Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

ScienceCinema

Tringe, Susannah

2018-02-14

Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

Resources for Biological Annotation of the Drosophila Genome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerald M. Rubin

2005-08-08

This project supported seed money for the development of cDNA and genetic resources to support studies of the Drosophila melanogaster genome. Key publications supported by this work that provide additional detail: (1) ''The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes''; and (2) ''The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes''.

The structure of a cholesterol-trapping protein

Science.gov Websites

Date February 28, 2003 Date Berkeley Lab Science Beat Berkeley Lab Science Beat The structure of a Institute researchers determined the three-dimensional structure of a protein that controls cholesterol level in the bloodstream. Knowing the structure of the protein, a cellular receptor that ensnares

Subsurface Microbes Expanding the Tree of Life

ScienceCinema

Banfield, Jillian

2018-02-14

Jillian Banfield, Ph.D., UC Berkeley Professor and Berkeley Lab Earth Sciences Division staff scientist and long-time user of the DOE Joint Genome Institute’s resources shares her perspective on how the DOE JGI helps advance her research addressing knowledge gaps related to the roles of subsurface microbial communities in biogeochemical cycling. The video was filmed near the town of Rifle, Colorado at the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 sponsored by the DOE Office of Biological and Environmental Research.

Microbes to Biomes at Berkeley Lab

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2015-10-28

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pereira, Jose H.; McAndrew, Ryan P.; Tomaleri, Giovani P.

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography programmore » at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.« less

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

DOE PAGES

Pereira, Jose H.; McAndrew, Ryan P.; Tomaleri, Giovani P.; ...

2017-09-05

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography programmore » at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.« less

Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Glass, N. Louise; Pennacchio, Len

2018-02-13

N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

From Shakespeare to Viruses

ScienceCinema

Kim, Sung-Hou

2017-12-11

Berkeley Lab scientists have created a unique new tool for analyzing and comparing long sets of data, be it the genomes of mammals or viruses, or the works of Shakespeare. The results of the Shakespeare analysis surprised scholars with their accuracy.

From Shakespeare to Viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sung-Hou Kim

2009-02-09

Berkeley Lab scientists have created a unique new tool for analyzing and comparing long sets of data, be it the genomes of mammals or viruses, or the works of Shakespeare. The results of the Shakespeare analysis surprised scholars with their accuracy

From Shakespeare to Viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Sung-Hou

2009-02-09

Berkeley Lab scientists have created a unique new tool for analyzing and comparing long sets of data, be it the genomes of mammals or viruses, or the works of Shakespeare. The results of the Shakespeare analysis surprised scholars with their accuracy.

DEGAS: Dynamic Exascale Global Address Space Programming Environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demmel, James

The Dynamic, Exascale Global Address Space programming environment (DEGAS) project will develop the next generation of programming models and runtime systems to meet the challenges of Exascale computing. The Berkeley part of the project concentrated on communication-optimal code generation to optimize speed and energy efficiency by reducing data movement. Our work developed communication lower bounds, and/or communication avoiding algorithms (that either meet the lower bound, or do much less communication than their conventional counterparts) for a variety of algorithms, including linear algebra, machine learning and genomics. The Berkeley part of the project concentrated on communication-optimal code generation to optimize speedmore » and energy efficiency by reducing data movement. Our work developed communication lower bounds, and/or communication avoiding algorithms (that either meet the lower bound, or do much less communication than their conventional counterparts) for a variety of algorithms, including linear algebra, machine learning and genomics.« less

Lawrence Berkeley National Laboratory 2015 Annual Financial Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Kim, P

FY2015 financial results reflect a year of significant scientific, operational and financial achievement for Lawrence Berkeley National Laboratory. Complementing many scientific accomplishments, Berkeley Lab completed construction of four new research facilities: the General Purpose Laboratory, Chu Hall, Wang Hall and the Flexlab Building Efficiency Testbed. These state-of-the-art facilities allow for program growth and enhanced collaboration, in part by enabling programs to return to the Lab’s Hill Campus from offsite locations. Detailed planning began for the new Integrative Genomics Building (IGB) that will house another major program currently located offsite. Existing site infrastructure was another key focus area. The Lab prioritizedmore » and increased investments in deferred maintenance in alignment with the Berkeley Lab Infrastructure Plan, which was developed under the leadership of the DOE Office of Science. With the expiration of American Recovery and Reinvestment Act (ARRA) funds, we completed the close-out of all of our 134 ARRA projects, recording total costs of $331M over the FY2009-2015 period. Download the report to read more.« less

Microbes to Biomes at Berkeley Lab

ScienceCinema

None

2018-06-21

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

ScienceCinema

Jansson, Janet

2018-01-04

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urban, Jeff

Berkeley Lab materials scientist, Jeff Urban presents his research on using metal-organic frameworks to capture carbon at Berkeley Lab's Cleantech Pitchfest on June 1, 2016. Removing excess carbon from an overheating atmosphere is an urgent and complicated problem. The answer, according to Berkeley Lab’s Jeff Urban, could lie at the nanoscale, where specially designed cage-like structures called metal organic frameworks, or MOFs, can trap large amounts of carbon in microscopically tiny structures. A Harvard PhD with expertise in thermoelectrics, gas separation and hydrogen storage, Urban directs teams at the Molecular Foundry’s Inorganic Materials Facility.

Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample

PubMed Central

Gilks, William P.; Pennell, Tanya M.; Flis, Ilona; Webster, Matthew T.; Morrow, Edward H.

2016-01-01

As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LH M). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics ( https://zenodo.org/communities/sussex_drosophila_sequencing/). PMID:27928499

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jansson, Janet

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI inmore » Walnut Creek, CA on Sept. 9, 2009.« less

Genome Science and Personalized Cancer Treatment (LBNL Summer Lecture Series)

ScienceCinema

Gray, Joe [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division and Associate Lab. Director for Life and Environmental Sciences

2018-05-04

Summer Lecture Series 2009: Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Labs Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, will focus on this approach, its promise, and its current roadblocks — particularly with regard to breast cancer.

POWER AND AUTHORITY--EMERGING TRENDS AND ASPIRATIONS, PROCEEDINGS OF THE STANFORD-BERKELEY SEMINAR FOR JUNIOR COLLEGE PRESIDENTS (2D, BERKELEY, JUNE 19-21, 1964).

ERIC Educational Resources Information Center

MEDSKER, LELAND L.; TILLERY, HARRY DALE

FIVE PAPERS ARE REPRODUCED IN THIS REPORT. DR. DONALD D. JACKSON DISCUSSED THE CHANGING POWER STRUCTURE IN MODERN SOCIETIES, AS PREPARATION FOR THE EXAMINATION OF TRENDS RELEVANT TO CRUCIAL ASPECTS OF THE COLLEGE COMMUNITY. GORDON W. BLACKWELL DESCRIBED THE FORMAL POWER STRUCTURE, THE INFORMAL POWER STRUCTURE, AND AREAS OF TENSION IN STATE…

Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Dehal, Paramvir

2018-02-06

Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

SF Cleantech Pitchfest: Nano Sponges for Carbon Capture

ScienceCinema

Urban, Jeff

2018-01-16

Berkeley Lab materials scientist, Jeff Urban presents his research on using metal-organic frameworks to capture carbon at Berkeley Lab's Cleantech Pitchfest on June 1, 2016. Removing excess carbon from an overheating atmosphere is an urgent and complicated problem. The answer, according to Berkeley Lab’s Jeff Urban, could lie at the nanoscale, where specially designed cage-like structures called metal organic frameworks, or MOFs, can trap large amounts of carbon in microscopically tiny structures. A Harvard PhD with expertise in thermoelectrics, gas separation and hydrogen storage, Urban directs teams at the Molecular Foundry’s Inorganic Materials Facility.

Life sciences and environmental sciences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-02-01

The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER's mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment,more » applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.« less

The Gulf Oil Spill: Ecogenomics and Ecoresilience (Keynote - 2011 JGI User Meeting)

ScienceCinema

Hazen, Terry [LBNL

2018-04-25

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Berkeley Lab microbial ecologist Terry Hazen delivers a keynote on "The Gulf Oil Spill: Ecogenomics and Ecoresilience" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011.

Sustainable Systems SFA 2.0

ScienceCinema

Hubbard, Susan

2018-05-07

Berkeley Lab Earth Sciences Division Director Susan Hubbard, the Project Lead for the Sustainable Systems Scientific Focus Area (SFA) 2.0, gives an overview of the project and its mission to develop a predictive understanding of terrestrial environments, from the genome to the watershed scales, to enable a new class of solutions for environmental and energy solutions.

Sustainable Systems SFA 2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hubbard, Susan

2015-12-19

Berkeley Lab Earth Sciences Division Director Susan Hubbard, the Project Lead for the Sustainable Systems Scientific Focus Area (SFA) 2.0, gives an overview of the project and its mission to develop a predictive understanding of terrestrial environments, from the genome to the watershed scales, to enable a new class of solutions for environmental and energy solutions.

Gobe: an interactive, web-based tool for comparative genomic visualization.

PubMed

Pedersen, Brent S; Tang, Haibao; Freeling, Michael

2011-04-01

Gobe is a web-based tool for viewing comparative genomic data. It supports viewing multiple genomic regions simultaneously. Its simple text format and flash-based rendering make it an interactive, exploratory research tool. Gobe can be used without installation through our web service, or downloaded and customized with stylesheets and javascript callback functions. Gobe is a flash application that runs in all modern web-browsers. The full source-code, including that for the online web application is available under the MIT license at: http://github.com/brentp/gobe. Sample applications are hosted at http://try-gobe.appspot.com/ and http://synteny.cnr.berkeley.edu/gobe-app/.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor; Glass, N. Louise; Martin, Francis

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) managed by Lawrence Berkeley National Laboratory, is the only user facility in the world devoted to problems of energy and environment. With over one million species, fungi—which include mushrooms—represent one of the largest under-explored branches of the Tree of Life. Together with its community of more than 1,000 scientific collaborators, JGI helping to unlock the secrets encoded in the genomes of fungi to advance a better understanding of the global carbon cycle and to develop new biotechnology products, next-generation biofuels, and medicines.

Hybrid Memory Management for Parallel Execution of Prolog on Shared Memory Multiprocessors

DTIC Science & Technology

1990-06-01

organizing data to increase locality. The stack structure exhibits greater locality than the heap structure. Tradeoff decisions can also be made on...PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES...University of California at Berkeley,Department of Electrical Engineering and Computer Sciences,Berkeley,CA,94720 8. PERFORMING ORGANIZATION REPORT

Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Canon, Shane

2018-01-24

DOE JGI's Zhong Wang, chair of the High-performance Computing session, gives a brief introduction before Berkeley Lab's Shane Canon talks about "Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Peppytides: Interactive Models of Polypeptide Chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

2014-01-21

Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

Peppytides: Interactive Models of Polypeptide Chains

ScienceCinema

Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

2018-06-08

Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

Health Detectives: Uncovering the Mysteries of Disease (LBNL Science at the Theater)

ScienceCinema

Bissell, Mina; Canaria, Christie; Celnicker, Susan; Karpen, Gary

2018-06-20

In this April 23, 2012 Science at the Theater event, Berkeley Lab scientists discuss how they uncover the mysteries of disease in unlikely places. Speakers and topics include: World-renowned cancer researcher Mina Bissell's pioneering research on the role of the cellular microenvironment in breast cancer has changed the conversation about the disease. How does DNA instability cause disease? To find out, Christie Canaria images neural networks to study disorders such as Huntington's disease. Fruit flies can tell us a lot about ourselves. Susan Celniker explores the fruit fly genome to learn how our genome works. DNA is not destiny. Gary Karpen explores how environmental factors shape genome function and disease through epigenetics.

Blasting Rocks and Blasting Cars Applied Engineering

ScienceCinema

LBNL

2017-12-09

June 30, 2004 Berkeley Lab lecture: Deb Hopkins works with industries like automobile, mining and paper to improve their evaluation and measuring techniques. For several years, she has coordinated ... June 30, 2004 Berkeley Lab lecture: Deb Hopkins works with industries like automobile, mining and paper to improve their evaluation and measuring techniques. For several years, she has coordinated a program at Berkeley Lab funded under the Partnership for a New Generation of Vehicles, a collaboration between the federal government and the U.S. Council for Automotive Research. Nondestructive evaluation techniques to test a car's structural integrity are being developed for auto assembly lines.

Health Detectives: Uncovering the Mysteries of Disease (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bissell, Mina; Canaria, Christie; Celnicker, Susan

In this April 23, 2012 Science at the Theater event, Berkeley Lab scientists discuss how they uncover the mysteries of disease in unlikely places. Speakers and topics include: World-renowned cancer researcher Mina Bissell's pioneering research on the role of the cellular microenvironment in breast cancer has changed the conversation about the disease. How does DNA instability cause disease? To find out, Christie Canaria images neural networks to study disorders such as Huntington's disease. Fruit flies can tell us a lot about ourselves. Susan Celniker explores the fruit fly genome to learn how our genome works. DNA is not destiny. Garymore » Karpen explores how environmental factors shape genome function and disease through epigenetics.« less

VIZARD: analysis of Affymetrix Arabidopsis GeneChip data

NASA Technical Reports Server (NTRS)

Moseyko, Nick; Feldman, Lewis J.

