78 FR 22286 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

Science.gov (United States)

2013-04-15

....R50000] Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA..., Department of Anthropology, has completed an inventory of human remains, in consultation with the appropriate... acting on behalf of the University of Washington, Department of Anthropology. If no additional requestors...

78 FR 59963 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2013-09-30

... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-13770; PPWOCRADN0-PCU00RP14.R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of..., Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum, University of...

76 FR 58033 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2011-09-19

... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum (Burke...

75 FR 36671 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2010-06-28

... DEPARTMENT OF THE INTERIOR National Park Service Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA; Correction AGENCY: National Park... human remains and associated funerary objects in the possession of the Thomas Burke Memorial Washington...

76 FR 58034 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2011-09-19

... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum (Burke...

76 FR 58039 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2011-09-19

... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum (Burke...

77 FR 46117 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2012-08-02

... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-10823; 2200-1100-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington...

78 FR 11675 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2013-02-19

... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-12080;2200-1100-665] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington...

Composition at Washington State University: Building a Multimodal Bricolage

Science.gov (United States)

Ericsson, Patricia; Hunter, Leeann Downing; Macklin, Tialitha Michelle; Edwards, Elizabeth Sue

2016-01-01

Multimodal pedagogy is increasingly accepted among composition scholars. However, putting such pedagogy into practice presents significant challenges. In this profile of Washington State University's first-year composition program, we suggest a multi-vocal and multi-theoretical approach to addressing the challenges of multimodal pedagogy. Patricia…

The University of Washington Mobile Planetarium: A Do-it-yourself Guide

Science.gov (United States)

Rosenfield, P.; Gaily, J.; Fraser, O.; Wisniewski, J.

2014-07-01

The University of Washington mobile planetarium project is a student-driven effort to bring astronomy to secondary schools, and the community, in Seattle, USA. This paper presents the solution that was designed and built in order to use the World- Wide Telescope — a computer program created by Microsoft that displays the astronomical sky as maps, the 3D Universe, and earth science data — from a laptop and an off-the-shelf high-definition (HD) projector located in an inflatable plane- tarium. In the first six months of operation, undergraduates at the University of Washington presented planetarium shows to over 1500 people, and 150 secondary school students created and presented their own astronomy projects in our dome, at their school. This paper aims to share the technical aspects of the project so that others can replicate the model or adapt it to their needs. This project was made possible thanks to a NASA/ESA Hubble Space Telescope education/public outreach grant.

77 FR 51563 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

Science.gov (United States)

2012-08-24

... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains and associated funerary objects, in consultation with... of Washington, Department of Anthropology. Disposition of the human remains and associated funerary...

78 FR 5198 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

Science.gov (United States)

2013-01-24

... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains and associated funerary objects, in consultation with... of Washington, Department of Anthropology. Disposition of the human remains to the Indian tribes...

78 FR 19298 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

Science.gov (United States)

2013-03-29

...-PPWOCRADN0] Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA..., Department of Anthropology, has completed an inventory of human remains, in consultation with the appropriate... Washington, Department of Anthropology. Disposition of the human remains to the Indian tribes stated below...

78 FR 45958 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2013-07-30

... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-13406; PPWOCRADN0-PCU00RP14.R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke...

78 FR 44595 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2013-07-24

... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-NAGPRA-13407; PPWOCRADN0-PCU00RP14.R50000] Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke...

Ethical issues in human genome epidemiology: a case study based on the Japanese American Family Study in Seattle, Washington.

Science.gov (United States)

Austin, Melissa A

2002-04-01

Recent completion of the draft sequence of the human genome has been greeted with both excitement and skepticism, and the potential of this accomplishment for advancing public health has been tempered by ethical concerns about the protection of human subjects. This commentary explores ethical issues arising in human genome epidemiology by using a case study approach based on the ongoing Japanese American Family Study at the University of Washington in Seattle (1994-2003). Ethical issues encountered in designing the study, collecting the data, and reporting the study results are considered. When developing studies, investigators must consider whether to restrict the study to specific racial or ethnic groups and whether community involvement is appropriate. Once the study design is in place, further ethical issues emerge, including obtaining informed consent for DNA banking and protecting the privacy and confidentiality of family members. Finally, investigators must carefully consider whether to report genotype results to study participants and whether pedigrees illustrating the results of the study will be published. Overall, the promise of genomics for improving public health must be pursued based on the fundamental ethical principles of respect for persons, beneficence, and justice.

Washington State University Algae Biofuels Research

Energy Technology Data Exchange (ETDEWEB)

chen, Shulin [Washington State Univ., Pullman, WA (United States). Dept. of Biological Systems Engineering; McCormick, Margaret [Targeted Growth, Inc., Seattle, WA (United States); Sutterlin, Rusty [Inventure Renewables, Inc., Gig Harbor, WA (United States)

2012-12-29

The goal of this project was to advance algal technologies for the production of biofuels and biochemicals by establishing the Washington State Algae Alliance, a collaboration partnership among two private companies (Targeted Growth, Inc. (TGI), Inventure Chemicals (Inventure) Inc (now Inventure Renewables Inc) and Washington State University (WSU). This project included three major components. The first one was strain development at TGI by genetically engineering cyanobacteria to yield high levels of lipid and other specialty chemicals. The second component was developing an algal culture system at WSU to produce algal biomass as biofuel feedstock year-round in the northern states of the United States. This system included two cultivation modes, the first one was a phototrophic process and the second a heterotrophic process. The phototrophic process would be used for algae production in open ponds during warm seasons; the heterotrophic process would be used in cold seasons so that year-round production of algal lipid would be possible. In warm seasons the heterotrophic process would also produce algal seeds to be used in the phototrophic culture process. Selected strains of green algae and cyanobacteria developed by TGI were tested in the system. The third component was downstream algal biomass processing by Inventure that included efficiently harvesting the usable fuel fractions from the algae mass and effectively isolating and separating the usable components into specific fractions, and converting isolated fractions into green chemicals.

Now It's Necessary: Virtual Reference Services at Washington State University, Pullman

Science.gov (United States)

Nicol, Erica Carlson; Crook, Linda

2013-01-01

While virtual reference services (VRS) are becoming more and more common in academic libraries, implementing and maintaining well-used and effective VRS can be a challenge in the face of competing demands on time, staffing, and funding. Between 2011 and 2012, librarians at Washington State University, Pullman (WSU) have overhauled and reorganized…

Universal pacemaker of genome evolution.

Science.gov (United States)

Snir, Sagi; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome. This correlation could be explained by a model that we denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, the correlation between the evolutionary rates of genes could be a simple consequence of molecular clock (MC). We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in the evolution of archaea and bacteria and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, although similarly to the MC, the UPM is strongly overdispersed. Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life.

The FLIP fuel experience at Washington State University

International Nuclear Information System (INIS)

Lovas, Thomas A.

1977-01-01

The Washington State University TRIGA-fueled modified G.E. reactor was refueled with a partial TRIGA-FLIP core in February, 1976. The final core loading consisted of 35 FLIP and 75 Standard TRIGA fuel rods and provided a core excess reactivity of $7.98. The observed performance of the reactor did not deviate significantly from the design predictions and specifications. Pulsing tests revealed a maximum power output of 1850 MW with a fuel temperature of 449 deg. C from a $2.50 pulse. Slight power fluctuations at 1 Megawatt steady-state operation and post-pulse power oscillations were observed. (author)

Sociology at Washington University in St. Louis: History and Reflections, 1906-1989.

Science.gov (United States)

Pittman, David J.; Boden, Deirdre

1990-01-01

Traces the history of sociology at Washington University (Missouri) from 1906 to 1989 in relation to the decision to abolish the department. Maintains that this decision began in 1968. Defines the contours of the sociology department, including a discussion of prominent scholars, contending that the decision will harm the discipline in the long…

Sulfates, Clouds and Radiation Brazil (SCAR-B) University of Washington C131A Data

Data.gov (United States)

National Aeronautics and Space Administration — SCAR_B_UWC131A data are Smoke/Sulfates, Clouds and Radiation Experiment in Brazil data from instruments on board the University of Washington C131A aircraft in...

Development of the University of Washington Biofuels and Biobased Chemicals Process Laboratory

Energy Technology Data Exchange (ETDEWEB)

Gustafson, Richard [University of Washington

2014-02-04

The funding from this research grant enabled us to design and build a bioconversion steam explosion reactor and ancillary equipment such as a high pressure boiler and a fermenter to support the bioconversion process research. This equipment has been in constant use since its installation in 2012. Following are research projects that it has supported: • Investigation of novel chip production method in biofuels production • Investigation of biomass refining following steam explosion • Several studies on use of different biomass feedstocks • Investigation of biomass moisture content on pretreatment efficacy. • Development of novel instruments for biorefinery process control Having this equipment was also instrumental in the University of Washington receiving a $40 million grant from the US Department of Agriculture for biofuels development as well as several other smaller grants. The research that is being done with the equipment from this grant will facilitate the establishment of a biofuels industry in the Pacific Northwest and enable the University of Washington to launch a substantial biofuels and bio-based product research program.

The power professorship program at Washington State University

International Nuclear Information System (INIS)

Mosher, C.C.; Shamash, Y.

1993-01-01

As with most electric power programs, Washington State University's has existed since the beginning of the engineering program 100 years ago. It has grown and developed largely through the efforts of a few dedicated individuals. The Power Professorship Program has existed since 1972. The Power Professor has been Dr. Clifford C. Mosher until his recent semi-retirement. The Power Professorship was conceived of as an avenue for joint university-industry interaction. Considerable time and ingenuity by visionary engineers and others have resulted in development of a financial base for the Power Professorship Program. The program has been funded equally by public and investor-utility sectors. Following financial difficulties stemming from the Washington Public Power Supply System financial default on public utility bonds for several nuclear projects, funding for the program from the public sector was canceled. After several lean years, public-sector support was again restored by WSU's electrical engineering department offering a contract for services to the utilities in exchange for funding. This contract has been renewed annually, with costs and benefits firmly established through careful analysis and consultation. Problems facing the power industry in the early 1970s with regard to establishing a pipeline of future human resources, were almost identical with those of the present time: indifferent feelings about the industry in general, students being attracted to more glamorous disciplines, and a decline in educational opportunities available in the power area. A 1985 article in the IEEE Power Engineering Review describing today's declining enrollment in power engineering applies equally well to previous periods. A major driving force for initiating utility-industry participation in the Power Professorship Program was the concern for maintaining a source of entry-level engineers with a background in power engineering

Nuclear Physics Laboratory, University of Washington annual report

International Nuclear Information System (INIS)

1998-04-01

The Nuclear Physics Laboratory at the University of Washington in Seattle pursues a broad program of nuclear physics. These activities are conducted locally and at remote sites. The current programs include in-house research using the local tandem Van de Graaff and superconducting linac accelerators and non-accelerator research in solar neutrino physics at the Sudbury Neutrino Observatory in Canada and at SAGE in Russia, and gravitation as well as user-mode research at large accelerators and reactor facilities around the world. Summaries of the individual research projects are included. Areas of research covered are: fundamental symmetries, weak interactions and nuclear astrophysics; neutrino physics; nucleus-nucleus reactions; ultra-relativistic heavy ions; and atomic and molecular clusters

Sample preparation for accelerator mass spectrometry at the University of Washington

International Nuclear Information System (INIS)

Grootes, P.M.; Stuiver, M.; Farwell, G.W.; Schmidt, F.H.

1981-01-01

The adaptation of the University of Washington FN tandem Van de Graaff to accelerator mass spectrometry (AMS), as well as some of the results obtained, are described in another paper in this volume (Farwell et al., 1981). Here we discuss our experiences in preparing carbon and beryllium samples that give large and stable ion beams when used in our Extrion cesium sputter source with an inverted cesium beam geometry

Radiochemistry Education at Washington State University: Sustaining Academic Radiochemistry for the Nation

International Nuclear Information System (INIS)

Clark, Sue B.; Nash, Ken; Benny, Paul; Clark, Aurora; Wall, Nathalie; Wall, Don; Yoo, Choong-Shik

2009-01-01

Since 2002, Washington State University has been building radiochemistry as a component of its overall chemistry program. Using an aggressive hiring strategy and leveraged funds from the state of Washington and federal agencies, six radiochemistry faculty members have been added to give a total of seven radiochemists out of a department of twenty-five faculty members. These faculty members contribute to a diverse curriculum in radiochemistry, and the Chemistry Department now enjoys a significant increase in the number of trainees, the quantity of research expenditures, and the volume and quality of peer-reviewed scientific literature generated by the radiochemistry faculty and the trainees. These three factors are essential for sustaining the radiochemistry education and research program at any academic institution.

Safety evaluation report related to the renewal of the operating license for the Washington State University TRIGA reactor. Docket No. 50-27

International Nuclear Information System (INIS)

1982-05-01

This Safety Evaluation Report for the application filed by the Washington State University (WSU) for a renewal of operating license number R-76 to continue to operate a research reactor has been prepared by the Office of Nuclear Reactor Regulation of the US Nuclear Regulatory Commission. The facility is owned and operated by the Washington State University and is located on the WSU campus in Pullman, Whitman County, Washington. The staff concludes that the TRIGA reactor facility can continue to be operated by WSU without endangering the health and safety of the public

Total body composition measurements using in vivo neutron activation at the University of Washington

International Nuclear Information System (INIS)

Lewellen, T.L.

1986-01-01

The University of Washington Division of Nuclear Medicine has been using in vivo irradiation to study whole body calcium since 1969. Over 350 patients have been studied and currently five patients per week are being measured in support of research programs on bone wasting disease. (author)

Psychometric Properties of the Persian Version of the Padua Inventory: Washington State University Revision (PI-WSUR)

OpenAIRE

Shams, Giti; Kaviani, Hosein; Esmaili, Yaghob; Ebrahimkhani, Narges; Manesh, Alireza Amin

2011-01-01

Objective The psychometric properties and factor structure of the Persian Padua Inventory Washington State University Revision (PI-WSUR), a measure of obsessive- compulsive phenomena, was examined in a non-clinical sample of 348 Iranian university students. Method The PI-WSUR was translated into Persian, and its back translation was controlled by the author inventory. A pilot study based on cultural differences was carried out on twenty students. The study subjects consisted of 348 university...

78 FR 11673 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

Science.gov (United States)

2013-02-19

... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains and associated funerary objects, in consultation with... Anthropology. Disposition of the human remains and associated funerary objects to the Indian tribes stated...

78 FR 5201 - Notice of Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA

Science.gov (United States)

2013-01-24

... Inventory Completion: University of Washington, Department of Anthropology, Seattle, WA AGENCY: National... Anthropology, has completed an inventory of human remains, in consultation with the appropriate Indian tribes..., Department of Anthropology. Disposition of the human remains to the Indian tribes stated below may occur if...

Washington State Biofuels Industry Development

Energy Technology Data Exchange (ETDEWEB)

Gustafson, Richard [Univ. of Washington, Seattle, WA (United States)

2017-04-09

The funding from this research grant enabled us to design, renovate, and equip laboratories to support University of Washington biofuels research program. The research that is being done with the equipment from this grant will facilitate the establishment of a biofuels industry in the Pacific Northwest and enable the University of Washington to launch a substantial biofuels and bio-based product research program.

Tropospheric Aerosol Radiative Forcing Observational eXperiment - University of Washington instrumented C-131A aircraft Data Set

Data.gov (United States)

National Aeronautics and Space Administration — TARFOX_UWC131A is the Tropospheric Aerosol Radiative Forcing Observational eXperiment (TARFOX) - University of Washington instrumented C-131A aircraft data set. The...

University of Washington, Nuclear Physics Laboratory annual report, 1995

International Nuclear Information System (INIS)

1995-04-01

The Nuclear Physics Laboratory of the University of Washington supports a broad program of experimental physics research. The current program includes in-house research using the local tandem Van de Graff and superconducting linac accelerators and non-accelerator research in double beta decay and gravitation as well as user-mode research at large accelerator and reactor facilities around the world. This book is divided into the following areas: nuclear astrophysics; neutrino physics; nucleus-nucleus reactions; fundamental symmetries and weak interactions; accelerator mass spectrometry; atomic and molecular clusters; ultra-relativistic heavy ion collisions; external users; electronics, computing, and detector infrastructure; Van de Graff, superconducting booster and ion sources; nuclear physics laboratory personnel; degrees granted for 1994--1995; and list of publications from 1994--1995

76 FR 73663 - Notice of Intent To Repatriate Cultural Items: Washington State University, Museum of...

Science.gov (United States)

2011-11-29

... below by December 29, 2011. ADDRESSES: Mary Collins, Director, Washington State University, Museum of... ethnographic collection from the Conner Museum to the Museum of Anthropology. In June of 2011, the curator of collections at the Conner Museum found four unassociated funerary items in the museum storage area and...

78 FR 78379 - Notice of Inventory Completion: Museum of Anthropology at Washington State University, Pullman, WA

Science.gov (United States)

2013-12-26

....R50000] Notice of Inventory Completion: Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Museum of Anthropology at... Indian tribes or Native Hawaiian organizations, and has determined that there is a cultural affiliation...

A new era in science at Washington University, St. Louis: Viktor Hamburger's zoology department in the 1940's.

Science.gov (United States)

Carson, H L

2001-04-01

In the early 1940s, the administration of the College of Arts and Sciences at Washington University, St. Louis was firmly in the hands of classical scholars who were not inclined to promote the development of modern research on scientific subjects. Funds supporting research in biology favored the School of Medicine and the Missouri Botanical Garden. Viktor Hamburger arrived at Washington University in 1935. At about the time he became the Acting Chairman of Zoology in 1942, research work in the biological departments began a dramatic surge that has continued to this day. For 65 years under his counsel and leadership, basic biology has thrived at this fine institution. As an early faculty recruit, I recount here a few personal recollections from those formative years.

The Installation of a P.E.T. Pharmacy at Washington University

International Nuclear Information System (INIS)

Gaehle, G.; Schwarz, S.; Mueller, M.; Margenau, B.; Welch, M.J.

2003-01-01

Washington University has produced radioisotopes for medical application since the early 1960s. In order to serve seven PET scanners and to meet more stringent government regulations we have installed a new PET pharmacy based on our past years of experiences. The new pharmacy was installed at the site of the 3.7 MeV tandem cascade accelerator that was decommissioned in April of 2001. The pharmacy consists of a production lab, quality control lab, reagent preparation lab, shipping and storage area and an office. Security and safety was a main consideration in the design of this PET pharmacy

The Pediatric Cancer Genome Project

Science.gov (United States)

Downing, James R; Wilson, Richard K; Zhang, Jinghui; Mardis, Elaine R; Pui, Ching-Hon; Ding, Li; Ley, Timothy J; Evans, William E

2013-01-01

The St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project (PCGP) is participating in the international effort to identify somatic mutations that drive cancer. These cancer genome sequencing efforts will not only yield an unparalleled view of the altered signaling pathways in cancer but should also identify new targets against which novel therapeutics can be developed. Although these projects are still deep in the phase of generating primary DNA sequence data, important results are emerging and valuable community resources are being generated that should catalyze future cancer research. We describe here the rationale for conducting the PCGP, present some of the early results of this project and discuss the major lessons learned and how these will affect the application of genomic sequencing in the clinic. PMID:22641210

The pre-history of the University of Washington Astronomy Department: 1891-1965

Science.gov (United States)

Sullivan, Woodruff T.

2015-01-01

The University of Washington (UW) created its first Professor of Astronomy (within the Mathematics Department) in 1891, only two years after Washington itself became a state. Joseph Taylor bought a Warner & Swasey refractor with a 6-inch John Brashear lens, and installed it in a dome in 1895 when the university moved to a new campus outside of downtown Seattle. The small observatory became only the second building on the present campus, and is listed on the State Register of Historical Buildings. Over succeeding decades, Taylor was followed, amongst others, by Samuel Boothroyd (who after nine years left for Cornell in 1921) and for two years by Herman Zanstra (of "Zanstra method" fame). In 1928 Theodor Jacobsen joined the faculty after having obtained his Ph.D. at the University of California (Berkeley) and spending two years as a staff member at Lick Observatory. Jacobsen's research over the years focused on the spectra and motions of variable stars, especially of the Cepheid type. In the 1970s Jacobsen published a paper about secular changes in one particular Cepheid variable still using his own data extending as far back as the 1920s. For 42 years until his retirement, Jacobsen taught courses in astronomy (although there never was an astronomy major and only two graduate degrees were ever awarded), navigation, and a variety of mathematical topics. In the decade following Sputnik and the birth of NASA, UW astronomy ceased to be a one-man effort with the creation of a modern department, founding of a graduate program, and hiring of two new faculty members: George Wallerstein and Paul Hodge came from Berkeley in 1965 and are both still engaged in research 50 years later.

Nonproliferation Education at the University of Washington

International Nuclear Information System (INIS)

Jones, Chris D.; Leek, K.M.

2006-01-01

The nonproliferation curriculum at the University of Washington (UW) is the product of collaboration between Pacific Northwest Center for Global Security (PNWCGS) at the Pacific Northwest National Laboratory (PNNL) and the Jackson School of International Studies (JSIS) and Department of Political Science at the University of Washington. This collaboration began in 2001 with the establishment the Institute for Global and Regional Security Studies (IGRSS). IGRSS is housed in the Jackson School, which will celebrate its centenary in 2008 as a center for the study of world regions. PNNL also engages in a number of collaborative relationships with UW units in the natural and applied sciences. The principal goal of IGRSS has been to develop courses that draw graduates and undergraduates into careers in the field of nonproliferation. Since offering its first courses in 2002, IGRSS has assisted a substantial number of UW graduate students in submitting successful applications for nonproliferation positions in U.S. government agencies, including the Nonproliferation Graduate Program at the National Nuclear Security Administration. Since 2001, several UW undergraduates have begun careers in the field of nonproliferation, either by working at national laboratories or enrolling in non-UW graduate programs. The UW brought to its nonproliferation partnership with PNNL long-established programs in a wide range of professional programs and academic disciplines, including the 14 interdisciplinary regional and topical programs of the Jackson School of International Studies. The JSIS is an interdisciplinary and interdepartmental enterprise that brings together faculty and students from across the UW. Since the late 1940s the UW has trained experts for the nation's foreign policy community in programs focused in the languages, cultures, and histories of regions deemed critical to U.S. national security. However, since the termination of its program in nuclear engineering several

Universal and idiosyncratic characteristic lengths in bacterial genomes

Science.gov (United States)

Junier, Ivan; Frémont, Paul; Rivoire, Olivier

2018-05-01

In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10–20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures.

MRFM (Magnetic Resonance Force Microscopy) MURI ARO Final Report (Grant W911NF-05-1-0403, University of Washington)

Science.gov (United States)

2012-10-14

University of Michigan; Ann Arbor, Michigan. • Faculty: 4 – Prof. John A. Sidles Department of Orthopaedics and Sports Medicine; University of Washington...electric field in the sample [17]; over a silicon sample the dissipation was shown to be proportional to the sample’s doping level [26]. 21 filename...nm thick film of perdeuterated polystyrene was doped with the free-radical TEMPAMINE at a concentration of 40 mM. An attonewton-sensitivity

The Zoology Department at Washington University (1944-1954): from undergraduate to graduate studies with Viktor Hamburger.

Science.gov (United States)

Dunnebacke, T H

2001-04-01

Beginning from an undergraduate's perspective and continuing through graduate school, this student's experiences in the Department of Zoology at Washington University in St. Louis, Missouri was a time of many rewarding experiences. Now, on this occasion of his 100th birthday, I wish to express my appreciation to the Chairman, Dr. Viktor Hamburger, for his teachings, his encouragement, and his friendship that has lasted over the past 56 years.

Epithermal neutron beam for BNCT research at the Washington State University TRIGA research reactor

International Nuclear Information System (INIS)

Nigg, D.W.; Venhuizen, J.R.; Wheeler, F.J.; Wemple, C.A.; Tripard, G.E.; Gavin, P.R.

2000-01-01

A new epithermal-neutron beam facility for BNCT (Boron Neutron Capture Therapy) research and boronated agent screening in animal models is in the final stages of construction at Washington State University (WSU). A key distinguishing feature of the design is the incorporation of a new, high-efficiency, neutron moderating and filtering material, Fluental, developed by the Technical Research Centre of Finland. An additional key feature is the provision for adjustable filter-moderator thickness to systematically explore the radiobiological consequences of increasing the fast-neutron contamination above the nominal value associated with the baseline system. (author)

76 FR 14045 - Notice of Intent To Repatriate a Cultural Item: Museum of Anthropology at Washington State...

Science.gov (United States)

2011-03-15

...: Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park Service... Museum of Anthropology at Washington State University, Pullman, WA, that meets the definition of..., a copper pendant was given to the Museum of Anthropology at Washington State University for intended...

University of Washington Lab Report to SNEAP, 1999

International Nuclear Information System (INIS)

Amsbaugh, J.F.; Harper, G.C.; Linder, C.E.; Myers, A.W.; Storns, D.W.; Wechel, T.D. van; Will, D.I.

2000-01-01

OAK-B135 University of Washington Lab Report to SNEAP, 1999. The NPL tandem Van de Graaff accelerator chains ran 1869 hours between 9/1/98 and 8/31/99. The DEIS ran 356 hours and the SpIS ran 667. There were 28 experiment-days in which the LINAC and tandem were used together and seven days when the tandem was used, with one of the external ion sources, as a tandem. Four of these were with light ions and three with heavy ions. There were 68 days of Tandem Terminal Ion Source (TIS) development or repair, and 46 days of TIS installation or removal or changing TIS ion species. The TIS/tandem was used a total of 70 days to deliver p, d, 3 He, or 4 He beams for use by an experimenter. There were 47 experiment-days during which the injector deck was used to generate C 60 or LiF 3 clusters, which were then investigated without further acceleration. They had 25 tank openings over the year. There were three scheduled openings for the installation or removal of the TIS, and seven to change the TIS ion species. There were 10 openings for 4 He ion source and column resistor gradient development. There were four openings for various repairs other than ion source, and one to replace the LE grid, which was found undamaged after all

Interview with David Tauben: University of Washington, Chief of the Division of Pain Medicine.

Science.gov (United States)

Tauben, David

2017-07-01

Dr Tauben is Clinical Professor jointly appointed in the Departments of Medicine and Anesthesia & Pain Medicine, and is the Hughes M & Katherine G Blake Endowed Professor, board certified in both Internal Medicine and Pain Medicine. He is also University of Washington (UW) Director of Medical Student and Resident Education in Pain Medicine, and Medical Director of UW TelePain, a tele-video-conferencing program intended to provide innovative pain education and consultative support to a five-state northwest regional primary care providers. He served as a member of the NIH National Pain Strategy task force on pain education and is principal investigator for the UW's prestigious NIH Pain Consortium Center of Excellence for Pain Education, leading curriculum development to extend the pain proficiency qualifications of interprofessional primary care providers. Dr Tauben is a member of the American Pain Society and the International Association for the Study of Pain special interest study groups on Pain Education. He is a founding member of the State of Washington Agency Medical Directors panel of medical experts developing opioid prescription guidelines for the state, and a regular clinical and content expert for regulatory and legislative bodies involved in public policy regarding pain medicine practice and standards. He speaks as a clinical expert in medical management of chronic pain, especially as it applies to primary care practices. Dr Tauben served as an expert for several US Centers for Disease Control clinical outreach programs and policy reviews advising primary care providers on how to prescribe opioids for chronic noncancer pain. He is annually recognized by his peers as recipient of regional awards in care of pain patients, and brings decades of clinical experience of best practice medication management of acute and chronic pain. Dr Tauben received his bachelors degree in philosophy from Yale University, medical degree from Tufts University School of

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Department of Biological Sciences, George Washington University, 333 Lisner Hall, 2023 G St. NW, Washington, DC 20052, USA; Institute for Neuroscience, George Washington University, 636 Ross Hall, 2300 I St. NW, Washington DC 20037, USA; Department of Biology, Genome Evolution Laboratory, National University ...

Promoting academic excellence through leadership development at the University of Washington: the Teaching Scholars Program.

Science.gov (United States)

Robins, Lynne; Ambrozy, Donna; Pinsky, Linda E

2006-11-01

The University of Washington Teaching Scholars Program (TSP) was established in 1995 to prepare faculty for local and national leadership and promote academic excellence by fostering a community of educational leaders to innovate, enliven, and enrich the environment for teaching and learning at the University of Washington (UW). Faculty in the Department of Medical Education and Biomedical Informatics designed and continue to implement the program. Qualified individuals from the UW Health Sciences Professional Schools and foreign scholars who are studying at the UW are eligible to apply for acceptance into the program. To date, 109 faculty and fellows have participated in the program, the majority of whom have been physicians. The program is committed to interprofessional education and seeks to diversify its participants. The curriculum is developed collaboratively with each cohort and comprises topics central to medical education and an emergent set of topics related to the specific interests and teaching responsibilities of the participating scholars. Core sessions cover the history of health professions education, learning theories, educational research methods, assessment, curriculum development, instructional methods, professionalism, and leadership. To graduate, scholars must complete a scholarly project in curriculum development, faculty development, or educational research; demonstrate progress towards construction of a teaching portfolio; and participate regularly and actively in program sessions. The TSP has developed and nurtured an active cadre of supportive colleagues who are transforming educational practice, elevating the status of teaching, and increasing the recognition of teachers. Graduates fill key teaching and leadership positions at the UW and in national and international professional organizations.

Grassroots Engagement and the University of Washington: Evaluating Science Communication Training Created by Graduate Students for Graduate Students

Science.gov (United States)

Rohde, J. A.; Clarkson, M.; Houghton, J.; Chen, W.

2016-12-01

Science graduate students increasingly seek science communication training, yet many do not have easy access to training programs. Students often rely on a "do it yourself" approach to gaining communication skills, and student created science communication programs are increasingly found at universities and institutions across the U.S. In 2010, graduate students at the University of Washington led a grassroots effort to improve their own communication and outreach by creating "The Engage Program." With a focus on storytelling and public speaking, this graduate level course not only trains students in science communication but also gives them real world experience practicing that training at a public speaker series at Town Hall Seattle. The Engage Program was fortunate in that it was able to find institutional champions at University of Washington and secure funding to sustain the program over the long-term. However, many grassroots communication programs find it difficult to gain institutional support if there is a perceived lack of alignment with university priorities or lack of return on investment. In order to justify and incentivize institutional support for instruction in science communication, student leaders within the program initiated, designed and carried out an evaluation of their own program focused on assessing the impact of student communication, evaluating the effectiveness of the program in teaching communication skills, and quantifying the benefits of communication training to both the students and their institution. Project leaders created the opportunity for this evaluation by initiating a crowdfunding campaign, which has helped to further engage public support of science communication and incentivized student participation in the program, and may also inspire future program leaders to pursue similar program optimizations.

76 FR 28066 - Notice of Intent To Repatriate a Cultural Item: Museum of Anthropology at Washington State...

Science.gov (United States)

2011-05-13

... Cultural Item: Museum of Anthropology at Washington State University, Pullman, WA AGENCY: National Park... possession of the Museum of Anthropology at Washington State University, Pullman, WA, that meets the... notice. One lot of stone, bone, and glass beads was given to the Museum of Anthropology at Washington...

A universal genomic coordinate translator for comparative genomics.

Science.gov (United States)

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

Legume Genome Initiative at the University of Oklahoma

Energy Technology Data Exchange (ETDEWEB)

Bruce A. Roe

2004-02-27

Consolidated Appropriations Resolution, 2003 Conference Report for the Department of Energy's Biological and Environmental Research (BER) program provided $481,000 for the Legume Genome Initiative at the University of Oklahoma. These funds were used to support our research that is aimed at determining the entire sequence of the gene rich regions of the genome of the legume, Medicago truncatula, by allowing us to obtain a greater degree of finished BAC sequences from the draft sequences we have already obtained through research funded by the Noble Foundation. During the funding period we increased the number of Medicago truncatula BACs with finished (Bermuda standard) sequences from 109 to 359, and the total number of BACs for which we collected sequence data from 584 to 842, 359 of which reached phase 2 (ordered and oriented contigs). We also sequenced a series of pooled BAC clones that cover additional euchromatic (gene rich) genomic regions. This work resulted in 6 refereed publications, see below. Genes whose sequence was determined during this study included multiple members of the plant disease resistance (R-gene) family as well as several genes involved in flavinoid biosynthesis, nitrogen fixation and plant-microbial symbosis. This work also served as a prelude to obtaining NSF funding for the international collaborative effort to complete the entire sequence of the Medicago truncatula genomic euchromatic regions using a BAC based approach.

Training the teachers. The clinician-educator track of the University of Washington Pulmonary and Critical Care Medicine Fellowship Program.

Science.gov (United States)

Adamson, Rosemary; Goodman, Richard B; Kritek, Patricia; Luks, Andrew M; Tonelli, Mark R; Benditt, Joshua

2015-04-01

The University of Washington was the first pulmonary and critical care medicine fellowship training program accredited by the Accreditation Council for Graduate Medical Education to create a dedicated clinician-educator fellowship track that has its own National Residency Matching Program number. This track was created in response to increasing demand for focused training in medical education in pulmonary and critical care. Through the Veterans Health Administration we obtained a stipend for a clinician-educator fellow to dedicate 12 months to training in medical education. This takes place predominantly in the second year of fellowship and is composed of several core activities: fellows complete the University of Washington's Teaching Scholars Program, a professional development program designed to train leaders in medical education; they teach in a variety of settings and receive feedback on their work from clinician-educator faculty and the learners; and they engage in scholarly activity, which may take the form of scholarship of teaching, integration, or investigation. Fellows are guided throughout this process by a primary mentor and a mentoring committee. Since funding became available in 2009, two of the three graduates to date have successfully secured clinician-educator faculty positions. Graduates uniformly believe that the clinician-educator track met their training goals better than the research-based track would have.

Outreach at Washington State University: a case study in costs and attendance

Science.gov (United States)

Bernhardt, Elizabeth A.; Bollen, Viktor; Bersano, Thomas M.; Mossman, Sean M.

2016-09-01

Making effective and efficient use of outreach resources can be difficult for student groups in smaller rural communities. Washington State University's OSA/SPIE student chapter desires well attended yet cost-effective ways to educate and inform the public. We designed outreach activities focused on three different funding levels: low upfront cost, moderate continuing costs, and high upfront cost with low continuing costs. By featuring our activities at well attended events, such as a pre-football game event, or by advertising a headlining activity, such as a laser maze, we take advantage of large crowds to create a relaxed learning atmosphere. Moreover, participants enjoy casual learning while waiting for a main event. Choosing a particular funding level and associating with well-attended events makes outreach easier. While there are still many challenges to outreach, such as motivating volunteers or designing outreach programs, we hope overcoming two large obstacles will lead to future outreach success.

Universal features in the genome-level evolution of protein domains.

Science.gov (United States)

Cosentino Lagomarsino, Marco; Sellerio, Alessandro L; Heijning, Philip D; Bassetti, Bruno

2009-01-01

Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution.

