are dubious or negative toward the 45-15 pilot project; a slight majority of parents in the pilot schools…

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Informational laws of genome structures

Science.gov (United States)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

Musa sebagai Model Genom

Directory of Open Access Journals (Sweden)

RITA MEGIA

2005-12-01

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

A Snapshot of the Emerging Tomato Genome Sequence

Directory of Open Access Journals (Sweden)

Lukas A. Mueller

2009-03-01

Full Text Available The genome of tomato ( L. is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States as part of the larger “International Solanaceae Genome Project (SOL: Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN. Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L. sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

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.

Resource Roads demonstration project : final report

Energy Technology Data Exchange (ETDEWEB)

NONE

2009-07-15

British Columbia's vast network of resource roads are considered to be amongst the most dangerous, high-risk workplaces in the province. Resource roads, also known as industrial roads, forest service roads, or petroleum development roads, present several unique safety challenges as workplaces. They are built for the purpose of access, egress and transport of materials, resources, equipment and people. However, the lack the same diligence of enforcement and a consistent design, construction, maintenance and standard for use as public highways or municipal roads. There are also safety challenges related to public use of resource roads. This report presented a project, called ResourceRoads by WorkSafe BC that focused on the organization and implementation of a management structure that would provide a system of coordination and a process of compliance for the users of the defined road systems. The project was based on information gathered in two forest districts of Prince George and the South Peace Forest Districts. A committee consisting of the actual owner of the road and other users was formed. The report presented a history of British Columbia's resource road system, and discussed resource roads as industrial workplaces and worksites, as well as resource road fatality statistics. The demonstration project was outlined in terms of project leadership; scope; strategic objectives; project purpose; performance objectives; project communication; demonstration areas; and project stages. Project fundamentals and project findings were also presented along with recommendations and responses to the Auditor General report and the Forest Safety Ombudsman report. It was concluded that potential uses of new technologies for resource road vehicles should be reviewed. tabs., figs.

Smart Intelligent Aircraft Structures (SARISTU) : Proceedings of the Final Project Conference

CERN Document Server

Papadopoulos, Michael

2016-01-01

The book includes the research papers presented in the final conference of the EU funded SARISTU (Smart Intelligent Aircraft Structures) project, held at Moscow, Russia between 19-21 of May 2015. The SARISTU project, which was launched in September 2011, developed and tested a variety of individual applications as well as their combinations. With a strong focus on actual physical integration and subsequent material and structural testing, SARISTU has been responsible for important progress on the route to industrialization of structure integrated functionalities such as Conformal Morphing, Structural Health Monitoring and Nanocomposites. The gap- and edge-free deformation of aerodynamic surfaces known as conformal morphing has gained previously unrealized capabilities such as inherent de-icing, erosion protection and lightning strike protection, while at the same time the technological risk has been greatly reduced. Individual structural health monitoring techniques can now be applied at the part-manufacturin...

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.

Rhipicephalus microplus strain Deutsch, whole genome shotgun sequencing project Version 2

Science.gov (United States)

The cattle tick, Rhipicephalus (Boophilus) microplus, has a genome over 2.4 times the size of the human genome, and with over 70% of repetitive DNA, this genome would prove very costly to sequence at today's prices and difficult to assemble and analyze. Cot filtration/selection techniques were used ...

Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

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.

UCSD Performance in the Edge Plasma Simulation (EPSI) Project. Final Report

Energy Technology Data Exchange (ETDEWEB)

Tynan, George Robert [Univ. of California, San Diego, CA (United States). Center for Energy Research

2017-12-12

This report contains a final report on the activities of UC San Diego PI G.R. Tynan and his collaborators as part of the EPSI Project, that was led by Dr. C.S. Chang, from PPPL. As a part of our work, we carried out several experiments on the ALCATOR C-­MOD tokamak device, aimed at unraveling the “trigger” or cause of the spontaneous transition from low-­mode confinement (L-­mode) to high confinement (H-­mode) that is universally observed in tokamak devices, and is planned for use in ITER.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Science.gov (United States)

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project

International Nuclear Information System (INIS)

Lakhssassi, K.; González-Recio, O.

2017-01-01

Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits.

A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project

Energy Technology Data Exchange (ETDEWEB)

Lakhssassi, K.; González-Recio, O.

2017-07-01

Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits.

The GenABEL Project for statistical genomics [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Lennart C. Karssen

2016-05-01

Full Text Available Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the “core team”, facilitating agile statistical omics methodology development and fast dissemination.

eHive: An Artificial Intelligence workflow system for genomic analysis

Science.gov (United States)

2010-01-01

Background The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. Results We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. Conclusions eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/. PMID:20459813

eHive: An Artificial Intelligence workflow system for genomic analysis

Directory of Open Access Journals (Sweden)

Gordon Leo

2010-05-01

Full Text Available Abstract Background The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. Results We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1 pairwise whole genome alignments, (2 multiple whole genome alignments and (3 gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. Conclusions eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/.

eHive: an artificial intelligence workflow system for genomic analysis.

Science.gov (United States)

Severin, Jessica; Beal, Kathryn; Vilella, Albert J; Fitzgerald, Stephen; Schuster, Michael; Gordon, Leo; Ureta-Vidal, Abel; Flicek, Paul; Herrero, Javier

2010-05-11

The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/.

The IGNITE network: a model for genomic medicine implementation and research.

Science.gov (United States)

Weitzel, Kristin Wiisanen; Alexander, Madeline; Bernhardt, Barbara A; Calman, Neil; Carey, David J; Cavallari, Larisa H; Field, Julie R; Hauser, Diane; Junkins, Heather A; Levin, Phillip A; Levy, Kenneth; Madden, Ebony B; Manolio, Teri A; Odgis, Jacqueline; Orlando, Lori A; Pyeritz, Reed; Wu, R Ryanne; Shuldiner, Alan R; Bottinger, Erwin P; Denny, Joshua C; Dexter, Paul R; Flockhart, David A; Horowitz, Carol R; Johnson, Julie A; Kimmel, Stephen E; Levy, Mia A; Pollin, Toni I; Ginsburg, Geoffrey S

2016-01-05

Patients, clinicians, researchers and payers are seeking to understand the value of using genomic information (as reflected by genotyping, sequencing, family history or other data) to inform clinical decision-making. However, challenges exist to widespread clinical implementation of genomic medicine, a prerequisite for developing evidence of its real-world utility. To address these challenges, the National Institutes of Health-funded IGNITE (Implementing GeNomics In pracTicE; www.ignite-genomics.org ) Network, comprised of six projects and a coordinating center, was established in 2013 to support the development, investigation and dissemination of genomic medicine practice models that seamlessly integrate genomic data into the electronic health record and that deploy tools for point of care decision making. IGNITE site projects are aligned in their purpose of testing these models, but individual projects vary in scope and design, including exploring genetic markers for disease risk prediction and prevention, developing tools for using family history data, incorporating pharmacogenomic data into clinical care, refining disease diagnosis using sequence-based mutation discovery, and creating novel educational approaches. This paper describes the IGNITE Network and member projects, including network structure, collaborative initiatives, clinical decision support strategies, methods for return of genomic test results, and educational initiatives for patients and providers. Clinical and outcomes data from individual sites and network-wide projects are anticipated to begin being published over the next few years. The IGNITE Network is an innovative series of projects and pilot demonstrations aiming to enhance translation of validated actionable genomic information into clinical settings and develop and use measures of outcome in response to genome-based clinical interventions using a pragmatic framework to provide early data and proofs of concept on the utility of these

Telephone Flat Geothermal Development Project Environmental Impact Statement Environmental Impact Report. Final: Comments and Responses to Comments

Energy Technology Data Exchange (ETDEWEB)

None

1999-02-01

This document is the Comments and Responses to Comments volume of the Final Environmental Impact Statement and Environmental Impact Report prepared for the proposed Telephone Flat Geothermal Development Project (Final EIS/EIR). This volume of the Final EIS/EIR provides copies of the written comments received on the Draft EIS/EIR and the leady agency responses to those comments in conformance with the requirements of the National Environmental Policy Act (NEPA) and the California Environmental Quality Act (CEQA).

Harmony in Career Learning and Scholastic System (Project HI-CLASS). Final Evaluation Report 1992-93. OREA Report.

