This system will be undergoing maintenance Friday, March 31 from 9:00 AM to 10:00 AM CDT.

Search Results

Evolutionary Genomics of Life in (and from) the Sea

Description: High throughput genome sequencing centers that were originally built for the Human Genome Project (Lander et al., 2001; Venter et al., 2001) have now become an engine for comparative genomics. The six largest centers alone are now producing over 150 billion nucleotides per year, more than 50 times the amount of DNA in the human genome, and nearly all of this is directed at projects that promise great insights into the pattern and processes of evolution. Unfortunately, this data is being produced at a pace far exceeding the capacity of the scientific community to provide insightful analysis, and few scientists with training and experience in evolutionary biology have played prominent roles to date. One of the consequences is that poor quality analyses are typical; for example, orthology among genes is generally determined by simple measures of sequence similarity, when this has been discredited by molecular evolutionary biologists decades ago. Here we discuss the how genomes are chosen for sequencing and how the scientific community can have input. We describe the PhIGs database and web tools (Dehal and Boore 2005a; http://PhIGs.org), which provide phylogenetic analysis of all gene families for all completely sequenced genomes and the associated 'Synteny Viewer', which allows comparisons of the relative positions of orthologous genes. This is the best tool available for inferring gene function across multiple genomes. We also describe how we have used the PhIGs methods with the whole genome sequences of a tunicate, fish, mouse, and human to conclusively demonstrate that two rounds of whole genome duplication occurred at the base of vertebrates (Dehal and Boore 2005b). This evidence is found in the large scale structure of the positions of paralogous genes that arose from duplications inferred by evolutionary analysis to have occurred at the base of vertebrates.
Date: January 9, 2006
Creator: Boore, Jeffrey L.; Dehal, Paramvir & Fuerstenberg, Susan I.
Item Type: Report
Partner: UNT Libraries Government Documents Department

COMPARISONS OF CODED APERTURE IMAGING USING VARIOUS APERTURES AND DECODING METHODS

Description: The utility of coded aperture imaging of radioisotope distributions in Nuclear Medicine is in its ability to give depth information about a three dimensional source. We have calculated imaging with Fresnel zone plate and multiple pinhole apertures to produce coded shadows and reconstruction of these shadows using correlation, Fresnel diffraction, and Fourier transform deconvolution. Comparisons of the coded apertures and decoding methods are made by evaluating their point response functions both for in-focus and out-of-focus image planes. Background averages and standard deviations were calculated. In some cases, background subtraction was made using combinations of two complementary apertures. Results using deconvolution reconstruction for finite numbers of events are also given.
Date: July 1, 1976
Creator: Chang, L.-T.; Macdonald, B. & Perez-Mendez, V.
Item Type: Article
Partner: UNT Libraries Government Documents Department

Chemistry and Materials Science 2004 Annual Report, Preview Edition

Description: Thriving from change is a constant element at LLNL. Through our commitment to scientific accomplishments, we have met the challenges posed by our evolving missions in 2004. It is the scientific breakthroughs that substantiate our strategic directions. Investments based on our strategic directions are bearing fruit, as illustrated in this preview of the 2004 Annual Report. We describe how our science is built around a strategic plan with four organizing themes: {sm_bullet} Materials properties and performance under extreme conditions {sm_bullet} Chemistry under extreme conditions and chemical engineering in support of national-security programs {sm_bullet} Science supporting national objectives at the intersection of chemistry, materials science, and biology {sm_bullet} Applied nuclear science for human health and national security We are particularly pleased with achievements within the 'intersection of chemistry, materials science, and biology,' an emerging area of science that may reshape the landscape of our national-security mission. CMS continues to have an unambiguous role both as a technology leader and as a partner for all of the four theme areas. We look forward to expanding the frontiers of science and continuing our partnership with the worldwide scientific community, as we firmly respond to the changing environment with agility and flexibility.
Date: May 16, 2005
Creator: Shang, S; Diaz de la Rubia, T & Rennie, G
Item Type: Report
Partner: UNT Libraries Government Documents Department