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Science.gov (United States)

Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L.M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David

2010-01-01

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students. PMID:20194808

Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

Directory of Open Access Journals (Sweden)

Hong-Da Chen

Full Text Available BACKGROUND: Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed. METHODS/PRINCIPAL FINDINGS: Here, we show that equivalent length, or L(e, a quantity determined by the variance of fluctuating part of the distribution of the k-mer frequencies in a genome, characterizes the latter's global structure. We computed the L(es of 865 complete chromosomes and found that they have nearly universal but (k-dependent values. The differences among the L(e of a chromosome and those of its coding and non-coding parts were found to be slight. CONCLUSIONS: We verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative "point" mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (1-5 x 10(-3/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

A Partnership for Modeling the Marine Environment of Puget Sound, Washington

Science.gov (United States)

2009-03-30

Northwest National Marine Renewable Energy Center, a joint University of Washington - Oregon State project funded by the U.S. Department of Energy. e. A... Marine Renewable Energy Center (NNMREC), a joint Washington - Oregon State project to investigate extraction of wave and tidal energy sponsored by

An expanding universe of the non-coding genome in cancer biology.

Science.gov (United States)

Xue, Bin; He, Lin

2014-06-01

Neoplastic transformation is caused by accumulation of genetic and epigenetic alterations that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential and invasive growth [Hanahan,D. et al. (2011) Hallmarks of cancer: the next generation. Cell, 144, 646-674]. Although the majority of the cancer studies have focused on the functions of protein-coding genes, emerging evidence has started to reveal the importance of the vast non-coding genome, which constitutes more than 98% of the human genome. A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs, including small ncRNAs and long ncRNAs (lncRNAs), play an important role in cancer development by regulating protein-coding gene expression through diverse mechanisms. In addition to ncRNAs, nearly half of the mammalian genomes consist of transposable elements, particularly retrotransposons. Once depicted as selfish genomic parasites that propagate at the expense of host fitness, retrotransposon elements could also confer regulatory complexity to the host genomes during development and disease. Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor development. Taken together, the functional significance of non-coding genome in tumorigenesis has been previously underestimated, and diverse transcripts derived from the non-coding genome could act as integral functional components of the oncogene and tumor suppressor network. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Migration to Alma/Primo: A Case Study of Central Washington University

Directory of Open Access Journals (Sweden)

Ping Fu

2015-12-01

Full Text Available This paper describes how Central Washington University Libraries (CWUL interacted and collaborated with the Orbis Cascade Alliance (OCA Shared Integrated Library System’s (SILS Implementation Team and Ex Libris to process systems and data migration from Innovative Interfaces Inc.’s Millennium integrated library system to Alma/Primo, Ex Libris’ next-generation library management solution and discovery and delivery solution. A chronological review method was used for this case study to provide an overall picture of key migration events, tasks, and implementation efforts, including pre-migration cleanup, migration forms, integration with external systems, testing, cutover, post-migration cleanup, and reporting and fixing outstanding issues. A three-phase migration model was studied, and a questionnaire was designed to collect data from functional leads to determine staff time spent on the migration tasks. Staff time spent on each phase was analyzed and quantitated, with some top essential elements for the success of the migration identified through the case review and data analysis. An analysis of the Ex Libris’ Salesforce cases created during the migration and post-migration was conducted to be used for identifying roles of key librarians and staff functional leads during the migration.

78 FR 2429 - Notice of Inventory Completion: The Museum of Anthropology at Washington State University...

Science.gov (United States)

2013-01-11

... construction. Archaeologists working for the Washington Archaeological Research Center at Washington State... Reservation. Historical, ethnographic, linguistic, and archaeological information links the site to the...

Program in Functional Genomics of Autoimmunity and Immunology of yhe University of Kentucky and the University of Alabama

Energy Technology Data Exchange (ETDEWEB)

Alan M Kaplan

2012-10-12

This grant will be used to augment the equipment infrastructure and core support at the University of Kentucky and the University of Alabama particularly in the areas of genomics/informatics, molecular analysis and cell separation. In addition, we will promote collaborative research interactions through scientific workshops and exchange of scientists, as well as joint exploration of the role of immune receptors as targets in autoimmunity and host defense, innate and adaptive immune responses, and mucosal immunity in host defense.

Program and curriculum development in radiochemistry at Washington State University to educate the next generation of radiochemists in the US

International Nuclear Information System (INIS)

Clark, S.B.; Nash, K.; Benny, P.; Elliston, J.; Buckely, P.

2005-01-01

Washington State University (WSU) has -been the recipient of grant funds from the U.S. Department of Energy's Office of Nuclear Science and Technology to enhance its curriculum and service activities in radiochemistry. These funds have been used to hire new faculty, redesign undergraduate and graduate courses in radiochemistry, and initiate summer programs in radiochemistry for regional college faculty and high school teachers. The funds received from the federal government were matched by investments from the state of Washington. These investments have resulted in many positive changes in the Chemistry Department and the Nuclear Radiation Center at WSU. The number of students graduating from our radiochemistry programs has increased markedly, and the level of additional extra mural funding for our programs has also increased. These activities will be described, and feedback from employers of our radiochemistry graduates will be provided. Plans for future radiochemistry program development will also be discussed.

Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases.

Science.gov (United States)

Huang, Erwen; Liu, Changhui; Zheng, Jingjing; Han, Xiaolong; Du, Weian; Huang, Yuanjian; Li, Chengshi; Wang, Xiaoguang; Tong, Dayue; Ou, Xueling; Sun, Hongyu; Zeng, Zhaoshu; Liu, Chao

2018-04-03

Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population. For 116 of the 117 SNPs, cumulative match probability (CMP) ranged from 2.01 × 10-48 to 1.93 × 10-50 and cumulative exclusion probability (CEP) ranged from 0.9999999996653 to 0.9999999999945. In 134 tested Han samples, 110 of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with CMP = 4.70 × 10-47 and CEP = 0.999999999862. By analyzing the same number of autosomal SNPs as in the HID-Ion AmpliSeq Identity Panel, i.e. 90 randomized out of the 110 SNPs, our panel yielded preferable CMP and CEP. Taken together, the 110-SNPs panel is advantageous for forensic test, and this study provided plenty of highly informative SNPs for compiling final universal panels.

76 FR 58031 - Notice of Intent To Repatriate Cultural Items: Thomas Burke Memorial Washington State Museum...

Science.gov (United States)

2011-09-19

... DEPARTMENT OF THE INTERIOR National Park Service [2253-665] Notice of Intent To Repatriate Cultural Items: Thomas Burke Memorial Washington State Museum, University of Washington, Seattle, WA AGENCY: National Park Service, Interior. ACTION: Notice. SUMMARY: The Thomas Burke Memorial Washington State Museum...

Overcoming institutional challenges through continuous professionalism improvement: the University of Washington experience.

Science.gov (United States)

Fryer-Edwards, Kelly; Van Eaton, Erik; Goldstein, Erika A; Kimball, Harry R; Veith, Richard C; Pellegrini, Carlos A; Ramsey, Paul G

2007-11-01

The University of Washington (UW) School of Medicine is in the midst of an emerging ecology of professionalism. This initiative builds on prior work focusing on professionalism at the student level and moves toward the complete integration of a culture of professionalism within the UW medical community of including staff, faculty, residents, and students. The platform for initiating professionalism as institutional culture is the Committee on Continuous Professionalism Improvement, established in November 2006. This article reviews three approaches to organizational development used within and outside medicine and highlights features that are useful for enhancing an institutional culture of professionalism: organizational culture, safety culture, and appreciative inquiry. UW Medicine has defined professional development as a continuous process, built on concrete expectations, using mechanisms to facilitate learning from missteps and highlighting strengths. To this end, the school of medicine is working toward improvements in feedback, evaluation, and reward structures at all levels (student, resident, faculty, and staff) as well as creating opportunities for community dialogues on professionalism issues within the institution. Throughout all the Continuous Professionalism Improvement activities, a two-pronged approach to cultivating a culture of professionalism is taken: celebration of excellence and attention to accountability.

Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

OpenAIRE

Aljanabi, S M; Martinez, I

1997-01-01

A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even i...

Toward a Modern Science of Obesity at Washington University: How We Do It and What is the Payoff?

Science.gov (United States)

Colditz, Graham A; Gehlert, Sarah; Bowen, Deborah J; Carson, Kenneth; Hovmand, Peter S; Lee, Jung Ae; Moley, Kelle H

2016-07-01

In our Cancer Prevention Program at Washington University in Saint Louis (WUSTL), we have made extraordinary efforts to create the kind of cancer prevention and control program that is both translational and transdisciplinary in nature, to accelerate the march from basic discoveries to population change. Here we present an overview of our obesity-related research currently ongoing in our Center, paying particular attention to both the translational- transdisciplinary process and to community-based participatory research. We end with our future directions for improving obesity-related cancer outcomes research. Cancer Prev Res; 9(7); 503-8. ©2016 AACR. ©2016 American Association for Cancer Research.

Comprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositories.

Science.gov (United States)

McDonald, Sandra A; Mardis, Elaine R; Ota, David; Watson, Mark A; Pfeifer, John D; Green, Jonathan M

2012-07-01

As part of the molecular revolution sweeping medicine, comprehensive genomic studies are adding powerful dimensions to medical research. However, their power exposes new regulatory, strategic, and quality assurance challenges for biorepositories. A key issue is that unlike other research techniques commonly applied to banked specimens, nucleic acid sequencing, if sufficiently extensive, yields data that could identify a patient. This evolving paradigm renders the concepts of anonymized and anonymous specimens increasingly outdated. The challenges for biorepositories in this new era include refined consent processes and wording, selection and use of legacy specimens, quality assurance procedures, institutional documentation, data sharing, and interaction with institutional review boards. Given current trends, biorepositories should consider these issues now, even if they are not currently experiencing sample requests for genomic analysis. We summarize our current experiences and best practices at Washington University Medical School, St Louis, MO, our perceptions of emerging trends, and recommendations.

From the Bench to the Clinic Part 1: Martin McIntosh, Ph.D., Introduces His Lab's Immunotherapy Research | Office of Cancer Genomics

Science.gov (United States)

The field of immunotherapy is rapidly advancing and genomics techniques are being incorporated to add a “precision” approach. OCG spoke with two CTD2 investigators from the Fred Hutchinson Cancer Research Center (FHCRC) about new advances in immunotherapy. For the first article of this two-part series, we interviewed Martin McIntosh, Ph.D., member of the Fred Hutchinson Translational Research program and previously Program Head in Computational Biology at FHCRC/University of Washington Comprehensive Cancer Center.

Climate Change Education at the University of Washington: Bridging Academic Degrees, Departments and Disciplines

Science.gov (United States)

Thompson, L.; Bertram, M. A.

2012-12-01

Education on climate change occurs in many departments at large research universities, but providing a coordinated educational experience for students in this topic is challenging. Departmental boundaries, accounting for student credit hours, and curricula inertia create roadblocks to the creation of interdisciplinary curriculum for both graduate and undergraduate students. We describe a hierarchy of interdisciplinary programs that reach students from seniors in high school to graduate students, targeting students from a variety of disciplines. The UWHS (University of Washington in the High School) program allows high school teachers to be trained to teach UW courses to their own high school students at their own school. The students who enroll receive a UW grade and credit for the course (as well as high school credit). A UWHS course on Climate and Climate Change (Atmospheric Sciences 211) was created in 2011 supported by training to high school science teachers on the fundamentals of climate science. For the 2012-13 academic year we anticipate at least 5 schools in Washington State will be offering this course. Once students matriculate at UW, 211 serves as a prerequisite for the Climate Minor that began in 2011. The minor is hosted by the departments of Atmospheric Sciences, Earth and Space Sciences and Oceanography, offering instruction in three focus areas: climate chemistry and biology, the physical climate, and past climate and ice. Students also take an integrative seminar where they are required to communicate to both scientific and non-scientific audiences some topic in climate science. Students enrolled in graduate programs at UW can participate in the Graduate Certificate in Climate Science that began 2008. The certificate gives students instruction in climate science covering the same topic areas as the minor and with a capstone project where student communicate some aspect of climate science to a non-physical science audience. Projects have included

Going from Microbial Ecology to Genome Data and Back: Studies on a Haloalkaliphilic Bacterium Isolated from Soap Lake, Washington State

Directory of Open Access Journals (Sweden)

Melanie R. Mormile

2014-11-01

Full Text Available Soap Lake is a meromictic, alkaline (~pH 9.8 and saline (~14 to 140 g liter-1 lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years and the extremely high sulfide level (~140 mM in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. H. hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment.

[Overview of patents on targeted genome editing technologies and their implications for innovation and entrepreneurship education in universities].

Science.gov (United States)

Fan, Xiang-yu; Lin, Yan-ping; Liao, Guo-jian; Xie, Jian-ping

2015-12-01

Zinc finger nuclease, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats/Cas9 nuclease are important targeted genome editing technologies. They have great significance in scientific research and applications on aspects of functional genomics research, species improvement, disease prevention and gene therapy. There are past or ongoing disputes over ownership of the intellectual property behind every technology. In this review, we summarize the patents on these three targeted genome editing technologies in order to provide some reference for developing genome editing technologies with self-owned intellectual property rights and some implications for current innovation and entrepreneurship education in universities.

78 FR 26249 - Drawbridge Operation Regulation; Lake Washington Ship Canal, Seattle, WA

Science.gov (United States)

2013-05-06

...The Coast Guard has issued a temporary deviation from the operating schedule that governs the Montlake Bridge across the Lake Washington Ship Canal, mile 5.2, at Seattle, WA, and the University Bridge across the Lake Washington Ship Canal, mile 4.3, at Seattle, WA. This deviation is necessary to accommodate the ``Beat the Bridge'' foot race. This deviation allows the bridges to remain in the closed position to allow safe movement of event participants.

Annual report of the Nuclear Physics Laboratory, University of Washington

International Nuclear Information System (INIS)

Snover, K.; Fulton, B.

1996-04-01

The Nuclear Physics Laboratory of the University of Washington has for over 40 years supported a broad program of experimental physics research. Some highlights of the research activities during the past year are given. Work continues at a rapid pace toward completion of the Sudbury Neutrino Observatory in January 1997. Following four years of planning and development, installation of the acrylic vessel began last July and is now 50% complete, with final completion scheduled for September. The Russian-American Gallium Experiment (SAGE) has completed a successful 51 Cr neutrino source experiment. The first data from 8 B decay have been taken in the Mass-8 CVC/Second Class Current study. The analysis of the measured barrier distributions for Ca-induced fission of prolate 192 Os and oblate 194 Pt has been completed. In a collaboration with a group from the Bhabha Atomic Research Centre they have shown that fission anisotropies at energies well above the barrier are not influenced by the mass asymmetry of the entrance channel relative to the Businaro-Gallone critical asymmetry. They also have preliminary evidence at higher bombarding energy that noncompound nucleus fission scales with the mean square angular momentum, in contrast to previous suggestions. The authors have measured proton and alpha particle emission spectra from the decay of A ∼ 200 compound nuclei at excitation energies of 50--100 MeV, and used these measurements to infer the nuclear temperature. The investigations of multiparticle Bose-Einstein interferometry have led to a new algorithm for putting Bose-Einstein and Coulomb correlations of up to 6th order into Monte Carlo simulations of ultra-relativistic collision events, and to a new fast algorithm for extracting event temperatures

The Impact of NSF-funded Physics Education Research at the University of Washington

Science.gov (United States)

Heron, Paula

2015-03-01

It is now well known that many students who complete introductory physics courses are unable to apply fundamental concepts in situations that involve qualitative reasoning. Systematic investigations have helped researchers understand why so many students fail to develop robust and coherent conceptual frameworks, and have led to the development of new teaching practices and materials that are far more effective than conventional ones. The Physics Education Group at the University of Washington has played a leading role in raising awareness of the need to improve instruction, and in supporting physics faculty in their efforts to do so. With support from the National Science Foundation, the group has helped build a research base that instructors can draw on, and has produced practical, flexible instructional materials that promote deeper learning in physics classrooms. Both ``Tutorials in Introductory Physics'' (Pearson, 2002) and ``Physics by Inquiry'' (Wiley, 1996) have been developed in an iterative process in which ongoing assessment of student learning plays an integral role. These materials have had a widespread and significant impact on physics teaching and on student learning from kindergarten through graduate school. In this talk I will describe the role of research in curriculum development, and speculate on the next generation of tools and resources to support physics teaching and learning.

Origins of the Human Genome Project.

Science.gov (United States)

Watson, J D; Cook-Deegan, R M

1991-01-01

Caenorhabditis elegans by a collaboration between Washington University and the Medical Research Council laboratory in Cambridge, U.K. This project is now turning to sequencing C. elegans DNA as a logical extension of this work. These are but the first fruits of the genome project. There is much more to come.

Structural genomics of infectious disease drug targets: the SSGCID

International Nuclear Information System (INIS)

Stacy, Robin; Begley, Darren W.; Phan, Isabelle; Staker, Bart L.; Van Voorhis, Wesley C.; Varani, Gabriele; Buchko, Garry W.; Stewart, Lance J.; Myler, Peter J.

2011-01-01

An introduction and overview of the focus, goals and overall mission of the Seattle Structural Genomics Center for Infectious Disease (SSGCID) is given. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium of researchers at Seattle BioMed, Emerald BioStructures, the University of Washington and Pacific Northwest National Laboratory that was established to apply structural genomics approaches to drug targets from infectious disease organisms. The SSGCID is currently funded over a five-year period by the National Institute of Allergy and Infectious Diseases (NIAID) to determine the three-dimensional structures of 400 proteins from a variety of Category A, B and C pathogens. Target selection engages the infectious disease research and drug-therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. The protein-expression systems, purified proteins, ligand screens and three-dimensional structures produced by SSGCID constitute a valuable resource for drug-discovery research, all of which is made freely available to the greater scientific community. This issue of Acta Crystallographica Section F, entirely devoted to the work of the SSGCID, covers the details of the high-throughput pipeline and presents a series of structures from a broad array of pathogenic organisms. Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented

Universal internucleotide statistics in full genomes: a footprint of the DNA structure and packaging?

Directory of Open Access Journals (Sweden)

Mikhail I Bogachev

Full Text Available Uncovering the fundamental laws that govern the complex DNA structural organization remains challenging and is largely based upon reconstructions from the primary nucleotide sequences. Here we investigate the distributions of the internucleotide intervals and their persistence properties in complete genomes of various organisms from Archaea and Bacteria to H. Sapiens aiming to reveal the manifestation of the universal DNA architecture. We find that in all considered organisms the internucleotide interval distributions exhibit the same [Formula: see text]-exponential form. While in prokaryotes a single [Formula: see text]-exponential function makes the best fit, in eukaryotes the PDF contains additionally a second [Formula: see text]-exponential, which in the human genome makes a perfect approximation over nearly 10 decades. We suggest that this functional form is a footprint of the heterogeneous DNA structure, where the first [Formula: see text]-exponential reflects the universal helical pitch that appears both in pro- and eukaryotic DNA, while the second [Formula: see text]-exponential is a specific marker of the large-scale eukaryotic DNA organization.

Working Together: Wellness and Academic Achievement at Tribal Colleges and Universities

Science.gov (United States)

Duran, Bonnie; Magarati, Maya; Parker, Myra; Egashira, Leo; Kipp, Billie Jo

2013-01-01

This article describes the activities of the Indigenous Wellness Research Institute (IWRI) at the University of Washington, Washington State, in collaborating with tribal colleges and universities (TCUs) to examine alcohol, drug, and mental health issues among Native students. The authors provide first steps for the development of culturally…

Are there laws of genome evolution?

Directory of Open Access Journals (Sweden)

Eugene V Koonin

2011-08-01

Full Text Available Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

Researcher Interview: Elaine Mardis

Science.gov (United States)

Elaine Mardis Ph.D., Professor of Medicine at Washington University School of Medicine, discusses her translational research applying genomics techniques to clinical trials, and forecasts the future of team science and cancer genomics.

Structures of the major capsid proteins of the human Karolinska Institutet and Washington University polyomaviruses.

Science.gov (United States)

Neu, Ursula; Wang, Jianbo; Macejak, Dennis; Garcea, Robert L; Stehle, Thilo

2011-07-01

The Karolinska Institutet and Washington University polyomaviruses (KIPyV and WUPyV, respectively) are recently discovered human viruses that infect the respiratory tract. Although they have not yet been linked to disease, they are prevalent in populations worldwide, with initial infection occurring in early childhood. Polyomavirus capsids consist of 72 pentamers of the major capsid protein viral protein 1 (VP1), which determines antigenicity and receptor specificity. The WUPyV and KIPyV VP1 proteins are distant in evolution from VP1 proteins of known structure such as simian virus 40 or murine polyomavirus. We present here the crystal structures of unassembled recombinant WUPyV and KIPyV VP1 pentamers at resolutions of 2.9 and 2.55 Å, respectively. The WUPyV and KIPyV VP1 core structures fold into the same β-sandwich that is a hallmark of all polyomavirus VP1 proteins crystallized to date. However, differences in sequence translate into profoundly different surface loop structures in KIPyV and WUPyV VP1 proteins. Such loop structures have not been observed for other polyomaviruses, and they provide initial clues about the possible interactions of these viruses with cell surface receptors.

University of Washington's radioecological studies in the Marshall Islands, 1946-1977.

Science.gov (United States)

Donaldson, L R; Seymour, A H; Nevissi, A E

1997-07-01

Since 1946, personnel from the School of Fisheries, University of Washington (Applied Fisheries Laboratory, 1943-1958; Laboratory of Radiation Biology, 1958-1967; and Laboratory of Radiation Ecology, since 1967), have studied the effects of nuclear detonations and the ensuing radioactivity on the marine and terrestrial environments throughout the Central Pacific. A collection of reports and publications about these activities plus a collection of several thousand samples from these periods are kept at the School of Fisheries. General findings from the surveys show that (1) fission products were prevalent in organisms of the terrestrial environment whereas activation products were prevalent in marine organisms; (2) the best biological indicators of fallout radionuclides by environments were (a) terrestrial-coconuts, land crabs; (b) reef-algae, invertebrates; and (c) marine-plankton, fish. Studies of plutonium and americium in Bikini Atoll showed that during 1971-1977 the highest concentrations of 241Am, 2.85 Bq g(-1) (77 pCi g(-1)) and 239,240Pu, 4.44 Bq g(-1) (120 pCi g(-1)), in surface sediments were found in the northwest part of the lagoon. The concentrations in the bomb craters were substantially lower than these values. Concentrations of soluble and particulate plutonium and americium in surface and deep water samples showed distributions similar to the sediment samples. That is, the highest concentration of these radionuclides in the water column were at locations with highest sediment concentration. Continuous circulation of water in the lagoon and exchange of water with open ocean resulted in removal of 111 G Bq y(-1) (3 Ci y(-1)) 241Am and 222 G Bq y(-1) (6 Ci y(-1)) 239,240Pu into the North Equatorial Current. A summary of the surveys, findings, and the historical role of the Laboratory in radioecological studies of the Marshall Islands are presented.

78 FR 15053 - Simpson Lumber Company, LLC, Shelton, Washington; Simpson Lumber Company, LLC, Tacoma, Washington...

Science.gov (United States)

2013-03-08

...,372B] Simpson Lumber Company, LLC, Shelton, Washington; Simpson Lumber Company, LLC, Tacoma, Washington; Simpson Lumber Company, LLC, Longview, Washington; Notice of Revised Determination on Reconsideration On... Reconsideration for the workers and former workers of Simpson Lumber Company, LLC, Shelton, Washington (TA-W-81...

Universal Internucleotide Statistics in Full Genomes: A Footprint of the DNA Structure and Packaging?

OpenAIRE

Bogachev, Mikhail I.; Kayumov, Airat R.; Bunde, Armin

2014-01-01

Uncovering the fundamental laws that govern the complex DNA structural organization remains challenging and is largely based upon reconstructions from the primary nucleotide sequences. Here we investigate the distributions of the internucleotide intervals and their persistence properties in complete genomes of various organisms from Archaea and Bacteria to H. Sapiens aiming to reveal the manifestation of the universal DNA architecture. We find that in all considered organisms the internucleot...

Climate change vulnerability and adaptation in the North Cascades region, Washington

Science.gov (United States)

Crystal L. Raymond; David L. Peterson; Regina M. Rochefort

2014-01-01

The North Cascadia Adaptation Partnership (NCAP) is a science-management partnership consisting of the U.S. Department of Agriculture Forest Service Mount Baker-Snoqualmie and Okanogan-Wenatchee National Forests and Pacific Northwest Research Station; North Cascades National Park Complex; Mount Rainier National Park; and University of Washington Climate Impacts Group....

78 FR 59955 - Notice of Inventory Completion: Thomas Burke Memorial Washington State Museum, University of...

Science.gov (United States)

2013-09-30

... responsibilities under NAGPRA, 25 U.S.C. 3003(d)(3). The determinations in this notice are the sole responsibility... Reservation, Washington) that this notice has been published. Dated: August 20, 2013. Sherry Hutt, Manager...

Physical data collected from Seaglider SG005 during Washington Coast June 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-06-24 to 2004-07-28 (NCEI Accession 0155971)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG005 during Washington Coast, September 2002 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2002-09-11 to 2002-11-03 (NCEI Accession 0155983)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG005 during Washington Coast August 2003 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2003-08-21 to 2004-01-20 (NCEI Accession 0155930)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG012 during Washington Coast, December 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-12-23 to 2005-01-25 (NCEI Accession 0156003)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG005 during Washington Coast, February 2003 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2003-02-08 to 2003-02-12 (NCEI Accession 0155963)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG002 during Washington Coast, December 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-12-23 to 2004-12-30 (NCEI Accession 0155944)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG002 during Washington Coast, January 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-01-20 to 2004-06-24 (NCEI Accession 0155959)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG030 during Washington Coast 8 November 2006 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2006-11-09 to 2006-12-17 (NCEI Accession 0156188)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG005 during Washington Coast, 8 November 2006 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2006-11-09 to 2007-03-15 (NCEI Accession 0155980)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG005 during Washington Coast, 10 September 2007 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2007-09-10 to 2008-01-17 (NCEI Accession 0155995)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG014 during Washington Coast, 15 March 2007 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2007-03-15 to 2007-09-10 (NCEI Accession 0156140)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Exploratory Factor Analysis of NRG Oncology's University of Washington Quality of Life Questionnaire – RTOG Modification

Science.gov (United States)

Pugh, Stephanie L.; Wyatt, Gwen; Wong, Raimond K. W.; Sagar, Stephen M.; Yueh, Bevan; Singh, Anurag K.; Yao, Min; Nguyen-Tan, Phuc Felix; Yom, Sue S.; Cardinale, Francis S.; Sultanem, Khalil; Hodson, D. Ian; Krempl, Greg A.; Chavez, Ariel; Yeh, Alexander M.; Bruner, Deborah W.

2016-01-01

Context The 15-item University of Washington Quality of Life questionnaire – Radiation Therapy Oncology Group (RTOG) modification (UW-QOL-RTOG modification) has been used in several trials of head and neck cancer conducted by NRG Oncology such as RTOG 9709, RTOG 9901, RTOG 0244, and RTOG 0537. Objectives This study is an exploratory factor analysis (EFA) to establish validity and reliability of the instrument subscales. Methods EFA on the UW-QOL - RTOG modification was conducted using baseline data from NRG Oncology's RTOG 0537, a trial of acupuncture-like transcutaneous electrical nerve stimulation in treating radiation-induced xerostomia. Cronbach's α coefficient was calculated to measure reliability; correlation with the University of Michigan Xerostomia Related Quality of Life Scale (XeQOLS) was used to evaluate concurrent validity; and correlations between consecutive time points were used to assess test-retest reliability. Results The 15-item EFA of the modified tool resulted in 11 items split into 4 factors: mucus, eating, pain, and activities. Cronbach's α ranged from 0.71 to 0.93 for the factors and total score, consisting of all 11 items. There were strong correlations (ρ≥0.60) between consecutive time points and between total score and the XeQOLS total score (ρ>0.65). Conclusion The UW-QOL-RTOG modification is a valid tool that can be used to assess symptom burden of head and neck cancer patients receiving radiation therapy or those who have recently completed radiation. The modified tool has acceptable reliability, concurrent validity, and test-retest reliability in this patient population, as well as the advantage of having being shortened from 15 to 11 items. PMID:27899312

12 CFR 4.4 - Washington office.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Washington office. 4.4 Section 4.4 Banks and... EXAMINERS Organization and Functions § 4.4 Washington office. The Washington office of the OCC is the main office and headquarters of the OCC. The Washington office directs OCC policy, oversees OCC operations...

Historical changes to Lake Washington and route of the Lake Washington Ship Canal, King County, Washington

Science.gov (United States)

Chrzastowski, Michael J.

1983-01-01

Lake Washington, in the midst of the greater Seattle metropolitan area of the Puget Sound region (fig. 1), is an exceptional commercial, recreational, and esthetic resource for the region . In the past 130 years, Lake Washington has been changed from a " wild " lake in a wilderness setting to a regulated lake surrounded by a growing metropolis--a transformation that provides an unusual opportunity to study changes to a lake's shoreline and hydrologic characteristics -resulting from urbanization.

Promoting fundamental clinical skills: a competency-based college approach at the University of Washington.

Science.gov (United States)

Goldstein, Erika A; Maclaren, Carol F; Smith, Sherilyn; Mengert, Terry J; Maestas, Ramoncita R; Foy, Hugh M; Wenrich, Marjorie D; Ramsey, Paul G

2005-05-01

The focus on fundamental clinical skills in undergraduate medical education has declined over the last several decades. Dramatic growth in the number of faculty involved in teaching and increasing clinical and research commitments have contributed to depersonalization and declining individual attention to students. In contrast to the close teaching and mentoring relationship between faculty and students 50 years ago, today's medical students may interact with hundreds of faculty members without the benefit of a focused program of teaching and evaluating clinical skills to form the core of their four-year curriculum. Bedside teaching has also declined, which may negatively affect clinical skills development. In response to these and other concerns, the University of Washington School of Medicine has created an integrated developmental curriculum that emphasizes bedside teaching and role modeling, focuses on enhancing fundamental clinical skills and professionalism, and implements these goals via a new administrative structure, the College system, which consists of a core of clinical teachers who spend substantial time teaching and mentoring medical students. Each medical student is assigned a faculty mentor within a College for the duration of his or her medical school career. Mentors continuously teach and reflect with students on clinical skills development and professionalism and, during the second year, work intensively with them at the bedside. They also provide an ongoing personal faculty contact. Competency domains and benchmarks define skill areas in which deepening, progressive attention is focused throughout medical school. This educational model places primary focus on the student.

Physical data collected from Seaglider SG012 during Washington Coast, launched 07 February 2005 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2005-02-07 to 2005-06-08 (NCEI Accession 0156075)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Work-based learning experiences help students with disabilities transition to careers: a case study of University of Washington projects.

Science.gov (United States)

Bellman, Scott; Burgstahler, Sheryl; Ladner, Richard

2014-01-01

This case study describes evidence-based practices employed by a collection of University of Washington projects that engage high school and postsecondary students with disabilities in work-based learning experiences such as industry and research internships, career development activities, job shadows, field trips, and mock interviews. The purpose of the article is two-fold. First, authors share best practices with others who wish to increase the participation of students with disabilities in work-based learning and thereby contribute to their academic and career success. The article discusses methods used to recruit students, employers and mentors, match students with specific opportunities, and prepare students for success. Second, authors share outcomes from studies regarding participation in these work-based learning opportunities, which include increased employment success, motivation to work toward a career, knowledge about careers and the workplace, job-related skills, ability to work with supervisors and coworkers, skills in self-advocating for accommodations, and perceived career options.

Death with dignity in Washington patients with amyotrophic lateral sclerosis.

Science.gov (United States)

Wang, Leo H; Elliott, Michael A; Jung Henson, Lily; Gerena-Maldonado, Elba; Strom, Susan; Downing, Sharon; Vetrovs, Jennifer; Kayihan, Paige; Paul, Piper; Kennedy, Kate; Benditt, Joshua O; Weiss, Michael D

2016-11-15

To describe the amyotrophic lateral sclerosis (ALS) patients who sought medication under the Washington State Death with Dignity (DWD) Act since its inception in 2009. Chart review at 3 tertiary medical centers in the Seattle/Puget Sound region and comparison to publicly available data of ALS and all-cause DWD cohorts from Washington and Oregon. In Washington State, 39 patients with ALS requested DWD from the University of Washington, Virginia Mason, and Swedish Medical Centers beginning in 2009. The median age at death was 65 years (range 46-86). Seventy-seven percent of the patients used the prescriptions. All of the patients who used the medications passed away without complications. The major reasons for patients to request DWD as reported by participating physicians were loss of autonomy and dignity and decrease in enjoyable activities. Inadequate pain control, financial cost, and loss of bodily control were less commonly indicated. These findings were similar to those of the 92 patients who sought DWD in Oregon. In Washington and Oregon, the percentage of patients with ALS seeking DWD is higher compared to the cancer DWD cohort. Furthermore, compared to the all-cause DWD cohort, patients with ALS are more likely to be non-Hispanic white, married, educated, enrolled in hospice, and to have died at home. Although a small number, ALS represents the disease with the highest proportion of patients seeking to participate in DWD. Patients with ALS who choose DWD are well-educated and have access to palliative or life-prolonging care. The use of the medications appears to be able to achieve the patients' goals without complications. © 2016 American Academy of Neurology.

Structural genomics: keeping up with expanding knowledge of the protein universe

Science.gov (United States)

Grabowski, Marek; Joachimiak, Andrzej; Otwinowski, Zbyszek; Minor, Wladek

2010-01-01

Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space — a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a reassessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006. PMID:17587562

Structural genomics: keeping up with expanding knowledge of the protein universe.

Science.gov (United States)

Grabowski, Marek; Joachimiak, Andrzej; Otwinowski, Zbyszek; Minor, Wladek

2007-06-01

Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space--a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a re-assessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006.

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.

Development and design of a computer-assisted information management system for radiation safety management at the University of Washington

International Nuclear Information System (INIS)

Riches, C.G.; Riordan, F.J.; Robb, D.; Grieb, C.; Pence, G.; O'Brien, M.J.

1984-01-01

The Radiation Safety Office (RSO) at the University of Washington (UW) found that it needed a computerized information system to help manage the campus radiation safety program and to help provide the records necessary to show compliance with regulations and license requirements. The John L. Locke Computer Center at the UW had just developed the GLAMOR system to aid information entry and query for their computer when the RSO turned to them for assistance. The module that was developed provided a mechanism for controlling and monitoring radioactive materials on campus. This became one part of a multi-faceted system that registers users, employees, sealed sources and radiation-producing machines. The system is designed to be interactive, for immediate information recall, and powerful enough to provide routine and special reports on compliance status. The RSO information system is designed to be flexible and can easily incorporate additional features. Some future features include an interactive SNM control program, an interface to the information system currently being developed for the occupational safety and health program and an interface to the database provided by the commercial film badge service used by the University. Development of this program lead the RSO to appreciate the usefulness of having health physics professionals on the staff who were also knowledgeable about computers and who could develop programs and reports necessary to their activities

Better Jobs, Brighter Futures, a Stronger Washington. Washington's Community and Technical Colleges

Science.gov (United States)

Washington State Board for Community and Technical Colleges, 2015

2015-01-01

The world is changing rapidly. With changes in technology, demographics, and workforce trends, Washington needs colleges to not only keep pace, but lead the way. Washington's 34 community and technical colleges answer that call. The community and technical colleges have proven uniquely positioned to adapt to, embrace, and ignite change. Community…

Oil spill response issues in Washington State

International Nuclear Information System (INIS)

Lempriere, P.R.