Science.gov (United States)

Duque, Diana L.

Harmony in Career Learning and Scholastic System (Project HI-CLASS) was a Transitional Bilingual Education Title VII-funded program in its fifth and final year in 1992-93. The project offered instructional and support services to 641 students of limited English proficiency (LEP) at three sites, all of which had many immigrant students, in…

Kansas Advanced Semiconductor Project: Final Report

International Nuclear Information System (INIS)

Baringer, P.; Bean, A.; Bolton, T.; Horton-Smith, G.; Maravin, Y.; Ratra, B.; Stanton, N.; von Toerne, E.; Wilson, G.

2007-01-01

KASP (Kansas Advanced Semiconductor Project) completed the new Layer 0 upgrade for D0, assumed key electronics projects for the US CMS project, finished important new physics measurements with the D0 experiment at Fermilab, made substantial contributions to detector studies for the proposed e+e- international linear collider (ILC), and advanced key initiatives in non-accelerator-based neutrino physics.

National human genome projects: an update and an agenda

OpenAIRE

An, Joon Yong

2017-01-01

Population genetic and human genetic studies are being accelerated with genome technology and data sharing. Accordingly, in the past 10 years, several countries have initiated genetic research using genome technology and identified the genetic architecture of the ethnic groups living in the corresponding country or suggested the genetic foundation of a social phenomenon. Genetic research has been conducted from epidemiological studies that previously described the health or disease conditions...

Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

Science.gov (United States)

Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

2008-09-01

A method to functionally annotate structural genomics targets, based on a novel structural alignment scoring function, is proposed. In the proposed score, position-specific scoring matrices are used to weight structurally aligned residue pairs to highlight evolutionarily conserved motifs. The functional form of the score is first optimized for discriminating domains belonging to the same Pfam family from domains belonging to different families but the same CATH or SCOP superfamily. In the optimization stage, we consider four standard weighting functions as well as our own, the "maximum substitution probability," and combinations of these functions. The optimized score achieves an area of 0.87 under the receiver-operating characteristic curve with respect to identifying Pfam families within a sequence-unique benchmark set of domain pairs. Confidence measures are then derived from the benchmark distribution of true-positive scores. The alignment method is next applied to the task of functionally annotating 230 query proteins released to the public as part of the Protein 3000 structural genomics project in Japan. Of these queries, 78 were found to align to templates with the same Pfam family as the query or had sequence identities > or = 30%. Another 49 queries were found to match more distantly related templates. Within this group, the template predicted by our method to be the closest functional relative was often not the most structurally similar. Several nontrivial cases are discussed in detail. Finally, 103 queries matched templates at the fold level, but not the family or superfamily level, and remain functionally uncharacterized. 2008 Wiley-Liss, Inc.

A locally funded Puerto Rican parrot (Amazona vittata genome sequencing project increases avian data and advances young researcher education

Directory of Open Access Journals (Sweden)

Oleksyk Taras K

2012-09-01

Full Text Available Abstract Background Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp, which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp. This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.

DIMEC - Final Report

DEFF Research Database (Denmark)

Conrad, Finn

1997-01-01

Final report of the research project DIMEC - Danish InfoMechatronic Control supported by the Danish Technical Research Council, STVF.......Final report of the research project DIMEC - Danish InfoMechatronic Control supported by the Danish Technical Research Council, STVF....

Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999

Energy Technology Data Exchange (ETDEWEB)

Harger, Carol A.

1999-10-28

Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence. [The annual report for June 1996 to August 1997 is included as an attachment to this final report.

77 FR 23740 - Sears Point Wetland and Watershed Restoration Project, Sonoma County, CA; Final Environmental...

Science.gov (United States)

2012-04-20

...-FF08RSFC00] Sears Point Wetland and Watershed Restoration Project, Sonoma County, CA; Final Environmental... environmental impact report and environmental impact statement (EIR/EIS) for the Sears Point Wetland and..., while providing public access and recreational and educational opportunities compatible with ecological...

Virginia Solar Pathways Project Final Technical Report

Energy Technology Data Exchange (ETDEWEB)

Bond, Katharine; Cosby, Sarah

2018-03-28

This Report provides a technical review of the final results of a funding award to Virginia Electric and Power Company (Dominion Energy Virginia (DEV) or the Company) for a project under the U.S. Department of Energy’s Solar Energy Technologies Office. The three-year project was formally known as the Virginia Solar Pathways Project (VSPP or the Project). The purpose of the VSPP was to develop a collaborative utility-administered solar strategy (Solar Strategy) for DEV’s service territory in the Commonwealth that could serve as a replicable model for other states with similar policy environments. The U.S. Department of Energy (DOE) funding award enabled DEV to take a focused approach to developing the Solar Strategy for its Virginia service territory. The structure and funding from the DOE award also facilitated valuable input from a formal stakeholder team convened to serve as advisors (Advisory Team) to the VSPP and contribute their perspectives and expertise to both the analysis and strategy development aspects of the Project. The development of the Solar Strategy involved three main goals: • Establish a policy and program framework that would integrate existing solar programs with new options appropriate for the Commonwealth’s policy environment and broader economic development objectives; • Promote wider deployment of solar within a low retail electric rate environment; and • Serve as a sustainable, utility-administered solar model that could be replicated in other states with similar policy environments, including, but not limited to, the entire Southeast region. In support of the VSPP goals, the Project Team commissioned four studies to support the Solar Strategy development. Two studies, completed by Navigant Consulting, focused on the integration of solar into the electric grid. The first solar integration study focused on integration of solar into the distribution grid where the utility system directly connects to and serves end-use customers

High participation rate among 25 721 patients with broad age range in a hospital-based research project involving whole-genome sequencing - the Lausanne Institutional Biobank.

Science.gov (United States)

Bochud, Murielle; Currat, Christine; Chapatte, Laurence; Roth, Cindy; Mooser, Vincent

2017-10-24

We aimed to evaluate the interest of adult inpatients and selected outpatients in engaging in a large, real-life, hospital-based, genomic medicine research project and in receiving clinically actionable incidental findings. Within the framework of the cross-sectional Institutional Biobank of Lausanne, Switzerland, a total of 25721 patients of the CHUV University Hospital were systematically invited to grant researchers access to their biomedical data and to donate blood for future analyses, including whole-genome sequencing. Multivariable logistic regression analysis was used to identify personal factors, including age, gender, religion, ethnicity, citizenship, education level and mode of admission, associated with willingness to participate in this genomic research project and with interest in receiving clinically actionable incidental findings. The overall participation rate was 79% (20343/25721). Participation rate declined progressively with age, averaging 83%, 75%, 67% and 62% in patients aged rate, but not with higher willingness to receive incidental findings within the population who had agreed to participate. A large proportion of adult patients, even among the elderly, are willing to actively participate and receive incidental findings in this systematic hospital-based precision and genomic medicine research program with broad consent.

Project Execution Plan,Rev. 3; FINAL

International Nuclear Information System (INIS)

IT Corporation, Las Vegas

2002-01-01

This plan addresses project activities encompassed by the U.S. Department of Energy's (DOE's), National Nuclear Security Administration Nevada Operations Office, Environmental Restoration Division and conforms to the requirements contained in the Life-Cycle Asset Management, DOE Order 430.1A; The Joint Program Office Policy on Project Management in Support of DOE Order 430.1; Program and Project Management for the Acquisition of Capital Assets, DOE Order 413.3; the Project Execution and Engineering Management Planning Guide, GPG-FM-010; and other applicable Good Practice Guides; and the FY 2001 Integrated Planning, Accountability, and Budgeting System Policy Guidance. The plan also reflects the milestone philosophies of the Federal Facility Agreement and Consent Order, as agreed to by the State of Nevada, the DOE, and the U.S. Department of Defense; and traditional project management philosophies such as the development of life-cycle costs, schedules, and work scope; identification o f roles and responsibilities; and baseline management and controls

Smart Gun Technology project. Final report

Energy Technology Data Exchange (ETDEWEB)

Weiss, D.R.