Characterization of Pathogenicity, Virulence and Host-Pathogen Interractions

Description: The threats of bio-terrorism and newly emerging infectious diseases pose serious challenges to the national security infrastructure. Rapid detection and diagnosis of infectious disease in human populations, as well as characterizing pathogen biology, are critical for reducing the morbidity and mortality associated with such threats. One of the key challenges in managing an infectious disease outbreak, whether through natural causes or acts of overt terrorism, is detection early enough to initiate effective countermeasures. Much recent attention has been directed towards the utility of biomarkers or molecular signatures that result from the interaction of the pathogen with the host for improving our ability to diagnose and mitigate the impact of a developing infection during the time window when effective countermeasures can be instituted. Host responses may provide early signals in blood even from localized infections. Multiple innate and adaptive immune molecules, in combination with other biochemical markers, may provide disease-specific information and new targets for countermeasures. The presence of pathogen specific markers and an understanding of the molecular capabilities and adaptations of the pathogen when it interacts with its host may likewise assist in early detection and provide opportunities for targeting countermeasures. An important question that needs to be addressed is whether these molecular-based approaches will prove useful for early diagnosis, complement current methods of direct agent detection, and aid development and use of countermeasures. Lawrence Livermore National Laboratory (LLNL) will host a workshop to explore the utility of host- and pathogen-based molecular diagnostics, prioritize key research issues, and determine the critical steps needed to transition host-pathogen research to tools that can be applied towards a more effective national bio-defense strategy. The workshop will bring together leading researchers/scientists in the area of host-pathogen interactions as well as policy makers from federal agencies. The main objectives of the workshop are: (1) to ...
Date: July 27, 2006
Creator: Krishnan, A & Folta, P
Item Type: Article
Partner: UNT Libraries Government Documents Department

Biotechnology development for biomedical applications.

Description: Sandia's scientific and engineering expertise in the fields of computational biology, high-performance prosthetic limbs, biodetection, and bioinformatics has been applied to specific problems at the forefront of cancer research. Molecular modeling was employed to design stable mutations of the enzyme L-asparaginase with improved selectivity for asparagine over other amino acids with the potential for improved cancer chemotherapy. New electrospun polymer composites with improved electrical conductivity and mechanical compliance have been demonstrated with the promise of direct interfacing between the peripheral nervous system and the control electronics of advanced prosthetics. The capture of rare circulating tumor cells has been demonstrated on a microfluidic chip produced with a versatile fabrication processes capable of integration with existing lab-on-a-chip and biosensor technology. And software tools have been developed to increase the calculation speed of clustered heat maps for the display of relationships in large arrays of protein data. All these projects were carried out in collaboration with researchers at the University of Texas M. D. Anderson Cancer Center in Houston, TX.
Date: November 1, 2010
Creator: Kuehl, Michael; Brozik, Susan Marie; Rogers, David Michael; Rempe, Susan L.; Abhyankar, Vinay V.; Hatch, Anson V. et al.
Item Type: Report
Partner: UNT Libraries Government Documents Department

Chemical Force Microscopy of Chemical and Biological Interactions

Description: Interactions between chemical functionalities define outcomes of the vast majority of important events in chemistry, biology and materials science. Chemical Force Microscopy (CFM)--a technique that uses direct chemical functionalization of AFM probes with specific functionalities--allows researchers to investigate these important interactions directly. We review the basic principles of CFM, some examples of its application, and theoretical models that provide the basis for understanding the experimental results. We also emphasize application of modern kinetic theory of non-covalent interactions strength to the analysis of CFM data.
Date: January 2, 2006
Creator: Noy, A
Item Type: Article
Partner: UNT Libraries Government Documents Department

DOE Joint Genome Institute 2008 Progress Report

Description: While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic ...
Date: March 12, 2009
Creator: Gilbert, David
Item Type: Report
Partner: UNT Libraries Government Documents Department

2007 Microbial Population Biology (July 22-26, 2007)

Description: Microbial Population Biology covers a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.
Date: April 1, 2008
Creator: Dean, Anthony M. & Gray, Nancy Ryan
Item Type: Article
Partner: UNT Libraries Government Documents Department

2007 Archaea: Ecology, Metabolism and Molecular Biology

Description: The Archaea are a fascinating and diverse group of prokaryotic organisms with deep roots overlapping those of eukaryotes. The focus of this GRC conference, 'Archaea: Ecology Metabolism & Molecular Biology', expands on a number of emerging topics highlighting the evolution and composition of microbial communities and novel archaeal species, their impact on the environment, archaeal metabolism, and research that stems from sequence analysis of archaeal genomes. The strength of this conference lies in its ability to couple reputable areas with new scientific topics in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.
Date: September 18, 2008
Creator: Gray, Imke Schroeder Nancy Ryan
Item Type: Article
Partner: UNT Libraries Government Documents Department