1997-01-01

Washington State statutes and regulations applicable to oil transport and oil spills were described. Specific provisions of the statutes and regulations and other relevant matters were also discussed. Among these were: (1) Washington State oil spill prevention plans, (2) Washington State oil spill contingency plans, (3) best achievable protection, (4) Intertanko's lawsuit against Washington State, (5) oil spill removal organizations, (6) certificates of financial responsibility in Washington State, (7) extent of potential liability under Washington Law, (8) disposal of cleanup materials, and (9) definition of 'qualified individuals' on marine vessels having the authority to implement removal actions

Experiential Learning for Native American Students at Tribal Colleges and Universities

Science.gov (United States)

Sauve, M. L.; Moore, K.

2003-12-01

In reaffirming its commitment to Indian tribes and Alaska Native entities, the Federal Government issued Executive Order 13270 of July 3, 2002, stating the policy that " this Nation's commitment to education excellence and opportunity must extend as well to the tribal colleges and universities." Further, the Federal Government has called on the private sector to contribute to these colleges' educational and cultural mission. American University, through its American Indian Internship Program, has responded to this call. American University, a private liberal arts institution of higher education in the Nation's capital, has long ago recognized the importance of experiential learning in undergraduate education. For over 50 years, its Washington Semester Program brings students from other universities around the country and the world to American University's campus and to Washington, D.C. for a unique academic experience. The Washington Semester Program combines academic seminars in various fields of concentration with internship work in government agencies, congressional offices, non-profit organizations, foundations and research institutions in the Nation's capital. Students in this Program get to meet the Nation's leaders, experts in the field, and notable newsmakers while incorporating their academic skills and courses in practice at their internship assignments. The American Indian Internship Program (also knows as Washington Internship for Native Students-WINS) is one of the programs in Washington Semester. This program is designed to give American Indian students the chance to study issues of interest to the Native community and to gain valuable work experience through an internship in the Nation's capital. All costs to attend the program are paid by the internship sponsors and American University, including transportation between the students' home and Washington, DC, tuition and program fees for 6 credit hours in the summer and 12 credit hours in fall

Genomic Data Commons launches

Science.gov (United States)

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

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

Science.gov (United States)

Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

/jgen/088/01/0001-0007. Keywords. Down syndrome; trisomy 21; meiosis; Penrose; parental age; nondisjunction; human genetics. Author Affiliations. Santhosh Girirajan1. Department of Genome Sciences, University of Washington, Seattle, ...

77 FR 25590 - Drawbridge Operation Regulation; Lake Washington Ship Canal, Seattle, WA

Science.gov (United States)

2012-05-01

...The Coast Guard has issued a temporary deviation from the operating schedule that governs University Bridge across the Lake Washington Ship Canal, mile 4.3, at Seattle, WA. This deviation is necessary to accommodate the Beat the Bridge charity foot race scheduled for Sunday, May 20, 2012. This deviation allows the bridge to remain in the closed position to allow safe movement of event participants.

Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

Energy Technology Data Exchange (ETDEWEB)

Reeve, Wayne [Murdoch University

2013-03-01

Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

On the analysis of genome-wide association studies in family-based designs: a universal, robust analysis approach and an application to four genome-wide association studies.

Directory of Open Access Journals (Sweden)

Sungho Won

2009-11-01

Full Text Available For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1 in 4 genome-wide association studies.

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The founding charter of the Genomic Observatories Network.

Science.gov (United States)

Davies, Neil; Field, Dawn; Amaral-Zettler, Linda; Clark, Melody S; Deck, John; Drummond, Alexei; Faith, Daniel P; Geller, Jonathan; Gilbert, Jack; Glöckner, Frank Oliver; Hirsch, Penny R; Leong, Jo-Ann; Meyer, Chris; Obst, Matthias; Planes, Serge; Scholin, Chris; Vogler, Alfried P; Gates, Ruth D; Toonen, Rob; Berteaux-Lecellier, Véronique; Barbier, Michèle; Barker, Katherine; Bertilsson, Stefan; Bicak, Mesude; Bietz, Matthew J; Bobe, Jason; Bodrossy, Levente; Borja, Angel; Coddington, Jonathan; Fuhrman, Jed; Gerdts, Gunnar; Gillespie, Rosemary; Goodwin, Kelly; Hanson, Paul C; Hero, Jean-Marc; Hoekman, David; Jansson, Janet; Jeanthon, Christian; Kao, Rebecca; Klindworth, Anna; Knight, Rob; Kottmann, Renzo; Koo, Michelle S; Kotoulas, Georgios; Lowe, Andrew J; Marteinsson, Viggó Thór; Meyer, Folker; Morrison, Norman; Myrold, David D; Pafilis, Evangelos; Parker, Stephanie; Parnell, John Jacob; Polymenakou, Paraskevi N; Ratnasingham, Sujeevan; Roderick, George K; Rodriguez-Ezpeleta, Naiara; Schonrogge, Karsten; Simon, Nathalie; Valette-Silver, Nathalie J; Springer, Yuri P; Stone, Graham N; Stones-Havas, Steve; Sansone, Susanna-Assunta; Thibault, Kate M; Wecker, Patricia; Wichels, Antje; Wooley, John C; Yahara, Tetsukazu; Zingone, Adriana

2014-03-07

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

The UCSC Genome Browser Database: update 2006

DEFF Research Database (Denmark)

Hinrichs, A S; Karolchik, D; Baertsch, R

2006-01-01

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

MCNP6 model of the University of Washington clinical neutron therapy system (CNTS).

Science.gov (United States)

Moffitt, Gregory B; Stewart, Robert D; Sandison, George A; Goorley, John T; Argento, David C; Jevremovic, Tatjana

2016-01-21

A MCNP6 dosimetry model is presented for the Clinical Neutron Therapy System (CNTS) at the University of Washington. In the CNTS, fast neutrons are generated by a 50.5 MeV proton beam incident on a 10.5 mm thick Be target. The production, scattering and absorption of neutrons, photons, and other particles are explicitly tracked throughout the key components of the CNTS, including the target, primary collimator, flattening filter, monitor unit ionization chamber, and multi-leaf collimator. Simulations of the open field tissue maximum ratio (TMR), percentage depth dose profiles, and lateral dose profiles in a 40 cm × 40 cm × 40 cm water phantom are in good agreement with ionization chamber measurements. For a nominal 10 × 10 field, the measured and calculated TMR values for depths of 1.5 cm, 5 cm, 10 cm, and 20 cm (compared to the dose at 1.7 cm) are within 0.22%, 2.23%, 4.30%, and 6.27%, respectively. For the three field sizes studied, 2.8 cm × 2.8 cm, 10.4 cm × 10.3 cm, and 28.8 cm × 28.8 cm, a gamma test comparing the measured and simulated percent depth dose curves have pass rates of 96.4%, 100.0%, and 78.6% (depth from 1.5 to 15 cm), respectively, using a 3% or 3 mm agreement criterion. At a representative depth of 10 cm, simulated lateral dose profiles have in-field (⩾ 10% of central axis dose) pass rates of 89.7% (2.8 cm × 2.8 cm), 89.6% (10.4 cm × 10.3 cm), and 100.0% (28.8 cm × 28.8 cm) using a 3% and 3 mm criterion. The MCNP6 model of the CNTS meets the minimum requirements for use as a quality assurance tool for treatment planning and provides useful insights and information to aid in the advancement of fast neutron therapy.

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

Brief research report: sociodemographic factors associated with HIV status among African American women in Washington, DC

Directory of Open Access Journals (Sweden)

Perkins EL

2013-09-01

Full Text Available Emory L Perkins,1 Dexter R Voisin,2 Kesslyn A Brade Stennis1 1Department of Social Work, Bowie State University, Bowie, MD, USA; 2School of Social Service Administration, University of Chicago, Chicago, IL, USA Introduction: African American women living in Washington, DC have one of the highest Human immunodeficiency virus (HIV incidence rates in the US. However, this population has been understudied, especially as it relates to factors associated with HIV status. Methods: This cross-sectional study examined sociodemographic factors that were associated with having a negative or positive HIV status among a sample of 115 African American women between the ages of 24 and 44 years. We assessed such factors as age, education, sexual orientation, household income, sources of income, number of children, length of residency tenure in Washington, DC, and level of HIV-prevention knowledge. Results: Among the overall sample, 53 women self-identified as HIV-positive and 62 as HIV-negative. Compared to their HIV-negative counterparts, women who reported being HIV-positive were less educated, had lower household income, and had longer residency tenure in Washington, DC. There were no differences in HIV knowledge between HIV-positive and -negative study participants. Conclusion: These findings may provide important directions for targeting specific subpopulations of African Americans for HIV-prevention/intervention programs. Keywords: HIV status, African American women, sociodemographic factors

Insights into structural variations and genome rearrangements in prokaryotic genomes.

Science.gov (United States)

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Excellence Initiatives to Establish World-Class Universities: Evaluation of Recent Experiences

OpenAIRE

Jamil Salmi; Isak Froumin

2013-01-01

Jamil Salmi, Ph. D., coordinator of the World Banks tertiary education program (NW, Washington, D.C., United States), member of the International Advisory Panel, National Research University -Higher School of Economics, Moscow, Russian Federation. Email: Address: The World Bank Institute, 1818 H Street, NW, Washington, D.C. 20433, United States.Isak Froumin, Ped.D., Professor, Director of Research and Development at the Education Institute, National Research Unive...

The UCSC genome browser database: update 2007

DEFF Research Database (Denmark)

Kuhn, R M; Karolchik, D; Zweig, A S

2006-01-01

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up t...

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.

A Symposium Associated with the Opening of the Play Copenhagen in Washington

International Nuclear Information System (INIS)

Schwartz, Brian

2002-01-01

On March 2, 2002 a special all day symposium was held in conjunction with the opening of the play Copenhagen in Washington. The play Copenhagen reenacts the 1941 visit of Werner Heisenberg, who was then in charge of the Nazi nuclear power program, to Niels Bohr, his mentor, and collaborator in creating quantum mechanics, complementarity, and the uncertainty principle, in German-occupied Denmark. The symposium entitled: THE COPENHAGEN INTERPRETATION: SCIENCE AND HISTORY ON STAGE was presented at the Baird Auditorium, in the National Museum of Natural History of the Smithsonian Institution. The program consisted of three two-hour sessions: (1) The Science of Copenhagen and its Influence of the 20th Century. (2) Bohr and Heisenberg: A strong Interaction. (3) Theater as Science ??? Science as Theater. The speakers included: Robert C. Card, Under Secretary of Energy; Ulrik Federspiel, Danish Ambassador to the US; John Marburger, III, Science Advisor President Bush; Jerome I. Friedman, MIT; Lene Vestergaard Hau, Harvard University; Richard Rhodes, Author; Rita Colwell, Director, NSF; Jeremy Bernstein, Author; Jochen H. Heisenberg, University of New Hampshire; Finn Aaserud, Director of the Niels Bohr Archive; Vilhelm A. Bohr, NIH; Thomas Powers, Author; Paul Lawrence Rose, Penn State University; Steven Barfield, University of Westminster, Jennifer Uphoff Gray, Associate Director, Copenhagen; Elizabeth Ireland McCann, Producer, Copenhagen; Lloyd Rose, Washington Post. Details of he program and useful information on the play Copenhagen are available on the web site http://web.gc.cuny.edu/ashp/nml/artsci/copenhagen.shtml . The complete symposium was video recorded and the set of 3 two-hour tapes can be obtained through the web site. The symposium was organized by Brian Schwartz, The Graduate Center, CUNY, Harry Lustig, Provost Emeritus at the City College of New York and Arthur Molella, Director, Lemelson Center, Smithsonian Institution. For further information contact Brian

A Symposium Associated with the Opening of the Play Copenhagen in Washington

Energy Technology Data Exchange (ETDEWEB)

Schwartz, Brian

2002-12-31

On March 2, 2002 a special all day symposium was held in conjunction with the opening of the play Copenhagen in Washington. The play Copenhagen reenacts the 1941 visit of Werner Heisenberg, who was then in charge of the Nazi nuclear power program, to Niels Bohr, his mentor, and collaborator in creating quantum mechanics, complementarity, and the uncertainty principle, in German-occupied Denmark. The symposium entitled: THE COPENHAGEN INTERPRETATION: SCIENCE AND HISTORY ON STAGE was presented at the Baird Auditorium, in the National Museum of Natural History of the Smithsonian Institution. The program consisted of three two-hour sessions: (1) The Science of Copenhagen and its Influence of the 20th Century. (2) Bohr and Heisenberg: A strong Interaction. (3) Theater as Science ??? Science as Theater. The speakers included: Robert C. Card, Under Secretary of Energy; Ulrik Federspiel, Danish Ambassador to the US; John Marburger, III, Science Advisor President Bush; Jerome I. Friedman, MIT; Lene Vestergaard Hau, Harvard University; Richard Rhodes, Author; Rita Colwell, Director, NSF; Jeremy Bernstein, Author; Jochen H. Heisenberg, University of New Hampshire; Finn Aaserud, Director of the Niels Bohr Archive; Vilhelm A. Bohr, NIH; Thomas Powers, Author; Paul Lawrence Rose, Penn State University; Steven Barfield, University of Westminster, Jennifer Uphoff Gray, Associate Director, Copenhagen; Elizabeth Ireland McCann, Producer, Copenhagen; Lloyd Rose, Washington Post. Details of he program and useful information on the play Copenhagen are available on the web site http://web.gc.cuny.edu/ashp/nml/artsci/copenhagen.shtml . The complete symposium was video recorded and the set of 3 two-hour tapes can be obtained through the web site. The symposium was organized by Brian Schwartz, The Graduate Center, CUNY, Harry Lustig, Provost Emeritus at the City College of New York and Arthur Molella, Director, Lemelson Center, Smithsonian Institution. For further information contact Brian

Discordance in selected designee for return of genomic findings in the event of participant death and estate executor.

Science.gov (United States)

Goodman, Jessie L; Amendola, Laura M; Horike-Pyne, Martha; Trinidad, Susan B; Fullerton, Stephanie M; Burke, Wylie; Jarvik, Gail P

2017-03-01

Legal and ethical questions arise regarding disseminating genetic research results to family members in the event of a research participant's death; failure to return or return to legal next of kin or estate executor may not reflect participant desires. We sought to determine participant preferences for whether and to whom they would like their data released in the case of their death prior to receiving genomic results, focusing on whether the person selected was also their estate executor. The University of Washington NEXT Medicine Study of the Clinical Sequencing Exploratory Research program previously reported participant preferences regarding designating an individual to receive genomic results in the event of death, including whether they want results shared, and if so, with what person. Participants were also asked whether this designee is executor of their will or estate. To date, 61 individuals were asked about the concordance of their study designee and legal representative: 42 (69%) reported having a will or estate plan and of these, 14 (33%) chose someone other than their executor to receive their results. For the 14 who chose someone other than their estate executor to receive genetic results, 12 (86%) chose a family member, typically a biological relative, as their designee. Those with a different genomic designee than their executor were less likely to be partnered ( P  = 0.0024). For those partnered participants without an estate plan, spouses were not always chosen for return of genomic results. For one-third of our participants, the individual deemed most appropriate by the participant to receive their genomic results was not the executor. In the absence of an explicit designation, HIPAA may prohibit access to genomic results to persons other than the executor; hence asking for designation at the time of study enrollment (or initiation of clinical testing) is important.

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

Science.gov (United States)

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Procurement of Human Tissues for Research Banking in the Surgical Pathology Laboratory: Prioritization Practices at Washington University Medical Center

Science.gov (United States)

Chernock, Rebecca D.; Leach, Tracey A.; Kahn, Ajaz A.; Yip, James H.; Rossi, Joan; Pfeifer, John D.

2011-01-01

Academic hospitals and medical schools with research tissue repositories often derive many of their internal human specimen acquisitions from their site's surgical pathology service. Typically, such acquisitions come from appropriately consented tissue discards sampled from surgical resections. Because the practice of surgical pathology has patient care as its primary mission, competing needs for tissue inevitably arise, with the requirement to preserve adequate tissue for clinical diagnosis being paramount. A set of best-practice gross pathology guidelines are summarized here, focused on the decision for tissue banking at the time specimens are macroscopically evaluated. These reflect our collective experience at Washington University School of Medicine, and are written from the point of view of our site biorepository. The involvement of trained pathology personnel in such procurements is very important. These guidelines reflect both good surgical pathology practice (including the pathologic features characteristic of various anatomic sites) and the typical objectives of research biorepositories. The guidelines should be helpful to tissue bank directors, and others charged with the procurement of tissues for general research purposes. We believe that appreciation of these principles will facilitate the partnership between surgical pathologists and biorepository directors, and promote both good patient care and strategic, value-added banking procurements. PMID:23386925

Parental-age effects in Down syndrome

Indian Academy of Sciences (India)

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Introduction .... currence risk for younger women, by the age of 40, the re- currence risk is not ..... Published on the Web: 30 March 2009. Journal of Genetics ...

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

University of Washington's eScience Institute Promotes New Training and Career Pathways in Data Science

Science.gov (United States)

Stone, S.; Parker, M. S.; Howe, B.; Lazowska, E.

2015-12-01

Rapid advances in technology are transforming nearly every field from "data-poor" to "data-rich." The ability to extract knowledge from this abundance of data is the cornerstone of 21st century discovery. At the University of Washington eScience Institute, our mission is to engage researchers across disciplines in developing and applying advanced computational methods and tools to real world problems in data-intensive discovery. Our research team consists of individuals with diverse backgrounds in domain sciences such as astronomy, oceanography and geology, with complementary expertise in advanced statistical and computational techniques such as data management, visualization, and machine learning. Two key elements are necessary to foster careers in data science: individuals with cross-disciplinary training in both method and domain sciences, and career paths emphasizing alternative metrics for advancement. We see persistent and deep-rooted challenges for the career paths of people whose skills, activities and work patterns don't fit neatly into the traditional roles and success metrics of academia. To address these challenges the eScience Institute has developed training programs and established new career opportunities for data-intensive research in academia. Our graduate students and post-docs have mentors in both a methodology and an application field. They also participate in coursework and tutorials to advance technical skill and foster community. Professional Data Scientist positions were created to support research independence while encouraging the development and adoption of domain-specific tools and techniques. The eScience Institute also supports the appointment of faculty who are innovators in developing and applying data science methodologies to advance their field of discovery. Our ultimate goal is to create a supportive environment for data science in academia and to establish global recognition for data-intensive discovery across all fields.

Carotid Consensus Panel duplex criteria can replace modified University of Washington criteria without affecting accuracy.

Science.gov (United States)

Kim, Ann H; Augustin, Gener; Shevitz, Andrew; Kim, Hannah; Trivonovich, Michael R; Powell, Alexis R; Kumins, Norman; Tarr, Robert; Kashyap, Vikram S

2018-04-01

The decision to intervene for internal carotid stenosis often depends on the degree of stenosis seen on duplex ultrasound (US). The aim of this study is to compare the diagnostic accuracy of two criteria: modified University of Washington (UW) and 2003 Carotid Consensus Panel (CCP). All patients undergoing US in an accredited (IAC) vascular laboratory from January 2010 to June 2015 were reviewed ( n=18,772 US exams). Patients receiving a neck computed tomography angiography (CTA) within 6 months of the US were included in the study ( n=254). The degree of stenosis was determined by UW/CCP criteria and confirmed on CTA images using North American Symptomatic Carotid Endarterectomy Trial (NASCET)/European Carotid Surgery Trial (ECST) schema. Kappa analysis with 95% confidence intervals (CIs) were utilized to determine duplex-CTA agreement. A total of 417 carotid arteries from 221 patients were assessed in this study. The modified UW criteria accurately classified 266 (63.9%, kappa = 0.321, 95% CI 0.255 to 0.386) cases according to NASCET-derived measurements. The sensitivity, specificity, and accuracy at ≥ 60% stenosis were 65.7%, 81.3%, and 81.9%. The CCP criteria resulted in 296 (70.9%) accurate diagnoses (kappa = 0.359, 95% CI 0.280 to 0.437). At ≥ 70% stenosis, the sensitivity, specificity and accuracy were 38.8%, 91.6%, and 87.1% for NASCET. Comparison of the duplex results to ECST-derived CTA measurements revealed a similar trend (UW 53.1%, κ = 0.301 vs CCP 62.1%, κ = 0.315). The CCP criteria demonstrate a higher concordance rate with measurements taken from CTAs. The CCP criteria may be more sensitive in classifying clinically significant degrees of stenosis without a loss in diagnostic accuracy.

Piscine reovirus: Genomic and molecular phylogenetic analysis from farmed and wild salmonids collected on the Canada/US Pacific Coast

Science.gov (United States)

Siah, Ahmed; Morrison, Diane B.; Fringuelli, Elena; Savage, Paul S.; Richmond, Zina; Purcell, Maureen K.; Johns, Robert; Johnson, Stewart C.; Sakasida, Sonja M.

2015-01-01

Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

Washington Tsunami Hazard Mitigation Program

Science.gov (United States)

Walsh, T. J.; Schelling, J.

2012-12-01

Washington State has participated in the National Tsunami Hazard Mitigation Program (NTHMP) since its inception in 1995. We have participated in the tsunami inundation hazard mapping, evacuation planning, education, and outreach efforts that generally characterize the NTHMP efforts. We have also investigated hazards of significant interest to the Pacific Northwest. The hazard from locally generated earthquakes on the Cascadia subduction zone, which threatens tsunami inundation in less than hour following a magnitude 9 earthquake, creates special problems for low-lying accretionary shoreforms in Washington, such as the spits of Long Beach and Ocean Shores, where high ground is not accessible within the limited time available for evacuation. To ameliorate this problem, we convened a panel of the Applied Technology Council to develop guidelines for construction of facilities for vertical evacuation from tsunamis, published as FEMA 646, now incorporated in the International Building Code as Appendix M. We followed this with a program called Project Safe Haven (http://www.facebook.com/ProjectSafeHaven) to site such facilities along the Washington coast in appropriate locations and appropriate designs to blend with the local communities, as chosen by the citizens. This has now been completed for the entire outer coast of Washington. In conjunction with this effort, we have evaluated the potential for earthquake-induced ground failures in and near tsunami hazard zones to help develop cost estimates for these structures and to establish appropriate tsunami evacuation routes and evacuation assembly areas that are likely to to be available after a major subduction zone earthquake. We intend to continue these geotechnical evaluations for all tsunami hazard zones in Washington.

Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

Science.gov (United States)

Smith, David Roy

2017-05-01

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

Perception of Natural Hazards and Risk among University of Washington Students

Science.gov (United States)

Herr, K.; Brand, B.; Hamlin, N.; Ou, J.; Thomas, B.; Tudor, E.

2012-12-01

Familiarity with a given population's perception of natural hazards and the threats they present is vital for the development of effective education prior to and emergency management response after a natural event. While much work has been done in other active tectonic regions, perception of natural hazards and risk among Pacific Northwest (PNW) residents is poorly constrained. The objective of this work is to assess the current perception of earthquake and volcanic hazards and risk in the PNW, and to better understand the factors which drive the public's behavior concerning preparedness and response. We developed a survey to assess the knowledge of natural hazards common to the region, their perception of risk concerning these hazards, and their level of preparedness should a natural hazard occur. The survey was distributed to University of Washington students and employees via an internet link as part of a class project in 'Living with Volcanoes' (ESS 106) in March of 2012, which returned more than 900 responses. The UW student population was chosen as our first "population" to assess because of their uniqueness as a large, semi-transient population (typical residence of less than 5 years). Only 50% of participants correctly reported their proximity to an active volcano, indicating either lack of knowledge of active volcanoes in the region or poor spatial awareness. When asked which area were most at risk to lahars, respondents indicated that all areas close to the hazard source, including topographically elevated regions, were at a higher risk than more distal and low-lying localities that are also at high risk, indicating a lack of knowledge concerning the topographic dependency of this hazard. Participants perceived themselves to be able to cope better with an earthquake than a volcanic event. This perception may be due to lack of knowledge of volcanic hazards and their extent or due to a false sense of security concerning earthquakes fostered by regular

Modeling hazardous mass flows Geoflows09: Mathematical and computational aspects of modeling hazardous geophysical mass flows; Seattle, Washington, 9–11 March 2009

Science.gov (United States)

Iverson, Richard M.; LeVeque, Randall J.

2009-01-01

A recent workshop at the University of Washington focused on mathematical and computational aspects of modeling the dynamics of dense, gravity-driven mass movements such as rock avalanches and debris flows. About 30 participants came from seven countries and brought diverse backgrounds in geophysics; geology; physics; applied and computational mathematics; and civil, mechanical, and geotechnical engineering. The workshop was cosponsored by the U.S. Geological Survey Volcano Hazards Program, by the U.S. National Science Foundation through a Vertical Integration of Research and Education (VIGRE) in the Mathematical Sciences grant to the University of Washington, and by the Pacific Institute for the Mathematical Sciences. It began with a day of lectures open to the academic community at large and concluded with 2 days of focused discussions and collaborative work among the participants.

RadGenomics project

Energy Technology Data Exchange (ETDEWEB)

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

2002-06-01

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

RadGenomics project

International Nuclear Information System (INIS)

Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

2002-01-01

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

A web-based decision support system to enhance IPM programs in Washington tree fruit.

Science.gov (United States)

Jones, Vincent P; Brunner, Jay F; Grove, Gary G; Petit, Brad; Tangren, Gerald V; Jones, Wendy E

2010-06-01

Integrated pest management (IPM) decision-making has become more information intensive in Washington State tree crops in response to changes in pesticide availability, the development of new control tactics (such as mating disruption) and the development of new information on pest and natural enemy biology. The time-sensitive nature of the information means that growers must have constant access to a single source of verified information to guide management decisions. The authors developed a decision support system for Washington tree fruit growers that integrates environmental data [140 Washington State University (WSU) stations plus weather forecasts from NOAA], model predictions (ten insects, four diseases and a horticultural model), management recommendations triggered by model status and a pesticide database that provides information on non-target impacts on other pests and natural enemies. A user survey in 2008 found that the user base was providing recommendations for most of the orchards and acreage in the state, and that users estimated the value at $ 16 million per year. The design of the system facilitates education on a range of time-sensitive topics and will make it possible easily to incorporate other models, new management recommendations or information from new sensors as they are developed.

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

Directory of Open Access Journals (Sweden)

Kim Seungill

2008-12-01

Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

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

The UCSC Genome Browser Database: 2008 update

DEFF Research Database (Denmark)

Karolchik, D; Kuhn, R M; Baertsch, R

2007-01-01

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrat...

A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

Directory of Open Access Journals (Sweden)

Guangtu Gao

2018-04-01

Full Text Available Single-nucleotide polymorphisms (SNPs are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss, SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD libraries, reduced representation libraries (RRL and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1 which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs and multi-sequence variants (MSVs. Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25. The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and

Father Secchi Goes to Washington

Science.gov (United States)

McCarthy, M. F.

1994-12-01

In 1848 a small group of Jesuit refugees arrived at Georgetown College near Washington, D.C. Among them was a young priest, Angelo Secchi, who had finished theology studies in Rome, but had not been able to complete his final examinations. This done successfully, Secchi turned to astronomy and the new facilities of the Georgetown College Observatory, directed by its founder, Fr. James Curley. During his two years in Washington, Secchi studied physics, wrote an article on Electrical Rheometry for the Smithsonian Institution, and formed a friendship with Matthew Fontaine Maury of the U.S. Navy, who headed the Chart Service and in 1844 was named superintendent of the National Observatory. This was later named the U.S. Naval Observatory. Secchi's friendships formed during the Washington visit proved most helpful for relations between European astronomers and U.S. colleagues. Secchi, after his return to Rome constructed the Observatory of the Collegio Romano atop the baroque Church of St. Ignatius in Rome and began his work in spectral classification of stars.

Corrections Education. Washington's Community and Technical Colleges

Science.gov (United States)

Washington State Board for Community and Technical Colleges, 2015

2015-01-01

The Washington State Department of Corrections contracts with community colleges to provide basic education and job training at each of the state's 12 adult prisons so upon release, individuals are more likely to get jobs and less likely to return. Washington State community colleges build a bridge for offenders to successfully re-enter…

Aerospace Training. Washington's Community and Technical Colleges

Science.gov (United States)

Washington State Board for Community and Technical Colleges, 2014

2014-01-01

Aerospace is an economic powerhouse that generates jobs and fuels our economy. Washington's community and technical colleges produce the world-class employees needed to keep it that way. With about 1,250 aerospace-related firms employing more than 94,000 workers, Washington has the largest concentration of aerospace expertise in the nation. To…

76 FR 16323 - Irish Potatoes Grown in Washington; Continuance Referendum

Science.gov (United States)

2011-03-23

...; FV11-946-1 CR] Irish Potatoes Grown in Washington; Continuance Referendum AGENCY: Agricultural... conducted among eligible Washington potato growers to determine whether they favor continuance of the marketing order regulating the handling of Irish potatoes grown in Washington. DATES: The referendum will be...

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

Genomes Project, as well as to other human genome projects. © The Authors 2017. Published by Oxford University Press.

A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

Energy Technology Data Exchange (ETDEWEB)

Mockler, Todd [Oregon State Univ., Corvallis, OR (United States)

2017-04-17

Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes of plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.

A Genome-Wide Landscape of Retrocopies in Primate Genomes.

Science.gov (United States)

Navarro, Fábio C P; Galante, Pedro A F

2015-07-29

Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

THE ROLE OF HISTORICAL AERIAL PHOTOGRAPHS IN THE REMEDIATION OF WWI CHEMICAL CONTAMINATION IN THE SPRING VALLEY SUPERFUND SITE, WASHINGTON, DC

Science.gov (United States)

During World War 1, The American University in Washington D.C. was used by the U.S. Army as an experiment station for the development and testing of a variety of battlefield munitions including chemical weapons such as Mustard Gas, Phosgene, Ricin and Lewisite, among others. Afte...

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

NARCIS (Netherlands)

Taylor, Alison M.; Shih, Juliann; Ha, Gavin; Gao, Galen F.; Zhang, Xiaoyang; Berger, Ashton C.; Schumacher, Steven E.; Wang, Chen; Hu, Hai; Liu, Jianfang; Lazar, Alexander J.; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Parker, Joel S.; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David A.; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Angulo Gonzalez, Ana Maria; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, Jonathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Mora Pinero, Edna M.; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz; Cherniack, Andrew D.; Beroukhim, Rameen; Meyerson, Matthew

2018-01-01

Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was

The language of the protein universe.

Science.gov (United States)

Scaiewicz, Andrea; Levitt, Michael

2015-12-01

Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

76 FR 377 - Land Acquisitions; Cowlitz Indian Tribe of Washington

Science.gov (United States)

2011-01-04

... State of Washington by Auditor's File Nos. G 450664 and G 147358. Parcel II That portion of the... thereof acquired by the State of Washington by deed recorded under Auditor's File Nos. G 140380 and D... recorded under Auditor's File No. F 38759, records of Clark County, Washington, described as follows...

Microbial genome analysis: the COG approach.

Science.gov (United States)

Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2017-09-14

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Recent developments: Washington focus

International Nuclear Information System (INIS)

Anon.

1990-01-01

November was a quiet month in Washington. Although Congress has recessed until 1991, the Senate filled vacancies in party leadership positions created by November's elections. The House is expected to proceed with its changes in early December. The Nuclear Energy Forum was held in Washington, DC on November 11-14 to discuss the status of the nuclear industry in the USA. The Forum, held in conjunction with the American Nuclear Society's annual meeting, assembled a large number of CEO's from US, European, and Far Eastern utilities and vendors. The meeting concluded with an announcement by Philip Bayne, President of NYPA and chairman of the Nuclear Power Oversight Committee (NPOC), of the results of a year-long NPOC study entitled a open-quotes Strategic Plan for Building New Nuclear Power Plants.close quotes

A universal, rapid, and inexpensive method for genomic DNA ...

Indian Academy of Sciences (India)

MOHAMMED BAQUR SAHIB A. AL-SHUHAIB

gels, containing 7% glycerol, and 1×TBE buffer. The gels were run under 200 .... Inc. Germany, GeneaidTM DNA Isolation Kit, Geneaid. Biotech., New Taipei City, .... C. L. and Arsenos G. 2015 Comparison of eleven methods for genomic DNA ...

76 FR 56157 - Brandeis University, et al.; Notice of Consolidated Decision on Applications for Duty-Free Entry...

Science.gov (United States)

2011-09-12

... DEPARTMENT OF COMMERCE International Trade Administration Brandeis University, et al.; Notice of Consolidated Decision on Applications for Duty-Free Entry of Electron Microscope This is a decision... Constitution Avenue, NW., Washington, DC. Docket Number: 11-042. Applicant: Brandeis University, Waltham, MA...

Genome Variation Map: a data repository of genome variations in BIG Data Center.

Science.gov (United States)

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2018-01-04

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Opportunities for addressing laminated root rot caused by Phellinus sulphuracens in Washington's forests: A Report from the Washington State Academy of Sciences in cooperation with the Washington State Department of Natural Resources

Science.gov (United States)

R. James Cook; Robert L. Edmonds; Ned B. Klopfenstein; Willis Littke; Geral McDonald; Daniel Omdahl; Karen Ripley; Charles G. Shaw; Rona Sturrock; Paul Zambino

2013-01-01

This report from the Washington State Academy of Sciences (WSAS) is in response to a request from the Washington State Department of Natural Resources (DNR) to "identify approaches and opportunities ripe for research on understanding and managing root diseases of Douglas-fir." Similar to the process used by the National Research Council, the WSAS upon...

The Saccharomyces Genome Database Variant Viewer.

Science.gov (United States)

Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

2016-01-04

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

Science.gov (United States)

Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

2012-01-01

Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

Researcher Mobility at a US Research-Intensive University: Implications for Research and Internationalization Strategies

Science.gov (United States)

Payumo, Jane G.; Lan, George; Arasu, Prema

2018-01-01

This study offers a unique lens on the patterns, productivity, and impact of researcher mobility at a US research-intensive university. Bibliometric data for Washington State University (WSU) was extracted from Elsevier's Scopus database and analyzed for the 10-year period from 2002 to 2012. We grouped researchers into four categories based on…

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 Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution.

Science.gov (United States)

Baniaga, Anthony E; Arrigo, Nils; Barker, Michael S

2016-06-03

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

ENCODE whole-genome data in the UCSC genome browser (2011 update).

Science.gov (United States)

Raney, Brian J; Cline, Melissa S; Rosenbloom, Kate R; Dreszer, Timothy R; Learned, Katrina; Barber, Galt P; Meyer, Laurence R; Sloan, Cricket A; Malladi, Venkat S; Roskin, Krishna M; Suh, Bernard B; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Kirkup, Vanessa; Fujita, Pauline A; Rhead, Brooke; Smith, Kayla E; Pohl, Andy; Kuhn, Robert M; Karolchik, Donna; Haussler, David; Kent, W James

2011-01-01

The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access.

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

Science.gov (United States)

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

Science.gov (United States)

Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

2017-06-01

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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.

The Modern Synthesis in the Light of Microbial Genomics.

Science.gov (United States)

Booth, Austin; Mariscal, Carlos; Doolittle, W Ford

2016-09-08

We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions. We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in lieu of any grand unified theory updated to include microbial genomics.

Drivers' use of marijuana in Washington state : traffic tech.