1996-05-01

The goal of the Smart Gun Technology project is to eliminate the capability of an unauthorized user form firing a law officer`s firearm by implementing user-recognizing-and-authorizing (or {open_quotes}smart{close_quotes}) surety technologies. This project was funded by the National Institute of Justice. This report lists the findings and results of the project`s three primary objectives. First, to find and document the requirements for a smart firearm technology that law enforcement officers will value. Second, to investigate, evaluate, and prioritize technologies that meet the requirements for a law enforcement officer`s smart firearm. Third, to demonstrate and document the most promising technology`s usefulness in models of a smart firearm.

Final Report Sustained Spheromak Physics Project FY 1997 - FY 1999

International Nuclear Information System (INIS)

Hooper, E.B.; Hill, D.N.

2000-01-01

This is the final report on the LDRD SI-funded Sustained Spheromak Physics Project for the years FY1997-FY1999, during which the SSPX spheromak was designed, built, and commissioned for operation at LLNL. The specific LDRD project covered in this report concerns the development, installation, and operation of specialized hardware and diagnostics for use on the SSPX facility in order to study energy confinement in a sustained spheromak plasma configuration. The USDOE Office of Fusion Energy Science funded the construction and routine operation of the SSPX facility. The main distinctive feature of the spheromak is that currents in the plasma itself produce the confining toroidal magnetic field, rather than external coils, which necessarily thread the vacuum vessel. There main objective of the Sustained Spheromak Physics Project was to test whether sufficient energy confinement could be maintained in a spheromak plasma sustained by DC helicity injection. Achieving central electron temperatures of several hundred eV would indicate this. In addition, we set out to determine how the energy confinement scales with T c and to relate the confinement time to the level of internal magnetic turbulence. Energy confinement and its scaling are the central technical issues for the spheromak as a fusion reactor concept. Pending the outcome of energy confinement studies now under way, the spheromak could be the basis for an attractive fusion reactor because of its compact size, simply-connected magnetic geometry, and potential for steady-state current drive

BIOETHICS METHODS IN THE ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS OF THE HUMAN GENOME PROJECT LITERATURE

Science.gov (United States)

Walker, Rebecca; Morrissey, Clair

2013-01-01

While bioethics as a field has concerned itself with methodological issues since the early years, there has been no systematic examination of how ethics is incorporated into research on the Ethical, Legal and Social Implications (ELSI) of the Human Genome Project. Yet ELSI research may bear a particular burden of investigating and substantiating its methods given public funding, an explicitly cross-disciplinary approach, and the perceived significance of adequate responsiveness to advances in genomics. We undertook a qualitative content analysis of a sample of ELSI publications appearing between 2003-2008 with the aim of better understanding the methods, aims, and approaches to ethics that ELSI researchers employ. We found that the aims of ethics within ELSI are largely prescriptive and address multiple groups. We also found that the bioethics methods used in the ELSI literature are both diverse between publications and multiple within publications, but are usually not themselves discussed or employed as suggested by bioethics method proponents. Ethics in ELSI is also sometimes undistinguished from related inquiries (such as social, legal, or political investigations). PMID:23796275

The Yeast Deletion Collection: A Decade of Functional Genomics

Science.gov (United States)

Giaever, Guri; Nislow, Corey

2014-01-01

The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MATa and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general. PMID:24939991

The BDGP gene disruption project: Single transposon insertions associated with 40 percent of Drosophila genes

Energy Technology Data Exchange (ETDEWEB)

Bellen, Hugo J.; Levis, Robert W.; Liao, Guochun; He, Yuchun; Carlson, Joseph W.; Tsang, Garson; Evans-Holm, Martha; Hiesinger, P. Robin; Schulze, Karen L.; Rubin, Gerald M.; Hoskins, Roger A.; Spradling, Allan C.

2004-01-13

The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in more than 30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6,300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7,140 lines. It now includes individual lines predicted to disrupt 5,362 of the 13,666 currently annotated Drosophila genes (39 percent). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene mis-expression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.

Spent fuel stability under repository conditions - final report of the european project

International Nuclear Information System (INIS)

Poinssot, Ch.; Ferry, C.; Kelm, M.; Cavedon, J.M.; Corbel, C.; Jegou, Ch.; Lovera, P.; Miserque, F.; Poulesquen, A.; Grambow, B.; Andriambololona, Z.; Martinez-Esparza, A.; Kelm, M.; Loida, A.; Rondinella, V.; Wegen, D.; Spahiu, K.; Johnson, L.; Cachoir, Ch.; Lemmens, K.; Quinones, J.; Bruno, J.; Christensen, H.; Grambow, B.; Pablo, J. de

2005-01-01

This report is the final report of the European Project 'Spent Fuel Stability under Repository Conditions' (FIKW-CT-2001-00192 SFS) funded by the European Commission from Nov.2000 to Oct.2004. Gathering the work performed by 13 partners from 6 countries, it aims to specifically focus on the spent nuclear fuel long term alteration in deep repository and the subsequent radionuclides release rate as a function of time. This report synthesised the wide experimental work performed within this project and enlightens the major outcomes, which can be summarised as follow: - A new model for defining the Instant Release Fraction was developed in order to consider the potential fuel evolution before the water penetrates the canister. Quantitative assessment has been produced and shows a significant contribution to the long term dose; - Based on new experimental data, kinetic radiolytic scheme have been upgraded and are used to determine the amount of oxidants produced at the fuel/water interface; - The existence of a dose threshold below which the water radiolysis does not influence the fuel alteration has been demonstrated and occurs between 3.5 and 33 MBq.g UO21. Above the threshold, the fuel alteration rates is directly related to the dose rate. - Hydrogen was experimentally demonstrated to be an efficient oxidants scavenger preventing therefore the fuel oxidation. Molecular mechanism still need to be understood. - Finally, a new Matrix Alteration Model integrating most of the SFS results (apart of the hydrogen effect) has been developed and used to assess the fuel long tern stability in representative conditions of deep repository in salt, clay-rock and granite. The breadth of the results and the significance of the conclusions testify of the success of the collaboration within the project. (authors)

Umatilla Satellite and Release Sites Project : Final Siting Report.

Energy Technology Data Exchange (ETDEWEB)

Montgomery, James M.

1992-04-01

This report presents the results of site analysis for the Umatilla Satellite and Release Sites Project. The purpose of this project is to provide engineering services for the siting and conceptual design of satellite and release facilities for the Umatilla Basin hatchery program. The Umatilla Basin hatchery program consists of artificial production facilities for salmon and steelhead to enhance production in the Umatilla River as defined in the Umatilla master plan approved in 1989 by the Northwest Power Planning Council. Facilities identified in the master plan include adult salmon broodstock holding and spawning facilities, facilities for recovery, acclimation, and/or extended rearing of salmon juveniles, and development of river sites for release of hatchery salmon and steelhead. The historic and current distribution of fall chinook, summer chinook, and coho salmon and steelhead trout was summarized for the Umatilla River basin. Current and future production and release objectives were reviewed. Twenty seven sites were evaluated for the potential and development of facilities. Engineering and environmental attributes of the sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.

Human genetics: international projects and personalized medicine.

Science.gov (United States)

Apellaniz-Ruiz, Maria; Gallego, Cristina; Ruiz-Pinto, Sara; Carracedo, Angel; Rodríguez-Antona, Cristina

2016-03-01

In this article, we present the progress driven by the recent technological advances and new revolutionary massive sequencing technologies in the field of human genetics. We discuss this knowledge in relation with drug response prediction, from the germline genetic variation compiled in the 1000 Genomes Project or in the Genotype-Tissue Expression project, to the phenome-genome archives, the international cancer projects, such as The Cancer Genome Atlas or the International Cancer Genome Consortium, and the epigenetic variation and its influence in gene expression, including the regulation of drug metabolism. This review is based on the lectures presented by the speakers of the Symposium "Human Genetics: International Projects & New Technologies" from the VII Conference of the Spanish Pharmacogenetics and Pharmacogenomics Society, held on the 20th and 21st of April 2015.

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

Science.gov (United States)

Salzberg, Steven L; Dunning Hotopp, Julie C; Delcher, Arthur L; Pop, Mihai; Smith, Douglas R; Eisen, Michael B; Nelson, William C

2005-01-01

The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

Final Year Project Report

Energy Technology Data Exchange (ETDEWEB)

Hubsch, Tristan [Howard University

2013-06-20

In the last years of this eighteen-year grant project, the research efforts have focused mostly on the study of off-shell representations of supersymmetry, both on the worldline and on the world- sheet, i.e., both in supersymmetric quantum mechanics and in supersymmetric field theory in 1+1-dimensional spacetime.