2002-01-01

SUMMARY: The Affymetrix GeneChip Arabidopsis genome array has proved to be a very powerful tool for the analysis of gene expression in Arabidopsis thaliana, the most commonly studied plant model organism. VIZARD is a Java program created at the University of California, Berkeley, to facilitate analysis of Arabidopsis GeneChip data. It includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for the discovery of regulatory motifs in upstream sequences. VIZARD also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis GeneChip array. AVAILABILITY: VIZARD is available free of charge for educational, research, and not-for-profit purposes, and can be downloaded at http://www.anm.f2s.com/research/vizard/ CONTACT: moseyko@uclink4.berkeley.edu.

Blasting Rocks and Blasting Cars Applied Engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

LBNL

2008-07-02

June 30, 2004 Berkeley Lab lecture: Deb Hopkins works with industries like automobile, mining and paper to improve their evaluation and measuring techniques. For several years, she has coordinated ... June 30, 2004 Berkeley Lab lecture: Deb Hopkins works with industries like automobile, mining and paper to improve their evaluation and measuring techniques. For several years, she has coordinated a program at Berkeley Lab funded under the Partnership for a New Generation of Vehicles, a collaboration between the federal government and the U.S. Council for Automotive Research. Nondestructive evaluation techniques to test a car's structural integrity are being developed formore » auto assembly lines.« less

Hope or Hype? What is Next for Biofuels? (LBNL Science at the Theater)

ScienceCinema

Keasling, Jay; Bristow, Jim; Tringe, Susannah Green

2017-12-09

Science at the Theater: From the sun to your gas tank: A new breed of biofuels may help solve the global energy challenge and reduce the impact of fossil fuels on global warming. KTVU Channel 2 health and science editor John Fowler will moderate a panel of Lawrence Berkeley National Laboratory scientists who are developing ways to convert the solar energy stored in plants into liquid fuels. Jay Keasling is one of the foremost authorities in the field of synthetic biology. He is applying this research toward the production of advanced carbon-neutral biofuels that can replace gasoline on a gallon-for-gallon basis. Keasling is Berkeley Labs Acting Deputy Director and the Chief Executive Officer of the U.S. Department of Energys Joint BioEnergy Institute. Jim Bristow is deputy director of programs for the U.S. Department of Energy Joint Genome Institute (JGI), a national user facility in Walnut Creek, CA. He developed and implemented JGIs Community Sequencing Program, which provides large-scale DNA sequencing and analysis to advance genomics related to bioenergy and environmental characterization and cleanup. Susanna Green Tringe is a computational biologist with the U.S. Department of Energy Joint Genome Institute (JGI). She helped pioneer the field of metagenomics, a new strategy for isolating, sequencing, and characterizing DNA extracted directly from environmental samples, such as the contents of the termite gut, which yielded enzymes responsible for breakdown of wood into fuel.

Construction of transplastomic lettuce (Lactuca sativa) dominantly producing astaxanthin fatty acid esters and detailed chemical analysis of generated carotenoids.

PubMed

Harada, Hisashi; Maoka, Takashi; Osawa, Ayako; Hattan, Jun-Ichiro; Kanamoto, Hirosuke; Shindo, Kazutoshi; Otomatsu, Toshihiko; Misawa, Norihiko

2014-04-01

The plastid genome of lettuce (Lactuca sativa L.) cv. Berkeley was site-specifically modified with the addition of three transgenes, which encoded β,β-carotenoid 3,3'-hydroxylase (CrtZ) and β,β-carotenoid 4,4'-ketolase (4,4'-oxygenase; CrtW) from a marine bacterium Brevundimonas sp. strain SD212, and isopentenyl diphosphate isomerase from a marine bacterium Paracoccus sp. strain N81106. Constructed transplastomic lettuce plants were able to grow on soil at a growth rate similar to that of non-transformed lettuce cv. Berkeley and generate flowers and seeds. The germination ratio of the lettuce transformants (T0) (98.8%) was higher than that of non-transformed lettuce (93.1 %). The transplastomic lettuce (T1) leaves produced the astaxanthin fatty acid (myristate or palmitate) diester (49.2% of total carotenoids), astaxanthin monoester (18.2%), and the free forms of astaxanthin (10.0%) and the other ketocarotenoids (17.5%), which indicated that artificial ketocarotenoids corresponded to 94.9% of total carotenoids (230 μg/g fresh weight). Native carotenoids were there lactucaxanthin (3.8%) and lutein (1.3 %) only. This is the first report to structurally identify the astaxanthin esters biosynthesized in transgenic or transplastomic plants producing astaxanthin. The singlet oxygen-quenching activity of the total carotenoids extracted from the transplastomic leaves was similar to that of astaxanthin (mostly esterified) from the green algae Haematococcus pluvialis.

Harnessing the Flow of Data from Fungi at JGI

ScienceCinema

Grigoriev, Igor; Glass, N. Louise; Martin, Francis; Turgeon, Gillian; Spatafora, Joey; Berka, Randy

2018-06-12

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) managed by Lawrence Berkeley National Laboratory, is the only user facility in the world devoted to problems of energy and environment. With over one million species, fungi—which include mushrooms—represent one of the largest under-explored branches of the Tree of Life. Together with its community of more than 1,000 scientific collaborators, JGI helping to unlock the secrets encoded in the genomes of fungi to advance a better understanding of the global carbon cycle and to develop new biotechnology products, next-generation biofuels, and medicines.

Comparative whole genome analysis of six diagnostic brucellaphages.

PubMed

Farlow, Jason; Filippov, Andrey A; Sergueev, Kirill V; Hang, Jun; Kotorashvili, Adam; Nikolich, Mikeljon P

2014-05-15

Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic comparisons including recently described genomes of the Tb phage from Mexico (TbM) and Pr phage to elucidate genomic diversity and candidate host range determinants. Comparative whole genome analysis revealed high sequence homogeneity among these brucellaphage genomes and resolved three genetic groups consistent with defined host range phenotypes. Group I was composed of Tb and Fz phages that are predominantly lytic for Brucella abortus and Brucella neotomae; Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus, Brucella melitensis and Brucella suis; Group III was composed of Wb and S708 phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the putative phage collar protein is a variable locus with features that may be contributing to the host specificities exhibited by different brucellaphage groups. The presence of several candidate host range determinants is illustrated herein for future dissection of the differential host specificity observed among these phages. Published by Elsevier B.V.

Harold F. Weaver: California Astronomer

NASA Astrophysics Data System (ADS)

Shields, J. C.

1993-05-01

This talk will give an overview of an oral history recently completed with Harold F. Weaver, Professor Emeritus of Astronomy at the University of California at Berkeley. Weaver grew up in California and studied as an undergraduate at Berkeley, where he also pursued graduate work incorporating research at Lick and Mount Wilson Observatories. After pursuing postdoctoral research at Yerkes Observatory and war work in Cambridge (Massachusetts) and Berkeley, Weaver was appointed to the staff of Lick Observatory. In 1951 he joined the faculty at Berkeley, where he later played a major role in founding Hat Creek Radio Observatory. As Director of the Berkeley Radio Astronomy Laboratory, Weaver oversaw construction of the 85-foot telescope at Hat Creek, which is the subject of a special session at this meeting. Two aspects of Weaver's career will be highlighted. The first is the somewhat unusual and very successful transition in Weaver's observational research from emphasis on classical photographic techniques at optical wavelengths to use of emerging radio technology for the study of Galactic structure. The second is service provided by Weaver to the American Astronomical Society and Astronomical Society of the Pacific at several key junctures in the development of both organizations.

INDC International Nuclear Data Committee

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nichols, A.; McCutchan, E.; Dimitriou, P.

The 22nd meeting of the International Network of Nuclear Structure and Decay Data Evaluators was convened at the Lawrence Berkeley National Laboratory, Berkeley, USA, from 22 to 26 May 2017 under the auspices of the IAEA Nuclear Data Section. This meeting was attended by 38 scientists from 12 Member States and the IAEA, all of whom are concerned primarily with the measurement, evaluation and dissemination of nuclear structure and decay data. A summary of the meeting, data centre reports, various proposals considered, technical discussions, actions agreed by the participants, and the resulting recommendations/conclusions are presented within this document.

Control system for the 2nd generation Berkeley AutoMounters (BAM2) at GM/CA CAT macromolecular crystallography beamlines

PubMed Central

Makarov, O.; Hilgart, M.; Ogata, C.; Pothineni, S.; Cork, C.

2011-01-01

GM/CA CAT at Sector 23 of the Advanced Photon Source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction. A second generation Berkeley automounter is being integrated into the beamline control system at the 23-BM experimental station. This new device replaces the previous all-pneumatic gripper motions with a combination of pneumatics and XYZ motorized linear stages. The latter adds a higher degree of flexibility to the robot including auto-alignment capability, accommodation of a larger capacity sample Dewar of arbitrary shape, and support for advanced operations such as crystal washing, while preserving the overall simplicity and efficiency of the Berkeley automounter design. PMID:21822343

Immobilization of Radionuclides Through Anaerobic Bio-oxidation of Fe(ll)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coates, John D.

2005-06-01

Over the last year we have focused our efforts on two independent aspects (a) further investigation of the microbiology and geochemistry of nitrate-dependent Fe(II) oxidation and (b) assembling the sequenced genome of Dechloromonas aromatica strain RCB. This work has been performed in a cooperative fashion amongst the independent labs of the three PI's with the UC Berkeley lab taking the lead under the guidance of J.D. Coates.

Integrated Approach to Reconstruction of Microbial Regulatory Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodionov, Dmitry A; Novichkov, Pavel S

2013-11-04

This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated inmore » RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.« less

76 FR 37650 - Safety Zone; 4th of July Festival Berkeley Marina Fireworks Display Berkeley, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

...-AA00 Safety Zone; 4th of July Festival Berkeley Marina Fireworks Display Berkeley, CA AGENCY: Coast... the 4th of July Festival Berkeley Marina Fireworks Display. Unauthorized persons or vessels are... display. Background and Purpose The City of Berkeley Marina will sponsor the 4th of July Festival Berkeley...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

This volume contains the proceedings of the fourth Contractor-Grantee Workshop for the Department of Energy (DOE) Human Genome Program. Of the 204 abstracts in this book, some 200 describe the genome research of DOE-funded grantees and contractors located at the multidisciplinary centers at Lawrence Berkeley Laboratory, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory; other DOE-supported laboratories; and more than 54 universities, research organizations, and companies in the United States and abroad. Included are 16 abstracts from ongoing projects in the Ethical, Legal, and Social Issues (ELSI) component, an area that continues to attract considerable attention from a widemore » variety of interested parties. Three abstracts summarize work in the new Microbial Genome Initiative launched this year by the Office of Health and Environmental Research (OHER) to provide genome sequence and mapping data on industrially important microorganisms and those that live under extreme conditions. Many of the projects will be discussed at plenary sessions held throughout the workshop, and all are represented in the poster sessions.« less

Fun and games in Berkeley: the early years (1956-2013).

PubMed

Tinoco, Ignacio

2014-01-01

Life at Berkeley for the past 57 years involved research on the thermodynamics, kinetics, and spectroscopic properties of RNA to better understand its structures, interactions, and functions. We (myself and all the graduate students and postdocs who shared in the fun) began with dinucleoside phosphates and slowly worked our way up to megadalton-sized RNA molecular motors. We used UV absorption, circular dichroism, circular intensity differential scattering, fluorescence, NMR, and single-molecule methods. We learned a lot and had fun doing it.

Proceedings of the High Energy Density Matter (HEDM) Contractor’s Conference Held in Woods Hole, Massachusetts on 6-8 June 1993

DTIC Science & Technology

1993-11-01

SRI International 75 "The Dodecahedral N20 Molecule: Some Theoretical Predictions" Henry F. Schaefer II1, University of Georgia 94 "Theoretical...and P20 Molecules: Some Theoretical Predictions," Henry Schaefer, University of Georgia 2 -2:30 c Investigations of the Structure and Dynamics of...Department of Chemistry APD Cryogenics, Inc. University of California, Berkeley 1833 Vultee Street Berkeley, CA 94708 Allentown, PA 18103 8 Henry F

Interactive Exploration on Large Genomic Datasets.

PubMed

Tu, Eric

2016-01-01

The prevalence of large genomics datasets has made the the need to explore this data more important. Large sequencing projects like the 1000 Genomes Project [1], which reconstructed the genomes of 2,504 individuals sampled from 26 populations, have produced over 200TB of publically available data. Meanwhile, existing genomic visualization tools have been unable to scale with the growing amount of larger, more complex data. This difficulty is acute when viewing large regions (over 1 megabase, or 1,000,000 bases of DNA), or when concurrently viewing multiple samples of data. While genomic processing pipelines have shifted towards using distributed computing techniques, such as with ADAM [4], genomic visualization tools have not. In this work we present Mango, a scalable genome browser built on top of ADAM that can run both locally and on a cluster. Mango presents a combination of different optimizations that can be combined in a single application to drive novel genomic visualization techniques over terabytes of genomic data. By building visualization on top of a distributed processing pipeline, we can perform visualization queries over large regions that are not possible with current tools, and decrease the time for viewing large data sets. Mango is part of the Big Data Genomics project at University of California-Berkeley [25] and is published under the Apache 2 license. Mango is available at https://github.com/bigdatagenomics/mango.