Science.gov (United States)

2016-08-01

In July 2014, Washington State allowed legal sales of : recreational marijuana. Working with the Washington : Traffic Safety Commission, NHTSA assisted the State in : conducting a roadside study to examine the prevalence : of marijuana use before and...

A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae.

Science.gov (United States)

Pellicer, Jaume; Kelly, Laura J; Leitch, Ilia J; Zomlefer, Wendy B; Fay, Michael F

2014-03-01

• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Facilities for Study and Research in the Offices of the United States Government at Washington. Bulletin, 1909, No. 1. Whole Number 398

Science.gov (United States)

Hadley, Arthur Twining

1909-01-01

This bulletin contains a report prepared by President Hadley of Yale University on the facilities for advanced study and research in the offices of the National Government at Washington. Especial interest attaches to this publication. It sets forth, in compact form, information which has frequently been sought by institutions and individuals…

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

Science.gov (United States)

Lajugie, Julien; Fourel, Nicolas; Bouhassira, Eric E

2015-01-01

Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Coordinated Collection Development via CD-ROM. A Pilot Project Granted by LSCA Title III Funds to Crosby Library, Gonzaga University. Final Narrative Report.

Science.gov (United States)

Peterson, Elaine; Carr, Mary M.

Three colleges in the state of Washington--Gonzaga College (Crosby Library), Whitworth College, and Eastern Washington University--received grants from the Fred Meyer Charitable Trust and the Library Services and Construction Act to facilitate coordinated collection development in the areas of education and business/economics, so that their…

Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.

Science.gov (United States)

Kravatsky, Yuri V; Chechetkin, Vladimir R; Tchurikov, Nikolai A; Kravatskaya, Galina I

2015-02-01

The broad class of tasks in genetics and epigenetics can be reduced to the study of various features that are distributed over the genome (genome tracks). The rapid and efficient processing of the huge amount of data stored in the genome-scale databases cannot be achieved without the software packages based on the analytical criteria. However, strong inhomogeneity of genome tracks hampers the development of relevant statistics. We developed the criteria for the assessment of genome track inhomogeneity and correlations between two genome tracks. We also developed a software package, Genome Track Analyzer, based on this theory. The theory and software were tested on simulated data and were applied to the study of correlations between CpG islands and transcription start sites in the Homo sapiens genome, between profiles of protein-binding sites in chromosomes of Drosophila melanogaster, and between DNA double-strand breaks and histone marks in the H. sapiens genome. Significant correlations between transcription start sites on the forward and the reverse strands were observed in genomes of D. melanogaster, Caenorhabditis elegans, Mus musculus, H. sapiens, and Danio rerio. The observed correlations may be related to the regulation of gene expression in eukaryotes. Genome Track Analyzer is freely available at http://ancorr.eimb.ru/. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Washington biofuel feedstock crop supply under output price and quantity uncertainty

International Nuclear Information System (INIS)

Zheng Qiujie; Shumway, C. Richard

2012-01-01

Subsidized development of an in-state biofuels industry has received some political support in the state of Washington, USA. Utilizing in-state feedstock supplies could be an efficient way to stimulate biofuel industries and the local economy. In this paper we estimate supply under output price and quantity uncertainty for major biofuel feedstock crops in Washington. Farmers are expected to be risk averse and maximize the utility of profit and uncertainty. We estimate very large Washington price elasticities for corn and sugar beets but a small price elasticity for a third potential feedstock, canola. Even with the large price elasticities for two potential feedstocks, their current and historical production levels in the state are so low that unrealistically large incentives would likely be needed to obtain sufficient feedstock supply for a Washington biofuel industry. Based on our examination of state and regional data, we find low likelihood that a Washington biofuels industry will develop in the near future primarily using within-state biofuel feedstock crops. - Highlights: ► Within-state feedstock crop supplies insufficient for Washington biofuel industry. ► Potential Washington corn and sugar beet supplies very responsive to price changes. ► Feedstock supplies more responsive to higher expected profit than lower risk. ► R and D for conversion of waste cellulosic feedstocks is potentially important policy.

Promoting Climate And Data Literacy: University Courses Engaging Students In Effective Teaching, Learning, Communication And Outreach Practices.

Science.gov (United States)

Halversen, C.; McDonnell, J. D.; Apple, J. K.; Weiss, E. L.

2016-02-01

Two university courses, 1) Promoting Climate Literacy and 2) Climate and Data Literacy, developed by the University of California Berkeley provide faculty across the country with course materials to help their students delve into the science underlying global environmental change. The courses include culturally responsive content, such as indigenous and place-based knowledge, and examine how people learn and consequently, how we should teach and communicate science. Promoting Climate Literacy was developed working with Scripps Institution of Oceanography, University of Washington, and Western Washington University. Climate and Data Literacy was developed with Rutgers University and Padilla Bay National Estuarine Research Reserve, WA. The Climate and Data Literacy course also focuses on helping students in science majors participating in U-Teach programs and students in pre-service teacher education programs gain skills in using real and near-real time data through engaging in investigations using web-based and locally-relevant data resources. The course helps these students understand and apply the scientific practices, disciplinary concepts and big ideas described in the Framework for K-12 Science Education and the Next Generation Science Standards (NGSS). This course focuses on students interested in teaching middle school science for three reasons: (1) teachers often have relatively weak understandings of the practices of science, and of complex Earth systems science and climate change; (2) the concepts that underlie climate change align well with the NGSS; and (3) middle school is a critical time for promoting student interest in science and for recruitment to STEM careers and lifelong climate literacy. This course is now being field tested in a number of U-Teach programs including Florida State University, Louisiana State University, as well as pre-service teacher education programs at California State University East Bay, and Western Washington University

THE APPLE JUICE CONCENTRATE ANTI-DUMPING CASE AGAINST CHINA: AN ESTIMATE OF CHANGE IN WASHINGTON'S REVENUES

OpenAIRE

van Voorthuizen, Hilde; Cho, Sung-Yeol; Schotzko, R. Thomas; Mittelhammer, Ronald C.

2001-01-01

Increasing volumes of apple juice concentrate imports from China into the U.S. began in the mid 90s as a result of low Chinese prices. In 1999, the U.S. Apple Association launched a complaint with the US International Trade Commission (USITC) regarding the Chinese price strategy. During the course of investigation, the U.S. Apple Association requested that the Department of Agricultural Economics at Washington State University analyze the impact on the total value of juice apples utilized in ...

An assessment of interstate safety investment properties in Washington state.

Science.gov (United States)

2014-12-01

The Washington State Department of Transportation (WSDOT) commissioned the current study, targeting the entire interstate : mainline network in Washington State, to provide strategic direction to multi-biennial investment interstate locations that of...

Expanding Access and Opportunity: The Washington State Achievers Program

Science.gov (United States)

Ramsey, Jennifer; Gorgol, Laura

2010-01-01

In 2001, the Bill & Melinda Gates Foundation launched a 10-year, multi-million dollar initiative, the Washington State Achievers Program (WSA), to increase opportunities for low-income students to attend postsecondary institutions in Washington State. The Bill & Melinda Gates Foundation granted funds to the College Success Foundation…

Expanding Access and Opportunity: The Washington State Achievers Scholarship

Science.gov (United States)

O'Brien, Colleen

2011-01-01

In 2001, the Bill & Melinda Gates Foundation launched the multi-year, multi-million dollar Washington State Achievers Scholarship program. Concerned about disparities in college participation for low-income students in the state of Washington versus their wealthier peers, the Gates Foundation partnered with the College Success Foundation…

gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.

Science.gov (United States)

Nakagawa, So; Takahashi, Mahoko Ueda

2016-01-01

In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp. © The Author(s) 2016. Published by Oxford University Press.

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

Science.gov (United States)

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2015-01-01

The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Theory of microbial genome evolution

Science.gov (United States)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

Genome Island: A Virtual Science Environment in Second Life

Science.gov (United States)

Clark, Mary Anne

2009-01-01

Mary Anne CLark describes the organization and uses of Genome Island, a virtual laboratory complex constructed in Second Life. Genome Island was created for teaching genetics to university undergraduates but also provides a public space where anyone interested in genetics can spend a few minutes, or a few hours, interacting with genetic…

75 FR 71139 - Land Acquisitions; Puyallup Tribe of Washington

Science.gov (United States)

2010-11-22

... Auditor, in Pierce County, Washington. Except that portion of Lot 3 conveyed to the State of Washington by Deeds recorded under Auditor's file number 689865 and 689858. Together with the East half of the... amendment of Short Plat Nos. 8502210395 and 8403080186, filed with the Pierce County Auditor, in Pierce...

Institutional Responsibility and the Flawed Genomic Biomarkers at Duke University: A Missed Opportunity for Transparency and Accountability.

Science.gov (United States)

DeMets, David L; Fleming, Thomas R; Geller, Gail; Ransohoff, David F

2017-08-01

When there have been substantial failures by institutional leadership in their oversight responsibility to protect research integrity, the public should demand that these be recognized and addressed by the institution itself, or the funding bodies. This commentary discusses a case of research failures in developing genomic predictors for cancer risk assessment and treatment at a leading university. In its review of this case, the Office of Research Integrity, an agency within the US Department of Health and Human Services, focused their report entirely on one individual faculty member and made no comment on the institution's responsibility and its failure to provide adequate oversight and investigation. These actions missed an important opportunity to emphasize the institution's critical responsibilities in oversight of research integrity and the importance of institutional transparency and accountability.

Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

Energy Technology Data Exchange (ETDEWEB)

Pop, Mihai

2011-10-13

University of Maryland's Mihai Pop on Genome Assembly Forensics: Metrics for Assessing Assembly Correctness at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Educator Supply and Demand in Washington State. 2004 Report

Science.gov (United States)

Lashway, Larry; Maloney, Rick; Hathaway, Randy; Bryant, B. J.

2005-01-01

This report describes the findings of the third Educator Supply and Demand Research study in the State of Washington. The intent of these Washington studies is to provide data to inform and shape decisions and activities in the following ways: (1) Provide useful information for educational policymakers, including the legislature, the State Board…

Deleterious mutation accumulation in organelle genomes.

Science.gov (United States)

Lynch, M; Blanchard, J L

1998-01-01

It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population size induced by uniparental inheritance. Because of the very low mutation rates of organelle genomes (on the order of 10(-4) per genome per year), the reduction in fitness resulting from mutation accumulation in such genomes is a very long-term process, not likely to imperil many species on time scales of less than a million years, but perhaps playing some role in phylogenetic lineage sorting on time scales of 10 to 100 million years.

Trends and determinants of cycling in the Washington, DC region.

Science.gov (United States)

2011-01-01

This report analyzes cycling trends, policies, and commuting in the Washington, DC area. The analysis is divided into two parts. : Part 1 focuses on cycling trends and policies in Washington (DC), Alexandria (VA), Arlington County (VA), Fairfax Count...

Alternative Fuels for Washington's School Buses: A Report to the Washington State Legislature.

Science.gov (United States)

Lyons, John Kim; McCoy, Gilbert A.

This document presents findings of a study that evaluated the use of both propane and compressed natural gas as alternative fuels for Washington State school buses. It discusses air quality improvement actions by state- and federal-level regulators and summarizes vehicle design, development, and commercialization activities by all major engine,…

Residential Energy Efficiency Potential: Washington

Energy Technology Data Exchange (ETDEWEB)

Wilson, Eric J [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

2017-11-27

Energy used by Washington single-family homes that can be saved through cost-effective improvements. Prepared by Eric Wilson and Noel Merket, NREL, and Erin Boyd, U.S. Department of Energy Office of Energy Policy and Systems Analysis.

Results of the Washington Passive Solar Design/Build Competition

Energy Technology Data Exchange (ETDEWEB)

Nylen, N.

1981-01-01

In an effort to encourage the design, construction, and marketing of moderately priced passive solar homes in Washington state, the Western Solar Utilization Network (Western SUN) recently sponsored the Washington Passive Solar Design/Build Competition. The competition drew an overwhelming response from designers and builders throughout Washington. Thermal performance of the designs was evaluated by a technical review committee, and final selections were made by the Competition Jury in accordance with the following criteria: perceived market acceptance, thermal performance, cost effectiveness, simplicity of design and operation, and completeness of the passive concept. Design contract awards totaling $50,000 were made available to winners in four categories, including single and multi-family, new and remodeled residences. In order to receive the award in its entirety, winning design/build teams are required to construct their design by April, 1983. As a result of the competition, a great deal was learned about the attitudes and knowledge of professionals and the general public regarding the use of solar energy in Washington state. Among the points that will be highlighted in this paper are the following: (1) a design/build competition is an effective vehicle for promoting solar energy among professionals in the housing community as well as the general public; (2) passive solar techniques can contribute significantly to the heating and cooling needs of residential housing throughout the state of Washington; (3) there is a great deal of interest and talent among the designers and builders of solar residences in Washington; and (4) follow-up activities, including the promotion of winning designs, the systematic collection of performance data, and identification of the major obstacles confronting designers and builders of solar homes, are critical to the success of the program in achieving both its short-term and long-term goals.

75 FR 76699 - The University of Texas at Austin, et al.; Notice of Decision on Applications for Duty-Free Entry...

Science.gov (United States)

2010-12-09

... DEPARTMENT OF COMMERCE International Trade Administration The University of Texas at Austin, et al..., NW., Washington, DC. Docket Number: 10-064. Applicant: The University of Texas at Austin, Center for Electromechanics, Pickle Research Campus, 10100 Burnet Road, Building 133, Austin, Texas 78758-4497. Instrument...

Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae).

Science.gov (United States)

Krahulcová, Anna; Trávnícek, Pavel; Krahulec, František; Rejmánek, Marcel

2017-04-01

Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa. The same chromosome number, 2 n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum , confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C -1 in A. parviflora to 1·275 pg 2C -1 in A. glabra var. glabra. The chromosome number of 2 n = 40 seems to be conclusively the universal 2 n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For

Physical data collected from Seaglider SG189 during Cuddy Survey in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2014-01-16 to 2014-04-27 (NCEI Accession 0162344)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG194 during Cuddy Survey in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2013-10-25 to 2014-05-10 (NCEI Accession 0162349)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG195 during Cuddy Survey in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2013-10-25 to 2014-02-22 (NCEI Accession 0162357)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Washington State Briefing Book for low-level radioactive waste management

Energy Technology Data Exchange (ETDEWEB)

1980-12-01

The Washington State Briefing Book is one of a series of state briefing books on low-level radioactive waste management practices. It has been prepared to assist state and federal agency officials in planning for safe low-level radioactive waste disposal. The report contains a profile of low-level radioactive waste generators in Washington. The profile is the result of a survey of NRC licensees in Washington. The briefing book also contains a comprehensive assessment of low-level radioactive waste management issues and concerns as defined by all major interested parties including industry, government, the media, and interest groups. The assessment was developed through personal communications with representatives of interested parties, and through a review of media sources. Lastly, the briefing book provides demographic and socioeconomic data and a discussion of relevant government agencies and activities, all of which may impact waste management practices in Washington.

Washington State Briefing Book for low-level radioactive waste management

International Nuclear Information System (INIS)

1980-12-01

The Washington State Briefing Book is one of a series of state briefing books on low-level radioactive waste management practices. It has been prepared to assist state and federal agency officials in planning for safe low-level radioactive waste disposal. The report contains a profile of low-level radioactive waste generators in Washington. The profile is the result of a survey of NRC licensees in Washington. The briefing book also contains a comprehensive assessment of low-level radioactive waste management issues and concerns as defined by all major interested parties including industry, government, the media, and interest groups. The assessment was developed through personal communications with representatives of interested parties, and through a review of media sources. Lastly, the briefing book provides demographic and socioeconomic data and a discussion of relevant government agencies and activities, all of which may impact waste management practices in Washington

Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses.

Science.gov (United States)

Weber, K Scott; Jensen, Jamie L; Johnson, Steven M

2015-01-01

An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.

LOW-ENERGY NUCLEAR PHYSICS NATIONAL HPC INITIATIVE: BUILDING A UNIVERSAL NUCLEAR ENERGY DENSITY FUNCTIONAL (UNEDF)

Energy Technology Data Exchange (ETDEWEB)

Bulgac, A

2013-03-27

This document is a summary of the physics research carried out by the University of Washington centered group. Attached are reports for the previous years as well as the full exit report of the entire UNEDF collaboration.

77 FR 50157 - Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting

Science.gov (United States)

2012-08-20

...; HAG 12-0260] Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting AGENCY.... Department of the Interior, Bureau of Land Management (BLM) Eastern Washington Resource Advisory Council... Bureau of Land Management's Eastern Washington and San Juan Resource Management Plan and the U.S. Forest...

The Significance of UNESCO’s Universal Declaration on the Human Genome & Human Rights

Directory of Open Access Journals (Sweden)

Shawn H.E. Harmon

2005-03-01

Full Text Available Modern medical research, particularly genetic research, is changing the nature of medicine. Concerns surrounding these changes and their potential negative impact on human rights led UNESCO to spearhead collaboration by experts in the creation of an international instrument intended to provide guidance for the promotion of bioethics and the protection of human rights in the genetic context. The result was the Universal Declaration of the Human Genome and Human Rights. This article briefly highlights the scientific and social setting into which the Declaration was injected. This is followed by a consideration of the drafting body (the IBC so as to assess whether UNESCO was the appropriate body to lead this project. The process by which the Declaration was created is also considered so as to assess whether it represents an example of ethical and democratic drafting. Finally, the substantive content of the Declaration is considered and measured against the pre-existing regime so as to assess whether it represents an intelligible and coherent response to the concerns raised capable of offering guidance now and into the future. By assessing these procedural and substantive matters, one can draw some tentative conclusions about the utility and significance of the Declaration.

Analysis of radiation-induced genome alterations in Vigna unguiculata

Directory of Open Access Journals (Sweden)

van der Vyver C

2011-09-01

Full Text Available Christell van der Vyver1, B Juan Vorster2, Karl J Kunert3, Christopher A Cullis41Institute for Plant Biotechnology, Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa; 2Department of Plant Production and Soil Science, and 3Department of Plant Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa; 4Case Western Reserve University, Department of Biology, Cleveland, OH, USAAbstract: Seeds from an inbred Vigna unguiculata (cowpea cultivar were gamma-irradiated with a dose of 180 Gy in order to identify and characterize possible mutations. Three techniques, ie, random amplified polymorphic DNA, microsatellites, and representational difference analysis, were used to characterize possible DNA variation among the mutants and nonirradiated control plants both immediately after irradiation and in subsequent generations. A large portion of putative radiation-induced genome changes had significant similarities to chloroplast sequences. The frequency of mutation at three of these isolated polymorphic regions with chloroplast similarity was further determined by polymerase chain reaction screening using a large number of individual parental, M1, and M2 plants. Analysis of these sequences indicated that the rate at which various regions of the genome is mutated in irradiation experiments differs significantly and also that mutations have variable “repair” rates. Furthermore, regions of the nuclear DNA derived from the chloroplast genome are highly susceptible to modification by radiation treatment. Overall, data have provided detailed information on the effects of gamma irradiation on the cowpea genome and about the ability of the plant to repair these genome changes in subsequent plant generations.Keywords: mutation breeding, gamma radiation, genetic mutations, cowpea, representational difference analysis

77 FR 23495 - Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting

Science.gov (United States)

2012-04-19

...; HAG 12-0164] Notice of Public Meeting, Eastern Washington Resource Advisory Council Meeting AGENCY... 1972, the U.S. Department of the Interior, Bureau of Land Management (BLM) Eastern Washington Resource... of Land Management's Eastern Washington and San Juan Resource Management Plan, and the U.S. Forest...

Evolution of the Largest Mammalian Genome.

Science.gov (United States)

Evans, Ben J; Upham, Nathan S; Golding, Goeffrey B; Ojeda, Ricardo A; Ojeda, Agustina A

2017-06-01

The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects-including during the evolution of hypersaline dietary tolerance in T. barrerae. ©The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Physical data collected from Seaglider SG030 during Cascadia September 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-09-15 to 2008-09-19 (NCEI Accession 0156193)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Heat-related illness in Washington State agriculture and forestry sectors.

Science.gov (United States)

Spector, June T; Krenz, Jennifer; Rauser, Edmund; Bonauto, David K

2014-08-01

We sought to describe heat-related illness (HRI) in agriculture and forestry workers in Washington State. Demographic and clinical Washington State Fund workers' compensation agriculture and forestry HRI claims data (1995-2009) and Washington Agriculture Heat Rule citations (2009-2012) were accessed and described. Maximum daily temperature (Tmax) and Heat Index (HImax) were estimated by claim date and location using AgWeatherNet's weather station network. There were 84 Washington State Fund agriculture and forestry HRI claims and 60 Heat Rule citations during the study period. HRI claims and citations were most common in crop production and support subsectors. The mean Tmax (HImax) was 95°F (99°F) for outdoor HRI claims. Potential HRI risk factors and HRI-related injuries were documented for some claims. Agriculture and forestry HRI cases are characterized by potential work-related, environmental, and personal risk factors. Further work is needed to elucidate the relationship between heat exposure and occupational injuries. © 2014 Wiley Periodicals, Inc.

Reaching Higher. A Parent's Guide to the Washington Assessment of Learning. Revised = Para llegar mas arriba. Una guia para padres sobre la evaluacion del aprendizaje de los estudiantes del estado de Washington (Washington Assessment of Student Learning). Revisado.

Science.gov (United States)

Washington Office of the State Superintendent of Public Instruction, Olympia.

This guide in English and Spanish is designed to answer questions parents may have about the Washington Assessment of Student Learning (WASL), including how it will help improve their children's education, how it is scored, and how to use the information it provides. In Washington, clear educational goals for subject content, thinking skills, and…

Promoting Inclusivity in STEM through Active Recruiting and Mentoring: The Pre-Major in Astronomy Program (Pre-MAP) at the University of Washington

Science.gov (United States)

Schwieterman, Edward; Binder, Breanna A.; Pre-Major in Astronomy Program

2016-01-01

The Pre-Major in Astronomy Program (Pre-MAP) is a research and mentoring program for entering undergraduate students offered by the University of Washington Astronomy Department since 2005. The primary goal of Pre-MAP is to recruit and retain students from groups traditionally underrepresented in science, technology, engineering, and mathematics (STEM) through early exposure to guided research projects. The Pre-MAP seminar is the core component of the program and offers instruction in computing skills, data manipulation, science writing, statistical analysis, and scientific speaking and presentation skills. Students choose research projects proposed by faculty, post-docs and graduate students in areas related to astrophysics, planetary science, and astrobiology. Pre-MAP has been successful in retaining underrepresented students in STEM fields relative to the broader UW population, and we've found these students are more likely to graduate and excel academically than their peers. As of fall 2015, more than one hundred students have taken the Pre-MAP seminar, and both internal and external evaluations have shown that all groups of participating students report an increased interest in astronomy and science careers at the end of the seminar. This talk will provide an overview of the program and the structure of the core seminar. In particular, the talk will focus on additions and revisions to the seminar course over the last few years, such as the introduction of a public speaking coach, career and internship modules, and the formalization of external lab tours.

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

Energy Technology Data Exchange (ETDEWEB)

Quake, Steve

2011-10-12

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Marijuana, other drugs, and alcohol use by drivers in Washington State.

Science.gov (United States)

2016-07-01

In Washington State legal sales of marijuana began July 8, 2014. A voluntary, anonymous roadside study was conducted to assess the prevalence of drivers testing positive for alcohol and other drugs, including marijuana, on Washingtons roads. Data ...

Physical data collected from Seaglider SG119 during WA Coast September 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-09-15 to 2009-01-07 (NCEI Accession 0156194)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG005 during WA Coast June 2005 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2005-06-08 to 2005-11-16 (NCEI Accession 0155972)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG014 during WA Coast April 2006 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2006-04-24 to 2006-11-09 (NCEI Accession 0156076)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG012 during WA Coast November 2005 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2005-11-16 to 2006-03-04 (NCEI Accession 0156521)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG005 during WA Coast August 2004 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2004-08-30 to 2004-12-23 (NCEI Accession 0155941)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG101 during WA Coast, April 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-04-01 to 2008-07-31 (NCEI Accession 0156172)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

Physical data collected from Seaglider SG030 during Cascadia 17 January 2008 in the North Pacific Ocean, Coastal Waters of Washington/Oregon deployed from 2008-01-17 to 2008-01-22 (NCEI Accession 0156178)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Seaglider is a buoyancy driven autonomous underwater vehicle (AUV) developed by scientists and engineers at the University of Washington's School of Oceanography and...

10KP: A phylodiverse genome sequencing plan.

Science.gov (United States)

Cheng, Shifeng; Melkonian, Michael; Smith, Stephen A; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Li, Fay-Wei; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun; Wong, Gane Ka-Shu

2018-03-01

Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here.

10KP: A phylodiverse genome sequencing plan

Science.gov (United States)

Cheng, Shifeng; Melkonian, Michael; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun

2018-01-01

Abstract Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here. PMID:29618049

Southwestern Washington 6 arc-second DEM

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The 6-second Southwest Washington Elevation Grid provides bathymetric data in ASCII raster format of 6-second resolution in geographic coordinates. This grid is...

Microbial Genomics: The Expanding Universe of Bacterial Defense Systems.

Science.gov (United States)

Forsberg, Kevin J; Malik, Harmit S

2018-04-23

Bacteria protect themselves against infection using multiple defensive systems that move by horizontal gene transfer and accumulate in genomic 'defense islands'. A recent study exploited these features to uncover ten novel defense systems, substantially expanding the catalog of bacterial defense systems and predicting the discovery of many more. Copyright © 2018 Elsevier Ltd. All rights reserved.

77 FR 37317 - Drawbridge Operation Regulation; Lake Washington, Seattle, WA

Science.gov (United States)

2012-06-21

..., 2012. The deviation allows the floating draw span of the SR 520 Lake Washington Bridge to remain in the... schedule that governs the State Route 520 (SR 520) Bridge across Lake Washington at Seattle, WA. This... allows the bridge to remain in the closed position to allow safe movement of event participants. DATES...

Timber resource statistics for southwest Washington.

Science.gov (United States)

Patricia M. Bassett; Daniel D. Oswald

1981-01-01

This report summarizes a 1978 timber-resource inventory of six counties in southwest Washington: Clark, Cowlitz, Lewis, Pacific, Skamania, and Wahkiakum. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

Genome sequence of vibrio cholerae G4222, a South African clinical isolate

CSIR Research Space (South Africa)

Le Rouw, Wouter J

2013-03-01

Full Text Available of Microbiology and Plant Pathology, University of Pretoria, South Africab; Center for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, South Africac Vibrio cholerae, a Gram-negative pathogen autochthonous to the aquatic environment..., is the causative agent of cholera. Here, we report the complete genome sequence of V. choleraeG4222, a clinical isolate from South Africa. Received 17 January 2013 Accepted 8 February 2013 Published 14 March 2013 Citation le Roux WJ, Chan WY, De Maayer P, Venter SN...

Evolution and Diversity of Transposable Elements in Vertebrate Genomes.

Science.gov (United States)

Sotero-Caio, Cibele G; Platt, Roy N; Suh, Alexander; Ray, David A

2017-01-01

Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

To Be a Slave: The Boyhood of Booker T. Washington.

Science.gov (United States)

National Park Service (Dept. of Interior), Washington, DC.

The Booker T. Washington National Monument preserves and protects the birth site and childhood home of Booker T. Washington, while interpreting his life experiences and significance in U.S. history as the most powerful African American between 1895 and 1915. The park provides a resource for public education and a focal point for continuing…

Population Genomics of Paramecium Species.

Science.gov (United States)

Johri, Parul; Krenek, Sascha; Marinov, Georgi K; Doak, Thomas G; Berendonk, Thomas U; Lynch, Michael

2017-05-01

Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess genomic variation in Paramecium, one of the most well-studied ciliate genera. The Paramecium aurelia complex consists of ∼15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs, as long as 320 MYA) and possess extremely streamlined genomes. We examine patterns of both nuclear and mitochondrial polymorphism, by sequencing whole genomes of 10-13 worldwide isolates of each of three species belonging to the P. aurelia complex: P. tetraurelia, P. biaurelia, P. sexaurelia, as well as two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Intergenic regions are highly constrained relative to coding sequences, especially in P. caudatum and P. multimicronucleatum that have shorter intergenic distances. Sequence diversity and divergence are reduced up to ∼100-150 bp both upstream and downstream of genes, suggesting strong constraints imposed by the presence of densely packed regulatory modules. In addition, comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species. This study presents the first genome-wide population-genomic analysis in ciliates and provides a valuable resource for future studies in evolutionary and functional genetics in Paramecium. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Timber resource statistics for eastern Washington.

Science.gov (United States)

Patricia M. Bassett; Daniel D. Oswald

1983-01-01

This report summarizes a 1980 timber resource inventory of the 16 forested counties in Washington east of the crest of the Cascade Range. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

40 CFR 81.348 - Washington.

Science.gov (United States)

2010-07-01

... 5/14/01 Attainment The City of Kent and a portion of the Green River valley bounded on the east and... Type Seattle-Tacoma Area: Seattle-Tacoma Urban Area (as defined by the Washington Department of Transportation urban area maps) King County (part) Attainment Pierce County (part) Attainment Snohomish County...

Genomic and Functional Approaches to Understanding Cancer Aneuploidy.

Science.gov (United States)

Taylor, Alison M; Shih, Juliann; Ha, Gavin; Gao, Galen F; Zhang, Xiaoyang; Berger, Ashton C; Schumacher, Steven E; Wang, Chen; Hu, Hai; Liu, Jianfang; Lazar, Alexander J; Cherniack, Andrew D; Beroukhim, Rameen; Meyerson, Matthew

2018-04-09

Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was anti-correlated with expression of immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss of chromosome arm 3p in squamous cancers. We applied genome engineering to delete 3p in lung cells, causing decreased proliferation rescued in part by chromosome 3 duplication. This study defines genomic and phenotypic correlates of cancer aneuploidy and provides an experimental approach to study chromosome arm aneuploidy. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Simultaneous gene finding in multiple genomes.

Science.gov (United States)

König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

2016-11-15

As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Fourteenth-Sixteenth Microbial Genomics Conference-2006-2008

Energy Technology Data Exchange (ETDEWEB)

Miller, Jeffrey H

2011-04-18

The concept of an annual meeting on the E. coli genome was formulated at the Banbury Center Conference on the Genome of E. coli in October, 1991. The first meeting was held on September 10-14, 1992 at the University of Wisconsin, and this was followed by a yearly series of meetings, and by an expansion to include The fourteenth meeting took place September 24-28, 2006 at Lake Arrowhead, CA, the fifteenth September 16-20, 2007 at the University of Maryland, College Park, MD, and the sixteenth September 14-18, 2008 at Lake Arrowhead. The full program for the 16th meeting is attached. There have been rapid and exciting advances in microbial genomics that now make possible comparing large data sets of sequences from a wide variety of microbial genomes, and from whole microbial communities. Examining the “microbiomes”, the living microbial communities in different host organisms opens up many possibilities for understanding the landscape presented to pathogenic microorganisms. For quite some time there has been a shifting emphasis from pure sequence data to trying to understand how to use that information to solve biological problems. Towards this end new technologies are being developed and improved. Using genetics, functional genomics, and proteomics has been the recent focus of many different laboratories. A key element is the integration of different aspects of microbiology, sequencing technology, analysis techniques, and bioinformatics. The goal of these conference is to provide a regular forum for these interactions to occur. While there have been a number of genome conferences, what distinguishes the Microbial Genomics Conference is its emphasis on bringing together biology and genetics with sequencing and bioinformatics. Also, this conference is the longest continuing meeting, now established as a major regular annual meeting. In addition to its coverage of microbial genomes and biodiversity, the meetings also highlight microbial communities and the use of

Refining aging criteria for northern sea otters in Washington State

Science.gov (United States)

Schuler, Krysten L.; Baker, Bridget B.; Mayer, Karl A.; Perez-Heydrich, Carolina; Holahan, Paula M.; Thomas, Nancy J.; White, C. LeAnn

2018-01-01

Measurement of skull ossification patterns is a standard method for aging various mammalian species and has been used to age Russian, Californian, and Alaskan sea otter populations. Cementum annuli counts have also been verified as an accurate aging method for the Alaskan sea otter population. In this study, cementum annuli count results and skull ossification patterns were compared as methods for aging the northern sea otter (Enhydra lutris kenyoni) population in Washington State. Significant agreement was found between the two methods suggesting that either method could be used to age the Washington population of otters. This study also found that ossification of the squamosal-jugal suture at the ventral glenoid fossa can be used to differentiate male subadults from adults. To assist field biologists or others without access to cementum annuli or skull ossification analysis techniques, a suite of morphologic, physiologic, and developmental characteristics were analyzed to assess whether a set of these more easily accessible parameters could also predict age class for the Washington population of otters. Tooth condition score, evidence of reproductive activity in females, and tooth eruption pattern were identified as the most useful criteria for classifying Washington sea otters as pups, juveniles, subadults, or adults/aged adults. A simple decision tree based on characteristics accessible in the field or at necropsy was created that can be used to reliably predict age class of Washington sea otters as determined by cementum annuli.

76 FR 18001 - Irish Potatoes Grown in Washington; Decreased Assessment Rate

Science.gov (United States)

2011-04-01

... IR] Irish Potatoes Grown in Washington; Decreased Assessment Rate AGENCY: Agricultural Marketing... rate established for the State of Washington Potato Committee (Committee) for the 2011-2012 and subsequent fiscal periods from $0.0035 to $0.003 per hundredweight of potatoes handled. The Committee locally...

76 FR 41589 - Irish Potatoes Grown in Washington; Decreased Assessment Rate

Science.gov (United States)

2011-07-15

... FIR] Irish Potatoes Grown in Washington; Decreased Assessment Rate AGENCY: Agricultural Marketing... established for the State of Washington Potato Committee (Committee) for the 2011-2012 and subsequent fiscal periods from $0.0035 to $0.003 per hundredweight of potatoes handled. The Committee locally administers...

Booker T. Washington's Educational Contributions to Contemporary Practices of Sustainable Development

Science.gov (United States)

Grant, Brett G.

2014-01-01

This article discusses Booker T. Washington's educational contributions to contemporary practices of sustainable development. In particular, the article looks at Washington's contributions in the areas of economic sustainability and entrepreneurship, character development, and aesthetics. As states continue to contemplate and evaluate the value of…

Genome Annotation and Transcriptomics of Oil-Producing Algae

Science.gov (United States)

2015-03-16

AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

Simple, quick and cost-efficient: A universal RT-PCR and sequencing strategy for genomic characterisation of foot-and-mouth disease viruses.

Science.gov (United States)

Dill, V; Beer, M; Hoffmann, B

2017-08-01

Foot-and-mouth disease (FMD) is a major contributor to poverty and food insecurity in Africa and Asia, and it is one of the biggest threats to agriculture in highly developed countries. As FMD is extremely contagious, strategies for its prevention, early detection, and the immediate characterisation of outbreak strains are of great importance. The generation of whole-genome sequences enables phylogenetic characterisation, the epidemiological tracing of virus transmission pathways and is supportive in disease control strategies. This study describes the development and validation of a rapid, universal and cost-efficient RT-PCR system to generate genome sequences of FMDV, reaching from the IRES to the end of the open reading frame. The method was evaluated using twelve different virus strains covering all seven serotypes of FMDV. Additionally, samples from experimentally infected animals were tested to mimic diagnostic field samples. All primer pairs showed a robust amplification with a high sensitivity for all serotypes. In summary, the described assay is suitable for the generation of FMDV sequences from all serotypes to allow immediate phylogenetic analysis, detailed genotyping and molecular epidemiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102.