2007 GRC on Cellulases and Cellulosomes (July 29-August 3, 2007)

Description: Cellulose, a key component of the plant cell wall, comprises the most abundant source of organic carbon on the planet and its microbial degradation is of considerable biological and industrial importance. Indeed, the microbial degradation of cellulose and other plant structural polysaccharides is critical to the maintenance of the carbon cycle in terrestrial and marine microbial ecosystems, host invasion by several phytopathogens, and herbivore nutrition. While the enzymes that attack cellulose are already widely used in several biotechnology-based industries, the major future application of these biocatalysts is the conversion of plant biomass into bio-ethanol and other forms of energy. In that context, the 2007 Conference will present the latest breakthroughs in our understanding of the enzymology, structural biology and (meta)genomics underpinning the conversion of plant structural polysaccharides into fermentable sugars, both in natural and engineered processes. There is also an increased emphasis on the roles of other carbohydrate active enzymes in plant biomass conversion. The themes for the scientific sessions include: (1) crystallographic and biochemical analyses of enzyme structure and function; (2) molecular mechanisms underpinning enzyme catalysis, processivity and specificity; (3) functional and comparative analyses of carbohydrate binding modules and enzyme-substrate interactions; (4) directed evolution for the development of catalytically superior glycoside hydrolases; (5) biophysical and structural analyses of native and chemically pretreated plant biomass and component polysaccharides; (6) genomics of specialist polysaccharide degrading microbes; (7) metagenomics and ecophysiology of plant biomass degradation in natural and engineered processes and; (8) enhancement of industrial bioprocesses by metabolic engineering and related approaches. While the Conference draws many of its participants from academia and government agencies, colleagues from industry have made many important and valuable contributions to the success of all the Conferences. This makes the Conference a truly interactive and productive venue for all sectors interested in the fundamental and applied sciences ...
Date: September 22, 2008
Creator: Gray, Mark Morrison Nancy Ryan
Item Type: Article
Partner: UNT Libraries Government Documents Department

04-ERD-052-Final Report

Description: Generating the sequence of the human genome represents a colossal achievement for science and mankind. The technical use for the human genome project information holds great promise to cure disease, prevent bioterror threats, as well as to learn about human origins. Yet converting the sequence data into biological meaningful information has not been immediately obvious, and we are still in the preliminary stages of understanding how the genome is organized, what are the functional building blocks and how do these sequences mediate complex biological processes. The overarching goal of this program was to develop novel methods and high throughput strategies for determining the functions of ''anonymous'' human genes that are evolutionarily deeply conserved in other vertebrates. We coupled analytical tool development and computational predictions regarding gene function with novel high throughput experimental strategies and tested biological predictions in the laboratory. The tools required for comparative genomic data-mining are fundamentally the same whether they are applied to scientific studies of related microbes or the search for functions of novel human genes. For this reason the tools, conceptual framework and the coupled informatics-experimental biology paradigm we developed in this LDRD has many potential scientific applications relevant to LLNL multidisciplinary research in bio-defense, bioengineering, bionanosciences and microbial and environmental genomics.
Date: February 26, 2007
Creator: Loots, G G; Ovcharenko, I; Collette, N; Babu, P; Chang, J; Stubbs, L et al.
Item Type: Report
Partner: UNT Libraries Government Documents Department

Advances in Genome Biology & Technology

Description: This year's meeting focused on the latest advances in new DNA sequencing technologies and the applications of genomics to disease areas in biology and biomedicine. Daytime plenary sessions highlighted cutting-edge research in areas such as complex genetic diseases, comparative genomics, medical sequencing, massively parallel DNA sequencing, and synthetic biology. Technical approaches being developed and utilized in contemporary genomics research were presented during evening concurrent sessions. Also, as in previous years, poster sessions bridged the morning and afternoon plenary sessions. In addition, for the third year in a row, the Advances in Genome Biology and Technology (AGBT) meeting was preceded by a pre-meeting workshop that aimed to provide an introductory overview for trainees and other meeting attendees. This year, speakers at the workshop focused on next-generation sequencing technologies, including their experiences, findings, and helpful advise for others contemplating using these platforms in their research. Speakers from genome centers and core sequencing facilities were featured and the workshop ended with a roundtable discussion, during which speakers fielded questions from the audience.
Date: December 1, 2007
Creator: Thomas J. Albert, Jon R. Armstrong, Raymond K. Auerback, W. Brad Barbazuk, et al.
Item Type: Article
Partner: UNT Libraries Government Documents Department