77 FR 37604 - Safety Zone; Fourth of July Fireworks, Berkeley Marina, Berkeley, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-22

...: The Coast Guard will enforce a 1,000 foot safety zone around the Berkeley Pier in position 37[deg]51... Zone; Fourth of July Fireworks, Berkeley Marina, Berkeley, CA AGENCY: Coast Guard, DHS. ACTION: Notice of enforcement of regulation. SUMMARY: The Coast Guard will enforce the safety zone for the Berkeley...

Optimizing Excited-State Electronic-Structure Codes for Intel Knights Landing: A Case Study on the BerkeleyGW Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deslippe, Jack; da Jornada, Felipe H.; Vigil-Fowler, Derek

2016-10-06

We profile and optimize calculations performed with the BerkeleyGW code on the Xeon-Phi architecture. BerkeleyGW depends both on hand-tuned critical kernels as well as on BLAS and FFT libraries. We describe the optimization process and performance improvements achieved. We discuss a layered parallelization strategy to take advantage of vector, thread and node-level parallelism. We discuss locality changes (including the consequence of the lack of L3 cache) and effective use of the on-package high-bandwidth memory. We show preliminary results on Knights-Landing including a roofline study of code performance before and after a number of optimizations. We find that the GW methodmore » is particularly well-suited for many-core architectures due to the ability to exploit a large amount of parallelism over plane-wave components, band-pairs, and frequencies.« less

Berkeley Lab Training

Science.gov Websites

Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Help Berkeley Lab Training Welcome Welcome to Berkeley Lab Training! Login to access your LBNL Training Profile. This provides quick access to all of the courses you need. Look below, to learn about different types of training available at

Trading Carbon: Can Cookstoves Light the Way (LBNL Science at the Theater)

ScienceCinema

Gadgil, Ashok; Booker, Kayje; Rausch, Adam

2018-06-08

Science at the Theater: Get smart about carbon! Learn how families in Africa, using stoves designed by Berkeley Lab, are at the forefront of global carbon reduction. Ashok Gadgil is the driving force behind the Berkeley-Darfur Cookstove. He is a researcher, inventor, renowned humanitarian, and director of Berkeley Lab's Environmental Energy Technologies Division. Kayje Booker is a Berkeley Lab researcher and UC Berkeley graduate student in ecosystem sciences. She is exploring how carbon markets can serve as catalysts for innovation in technologies for the poor. Adam Rausch is a Berkeley Lab researcher and UC Berkeley graduate student in civil environmental engineering. He helps to design and test stove designs in Ethiopia and elsewhere.

DNA Everywhere. A Guide for Simplified Environmental Genomic DNA Extraction Suitable for Use in Remote Areas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gabrielle N. Pecora; Francine C. Reid; Lauren M. Tom

2016-05-01

Collecting field samples from remote or geographically distant areas can be a financially and logistically challenging. With participation of a local organization where the samples are originated from, gDNA samples can be extracted from the field and shipped to a research institution for further processing and analysis. The ability to set up gDNA extraction capabilities in the field can drastically reduce cost and time when running long-term microbial studies with a large sample set. The method outlined here has developed a compact and affordable method for setting up a “laboratory” and extracting and shipping gDNA samples from anywhere in themore » world. This white paper explains the process of setting up the “laboratory”, choosing and training individuals with no prior scientific experience how to perform gDNA extractions and safe methods for shipping extracts to any research institution. All methods have been validated by the Andersen group at Lawrence Berkeley National Laboratory using the Berkeley Lab PhyloChip.« less

71. Joe Moore, Photographer. September, 1996. BEVATRON ROOF SHIELDING AND ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

71. Joe Moore, Photographer. September, 1996. BEVATRON ROOF SHIELDING AND BUILDING TRUSS STRUCTURE - University of California Radiation Laboratory, Bevatron, 1 Cyclotron Road, Berkeley, Alameda County, CA

Use of a personal computer for the real-time reception and analysis of data from a sounding rocket experiment

NASA Technical Reports Server (NTRS)

Herrick, W. D.; Penegor, G. T.; Cotton, D. M.; Kaplan, G. C.; Chakrabarti, S.

1990-01-01

In September 1988 the Earth and Planetary Atmospheres Group of the Space Sciences Laboratory of the University of California at Berkeley flew an experiment on a high-altitude sounding rocket launched from the NASA Wallops Flight Facility in Virginia. The experiment, BEARS (Berkeley EUV Airglow Rocket Spectrometer), was designed to obtain spectroscopic data on the composition and structure of the earth's upper atmosphere. Consideration is given to the objectives of the BEARS experiment; the computer interface and software; the use of remote data transmission; and calibration, integration, and flight operations.

Trading Carbon: Can Cookstoves Light the Way (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gadgil, Ashok; Booker, Kayje; Rausch, Adam

2010-09-20

Science at the Theater: Get smart about carbon! Learn how families in Africa, using stoves designed by Berkeley Lab, are at the forefront of global carbon reduction. Ashok Gadgil is the driving force behind the Berkeley-Darfur Cookstove. He is a researcher, inventor, renowned humanitarian, and director of Berkeley Lab's Environmental Energy Technologies Division. Kayje Booker is a Berkeley Lab researcher and UC Berkeley graduate student in ecosystem sciences. She is exploring how carbon markets can serve as catalysts for innovation in technologies for the poor. Adam Rausch is a Berkeley Lab researcher and UC Berkeley graduate student in civil environmentalmore » engineering. He helps to design and test stove designs in Ethiopia and elsewhere.« less

SFA 2.0- Watershed Structure and Controls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Ken

2015-01-23

Berkeley Lab Earth Scientist Ken Williams explains the watershed research within the Sustainable Systems SFA 2.0 project—including identification and monitoring of primary factors that control watershed biogeochemical functioning.

Site Environmental Report for 2005 Volume I and Volume II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruggieri, Michael

2006-07-07

Each year, Ernest Orlando Lawrence Berkeley National Laboratory prepares an integrated report on its environmental programs to satisfy the requirements of United States Department of Energy Order 231.1A, ''Environment, Safety, and Health Reporting''. The ''Site Environmental Report for 2005'' summarizes Berkeley Lab's environmental management performance, presents environmental monitoring results, and describes significant programs for calendar year 2005. (Throughout this report, Ernest Orlando Lawrence Berkeley National Laboratory is referred to as ''Berkeley Lab'', ''the Laboratory'', ''Lawrence Berkeley National Laboratory'', and ''LBNL''.) The report is separated into two volumes. Volume I contains an overview of the Laboratory, the status of environmental programs,more » and summarized results from surveillance and monitoring activities. This year's Volume I text body is organized into an executive summary followed by six chapters. The report's structure has been reorganized this year, and it now includes a chapter devoted to environmental management system topics. Volume II contains individual data results from surveillance and monitoring activities. The ''Site Environmental Report'' is distributed by releasing it on the Web from the Berkeley Lab Environmental Services Group (ESG) home page, which is located at http://www.lbl.gov/ehs/esg/. Many of the documents cited in this report also are accessible from the ESG Web page. CD and printed copies of this Site Environmental Report are available upon request. The report follows the Laboratory's policy of using the International System of Units (SI), also known as the metric system of measurements. Whenever possible, results are also reported using the more conventional (non-SI) system of measurements, because the non-SI system is referenced by several current regulatory standards and is more familiar to some readers. Two tables are provided at the end of the Glossary to help readers: the first defines the prefixes used with SI units of measurement, and the second provides conversions to non-SI units.« less

Weak Interactions Group

Science.gov Websites

Weak Interactions Group UC Berkeley UC Berkeley Physics Lawrence Berkeley Lab Nuclear Science Division at LBL Physics Division at LBL Phonebook A-Z Index Navigation Home Members Research Projects CUORE Design Concept Berkeley Projects People Publications Contact Links KamLAND Physics Impact Neutrino

Lawrence Berkeley National Laboratory 2016 Annual Financial Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Kim, P.; Williams, Kim, P.

FY2016 was a year of significant change and progress at Berkeley Lab. In March, Laboratory Director Michael Witherell assumed his new role when former Lab Director Paul Alivisatos became Vice Chancellor for Research at UC Berkeley. Dr. Witherell has solidified the Lab’s strategy, with a focus on long term science and technology priorities. Large-scale science efforts continued to expand at the Lab, including the Dark Energy Spectroscopic Instrument now heading towards construction, and the LUX-ZEPLIN dark matter detector to be built underground in South Dakota. Another proposed project, the Advanced Light Source-Upgrade, was given preliminary approval and will be themore » Lab’s largest scientific investment in years. Construction of the Integrative Genomics Building began, and will bring together researchers from the Lab’s Joint Genome Institute, now based in Walnut Creek, and the Systems Biology Knowledgebase (K-Base) under one roof. Investment in the Lab’s infrastructure also continues, informed by the Lab’s Infrastructure Strategic Plan. Another important focus is on developing the next generation of scientists with the talent and diversity needed to sustain Berkeley Lab’s scientific leadership and mission contributions to DOE and the Nation. Berkeley Lab received $897.5M in new FY2016 funding, a 12.5% increase over FY2015, for both programmatic and infrastructure activities. While the Laboratory experienced a substantial increase in funding, it was accompanied by only a modest increase in spending, as areas of growth were partially offset by the completion of several major efforts in FY2015. FY2016 costs were $826.9M, an increase of 1.9% over FY2015. Similar to the prior year, the indirect-funded Operations units worked with generally flat budgets to yield more funding for strategic needs. A key challenge for Berkeley Lab continues to be achieving the best balance to fund essential investments, deliver highly effective operational mission support and remain cost-competitive. Through a comprehensive approach to prioritize competing needs, the Lab ended the year in a favorable financial position. The Office of the Chief Financial Officer (OCFO) played a key role in providing analysis and decision support to Executive Leadership, enabling the Lab to enhance its financial management strategies. In FY2016, the OCFO updated its analytic approaches and models to enhance long term financial projections under various funding and investment scenarios, and to assess total cost of ownership for major proposed investments. These improvements provided the new Lab Director and Senior Leadership with more comprehensive information and analytic support for planning and prioritization efforts. Within the OCFO, we focused on core operations and key initiatives defined in our OCFO Strategic Roadmap. The Lab’s Financial System transitioned from stabilization to optimization, with a focus on expanding the financial reporting capabilities considerably. We completed implementation of the eCommerce platform, achieving a notable outcome for the Lab in close partnership with DOE’s Office of Science. In other accomplishments, we launched a financial literacy program to enable Lab managers and staff to understand and execute their financial management and stewardship responsibilities more effectively; made substantial progress in enhancing our Field Finance model that provides financial support to client divisions and areas; developed a business process governance model to define OCFO business processes, clarify roles, and strengthen service delivery; and implemented a Partners in Leadership training program to build leadership capacity among our staff. We completed a ‘refresh’ of our Strategic Roadmap, which now defines our priorities for FY2017-FY2019. As a part of this effort, we made a subtle but important change to the OCFO mission statement to call out the Lab’s research and stewardship mission to sustain the Lab’s science and technology capabilities now and into the future. Berkeley Lab’s FY2016 progress on all fronts - scientific, operations, and financial management – position the Lab to continue bringing science solutions to the world as we charge into the 21st Century.« less

Sneak Preview of Berkeley Lab's Science at the Theatre on June 6th, 2011

ScienceCinema

Sanii, Babak

2017-12-11

Babak Sanii provides a sneak preview of Berkeley Lab's next Science at the Theater Event: Big Thinking: The Power of Nanoscience. Berkeley Lab scientists reveal how nanoscience will bring us cleaner energy, faster computers, and improved medicine. Berkeley Repertory Theatre on June 6th, 2011.

Sneak Preview of Berkeley Lab's Science at the Theatre on June 6th, 2011

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanii, Babak

Babak Sanii provides a sneak preview of Berkeley Lab's next Science at the Theater Event: Big Thinking: The Power of Nanoscience. Berkeley Lab scientists reveal how nanoscience will bring us cleaner energy, faster computers, and improved medicine. Berkeley Repertory Theatre on June 6th, 2011.

SFA 2.0- Watershed Structure and Controls

ScienceCinema

Williams, Ken

2018-05-23

Berkeley Lab Earth Scientist Ken Williams explains the watershed research within the Sustainable Systems SFA 2.0 project—including identification and monitoring of primary factors that control watershed biogeochemical functioning.

Differences in STEM doctoral publication by ethnicity, gender and academic field at a large public research university.