Science.gov (United States)

Brown, Nathan M; Mueller, Ryan S; Shepardson, Jonathan W; Landry, Zachary C; Morré, Jeffrey T; Maier, Claudia S; Hardy, F Joan; Dreher, Theo W

2016-06-13

Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013 and maintained in non-axenic culture. The Anabaena sp. WA102 5.7 Mbp genome assembly has been closed with long-read, single-molecule sequencing and separately a draft genome assembly has been produced with short-read sequencing technology. The closed and draft genome assemblies are compared, showing a correlation between long repeats in the genome and the many gaps in the short-read assembly. Anabaena sp. WA102 encodes anatoxin-a biosynthetic genes, as does its close relative Anabaena sp. AL93 (also introduced in this study). These strains are distinguished by differences in the genes for light-harvesting phycobilins, with Anabaena sp. AL93 possessing a phycoerythrocyanin operon. Biologically relevant structural variants in the Anabaena sp. WA102 genome were detected only by long-read sequencing: a tandem triplication of the anaBCD promoter region in the anatoxin-a synthase gene cluster (not triplicated in Anabaena sp. AL93) and a 5-kbp deletion variant present in two-thirds of the population. The genome has a large number of mobile elements (160). Strikingly, there was no synteny with the genome of its nearest fully assembled relative, Anabaena sp. 90. Structural and functional genome analyses indicate that Anabaena sp. WA102 has a flexible genome. Genome closure, which can be readily achieved with long-read sequencing, reveals large scale (e.g., gene order) and local structural features that should be considered in understanding genome evolution and function.

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes

Directory of Open Access Journals (Sweden)

Wang Zhengyuan

2008-11-01

Full Text Available Abstract Background Nematode.net http://www.nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes. Beyond the well-characterized model nematode C. elegans, over 500,000 expressed sequence tags (ESTs and nearly 600,000 genome survey sequences (GSSs have been generated from 36 nematode species as part of the Parasitic Nematode Genomics Program undertaken by the Genome Center at Washington University School of Medicine. However, these sequencing data are not present in most publicly available protein databases, which only include sequences in Swiss-Prot. Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes or full-length proteins. Description Here we present the NemaPath pathway server, a web-based pathway-level visualization tool for navigating putative metabolic pathways for over 30 nematode species, including 27 parasites. The NemaPath approach consists of two parts: 1 a backend tool to align and evaluate nematode genomic sequences (curated EST contigs against the annotated Kyoto Encyclopedia of Genes and Genomes (KEGG protein database; 2 a web viewing application that displays annotated KEGG pathway maps based on desired confidence levels of primary sequence similarity as defined by a user. NemaPath also provides cross-referenced access to nematode genome information provided by other tools available on Nematode.net, including: detailed NemaGene EST cluster information; putative translations; GBrowse EST cluster views; links from nematode data to external databases for corresponding synonymous C. elegans counterparts, subject matches in KEGG's gene database, and also KEGG Ontology (KO identification. Conclusion The NemaPath server hosts metabolic pathway mappings for 30 nematode species and is available on the World Wide Web at http://nematode.net/cgi-bin/keggview.cgi. The nematode source sequences used for the metabolic pathway

Economic Impact of Pacific Northwest National Laboratory on the State of Washington in Fiscal Year 2014

Energy Technology Data Exchange (ETDEWEB)

Scott, Michael J.; Niemeyer, Jackie M.

2015-11-09

PNNL is a large economic entity with a total of 4,308 employees, $939 million (M) in total funding, and $1.02 billion (B) in total spending during FY 2014. The number of employees that live in Washington State is 4,026 or 93 percent of the Laboratory staff. he Laboratory directly and indirectly supported $1.45 billion in economic output, 6,832 jobs, and $517 million in Washington State wage income from current operations. The state also gained more than $1.19 billion in output, over 6,200 jobs, and $444 million in income through closely related economic activities such as visitors, health care spending, spending by resident retirees, and spinoff companies. PNNL affects Washington’s economy through commonly recognized economic channels, including spending on payrolls and other goods and services that support Laboratory operations. Less commonly recognized channels also have their own impacts and include company-supported spending on health care for its staff members and retirees, spending of its resident retirees, Laboratory visitor spending, and the economic activities in a growing constellation of “spinoff” companies founded on PNNL research, technology, and managerial expertise. PNNL also has a significant impact on science and technology education and community not-for-profit organizations. PNNL is an active participant in the future scientific enterprise in Washington with the state’s K-12 schools, colleges, and universities. The Laboratory sends staff members to the classroom and brings hundreds of students to the PNNL campus to help train the next generation of scientists, engineers, mathematicians, and technicians. This investment in human capital, though difficult to measure in terms of current dollars of economic output, is among the important lasting legacies of the Laboratory. Finally, PNNL contributes to the local community with millions of dollars’ worth of cash and in-kind corporate and staff contributions, all of which strengthen the

Promoting synergistic research and education in genomics and bioinformatics.

Science.gov (United States)

Yang, Jack Y; Yang, Mary Qu; Zhu, Mengxia Michelle; Arabnia, Hamid R; Deng, Youping

2008-01-01

scientific achievements by bridging these two very important disciplines into an interactive and attractive forum. Keeping this objective in mind, Biocomp 2007 aims to promote interdisciplinary and multidisciplinary education and research. 25 high quality peer-reviewed papers were selected from 400+ submissions for this supplementary issue of BMC Genomics. Those papers contributed to a wide-range of important research fields including gene expression data analysis and applications, high-throughput genome mapping, sequence analysis, gene regulation, protein structure prediction, disease prediction by machine learning techniques, systems biology, database and biological software development. We always encourage participants submitting proposals for genomics sessions, special interest research sessions, workshops and tutorials to Professor Hamid R. Arabnia (hra@cs.uga.edu) in order to ensure that Biocomp continuously plays the leadership role in promoting inter/multidisciplinary research and education in the fields. Biocomp received top conference ranking with a high score of 0.95/1.00. Biocomp is academically co-sponsored by the International Society of Intelligent Biological Medicine and the Research Laboratories and Centers of Harvard University--Massachusetts Institute of Technology, Indiana University--Purdue University, Georgia Tech--Emory University, UIUC, UCLA, Columbia University, University of Texas at Austin and University of Iowa etc. Biocomp--Worldcomp brings leading scientists together across the nation and all over the world and aims to promote synergistic components such as keynote lectures, special interest sessions, workshops and tutorials in response to the advances of cutting-edge research.

Microbial species delineation using whole genome sequences.

Science.gov (United States)

Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

2015-08-18

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

An annotated checklist of the vascular flora of Washington County Mississippi

Science.gov (United States)

Field explorations have yielded 257 species new to Washington County, Mississippi and Calandrinia ciliata (Ruiz & Pav.) DC. and Ruellia nudiflora (Engelm. & Gray) Urban new to the state. An annotated list of 796 taxa for Washington County is provided and excludes 62 species that were reported from ...

Washington: a guide to geothermal energy development

Energy Technology Data Exchange (ETDEWEB)

Bloomquist, R.G.; Basescu, N.; Higbee, C.; Justus, D.; Simpson, S.

1980-06-01

Washington's geothermal potential is discussed. The following topics are covered: exploration, drilling, utilization, legal and institutional setting, and economic factors of direct use projects. (MHR)

Non-Random Inversion Landscapes in Prokaryotic Genomes Are Shaped by Heterogeneous Selection Pressures.

Science.gov (United States)

Repar, Jelena; Warnecke, Tobias

2017-08-01

Inversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1,651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased toward (symmetric) inversions around the origin-terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus-Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favoring symmetric rearrangements in archaea with a single origin of replication. Within clades, we find strong but clade-specific relationships between symmetric inversion bias and different features of adaptive genome architecture, including the distance of essential genes to the origin of replication and the preferential localization of genes on the leading strand. We suggest that heterogeneous selection pressures have converged to produce similar patterns of structural genome evolution across prokaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

WashingtonOnline Virtual Campus: Infusing Culture in Dispersed Web-Based Higher Education

Directory of Open Access Journals (Sweden)

Shalin Hai-Jew

2004-08-01

Full Text Available Started in 1997, WashingtonOnline Virtual Campus (WAOL consists of a consortium of 34 community colleges around Washington State to provide asynchronous online learning. WAOL bears many of the features of a loosely coupled organization with its geographically dispersed frontline instructors, fragmented external environment, modularity of courses and supervision, and its use of enhanced leadership and technology to communicate a culture. Recent surveys of its administration, instructors, and staff found disparities in various constituencies’ perspectives on the organization’s culture, decision-making, values, brand or reputation, communications, and WAOL’s authorizing environment. Research suggests that WAOL benefits from some aspects of loose coupling: greater adaptive abilities and responsiveness to the State’s college system; “fast” course development and launching; and isolated breakdowns. There is, however, a persistent difficulty in conveying a cohesive culture. There is a perception of WAOL’s invisibility among its varied constituencies. This organization is at a crossroads, with the threat of colleges disconnecting from this consortium. WAOL should redefine its direction and purpose, such as coupling with local universities to provide not only associates degrees but full Baccalaureate and/ or Masters degrees. It may strengthen its position by improving learner supports, publicizing its decisions, creating a stronger sense of virtual community among the instructors (as in its recent creation of an online community for instructors, increased participative decision-making and use of line faculty and staff insights, and greater course varieties.

Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes.

Science.gov (United States)

Christie, Joshua R; Beekman, Madeleine

2017-03-01

Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Privacy-preserving techniques of genomic data-a survey.

Science.gov (United States)

Aziz, Md Momin Al; Sadat, Md Nazmus; Alhadidi, Dima; Wang, Shuang; Jiang, Xiaoqian; Brown, Cheryl L; Mohammed, Noman

2017-11-07

Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regarding the collection, storage and analysis of such sensitive human data. Recent results show that given some background information, it is possible for an adversary to reidentify an individual from a specific genomic data set. This can reveal the current association or future susceptibility of some diseases for that individual (and sometimes the kinship between individuals) resulting in a privacy violation. Regardless of these risks, our genomic data hold much importance in analyzing the well-being of us and the future generation. Thus, in this article, we discuss the different privacy and security-related problems revolving around human genomic data. In addition, we will explore some of the cardinal cryptographic concepts, which can bring efficacy in secure and private genomic data computation. This article will relate the gaps between these two research areas-Cryptography and Genomics. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

78 FR 48285 - Irish Potatoes Grown in Washington; Decreased Assessment Rate

Science.gov (United States)

2013-08-08

...; FV13-946-1 FIR] Irish Potatoes Grown in Washington; Decreased Assessment Rate AGENCY: Agricultural... established for the State of Washington Potato Committee (Committee) for the 2013-2014 fiscal year and all subsequent fiscal periods from $0.003 to $0.0025 per hundredweight of potatoes handled. The Committee locally...

Marijuana, other drugs, and alcohol use by drivers in Washington state : appendices.

Science.gov (United States)

2016-07-01

In Washington State legal sales of marijuana began July 8, 2014. A voluntary, anonymous roadside study was conducted to assess the prevalence of drivers testing positive for alcohol and other drugs, including marijuana, on Washingtons roads. Data ...

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes.

Science.gov (United States)

Francis, Warren R; Wörheide, Gert

2017-06-01

One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Impact of Interstate Migration on Human Capital Development in Washington

Science.gov (United States)

Spaulding, Randy

2010-01-01

Washington State is a leader in the innovation economy largely due to the combination of aerospace, software, and biomedical industries centered in the greater Seattle area; and, the state's high level of international trade. Despite Washington's national ranking, the state is overly reliant on importing educated workers from other states and…

Washington Schools Learn from Value Engineering.

Science.gov (United States)

Doleae, Michael L.; Childs, Harvey C.

1983-01-01

Results of two value engineering studies have shown that a review early in the design process can help save costs in school construction, maintenance, operation, and replacement. The value engineering concepts and technical manual are being presented throughout the state of Washington. (MLF)

Bridging the gap between university and industry: experiences with a senior level undergraduate supply chain course

NARCIS (Netherlands)

Steenhuis, H.J.; de Bruijn, E.J.

2005-01-01

Teaching operations and supply chain management courses can be challenging especially because textbook materials and “real” life experiences don’t always coincide. At Eastern Washington University a new approach has been introduced with a heavy emphasis on practical knowledge, i.e. oriented towards

Integrated Digital English Acceleration (I-DEA). Washington's Community and Technical Colleges

Science.gov (United States)

Washington State Board for Community and Technical Colleges, 2015

2015-01-01

Washington state has a large and rapidly growing foreign-born population. In 2011, immigrants made up 16.5 percent of Washington's civilian employed workforce, up from 7.1 percent in 1990. These new arrivals create jobs by forming businesses, spending income in local economies and raising employers' productivity. Thanks to project I-DEA…

Organelles genome stability of wheat plantlets produced by anther ...

African Journals Online (AJOL)

Yomi

2012-03-15

Mar 15, 2012 ... 1Department of Biotechnology, Faculty of Agricultural Technology, Al-Balqa' Applied University, ... genetic stability of wheat organelles genomes for plantlets produced by anther culture using restriction ..... of transgenic plants.

Hydrographic and biological observations on the Washington continental shelf and slope during the periods: 30 March-5 April, 8-15 June, and 6-11 September 1978

Energy Technology Data Exchange (ETDEWEB)

Postel, J.R.; Peterson, W.K. (comps.)

1981-01-01

During 1978 several cruises were successfully completed along a shelf-slope section off the Washington coast. These cruises were undertaken to collect seasonal information on the processes affecting phytoplankton production and distribution and data on the settling rate of organic matter in the sea during spring, early summer, and autumn conditions. This report summarizes the data collected on three cruises aboard the R/V CAYUSE, which was operated by Oregon State University. All three cruises originated and terminated in Newport, Oregon. Sampling was conducted at established station locations along a transect off Copalis Beach, Washington. Water depth varied from about 10 m at the innermost station (approx. 3 km from the beach) to over 1500 m at the outermost station (approx. 120 km from the beach).

KnowEnG: a knowledge engine for genomics.

Science.gov (United States)

Sinha, Saurabh; Song, Jun; Weinshilboum, Richard; Jongeneel, Victor; Han, Jiawei

2015-11-01

We describe here the vision, motivations, and research plans of the National Institutes of Health Center for Excellence in Big Data Computing at the University of Illinois, Urbana-Champaign. The Center is organized around the construction of "Knowledge Engine for Genomics" (KnowEnG), an E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. The scientist will come to KnowEnG with their own data sets in the form of spreadsheets and ask KnowEnG to analyze those data sets in the light of a massive knowledge base of community data sets called the "Knowledge Network" that will be at the heart of the system. The Center is undertaking discovery projects aimed at testing the utility of KnowEnG for transforming big data to knowledge. These projects span a broad range of biological enquiry, from pharmacogenomics (in collaboration with Mayo Clinic) to transcriptomics of human behavior. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Washington (Wash) C. Winn: In Memoriam

Centers for Disease Control (CDC) Podcasts

2012-03-08

Dr. Mike Miller and Dr. David Walker dicuss the career and life of noted clinical biologist, Dr. Washington C. Winn Jr.  Created: 3/8/2012 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 3/12/2012.

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

Science.gov (United States)

Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; Sivarajan, Sajeevan Radha; Patrignani, Andrea; Grüter, Simon; Poveda, Lucy; Shimizu-Inatsugi, Rie; Baeten, John; Francoijs, Kees-Jan; Nataraja, Karaba N; Reddy, Yellodu A Nanja; Phadnis, Shamprasad; Ravikumar, Ramapura L; Schlapbach, Ralph; Sreeman, Sheshshayee M; Shimizu, Kentaro K

2017-09-05

Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq.

Science.gov (United States)

Logan, Grace; Freimanis, Graham L; King, David J; Valdazo-González, Begoña; Bachanek-Bankowska, Katarzyna; Sanderson, Nicholas D; Knowles, Nick J; King, Donald P; Cottam, Eleanor M

2014-09-30

Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region. We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment.

"Harnessing genomics to improve health in India" – an executive course to support genomics policy

Directory of Open Access Journals (Sweden)

Acharya Tara

2004-05-01

Full Text Available Abstract Background The benefits of scientific medicine have eluded millions in developing countries and the genomics revolution threatens to increase health inequities between North and South. India, as a developing yet also industrialized country, is uniquely positioned to pioneer science policy innovations to narrow the genomics divide. Recognizing this, the Indian Council of Medical Research and the University of Toronto Joint Centre for Bioethics conducted a Genomics Policy Executive Course in January 2003 in Kerala, India. The course provided a forum for stakeholders to discuss the relevance of genomics for health in India. This article presents the course findings and recommendations formulated by the participants for genomics policy in India. Methods The course goals were to familiarize participants with the implications of genomics for health in India; analyze and debate policy and ethical issues; and develop a multi-sectoral opinion leaders' network to share perspectives. To achieve these goals, the course brought together representatives of academic research centres, biotechnology companies, regulatory bodies, media, voluntary, and legal organizations to engage in discussion. Topics included scientific advances in genomics, followed by innovations in business models, public sector perspectives, ethics, legal issues and national innovation systems. Results Seven main recommendations emerged: increase funding for healthcare research with appropriate emphasis on genomics; leverage India's assets such as traditional knowledge and genomic diversity in consultation with knowledge-holders; prioritize strategic entry points for India; improve industry-academic interface with appropriate incentives to improve public health and the nation's wealth; develop independent, accountable, transparent regulatory systems to ensure that ethical, legal and social issues are addressed for a single entry, smart and effective system; engage the public and

NSA Diana Wueger Published in Washington Quarterly

OpenAIRE

Grant, Catherine L.

2016-01-01

National Security Affairs (NSA) News NSA Faculty Associate for Research Diana Wueger has recently had an article titled “India’s Nuclear-Armed Submarines: Deterrence or Danger?” published in the Washington Quarterly.

Bibliography of the geology of the Columbia Basin and surrounding areas of Washington

International Nuclear Information System (INIS)

Tucker, G.B.; Rigby, J.G.

1979-07-01

In the fall of 1977, the Washington State Department of Natural Resources, Division of Geology and Earth Resources (WDGER), entered into a contract with the US Department of Energy, administered by Rockwell Hanford Operations (Rockwell) in Richland, Washington, as a principal contributor to a geologic study of feasibility of storing radioactive waste within Columbia River basalt. WDGER's responsibility was the production of this bibliography and a reconnaissance geologic map of the sediments overlying the Columbia River Basalt Group in the State of Washington. This bibliography is a compilation of all known published, unpublished, and open-file references dealing with geology and geophysics of the Columbia Basin of eastern Washington. The citations were obtained primarily from the WDGER and Washington State libraries; the Geo-Ref bibliographic system was also utilized. Because the WDGER portion of the study included preparation of a reconnaissance geologic map of surficial deposits in the Columbia Basin, available references dealing with this subject have been annotated. Many abstracts in the annotated section are quotations and have been copied directly from their respective publications

Bibliography of the geology of the Columbia Basin and surrounding areas of Washington

Energy Technology Data Exchange (ETDEWEB)

Tucker, G.B.; Rigby, J.G.

1979-07-01

In the fall of 1977, the Washington State Department of Natural Resources, Division of Geology and Earth Resources (WDGER), entered into a contract with the US Department of Energy, administered by Rockwell Hanford Operations (Rockwell) in Richland, Washington, as a principal contributor to a geologic study of feasibility of storing radioactive waste within Columbia River basalt. WDGER's responsibility was the production of this bibliography and a reconnaissance geologic map of the sediments overlying the Columbia River Basalt Group in the State of Washington. This bibliography is a compilation of all known published, unpublished, and open-file references dealing with geology and geophysics of the Columbia Basin of eastern Washington. The citations were obtained primarily from the WDGER and Washington State libraries; the Geo-Ref bibliographic system was also utilized. Because the WDGER portion of the study included preparation of a reconnaissance geologic map of surficial deposits in the Columbia Basin, available references dealing with this subject have been annotated. Many abstracts in the annotated section are quotations and have been copied directly from their respective publications.

Geologic Map of Northeastern Seattle (Part of the Seattle North 7.5' x 15' Quadrangle), King County, Washington

Science.gov (United States)

Booth, Derek B.; Troost, Kathy Goetz; Shimel, Scott A.

2009-01-01

This geologic map, approximately coincident with the east half of the Seattle North 7.5 x 15' quadrangle (herein, informally called the 'Seattle NE map'), covers nearly half of the City of Seattle and reaches from Lake Washington across to the Puget Sound shoreline. Land uses are mainly residential, but extensive commercial districts are located in the Northgate neighborhood, adjacent to the University of Washington, and along the corridors of Aurora Avenue North and Lake City Way. Industrial activity is concentrated along the Lake Washington Ship Canal and around Lake Union. One small piece of land outside of the quadrangle boundaries, at the west edge of the Bellevue North quadrangle, is included on this map for geographic continuity. Conversely, a small area in the northeast corner of the Seattle North quadrangle, on the eastside of Lake Washington, is excluded from this map. Within the boundaries of the map area are two large urban lakes, including the most heavily visited park in the State of Washington (Green Lake Park); a stream (Thornton Creek) that still hosts anadromous salmon despite having its headwaters in a golfcourse and a shopping center; parts of three cities, with a combined residential population of about 300,000 people; and the region's premier research institution, the University of Washington. The north boundary of the map is roughly NE 168th Street in the cities of Shoreline and Lake Forest Park, and the south boundary corresponds to Mercer Street in Seattle. The west boundary is 15th Avenue W (and NW), and the east boundary is formed by Lake Washington. Elevations range from sea level to a maximum of 165 m (541 ft), the latter on a broad till-covered knob in the city of Shoreline near the northwest corner of the map. Previous geologic maps of this area include those of Waldron and others (1962), Galster and Laprade (1991), and Yount and others (1993). Seattle lies within the Puget Lowland, an elongate structural and topographic basin between

The Politics of Information: Building a Relational Database To Support Decision-Making at a Public University.

Science.gov (United States)

Friedman, Debra; Hoffman, Phillip

2001-01-01

Describes creation of a relational database at the University of Washington supporting ongoing academic planning at several levels and affecting the culture of decision making. Addresses getting started; sharing the database; questions, worries, and issues; improving access to high-demand courses; the advising function; management of instructional…

Fuel management at Washington State Ferries

International Nuclear Information System (INIS)

Brodeur, P.; Olds, J.

2008-01-01

This presentation discussed Washington State Ferry (WSF) operations and provided details of a biodiesel research and demonstration project. Washington has the largest ferry system in the United States, with a total of 28 vessels that operate on 10 routes through 20 terminals. Routes vary by transit times, navigational challenges, and the proximity to population centres. WSF fuel and emissions management initiatives include exhaust emission studies, clean fuel initiatives, machinery upgrades, fuel conservation initiatives, and biodiesel testing. The organization is also using waste heat recovery and a positive restraint system. The WSF biodiesel pilot program was conducted using soy-derived fuels with a purifier disk stack. The program is in agreement with recent legislation requiring that 2 per cent of annual diesel fuel sales are from biodiesel fuels, and state legislation requiring that state agencies use a minimum of 20 per cent biodiesel blends in diesel-powered vessels and vehicles. Details of project partnerships were included. tabs., figs

Low-temperature geothermal resources of Washington

Energy Technology Data Exchange (ETDEWEB)

Schuster, J.E. [Washington State Dept. of Natural Resources, Olympia, WA (United States). Div. of Geology and Earth Resources; Bloomquist, R.G. [Washington State Energy Office, Olympia, WA (United States)

1994-06-01

This report presents information on the location, physical characteristics, and water chemistry of low-temperature geothermal resources in Washington. The database includes 941 thermal (>20C or 68F) wells, 34 thermal springs, lakes, and fumaroles, and 238 chemical analyses. Most thermal springs occur in the Cascade Range, and many are associated with stratovolcanoes. In contrast, 97 percent of thermal wells are located in the Columbia Basin of southeastern Washington. Some 83.5 percent are located in Adams, Benton, Franklin, Grant, Walla Walla, and Yakima Counties. Yakima County, with 259 thermal wells, has the most. Thermal wells do not seem to owe their origin to local sources of heat, such as cooling magma in the Earth`s upper crust, but to moderate to deep circulation of ground water in extensive aquifers of the Columbia River Basalt Group and interflow sedimentary deposits, under the influence of a moderately elevated (41C/km) average geothermal gradient.

Enhancing faba bean (Vicia faba L.) genome resources.

Science.gov (United States)

Cooper, James W; Wilson, Michael H; Derks, Martijn F L; Smit, Sandra; Kunert, Karl J; Cullis, Christopher; Foyer, Christine H

2017-04-01

Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly. Genomic reads were assembled de novo into contigs with a size range of 50-5000 bp. Over 85% of sequences did not align to known genes, of which ~10% could be aligned to known repetitive genetic elements. Over 26 000 of the reference transcriptome unigenes could be aligned to DNA-sequencing (DNA-seq) reads with high confidence. Moreover, this comparison identified 56 668 potential splice points in all identified unigenes. Sequence length data were extended at 461 putative loci through alignment of DNA-seq contigs to full-length, publicly available linkage marker sequences. Reads also yielded coverages of 3466× and 650× for the chloroplast and mitochondrial genomes, respectively. Inter- and intraspecies organelle genome comparisons established core legume organelle gene sets, and revealed polymorphic regions of faba bean organelle genomes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Locating inputs of freshwater to Lynch Cove, Hood Canal, Washington, using aerial infrared photography

Science.gov (United States)

Sheibley, Rich W.; Josberger, Edward G.; Chickadel, Chris

2010-01-01

The input of freshwater and associated nutrients into Lynch Cove and lower Hood Canal (fig. 1) from sources such as groundwater seeps, small streams, and ephemeral creeks may play a major role in the nutrient loading and hydrodynamics of this low dissolved-oxygen (hypoxic) system. These disbursed sources exhibit a high degree of spatial variability. However, few in-situ measurements of groundwater seepage rates and nutrient concentrations are available and thus may not represent adequately the large spatial variability of groundwater discharge in the area. As a result, our understanding of these processes and their effect on hypoxic conditions in Hood Canal is limited. To determine the spatial variability and relative intensity of these sources, the U.S. Geological Survey Washington Water Science Center collaborated with the University of Washington Applied Physics Laboratory to obtain thermal infrared (TIR) images of the nearshore and intertidal regions of Lynch Cove at or near low tide. In the summer, cool freshwater discharges from seeps and streams, flows across the exposed, sun-warmed beach, and out on the warm surface of the marine water. These temperature differences are readily apparent in aerial thermal infrared imagery that we acquired during the summers of 2008 and 2009. When combined with co-incident video camera images, these temperature differences allow identification of the location, the type, and the relative intensity of the sources.

Southwestern Washington 1/3 arc-second DEM

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The 1/3-second Southwest Washington Elevation Grid provides bathymetric data in ASCII raster format of 1/3-second resolution in geographic coordinates. This grid is...

Global-Service Learning and Student-Athletes: A Model for Enhanced Academic Inclusion at the University of Washington.

Science.gov (United States)

Barker, Holly M

The University of Washington (UW) continues to create opportunities to engage all students in transformational undergraduate educational opportunities, such as study abroad. This article describes specific efforts to increase inclusion for student-athletes in study abroad, particularly for first-generation students, including low-income students of color. Given the overrepresentation of students of color in sports vis-à-vis the larger student body at predominantly white institutions (PWIs), like UW, service-learning in communities beyond campus boundaries provides opportunities to apply international learning to a local context and to create a continuum of learning. By coupling educational theories from the classroom-particularly theories related to power and privilege-with community-based leadership in local communities, students are better prepared to actively engage in improving their own institutions. During the summers of 2013, 2014, and 2015, the author was the instructor for study abroad courses to French Polynesia with student-athletes. The courses were for 12 days (10 days on the ground and 2 days of flying), the maximum time that football players could be away from required summer workouts. This paper examines student evaluations from the French Polynesia trip in 2015. Student-athlete evaluations of a study abroad experience underscored: the transformative impact of study abroad to their academic, social, and athletic lives; the benefit of creating family-like relationships outside the confines of their sport; an appreciation for the many forms where indigenous knowledge resides, such as in navigation, dance, fishing, weaving, and cooking; intense feelings of culture shock upon return to the US, even when the trip is short in duration; a desire to engage with the diverse communities in Seattle beyond the scope of the program's structure, and; frustration, particularly for the male student-athletes, about the ways coaches, family, and friends wanted to

A 2015 comparison of operational performance : Washington state ferries to ferry operators worldwide.

Science.gov (United States)

2015-03-01

This report provides an update to the 2010 report A Comparison of Operational Performance: : Washington State Ferries to Ferry Operators Worldwide, observing changes in Washington State : Ferries, 23 other ferry systems, and the ferry industry ...

Willapa Bay, Washington Benthic Habitats 1995 Biotic

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — In June 1995, the Columbia River Estuary Study Taskforce (CREST) acquired 295 true color aerial photographs (1:12,000) of Willapa Bay, Washington, from the State of...

Willapa Bay, Washington Benthic Habitats 1995 Geoform

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — In June 1995, the Columbia River Estuary Study Taskforce (CREST) acquired 295 true color aerial photographs (1:12,000) of Willapa Bay, Washington, from the State of...

Willapa Bay, Washington Benthic Habitats 1995 Substrate

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — In June 1995, the Columbia River Estuary Study Taskforce (CREST) acquired 295 true color aerial photographs (1:12,000) of Willapa Bay, Washington, from the State of...

LiDAR (Terrain), THURSTON COUNTY, WASHINGTON, USA

Data.gov (United States)

Federal Emergency Management Agency, Department of Homeland Security — Fugro EarthData Company furnished the collection, processing, and development of LiDAR for 825 square miles in Washington (805 square miles of Thurston County and 20...

Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q.

Science.gov (United States)

Xie, Wen; Chen, Chunhai; Yang, Zezhong; Guo, Litao; Yang, Xin; Wang, Dan; Chen, Ming; Huang, Jinqun; Wen, Yanan; Zeng, Yang; Liu, Yating; Xia, Jixing; Tian, Lixia; Cui, Hongying; Wu, Qingjun; Wang, Shaoli; Xu, Baoyun; Li, Xianchun; Tan, Xinqiu; Ghanim, Murad; Qiu, Baoli; Pan, Huipeng; Chu, Dong; Delatte, Helene; Maruthi, M N; Ge, Feng; Zhou, Xueping; Wang, Xiaowei; Wan, Fanghao; Du, Yuzhou; Luo, Chen; Yan, Fengming; Preisser, Evan L; Jiao, Xiaoguo; Coates, Brad S; Zhao, Jinyang; Gao, Qiang; Xia, Jinquan; Yin, Ye; Liu, Yong; Brown, Judith K; Zhou, Xuguo Joe; Zhang, Youjun

2017-05-01

The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 437 kb, and a total length of 658 Mb. Annotation of repetitive elements and coding regions resulted in 265.0 Mb TEs (40.3%) and 20 786 protein-coding genes with putative gene family expansions, respectively. Phylogenetic analysis based on orthologs across 14 arthropod taxa suggested that MED/Q is clustered into a hemipteran clade containing A. pisum and is a sister lineage to a clade containing both R. prolixus and N. lugens. Genome completeness, as estimated using the CEGMA and Benchmarking Universal Single-Copy Orthologs pipelines, reached 96% and 79%. These MED/Q genomic resources lay a foundation for future 'pan-genomic' comparisons of invasive vs. noninvasive, invasive vs. invasive, and native vs. exotic Bemisia, which, in return, will open up new avenues of investigation into whitefly biology, evolution, and management. © The Author 2017. Published by Oxford University Press.

30 years of Physics Education Research at the University of Washington

Science.gov (United States)

Shaffer, Peter S.

2017-01-01

Over the past 30 years, members of the UW Physics Education Group have examined student learning in courses serving a wide range of populations. Most of the focus has been on elementary, middle, and high school teachers and students in introductory university physics courses, but more recently, the effort has expanded to include physics majors in upper-division courses on quantum mechanics and electrodynamics. In general, the group has taken a practical approach that focuses on identifying instructional strategies that are effective at promoting conceptual understanding and student reasoning ability. Examples will be drawn from across these courses to illustrate common themes and connections.

78 FR 17229 - Notice of Public Meeting, Eastern Washington Resource Advisory Council

Science.gov (United States)

2013-03-20

... DEPARTMENT OF THE INTERIOR Bureau of Land Management [LLORW00000 L102000000.ML0000 13XL1109AF.HAG13-0139] Notice of Public Meeting, Eastern Washington Resource Advisory Council AGENCY: Bureau of... the Eastern Washington Resource Advisory Council. The meeting on March 21, 2013, has been cancelled...

Improving Immunization Coverage in a Rural School District in Pierce County, Washington

Science.gov (United States)

Peterson, Robin M.; Cook, Carolyn; Yerxa, Mary E.; Marshall, James H.; Pulos, Elizabeth; Rollosson, Matthew P.

2012-01-01

Washington State has some of the highest percentages of school immunization exemptions in the country. We compared school immunization records in a rural school district in Pierce County, Washington, to immunization records in the state immunization information system (IIS) and parent-held records. Correcting school immunization records resulted…

GFVO: the Genomic Feature and Variation Ontology

KAUST Repository

Baran, Joachim

2015-05-05

Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

Draft genome of the gayal, Bos frontalis

Science.gov (United States)

Wang, Ming-Shan; Zeng, Yan; Wang, Xiao; Nie, Wen-Hui; Wang, Jin-Huan; Su, Wei-Ting; Xiong, Zi-Jun; Wang, Sheng; Qu, Kai-Xing; Yan, Shou-Qing; Yang, Min-Min; Wang, Wen; Dong, Yang; Zhang, Ya-Ping

2017-01-01

Abstract Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal. PMID:29048483

El Consenso de Washington: aciertos, yerros y omisiones

Directory of Open Access Journals (Sweden)

Juan Carlos Moreno-Brid

2004-12-01

Full Text Available This paper analyses the economic and social development of Latin America after nearly two decades of macroeconomic policies and reforms in line with the “Washington Consensus”. It shows that these policies did lower inflation and induced an export boom, but failed to boost domestic investment and to remove the balance of payments binding constraint on the region’s long–term path of economic expansion. Four alternative explanations of such poor performance of the Washington Consensus are compared. It is argued, in particular, that, contrary to mainstream opinion, in Latin America there is no clear association between the depth of macroeconomic reforms and economic growth performance.

Doctors of Osteopathy Licensed in Washington.

Science.gov (United States)

Senters, Jo

Based on information gathered by the Health Manpower Project through a survey cosponsored with the Washington Osteopathic Medical Association, this report begins with a statement of philosophy of osteopathic medicine and proceeds to comment on where such professional education is available. Remarks on the type of educational background of the…

Changing Housing Patterns in Metropolitan Washington

Science.gov (United States)

Grier, George; Grier, Eunice

1975-01-01

This testimony, before a public hearing of the New York City Commission on Human Rights in May 1974, summarizes extensive studies of changing minority residential patterns in metropolitan Washington and less extensive studies of other groups; the prospects for future desegregation and for using the growing economic potential of minority families…

Timber resource statistics for western Washington.