Technical approach to finalizing sensible soil cleanup levels at the Fernald Environmental Management Project

International Nuclear Information System (INIS)

Carr, D.; Hertel, B.; Jewett, M.; Janke, R.; Conner, B.

1996-01-01

The remedial strategy for addressing contaminated environmental media was recently finalized for the US Department of Energy's (DOE) Fernald Environmental Management Project (FEMP) following almost 10 years of detailed technical analysis. The FEMP represents one of the first major nuclear facilities to successfully complete the Remedial Investigation/Feasibility Study (RI/FS) phase of the environmental restoration process. A critical element of this success was the establishment of sensible cleanup levels for contaminated soil and groundwater both on and off the FEMP property. These cleanup levels were derived based upon a strict application of Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) regulations and guidance, coupled with positive input from the regulatory agencies and the local community regarding projected future land uses for the site. The approach for establishing the cleanup levels was based upon a Feasibility Study (FS) strategy that examined a bounding range of viable future land uses for the site. Within each land use, the cost and technical implications of a range of health-protective cleanup levels for the environmental media were analyzed. Technical considerations in driving these cleanup levels included: direct exposure routes to viable human receptors; cross- media impacts to air, surface water, and groundwater; technical practicality of attaining the levels; volume of affected media; impact to sensitive environmental receptors or ecosystems; and cost. This paper will discuss the technical approach used to support the finalization of the cleanup levels for the site. The final cleanup levels provide the last remaining significant piece to the puzzle of establishing a final site-wide remedial strategy for the FEMP, and positions the facility for the expedient completion of site-wide remedial activities

Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

DEFF Research Database (Denmark)

Olivares Hernandez, Roberto

Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been construc......Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been...

Identification of coding and non-coding mutational hotspots in cancer genomes.

Science.gov (United States)

Piraino, Scott W; Furney, Simon J

2017-01-05

The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

Decoding the human genome

CERN Multimedia

CERN. Geneva. Audiovisual Unit; Antonerakis, S E

2002-01-01

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

ACCESS Project: Final Report

Energy Technology Data Exchange (ETDEWEB)

Weller, Heiko [Robert Bosch, LLC, Farmington Hills, MI (United States)

2015-04-01

The ACCESS project addressed the development, testing, and demonstration of the proposed advanced technologies and the associated emission and fuel economy improvement at an engine dynamometer and on a full-scale vehicle. Improve fuel economy by 25% with minimum performance penalties Achieve SULEV level emissions with gasoline Demonstrate multi-mode combustion engine management system

Final project report for NEET pulsed ion beam project

Energy Technology Data Exchange (ETDEWEB)

Kucheyev, S. O. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2018-01-11

The major goal of this project was to develop and demonstrate a novel experimental approach to access the dynamic regime of radiation damage formation in nuclear materials. In particular, the project exploited a pulsed-ion-beam method in order to gain insight into defect interaction dynamics by measuring effective defect interaction time constants and defect diffusion lengths. This project had the following four major objectives: (i) the demonstration of the pulsed ion beam method for a prototypical nuclear ceramic material, SiC; (ii) the evaluation of the robustness of the pulsed beam method from studies of defect generation rate effects; (iii) the measurement of the temperature dependence of defect dynamics and thermally activated defect-interaction processes by pulsed ion beam techniques; and (iv) the demonstration of alternative characterization techniques to study defect dynamics. As we describe below, all these objectives have been met.

Long term Gas Supply Security in an Enlarged Europe. Final Report ENGAGED Project

International Nuclear Information System (INIS)

Van Oostvoorn, F.; Likachev, V.; Morgan, T.

2004-12-01

The title project concerned a study on the long-term gas supply security in Europe with a focus on the developments, risks and policies in the candidate countries in Eastern Europe. For that reason the report not only includes a European and EU-30 wide scenario analysis but also chapters on specific topics. One study (a chapter in this report) concerns the gas market and regulation developments in a number of relevant candidate countries. Another chapter presents a Russian vision on gas demand, production and supplies from Russia and also includes a paragraph on the supplies from other neighbours and the transit issues in the Ukraine. Finally, the report contains a chapter discussing the required network infrastructure for bringing the gas from external gas suppliers to the EU-30 markets. Hereby it analysis and tests the network flexibility to cope with some unlikely and unexpected supply interruptions in main pipelines to EU markets. The background information of the studies underlying the chapters can be partly found in the annexes and in the individual task reports. During the project the results of the study were discussed at several seminars in candidate countries and particularly on the final seminar in Prague, in June 2003, with different and important stakeholders and market actors

Human Genome Diversity Project. Summary of planning workshop 3(B): Ethical and human-rights implications

Energy Technology Data Exchange (ETDEWEB)

NONE

1993-12-31

The third planning workshop of the Human Genome Diversity Project was held on the campus of the US National Institutes of Health in Bethesda, Maryland, from February 16 through February 18, 1993. The second day of the workshop was devoted to an exploration of the ethical and human-rights implications of the Project. This open meeting centered on three roundtables, involving 12 invited participants, and the resulting discussions among all those present. Attendees and their affiliations are listed in the attached Appendix A. The discussion was guided by a schedule and list of possible issues, distributed to all present and attached as Appendix B. This is a relatively complete, and thus lengthy, summary of the comments at the meeting. The beginning of the summary sets out as conclusions some issues on which there appeared to be widespread agreement, but those conclusions are not intended to serve as a set of detailed recommendations. The meeting organizer is distributing his recommendations in a separate memorandum; recommendations from others who attended the meeting are welcome and will be distributed by the meeting organizer to the participants and to the Project committee.

Independent management and financial review, Yucca Mountain Project, Nevada. Final report, Appendix

International Nuclear Information System (INIS)

1995-01-01

The Nuclear Waste Policy Act of 1982 (Public Law 97-425), as amended by Public Law 100-203, December 22, 1987, established the Office of Civilian Radioactive Waste Management (OCRWM) within the Department of Energy (DOE), and directed the Office to investigate a site at Yucca Mountain, Nevada, to determine if this site is suitable for the construction of a repository for the disposal of high level nuclear waste. Work on site characterization has been under way for several years. Thus far, about $1.47 billion have been spent on Yucca Mountain programs. This work has been funded by Congressional appropriations from a Nuclear Waste Fund to which contributions have been made by electric utility ratepayers through electric utilities generating power from nuclear power stations. The Secretary of Energy and the Governor of the State of Nevada have appointed one person each to a panel to oversee an objective, independent financial and management evaluation of the Yucca Mountain Project. The Requirements for the work will include an analysis of (1) the Yucca Mountain financial and, contract management techniques and controls; (2) Project schedules and credibility of the proposed milestones; (3) Project organizational effectiveness and internal planning processes, and (4) adequacy of funding levels and funding priorities, including the cost of infrastructure and scientific studies. The recipient will provide monthly progress report and the following reports/documents will be presented as deliverables under the contract: (1) Financial and Contract Management Preliminary Report; (2) Project Scheduling Preliminary Report; (3)Project Organizational Effectiveness Preliminary Report; (4) Project Funding Levels and Funding Priorities Preliminary Report; and (5) Final Report

Independent management and financial review, Yucca Mountain Project, Nevada. Final report, Appendix

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-07-15

The Nuclear Waste Policy Act of 1982 (Public Law 97-425), as amended by Public Law 100-203, December 22, 1987, established the Office of Civilian Radioactive Waste Management (OCRWM) within the Department of Energy (DOE), and directed the Office to investigate a site at Yucca Mountain, Nevada, to determine if this site is suitable for the construction of a repository for the disposal of high level nuclear waste. Work on site characterization has been under way for several years. Thus far, about $1.47 billion have been spent on Yucca Mountain programs. This work has been funded by Congressional appropriations from a Nuclear Waste Fund to which contributions have been made by electric utility ratepayers through electric utilities generating power from nuclear power stations. The Secretary of Energy and the Governor of the State of Nevada have appointed one person each to a panel to oversee an objective, independent financial and management evaluation of the Yucca Mountain Project. The Requirements for the work will include an analysis of (1) the Yucca Mountain financial and, contract management techniques and controls; (2) Project schedules and credibility of the proposed milestones; (3) Project organizational effectiveness and internal planning processes, and (4) adequacy of funding levels and funding priorities, including the cost of infrastructure and scientific studies. The recipient will provide monthly progress report and the following reports/documents will be presented as deliverables under the contract: (1) Financial and Contract Management Preliminary Report; (2) Project Scheduling Preliminary Report; (3)Project Organizational Effectiveness Preliminary Report; (4) Project Funding Levels and Funding Priorities Preliminary Report; and (5) Final Report.