PubMed

Mendoza-Denton, Rodolfo; Patt, Colette; Fisher, Aaron; Eppig, Andrew; Young, Ira; Smith, Andrew; Richards, Mark A

2017-01-01

Two independent surveys of PhD students in STEM fields at the University of California, Berkeley, indicate that underrepresented minorities (URMs) publish at significantly lower rates than non-URM males, placing the former at a significant disadvantage as they compete for postdoctoral and faculty positions. Differences as a function of gender reveal a similar, though less consistent, pattern. A conspicuous exception is Berkeley's College of Chemistry, where publication rates are tightly clustered as a function of ethnicity and gender, and where PhD students experience a highly structured program that includes early and systematic involvement in research, as well as clear expectations for publishing. Social science research supports the hypothesis that this more structured environment hastens the successful induction of diverse groups into the high-performance STEM academic track.

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobecky, Patricia A.

2015-04-06

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Areamore » 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.« less

Berkeley Lab Scientist Named MacArthur "Genius" Fellow for Audio

Science.gov Websites

Preservation Research | Berkeley Lab Berkeley Lab A-Z Index Directory Submit Web People Navigation Berkeley Lab Search Submit Web People Close About the Lab Leadership/Organization Calendar News to digitally recover a 128-year-old recording of Alexander Graham Bell's voice, enabling people to

Adsorption of Dissolved Metals in the Berkeley Pit using Thiol-Functionalized Self-Assembled Monolayers on Mesoporous Supports (Thiol-SAMMS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Betancourt, Amaury P.; Mattigod, Shas V.; Wellman, Dawn M.

2010-03-07

The Berkeley Pit in Butte, Montana, is heavily contaminated with dissolved metals. Adsorption and extraction of these metals can be accomplished through the use of a selective adsorbent. For this research, the adsorbent used was thiol-functionalized Self-Assembled Monolayers on Mesoporous Supports (thiol-SAMMS), which was developed at Pacific Northwest National Laboratory (PNNL). Thiol-SAMMS selectively binds to numerous types of dissolved metals. The objective of this research was to evaluate the loading and kinetics of aluminum, beryllium, copper, and zinc on thiol-SAMMS. For the loading tests, a series of Berkeley Pit water to thiol-SAMMS ratios (mL:g) were tested. These ratios were 1000:1,more » 500:1, 100:1, and 50:1. Berkeley Pit water is acidic (pH {approx} 2.5). This can affect the performance of SAMMS materials. Therefore, the effect of pH was evaluated by conducting parallel series of loading tests wherein the Berkeley Pit water was neutralized before or after addition of thiol-SAMMS, and a series of kinetics tests wherein the Berkeley Pit water was neutralized before addition of thiol-SAMMS for the first test and was not neutralized for the second test. For the kinetics tests, one Berkeley Pit water to thiol-SAMMS ratio was tested, which was 2000:1. The results of the loading and kinetics tests suggest that a significant decrease in dissolved metal concentration at Berkeley Pit could be realized through neutralization of Berkeley Pit water. Thiol-SAMMS technology has a limited application under the highly acidic conditions posed by the Berkeley Pit. However, thiol-SAMMS could provide a secondary remedial technique which would complete the remedial system and remove dissolved metals from the Berkeley Pit to below drinking water standards.« less

The Undergraduate Origins of PhD Economists: The Berkeley Experience

ERIC Educational Resources Information Center

Olney, Martha L.

2015-01-01

The University of California, Berkeley sends more undergraduate students to economics PhD programs than any other public university. While this fact is surely a function of its size, there may be lessons from the Berkeley experience that others could adopt. To investigate why Berkeley generates so many economics PhD students, the author convened…

Microsoft Licenses Berkeley Lab's Home Energy Saver Code for Its Energy

Science.gov Websites

-based tool for calculating energy use in residential buildings. About one million people visit the Home Management Software | Berkeley Lab Berkeley Lab A-Z Index Directory Submit Web People Navigation Berkeley Lab Search Submit Web People Close About the Lab Leadership/Organization Calendar News

What Made Berkeley Great? The Sources of Berkeley's Sustained Academic Excellence. Research & Occasional Paper Series CSHE.3.11

ERIC Educational Resources Information Center

Breslauer, George W.

2011-01-01

University of California (UC) Berkeley's chief academic officer explores the historical sources of Berkeley' academic excellence. He identifies five key factors: (1) wealth from many sources; (2) supportive and skilled governors; (3) leadership from key UC presidents; (4) the pioneering ethos within the State of California; and (5) a process of…

Berkeley Lab's Saul Perlmutter wins Nobel Prize in Physics | Berkeley Lab

Science.gov Websites

astrophysics, dark energy, physics Connect twitter instagram LinkedIn facebook youtube This form needs Berkeley Lab's Saul Perlmutter wins Nobel Prize in Physics News Release Paul Preuss 510-486-6249 * October professor of physics at the University of California at Berkeley, has won the 2011 Nobel Prize in Physics

FY2014 LBNL LDRD Annual Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Darren

2015-06-01

Laboratory (Berkeley Lab or LBNL) is a multi-program national research facility operated by the University of California for the Department of Energy (DOE). As an integral element of DOE’s National Laboratory System, Berkeley Lab supports DOE’s missions in fundamental science, energy resources, and environmental quality. Berkeley Lab programs advance four distinct goals for DOE and the nation. The LDRD program supports Berkeley Lab’s mission in many ways. First, because LDRD funds can be allocated within a relatively short time frame, Berkeley Lab researchers can support the mission of the Department of Energy (DOE) and serve the needs of the nationmore » by quickly responding to forefront scientific problems. Second, LDRD enables Berkeley Lab to attract and retain highly qualified scientists and to support their efforts to carry out worldleading research. In addition, the LDRD program also supports new projects that involve graduate students and postdoctoral fellows, thus contributing to the education mission of Berkeley Lab.« less

The distributed annotation system.

PubMed

Dowell, R D; Jokerst, R M; Day, A; Eddy, S R; Stein, L

2001-01-01

Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

Cool Cities, Cool Planet (LBNL Science at the Theater)

ScienceCinema

Rosenfeld, Arthur; Pomerantz, Melvin; Levinson, Ronnen

2018-06-14

Science at the Theater: Berkeley Lab scientists discuss how cool roofs can cool your building, your city ... and our planet. Arthur Rosenfeld, Professor of Physics Emeritus at UC Berkeley, founded the Berkeley Lab Center for Building Science in 1974. He served on the California Energy Commission from 2000 to 2010 and is commonly referred to as California's godfather of energy efficiency. Melvin Pomerantz is a member of the Heat Island Group at Berkeley Lab. Trained as a physicist at UC Berkeley, he specializes in research on making cooler pavements and evaluating their effects. Ronnen Levinson is a staff scientist at Berkeley Lab and the acting leader of its Heat Island Group. He has developed cool roofing and paving materials and helped bring cool roof requirements into building energy efficiency standards.

Untitled Document

Science.gov Websites

, contact: Saul Perlmutter (saul(at)lbl(dot)gov) University of California Berkeley, CA 94720 A. Spadafora (alspadafora(at)lbl(dot)gov) Lawrence Berkeley National Laboratory 1 Cyclotron Rd. Berkeley, CA 94720

Tough Ceramic Mimics Mother of Pearl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ritchie, Robert

2008-12-05

Berkeley Lab scientists have mimicked the structure of mother of pearl to create what may well be the toughest ceramic ever produced. http://newscenter.lbl.gov/press-releases/2008/12/05/scientists-create-tough-ceramic-that-mimics-mother-of-pearl/

Tough Ceramic Mimics Mother of Pearl

ScienceCinema

Ritchie, Robert

2017-12-12

Berkeley Lab scientists have mimicked the structure of mother of pearl to create what may well be the toughest ceramic ever produced. http://newscenter.lbl.gov/press-releases/2008/12/05/scientists-create-tough-ceramic-that-mimics-mother-of-pearl/

Berkeley Lab - Materials Sciences Division

Science.gov Websites

Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Search MSD Go MSD - Materials Investigators Division Staff Facilities and Centers Staff Jobs Safety Personnel Resources Committees In Case of

ARC-2006-ACD06-0216-008

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASA Berkeley researcher Zack Gainsforth working with sample encased in aerogel

ARC-2006-ACD06-0216-003

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASA Berkeley researchers Zack Gainsforth working with sample encased in aerogel

ARC-2006-ACD06-0216-024

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASA Berkeley researcher Zack Gainsforth working with sample encased in aerogel

ARC-2006-ACD06-0216-025

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASA Berkeley researcher Zack Gainsforth working with sample encased in aerogel

Tradeoffs Between Synchronization, Communication, and Work in Parallel Linear Algebra Computations

DTIC Science & Technology

2014-01-25

Demmel Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2014- 8 http...www.eecs.berkeley.edu/Pubs/TechRpts/2014/EECS-2014- 8 .html January 25, 2014 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the...University of California at Berkeley,Electrical Engineering and Computer Sciences,Berkeley,CA,94720 8 . PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING

Evaluating the Impact of Open Access at Berkeley: Results from the 2015 Survey of Berkeley Research Impact Initiative (BRII) Funding Recipients

ERIC Educational Resources Information Center

Teplitzky, Samantha; Phillips, Margaret

2016-01-01

The Berkeley Research Impact Initiative (BRII) was one of the first campus-based open access (OA) funds to be established in North America and one of the most active, distributing more than $244,000 to support University of California (UC) Berkeley authors. In April 2015, we conducted a qualitative study of 138 individuals who had received BRII…

Berkeley Lab - Materials Sciences Division

Science.gov Websites

Synthesis Condensed Matter and Materials Physics Scattering and Instrumentation Science Centers Center for Berkeley National Laboratory 1 Cyclotron Road MS 66R0200 Berkeley CA 94720 510-486-4957 A U.S. Department

Nuclear Medicine at Berkeley Lab: From Pioneering Beginnings to Today (LBNL Summer Lecture Series)

ScienceCinema

Budinger, Thomas [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Nuclear Medicine & Functional Imaging

2018-01-23

Summer Lecture Series 2006: Thomas Budinger, head of Berkeley Lab's Center for Functional Imaging, discusses Berkeley Lab's rich history pioneering the field of nuclear medicine, from radioisotopes to medical imaging.

ARC-2006-ACD06-0216-006

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASA Berkeley researchers Zack Gainsforth (seated) and Chris Snead working with sample encased in aerogel

ARC-2006-ACD06-0216-009

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASA Berkeley researchers Zack Gainsforth (seated) and Chris Snead working with sample encased in aerogel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, Sabin; Schlegel, David

Lawrence Berkeley National Laboratory physicist and dark energy hunter David Schlegel chats with Sabin Russell, former San Francisco Chronicle reporter turned Berkeley Lab science writer, June 22, 2011. Their conversation is the first installment of "Sit Down With Sabin," a weekly conversation hosted by Russell. Over the course of five conversations with Berkeley Lab staff this summer, Russell will explore the ups and downs of innovative science — all without the aid of PowerPoint slides. Brought to you by Berkeley Lab Public Affairs.

Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tarver, Angela; Fern, Alison; Diego, Matthew San

2010-06-18

The U.S. Department of Energy (DOE) Joint Genome Institute?s (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation&more » Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.« less

Do Special Education Interventions Improve Learning of Secondary Content? A Meta-Analysis. Research to Practice. Structured Abstract No. 80

ERIC Educational Resources Information Center

Dragoo, Kyrie

2011-01-01

This is a structured abstract of a meta-analysis conducted by T. E. Scruggs, M. A. Mastropieri, S. Berkeley, and J. E. Graetz, published in "Remedial & Special Education" (2009). The authors of the original paper describe findings from a research synthesis on content area instruction for students with disabilities. Seventy studies…

40 CFR 81.341 - South Carolina.

Code of Federal Regulations, 2014 CFR

2014-07-01

... County X Anderson County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun... County X Berkeley County X Calhoun County X Charleston County X Cherokee County X Chester County X... Beaufort County Berkeley County Calhoun County Charleston County Cherokee County Chester County...

Investigation of Structure of Gd and Tb Nuclei using STARS and LiBerACE

NASA Astrophysics Data System (ADS)

Bonniwell, Cain; Pauerstein, Ben; Allmond, J. M.; Beausang, C. W.

2009-10-01

This experiment, performed at Livermore Berkeley National Lab as a collaboration of Livermore, Berkeley, and the University of Richmond, was designed to investigate the structure of gadolinium and terbium nuclei using the P + 156Gd reaction at E beam = 27 MeV. The experimental design included use of the STARS system for detecting charged particles as well as the LiBerACE clover array for detecting gamma rays. The master gate was set to record particle-gamma as well as gamma-gamma coincidences. The data is currently being analyzed using the RADWARE escl8r software package which has allowed the creation of extensive level schemes for several Gd and Tb nuclei. So far the data suggests new gamma ray transitions as well as new energy states in 154Gd and 155Tb. The project is ongoing, and the results will be presented. This work was supported by the US Department of Energy under grant numbers DE-FG52NA26206 and DE-FG02-05ER41379.