Science.gov (United States)

Coffin D. MacLean; Patricia M. Bassett; Glenn. Yeary

1992-01-01

This report summarizes a 1988-90 timber resource inventory of 19 counties in western Washington: Clallam, Clark, Cowlitz, Grays Harbor, Island, Jefferson, King, Kitsap, Lewis, Mason, Pacific, Pierce, San Juan, Skagit, Skamania, Snohomish, Thurston, Wahkiakum, and Whatcom. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

78 FR 53235 - 50th Anniversary of the March on Washington for Jobs and Freedom

Science.gov (United States)

2013-08-28

... Anniversary of the March on Washington for Jobs and Freedom By the President of the United States of America A... waters of the reflecting pool, to the proud base of the Washington Monument. They were men and women..., and justice for all. The March on Washington capped off a summer of discontent, a time when the...

A Grape Production Guide for Vocational Agriculture Instructors in Washington. Final Report.

Science.gov (United States)

Padelford, Stewart L.; Cvancara, Joseph G., Ed.

This curriculum guide is intended to provide vocational agriculture instructors with an up-to-date resource dealing with grape production in Washington. Addressed in the individual units of the guide are the following topics: the history of grape production; grape types important to Washington; site selection for a vineyard; establishment and…

Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm.

Science.gov (United States)

Jin, Jingjing; Lee, May; Bai, Bin; Sun, Yanwei; Qu, Jing; Rahmadsyah; Alfiko, Yuzer; Lim, Chin Huat; Suwanto, Antonius; Sugiharti, Maria; Wong, Limsoon; Ye, Jian; Chua, Nam-Hai; Yue, Gen Hua

2016-12-01

Oil palm is the world's leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Medicinal Cannabis: A Survey Among Health Care Providers in Washington State

Science.gov (United States)

Carlini, Beatriz H; Garrett, Sharon B; Carter, Gregory T

2017-02-01

Washington State allows marijuana use for medical (since 1998) and recreational (since 2012) purposes. The benefits of medicinal cannabis (MC) can be maximized if clinicians educate patients about dosing, routes of administration, side effects, and plant composition. However, little is known about clinicians' knowledge and practices in Washington State. An anonymous online survey assessed providers' MC knowledge, beliefs, clinical practices, and training needs. The survey was disseminated through health care providers' professional organizations in Washington State. Descriptive analysis compared providers who had and had not authorized MC for patients. Survey results informed the approach and content of an online training on best clinical practices of MC. Four hundred ninety-four health care providers responded to the survey. Approximately two-third were women, aged 30 to 60 years, and working in family or internal medicine. More than half of the respondents were legally allowed to write MC authorizations per Washington State law, and 27% of those had issued written MC authorizations. Overall, respondents reported low knowledge and comfort level related to recommending MC. Respondents rated MC knowledge as important and supported inclusion of MC training in medical/health provider curriculum. Most Washington State providers have not received education on scientific basis of MC or training on best clinical practices of MC. Clinicians who had issued MC authorizations were more likely to have received MC training than those who had not issued MC authorization. The potential of MCs to benefit some patients is hindered by the lack of comfort of clinicians to recommend it. Training opportunities are badly needed to address these issues.

National Nuclear Waste Policy Act of 1981. Hearings before the Committee on Environment and Public Works, United States Senate, Ninety-Seventh Congress, First Session on S. 1662, October 31, 1981, Richland, Washington; November 9, 1981, Washington, DC

International Nuclear Information System (INIS)

Anon.

1982-01-01

Hearings were held on October 31, 1981 in Richland, Washington and on November 9, 1981 in Washington, DC to discuss the effort in S. 1662 to establish a national policy and an environmentally acceptable program for managing nuclear wastes from domestic commercial activities. The Richland hearing was held in recognition that Washington State will bear the major impact of the legislation. Witnesses at the Washington, DC hearing included officials from states that are potential sites for radioactive waste storage and disposal facilities. The hearing record includes the testimony of 16 witnesses in Richland and seven in Washington, DC, followed by a reprint of S. 1662 and additional material submitted for the record

Economic Impact of Pacific Northwest National Laboratory on the State of Washington in Fiscal Year 2013

Energy Technology Data Exchange (ETDEWEB)

Scott, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Niemeyer, Jackie M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2014-12-01

Pacific Northwest National Laboratory (PNNL) is a large economic entity, with $1.06 billion in annual funding, $936 million in total spending, and 4,344 employees in fiscal year (FY) 2013. Four thousand, one hundred and one (4,101) employees live in Washington State. The Laboratory directly and indirectly supports almost $1.31 billion in economic output, 6,802 jobs, and $514 million in Washington State wage income from current operations. The state also gains more than $1.21 billion in output, more than 6,400 jobs, and $459 million in income through closely related economic activities, such as visitors, health care spending, spending by resident retirees, and spinoff companies. PNNL affects Washington’s economy through commonly recognized economic channels, including spending on payrolls and other goods and services that support Laboratory operations. Less-commonly recognized channels also have their own impacts and include company-supported spending on health care for its staff members and retirees, spending of its resident retirees, Laboratory visitor spending, and the economic activities in a growing constellation of “spinoff” companies founded on PNNL research, technology, and managerial expertise. PNNL also has a significant impact on science and technology education and community nonprofit organizations. PNNL is an active participant in the future scientific enterprise in Washington with the state’s K-12 schools, colleges, and universities. The Laboratory sends staff members to the classroom and brings hundreds of students to the PNNL campus to help train the next generation of scientists, engineers, mathematicians, and technicians. This investment in human capital, though difficult to measure in terms of current dollars of economic output, is among the important lasting legacies of the Laboratory. Finally, PNNL contributes to the local community with millions of dollars’ worth of cash and in-kind corporate and staff contributions, all of which

Washington Irving and the American Indian.

Science.gov (United States)

Littlefield, Daniel F., Jr.

1979-01-01

Some modern scholars feel that Washington Irving vacillated between romanticism and realism in his literary treatment of the American Indian. However, a study of all his works dealing with Indians, placed in context with his non-Indian works, reveals that his attitude towards Indians was intelligent and enlightened for his time. (CM)

University of Texas Southwestern Medical Center: High-Throughput siRNA Screening of a Non-Small Cell Lung Cancer (NSCLC) Cell Line Panel | Office of Cancer Genomics

Science.gov (United States)

The goal of this project is to use siRNA screens to identify NSCLC-selective siRNAs from two genome-wide libraries that will allow us to functionally define genetic dependencies of subtypes of NSCLC. Using bioinformatics tools, the CTD2 center at the University of Texas Southwestern Medical Center are discovering associations between this functional data (siRNAs) and NSCLC mutational status, methylation arrays, gene expression arrays, and copy number variation data that will help us identify new targets and enrollment biomarkers. 

The expanding universe of cohesin functions: a new genome stability caretaker involved in human disease and cancer.

Science.gov (United States)

Mannini, Linda; Menga, Stefania; Musio, Antonio

2010-06-01

Cohesin is responsible for sister chromatid cohesion, ensuring the correct chromosome segregation. Beyond this role, cohesin and regulatory cohesin genes seem to play a role in preserving genome stability and gene transcription regulation. DNA damage is thought to be a major culprit for many human diseases, including cancer. Our present knowledge of the molecular basis underlying genome instability is extremely limited. Mutations in cohesin genes cause human diseases such as Cornelia de Lange syndrome and Roberts syndrome/SC phocomelia, and all the cell lines derived from affected patients show genome instability. Cohesin mutations have also been identified in colorectal cancer. Here, we will discuss the human disorders caused by alterations of cohesin function, with emphasis on the emerging role of cohesin as a genome stability caretaker.

International team with Virginia Tech participation maps genome of dengue and yellow fever mosquito

OpenAIRE

Trulove, Susan

2007-01-01

Developing new strategies to prevent and control yellow fever and dengue fever has become more possible with the completion of the first draft of the genome sequence of Aedes aegypti mosquito by scientists led by Vishvanath Nene at The Institute for Genomic Research (TIGR) and David Severson at the University of Notre Dame. The genome is the complete set of genetic material including genes and other segments of DNA in an organism.

Report : public transportation in Washington State, 1984

Science.gov (United States)

1984-10-01

This report is an update of the Public Transportation in Washington State publication, dated December 1981. In order to reflect the changes that have occurred since that time, this report contains the most current data obtainable. Chapter One of this...

Scientific Framework for Stormwater Monitoring by the Washington State Department of Transportation

Science.gov (United States)

Sheibley, R.W.; Kelly, V.J.; Wagner, R.J.

2009-01-01

The Washington State Department of Transportation municipal stormwater monitoring program, in operation for about 8 years, never has received an external, objective assessment. In addition, the Washington State Department of Transportation would like to identify the standard operating procedures and quality assurance protocols that must be adopted so that their monitoring program will meet the requirements of the new National Pollutant Discharge Elimination System municipal stormwater permit. As a result, in March 2009, the Washington State Department of Transportation asked the U.S. Geological Survey to assess their pre-2009 municipal stormwater monitoring program. This report presents guidelines developed for the Washington State Department of Transportation to meet new permit requirements and regional/national stormwater monitoring standards to ensure that adequate processes and procedures are identified to collect high-quality, scientifically defensible municipal stormwater monitoring data. These include: (1) development of coherent vision and cooperation among all elements of the program; (2) a comprehensive approach for site selection; (3) an effective quality assurance program for field, laboratory, and data management; and (4) an adequate database and data management system.

Modeling the Risk of Radiation-Induced Acute Esophagitis for Combined Washington University and RTOG Trial 93-11 Lung Cancer Patients

International Nuclear Information System (INIS)

Huang, Ellen X.; Bradley, Jeffrey D.; El Naqa, Issam; Hope, Andrew J.; Lindsay, Patricia E.; Bosch, Walter R.; Matthews, John W.; Sause, William T.; Graham, Mary V.; Deasy, Joseph O.

2012-01-01

Purpose: To construct a maximally predictive model of the risk of severe acute esophagitis (AE) for patients who receive definitive radiation therapy (RT) for non–small-cell lung cancer. Methods and Materials: The dataset includes Washington University and RTOG 93-11 clinical trial data (events/patients: 120/374, WUSTL = 101/237, RTOG9311 = 19/137). Statistical model building was performed based on dosimetric and clinical parameters (patient age, sex, weight loss, pretreatment chemotherapy, concurrent chemotherapy, fraction size). A wide range of dose–volume parameters were extracted from dearchived treatment plans, including Dx, Vx, MOHx (mean of hottest x% volume), MOCx (mean of coldest x% volume), and gEUD (generalized equivalent uniform dose) values. Results: The most significant single parameters for predicting acute esophagitis (RTOG Grade 2 or greater) were MOH85, mean esophagus dose (MED), and V30. A superior–inferior weighted dose-center position was derived but not found to be significant. Fraction size was found to be significant on univariate logistic analysis (Spearman R = 0.421, p < 0.00001) but not multivariate logistic modeling. Cross-validation model building was used to determine that an optimal model size needed only two parameters (MOH85 and concurrent chemotherapy, robustly selected on bootstrap model-rebuilding). Mean esophagus dose (MED) is preferred instead of MOH85, as it gives nearly the same statistical performance and is easier to compute. AE risk is given as a logistic function of (0.0688 ∗ MED+1.50 ∗ ConChemo-3.13), where MED is in Gy and ConChemo is either 1 (yes) if concurrent chemotherapy was given, or 0 (no). This model correlates to the observed risk of AE with a Spearman coefficient of 0.629 (p < 0.000001). Conclusions: Multivariate statistical model building with cross-validation suggests that a two-variable logistic model based on mean dose and the use of concurrent chemotherapy robustly predicts acute esophagitis

Modeling the Risk of Radiation-Induced Acute Esophagitis for Combined Washington University and RTOG Trial 93-11 Lung Cancer Patients

Energy Technology Data Exchange (ETDEWEB)

Huang, Ellen X.; Bradley, Jeffrey D.; El Naqa, Issam [Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO (United States); Hope, Andrew J.; Lindsay, Patricia E. [Princess Margaret Hospital, Toronto, ON (Canada); Bosch, Walter R.; Matthews, John W. [Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO (United States); Sause, William T. [Department of Radiation Oncology, LDS Hospital, Salt Lake City, UT (United States); Graham, Mary V. [Department of Radiation Oncology, Phelps County Regional Hospital, Rolla, MO (United States); Deasy, Joseph O., E-mail: deasyj@mskcc.org [Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, NY (United States)

2012-04-01

Purpose: To construct a maximally predictive model of the risk of severe acute esophagitis (AE) for patients who receive definitive radiation therapy (RT) for non-small-cell lung cancer. Methods and Materials: The dataset includes Washington University and RTOG 93-11 clinical trial data (events/patients: 120/374, WUSTL = 101/237, RTOG9311 = 19/137). Statistical model building was performed based on dosimetric and clinical parameters (patient age, sex, weight loss, pretreatment chemotherapy, concurrent chemotherapy, fraction size). A wide range of dose-volume parameters were extracted from dearchived treatment plans, including Dx, Vx, MOHx (mean of hottest x% volume), MOCx (mean of coldest x% volume), and gEUD (generalized equivalent uniform dose) values. Results: The most significant single parameters for predicting acute esophagitis (RTOG Grade 2 or greater) were MOH85, mean esophagus dose (MED), and V30. A superior-inferior weighted dose-center position was derived but not found to be significant. Fraction size was found to be significant on univariate logistic analysis (Spearman R = 0.421, p < 0.00001) but not multivariate logistic modeling. Cross-validation model building was used to determine that an optimal model size needed only two parameters (MOH85 and concurrent chemotherapy, robustly selected on bootstrap model-rebuilding). Mean esophagus dose (MED) is preferred instead of MOH85, as it gives nearly the same statistical performance and is easier to compute. AE risk is given as a logistic function of (0.0688 Asterisk-Operator MED+1.50 Asterisk-Operator ConChemo-3.13), where MED is in Gy and ConChemo is either 1 (yes) if concurrent chemotherapy was given, or 0 (no). This model correlates to the observed risk of AE with a Spearman coefficient of 0.629 (p < 0.000001). Conclusions: Multivariate statistical model building with cross-validation suggests that a two-variable logistic model based on mean dose and the use of concurrent chemotherapy robustly predicts

Modeling the risk of radiation-induced acute esophagitis for combined Washington University and RTOG trial 93-11 lung cancer patients.

Science.gov (United States)

Huang, Ellen X; Bradley, Jeffrey D; El Naqa, Issam; Hope, Andrew J; Lindsay, Patricia E; Bosch, Walter R; Matthews, John W; Sause, William T; Graham, Mary V; Deasy, Joseph O

2012-04-01

To construct a maximally predictive model of the risk of severe acute esophagitis (AE) for patients who receive definitive radiation therapy (RT) for non-small-cell lung cancer. The dataset includes Washington University and RTOG 93-11 clinical trial data (events/patients: 120/374, WUSTL = 101/237, RTOG9311 = 19/137). Statistical model building was performed based on dosimetric and clinical parameters (patient age, sex, weight loss, pretreatment chemotherapy, concurrent chemotherapy, fraction size). A wide range of dose-volume parameters were extracted from dearchived treatment plans, including Dx, Vx, MOHx (mean of hottest x% volume), MOCx (mean of coldest x% volume), and gEUD (generalized equivalent uniform dose) values. The most significant single parameters for predicting acute esophagitis (RTOG Grade 2 or greater) were MOH85, mean esophagus dose (MED), and V30. A superior-inferior weighted dose-center position was derived but not found to be significant. Fraction size was found to be significant on univariate logistic analysis (Spearman R = 0.421, p < 0.00001) but not multivariate logistic modeling. Cross-validation model building was used to determine that an optimal model size needed only two parameters (MOH85 and concurrent chemotherapy, robustly selected on bootstrap model-rebuilding). Mean esophagus dose (MED) is preferred instead of MOH85, as it gives nearly the same statistical performance and is easier to compute. AE risk is given as a logistic function of (0.0688 MED+1.50 ConChemo-3.13), where MED is in Gy and ConChemo is either 1 (yes) if concurrent chemotherapy was given, or 0 (no). This model correlates to the observed risk of AE with a Spearman coefficient of 0.629 (p < 0.000001). Multivariate statistical model building with cross-validation suggests that a two-variable logistic model based on mean dose and the use of concurrent chemotherapy robustly predicts acute esophagitis risk in combined-data WUSTL and RTOG 93-11 trial datasets. Copyright �

Comparative genomic analysis of multidrug-resistant Streptococcus pneumoniae isolates

Directory of Open Access Journals (Sweden)

Pan F

2018-05-01

Full Text Available Fen Pan,1 Hong Zhang,1 Xiaoyan Dong,2 Weixing Ye,3 Ping He,4 Shulin Zhang,4 Jeff Xianchao Zhu,5 Nanbert Zhong1,2,6 1Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China; 2Department of Respiratory, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China; 3Shanghai Personal Biotechnology Co., Ltd, Shanghai, China; 4Department of Medical Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; 5Zhejiang Bioruida Biotechnology co. Ltd, Zhejiang, China; 6New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA Introduction: Multidrug resistance in Streptococcus pneumoniae has emerged as a serious problem to public health. A further understanding of the genetic diversity in antibiotic-resistant S. pneumoniae isolates is needed. Methods: We conducted whole-genome resequencing for 25 pneumococcal strains isolated from children with different antimicrobial resistance profiles. Comparative analysis focus on detection of single-nucleotide polymorphisms (SNPs and insertions and deletions (indels was conducted. Moreover, phylogenetic analysis was applied to investigate the genetic relationship among these strains. Results: The genome size of the isolates was ~2.1 Mbp, covering >90% of the total estimated size of the reference genome. The overall G+C% content was ~39.5%, and there were 2,200–2,400 open reading frames. All isolates with different drug resistance profiles harbored many indels (range 131–171 and SNPs (range 16,103–28,128. Genetic diversity analysis showed that the variation of different genes were associated with specific antibiotic resistance. Known antibiotic resistance genes (pbps, murMN, ciaH, rplD, sulA, and dpr were identified, and new genes (regR, argH, trkH, and PTS-EII closely related with antibiotic resistance were found, although these genes were primarily annotated

Westport, Washington Tsunami Forecast Grids for MOST Model

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Westport, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

The Path to Advanced Practice Licensure for Clinical Nurse Specialists in Washington State.

Science.gov (United States)

Schoonover, Heather

The aim of this study was to provide a review of the history and process to obtaining advanced practice licensure for clinical nurse specialists in Washington State. Before 2016, Washington State licensed certified nurse practitioners, certified nurse midwives, and certified nurse anesthetists under the designation of an advanced registered nurse practitioner; however, the state did not recognize clinical nurse specialists as advanced practice nurses. The work to drive the rule change began in 2007. The Washington Affiliate of the National Association of Clinical Nurse Specialists used the Power Elite Theory to guide advocacy activities, building coalitions and support for the desired rule changes. On January 8, 2016, the Washington State Nursing Care Quality Assurance Commission voted to amend the state's advanced practice rules, including clinical nurse specialists in the designation of an advanced practice nurse. Since the rule revision, clinical nurse specialists in Washington State have been granted advanced registered nurse practitioner licenses. Driving changes in state regulatory rules requires diligent advocacy, partnership, and a deep understanding of the state's rule-making processes. To be successful in changing rules, clinical nurse specialists must build strong partnerships with key influencers and understand the steps in practice required to make the desired changes.

Evaluating ballot initiative support for legalised marijuana: The case of Washington.

Science.gov (United States)

Collingwood, Loren; O'Brien, Ben Gonzalez; Dreier, Sarah

2018-03-11

In 2012, Washington and Colorado became the first U.S. states to legalise recreational marijuana. By 2016, eight states and the District of Columbia had legalised recreational marijuana, with more expected to consider it in 2018. Despite this trend, little academic research explains what drives ballot-initiative vote choice on marijuana legalisation. This paper uses a pre-election random sample voter survey to examine the individual characteristics that correlated with Washington voters' support for legal recreational marijuana. We find that voting on marijuana ballot initiatives largely reflects public opinion about marijuana and is particularly shaped voters' political ideology, party affiliation, religious affiliation and practice, and education. Notably, we find that those reporting experiences (i.e., someone they know) with the criminal justice system are more supportive of legalisation than those who do not. We conclude that marijuana legalisation voting behavior generally aligns with public opinion on the issue. However, one key aspect of Washington's legalisation campaign-the criminal injustices of marijuana illegality-helped shape Washington state voting behavior. Further research is needed to examine if, when, and in what contexts criminal justice campaign themes are likely to strengthen or undermine future states' marijuana legalisation efforts. Copyright © 2018 Elsevier B.V. All rights reserved.

Crash Fatality Rates After Recreational Marijuana Legalization in Washington and Colorado.

Science.gov (United States)

Aydelotte, Jayson D; Brown, Lawrence H; Luftman, Kevin M; Mardock, Alexandra L; Teixeira, Pedro G R; Coopwood, Ben; Brown, Carlos V R

2017-08-01

To evaluate motor vehicle crash fatality rates in the first 2 states with recreational marijuana legalization and compare them with motor vehicle crash fatality rates in similar states without recreational marijuana legalization. We used the US Fatality Analysis Reporting System to determine the annual numbers of motor vehicle crash fatalities between 2009 and 2015 in Washington, Colorado, and 8 control states. We compared year-over-year changes in motor vehicle crash fatality rates (per billion vehicle miles traveled) before and after recreational marijuana legalization with a difference-in-differences approach that controlled for underlying time trends and state-specific population, economic, and traffic characteristics. Pre-recreational marijuana legalization annual changes in motor vehicle crash fatality rates for Washington and Colorado were similar to those for the control states. Post-recreational marijuana legalization changes in motor vehicle crash fatality rates for Washington and Colorado also did not significantly differ from those for the control states (adjusted difference-in-differences coefficient = +0.2 fatalities/billion vehicle miles traveled; 95% confidence interval = -0.4, +0.9). Three years after recreational marijuana legalization, changes in motor vehicle crash fatality rates for Washington and Colorado were not statistically different from those in similar states without recreational marijuana legalization. Future studies over a longer time remain warranted.

Natural phenomena hazards, Hanford Site, Washington

International Nuclear Information System (INIS)

Conrads, T.J.

1998-01-01

This document presents the natural phenomena hazard loads for use in implementing DOE Order 5480.28, Natural Phenomena Hazards Mitigation, and supports development of double-shell tank systems specifications at the Hanford Site in south-central Washington State. The natural phenomena covered are seismic, flood, wind, volcanic ash, lightning, snow, temperature, solar radiation, suspended sediment, and relative humidity

Reefgenomics.Org - a repository for marine genomics data.

Science.gov (United States)

Liew, Yi Jin; Aranda, Manuel; Voolstra, Christian R

2016-01-01

Over the last decade, technological advancements have substantially decreased the cost and time of obtaining large amounts of sequencing data. Paired with the exponentially increased computing power, individual labs are now able to sequence genomes or transcriptomes to investigate biological questions of interest. This has led to a significant increase in available sequence data. Although the bulk of data published in articles are stored in public sequence databases, very often, only raw sequencing data are available; miscellaneous data such as assembled transcriptomes, genome annotations etc. are not easily obtainable through the same means. Here, we introduce our website (http://reefgenomics.org) that aims to centralize genomic and transcriptomic data from marine organisms. Besides providing convenient means to download sequences, we provide (where applicable) a genome browser to explore available genomic features, and a BLAST interface to search through the hosted sequences. Through the interface, multiple datasets can be queried simultaneously, allowing for the retrieval of matching sequences from organisms of interest. The minimalistic, no-frills interface reduces visual clutter, making it convenient for end-users to search and explore processed sequence data. DATABASE URL: http://reefgenomics.org. © The Author(s) 2016. Published by Oxford University Press.

Washington Windplant No. 1: Botanical resources field survey. Appendix B to Washington Windplant No. 1 EIS

International Nuclear Information System (INIS)

1994-12-01

KENETECH Windpower, Inc., has applied to Klickitat County for a conditional use permit to construct and operate a 115 Megawatt windfarm on an approximately 5110 hectare (12,630 acre) site in the Columbia Hills near Goldendale, Washington. A transmission services agreement between the Bonneville Power Administration (BPA) and utilities purchasing the Project's output will also be required. Klickitat County and BPA initiated the preparation of a joint SEPA/NEPA Environmental Impact Statement, under the authority of the Washington State Environmental Policy Act and the National Environmental Policy Act. The EIS addresses, among other issues, the Project's potential impact on rare, threatened or endangered, and sensitive plant species and communities as well as plant species of potential cultural importance. A field survey along potential impact corridors (turbine strings, roadways, and the transmission line alignment) was conducted between April and June, 1994 in order to identify rare plant species, high-quality native plant communities, and plant species of potential cultural importance present in these corridors. In addition, habitat maps of the entire 5110-ha project area were field verified. This report contains the results of that survey and an assessment of the potential project impacts

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.

Promoting Diversity in STEM through Active Recruiting and Mentoring: The Pre-Major in Astronomy Program (Pre-MAP) at the University of Washington

Science.gov (United States)

Schwieterman, Edward; Binder, Breanna; Tremmel, Michael; Garofali, Kristen; Agol, Eric; Meadows, Victoria

2015-11-01

The Pre-Major in Astronomy Program (Pre-MAP) is a research and mentoring program for underclassmen and transfer students offered by the University of Washington Astronomy Department since 2005. The primary goal of Pre-MAP is to recruit and retain students from groups traditionally underrepresented in science, technology, engineering, and mathematics (STEM) through early exposure to research. The Pre-MAP seminar is the core component of the program and offers instruction in computing skills, data manipulation, science writing, statistical analysis, and scientific speaking and presentation skills. Students choose research projects proposed by faculty, post-docs and graduate students in areas related to astrophysics, planetary science, and astrobiology. Pre-MAP has been successful in retaining underrepresented students in STEM fields relative to the broader UW population, and we've found these students are more likely to graduate and excel academically than their peers. As of spring 2015, more than one hundred students have taken the Pre-MAP seminar, and both internal and external evaluations have shown that all groups of participating students report an increased interest in astronomy and science careers at the end of the seminar. Several former Pre-MAP students have obtained or are pursuing doctoral and master’s degrees in STEM fields; many more work at NASA centers, teaching colleges, or as engineers or data analysts. Pre- MAP student research has produced dozens of publications in peer-reviewed research journals. This talk will provide an overview of the program: the structure of the seminar, examples of projects completed by students, cohort-building activities outside the seminar, funding sources, recruitment strategies, and the aggregate demographic and achievement data of our students. It is our hope that similar programs may be adopted successfully at other institutions.

Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae.

Science.gov (United States)

Nam, Bo-Hye; Kwak, Woori; Kim, Young-Ok; Kim, Dong-Gyun; Kong, Hee Jeong; Kim, Woo-Jin; Kang, Jeong-Ha; Park, Jung Youn; An, Cheul Min; Moon, Ji-Young; Park, Choul Ji; Yu, Jae Woong; Yoon, Joon; Seo, Minseok; Kim, Kwondo; Kim, Duk Kyung; Lee, SaetByeol; Sung, Samsun; Lee, Chul; Shin, Younhee; Jung, Myunghee; Kang, Byeong-Chul; Shin, Ga-Hee; Ka, Sojeong; Caetano-Anolles, Kelsey; Cho, Seoae; Kim, Heebal

2017-05-01

Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [ 1 ]. Abalone is an economically important fishery and aquaculture animal that is considered a highly prized seafood delicacy. The total global supply of abalone has increased 5-fold since the 1970s and farm production increased explosively from 50 mt to 103 464 mt in the past 40 years. Additionally, researchers have recently focused on abalone given their reported tumor suppression effect. However, despite the valuable features of this marine animal, no genomic information is available for the Haliotidae family and related research is still limited. To construct the H . discus hannai genome, a total of 580-G base pairs using Illumina and Pacbio platforms were generated with 322-fold coverage based on the 1.8-Gb estimated genome size of H . discus hannai using flow cytometry. The final genome assembly consisted of 1.86 Gb with 35 450 scaffolds (>2 kb). GC content level was 40.51%, and the N50 length of assembled scaffolds was 211 kb. We identified 29 449 genes using Evidence Modeler based on the gene information from ab initio prediction, protein homology with known genes, and transcriptome evidence of RNA-seq. Here we present the first Haliotidae genome, H . discus hannai , with sequencing data, assembly, and gene annotation information. This will be helpful for resolving the lack of genomic information in the Haliotidae family as well as providing more opportunities for understanding gastropod evolution. © The Authors 2017. Published by Oxford University Press.

Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

International Nuclear Information System (INIS)

Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

2000-01-01

A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society

Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

Energy Technology Data Exchange (ETDEWEB)

Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

2000-09-18

A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society.

Basic Education for Adults: Pathways to College and Careers for Washington's Emerging Workforce. Washington's Community and Technical Colleges

Science.gov (United States)

Washington State Board for Community and Technical Colleges, 2015

2015-01-01

This brief describes the Basic Education for Adults (BEdA) programs that bridge the gap between school and work, thereby creating pathways to college and careers for Washington's emerging workforce. BEdA programs teach foundational skills--reading, writing, math, technology and English language--so adults can move through college and into…

Genomic analyses of the CAM plant pineapple.

Science.gov (United States)

Zhang, Jisen; Liu, Juan; Ming, Ray

2014-07-01

The innovation of crassulacean acid metabolism (CAM) photosynthesis in arid and/or low CO2 conditions is a remarkable case of adaptation in flowering plants. As the most important crop that utilizes CAM photosynthesis, the genetic and genomic resources of pineapple have been developed over many years. Genetic diversity studies using various types of DNA markers led to the reclassification of the two genera Ananas and Pseudananas and nine species into one genus Ananas and two species, A. comosus and A. macrodontes with five botanical varieties in A. comosus. Five genetic maps have been constructed using F1 or F2 populations, and high-density genetic maps generated by genotype sequencing are essential resources for sequencing and assembling the pineapple genome and for marker-assisted selection. There are abundant expression sequence tag resources but limited genomic sequences in pineapple. Genes involved in the CAM pathway has been analysed in several CAM plants but only a few of them are from pineapple. A reference genome of pineapple is being generated and will accelerate genetic and genomic research in this major CAM crop. This reference genome of pineapple provides the foundation for studying the origin and regulatory mechanism of CAM photosynthesis, and the opportunity to evaluate the classification of Ananas species and botanical cultivars. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

An Examination of Gender Role Identity, Sexual Self-Esteem, Sexual Coercion and Sexual Victimization in a University Sample

Science.gov (United States)

Kelly, Theresa C.; Erickson, Chris D.

2007-01-01

The relationship between gender role identity, sexual self-esteem and sexual coercion was examined through a questionnaire. Participants were 84 undergraduate students from a university in Washington, DC. Contrary to what has been found in the literature, there were weak relationships between sexual coercion and masculinity, and sexual coercion…

Draft genome of the lined seahorse, Hippocampus erectus.

Science.gov (United States)

Lin, Qiang; Qiu, Ying; Gu, Ruobo; Xu, Meng; Li, Jia; Bian, Chao; Zhang, Huixian; Qin, Geng; Zhang, Yanhong; Luo, Wei; Chen, Jieming; You, Xinxin; Fan, Mingjun; Sun, Min; Xu, Pao; Venkatesh, Byrappa; Xu, Junming; Fu, Hongtuo; Shi, Qiong

2017-06-01

The lined seahorse, Hippocampus erectus , is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse ( H. comes ). We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior. © The Authors 2017. Published by Oxford University Press.

Science Technology Engineering and Math (STEM) Education MUST Begin in Early Childhood Education: A Systematic Analysis of Washington State Guidelines Used to Gauge the Development and Learning of Young Learners

Science.gov (United States)

Briseno, Luis Miguel

This paper reflects future direction for early Science Technology Engineering and Mathematics (STEM) education, science in particular. Washington State stakeholders use guidelines including: standards, curriculums and assessments to gauge young children's development and learning, in early childhood education (ECE). Next Generation Science Standards (NGSS), and the Framework for K-12 programs (National Research Council, 2011) emphasizes the need for reconfiguration of standards: "Too often standards are a long list of detailed and disconnected facts... this approach alienates young people, it also leaves them with fragments of knowledge and little sense of the inherent logic and consistency of science and of its universality." NGSS' position elevates the concern and need for learners to experience teaching and learning from intentionally designed cohesive curriculum units, rather than as a series of unrelated and isolated lessons. To introduce the argument the present study seeks to examine Washington State early learning standards. To evaluate this need, I examined balance and coverage/depth. Analysis measures the level of continuum in high-quality guidelines from which Washington State operates to serve its youngest citizens and their families.

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

Science.gov (United States)

Valach, Matus; Burger, Gertraud; Gray, Michael W; Lang, B Franz

2014-12-16

5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

High-speed and high-ratio referential genome compression.

Science.gov (United States)

Liu, Yuansheng; Peng, Hui; Wong, Limsoon; Li, Jinyan

2017-11-01

The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio. We present a high-performance referential genome compression algorithm named HiRGC. It is based on a 2-bit encoding scheme and an advanced greedy-matching search on a hash table. We compare the performance of HiRGC with four state-of-the-art compression methods on a benchmark dataset of eight human genomes. HiRGC takes compress about 21 gigabytes of each set of the seven target genomes into 96-260 megabytes, achieving compression ratios of 217 to 82 times. This performance is at least 1.9 times better than the best competing algorithm on its best case. Our compression speed is also at least 2.9 times faster. HiRGC is stable and robust to deal with different reference genomes. In contrast, the competing methods' performance varies widely on different reference genomes. More experiments on 100 human genomes from the 1000 Genome Project and on genomes of several other species again demonstrate that HiRGC's performance is consistently excellent. The C ++ and Java source codes of our algorithm are freely available for academic and non-commercial use. They can be downloaded from https://github.com/yuansliu/HiRGC. jinyan.li@uts.edu.au. 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

Integrated Basic Education and Skills Training (I-BEST). Washington's Community and Technical Colleges

Science.gov (United States)

Washington State Board for Community and Technical Colleges, 2014

2014-01-01

Washington's Integrated Basic Education and Skills Training Program (I-BEST) quickly teaches students literacy, work, and college-readiness skills so they can move through school and into living wage jobs faster. Pioneered by Washington's community and technical colleges, I-BEST uses a team-teaching approach to combine college-readiness classes…

Joint NEPA/SEPA draft environmental impact statement Washington Windplant No. 1

International Nuclear Information System (INIS)

1995-02-01

This is the draft Environmental Impact Statement for a proposed construction and operation of a 115 megawatt Washington Windplant No. 1 by KENETECH Windpower, Inc in Klickitat County, Washington. The Project would be constructed on private land (5,110 hectares) under easement to KENETECH Windpower, Inc., and would include approximately 345 type 33M-VS wind turbines. Alternatives to the Proposed Action include an alternative powerline route; a restricted areas alternative; a subarea development alternative; a no-action alternative

Plasma Science and Innovation Center at Washington, Wisconsin, and Utah State: Final Scientific Report for the University of Wisconsin-Madison

Energy Technology Data Exchange (ETDEWEB)

Sovinec, Carl R. [Univ. of Wisconsin, Madison, WI (United States)

2016-11-28

The University of Wisconsin-Madison component of the Plasma Science and Innovation Center (PSI Center) contributed to modeling capabilities and algorithmic efficiency of the Non-Ideal Magnetohydrodynamics with Rotation (NIMROD) Code, which is widely used to model macroscopic dynamics of magnetically confined plasma. It also contributed to the understanding of direct-current (DC) injection of electrical current for initiating and sustaining plasma in three spherical torus experiments: the Helicity Injected Torus-II (HIT-II), the Pegasus Toroidal Experiment, and the National Spherical Torus Experiment (NSTX). The effort was funded through the PSI Center's cooperative agreement with the University of Washington and Utah State University over the period of March 1, 2005 - August 31, 2016. In addition to the computational and physics accomplishments, the Wisconsin effort contributed to the professional education of four graduate students and two postdoctoral research associates. The modeling for HIT-II and Pegasus was directly supported by the cooperative agreement, and contributions to the NSTX modeling were in support of work by Dr. Bickford Hooper, who was funded through a separate grant. Our primary contribution to model development is the implementation of detailed closure relations for collisional plasma. Postdoctoral associate Adam Bayliss implemented the temperature-dependent effects of Braginskii's parallel collisional ion viscosity. As a graduate student, John O'Bryan added runtime options for Braginskii's models and Ji's K2 models of thermal conduction with magnetization effects and thermal equilibration. As a postdoctoral associate, O'Bryan added the magnetization effects for ion viscosity. Another area of model development completed through the PSI-Center is the implementation of Chodura's phenomenological resistivity model. Finally, we investigated and tested linear electron parallel viscosity, leveraged by support from

Endangered Species Case - Washington Toxics Coalition v. EPA

Science.gov (United States)

This Web page provides information on the Washington Toxics Coalition v. EPA case, related to protection of Pacific salmon and steelhead, and links to the biological opinions issued by the NMFS and EPA’s responses.