Comparative Genomics in Homo sapiens.

Science.gov (United States)

Oti, Martin; Sammeth, Michael

2018-01-01

Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

Genomics in health and disease | Shawky | Egyptian Journal of ...

African Journals Online (AJOL)

Genomics is the study of all person's genes including interactions of those genes ... Our environment and our biology are two factors that strongly influence our health. ... The completion of the Human Genome Project signaled that the genome ...

Final Status Survey for the Largest Decommissioning Project on Earth

International Nuclear Information System (INIS)

Dubiel, R.W.; Miller, J.; Quayle, D.

2006-01-01

To assist the United States Department of Energy's (US DOE's) re-industrialization efforts at its gaseous diffusion site in Oak Ridge, Tennessee, known as the East Tennessee Technology Park (ETTP), the US DOE awarded a 6-year Decontamination and Decommissioning (D and D) contract to BNG America (formerly BNFL Inc.) in 1997. The ETTP 3-Building D and D Project included the removal and disposition of the materials and equipment from the K-33, K-31, and K-29 Gaseous Diffusion Plant buildings. The three buildings comprise more than 4.8 million square feet (446,000 square meters) of floor surface area and more than 350 million pounds (148 million kilograms) of hazardous and radioactively contaminated material, making it the largest nuclear D and D project in progress anywhere in the world. The logistical hurdles involved in a project of this scope and magnitude required an extensive amount of Engineering and Health Physics professionals. In order to accomplish the Final Status Survey (FSS) for a project of this scope, the speed and efficiency of automated survey equipment was essential. Surveys of floors, structural steel and ceilings up to 60 feet (18 meters) were required. The FSS had to be expanded to include additional remediation and surveys due to characterization surveys and assumptions regarding the nature and extent of contamination provided by the US DOE. Survey design and technical bases had to consider highly variable constituents; including uranium from depleted to low enrichment, variable levels of Technetium-99 and transuranic nuclides, which were introduced into the cascade during the 1960's when recycled uranium (RU) from Savannah River was re-enriched at the facility. The RU was transported to unexpected locations from leaks in the cascade by complex building ventilation patterns. The primary survey tool used for the post remediation and FSS was the Surface Contamination Monitor (SCM) and the associated Survey Information Management System (SIMS

Genomic research in Eucalyptus.

Science.gov (United States)

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

2005-09-01

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

Big Data Analysis of Human Genome Variations

KAUST Repository

Gojobori, Takashi

2016-01-25

Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human genome variations: 1) HapMap Data (1,417 individuals) (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2010-08_phaseII+III/forward/), 2) HGDP (Human Genome Diversity Project) Data (940 individuals) (http://www.hagsc.org/hgdp/files.html), 3) 1000 genomes Data (2,504 individuals) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ If we can integrate all three data into a single volume of data, we should be able to conduct a more detailed analysis of human genome variations for a total number of 4,861 individuals (= 1,417+940+2,504 individuals). In fact, we successfully integrated these three data sets by use of information on the reference human genome sequence, and we conducted the big data analysis. In particular, we constructed a phylogenetic tree of about 5,000 human individuals at the genome level. As a result, we were able to identify clusters of ethnic groups, with detectable admixture, that were not possible by an analysis of each of the three data sets. Here, we report the outcome of this kind of big data analyses and discuss evolutionary significance of human genomic variations. Note that the present study was conducted in collaboration with Katsuhiko Mineta and Kosuke Goto at KAUST.

Hispanic Vocational Exploration Project. Final Report.

Science.gov (United States)

Centro De La Comunidad, Inc., New London, CT.

During its second year, the Hispanic Vocational Exploration Project recruited eighth and ninth grade Hispanic youth for a four-week cycle, after-school, career exploratory program at Southeastern Regional Vocational Technical School, Groton, Connecticut. A series of career education workshops was the other major project activity. Supportive…

Radiological and environmental consequences. Final report of the Nordic Nuclear Safety Research project BOK-2

International Nuclear Information System (INIS)

Palsson, S.E.

2002-11-01

Final report of the Nordic Nuclear Safety Research project BOK-2, Radiological and Environmental Consequences. The project was carried out 1998-2001 with participants from all the Nordic countries. Representatives from the Baltic States were also invited to some of the meetings and seminars. The project consisted of work on terrestrial and marine radioecology and had a broad scope in order to enable participation of research groups with various fields of interest. This report focuses on the project itself and gives a general summary of the studies undertaken. A separate technical report summarises the work done by each research group and gives references to papers published in scientific journals. The topics in BOK-2 included improving assessment of old and recent fallout, use of radionuclides as tracers in Nordic marine areas, improving assessment of internal doses and use of mass spectrometry in radioecology. (au)

Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study

DEFF Research Database (Denmark)

de Vries, Paul S; Sabater-Lleal, Maria; Chasman, Daniel I

2017-01-01

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In...

The ICE-CREAM Project : final report

NARCIS (Netherlands)

Janse, M.D.

2004-01-01

The ICE-CREAM project has been investigating how to make compelling experiences for end-users based on enabling technologies for interactive media, such as DVB-MHP, Internet and MPEG-4. The goals of the project were to extend the notion of interaction, to exploit domestic activities and familiar

Big Data Analysis of Human Genome Variations

KAUST Repository

Gojobori, Takashi

2016-01-01

Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human

HLA diversity in the 1000 genomes dataset.

Directory of Open Access Journals (Sweden)

Pierre-Antoine Gourraud

Full Text Available The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation by sequencing at a level that should allow the genome-wide detection of most variants with frequencies as low as 1%. However, in the major histocompatibility complex (MHC, only the top 10 most frequent haplotypes are in the 1% frequency range whereas thousands of haplotypes are present at lower frequencies. Given the limitation of both the coverage and the read length of the sequences generated by the 1000 Genomes Project, the highly variable positions that define HLA alleles may be difficult to identify. We used classical Sanger sequencing techniques to type the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genes in the available 1000 Genomes samples and combined the results with the 103,310 variants in the MHC region genotyped by the 1000 Genomes Project. Using pairwise identity-by-descent distances between individuals and principal component analysis, we established the relationship between ancestry and genetic diversity in the MHC region. As expected, both the MHC variants and the HLA phenotype can identify the major ancestry lineage, informed mainly by the most frequent HLA haplotypes. To some extent, regions of the genome with similar genetic or similar recombination rate have similar properties. An MHC-centric analysis underlines departures between the ancestral background of the MHC and the genome-wide picture. Our analysis of linkage disequilibrium (LD decay in these samples suggests that overestimation of pairwise LD occurs due to a limited sampling of the MHC diversity. This collection of HLA-specific MHC variants, available on the dbMHC portal, is a valuable resource for future analyses of the role of MHC in population and disease studies.

Human genome education model project. Ethical, legal, and social implications of the human genome project: Education of interdisciplinary professionals

Energy Technology Data Exchange (ETDEWEB)

Weiss, J.O. [Alliance of Genetic Support Groups, Chevy Chase, MD (United States); Lapham, E.V. [Georgetown Univ., Washington, DC (United States). Child Development Center

1996-12-31

This meeting was held June 10, 1996 at Georgetown University. The purpose of this meeting was to provide a multidisciplinary forum for exchange of state-of-the-art information on the human genome education model. Topics of discussion include the following: psychosocial issues; ethical issues for professionals; legislative issues and update; and education issues.

The final disposal of radioactive wastes as social, political and scientific project - an introduction

International Nuclear Information System (INIS)

Brunnengraeber, Achim

2015-01-01

The nuclear power production that was productive for two generations produces radioactive wastes that will be a hazardous and financial burden for many future generations. Science, politics, industry and the society are responsible to find a successful solution for the project of final disposal of radioactive wastes. With the fast development of renewable energies with the perspectives of sustainability and other advantages nuclear power will not have a remarkable future. The search for a final repository site is a tremendous governmental, economic and public challenge but can also be seen as a social chance. Democracy could be enforced by this process, public commitment, transparency, co-determination, confidence in political processes are indispensible premises.