Web Support

Science.gov Websites

Berkeley Lab Lawrence Berkeley National Laboratory A-Z Index Directory Submit Web People Navigation Berkeley Lab Search Submit Web People Close About the Lab Leadership/Organization Calendar News Center our response, please check the specific website or page in question for the name of the appropriate

78 FR 29022 - Safety Zone; Fourth of July Fireworks, Berkeley Marina, Berkeley, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-17

... Marina Fourth of July Fireworks display in the Captain of the Port, San Francisco area of responsibility... Guard will enforce a 1,000 foot safety zone around the Berkeley Pier in approximate position 37[deg]51... radius 1,000 [[Page 29023

Berkeley Lab - Materials Sciences Division

Science.gov Websites

Synthesis Condensed Matter and Materials Physics Scattering and Instrumentation Science Centers Center for Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Search MSD Go MSD - Materials Sciences Division About Organization Contact Research Core Programs Materials Discovery, Design and

Molecular Foundry Workshop draws overflow crowd to BerkeleyLab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, Art

2002-11-27

Nanoscale science and technology is now one of the top research priorities in the United States. With this background, it is no surprise that an overflow crowd or more than 350 registrants filled two auditoriums to hear about and contribute ideas for the new Molecular Foundry during a two-day workshop at the Lawrence Berkeley National Laboratory (Berkeley Lab). Scheduled to open for business at Berkeley Labin early 2006, the Molecular Foundry is one of three Nanoscale Science Research Centers (NSRCs) put forward for funding by the DOE's Office of Basic Energy Sciences (BES).

Berkeley Lab - Materials Sciences Division

Science.gov Websites

Postdoc Forum Research Highlights Awards Publications Database Events Calendar Newsletter Archive People ; Finance Templates Travel One-Stop Investigators Division Staff Facilities and Centers Staff Jobs People Division, please use the links here. An outline of the Division structure is available at the Organization

Excellence in Research: Creative Organizational Responses at Berkeley, Harvard, MIT, and Stanford. ASHE 1985 Annual Meeting Paper.

ERIC Educational Resources Information Center

Gardiner, John J.

Research environments of four leading universities were studied: University of California at Berkeley (UC-Berkeley), Harvard University, Massachusetts Institute of Technology (MIT), and Stanford University. Attention was directed to organizational responses for encouraging collaboration in research at these leading universities, as well as to…

Berkeley Lab - Lawrence Berkeley National Laboratory

Science.gov Websites

nanoparticles that could make solar panels more efficient by converting light usually missed by solar cells into of Methane's Increasing Greenhouse Effect A Berkeley Lab research team tracked a rise in the warming effect of methane - one of the most important greenhouse gases for the Earth's atmosphere - over a 10

A-Z Link

Science.gov Websites

Index (this page) 2. Use search.lbl.gov powered by Google. 3. Use DS The Directory of both People and Berkeley Lab Lawrence Berkeley National Laboratory A-Z Index Directory Submit Web People Navigation Berkeley Lab Search Submit Web People Close About the Lab Leadership/Organization Calendar News Center

Berkeley Lab - Materials Sciences Division

Science.gov Websites

Synthesis Condensed Matter and Materials Physics Scattering and Instrumentation Science Centers Center for materials and phenomena at multiple time and length scales. Through our core programs and research centers Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Search MSD Go MSD - Materials

ARC-2006-ACD06-0216-010

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASA Berkeley researchers Zack Gainsforth (seated) and Chris Snead working with sample encased in aerogel Note: Eric Land of NASA/AMES video crew in lower left corner providing sound support for event

City of Berkeley, California Municipal Tree Resource Analysis

Treesearch

S.E. Maco; E.G. McPherson; J.R. Simpson; P.J. Peper; Q. Xiao

2005-01-01

Vibrant, renowned for its livability and cultural wealth, the city of Berkeley maintains trees as an integral component of the urban infrastructure. Research indicates that healthy trees can mitigate impacts associated with the built environment by reducing stormwater runoff, energy consumption, and air pollutants. Put simply, trees improve urban life, making Berkeley...

Solutions that stick: activating cross-disciplinary collaboration in a graduate-level public health innovations course at the University of California, Berkeley.

PubMed

Sandhu, Jaspal S; Hosang, Robert Nap; Madsen, Kristine A

2015-03-01

Since 2011 we have taught a public health innovations course at the University of California, Berkeley. Students gain skills in systematic innovation, or human-centered design, while working in small interdisciplinary teams on domestic and global health projects with client organizations. To support acquisition of meaningful problem-solving skills, we structured the course so that the majority of learning happens in scenarios that do not involve faculty. Taken by students representing 26 graduate programs (as diverse as epidemiology, city planning, and mechanical engineering), it is one of the 10 highest-rated courses offered by the School of Public Health. We present the blueprints for our course with the hope that other institutions whose students could benefit will borrow from our model.

Polar Vortices Observed in Ferroelectric | Berkeley Lab

Science.gov Websites

vortices" that appear to be the electrical cousins of magnetic skyrmions holds intriguing structures are confined to magnetic systems and aren't possible in ferroelectric materials, but through the . Ferroic materials display unique electrical or magnetic properties - or both in the case of multiferroics

Teaching Database Management System Use in a Library School Curriculum.

ERIC Educational Resources Information Center

Cooper, Michael D.

1985-01-01

Description of database management systems course being taught to students at School of Library and Information Studies, University of California, Berkeley, notes course structure, assignments, and course evaluation. Approaches to teaching concepts of three types of database systems are discussed and systems used by students in the course are…

PUB-3000 | BERKELEY LAB HEALTH AND SAFETY MANUAL

Science.gov Websites

ES&H MANUAL (PUB-3000) Berkeley Lab Table of Contents Guide to Using the ES&H Manual Responsible Authors Log of ES&H Manual Changes Requesting a Change to the ES&H Manual Search the ES &H Manual Questions & Comments Lawrence Berkeley National Laboratory University of California

SB6.0: The 6th International meeting on Synthetic Biology, July 9-11, 2013

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kahl, Linda J.

The Synthetic Biology conference series (SBx.0) is the preeminent academic meeting in synthetic biology. Organized by the BioBricks Foundation, the SBx.0 conference series brings together leading researchers, students, industry executives, and policy makers from around the world to share, consider, debate, and plan efforts to make biology easier to engineer. Historically held every two years, the SBx.0 conferences are held in alternating locations in the United States, Europe, and Asia to encourage global participation and collaboration so that the ramifications of synthetic biology research and development are most likely to be safe ethical, and beneficial. On 9-11 July 2013, themore » 6th installment of the synthetic biology conference series (SB6.0) was held on the campus of Imperial College London (http://sb6.biobricks.org). The SB6.0 conference was attended by over 700 people, and many more were able to participate via video digital conference (http://sb6.biobricks.org/digital-conference/). Over the course of three days, the SB6.0 conference agenda included plenary sessions, workshops, and poster presentations covering topics ranging from the infrastructure needs arising when “Systematic Engineering Meets Biological Complexity” and design-led considerations for “Connecting People and Technologies” to discussions on “Engineering Biology for New Materials,” “Assessing Risk and Managing Biocontainment,” and “New Directions for Energy and Sustainability.” The $10,150 grant awarded by the U.S. Department of Energy (DE-SC0010233) to the BioBricks Foundation was used to provide partial reimbursement for the travel expenses of leading researchers from the United States to speak at the SB6.0 conference. A total of $9,450 was used to reimburse U.S. speakers for actual expenses related to the SB6.0 conference, including airfare (economy or coach only), ground transportation, hotel, and registration fees. In addition, $700 of the grant was used to offset direct administrative costs associated with selecting speakers (preparing announcements, evaluating abstract submissions) and handling travel arrangements. Leading U.S. researchers selected to speak at the SB6.0 conference included: Adam Arkin, Ph.D. Division Director of the Physical Biosciences Division at the Lawrence Berkeley National Laboratory and Professor in the Department of Bioengineering at UC Berkeley Jay Keasling, Ph.D. Professor in the Department of Bioengineering at Berkeley, Senior Faculty Scientist and Associate Laboratory Director of the Lawrence Berkeley National Laboratory, and Chief Executive Officer of the Joint BioEnergy Institute. Debra Mathews, Ph.D. Assistant Director for Science Programs for the Johns Hopkins Berman Institute of Bioethics, Assistant Professor in the Department of Pediatrics, and Affiliate Faculty in the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine. Richard Murray, Ph.D. Thomas E. and Doris Everhart Professor of Control & Dynamical Systems and Bioengineering at Caltech. Sarah Richardson, Ph.D. Distinguished Postdoctoral Fellow in Genomics at the Lawrence Berkeley National Laboratory and the Department of Energy Joint Genome Institute. and others (for a complete listing of speakers presenting at the SB6.0 conference see http://sb6.biobricks.org/speakers/) The SB6.0 conference was the largest synthetic biology conference to date, and highlights of the SB6.0 conference have been published in a special issue of ACS Synthetic Biology (http://pubs.acs.org/toc/asbcd6/3/3). The BioBricks Foundation appreciates the support of the U.S. Department of Energy in helping to make this most influential and important conference in the field of synthetic biology a success.« less

Changes in prices, sales, consumer spending, and beverage consumption one year after a tax on sugar-sweetened beverages in Berkeley, California, US: A before-and-after study.

PubMed

Silver, Lynn D; Ng, Shu Wen; Ryan-Ibarra, Suzanne; Taillie, Lindsey Smith; Induni, Marta; Miles, Donna R; Poti, Jennifer M; Popkin, Barry M

2017-04-01

Taxes on sugar-sweetened beverages (SSBs) meant to improve health and raise revenue are being adopted, yet evaluation is scarce. This study examines the association of the first penny per ounce SSB excise tax in the United States, in Berkeley, California, with beverage prices, sales, store revenue/consumer spending, and usual beverage intake. Methods included comparison of pre-taxation (before 1 January 2015) and first-year post-taxation (1 March 2015-29 February 2016) measures of (1) beverage prices at 26 Berkeley stores; (2) point-of-sale scanner data on 15.5 million checkouts for beverage prices, sales, and store revenue for two supermarket chains covering three Berkeley and six control non-Berkeley large supermarkets in adjacent cities; and (3) a representative telephone survey (17.4% cooperation rate) of 957 adult Berkeley residents. Key hypotheses were that (1) the tax would be passed through to the prices of taxed beverages among the chain stores in which Berkeley implemented the tax in 2015; (2) sales of taxed beverages would decline, and sales of untaxed beverages would rise, in Berkeley stores more than in comparison non-Berkeley stores; (3) consumer spending per transaction (checkout episode) would not increase in Berkeley stores; and (4) self-reported consumption of taxed beverages would decline. Main outcomes and measures included changes in inflation-adjusted prices (cents/ounce), beverage sales (ounces), consumers' spending measured as store revenue (inflation-adjusted dollars per transaction) in two large chains, and usual beverage intake (grams/day and kilocalories/day). Tax pass-through (changes in the price after imposition of the tax) for SSBs varied in degree and timing by store type and beverage type. Pass-through was complete in large chain supermarkets (+1.07¢/oz, p = 0.001) and small chain supermarkets and chain gas stations (1.31¢/oz, p = 0.004), partial in pharmacies (+0.45¢/oz, p = 0.03), and negative in independent corner stores and independent gas stations (-0.64¢/oz, p = 0.004). Sales-unweighted mean price change from scanner data was +0.67¢/oz (p = 0.00) (sales-weighted, +0.65¢/oz, p = 0.003), with +1.09¢/oz (p < 0.001) for sodas and energy drinks, but a lower change in other categories. Post-tax year 1 scanner data SSB sales (ounces/transaction) in Berkeley stores declined 9.6% (p < 0.001) compared to estimates if the tax were not in place, but rose 6.9% (p < 0.001) for non-Berkeley stores. Sales of untaxed beverages in Berkeley stores rose by 3.5% versus 0.5% (both p < 0.001) for non-Berkeley stores. Overall beverage sales also rose across stores. In Berkeley, sales of water rose by 15.6% (p < 0.001) (exceeding the decline in SSB sales in ounces); untaxed fruit, vegetable, and tea drinks, by 4.37% (p < 0.001); and plain milk, by 0.63% (p = 0.01). Scanner data mean store revenue/consumer spending (dollars per transaction) fell 18¢ less in Berkeley (-$0.36, p < 0.001) than in comparison stores (-$0.54, p < 0.001). Baseline and post-tax Berkeley SSB sales and usual dietary intake were markedly low compared to national levels (at baseline, National Health and Nutrition Examination Survey SSB intake nationally was 131 kcal/d and in Berkeley was 45 kcal/d). Reductions in self-reported mean daily SSB intake in grams (-19.8%, p = 0.49) and in mean per capita SSB caloric intake (-13.3%, p = 0.56) from baseline to post-tax were not statistically significant. Limitations of the study include inability to establish causal links due to observational design, and the absence of health outcomes. Analysis of consumption was limited by the small effect size in relation to high standard error and Berkeley's low baseline consumption. One year following implementation of the nation's first large SSB tax, prices of SSBs increased in many, but not all, settings, SSB sales declined, and sales of untaxed beverages (especially water) and overall study beverages rose in Berkeley; overall consumer spending per transaction in the stores studied did not rise. Price increases for SSBs in two distinct data sources, their timing, and the patterns of change in taxed and untaxed beverage sales suggest that the observed changes may be attributable to the tax. Post-tax self-reported SSB intake did not change significantly compared to baseline. Significant declines in SSB sales, even in this relatively affluent community, accompanied by revenue used for prevention suggest promise for this policy. Evaluation of taxation in jurisdictions with more typical SSB consumption, with controls, is needed to assess broader dietary and potential health impacts.