Diffusion through Carbon Nanotube Semipermeable membranes

Description: The goal of this project is to measure transport through CNTs and study effects of confinement at molecular scale. This work is motivated by several simulation papers in high profile journals that predict significantly higher transport rates of gases and liquids through carbon nanotubes as compared with similarly-sized nanomaterials (e.g. zeolites). The predictions are based on the effects of confinement, atomically smooth pore walls and high pore density. Our work will provide the first measurements that would compare to and hopefully validate the simulations. Gas flux is predicted to be >1000X greater for SWNTs versus zeolitesi. A high flux of 6-30 H2O/NT/ns {approx} 8-40 L/min for a 1cm{sup 2} membrane is also predicted. Neutron diffraction measurements indicate existence of a 1D water chain within a cylindrical ice sheet inside carbon nanotubes, which is consistent with the predictions of the simulation. The enabling experimental platform that we are developing is a semipermeable membrane made out of vertically aligned carbon nanotubes with gaps between nanotubes filled so that the transport occurs through the nanotubes. The major challenges of this project included: (1) Growth of CNTs in the suitable vertically aligned configuration, especially the single wall carbon nanotubes; (2) Development of a process for void-free filling gaps between CNTs; and (3) Design of the experiments that will probe the small amounts of analyte that go through. Knowledge of the behavior of water upon nanometer-scale confinement is key to understanding many biological processes. For example, the protein folding process is believed to involve water confined in a hydrophobic environment. In transmembrane proteins such as aquaporins, water transport occurs under similar conditions. And in fields as far removed as oil recovery and catalysis, an understanding of the nanoscale molecular transport occurring within the nanomaterials used (e.g. zeolites) is the key to process optimization. Furthermore, advancement ...
Date: February 13, 2006
Creator: Bakajin, O
Item Type: Report
Partner: UNT Libraries Government Documents Department

Evaluation of Cavity Collapse and Surface Crater Formation for Selected Lawrence Livermore National Laboratory Underground Nuclear Tests - 2006

Description: This report describes evaluation of collapse evolution for selected LLNL underground nuclear tests at the Nevada Test Site (NTS). The work is being done at the request of Bechtel Nevada and supports the Department of Energy National Nuclear Security Association Nevada Site Office Borehole Management Program (BMP). The primary objective of this program is to close (plug) weapons program legacy boreholes that are deemed no longer useful. Safety decisions must be made before a crater area, or potential crater area, can be reentered for any work. Our statements on cavity collapse and crater formation are input into their safety decisions. The BMP is an on-going program to address hundreds of boreholes at the NTS. Each year Bechtel Nevada establishes a list of holes to be addressed. They request the assistance of the Lawrence Livermore National Laboratory and Los Alamos National Laboratory Containment Programs to provide information related to the evolution of collapse history and make statements on completeness of collapse as relates to surface crater stability. These statements do not include the effects of erosion that may modify the collapse craters over time. They also do not address possible radiation dangers that may be present. Subject matter experts from the LLNL Containment Program and the Chemistry Biology and Nuclear Sciences Division who had been active in weapons testing activities performed these evaluations. Information used included drilling and hole construction, emplacement and stemming, timing and sequence of the selected test and nearby tests, geology, yield, depth of burial, collapse times, surface crater sizes, cavity and crater volume estimations, and ground motion. Both classified and unclassified data were reviewed. Various amounts of information are available for these tests, depending on their age and other associated activities. Lack of data can hamper evaluations and introduce uncertainty. We make no attempt to quantify this ...
Date: March 16, 2006
Creator: Pawloski, G. A. & Raschke, K.
Item Type: Report
Partner: UNT Libraries Government Documents Department

Science & Technology Review April/May 2010

Description: This month's issue has the following articles: (1) Fifty Years of Stellar Laser Research - Commentary by Edward I. Moses; (2) A Stellar Performance - By combining computational models with test shot data, scientists at the National Ignition Facility have demonstrated that the laser is spot-on for ignition; (3) Extracting More Power from the Wind - Researchers are investigating how atmospheric turbulence affects power production from wind turbines; (4) Date for a Heart Cell - Carbon-14 dating reveals that a significant number of heart muscle cells are regenerated over the course of our lives; and (5) Unique Marriage of Biology and Semiconductors - A new device featuring a layer of fat surrounding a thin silicon wire takes advantage of the communication properties of both biomolecules and semiconductors.
Date: March 8, 2010
Creator: Blobaum, K M
Item Type: Report
Partner: UNT Libraries Government Documents Department

SUMMARY STATEMENT OF FINDINGS RELATED TO THE DISTRIBUTION, CHARACTERISTICS, AND BIOLOGICAL AVAILABILITY OF FALLOUT DEBRIS ORIGINATING FROM TESTING PROGRAMS AT THE NEVADA TEST SITE