Annual genome conference. Final report, September 1, 1994--August 31, 1995

Energy Technology Data Exchange (ETDEWEB)

Gardiner, K.

1995-11-01

Tremendous progress has been made in the construction of physical and genetic maps of the human chromosomes. The next step in the solving of disease related problems, and in understanding the human genome as a whole, is the systematic isolation of transcribed sequences. Many investigators have already embarked upon comprehensive gene searches, and many more are considering the best strategies for undertaking such searches. Because these are likely to be costly and time consuming endeavors, it is important to determine the most efficient approaches. As a result, it is critical that investigators involved in the construction of transcriptional maps have the opportunity to discuss their experiences and their successes with both old and new technologies. This document contains the proceedings of the Fourth Annual Workshop on the Identification of Transcribed Sequences, held in Montreal, Quebec, October 16-18, 1994. Included are the workshop notebook, containing the agenda, abstracts presented and list of attendees. Topics included: Progress in the application of the hybridization based approaches and exon trapping; Progress in transcriptional map construction of selected genomic regions; Computer assisted analysis of genomic and protein coding sequences and additional new approaches; and, Sequencing and mapping of random cDNAs.

The Genomic Evolution of Prostate Cancer

Science.gov (United States)

2017-06-01

the proposed project : 1. To continue to acquire a comprehensive understanding of prostate cancer genomics . 2. To develop an understanding of... Genetics I • ECEV 35901 Evolutionary Genomics • Fundamentals of Clinical Research • HGEN 47400 Introduction to Probability and Statistics for Geneticists...Marc Gillard,2 David M. Hatcher,5 Westin R. Tom,5 Walter M. Stadler2 and Kevin P. White1,2,3 1Institute for Genomics and Systems Biology , Departments of

The final focus test beam project

International Nuclear Information System (INIS)

Burke, D.

1991-05-01

An overview is given of the Final Focus Test Beam (FFTB) that is being constructed as a prototype final focus system for a future electron-positron linear collider. This beam line will use as input the 50 GeV electron beam from the SLC linac, and is designed to reduce the transverse dimensions of the beam spot at the focal point to 1 μm. 5 refs., 2 figs., 1 tab

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

Project Elderly. Interim and Final Reports.

Science.gov (United States)

Miami-Dade Community Coll., FL.

This report examines Project Elderly, a project developed to provide job possibilities for the older adult in the labor market in metropolitan Miami (FL). A survey questionnaire was developed to (1) assess the opportunities of the elderly for re-entry into volunteer and paid employment positions; (2) determine the extent of the senior population…

FutureGen 2.0 Pipeline and Regional Carbon Capture Storage Project - Final Report

Energy Technology Data Exchange (ETDEWEB)

Burger, Chris [Patrick Engineering Inc., Lisle, IL (United States); Wortman, David [Patrick Engineering Inc., Lisle, IL (United States); Brown, Chris [Battelle Memorial Inst., Richland, WA (United States); Hassan, Syed [Gulf Interstate Engineering, Houston, TX (United States); Humphreys, Ken [Futuregen Industrial Alliance, Inc., Washington, D.C. (United States); Willford, Mark [Futuregen Industrial Alliance, Inc., Washington, D.C. (United States)

2016-03-31

The U.S. Department of Energy’s (DOE) FutureGen 2.0 Program involves two projects: (1) the Oxy-Combustion Power Plant Project and (2) the CO2 Pipeline and Storage Project. This Final Technical Report is focused on the CO2 Pipeline and Storage Project. The FutureGen 2.0 CO2 Pipeline and Storage Project evolved from an initial siting and project definition effort in Phase I, into the Phase II activity consisting permitting, design development, the acquisition of land rights, facility design, and licensing and regulatory approvals. Phase II also progressed into construction packaging, construction procurement, and targeted early preparatory activities in the field. The CO2 Pipeline and Storage Project accomplishments were significant, and in some cases unprecedented. The engineering, permitting, legal, stakeholder, and commercial learnings substantially advance the nation’s understanding of commercial-scale CO2 storage in deep saline aquifers. Voluminous and significant information was obtained from the drilling and the testing program of the subsurface, and sophisticated modeling was performed that held up to a wide range of scrutiny. All designs progressed to the point of securing construction contracts or comfort letters attesting to successful negotiation of all contract terms and willing execution at the appropriate time all major project elements – pipeline, surface facilities, and subsurface – as well as operations. While the physical installation of the planned facilities did not proceed in part due to insufficient time to complete the project prior to the expiration of federal funding, the project met significant objectives prior to DOE’s closeout decision. Had additional time been available, there were no known, insurmountable obstacles that would have precluded successful construction and operation of the project. Due to the suspension of the project, site restoration activities were developed and the work was accomplished. The site restoration

ND-REAP/DOE cooperative project: final report

Energy Technology Data Exchange (ETDEWEB)

1979-01-01

The impacts of energy-related developments in North Dakota are having profound effects on the state. Among the most significant of these effects are those on the state's economy and its population. Knowledge of the total environmental effects of development is a necessary prerequisite for effective planning and decision making. This final report addresses the conceptual design and functional evolution of the Regional Environmental Assessment Program, the results of the REAP/DOE Cooperative Effort, as well as evolution of the REAP/DOE effort and recommendations for future directions. The Economic Demographic (E-D) Model was developed to give North Dakota decision makers a tool with which to evaluate the impacts of coal development. It projects social, economic, and characteristics of North Dakota. Refinements and expansion of the model are discussed in Section 1. Section 2 provides an evaluation of the model as applied to other states. Section 3 identifies and evaluates the use of REAP data and capabilities to date. The REAP Resources Reference System R/sup 3/S was developed to provide access to information systems and to past research and present studies about aspects of North Dakota. It is a computer-based library reference system. Its status and expansion potential is covered in Section 4. Section 5 makes recommendations for future efforts.

EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

Science.gov (United States)

Hu, Zhiqiang; Sun, Chen; Lu, Kuang-Chen; Chu, Xixia; Zhao, Yue; Lu, Jinyuan; Shi, Jianxin; Wei, Chaochun

2017-08-01

Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms. EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html . ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Project Final Report: HPC-Colony II

Energy Technology Data Exchange (ETDEWEB)

Jones, Terry R [ORNL; Kale, Laxmikant V [University of Illinois, Urbana-Champaign; Moreira, Jose [IBM T. J. Watson Research Center

2013-11-01

This report recounts the HPC Colony II Project which was a computer science effort funded by DOE's Advanced Scientific Computing Research office. The project included researchers from ORNL, IBM, and the University of Illinois at Urbana-Champaign. The topic of the effort was adaptive system software for extreme scale parallel machines. A description of findings is included.

Project CAREER/CAN. Final Evaluation Report.

Science.gov (United States)

National Educational Evaluation Services, Inc., Chestnut Hill, MA.

A description and evaluation of (1) the development of the 4-column process which completes the behavioral objective data base, (2) the development of the computer retrieval capability, and (3) the pilot testing of the product in high school classrooms are included in this summative evaluation of Project CAREER/CAN. (Goals of Project CAREER/CAN,…

DEFINING THE CHEMICAL SPACE OF PUBLIC GENOMIC ...

Science.gov (United States)

The current project aims to chemically index the genomics content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. By defining the chemical space of public genomic data, it is possible to identify classes of chemicals on which to develop methodologies for the integration of chemogenomic data into predictive toxicology. The chemical space of public genomic data will be presented as well as the methodologies and tools developed to identify this chemical space.

Next generation tools for genomic data generation, distribution, and visualization.

Science.gov (United States)

Nix, David A; Di Sera, Tonya L; Dalley, Brian K; Milash, Brett A; Cundick, Robert M; Quinn, Kevin S; Courdy, Samir J

2010-09-09

With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq.

The post-Human Genome Project mindset: race, reliability, and health care.