Seismic Analysis of Intake Towers

DTIC Science & Technology

1982-10-01

Experiment Station (WES) under the sponsorship of the Directorate of Civil Works of the Office, Chief of Engineers, U. S. Army. The work was funded under...the structural capacity of the intake S,-tower are contained in Engineer Technical Letter (ETL) 1110-2-265 " Civil Systems Incorporated, "Dynamic...Berkeley, Calif. " ___ 1975. "Earthquake Resistant Design of Intake-Outlet Towers," Journal of the Structural Division_ American Society of Civil

Mendelevium: The Way It Was

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

A reel of black & white film shot nearly 60 years ago has surfaced at Berkeley Lab, depicting the discovery of Mendelevium - or Element 101 - as reenacted by some of the legendary scientists who did the actual work at that time. Since the 1940s, Berkeley Lab scientists were locked in a race to synthesize new elements, and more often than not, they came out winners. Sixteen elements, most of them in the actinide series at the bottom of the periodic table, were discovered and synthesized by its researchers. Retired Berkeley Lab physicist Claude Lyneis found the reel inmore » a box of dusty and deteriorating films slated for disposal. Using digital editing skills he acquired to make videos of his son's lacrosse team, Lyneis has produced and narrated an excerpt of this nearly-lost footage. It is an entertaining and informative look at the pioneering physics performed at UC Berkeley and Lawrence Berkeley National Laboratory's hillside campus.« less

Laboratory Directed Research and Development Program FY 2006

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansen

2007-03-08

The Ernest Orlando Lawrence Berkeley National Laboratory (Berkeley Lab or LBNL) is a multi-program national research facility operated by the University of California for the Department of Energy (DOE). As an integral element of DOE's National Laboratory System, Berkeley Lab supports DOE's missions in fundamental science, energy resources, and environmental quality. Berkeley Lab programs advance four distinct goals for DOE and the nation: (1) To perform leading multidisciplinary research in the computing sciences, physical sciences, energy sciences, biosciences, and general sciences in a manner that ensures employee and public safety and protection of the environment. (2) To develop and operatemore » unique national experimental facilities for qualified investigators. (3) To educate and train future generations of scientists and engineers to promote national science and education goals. (4) To transfer knowledge and technological innovations and to foster productive relationships among Berkeley Lab's research programs, universities, and industry in order to promote national economic competitiveness.« less

Mendelevium: The Way It Was

ScienceCinema

None

2018-05-30

A reel of black & white film shot nearly 60 years ago has surfaced at Berkeley Lab, depicting the discovery of Mendelevium - or Element 101 - as reenacted by some of the legendary scientists who did the actual work at that time. Since the 1940s, Berkeley Lab scientists were locked in a race to synthesize new elements, and more often than not, they came out winners. Sixteen elements, most of them in the actinide series at the bottom of the periodic table, were discovered and synthesized by its researchers. Retired Berkeley Lab physicist Claude Lyneis found the reel in a box of dusty and deteriorating films slated for disposal. Using digital editing skills he acquired to make videos of his son's lacrosse team, Lyneis has produced and narrated an excerpt of this nearly-lost footage. It is an entertaining and informative look at the pioneering physics performed at UC Berkeley and Lawrence Berkeley National Laboratory's hillside campus.

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of a novel plant-type ferredoxin/thioredoxin reductase-like protein from Methanosarcina acetivorans

PubMed Central

Kumar, Adepu K.; Yennawar, Neela H.; Yennawar, Hemant P.; Ferry, James G.

2011-01-01

The genome of Methanosarcina acetivorans contains a gene (ma1659) that is predicted to encode an uncharacterized chimeric protein containing a plant-type ferredoxin/thioredoxin reductase-like catalytic domain in the N-terminal region and a bacterial-like rubredoxin domain in the C-terminal region. To understand the structural and functional properties of the protein, the ma1659 gene was cloned and overexpressed in Escherichia coli. Crystals of the MA1659 protein were grown by the sitting-drop method using 2 M ammonium sulfate, 0.1 M HEPES buffer pH 7.5 and 0.1 M urea. Diffraction data were collected to 2.8 Å resolution using the remote data-collection feature of the Advanced Light Source, Lawrence Berkeley National Laboratory. The crystal belonged to the primitive cubic space group P23 or P213, with unit-cell parameters a = b = c = 92.72 Å. Assuming the presence of one molecule in the asymmetric unit gave a Matthews coefficient (V M) of 3.55 Å3 Da−1, corresponding to a solvent content of 65%. PMID:21795791

Characterizing Crowd Participation and Productivity of Foldit Through Web Scraping

DTIC Science & Technology

2016-03-01

Berkeley Open Infrastructure for Network Computing CDF Cumulative Distribution Function CPU Central Processing Unit CSSG Crowdsourced Serious Game...computers at once can create a similar capacity. According to Anderson [6], principal investigator for the Berkeley Open Infrastructure for Network...extraterrestrial life. From this project, a software-based distributed computing platform called the Berkeley Open Infrastructure for Network Computing

Participatory Classification in a System for Assessing Multimodal Transportation Patterns

DTIC Science & Technology

2015-02-17

Culler Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2015-8 http...California at Berkeley,Electrical Engineering and Computer Sciences,Berkeley,CA,94720 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING...confirmation screen This section sketches the characteristics of the data that was collected, computes the accuracy of the auto- mated inference algorithm

Site Environmental Report for 2004. Volume 1, Environment, Health, and Safety Division

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2005-09-30

Each year, Ernest Orlando Lawrence Berkeley National Laboratory prepares an integrated report on its environmental programs to satisfy the requirements of United States Department of Energy Order 231.1A, Environment, Safety, and Health Reporting.1 The Site Environmental Report for 2004 summarizes Berkeley Lab’s environmental management performance, presents environmental monitoring results, and describes significant programs for calendar year 2004. (Throughout this report, Ernest Orlando Lawrence Berkeley National Laboratory is referred to as “Berkeley Lab,” “the Laboratory,” “Lawrence Berkeley National Laboratory,” and “LBNL.”) The report is separated into two volumes. Volume I contains an overview of the Laboratory, the status of environmental programs,more » and summarized results from surveillance and monitoring activities. Volume II contains individual data results from these activities. This year, the Site Environmental Report was distributed by releasing it on the Web from the Berkeley Lab Environmental Services Group (ESG) home page, which is located at http://www.lbl.gov/ehs/esg/. Many of the documents cited in this report also are accessible from the ESG Web page. CD and printed copies of this Site Environmental Report are available upon request.« less

Identification and partial characterization of the enzyme of omega: one of five putative DPP IV genes in Drosophila melanogaster

PubMed Central

Chihara, Carol J.; Song, Chunyan; LaMonte, Greg; Fetalvero, Kristina; Hinchman, Kristy; Phan, Helen; Pineda, Mario; Robinson, Kelly; Schneider, Gregory P.

2005-01-01

The omega (ome) gene product is a modifier of larval cuticle protein 5 and its alleles (and duplicates) in the third instar of Drosophila melanogaster. Using deletion mapping the locus mapped to 70F-71A on the left arm of chromosome 3. A homozygote null mutant (ome 1) shows a pleiotropic phenotype that affected the size, developmental time of the flies, and the fertility (or perhaps the behavior) of homozygous mutant males. The omega gene was verified as producing a dipeptidyl peptidase IV (DPPIV) by genetic analysis, substrate specificity and pH optimum. The identity of the gene was confirmed as CG32145 (cytology 70F4) in the Celera Database (Berkeley Drosophila Genome Project), which is consistent with its deletion map position. The genomic structure of the gene is described and the decrease in DPPIV activity in the mutant ome1 is shown to be due to the gene CG32145 (omega). The D. melanogaster omega DPPIV enzyme was partially purified and characterized. The exons of the ome1 mutant were sequenced and a base substitution mutation in exon 4 was identified that would yield a truncated protein caused by a stop codon. A preliminary study of the compartmentalization of the omega DPPIV enzyme in several organs is also reported. Abbreviations: DPPIV dipeptidyl peptidase IV LCP5 & LCP6 third instar larval cuticle proteins 5 & 6 ome & ome1 omega locus name (CG32145) and mutant allele in D. melanogaster pNA paranotroanilide PMID:17119608

Star Formation near Berkeley 59: Embedded Protostars

NASA Astrophysics Data System (ADS)

Rosvick, J. M.; Majaess, D.

2013-12-01

A group of suspected protostars in a dark cloud northwest of the young (~2 Myr) cluster Berkeley 59 and two sources in a pillar south of the cluster have been studied in order to determine their evolutionary stages and ascertain whether their formation was triggered by Berkeley 59. Narrowband near-infrared observations from the Observatoire du Mont Mégantic, 12CO (J = 3-2) and SCUBA-2 (450 and 850 μm) observations from the JCMT, 2MASS, and WISE images, and data extracted from the IPHAS survey catalog were used. Of 12 sources studied, two are Class I objects, while three others are flat/Class II, one of which is a T Tauri candidate. A weak CO outflow and two potential starless cores are present in the cloud, while the pillar possesses substructure at different velocities, with no outflows present. The CO spectra of both regions show peaks in the range v LSR = -15 to -17 km s-1, which agrees with the velocity adopted for Berkeley 59 (-15.7 km s-1), while spectral energy distribution models yield an average interstellar extinction AV and distance of 15 ± 2 mag and 830 ± 120 pc, respectively, for the cloud, and 6.9 mag and 912 pc for the pillar, indicating that the regions are in the same vicinity as Berkeley 59. The formation of the pillar source appears to have been triggered by Berkeley 59. It is unclear whether Berkeley 59 triggered the association's formation.

Changes in prices, sales, consumer spending, and beverage consumption one year after a tax on sugar-sweetened beverages in Berkeley, California, US: A before-and-after study

PubMed Central

Ryan-Ibarra, Suzanne; Taillie, Lindsey Smith; Induni, Marta

2017-01-01

Background Taxes on sugar-sweetened beverages (SSBs) meant to improve health and raise revenue are being adopted, yet evaluation is scarce. This study examines the association of the first penny per ounce SSB excise tax in the United States, in Berkeley, California, with beverage prices, sales, store revenue/consumer spending, and usual beverage intake. Methods and findings Methods included comparison of pre-taxation (before 1 January 2015) and first-year post-taxation (1 March 2015–29 February 2016) measures of (1) beverage prices at 26 Berkeley stores; (2) point-of-sale scanner data on 15.5 million checkouts for beverage prices, sales, and store revenue for two supermarket chains covering three Berkeley and six control non-Berkeley large supermarkets in adjacent cities; and (3) a representative telephone survey (17.4% cooperation rate) of 957 adult Berkeley residents. Key hypotheses were that (1) the tax would be passed through to the prices of taxed beverages among the chain stores in which Berkeley implemented the tax in 2015; (2) sales of taxed beverages would decline, and sales of untaxed beverages would rise, in Berkeley stores more than in comparison non-Berkeley stores; (3) consumer spending per transaction (checkout episode) would not increase in Berkeley stores; and (4) self-reported consumption of taxed beverages would decline. Main outcomes and measures included changes in inflation-adjusted prices (cents/ounce), beverage sales (ounces), consumers’ spending measured as store revenue (inflation-adjusted dollars per transaction) in two large chains, and usual beverage intake (grams/day and kilocalories/day). Tax pass-through (changes in the price after imposition of the tax) for SSBs varied in degree and timing by store type and beverage type. Pass-through was complete in large chain supermarkets (+1.07¢/oz, p = 0.001) and small chain supermarkets and chain gas stations (1.31¢/oz, p = 0.004), partial in pharmacies (+0.45¢/oz, p = 0.03), and negative in independent corner stores and independent gas stations (−0.64¢/oz, p = 0.004). Sales-unweighted mean price change from scanner data was +0.67¢/oz (p = 0.00) (sales-weighted, +0.65¢/oz, p = 0.003), with +1.09¢/oz (p < 0.001) for sodas and energy drinks, but a lower change in other categories. Post-tax year 1 scanner data SSB sales (ounces/transaction) in Berkeley stores declined 9.6% (p < 0.001) compared to estimates if the tax were not in place, but rose 6.9% (p < 0.001) for non-Berkeley stores. Sales of untaxed beverages in Berkeley stores rose by 3.5% versus 0.5% (both p < 0.001) for non-Berkeley stores. Overall beverage sales also rose across stores. In Berkeley, sales of water rose by 15.6% (p < 0.001) (exceeding the decline in SSB sales in ounces); untaxed fruit, vegetable, and tea drinks, by 4.37% (p < 0.001); and plain milk, by 0.63% (p = 0.01). Scanner data mean store revenue/consumer spending (dollars per transaction) fell 18¢ less in Berkeley (−$0.36, p < 0.001) than in comparison stores (−$0.54, p < 0.001). Baseline and post-tax Berkeley SSB sales and usual dietary intake were markedly low compared to national levels (at baseline, National Health and Nutrition Examination Survey SSB intake nationally was 131 kcal/d and in Berkeley was 45 kcal/d). Reductions in self-reported mean daily SSB intake in grams (−19.8%, p = 0.49) and in mean per capita SSB caloric intake (−13.3%, p = 0.56) from baseline to post-tax were not statistically significant. Limitations of the study include inability to establish causal links due to observational design, and the absence of health outcomes. Analysis of consumption was limited by the small effect size in relation to high standard error and Berkeley’s low baseline consumption. Conclusions One year following implementation of the nation’s first large SSB tax, prices of SSBs increased in many, but not all, settings, SSB sales declined, and sales of untaxed beverages (especially water) and overall study beverages rose in Berkeley; overall consumer spending per transaction in the stores studied did not rise. Price increases for SSBs in two distinct data sources, their timing, and the patterns of change in taxed and untaxed beverage sales suggest that the observed changes may be attributable to the tax. Post-tax self-reported SSB intake did not change significantly compared to baseline. Significant declines in SSB sales, even in this relatively affluent community, accompanied by revenue used for prevention suggest promise for this policy. Evaluation of taxation in jurisdictions with more typical SSB consumption, with controls, is needed to assess broader dietary and potential health impacts. PMID:28419108