Description: Summary statements are given of significant findings related to the distribution characteristics, and biological availability of fall-out debris originating from testing programs at the Nevada Test Site during the past decade. The delineation of fall-out patterns has been accomplished by the use of aenial and ground monitoring surveys. Only about 25% of the total amount of fission products produced by tower-supported detonations were deposited within distances corresponding to fall-out time of H + 12 hr; a much smaller quantity was deposited by halloon-supported detonations. Fall-out particles less than 44 (For in diameter are presumed to be of the greatest biological significance. About 30% of the fall-out radioactivity from tower-supported detonations was contained in the 0 to 44 (For particles as compared to almost 70% for balloon-supported detonations. Fall-out debris from halloon- supported detonations was also much more water and acid soluble than was the debris from towel-supported detonations. The <44 (For fallout particles contained a higher percentage of Sr/sup 89/, Sr/sup 90/, Ru/sup 10/ / sup 3/, and Ru/sup 106/ than did larger sized particles. There was a higher percentage of these radioelements in the particles from balloon-supported detonations. Within distances corresponding to H + 12 hr fall-out time, balloon- supported detonations deposited a maximum of 0.13% of the theoretical total Sr/ sup 89/ produced; tower-supported detonations deposited a maximum of 2%. Tower- supported detonations also deposited a maximum of 7.2% of the theoretical total amount of Sr/sup 90/ produced. Beta decay curves approximated the T/sup -1.//sup 2/ decay expression from H + 12 to H + 6000 hr; gamma decay curves deviated to the extent that irradiation doses calculated by the observed decay values were 1.5 to 2 times > those calculated by the T/sup -1.//sup 2/ relationship. Fall- out radioactivity is apparently confined to the first 2 in. ...
Date: September 14, 1960
Creator: Larson, K.H. & Neel, J.W.
Item Type: Report
Partner: UNT Libraries Government Documents Department

Stability of biological networks as represented in Random Boolean Nets.

Description: We explore stability of Random Boolean Networks as a model of biological interaction networks. We introduce surface-to-volume ratio as a measure of stability of the network. Surface is defined as the set of states within a basin of attraction that maps outside the basin by a bit-flip operation. Volume is defined as the total number of states in the basin. We report development of an object-oriented Boolean network analysis code (Attract) to investigate the structure of stable vs. unstable networks. We find two distinct types of stable networks. The first type is the nearly trivial stable network with a few basins of attraction. The second type contains many basins. We conclude that second type stable networks are extremely rare.
Date: September 1, 2004
Creator: Slepoy, Alexander & Thompson, Marshall
Item Type: Report
Partner: UNT Libraries Government Documents Department

RADIATION SAFETY IN THE DEVELOPMENT AND USE OF NUCLEAR ENERGY FOR ROCKET PROPULSION

Description: A vigorous safety program is being conducted concurrently with engineering development of prototype nuclear propulsion reactors, and some of its conclusions are discussed. The problem areas are delineated and reasonably sound predictions are presented of the potential radiation hazards of testing and flying a minimal performance system capable of producing 1000 Mw power for an operating cycle of 5 min. The reactor, although containing more U/sup 2//sup 3// sup 5/ than an atomic bomb, could not produce a significant nuclear explosion under the most drastic accident conditions. At most, the energy release would be only approximately -3% of the maximum power rating. Prompt neutron and gamma radiation during operation, although lethal at short distances, will not deliver significant exposure to test and launch crews at a distance of 1 mile. Accidental release of accummulated fission products during static testing, launch pad failure, or early mission abort would result in considerable contamination of the facilities, and extensive decontamination operations would be necessary. Impact outside the controlled area of an operated reactor, either as a result of late mission failure or re-entry from orbit, constitute a problem requiring further study. Choice of seacoast, ocean, and island-based launching sites, controlled re-entry and impact, and reactor burn-up or fission prcduct boil-off in space are possibilities. General biospheric contamination from nuclear rocket operations is an insignificant problem compared to that created by nuclear weapon tests. (D.L.C.)
Date: January 1, 1961
Creator: Langham, W.H.
Item Type: Report
Partner: UNT Libraries Government Documents Department

Sage-Grouse and Wind Energy: Biology, Habits, and Potential Effects from Development

Description: Proposed development of domestic energy resources, including wind energy, is expected to impact the sagebrush steppe ecosystem in the western United States. The greater sage-grouse relies on habitats within this ecosystem for survival, yet very little is known about how wind energy development may affect sage-grouse. The purpose of this report is to inform organizations of the impacts wind energy development could have on greater sage-grouse populations and identify information needed to fill gaps in knowledge.
Date: July 15, 2009
Creator: Becker, James M.; Tagestad, Jerry D.; Duberstein, Corey A. & Downs, Janelle L.
Item Type: Report
Partner: UNT Libraries Government Documents Department