Science.gov (United States)

Kimmelman, J

2006-11-01

The following essay reports on the first session of a 2-day workshop on genetic diversity and science communication, organized by the Institute of Genetics. I argue that the four talks in this session reflected two different facets of a 'post-Human Genome Project (HGP)' view of human genetics. The first is characterized by an increasing interest in genetic differences. Two speakers - Troy Duster and Jasber Singh - expressed skepticism about one aspect of this trend: an emphasis on race in medicine and genetics. The other two speakers - Kenneth Weiss and Gustavo Turecki - spoke to a second facet of the post-HGP view: a recognition of the difficulty in translating genetic discovery into medical or public health applications. Though both sets of talks were highly critical of current trends in genetic research, they pulled in opposite directions: one warned about the role of genetics in stabilizing racial categories, while the other lamented the failure of any genetic claims or categories to stabilize at all. I argue that the use of racial categories in medicine seems likely to encounter scientific, medical, and social challenges.

Learning about the Human Genome. Part 2: Resources for Science Educators. ERIC Digest.

Science.gov (United States)

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…

Genome-wide DNA polymorphism analyses using VariScan

Directory of Open Access Journals (Sweden)

Vilella Albert J

2006-09-01

Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

Science.gov (United States)

Card, Daren C; Schield, Drew R; Reyes-Velasco, Jacobo; Fujita, Matthew K; Andrew, Audra L; Oyler-McCance, Sara J; Fike, Jennifer A; Tomback, Diana F; Ruggiero, Robert P; Castoe, Todd A

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

Science.gov (United States)

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthre K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Final report of the project performance assessment and economic evaluation of nuclear waste management

International Nuclear Information System (INIS)

Rasilainen, K.; Anttila, M.; Hautojaervi, A.

1993-05-01

The publication is the final report of project Performance Assessment and Economic Evaluation of Nuclear Waste Management (TOKA) at the Nuclear Engineering Laboratory of VTT (Technical Research Centre of Finland), forming part of the Publicly Financed Nuclear Waste Management Research Programme (JYT). The project covers safety and cost aspects of all phases of nuclear waste management. The main emphasis has been on developing an integrated system of models for performance assessment of nuclear waste repositories. During the four years the project has so far been in progress, the total amount of work has been around 14 person-years. Computer codes are the main tools in the project, they are either developed by the project team or acquired from abroad. In-house model development has been especially active in groundwater flow, near-field and migration modelling. The quantitative interpretation of Finnish tracer experiments in the laboratory and natural analogue studies at Palmottu support performance assessments via increased confidence in the migration concepts used. The performance assessment philosophy adopted by the team consists of deterministic modelling and pragmatic scenario analysis. This is supported by the long-term experience in practical performance assessment of the team, and in theoretical probabilistic modelling exercises. The radiological risks of spent fuel transportation from the Loviisa nuclear power plant to Russia have been analysed using a probabilistic computer code and Finnish traffic accident statistics. The project assists the authorities in the annual assessment of utility estimates of funding needs for future nuclear waste management operations. The models and methods used within the project are tested in international verification/validation projects

Genomics and fish adaptation

Directory of Open Access Journals (Sweden)

Agostinho Antunes

2015-12-01

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

Annotating non-coding regions of the genome.

Science.gov (United States)

Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B

2010-08-01

Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.

Peanut (Arachis hypogaea Expressed Sequence Tag Project: Progress and Application

Directory of Open Access Journals (Sweden)

Suping Feng

2012-01-01

Full Text Available Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function.

An efficient approach to BAC based assembly of complex genomes.

Science.gov (United States)

Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; Batley, Jacqueline; Šimková, Hana; Doležel, Jaroslav; Edwards, David

2016-01-01

There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.

Snake Genome Sequencing: Results and Future Prospects.

Science.gov (United States)

Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

2016-12-01

Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Snake Genome Sequencing: Results and Future Prospects

Directory of Open Access Journals (Sweden)

Harald M. I. Kerkkamp

2016-12-01

Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

The Final Year Project (FYP) in Social Sciences: Establishment of Its Associated Competences and Evaluation Standards

Science.gov (United States)

Mateo, Joan; Escofet, Anna; Martinez, Francesc; Ventura, Javier; Vlachopoulos, Dimitrios

2012-01-01

This paper presents the fundamental characteristics of the Final Year Project (FYP), its associated competences and some evaluation standards that derived from a research conducted by the regional government of Catalonia (Spain) and the Catalan University Quality Assurance Agency. More analytically, the paper begins with the definition of the…

From Genes to Genomes Chances and boundaries of the New Biology

CERN Document Server

Winnaker, E L

1997-01-01

The goal of my lecture is to show the new dimensions of genome research. It is replacing classic recombinant DNA technologies. The search for single genes is being replaced by the analysis of gene activities of whole cells, organs or organisms. This development changes radically basic biomedical research and points to new therapeutic strategies (examples:cancer,Alzheimer's disease). I will also show the rapid changes of our understanding of gene activity. Mendel's definition of genes is now replaced by molecular terms which teach us how gene expression is regulated and controlled. Finally I will try to outline the limits of genetic analysis and how it raises ethical and moral questions. If the analysis of changes in the genetic read-out are related to diseases for which there is no therapy or if such knowledge only predisposes to genetic diseases the handling of such information requires extraordinary care. The genome projects thus have to be and are being pursued in conjunction with careful ethical analyses ...

Analysing human genomes at different scales

DEFF Research Database (Denmark)

Liu, Siyang

The thriving of the Next-Generation sequencing (NGS) technologies in the past decade has dramatically revolutionized the field of human genetics. We are experiencing a wave of several large-scale whole genome sequencing studies of humans in the world. Those studies vary greatly regarding cohort...... will be reflected by the analysis of real data. This thesis covers studies in two human genome sequencing projects that distinctly differ in terms of studied population, sample size and sequencing depth. In the first project, we sequenced 150 Danish individuals from 50 trio families to 78x coverage....... The sophisticated experimental design enables high-quality de novo assembly of the genomes and provides a good opportunity for mapping the structural variations in the human population. We developed the AsmVar approach to discover, genotype and characterize the structural variations from the assemblies. Our...

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

Science.gov (United States)

Jongeneel, C Victor; Achinike-Oduaran, Ovokeraye; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Akanle, Bola; Aron, Shaun; Ashano, Efejiro; Bendou, Hocine; Botha, Gerrit; Chimusa, Emile; Choudhury, Ananyo; Donthu, Ravikiran; Drnevich, Jenny; Falola, Oluwadamila; Fields, Christopher J; Hazelhurst, Scott; Hendry, Liesl; Isewon, Itunuoluwa; Khetani, Radhika S; Kumuthini, Judit; Kimuda, Magambo Phillip; Magosi, Lerato; Mainzer, Liudmila Sergeevna; Maslamoney, Suresh; Mbiyavanga, Mamana; Meintjes, Ayton; Mugutso, Danny; Mpangase, Phelelani; Munthali, Richard; Nembaware, Victoria; Ndhlovu, Andrew; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Panji, Sumir; Pillay, Venesa; Rendon, Gloria; Sengupta, Dhriti; Mulder, Nicola

2017-06-01

The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

The Arab genome: Health and wealth.

Science.gov (United States)

Zayed, Hatem

2016-11-05

The 22 Arab nations have a unique genetic structure, which reflects both conserved and diverse gene pools due to the prevalent endogamous and consanguineous marriage culture and the long history of admixture among different ethnic subcultures descended from the Asian, European, and African continents. Human genome sequencing has enabled large-scale genomic studies of different populations and has become a powerful tool for studying disease predictions and diagnosis. Despite the importance of the Arab genome for better understanding the dynamics of the human genome, discovering rare genetic variations, and studying early human migration out of Africa, it is poorly represented in human genome databases, such as HapMap and the 1000 Genomes Project. In this review, I demonstrate the significance of sequencing the Arab genome and setting an Arab genome reference(s) for better understanding the molecular pathogenesis of genetic diseases, discovering novel/rare variants, and identifying a meaningful genotype-phenotype correlation for complex diseases. Copyright © 2016. Published by Elsevier B.V.