The Berkeley Out-of-Order Machine (BOOM): An Industry-Competitive, Synthesizable, Parameterized RISC-V Processor

DTIC Science & Technology

2015-06-13

The Berkeley Out-of-Order Machine (BOOM): An Industry- Competitive, Synthesizable, Parameterized RISC-V Processor Christopher Celio David A...Synthesizable, Parameterized RISC-V Processor Christopher Celio, David Patterson, and Krste Asanović University of California, Berkeley, California 94720...Order Machine BOOM is a synthesizable, parameterized, superscalar out- of-order RISC-V core designed to serve as the prototypical baseline processor

Berkeley Lab - Materials Sciences Division

Science.gov Websites

Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Search MSD Go MSD - Materials Investigators Ager, Joel W » Alivisatos, A Paul » Altman, Ehud » Analytis, James » Anderson, Christopher  , Naomi » Gullikson, Eric M » Harris, Stephen J » Hasan, M. Zahid » Hellman, Frances » Helms, Brett A

A Profile of Minority Graduate Students at the University of California, Berkeley: Recruitment, Selection, Fields of Study and Financial Support.

ERIC Educational Resources Information Center

Collins, O. R.

This paper presents a profile of minority graduate students at the University of California, Berkeley. Following a brief overview of Berkeley's Graduate Minority Program (GMP), data is presented concerning the number of GMP students supported; available funds and average grants for students from 1968-69 to 1973-74; distribution of GMP students…

Exploring Your Sense of Smell. Science Study Aid No. 10.

ERIC Educational Resources Information Center

Boeschen, John; And Others

This Science Study Aid (SSA), structured for grade levels 7-9, is based on work of the U.S. Department of Agriculture's Agricultural Research Service (ARS) conducted at the Western Regional Research Center in Berkeley, California. It is concerned with food aroma, its intensity and character, and olfactory threshold determinations. The SSA provides…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, Iain; Regnier, Cindy

Science at the Theater: Berkeley Lab scientists reveal the latest research on how to reduce your carbon footprint at home, work, and when you shop. Learn how even small choices can have a big impact. Iain Walker's research focuses on optimizing the energy use and comfort of buildings. He's a staff scientist in the Energy Performance of Buildings Group, which is part of Berkeley Lab's Environmen...tal Energy Technologies Division. He's also executive editor of Home Energy Magazine. Cindy Regnier is a Project Manager in the Environmental Energy Technologies Division at Berkeley Lab. She has over 13 years of mechanical engineeringmore » design experience, with a focus on low-energy buildings. Her projects have included several LEED Platinum buildings and the design of a 200,000 sf carbon neutral, net-zero energy science museum in San Francisco. Eric Masanet is Acting Deputy Leader of the International Energy Studies Group at Berkeley Lab. His research focuses on life-cycle assessments and energy efficiency analysis. He holds a joint research appointment in the Institute of Transportation Studies at UC Berkeley.« less

Site Environmental Report for 2006. Volume I, Environment, Health, and Safety Division

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2007-09-30

Each year, Ernest Orlando Lawrence Berkeley National Laboratory prepares an integrated report on its environmental programs to satisfy the requirements of United States Department of Energy Order 231.1A, Environment, Safety, and Health Reporting.1 The Site Environmental Report for 2006 summarizes Berkeley Lab’s environmental management performance, presents environmental monitoring results, and describes significant programs for calendar year 2006. (Throughout this report, Ernest Orlando Lawrence Berkeley National Laboratory is referred to as “Berkeley Lab,” “the Laboratory,” “Lawrence Berkeley National Laboratory,” and “LBNL.”) The report is separated into two volumes. Volume I is organized into an executive summary followed by six chapters thatmore » contain an overview of the Laboratory, a discussion of the Laboratory’s environmental management system, the status of environmental programs, and summarized results from surveillance and monitoring activities. Volume II contains individual data results from surveillance and monitoring activities.« less

Laboratory directed research and development program FY 1999

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansen, Todd; Levy, Karin

2000-03-08

The Ernest Orlando Lawrence Berkeley National Laboratory (Berkeley Lab or LBNL) is a multi-program national research facility operated by the University of California for the Department of Energy (DOE). As an integral element of DOE's National Laboratory System, Berkeley Lab supports DOE's missions in fundamental science, energy resources, and environmental quality. Berkeley Lab programs advance four distinct goals for DOE and the nation: (1) To perform leading multidisciplinary research in the computing sciences, physical sciences, energy sciences, biosciences, and general sciences in a manner that ensures employee and public safety and protection of the environment. (2) To develop and operatemore » unique national experimental facilities for qualified investigators. (3) To educate and train future generations of scientists and engineers to promote national science and education goals. (4) To transfer knowledge and technological innovations and to foster productive relationships among Berkeley Lab's research programs, universities, and industry in order to promote national economic competitiveness. This is the annual report on Laboratory Directed Research and Development (LDRD) program for FY99.« less

Impact of the Berkeley Excise Tax on Sugar-Sweetened Beverage Consumption

PubMed Central

Falbe, Jennifer; Thompson, Hannah R.; Becker, Christina M.; Rojas, Nadia; McCulloch, Charles E.

2016-01-01

Objectives. To evaluate the impact of the excise tax on sugar-sweetened beverage (SSB) consumption in Berkeley, California, which became the first US jurisdiction to implement such a tax ($0.01/oz) in March 2015. Methods. We used a repeated cross-sectional design to examine changes in pre- to posttax beverage consumption in low-income neighborhoods in Berkeley versus in the comparison cities of Oakland and San Francisco, California. A beverage frequency questionnaire was interviewer administered to 990 participants before the tax and 1689 after the tax (approximately 8 months after the vote and 4 months after implementation) to examine relative changes in consumption. Results. Consumption of SSBs decreased 21% in Berkeley and increased 4% in comparison cities (P = .046). Water consumption increased more in Berkeley (+63%) than in comparison cities (+19%; P < .01). Conclusions. Berkeley’s excise tax reduced SSB consumption in low-income neighborhoods. Evaluating SSB taxes in other cities will improve understanding of their public health benefit and their generalizability. PMID:27552267

From Relational Interfaces to Assume-Guarantee Contracts

DTIC Science & Technology

2014-03-18

Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2014-21 http://www.eecs.berkeley.edu/Pubs...5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) University of California at Berkeley, Electrical Engineering...design,” in EMSOFT’01. Springer, LNCS 2211, 2001. [2] A. Sangiovanni-Vincentelli et al., “Taming Dr. Frankenstein : Contract-Based Design for Cyber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeff Neaton

Jan. 22, 2010: Host Alice Egan of Berkeley Lab's Materials Sciences Division interviews scientists about their lives and work in language everyone can understand. Her guest Berkeley Lab's MIke Crommie.

iScreen: Image-Based High-Content RNAi Screening Analysis Tools.

PubMed

Zhong, Rui; Dong, Xiaonan; Levine, Beth; Xie, Yang; Xiao, Guanghua

2015-09-01

High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well. This image-based high-content screening technology has led to genome-wide functional annotation in a wider spectrum of biological research studies, as well as in drug and target discovery, so that complex cellular phenotypes can be measured in a multiparametric format. Despite these advances, data analysis and visualization tools are still largely lacking for these types of experiments. Therefore, we developed iScreen (image-Based High-content RNAi Screening Analysis Tool), an R package for the statistical modeling and visualization of image-based high-content RNAi screening. Two case studies were used to demonstrate the capability and efficiency of the iScreen package. iScreen is available for download on CRAN (http://cran.cnr.berkeley.edu/web/packages/iScreen/index.html). The user manual is also available as a supplementary document. © 2014 Society for Laboratory Automation and Screening.

The DNA Files: Report from Genome Radio Project, March--June 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

The Genome Radio Project (GRP) core staff are now all in place and the office infrastructure has been set up. The project logo, stationery, and letterhead have all been approved. The name of the series has been identified: The DNA Files. Weekly staff planning meetings and work plans have been initiated; the research component has been launched; interviews of potential production personnel are being conducted. The first three months of the GRP were principally devoted to the further development of the entire two-year project, specifically by pursuing full funding for this project from sources other than DOE. The principal purposemore » of this planning grant includes the following: produce a pilot documentary which can be used to strengthen the marketing strategy of the overall project; create concrete strategies for best engaging the talents and energies of the project`s advisors; and identify concrete collaborations that maximize the efficacy of a well-designed set of ancillary materials. During this period, GRP collaborated with the Exploratorium in San Francisco to record their series of evening lectures on the social implications of genetic research and its applications. Project staff also attended Lawrence Berkeley Lab.`s Genome Educators Workshops, and the Public Radio Conference.« less

Letting the cat out of the bag: a personal journey in Biophysics.

PubMed

Bustamante, Carlos J

2014-10-08

When the author arrived in Berkeley, in the mid 1970s, to study Biophysics he soon felt as if he was engaging himself in a somewhat marginal activity. Biology was then entering another of its cyclical periods of annotation that was to culminate with the human genome project. Two decades later, however, at the end of this process, it had become clear that two main tasks were acquiring a central importance in biological research: a renewed push for a quantitative, precise description of biological systems at the molecular level, and efforts towards an integrated understanding of the operation, control, and coordination of cellular processes. Today, these have become two of the most fertile research areas in Biophysics.

A Context Menu for the Real World: Controlling Physical Appliances Through Head-Worn Infrared Targeting

DTIC Science & Technology

2013-12-10

Edward A. Lee Björn Hartmann Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2013-200...NAME(S) AND ADDRESS(ES) University of California at Berkeley, Electrical Engineering and Computer Sciences,Berkeley,CA,94720 8. PERFORMING...movement. PHYSICAL TARGET ACQUISITION STUDY To understand the accuracy and performance of head- orientation-based selection through our device, we car - ried

A Context Menu for the Real World: Controlling Physical Appliances through Head-Worn Infrared Targeting

DTIC Science & Technology

2013-11-04

Edward A. Lee Björn Hartmann Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2013-182...NAME(S) AND ADDRESS(ES) University of California at Berkeley, Electrical Engineering and Computer Sciences,Berkeley,CA,94720 8. PERFORMING...accuracy and performance of head- orientation-based selection through our device, we car - ried out a comparative target acquisition study, where

Sit Down with Sabin: Margaret Torn: The Carbon Cycle Like You've Never Seen It (LBNL Summer Lecture Series)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, Sabin; Torn, Margaret

2011-07-06

Lawrence Berkeley National Laboratory soil scientist Margaret Torn appears July 6, 2011 on "Sit Down with Sabin," a weekly conversation in which former reporter Sabin Russell chats with Berkeley Lab staff about innovative science. Torn discusses how she travels the world to learn more about soil's huge role in the global carbon cycle. Brought to you by Berkeley Lab Public Affairs.

An introduction to the nitrogen dynamics in controlled systems workshop. Life support and nitrogen: NASA's interest in nitrogen cycling

NASA Technical Reports Server (NTRS)

MacElroy, R. D.; Smernoff, D. T.

1996-01-01

A Workshop on "Nitrogen Dynamics in Controlled Systems" was held September 26-28, 1995 at the Lawrence Berkeley National Laboratory. The meetings were sponsored by the NASA Advanced Life Support program and the Lawrence Berkeley National Laboratory, and hosted by Prof. Lester Packer of the University of California at Berkeley, and of the Lawrence Berkeley National Laboratory. The Workshop participants were asked to: 1. summarize current knowledge on the cycling of nitrogen in closed systems; 2. identify the needs that closed systems may have for specific forms of nitrogen; 3. identify possible ways of generating and maintaining (or avoiding) specific forms and concentrations of nitrogen; 4. compare biological and physical/chemical methods of transforming nitrogen.

Visualizing Rhizosphere Soil Structure Around Living Roots

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2008-12-01

The rhizosphere, a thin layer of soil (0 to 2 mm) surrounding a living root, is an important interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 ìm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

Visualizing the impact of living roots on rhizosphere soil structure using X-ray microtomography

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2009-04-01

The rhizosphere is an interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 μm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

UC Berkeley's Adaptations to the Crisis of Public Higher Education in the US: Privatization? Commercialization? or Hybridization? Research & Occasional Paper Series: CSHE.17.13

ERIC Educational Resources Information Center

Breslauer, George W.