77 FR 61782 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

Science.gov (United States)

2012-10-11

... Washington State Parks and Recreation Commission at the address below by November 13, 2012. ADDRESSES: Alicia... affiliated with the human remains should contact Alicia Woods, Washington State Parks and Recreation...

RatMap--rat genome tools and data.

Science.gov (United States)

Petersen, Greta; Johnson, Per; Andersson, Lars; Klinga-Levan, Karin; Gómez-Fabre, Pedro M; Ståhl, Fredrik

2005-01-01

The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB-Genetics at Goteborg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. The database is under the supervision of the Rat Gene and Nomenclature Committee (RGNC); thus much attention is paid to rat gene nomenclature. RatMap presents information on rat idiograms, karyotypes and provides a unified presentation of the rat genome sequence and integrated rat linkage maps. A set of tools is also available to facilitate the identification and characterization of rat QTLs, as well as the estimation of exon/intron number and sizes in individual rat genes. Furthermore, comparative gene maps of rat in regard to mouse and human are provided.

RatMap—rat genome tools and data

Science.gov (United States)

Petersen, Greta; Johnson, Per; Andersson, Lars; Klinga-Levan, Karin; Gómez-Fabre, Pedro M.; Ståhl, Fredrik

2005-01-01

The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB–Genetics at Göteborg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. The database is under the supervision of the Rat Gene and Nomenclature Committee (RGNC); thus much attention is paid to rat gene nomenclature. RatMap presents information on rat idiograms, karyotypes and provides a unified presentation of the rat genome sequence and integrated rat linkage maps. A set of tools is also available to facilitate the identification and characterization of rat QTLs, as well as the estimation of exon/intron number and sizes in individual rat genes. Furthermore, comparative gene maps of rat in regard to mouse and human are provided. PMID:15608244

Genomic potential hypothesis of evolution: a concept of biogenesis in habitable spaces of the universe.

Science.gov (United States)

Schwabe, Christian

2002-11-01

The new hypothesis of evolution establishes a contiguity of life sciences with cosmology, physics, and chemistry, and provides a basis for the search for life on other planets. Chemistry is the sole driving force of the assembly of life, under the subtle guidance exerted by bonding orbital geometry. That phenomenon leads to multiple origins that function on the same principles but are different to the extent that their nucleic acid core varies. Thus, thoughts about the origins of life and the development of complexity have been transferred from the chance orientation of the past to the realm of atomic structures, which are subject to the laws of thermodynamics and kinetics. Evolution is a legitimate subject of basic science, and the complexity of life will submit to the laws of chemistry and physics as the problem is viewed from a new perspective. The paradigm connects life to the big events that formed every sphere of our living space and that keeps conditions fine-tuned for life to persist, perhaps a billion years or more. The "genomic potential" hypothesis leads to the prediction that life like ours is likely to exist in galaxies that are as distant from the origin of the universe as the Milky Way, and that the habitable zone of our galaxy harbors other living planets as well. Copyright 2002 Wiley-Liss, Inc.

78 FR 13887 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

Science.gov (United States)

2013-03-01

... Washington State Parks and Recreation Commission at the address below by April 1, 2013. ADDRESSES: Alicia... contact Alicia Woods, Washington State Parks and Recreation Commission, PO Box 42650, Olympia, WA 98504...

Washington Public Libraries Online: Collaborating in Cyberspace.

Science.gov (United States)

Wildin, Nancy

1997-01-01

Discussion of public libraries, the Internet, and the World Wide Web focuses on development of a Web site in Washington. Highlights include access to the Internet through online public access catalogs; partnerships between various types of libraries; hardware and software; HTML training; content design; graphics design; marketing; evaluation; and…

Phylogenetic classification and the universal tree.

Science.gov (United States)

Doolittle, W F

1999-06-25

From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

Distinguishing between "function" and "effect" in genome biology.

Science.gov (United States)

Doolittle, W Ford; Brunet, Tyler D P; Linquist, Stefan; Gregory, T Ryan

2014-05-09

Much confusion in genome biology results from conflation of possible meanings of the word "function." We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions. Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

Science.gov (United States)

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Timber resource statistics for the Olympic Peninsula, Washington.

Science.gov (United States)

Patricia M. Bassett; Daniel D. Oswald

1961-01-01

This report summarizes a 1978-79 timber resource inventory of five counties in the Olympic Peninsula of Washington: Clallam, Grays Harbor, Jefferson, Mason, and Thurston. Detailed tables of forest area, timber volume, growth, mortality, and harvest are presented.

Recidivism of Supermax Prisoners in Washington State

Science.gov (United States)

Lovell, David; Johnson, L. Clark; Cain, Kevin C.

2007-01-01

This study of recidivism among Washington supermax prisoners used a retrospective matched control design, matching supermax prisoners one-to-one with nonsupermax prisoners on mental illness status and up to eight recidivism predictors. Supermax prisoners committed new felonies at a higher rate than nonsupermax controls, but the difference was not…

78 FR 78808 - Proposed Flood Elevation Determinations for Pierce County, Washington, and Incorporated Areas

Science.gov (United States)

2013-12-27

...-2013-0002; Internal Agency Docket No. FEMA-B-7748] Proposed Flood Elevation Determinations for Pierce... proposed rule concerning proposed flood elevation determinations for Pierce County, Washington, and... sources in Pierce County, Washington. On April 16, 2012, FEMA published a proposed rulemaking at 77 FR...

77 FR 48535 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

Science.gov (United States)

2012-08-14

...: Alicia Woods, Washington State Parks and Recreation Commission, P.O. Box 42650, Olympia, WA 98504-2650... it satisfies the criteria in 43 CFR 10.11(c)(1) should contact Alicia Woods, Washington State Parks...

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.

LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES

Energy Technology Data Exchange (ETDEWEB)

Howard Ochman

2006-02-22

The aims of this research were to elucidate the role and extent of lateral transfer in the differentiation of bacterial strains and species, and to assess the impact of gene transfer on the evolution of bacterial genomes. The ultimate goal of the project is to examine the dynamics of a core set of protein-coding genes (i.e., those that are distributed universally among Bacteria) by developing conserved primers that would allow their amplification and sequencing in any bacterial taxa. In addition, we adopted a bioinformatic approach to elucidate the extent of lateral gene transfer in sequenced genome.

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.

High School Administrative Staffing in Washington State: Principal Perspectives on Resource Needs and Utilization

Science.gov (United States)

Steach, John C.

2011-01-01

This mixed methods study explored how high school principals prioritize their work and utilize available human resources to adjust to inadequate administrative staffing. Analysis of staffing levels across the state of Washington and specifically inside two eastern Washington districts framed interview questions for central office administration…

78 FR 76031 - Sweet Cherries Grown in Designated Counties in Washington; Decreased Assessment Rate

Science.gov (United States)

2013-12-16

... FIR] Sweet Cherries Grown in Designated Counties in Washington; Decreased Assessment Rate AGENCY... subsequent fiscal periods from $0.18 to $0.15 per ton of sweet cherries handled. The Committee locally administers the marketing order for sweet cherries grown in designated counties in Washington. The Committee's...

ERGC: an efficient referential genome compression algorithm.

Science.gov (United States)

Saha, Subrata; Rajasekaran, Sanguthevar

2015-11-01

Genome sequencing has become faster and more affordable. Consequently, the number of available complete genomic sequences is increasing rapidly. As a result, the cost to store, process, analyze and transmit the data is becoming a bottleneck for research and future medical applications. So, the need for devising efficient data compression and data reduction techniques for biological sequencing data is growing by the day. Although there exists a number of standard data compression algorithms, they are not efficient in compressing biological data. These generic algorithms do not exploit some inherent properties of the sequencing data while compressing. To exploit statistical and information-theoretic properties of genomic sequences, we need specialized compression algorithms. Five different next-generation sequencing data compression problems have been identified and studied in the literature. We propose a novel algorithm for one of these problems known as reference-based genome compression. We have done extensive experiments using five real sequencing datasets. The results on real genomes show that our proposed algorithm is indeed competitive and performs better than the best known algorithms for this problem. It achieves compression ratios that are better than those of the currently best performing algorithms. The time to compress and decompress the whole genome is also very promising. The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/∼rajasek/ERGC.zip. rajasek@engr.uconn.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genome-Based Microbial Taxonomy Coming of Age.

Science.gov (United States)

Hugenholtz, Philip; Skarshewski, Adam; Parks, Donovan H

2016-06-01

Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes

KAUST Repository

Qu, Hongzhu

2010-12-01

Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based scheme (DnaE1-DnaE1, DnaE2-DnaE1, and DnaE3-PolC), we investigated NCA and nucleotide composition gradients at three codon positions and found that there was universal G-enrichment on LeS among all groups. This was due to a strong selection for G-heading (codon position1 or cp1) codons and mutation pressure that led to more G-ending (cp3) codons. Moreover, a slight T-enrichment of LeS due to the mutation of cytosine deamination at cp3 was universal among DnaE1-DnaE1 and DnaE2-DnaE1 genomes, but was not clearly seen among DnaE3-PolC genomes, in which A-enrichment of LeS was proposed to be the effect of selections unique to polC and a mutation bias toward A-richness at cp1 that may be a result of transcription-coupled DNA repair mechanisms. Furthermore, strand-biased gene distribution enhances the purine-richness of LeS for DnaE3-PolC genomes and T-richness of LeS for DnaE1-DnaE1 and DnaE2-dnaE1 genomes. © 2010 Institut Pasteur.

Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes

KAUST Repository

Qu, Hongzhu; Wu, Hao; Zhang, Tongwu; Zhang, Zhang; Hu, Songnian; Yu, Jun

2010-01-01

Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based scheme (DnaE1-DnaE1, DnaE2-DnaE1, and DnaE3-PolC), we investigated NCA and nucleotide composition gradients at three codon positions and found that there was universal G-enrichment on LeS among all groups. This was due to a strong selection for G-heading (codon position1 or cp1) codons and mutation pressure that led to more G-ending (cp3) codons. Moreover, a slight T-enrichment of LeS due to the mutation of cytosine deamination at cp3 was universal among DnaE1-DnaE1 and DnaE2-DnaE1 genomes, but was not clearly seen among DnaE3-PolC genomes, in which A-enrichment of LeS was proposed to be the effect of selections unique to polC and a mutation bias toward A-richness at cp1 that may be a result of transcription-coupled DNA repair mechanisms. Furthermore, strand-biased gene distribution enhances the purine-richness of LeS for DnaE3-PolC genomes and T-richness of LeS for DnaE1-DnaE1 and DnaE2-dnaE1 genomes. © 2010 Institut Pasteur.

Early Restoration Public Meeting, Washington, DC | NOAA Gulf Spill

Science.gov (United States)

benefit injured marshes, coastal dune and nearshore habitats, oysters, and human uses (on water recreation . Department of Commerce Herbert Hoover Building Auditorium 1401 Constitution Ave., NW Washington, D.C. 20230

Psychiatric Boarding in Washington State and the Inadequacy of Mental Health Resources.

Science.gov (United States)

Bloom, Joseph D

2015-06-01

Psychiatric boarding is a term derived from emergency medicine that describes the holding of patients deemed in need of hospitalization in emergency departments for extended periods because psychiatric beds are not available. Such boarding has occurred for many years in the shadows of mental health care as both inpatient beds and community services have decreased. This article focuses on a 2014 Washington State Supreme Court decision that examined the interpretation of certain sections of the Washington state civil commitment statute that had been used to justify the extended boarding of detained psychiatric patients in general hospital emergency departments. The impact of this decision on the state of Washington should be significant and could spark a national debate about the negative impacts of psychiatric boarding on patients and on the nation's general hospital emergency services. © 2015 American Academy of Psychiatry and the Law.

Draft genome of the leopard gecko, Eublepharis macularius.

Science.gov (United States)

Xiong, Zijun; Li, Fang; Li, Qiye; Zhou, Long; Gamble, Tony; Zheng, Jiao; Kui, Ling; Li, Cai; Li, Shengbin; Yang, Huanming; Zhang, Guojie

2016-10-26

Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these 'rules' and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in 'typical' geckos. We report high-depth genome sequencing, assembly, and annotation for a male leopard gecko, Eublepharis macularius (Eublepharidae). Illumina sequence data were generated from seven insert libraries (ranging from 170 to 20 kb), representing a raw sequencing depth of 136X from 303 Gb of data, reduced to 84X and 187 Gb after filtering. The assembled genome of 2.02 Gb was close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes of 664 and 20 kb, respectively, were comparable to the previously published Gekko japonicus genome. Repetitive elements accounted for 42 % of the genome. Gene annotation yielded 24,755 protein-coding genes, of which 93 % were functionally annotated. CEGMA and BUSCO assessment showed that our assembly captured 91 % (225 of 248) of the core eukaryotic genes, and 76 % of vertebrate universal single-copy orthologs. Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.

The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.

Science.gov (United States)

Sakai, Hiroaki; Naito, Ken; Takahashi, Yu; Sato, Toshiyuki; Yamamoto, Toshiya; Muto, Isamu; Itoh, Takeshi; Tomooka, Norihiko

2016-01-01

The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high-salinity, acid or alkaline soil; drought; flooding; and pests and diseases. These features of the genus Vigna make it a good target for investigation of genetic diversity in adaptation to stressful environments; however, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ('VigGS', http://viggs.dna.affrc.go.jp), based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Port Angeles, Washington Tsunami Forecast Grids for MOST Model

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Port Angeles, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST)...

Xerostomia After Treatment for Oral and Oropharyngeal Cancer Using the University of Washington Saliva Domain and a Xerostomia-Related Quality-of-Life Scale

International Nuclear Information System (INIS)

Rogers, Simon N.; Johnson, Ian A.; Lowe, Derek

2010-01-01

Purpose: The first aim of this study was to identify which clinical factors are associated with xerostomia in patients after treatment for oral and oropharyngeal squamous cell carcinoma, using the Xerostomia-Related Quality-of-Life Scale (XeQoLS) and the University of Washington Quality-of-Life Questionnaire Version 4 dry mouth item (UW-QOL v4). The second aim was to compare these two questionnaires and postulate a cutoff in the UW-QOL below which patients are doing sufficient badly to warrant further evaluation and support. Methods and Materials: In all, 371 patients alive and disease free treated between 1992 and 2005 were sent the survey, of whom 250 (67%) responded. Various clinical factors correlated with xerostomia, particularly adjuvant radiotherapy and Pstage. Results: In logistic regression analyses to predict three or more problems on the XeQoLS, only adjuvant radiotherapy (p < 0.001) was significant at the 5% level. There were significant (p < 0.001) correlations between the XeQoLS scores (total average and domain) with all the UW-QOL domain scores, the strongest with swallowing (-0.69), taste (-0.64), chewing (-0.64), mood (-0.60), and saliva (-0.59) domains. Patients scoring <70 (i.e., 0 or 30) on the UW-QOL could be used as a screening cutoff because it formed 1 in 5 of all patients (49/242) but accounted for half (299/566) of the significant problems generated by the XeQoLS. This also identified 13/21 patients with 10 or more problems. Conclusion: The UW-QOL saliva domain seems to be a suitable means of screening for dry mouth in head-and-neck clinics and could be used to trigger interventions.

Timber resource statistics for eastern Washington, 1995.

Science.gov (United States)

Neil McKay; Patricia M. Bassett; Colin D. MacLean

1995-01-01

This report summarizes a 1990-91 timber resource inventory of Washington east of the crest of the Cascade Range. The inventory was conducted on all private and public lands except National Forests. Timber resource statistics from National Forest inventories also are presented. Detailed tables provide estimates of forest area, timber volume, growth, mortality, and...

Genomic restructuring in Hordeum chilense durum wheat hybrids ...

Indian Academy of Sciences (India)

ANDREIA DELGADO

4John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. 5Departament of Genetics and Biotechnology, University of Tras-os-Montes and Alto ... [Delgado A., Carvalho A., Martín A. C., Martín A. and Lima-Brito J. 2017 Genomic restructuring in F1 Hordeum chilense × durum ...... Academic Press, Burlington,.

78 FR 74163 - Harrison Medical Center, a Subsidiary of Franciscan Health System Bremerton, Washington; Notice...

Science.gov (United States)

2013-12-10

... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-83,070] Harrison Medical Center, a Subsidiary of Franciscan Health System Bremerton, Washington; Notice of Negative Determination... workers of Harrison Medical Center, a subsidiary of Franciscan Health System, Bremerton, Washington...

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich.

Science.gov (United States)

Luan, Ming-Bao; Jian, Jian-Bo; Chen, Ping; Chen, Jun-Hui; Chen, Jian-Hua; Gao, Qiang; Gao, Gang; Zhou, Ju-Hong; Chen, Kun-Mei; Guang, Xuan-Min; Chen, Ji-Kang; Zhang, Qian-Qian; Wang, Xiao-Fei; Fang, Long; Sun, Zhi-Min; Bai, Ming-Zhou; Fang, Xiao-Dong; Zhao, Shan-Cen; Xiong, He-Ping; Yu, Chun-Ming; Zhu, Ai-Guo

2018-05-01

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae. © 2018 John Wiley & Sons Ltd.

Genomics using the Assembly of the Mink Genome

DEFF Research Database (Denmark)

Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

2018-01-01

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

Neah Bay, Washington Tsunami Forecast Grids for MOST Model

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Neah Bay, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

Toke Point, Washington Tsunami Forecast Grids for MOST Model

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Toke Point, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

La Push, Washington Tsunami Forecast Grids for MOST Model

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The La Push, Washington Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

Validation of clinical testing for warfarin sensitivity: comparison of CYP2C9-VKORC1 genotyping assays and warfarin-dosing algorithms.

Science.gov (United States)

Langley, Michael R; Booker, Jessica K; Evans, James P; McLeod, Howard L; Weck, Karen E

2009-05-01

Responses to warfarin (Coumadin) anticoagulation therapy are affected by genetic variability in both the CYP2C9 and VKORC1 genes. Validation of pharmacogenetic testing for warfarin responses includes demonstration of analytical validity of testing platforms and of the clinical validity of testing. We compared four platforms for determining the relevant single nucleotide polymorphisms (SNPs) in both CYP2C9 and VKORC1 that are associated with warfarin sensitivity (Third Wave Invader Plus, ParagonDx/Cepheid Smart Cycler, Idaho Technology LightCycler, and AutoGenomics Infiniti). Each method was examined for accuracy, cost, and turnaround time. All genotyping methods demonstrated greater than 95% accuracy for identifying the relevant SNPs (CYP2C9 *2 and *3; VKORC1 -1639 or 1173). The ParagonDx and Idaho Technology assays had the shortest turnaround and hands-on times. The Third Wave assay was readily scalable to higher test volumes but had the longest hands-on time. The AutoGenomics assay interrogated the largest number of SNPs but had the longest turnaround time. Four published warfarin-dosing algorithms (Washington University, UCSF, Louisville, and Newcastle) were compared for accuracy for predicting warfarin dose in a retrospective analysis of a local patient population on long-term, stable warfarin therapy. The predicted doses from both the Washington University and UCSF algorithms demonstrated the best correlation with actual warfarin doses.

Validation of Clinical Testing for Warfarin Sensitivity

Science.gov (United States)

Langley, Michael R.; Booker, Jessica K.; Evans, James P.; McLeod, Howard L.; Weck, Karen E.

2009-01-01

Responses to warfarin (Coumadin) anticoagulation therapy are affected by genetic variability in both the CYP2C9 and VKORC1 genes. Validation of pharmacogenetic testing for warfarin responses includes demonstration of analytical validity of testing platforms and of the clinical validity of testing. We compared four platforms for determining the relevant single nucleotide polymorphisms (SNPs) in both CYP2C9 and VKORC1 that are associated with warfarin sensitivity (Third Wave Invader Plus, ParagonDx/Cepheid Smart Cycler, Idaho Technology LightCycler, and AutoGenomics Infiniti). Each method was examined for accuracy, cost, and turnaround time. All genotyping methods demonstrated greater than 95% accuracy for identifying the relevant SNPs (CYP2C9 *2 and *3; VKORC1 −1639 or 1173). The ParagonDx and Idaho Technology assays had the shortest turnaround and hands-on times. The Third Wave assay was readily scalable to higher test volumes but had the longest hands-on time. The AutoGenomics assay interrogated the largest number of SNPs but had the longest turnaround time. Four published warfarin-dosing algorithms (Washington University, UCSF, Louisville, and Newcastle) were compared for accuracy for predicting warfarin dose in a retrospective analysis of a local patient population on long-term, stable warfarin therapy. The predicted doses from both the Washington University and UCSF algorithms demonstrated the best correlation with actual warfarin doses. PMID:19324988

A novel program to design siRNAs simultaneously effective to highly variable virus genomes.

Science.gov (United States)

Lee, Hui Sun; Ahn, Jeonghyun; Jun, Eun Jung; Yang, Sanghwa; Joo, Chul Hyun; Kim, Yoo Kyum; Lee, Heuiran

2009-07-10

A major concern of antiviral therapy using small interfering RNAs (siRNAs) targeting RNA viral genome is high sequence diversity and mutation rate due to genetic instability. To overcome this problem, it is indispensable to design siRNAs targeting highly conserved regions. We thus designed CAPSID (Convenient Application Program for siRNA Design), a novel bioinformatics program to identify siRNAs targeting highly conserved regions within RNA viral genomes. From a set of input RNAs of diverse sequences, CAPSID rapidly searches conserved patterns and suggests highly potent siRNA candidates in a hierarchical manner. To validate the usefulness of this novel program, we investigated the antiviral potency of universal siRNA for various Human enterovirus B (HEB) serotypes. Assessment of antiviral efficacy using Hela cells, clearly demonstrates that HEB-specific siRNAs exhibit protective effects against all HEBs examined. These findings strongly indicate that CAPSID can be applied to select universal antiviral siRNAs against highly divergent viral genomes.

Visualization for genomics: the Microbial Genome Viewer.

NARCIS (Netherlands)

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

2004-01-01

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

Volatile substance misuse deaths in Washington State, 2003-2012.

Science.gov (United States)

Ossiander, Eric M

2015-01-01

Volatile substance misuse (VSM - also known as huffing or sniffing) causes some deaths, but because there are no specific cause-of-death codes for VSM, these deaths are rarely tabulated. Count and describe VSM deaths occurring in Washington State during 2003-2012. We used the textual cause-of-death information on death certificates to count VSM-associated deaths that occurred in Washington State during 2003-2012. We extracted records that contained words suggesting either a method of inhalation or a substance commonly used for VSM, and reviewed those records to identify deaths on which the inhalation of a volatile substance was mentioned. We conducted a descriptive analysis of those deaths. Fifty-six deaths involving VSM occurred in Washington State during 2003-2012. VSM deaths occurred primarily among adults age 20 and over (91%), males (88%), and whites (93%). Twelve different chemicals were associated with deaths, but 1 of them, difluoroethane, was named on 30 death certificates (54%), and its involvement increased during the study period. Gas duster products were named as the source of difluoroethane for 12 deaths; no source was named for the other 18 difluoroethane deaths. Most VSM deaths occurred among white male adults, and gas duster products containing difluoroethane were the primary source of inhalants. Approaches to deter VSM, such as the addition of bitterants to gas dusters, should be explored.

The 50th Annual Maize Genetics Conference

Energy Technology Data Exchange (ETDEWEB)

Cone, Karen

2014-03-26

The 50th Annual Maize Genetics Conference was held February 27 - March 2, 2008 at the Marriott Wardman Park Hotel in Washington, D.C. As the golden anniversary of the Conference and coinciding with the release of a draft of the maize genome sequence, this was a special meeting. To publicize this unique occasion, meeting organizers hosted a press conference, which was attended by members of the press representing science and non-science publications, and an evening reception at the Smithsonian National Museum of Natural History, where the draft sequence was announced and awards were presented to Dr. Mary Clutter and Senator Kit Bond to thank them for their outstanding contributions to maize genetics and genomics research. As usual, the Conference provided an invigorating forum for exchange of recent research results in many areas of maize genetics, e.g., cytogenetics, development, molecular genetics, transposable element biology, biochemical genetics, and genomics. Results were shared via both oral and poster presentations. Invited talks were given by four distinguished geneticists: Vicki Chandler, University of Arizona; John Doebley, University of Wisconsin; Susan Wessler, University of Georgia; and Richard Wilson, Washington University. There were 46 short talks and 241 poster presentations. The Conference was attended by over 500 participants. This included a large number of first-time participants in the meeting and an increasingly visible presence by individuals from underrepresented groups. Although we do not have concrete counts, there seem to be more African American, African and Hispanic/Latino attendees coming to the meeting than in years past. In addition, this meeting attracted many participants from outside the U.S. Student participation continues to be hallmark of the spirit of free exchange and cooperation characteristic of the maize genetics community. With the generous support provided by DOE, USDA NSF, and corporate/private donors, organizers were

Alternative Fuels Data Center: Washington Transportation Data for

Science.gov (United States)

stations in Washington with alternative fuels Fuel Public Private Biodiesel (B20 and above) 8 33 Compressed Partnerships Spark Biodiesel Success for Essential Baking Company Partnerships Spark Biodiesel Success for Videos on YouTube Video thumbnail for Seattle Bakery Delivers With Biodiesel Trucks Seattle Bakery

Dignity, death, and dilemmas: a study of Washington hospices and physician-assisted death.

Science.gov (United States)

Campbell, Courtney S; Black, Margaret A

2014-01-01

The legalization of physician-assisted death in states such as Washington and Oregon has presented defining ethical issues for hospice programs because up to 90% of terminally ill patients who use the state-regulated procedure to end their lives are enrolled in hospice care. The authors recently partnered with the Washington State Hospice and Palliative Care Organization to examine the policies developed by individual hospice programs on program and staff participation in the Washington Death with Dignity Act. This article sets a national and local context for the discussion of hospice involvement in physician-assisted death, summarizes the content of hospice policies in Washington State, and presents an analysis of these findings. The study reveals meaningful differences among hospice programs about the integrity and identity of hospice and hospice care, leading to different policies, values, understandings of the medical procedure, and caregiving practices. In particular, the authors found differences 1) in the language used by hospices to refer to the Washington statute that reflect differences among national organizations, 2) the values that hospice programs draw on to support their policies, 3) dilemmas created by requests by patients for hospice staff to be present at a patient's death, and 4) five primary levels of noninvolvement and participation by hospice programs in requests from patients for physician-assisted death. This analysis concludes with a framework of questions for developing a comprehensive hospice policy on involvement in physician-assisted death and to assist national, state, local, and personal reflection. Copyright © 2014 U.S. Cancer Pain Relief Committee. Published by Elsevier Inc. All rights reserved.

PLAZA 3.0: an access point for plant comparative genomics.

Science.gov (United States)

Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; Inzé, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas

2015-01-01

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

78 FR 44594 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

Science.gov (United States)

2013-07-24

..., 2013. ADDRESSES: Alicia Woods, Washington State Parks and Recreation Commission, PO Box 42650, Olympia, WA 98504-2650, telephone (360) 902- 0939, email Alicia[email protected] . SUPPLEMENTARY INFORMATION... to Alicia Woods, Washington State Parks and Recreation Commission, PO Box 42650, Olympia, WA 98504...

Cloud-based interactive analytics for terabytes of genomic variants data.

Science.gov (United States)

Pan, Cuiping; McInnes, Gregory; Deflaux, Nicole; Snyder, Michael; Bingham, Jonathan; Datta, Somalee; Tsao, Philip S

2017-12-01

Large scale genomic sequencing is now widely used to decipher questions in diverse realms such as biological function, human diseases, evolution, ecosystems, and agriculture. With the quantity and diversity these data harbor, a robust and scalable data handling and analysis solution is desired. We present interactive analytics using a cloud-based columnar database built on Dremel to perform information compression, comprehensive quality controls, and biological information retrieval in large volumes of genomic data. We demonstrate such Big Data computing paradigms can provide orders of magnitude faster turnaround for common genomic analyses, transforming long-running batch jobs submitted via a Linux shell into questions that can be asked from a web browser in seconds. Using this method, we assessed a study population of 475 deeply sequenced human genomes for genomic call rate, genotype and allele frequency distribution, variant density across the genome, and pharmacogenomic information. Our analysis framework is implemented in Google Cloud Platform and BigQuery. Codes are available at https://github.com/StanfordBioinformatics/mvp_aaa_codelabs. cuiping@stanford.edu or ptsao@stanford.edu. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

Washington Conference

International Nuclear Information System (INIS)

Anon.

1981-01-01

The 1981 Particle Accelerator Conference was held in Washington from 11-13 March. It was the ninth in the series of meetings organized in the USA which differ from the 'International' meetings in their coverage of the full range of accelerator engineering and technology, including applications outside e field of high energy physics. The Conference took place under the cloud of further budget cuts for Fiscal Year 1982 in the USA which the Department of Energy has applied in line with the financial policy of the new administration. Coming on top of many years of budget trimming which have reduced the number of high energy physics Laboratories funded by the DOE to three (Brookhaven, Fermilab, Stanford - Cornell is funded by the National Science Foundation) and reduced the exploitation of these Laboratories to less than half of their potential, the new cuts did not exactly help to boost morale. Nevertheless, the huge amount of tailed work in accelerator physics and technology which was presented at the Conference showed how alive the field is

Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis.

Science.gov (United States)

Facey, Paul D; Méric, Guillaume; Hitchings, Matthew D; Pachebat, Justin A; Hegarty, Matt J; Chen, Xiaorui; Morgan, Laura V A; Hoeppner, James E; Whitten, Miranda M A; Kirk, William D J; Dyson, Paul J; Sheppard, Sam K; Del Sol, Ricardo

2015-07-15

Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola. BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae. The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea. © The Author(s) 2015. Published by

VizieR Online Data Catalog: The Washington Visual Double Star Catalog (Mason+ 2001-2014)

Science.gov (United States)

Mason, B. D.; Wycoff, G. L.; Hartkopf, W. I.; Douglass, G. G.; Worley, C. E.

2018-05-01

The Washington Visual Double Star Catalog (WDS) is the successor to the Index Catalogue of Visual Double Stars, 1961.0 (IDS; Jeffers and van den Bos, Publ. Lick Obs. 21). Three earlier double star catalogs in XXth century, those by Burnham (BDS, 1906, "General Catalogue of Double Stars within 121 degrees of the North Pole", Carnegie Institution of Washington), Innes (SDS, 1927, "Southern Double Star Catalogue -19 to -90 degrees", Union Observatory, Johannesburg, South Africa), and Aitken (ADS, 1932 "New General Catalogue of Double Stars within 121 degrees of the North Pole", Carnegie Institution of Washington), each covered only a portion of the sky. Both the IDS and the WDS cover the entire sky, and the WDS is intended to contain all known visual double stars for which at least one differential measure has been published. The WDS is continually updated as published data become available. Prior to this, three major updates have been published (Worley and Douglass 1984, "Washington Visual Double Star Catalog, 1984.0", U.S. Naval Observatory, Washington; Worley and Douglass 1997A&AS..125..523W, Cat. I/237; Mason, Wycoff, Hartkopf, Douglass and Worley 2001AJ....122.3466M; and Mason et al. 2006.5). The Washington Double Star Catalog (WDS) has seen numerous changes since the last major release of the catalog. The application of many techniques and considerable industry over the past few years has yielded significant gains in both the number of systems and the number of measures. Is is maintained by the US Naval Observatory, and represents the world's principal database of astrometric double and multiple star information. The WDS contains positions (J2000), discoverer designations, epochs, position angles, separations, magnitudes, spectral types, proper motions, and, when available, Durchmusterung numbers and notes for the components of the systems. (3 data files).

The mitochondrial genome of the quiet-calling katydids, Xizicus ...

Indian Academy of Sciences (India)

College of Life Sciences, Hebei University, Baoding 071002, People's Republic of China. Abstract. To help determine whether the typical arthropod .... In the same way, the cycle was repeated to 'walk' around the rest of the genome. ..... Life Web Project (http://tolweb.org/). Hall T. A. 1999 BioEdit: a user-friendly biological ...

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Washington Wildlife Mitigation Projects : Final Programmatic Environmental Assessment and Finding of No Significant Impact.

Energy Technology Data Exchange (ETDEWEB)

United States. Bonneville Power Administration; Washington (State). Dept. of Fish and Wildlife.

1996-08-01

Bonneville Power Administration (BPA) proposes to fund the portion of the Washington Wildlife Mitigation Agreement (Agreement) pertaining to wildlife habitat mitigation projects to be undertaken in a cooperative effort with the Washington Department of Fish and Wildlife (WDFW). This Agreement serves to establish a monetary budget funded by BPA for projects proposed by Washington Wildlife Coalition members and approved by BPA to protect, mitigate, and improve wildlife and/or wildlife habitat within the State of Washington that has been affected by the construction of Federal dams along the Columbia River. This Environmental Assessment examines the potential environmental effects of acquiring and/or improving wildlife habitat within five different project areas. These project areas are located throughout Grant County and in parts of Okanogan, Douglas, Adams, Franklin, Kittias, Yakima, and Benton Counties. The multiple projects would involve varying combinations of five proposed site-specific activities (habitat improvement, operation and maintenance, monitoring and evaluation, access and recreation management, and cultural resource management). All required Federal, State, and tribal coordination, permits and/or approvals would be obtained prior to ground-disturbing activities.

Washington wildlife mitigation projects. Final programmatic environmental assessment and finding of no significant impact

International Nuclear Information System (INIS)

1996-08-01

Bonneville Power Administration (BPA) proposes to fund the portion of the Washington Wildlife Mitigation Agreement (Agreement) pertaining to wildlife habitat mitigation projects to be undertaken in a cooperative effort with the Washington Department of Fish and Wildlife (WDFW). This Agreement serves to establish a monetary budget funded by BPA for projects proposed by Washington Wildlife Coalition members and approved by BPA to protect, mitigate, and improve wildlife and/or wildlife habitat within the State of Washington that has been affected by the construction of Federal dams along the Columbia River. This Environmental Assessment examines the potential environmental effects of acquiring and/or improving wildlife habitat within five different project areas. These project areas are located throughout Grant County and in parts of Okanogan, Douglas, Adams, Franklin, Kittias, Yakima, and Benton Counties. The multiple projects would involve varying combinations of five proposed site-specific activities (habitat improvement, operation and maintenance, monitoring and evaluation, access and recreation management, and cultural resource management). All required Federal, State, and tribal coordination, permits and/or approvals would be obtained prior to ground-disturbing activities

NRGC: a novel referential genome compression algorithm.