Proposed modifications to the Lower Mokelumne River Project, California: FERC Project No. 2916-004. Final environmental impact statement

Energy Technology Data Exchange (ETDEWEB)

1993-11-01

This final environmental impact statement (FEIS) has been prepared for the Federal Energy Regulatory Commission (Commission) to consider modifications to the existing Lower Mokelumne River Project (LMRP) (FERC Project No. 2916-004) in California. Chinook salmon and steelhead trout populations in the lower Mokelumne River have experienced recent declines and fish kills associated, in part, with discharges from Camanche Dam. The California Department of Fish and Game and the California Sportfishing Protection Alliance have asked the Commission to investigate and correct these problems. A wide range of different mitigation actions has been proposed by parties participating in the scoping of this proceeding, and staff has evaluated these proposed actions in this assessment. The staff is recommending a combination of flow and non-flow modifications to the existing license, including new minimum flow and minimum pool elevation requirements at Camanche Reservoir, ramping rates on dam releases, interim attraction and out-migrant spike flows, instream habitat improvements, and a series of studies and monitoring to determine feasible means for solving off-site fish passage problems.

Next generation tools for genomic data generation, distribution, and visualization

Directory of Open Access Journals (Sweden)

Nix David A

2010-09-01

Full Text Available Abstract Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx; an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub; and a standalone Java Swing application (GWrap that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq.

The Banana Genome Hub

Science.gov (United States)

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

2013-01-01

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

Mechanisms of Low Dose Radio-Suppression of Genomic Instability

Energy Technology Data Exchange (ETDEWEB)

Engelward, Bevin P. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

2009-09-16

The major goal of this project is to contribute toward the elucidation of the impact of long term low dose radiation on genomic stability. We have created and characterized novel technologies for delivering long term low dose radiation to animals, and we have studied genomic stability by applying cutting edge molecular analysis technologies. Remarkably, we have found that a dose rate that is 300X higher than background radiation does not lead to any detectable genomic damage, nor is there any significant change in gene expression for genes pertinent to the DNA damage response. These results point to the critical importance of dose rate, rather than just total dose, when evaluating public health risks and when creating regulatory guidelines. In addition to these studies, we have also further developed a mouse model for quantifying cells that have undergone a large scale DNA sequence rearrangement via homologous recombination, and we have applied these mice in studies of both low dose radiation and space radiation. In addition to more traditional approaches for assessing genomic stability, we have also explored radiation and possible beneficial effects (adaptive response), long term effects (persistent effects) and effects on communication among cells (bystander effects), both in vitro and in vivo. In terms of the adaptive response, we have not observed any significant induction of an adaptive response following long term low dose radiation in vivo, delivered at 300X background. In terms of persistent and bystander effects, we have revealed evidence of a bystander effect in vivo and with researchers at and demonstrated for the first time the molecular mechanism by which cells “remember” radiation exposure. Understanding the underlying molecular mechanisms by which radiation can induce genomic instability is fundamental to our ability to assess the biological impact of low dose radiation. Finally, in a parallel set of studies we have explored the effects of heavy

WormBase: Annotating many nematode genomes.

Science.gov (United States)

Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W

2012-01-01

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

Mitogenomes from The 1000 Genome Project reveal new Near Eastern features in present-day Tuscans.

Directory of Open Access Journals (Sweden)

Alberto Gómez-Carballa

Full Text Available Genetic analyses have recently been carried out on present-day Tuscans (Central Italy in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000 and partial control region sequences (>180,000.Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%. Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.

Novalignin project. Final report

Energy Technology Data Exchange (ETDEWEB)

Stigsson, Lars [KIRAM AB, Saltsjoebaden (Sweden)

2002-02-01

The NovaFiber process is a new and sustainable technology for manufacturing of chemical pulp incorporating an efficient route for recovery of energy and pulping chemicals. The process is substantially sulphur chemicals free and this creates a great potential for recovery of sulphur free lignin for internal use as a fuel or export from the mill. The NovaLignin project has been launched to evaluate this potential from a technical and economical perspective. The NovaLignin research and development effort has been partly financed by NUTEK, Energimyndigheten and Mistra. A major feature of the new lignin is the absence of organically bound sulphur compounds in the material increasing the scope of potential uses for the lignin as a precursor for fine chemicals preparation or as a sulphur free biomass based fuel. Two major forest industry laboratories in Scandinavia have conducted the laboratory cooking and lignin extraction work in the present project. The lignin extracted from the NovaFiber process, NovaLignin, has been characterised and evaluated for use in different applications. The consequences of lignin extraction in different mill configurations with a recovery boiler or a black liquor gasification system for chemicals recovery is outlined below. The NovaFiber pulp mill is compared to a reference mill based on conventional kraft pulping on the same wood raw material. The mill capacity is 2000 t/d bleached softwood pulp. The lime kiln is fired with bark and the remaining falling bark is sold, or if there is a deficit, more bark is purchased. Initial laboratory studies conducted at ATO-DLO, the Netherlands, clearly show a great potential for NovaLignin as a functional additive in thermoplastics. NovaFiber and Kraft lignin act as an UV stabiliser for polyethylene at a comparable level as an expensive commercial stabiliser, such as HALS. This means that NovaFiber lignin has a very good price/performance ratio. Experiments show that NovaFiber lignin has good potential

TWTF project criticality task force final review and assessment

International Nuclear Information System (INIS)

McKinley, K.B.; Cannon, J.W.; Wheeler, F.J.; Worle, H.A.

1980-11-01

The Transuranic Waste Treatment Facility (TWTF) is being developed to process transuranic waste, stored and buried at the Idaho National Engineering Laboratory, into a chemically inert, physically stable basalt-like residue acceptable at a federal repository. A task force was assembled by the TWTF Project Division to review and assess all aspects of criticality safety for the TWTF. This document presents the final review, assessments, and recommendations of this task force. The following conclusions were made: Additional criticality studies are needed for the entire envelope of feed compositions and temperature effects. Safe operating k/sub eff/'s need to be determined for process components. Criticality analyses validation experiments may also be required. SRP neutron interrogation should be replaced by DDT neutron interrogation. Accuracy studies need to be performed for the proposed assaying techniques. Time-correlated neutron monitoring needs to be mocked up for process components to prove feasibility and determine accuracy. The criticality control techniques developed for the TWTF conceptual design are in compliance with ERDAM 0530, including the Double Contingency Rule. Detailed procedures and controls need to be developed

DNA Data Bank of Japan at work on genome sequence data.

Science.gov (United States)

Tateno, Y; Fukami-Kobayashi, K; Miyazaki, S; Sugawara, H; Gojobori, T

1998-01-01

We at the DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) have recently begun receiving, processing and releasing EST and genome sequence data submitted by various Japanese genome projects. The data include those for human, Arabidopsis thaliana, rice, nematode, Synechocystis sp. and Escherichia coli. Since the quantity of data is very large, we organized teams to conduct preliminary discussions with project teams about data submission and handling for release to the public. We also developed a mass submission tool to cope with a large quantity of data. In addition, to provide genome data on WWW, we developed a genome information system using Java. This system (http://mol.genes.nig.ac.jp/ecoli/) can in theory be used for any genome sequence data. These activities will facilitate processing of large quantities of EST and genome data.

Oncogenomic portals for the visualization and analysis of genome-wide cancer data.

Science.gov (United States)

Klonowska, Katarzyna; Czubak, Karol; Wojciechowska, Marzena; Handschuh, Luiza; Zmienko, Agnieszka; Figlerowicz, Marek; Dams-Kozlowska, Hanna; Kozlowski, Piotr

2016-01-05

Somatically acquired genomic alterations that drive oncogenic cellular processes are of great scientific and clinical interest. Since the initiation of large-scale cancer genomic projects (e.g., the Cancer Genome Project, The Cancer Genome Atlas, and the International Cancer Genome Consortium cancer genome projects), a number of web-based portals have been created to facilitate access to multidimensional oncogenomic data and assist with the interpretation of the data. The portals provide the visualization of small-size mutations, copy number variations, methylation, and gene/protein expression data that can be correlated with the available clinical, epidemiological, and molecular features. Additionally, the portals enable to analyze the gathered data with the use of various user-friendly statistical tools. Herein, we present a highly illustrated review of seven portals, i.e., Tumorscape, UCSC Cancer Genomics Browser, ICGC Data Portal, COSMIC, cBioPortal, IntOGen, and BioProfiling.de. All of the selected portals are user-friendly and can be exploited by scientists from different cancer-associated fields, including those without bioinformatics background. It is expected that the use of the portals will contribute to a better understanding of cancer molecular etiology and will ultimately accelerate the translation of genomic knowledge into clinical practice.