Science.gov (United States)

Saha, Subrata; Rajasekaran, Sanguthevar

2016-11-15

Next-generation sequencing techniques produce millions to billions of short reads. The procedure is not only very cost effective but also can be done in laboratory environment. The state-of-the-art sequence assemblers then construct the whole genomic sequence from these reads. Current cutting edge computing technology makes it possible to build genomic sequences from the billions of reads within a minimal cost and time. As a consequence, we see an explosion of biological sequences in recent times. In turn, the cost of storing the sequences in physical memory or transmitting them over the internet is becoming a major bottleneck for research and future medical applications. Data compression techniques are one of the most important remedies in this context. We are in need of suitable data compression algorithms that can exploit the inherent structure of biological sequences. Although standard data compression algorithms are prevalent, they are not suitable to compress biological sequencing data effectively. In this article, we propose a novel referential genome compression algorithm (NRGC) to effectively and efficiently compress the genomic sequences. We have done rigorous experiments to evaluate NRGC by taking a set of real human genomes. The simulation results show that our algorithm is indeed an effective genome compression algorithm that performs better than the best-known algorithms in most of the cases. Compression and decompression times are also very impressive. The implementations are freely available for non-commercial purposes. They can be downloaded from: http://www.engr.uconn.edu/~rajasek/NRGC.zip CONTACT: rajasek@engr.uconn.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

Science.gov (United States)

Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

2015-01-01

The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

Experience with Honeycrisp apple storage management in Washington

Science.gov (United States)

High demand and premium pricing have led to rapid increases in Honeycrisp plantings and fruit volume in Washington State, USA since introduction of the cultivar in 1999. Most fruit is packed and sold by January because of strong demand coupled with difficulties associated with extended storage. Howe...

Parallel computing in genomic research: advances and applications

Directory of Open Access Journals (Sweden)

Ocaña K

2015-11-01

Full Text Available Kary Ocaña,1 Daniel de Oliveira2 1National Laboratory of Scientific Computing, Petrópolis, Rio de Janeiro, 2Institute of Computing, Fluminense Federal University, Niterói, Brazil Abstract: Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. Keywords: high-performance computing, genomic research, cloud computing, grid computing, cluster computing, parallel computing

GeNemo: a search engine for web-based functional genomic data.

Science.gov (United States)

Zhang, Yongqing; Cao, Xiaoyi; Zhong, Sheng

2016-07-08

A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analisis TLC entre Colombia y Estados Unidos: Estados de Virginia y Washington

OpenAIRE

Pulecio Leon, Gloria Daniela

2016-01-01

el punto central de esta investigación será identificar las principales fortalezas y oportunidades de las empresas colombianas frente al Tratado de Libre Comercio con Estados Unidos, con miras al desarrollo de un proceso de exportación no tradicional e internacionalización, en los estados de Virginia y Washington. Para esto debemos primero reconocer las oportunidades que el mercado colombiano ha aprovechado en los estados de Virginia y Washington, segundo revisar si el tratado de libre ...

University of Washington/ Northwest National Marine Renewable Energy Center Tidal Current Technology Test Protocol, Instrumentation, Design Code, and Oceanographic Modeling Collaboration: Cooperative Research and Development Final Report, CRADA Number CRD-11-452

Energy Technology Data Exchange (ETDEWEB)

Driscoll, Frederick R. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

2016-11-01

The University of Washington (UW) - Northwest National Marine Renewable Energy Center (UW-NNMREC) and the National Renewable Energy Laboratory (NREL) will collaborate to advance research and development (R&D) of Marine Hydrokinetic (MHK) renewable energy technology, specifically renewable energy captured from ocean tidal currents. UW-NNMREC is endeavoring to establish infrastructure, capabilities and tools to support in-water testing of marine energy technology. NREL is leveraging its experience and capabilities in field testing of wind systems to develop protocols and instrumentation to advance field testing of MHK systems. Under this work, UW-NNMREC and NREL will work together to develop a common instrumentation system and testing methodologies, standards and protocols. UW-NNMREC is also establishing simulation capabilities for MHK turbine and turbine arrays. NREL has extensive experience in wind turbine array modeling and is developing several computer based numerical simulation capabilities for MHK systems. Under this CRADA, UW-NNMREC and NREL will work together to augment single device and array modeling codes. As part of this effort UW NNMREC will also work with NREL to run simulations on NREL's high performance computer system.

Status of birds at the Hanford Site in southeastern Washington

International Nuclear Information System (INIS)

Landeen, D.S.; Johnson, A.R.; Mitchell, R.M.

1992-06-01

The US Department of Energy has entered into agreements with the Washington State Department of Ecology, the US Environmental Protection Agency, and Hanford Site contractors to focus work activities on cleanup and stabilization of radioactive and hazardous waste sites located at the Hanford Site in southeastern Washington. Ecological characterization is an essential part of the remediation process, and the identification of biotic components such as bird species that could be impacted by cleanup activities is an important part of the initial environmental characterizations. Site characterization work has resulted in this list of 238 birds that have been observed at the Hanford Site. This list is presented with a status rating for abundance and seasonal occurrence

Mutant power: using mutant allele collections for yeast functional genomics.

Science.gov (United States)

Norman, Kaitlyn L; Kumar, Anuj

2016-03-01

The budding yeast has long served as a model eukaryote for the functional genomic analysis of highly conserved signaling pathways, cellular processes and mechanisms underlying human disease. The collection of reagents available for genomics in yeast is extensive, encompassing a growing diversity of mutant collections beyond gene deletion sets in the standard wild-type S288C genetic background. We review here three main types of mutant allele collections: transposon mutagen collections, essential gene collections and overexpression libraries. Each collection provides unique and identifiable alleles that can be utilized in genome-wide, high-throughput studies. These genomic reagents are particularly informative in identifying synthetic phenotypes and functions associated with essential genes, including those modeled most effectively in complex genetic backgrounds. Several examples of genomic studies in filamentous/pseudohyphal backgrounds are provided here to illustrate this point. Additionally, the limitations of each approach are examined. Collectively, these mutant allele collections in Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans promise insights toward an advanced understanding of eukaryotic molecular and cellular biology. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Genetic variation in steelhead (Salmo gairdneri) from the north coast of Washington

Science.gov (United States)

Reisenbichler, R.R.; Phelps, S.R.

1989-01-01

Steelhead (Salmo gairdneri) collected from various sites in nine drainages in northwestern Washington were genetically characterized at 65 protein-coding loci by starch-gel electrophoresis. Genetic differentiation within and among drainages was not significant, and genetic variation among drainages was much less than that reported in British Columbia; these results may be the consequence of gene flow from hatchery stocks that have been released in Washington since the 1940's. Allele frequencies varied significantly among year-classes (hence, genetic characterization studies must include data from several year-classes), and also between hatchery fish (including a stock developed with local wild fish) and wild fish, indicating that few wild fish have been successfully and routinely included in hatchery brood stocks. Conservation of genetic diversity along the north coast of Washington should be facilitated by reducing the numbers of hatchery fish that spawn in streams and by including wild fish in hatchery brood stocks.

78 FR 50099 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

Science.gov (United States)

2013-08-16

... at the address in this notice by September 16, 2013. ADDRESSES: Alicia Woods, Washington State Parks... Alicia[email protected] . SUPPLEMENTARY INFORMATION: Notice is here given in accordance with the Native... request Alicia Woods, Washington State Parks and Recreation Commission, PO Box 42650, Olympia, WA 98504...

78 FR 44593 - Notice of Inventory Completion: Washington State Parks and Recreation Commission, Olympia, WA

Science.gov (United States)

2013-07-24

...: Alicia Woods, Washington State Parks and Recreation Commission, PO Box 42650, Olympia, WA 98504-2650, telephone (360) 902- 0939, email Alicia[email protected] . SUPPLEMENTARY INFORMATION: Notice is here given... written request with information in support of the request to Alicia Woods, Washington State Parks and...

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.

Gain-of-function mutagenesis approaches in rice for functional genomics and improvement of crop productivity.

Science.gov (United States)

Moin, Mazahar; Bakshi, Achala; Saha, Anusree; Dutta, Mouboni; Kirti, P B

2017-07-01

The epitome of any genome research is to identify all the existing genes in a genome and investigate their roles. Various techniques have been applied to unveil the functions either by silencing or over-expressing the genes by targeted expression or random mutagenesis. Rice is the most appropriate model crop for generating a mutant resource for functional genomic studies because of the availability of high-quality genome sequence and relatively smaller genome size. Rice has syntenic relationships with members of other cereals. Hence, characterization of functionally unknown genes in rice will possibly provide key genetic insights and can lead to comparative genomics involving other cereals. The current review attempts to discuss the available gain-of-function mutagenesis techniques for functional genomics, emphasizing the contemporary approach, activation tagging and alterations to this method for the enhancement of yield and productivity of rice. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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...

Genomic dissection and prioritizing of candidate genes of QTL for ...

Indian Academy of Sciences (India)

of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA. 5Mudanjiang ..... Fragile X mental retardation gene 1,. −2.1 ... stimulus/stress and signalling associated with acute-phase response were .... This work was supported by the Center of Genomics and Bioinfor- matics and ...

Security, Violent Events, and Anticipated Surge Capabilities of Emergency Departments in Washington State

Science.gov (United States)

Weyand, Jonathan S.; Junck, Emily; Kang, Christopher S.; Heiner, Jason D.

2017-01-01

Introduction Over the past 15 years, violent threats and acts against hospital patients, staff, and providers have increased and escalated. The leading area for violence is the emergency department (ED) given its 24/7 operations, role in patient care, admissions gateway, and center for influxes during acute surge events. This investigation had three objectives: to assess the current security of Washington State EDs; to estimate the prevalence of and response to threats and violence in Washington State EDs; and to appraise the Washington State ED security capability to respond to acute influxes of patients, bystanders, and media during acute surge events. Methods A voluntary, blinded, 28-question Web-based survey developed by emergency physicians was electronically delivered to all 87 Washington State ED directors in January 2013. We evaluated responses by descriptive statistical analyses. Results Analyses occurred after 90% (78/87) of ED directors responded. Annual censuses of the EDs ranged from violent threats or acts occurring in their ED. Of these, 93% were directed towards nursing staff, 90% towards physicians, 74% towards security personnel, and 51% towards administrative personnel. Nearly half (48%) noted incidents directed towards another patient, and 50% towards a patient’s family or friend. These events were variably reported to the hospital administration. After an acute surge event, 35% believed the initial additional security response would not be adequate, with 26% reporting no additional security would be available within 15 minutes. Conclusion Our study reveals the variability of ED security staffing and a heterogeneity of capabilities throughout Washington State. These deficiencies and vulnerabilities highlight the need for other EDs and regional emergency preparedness planners to conduct their own readiness assessments. PMID:28435498

Unmet Student Financial Need in the State of Washington: A Study of the "Need Gap."

Science.gov (United States)

Fenske, Robert; And Others

A study of unmet student financial need in Washington State was conducted by the Washington Council for Postsecondary Education. "Unmet need" is the difference between need and the total amount of aid received by the student through federal, state, and institutional financial aid programs, privately funded scholarships, and nonsubsidized…

Harnessing genomics to improve health in the Eastern Mediterranean Region – an executive course in genomics policy

Directory of Open Access Journals (Sweden)

Singer Peter A

2005-01-01

Full Text Available Abstract Background While innovations in medicine, science and technology have resulted in improved health and quality of life for many people, the benefits of modern medicine continue to elude millions of people in many parts of the world. To assess the potential of genomics to address health needs in EMR, the World Health Organization's Eastern Mediterranean Regional Office and the University of Toronto Joint Centre for Bioethics jointly organized a Genomics and Public Health Policy Executive Course, held September 20th–23rd, 2003, in Muscat, Oman. The 4-day course was sponsored by WHO-EMRO with additional support from the Canadian Program in Genomics and Global Health. The overall objective of the course was to collectively explore how to best harness genomics to improve health in the region. This article presents the course findings and recommendations for genomics policy in EMR. Methods The course brought together senior representatives from academia, biotechnology companies, regulatory bodies, media, voluntary, and legal organizations to engage in discussion. Topics covered included scientific advances in genomics, followed by innovations in business models, public sector perspectives, ethics, legal issues and national innovation systems. Results A set of recommendations, summarized below, was formulated for the Regional Office, the Member States and for individuals. • Advocacy for genomics and biotechnology for political leadership; • Networking between member states to share information, expertise, training, and regional cooperation in biotechnology; coordination of national surveys for assessment of health biotechnology innovation systems, science capacity, government policies, legislation and regulations, intellectual property policies, private sector activity; • Creation in each member country of an effective National Body on genomics, biotechnology and health to: - formulate national biotechnology strategies - raise

Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

Science.gov (United States)

Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

2013-10-01

Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.

Avian use of proposed KENETECH and CARES wind farm sites in Klickitat County, Washington. Appendix C to Washington Windplant No. 1 EIS. Technical report

International Nuclear Information System (INIS)

1995-01-01

The Columbia Hills area above (north of) the Columbia River in Klickitat County, in southcentral Washington, is being considered for development of two wind power generation projects that could include the eventual placement of up to 436 wind turbines. The KENETECH Windpower Washington Windplant TM Number 1 project would include placing up to 345 KENETECH 33M-VS turbines, capable of producing up to 115 megawatts (MW), in 39 rows (strings) on a 5,110-hectare (12,630-acre) site. During scoping for these proposed developments, concerns were raised regarding the potential for avian mortality associated with wind farm development. Collision with wind turbine blade, towers, guy wires, and transmission lines, and electrocution from power lines have been identified as sources of avian mortality, particularly raptors, at existing wind farm facilities. To address these concerns, an avian study was conducted at the site in accordance with an avian study plan and protocol developed, with input from a national avian task force, state agencies (Washington Department of Fish and Wildlife [WDFW]), and federal agencies (USFWS). The study included four elements: (1) a winter raptor and waterfowl study, (2) spring migration and fall migration studies, (3) a summer resident study, and (4) a raptor breeding study. The study involved extensive field studies conducted by biologists experienced in identifying raptors and other birds

Hello Mr. President! Rollenspiele zwischen Hollywood und Washington

NARCIS (Netherlands)

Mehring, F.

2016-01-01

Hello Mr. President Rollenspiele zwischen Hollywood und Washington Am 8. November 2016 entscheidet sich, wer zum 58. Präsidenten der USA gewählt wird: Die ehemalige Außenministerin Hillary Clinton oder der republikanische Kandidat Donald Trump. In der heißen Phase des Wahlkampfs fällt besonders

Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data.

Science.gov (United States)

Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; Bazin, Eric; Blum, Michael G B

2016-04-01

To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Millimeter-Wave Radar Field Measurements and Inversion of Cloud Parameters for the 1999 Mt. Washington Icing Sensors Project

Science.gov (United States)

Pazmany, Andrew L.; Reehorst, Andrew (Technical Monitor)

2001-01-01

The Mount Washington Icing Sensors Project (MWISP) was a multi-investigator experiment with participants from Quadrant Engineering, NOAA Environmental Technology Laboratory (NOAA/ETL), the Microwave Remote Sensing Laboratory (MIRSL) of the University of Massachusetts (UMass), and others. Radar systems from UMass and NOAA/ETL were used to measure X-, Ka-, and W-band backscatter data from the base of Mt. Washington, while simultaneous in-situ particle measurements were made from aircraft and from the observatory at the summit. This report presents range and time profiles of liquid water content and particle size parameters derived from range profiles of radar reflectivity as measured at X-, Ka-, and W-band (9.3, 33.1, and 94.9 GHz) using an artificial neural network inversion algorithm. In this report, we provide a brief description of the experiment configuration, radar systems, and a review of the artificial neural network used to extract cloud parameters from the radar data. Time histories of liquid water content (LWC), mean volume diameter (MVD) and mean Z diameter (MZD) are plotted at 300 m range intervals for slant ranges between 1.1 and 4 km. Appendix A provides details on the extraction of radar reflectivity from measured radar power, and Appendix B provides summary logs of the weather conditions for each day in which we processed data.

The genome draft of coconut (Cocos nucifera).

Science.gov (United States)

Xiao, Yong; Xu, Pengwei; Fan, Haikuo; Baudouin, Luc; Xia, Wei; Bocs, Stéphanie; Xu, Junyang; Li, Qiong; Guo, Anping; Zhou, Lixia; Li, Jing; Wu, Yi; Ma, Zilong; Armero, Alix; Issali, Auguste Emmanuel; Liu, Na; Peng, Ming; Yang, Yaodong

2017-11-01

antiporter gene family and ion channel gene families between C. nucifera and Arabidopsis thaliana indicated that significant gene expansion may have occurred in the coconut involving Na+/H+ antiporter, carnitine/acylcarnitine translocase, potassium-dependent sodium-calcium exchanger, and potassium channel genes. Despite its agronomic importance, C. nucifera is still under-studied. In this report, we present a draft genome of C. nucifera and provide genomic information that will facilitate future functional genomics and molecular-assisted breeding in this crop species. © The Author 2017. Published by Oxford University Press.

Radiological Survey Results for Areas A1 North, A5A, A6, and B2 at the Molycorp Washington Remediation Project, Washington, Pennsylvania

International Nuclear Information System (INIS)

W.C. Adams

2007-01-01

Perform radiological surveys of the Molycorp Washington Remediation Project (MWRP) facility in Washington, Pennsylvania. The U.S. Nuclear Regulatory Commission (NRC) requested the Oak Ridge Institute for Science and Education (ORISE) to provide limited training pertaining to ORISE radiological soil scanning and sampling procedures to the Pennsylvania Department of Environmental Protection (PADEP) personnel. In addition, the NRC also requested that ORISE perform radiological surveys of the Molycorp Washington Remediation Project (MWRP) facility in Washington, Pennsylvania (Figure 1). ORISE has and will continue to interface with PADEP personnel in a joint effort to perform confirmatory radiological surveys, consisting of gamma scans and soil sampling, at the MWRP facility. PADEP personnel will continue to submit soil samples that they collect to ORISE for analyses. PADEP sample results, along with ORISE results, will be provided to the NRC and PADEP so that decisions regarding the radiological status of the surveyed areas can be determined. ORISE performed radiological surveys during the period of November 28 and 29, 2006. The survey unit (SU) available for ORISE radiological survey activities was Area A1 North. The MWRP final status survey (FSS) results for Area A1 North were reviewed prior to these survey activities. Prior to ORISE's survey activities, PADEP personnel had performed radiological surveys and collected soil samples from SU Areas A5A and A6. These samples were provided to ORISE for analyses while on site. After the ORISE radiological surveys, PADEP personnel collected soil samples from SU Areas A2 and B2 and these samples were shipped to ORISE for analyses in January 2007. Figure 2 depicts the MWRP Areas A through D; ORISE and PADEP personnel performed survey activities in portions of Areas A and B. For interlaboratory comparison analyses with MWRP's site contractor, Malcolm Pirnie (MP), ORISE requested soil samples from the Area A1 soil stockpiles

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

Parent's Guide to Special Education in Washington State, 1985-86 [and] Guia para Padres: Para Educacion Especial en el Estado de Washington.

Science.gov (United States)

Washington Office of the State Superintendent of Public Instruction, Olympia.

This pamphlet guides parents of children with disabilities through the procedures for acquiring special education services in the state of Washington. Following an overview of special education, the pamphlet presents information on notice and consent procedures, confidentiality of records, individualized education programs (IEP), the placement…

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

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

2004-07-22

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

Inimkatsed viisid eestlased Washington Posti esiküljele / Neeme Raud

Index Scriptorium Estoniae

Raud, Neeme, 1969-

2000-01-01

Eilne Washington Post kirjutas esiküljelt alanud artiklis Lääne farmaatsiagigantide kuritegelikest inimkatsetest, kasutades ühe näitena Postimehes ilmunud ülevaadet Šveitsi ravimifirma katsetest noorte eestlastega

Timber resource statistics for Washington, January 1, 1973.

Science.gov (United States)

Patricia M. Bassett; Grover A. Choate

1974-01-01

Timber resource statistics to January 1, 1973, for the State of Washington show total land area, commercial timberland area, and growing stock and sawtimber inventory volumes by county and owner group. Growth and removals are shown by Forest Survey inventory unit for 1972. Each National Forest is updated to January 1, 1973.

Clash of the Titans: Booker T. Washington and W. E. B. Du Bois. Curriculum Based Education Program, Grade 11.

Science.gov (United States)

National Park Service (Dept. of Interior), Washington, DC.

The Booker T. Washington National Monument preserves and protects the birth site and childhood home of Booker T. Washington while interpreting his life experiences and significance in U.S. history as the most powerful African American between 1895 and 1915. The programs and activities included in this guide about the Booker T. Washington and W. E.…

Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning.

Science.gov (United States)

Dozmorov, Mikhail G

2017-10-15

One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The interpretation of these genome-wide ROIs represents a challenge as the majority of them lie outside of functionally well-defined protein coding regions. Recent efforts by the members of the International Human Epigenome Consortium have generated volumes of functional/regulatory data (reference epigenomic datasets), effectively annotating the genome with epigenomic properties. Consequently, a wide variety of computational tools has been developed utilizing these epigenomic datasets for the interpretation of genomic data. The purpose of this review is to provide a structured overview of practical solutions for the interpretation of ROIs with the help of epigenomic data. Starting with epigenomic enrichment analysis, we discuss leading tools and machine learning methods utilizing epigenomic and 3D genome structure data. The hierarchy of tools and methods reviewed here presents a practical guide for the interpretation of genome-wide ROIs within an epigenomic context. mikhail.dozmorov@vcuhealth.org. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.

Science.gov (United States)

Nowell, Reuben W; Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J; Wheat, Christopher W; Saastamoinen, Marjo; Saccheri, Ilik J; Van't Hof, Arjen E; Wasik, Bethany R; Connahs, Heidi; Aslam, Muhammad L; Kumar, Sujai; Challis, Richard J; Monteiro, Antónia; Brakefield, Paul M; Blaxter, Mark

2017-07-01

The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html). © The Authors 2017. Published by Oxford University Press.

76 FR 21928 - Washington State University; Facility Operating License No. R-76; Washington State University...

Science.gov (United States)

2011-04-19

... late 2008, the site was surrounded for a distance of 400 meters (1300 feet) in all directions by... course is separated from the NRCR by 100 to 200 meters (330 to 660 feet) of land. There is a parcel of land abutting the NRCR of about 10,000 square meters (109,000 square feet) of virgin prairie land which...

One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions.

Science.gov (United States)

Mueller, Linda; Bertelli, Claire; Pillonel, Trestan; Salamin, Nicolas; Greub, Gilbert

2017-06-01

Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate-protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Different genome maintenance strategies in human and tobacco cells.

Science.gov (United States)

Pelczar, Pawel; Kalck, Véronique; Kovalchuk, Igor

2003-08-22

In this work, genome maintenance strategies of organisms belonging to different kingdoms (animals versus plants) but of similar genome size were investigated using a novel, universal double-strand break (DSB) repair assay. Different plasmids linearised with KpnI, Acc65I or EcoRV yielding either 3' or 5' protruding or blunt DNA termini, respectively, were transfected into HeLa cells and Nicotiana plumbaginifolia protoplasts and assayed for the efficiency and fidelity of DSB repair. We show that the mechanism of break sealing is similar but that drastic differences are seen in the fidelity of repair: in HeLa cells, 50-55% DSBs were repaired precisely, compared to as little as 15-30% in tobacco cells. Moreover, the DSB repair in plants resulted in 30-40% longer deletions and significantly shorter insertions. Combined, these led to more than twofold larger net DNA loss in tobacco cells. Our observations point to possible differences in the strategies of DSB repair and genome maintenance in plants and animals.

Final Report: Feasibility Study of Biomass in Snohomish County, Washington

Energy Technology Data Exchange (ETDEWEB)

Daryl Williams (Tulalip Tribes); Ray Clark (Clark Group)

2005-01-31

This report and its attachments summarizes the results of a unique tribal-farmer cooperative study to evaluate the feasibility of building one or more regional anaerobic digestion systems in Snohomish County, Washington.

77 FR 72907 - Western Washington Railroad, LLC-Lease and Operation Exemption-City of Tacoma, Department of...

Science.gov (United States)

2012-12-06

..., 2012, Western Washington Railroad, LLC (WWRR), a Washington limited liability company and noncarrier... allow for interchange with WWRR, BNSF Railway Company, the Puget Sound and Pacific Railroad, and Union Pacific Railroad Company, and also over the entire line for emergency routing. WWRR states that the...

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.

Routine environmental audit of the Hanford Site, Richland, Washington

Energy Technology Data Exchange (ETDEWEB)

1994-05-01

This report documents the results of the routine environmental audit of the Hanford Site (Hanford), Richland, Washington. During this audit, the activities conducted by the audit team included reviews of internal documents an reports from previous audits and assessments; interviews with US Department of Energy (DOE), State of Washington regulatory, and contractor personnel; and inspections and observations of selected facilities and operations. The onsite portion of the audit was conducted May 2--13, 1994, by the DOE Office of Environmental Audit (EH-24), located within the Office of Environment, Safety and Health (EH). The audit evaluated the status of programs to ensure compliance with Federal, State, and local environmental laws and regulations; compliance with DOE orders, guidance, and directives; and conformance with accepted industry practices and standards of performance. The audit also evaluated the status and adequacy of the management systems developed to address environmental requirements.

Routine environmental audit of the Hanford Site, Richland, Washington

International Nuclear Information System (INIS)

1994-05-01

This report documents the results of the routine environmental audit of the Hanford Site (Hanford), Richland, Washington. During this audit, the activities conducted by the audit team included reviews of internal documents an reports from previous audits and assessments; interviews with US Department of Energy (DOE), State of Washington regulatory, and contractor personnel; and inspections and observations of selected facilities and operations. The onsite portion of the audit was conducted May 2--13, 1994, by the DOE Office of Environmental Audit (EH-24), located within the Office of Environment, Safety and Health (EH). The audit evaluated the status of programs to ensure compliance with Federal, State, and local environmental laws and regulations; compliance with DOE orders, guidance, and directives; and conformance with accepted industry practices and standards of performance. The audit also evaluated the status and adequacy of the management systems developed to address environmental requirements

The State of Washington's Children. [Seventh Annual Report].

Science.gov (United States)

Marvinney, Sandy, Ed.

This KIDS COUNT seventh annual report examines statewide trends in the well-being of Washington's children. The statistical portrait is based 24 key indicators of well-being: (1) teen birth rate; (2) teen pregnancy rate; (3) births to unmarried mothers; (4) divorces involving children; (5) family foster caseload; (6) average real wages; (7) per…

The Sequenced Angiosperm Genomes and Genome Databases.

Science.gov (United States)

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

2018-01-01

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

Report on materials characterization center workshop on stress corrosion cracking for the Salt Repository Project, December 16-17, 1986, Seattle, Washington: Workshop summary

International Nuclear Information System (INIS)

Merz, M.D.; Shannon, D.W.

1986-09-01

The Materials Characterization Center (MCC) at Pacific Northwest Laboratory (PNL) conducted a Workshop on Stress Corrosion Cracking for the Salt Repository Project on December 16 and 17, 1986 in Seattle, Washington. The workshop was held to formulate recommendations for addressing stress corrosion cracking (SCC) in a salt repository. It was attended by 24 representatives from major laboratories, universities, and industry. This report presents the recommendations of the workshop, along with the agenda, list of participants, questions and comments, summaries of working groups on low-strength steel and alternate materials, and materials handed out by the speakers

CrisprGE: a central hub of CRISPR/Cas-based genome editing.

Science.gov (United States)

Kaur, Karambir; Tandon, Himani; Gupta, Amit Kumar; Kumar, Manoj

2015-01-01

CRISPR system is a powerful defense mechanism in bacteria and archaea to provide immunity against viruses. Recently, this process found a new application in intended targeting of the genomes. CRISPR-mediated genome editing is performed by two main components namely single guide RNA and Cas9 protein. Despite the enormous data generated in this area, there is a dearth of high throughput resource. Therefore, we have developed CrisprGE, a central hub of CRISPR/Cas-based genome editing. Presently, this database holds a total of 4680 entries of 223 unique genes from 32 model and other organisms. It encompasses information about the organism, gene, target gene sequences, genetic modification, modifications length, genome editing efficiency, cell line, assay, etc. This depository is developed using the open source LAMP (Linux Apache MYSQL PHP) server. User-friendly browsing, searching facility is integrated for easy data retrieval. It also includes useful tools like BLAST CrisprGE, BLAST NTdb and CRISPR Mapper. Considering potential utilities of CRISPR in the vast area of biology and therapeutics, we foresee this platform as an assistance to accelerate research in the burgeoning field of genome engineering. © The Author(s) 2015. Published by Oxford University Press.

75 FR 10442 - Sweet Cherries Grown in Designated Counties in Washington; Change in the Handling Regulation

Science.gov (United States)

2010-03-08

.... The existing paragraph (e) would be redesignated as paragraph (d), and the introductory sentence of... reported by the National Agricultural Statistics Service, USDA, and 1,500 Washington cherry producers, the... revise the introductory sentence of paragraph (g) to read as follows: Sec. 923.322 Washington cherry...

GenColors-based comparative genome databases for small eukaryotic genomes.

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Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

Science.gov (United States)

Manolio, Teri A

2016-10-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

"Harnessing genomics to improve health in Africa" – an executive course to support genomics policy

Directory of Open Access Journals (Sweden)

Singer Peter A

2005-01-01

Full Text Available Abstract Background Africa in the twenty-first century is faced with a heavy burden of disease, combined with ill-equipped medical systems and underdeveloped technological capacity. A major challenge for the international community is to bring scientific and technological advances like genomics to bear on the health priorities of poorer countries. The New Partnership for Africa's Development has identified science and technology as a key platform for Africa's renewal. Recognizing the timeliness of this issue, the African Centre for Technology Studies and the University of Toronto Joint Centre for Bioethics co-organized a course on Genomics and Public Health Policy in Nairobi, Kenya, the first of a series of similar courses to take place in the developing world. This article presents the findings and recommendations that emerged from this process, recommendations which suggest that a regional approach to developing sound science and technology policies is the key to harnessing genome-related biotechnology to improve health and contribute to human development in Africa. Methods The objectives of the course were to familiarize participants with the current status and implications of genomics for health in Africa; to provide frameworks for analyzing and debating the policy and ethical questions; and to begin developing a network across different sectors by sharing perspectives and building relationships. To achieve these goals the course brought together a diverse group of stakeholders from academic research centres, the media, non-governmental, voluntary and legal organizations to stimulate multi-sectoral debate around issues of policy. Topics included scientific advances in genomics innovation systems and business models, international regulatory frameworks, as well as ethical and legal issues. Results Seven main recommendations emerged: establish a network for sustained dialogue among participants; identify champions among politicians; use the

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Science.gov (United States)

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

Rodent malaria parasites : genome organization & comparative genomics

NARCIS (Netherlands)

Kooij, Taco W.A.

2006-01-01

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

A reference genome of the European beech (Fagus sylvatica L.).

Science.gov (United States)

Mishra, Bagdevi; Gupta, Deepak K; Pfenninger, Markus; Hickler, Thomas; Langer, Ewald; Nam, Bora; Paule, Juraj; Sharma, Rahul; Ulaszewski, Bartosz; Warmbier, Joanna; Burczyk, Jaroslaw; Thines, Marco

2018-06-01

The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany. Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum. The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.

Booker T. Washington's Audacious Vocationalist Philosophy

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Lewis, Theodore

2014-01-01

Booker T. Washington was born a slave in the American South, rising remarkably in the period after slavery to become a leader of his race. His advocacy of appeasement with the Southern white establishment incurred the ire of his black peers, given the withdrawal of the franchise from ex-slaves in southern states after a brief period of positive…

Genome size analyses of Pucciniales reveal the largest fungal genomes.

Science.gov (United States)

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

2014-01-01

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

Greenhouse gas mitigation options for Washington State

Energy Technology Data Exchange (ETDEWEB)

Garcia, N.

1996-04-01

President Clinton, in 1993, established a goal for the United States to return emissions of greenhouse gases to 1990 levels by the year 2000. One effort established to help meet this goal was a three part Environmental Protection Agency state grant program. Washington State completed part one of this program with the release of the 1990 greenhouse gas emissions inventory and 2010 projected inventory. This document completes part two by detailing alternative greenhouse gas mitigation options. In part three of the program EPA, working in partnership with the States, may help fund innovative greenhouse gas reduction strategies. The greenhouse gas control options analyzed in this report have a wide range of greenhouse gas reductions, costs, and implementation requirements. In order to select and implement a prudent mix of control strategies, policy makers need to have some notion of the potential change in climate, the consequences of that change and the uncertainties contained therein. By understanding the risks of climate change, policy makers can better balance the use of scarce public resources for concerns that are immediate and present against those that affect future generations. Therefore, prior to analyzing alternative greenhouse gas control measures, this report briefly describes the phenomenon and uncertainties of global climate change, and then projects the likely consequences for Washington state.

Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.

Science.gov (United States)

Bajaj, Deepak; Saxena, Maneesha S; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

2015-03-01

Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Absence of genome reduction in diverse, facultative endohyphal bacteria

Energy Technology Data Exchange (ETDEWEB)

Baltrus, David A. [Univ. of Arizona, Tucson, AZ (United States); Dougherty, Kevin [Univ. of Arizona, Tucson, AZ (United States); Arendt, Kayla R. [Univ. of Arizona, Tucson, AZ (United States); Huntemann, Marcel [Joint Genome Institute, Walnut Creek, CA (United States); Clum, Alicia [Joint Genome Institute, Walnut Creek, CA (United States); Pillay, Manoj [Joint Genome Institute, Walnut Creek, CA (United States); Palaniappan, Krishnaveni [Joint Genome Institute, Walnut Creek, CA (United States); Varghese, Neha [Joint Genome Institute, Walnut Creek, CA (United States); Mikhailova, Natalia [Joint Genome Institute, Walnut Creek, CA (United States); Stamatis, Dimitrios [Joint Genome Institute, Walnut Creek, CA (United States); Reddy, T. B. K. [Joint Genome Institute, Walnut Creek, CA (United States); Ngan, Chew Yee [Joint Genome Institute, Walnut Creek, CA (United States); Daum, Chris [Joint Genome Institute, Walnut Creek, CA (United States); Shapiro, Nicole [Joint Genome Institute, Walnut Creek, CA (United States); Markowitz, Victor [Joint Genome Institute, Walnut Creek, CA (United States); Ivanova, Natalia [Joint Genome Institute, Walnut Creek, CA (United States); Kyrpides, Nikos [Joint Genome Institute, Walnut Creek, CA (United States); Woyke, Tanja [Joint Genome Institute, Walnut Creek, CA (United States); Arnold, A. Elizabeth [Univ. of Arizona, Tucson, AZ (United States)

2017-02-28

Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.

The Ruby UCSC API: accessing the UCSC genome database using Ruby.