2013-01-01

The University of California at Berkeley now delivers more to the public of California than it ever has, and it does this on the basis of proportionally less funding by the State government than it has ever received. This claim may come as a surprise, since it is often said that Berkeley is in the process of privatizing, becoming less of a public…

In Conversation with Jeff Neaton

ScienceCinema

Jeff Neaton

2017-12-09

Jan. 22, 2010: Host Alice Egan of Berkeley Lab's Materials Sciences Division interviews scientists about their lives and work in language everyone can understand. Her guest Berkeley Lab's MIke Crommie.

Putting Carbon in its Place: What You Can Do (LBNL Science at the Theater)

ScienceCinema

Walker, Iain; Regnier, Cindy [LBNL, Environmental Energy Technologies Division; Miller, Jeff; Masanet, Eric

2018-06-28

Science at the Theater: Berkeley Lab scientists reveal the latest research on how to reduce your carbon footprint at home, work, and when you shop. Learn how even small choices can have a big impact. Iain Walker's research focuses on optimizing the energy use and comfort of buildings. He's a staff scientist in the Energy Performance of Buildings Group, which is part of Berkeley Lab's Environmen...tal Energy Technologies Division. He's also executive editor of Home Energy Magazine. Cindy Regnier is a Project Manager in the Environmental Energy Technologies Division at Berkeley Lab. She has over 13 years of mechanical engineering design experience, with a focus on low-energy buildings. Her projects have included several LEED Platinum buildings and the design of a 200,000 sf carbon neutral, net-zero energy science museum in San Francisco. Eric Masanet is Acting Deputy Leader of the International Energy Studies Group at Berkeley Lab. His research focuses on life-cycle assessments and energy efficiency analysis. He holds a joint research appointment in the Institute of Transportation Studies at UC Berkeley.

Seeing the Light (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brunger, Axel; Segalman, Rachel; Westphal, Andrew

2011-09-12

Berkeley Lab's Science at the Theater event "Seeing the Light" took place on Sept 12, 2011, at Berkeley Repertory's Roda Theatre. Learn how the Advanced Light Source is improving medicine, paving the way for clean energy, changing the future of computers, and much more. Featured speakers are Berkeley Lab's Roger Falcone, Rachel Segalman, Andrew Westphal, and Stanford University's Axel Brunger. Rachel Segalman: The future of clean energy technology relies on a better understanding of materials at the nanoscale. Berkeley Lab's Rachel Segalman uses the ALS to conduct this research, which could lead to improved photovoltaics and fuel cells. Axel Brunger:more » Improved treatment for human diseases hinges on understanding molecular-scale processes. Stanford University's Axel Brunger will discuss a new melanoma drug that was developed by a local company, Plexxikon, using the ALS for X-ray data collection. Andrew Westphal: What's comet dust made of? Andrew Westphal of UC Berkeley's Space Sciences Laboratory uses the ALS to study comet dust and interplanetary space dust collected by a NASA spacecraft. Moderated by Roger Falcone, Division Director of the Advanced Light Source« less

In Conversation with Mike Crommie

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mike Crommie

2010-02-16

Dec. 9 2009: Host Alice Egan of Berkeley Lab's Materials Sciences Division interviews scientists about their lives and work in language everyone can understand. Her guest is Berkeley Lab's Mike Crommie.

In Conversation with Mike Crommie

ScienceCinema

Mike Crommie

2017-12-09

Dec. 9 2009: Host Alice Egan of Berkeley Lab's Materials Sciences Division interviews scientists about their lives and work in language everyone can understand. Her guest is Berkeley Lab's Mike Crommie.

Sneak Preview of April 25 Science at the Theater

ScienceCinema

Ho, Shirley

2017-12-12

Berkeley Lab astrophysicist Shirley Ho offers a sneak preview of the Science at the Theatre event at the Berkeley Repertory Theatre on April 25. Three Berkeley Lab cosmologists and Bay Area astronomer Andrew Fraiknoi will gather at the Berkeley Rep on Monday, April 25, from 7 to 9 p.m. to shed light on the mystery of the accelerating universe. Topics will include hunting down Type 1a supernovae, measuring the universe using baryon oscillation, and whether dark energy is the true driver of the universe. If you have questions for the scientists, post them below, send them to friendsofberkeleylab@lbl.gov, or catch us on facebook: http://www.facebook.com/video/video.php?v=10150215592292354&oid=593833429...Your question might be answered at the April 25 talk if there's time.

Novel Adult Stem Cells for Peripheral Nerve Regeneration

DTIC Science & Technology

2012-09-01

were also positive for MSC surface marker CD29 and CD44 (Fig. 1F-G). However, CD29 and CD44 are also expressed in SMCs, so we will not use these non...tubulin. In addition, MVSCs were negative for perivascular MSC marker CD146 (Fig. 1H) and SMC progenitor marker Sca-1 (Fig. 1I). MVSCs were also...University of California, Berkeley, California 94720, USA. 2 UC Berkeley-UCSF Graduate Program in Bioengineering, Berkeley, California 94720, USA. 3

Space Radiation and Cataracts (LBNL Summer Lecture Series)

ScienceCinema

Blakely, Eleanor [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division

2018-01-23

Summer Lecture Series 2009: Eleanor Blakely, radiation biologist of the Life Sciences Division at Lawrence Berkeley National Laboratory, has been a scientist at Berkeley Lab since 1975. She is studying the effect of radiation on cataracts which concerns not only cancer patients, but also astronauts. As astronauts spend increasingly longer time in space, the effects of cosmic radiation exposure will become an increasingly important health issue- yet there is little human data on these effects. Blakely reviews this emerging field and the contributions made at Berkeley Lab

UC Berkeley's Celebration of the International Year of Astronomy 2009

NASA Astrophysics Data System (ADS)

Cobb, B. E.; Croft, S.; Silverman, J. M.; Klein, C.; Modjaz, M.

2010-08-01

We present the astronomy outreach efforts undertaken for the International Year of Astronomy 2009 at the University of California, Berkeley. Our department-wide endeavors included a monthly public lecture series by UC Berkeley astronomers and a major astronomy outreach event during a campus-wide university "open house," which included solar observing and a Starlab Planetarium. In addition to sharing our outreach techniques and outcomes, we discuss some of our unique strategies for advertising our events to the local community.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Todd DeSantis

Scientists at Berkeley Lab and the University of California, Merced are using an innovative DNA array developed at Berkeley Lab to catalog the microbes that live among coral in the tropical waters off the coast of Puerto Rico.

Berkeley Lab Search - Search engine for Berkeley Lab

Science.gov Websites

twitter instagram google plus facebook youtube A U.S. Department of Energy National Laboratory Managed by the University of California Questions & Comments Privacy & Security Notice twitter instagram

ARC-2006-ACD06-0216-017

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASABerkeley researcher Zack Gainsforth working with sample encased in aerogel

ARC-2006-ACD06-0216-022

NASA Image and Video Library

2006-11-29

Stardust sample analysis @ UC Berkeley clean room with Dr Scott Sandford, NASA Ames Astrophysicist - mission samples provided to UC Berkeley for analysis by NASABerkeley researcher Zack Gainsforth working with sample encased in aerogel

Federal, State, and Local Governments: University Patrons, Partners, or Protagonists? Research & Occasional Paper Series: CSHE.3.06

ERIC Educational Resources Information Center

Vest, Charles M.

2006-01-01

Charles Vest gave the first of three Clark Kerr Lectures on the Role of Higher Education in Society on April 19, 2005 on the Berkeley campus. This essay argues that research-intensive public and private universities increasingly have far more similarities than differences in missions, structures, and even financial support. For both, the federal…

Saul Perlmutter

Science.gov Websites

joined the UC Berkeley Physics Department in 2004. He is also an astrophysicist at Lawrence Berkeley Perlmutter won the Department of Energy's E. O. Lawrence Award in Physics. In 2003 he was awarded the

Sneak Preview of April 25 Science at the Theater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Shirley

Berkeley Lab astrophysicist Shirley Ho offers a sneak preview of the Science at the Theatre event at the Berkeley Repertory Theatre on April 25. Three Berkeley Lab cosmologists and Bay Area astronomer Andrew Fraiknoi will gather at the Berkeley Rep on Monday, April 25, from 7 to 9 p.m. to shed light on the mystery of the accelerating universe. Topics will include hunting down Type 1a supernovae, measuring the universe using baryon oscillation, and whether dark energy is the true driver of the universe. If you have questions for the scientists, post them below, send them to friendsofberkeleylab@lbl.gov, or catchmore » us on facebook: http://www.facebook.com/video/video.php?v=10150215592292354&oid=593833429...Your question might be answered at the April 25 talk if there's time.« less

Ernest Orlando Lawrence Berkeley National Laboratory Institutional Plan FY 2000-2004

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chartock, Mike; Hansen, Todd

1999-08-01

The FY 2000-2004 Institutional Plan provides an overview of the Ernest Orlando Lawrence Berkeley National Laboratory (Berkeley Lab, the Laboratory) mission, strategic plan, initiatives, and the resources required to fulfill its role in support of national needs in fundamental science and technology, energy resources, and environmental quality. To advance the Department of Energy's ongoing efforts to define the Integrated Laboratory System, the Berkeley Lab Institutional Plan reflects the strategic elements of our planning efforts. The Institutional Plan is a management report that supports the Department of Energy's mission and programs and is an element of the Department of Energy's strategicmore » management planning activities, developed through an annual planning process. The Plan supports the Government Performance and Results Act of 1993 and complements the performance-based contract between the Department of Energy and the Regents of the University of California. It identifies technical and administrative directions in the context of the national energy policy and research needs and the Department of Energy's program planning initiatives. Preparation of the plan is coordinated by the Office of Planning and Communications from information contributed by Berkeley Lab's scientific and support divisions.« less

Joint SSRTNet/ALS-MES Workshop report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shuh, David; Van Hove, Michel

2001-11-30

This joint workshop brought together experimentalists and theorists interested in synchrotron radiation and highlighted subjects relevant to molecular environmental science (MES). The strong mutual interest between the participants resulted in joint sessions on the first day, followed by more specialized parallel sessions on the second day. Held in conjunction with the Advanced Light Source (ALS) Users' Association Annual Meeting at the Lawrence Berkeley National Laboratory (Berkeley Lab), the Synchrotron Radiation Research Theory Network (SRRTNet) workshop was co-organized by Michel Van Hove (Berkeley Lab and University of California, Davis) and Andrew Canning (Berkeley Lab), while David Shuh (Berkeley Lab) organized themore » ALS-MES workshop. SRRTNet is a global network that promotes the interaction of theory and experiment (http://www.cse.clrc.ac.uk/Activity/SRRTnet). The ALS-MES project is constructing Beamline 11.0.2.1-2, a new soft x-ray beamline for MES investigations at photon energies from 75 eV to 2 keV, to provide photons for wet spectroscopy end stations and an upgraded scanning transmission x-ray microscope (STXM). The ALS-MES beamline and end stations will be available for users in the late fall of 2002.« less

Gerson Goldhaber: A Life in Science

NASA Astrophysics Data System (ADS)

Pavlish, Ursula

2011-06-01

I draw on my interviews in 2005-2007 with Gerson Goldhaber (1924-2010), his wife Judith, and his colleagues at Lawrence Berkeley National Laboratory. I discuss his childhood, early education, marriage to his first wife Sulamith (1923-1965), and his further education at the Hebrew University in Jerusalem (1942-1947) and his doctoral research at University of Wisconsin at Madison (1947-1950). He then was appointed to an instructorship in physics at Columbia University (1950-1953) before accepting a position in the physics department at the University of California at Berkeley and the Radiation Laboratory (later the Lawrence Berkeley Laboratory, today the Lawrence Berkeley National Laboratory), where he remained for the rest of his life. He made fundamental contributions to physics, including to the discovery of the antiproton in 1955, the GGLP effect in 1960, the psi particle in 1974, and charmed mesons in 1977, and to cosmology, including the discovery of the accelerating universe and dark energy in 1998. Beginning in the late 1960s, he also took up art, and he and his second wife Judith, whom he married in 1969, later collaborated in illustrating and writing two popular books. Goldhaber died in Berkeley, California, on July 19, 2010, at the age of 86.

PhyloChip Tackles Coral Disease

ScienceCinema

Todd DeSantis

2017-12-09

Scientists at Berkeley Lab and the University of California, Merced are using an innovative DNA array developed at Berkeley Lab to catalog the microbes that live among coral in the tropical waters off the coast of Puerto Rico.

Berkeley Lab Scientists Recipients of 2015 Breakthrough Prizes | Berkeley

Science.gov Websites

. Doudna and Charpentier have been at the forefront of research into a genetic element known as CRISPR , which stands for Clustered Regularly Interspaced Short Palindromic Repeats. The combination of CRISPR

Hot Technology, Cool Science (LBNL Science at the Theater)

ScienceCinema

Fowler, John

2018-06-08

Great innovations start with bold ideas. Learn how Berkeley Lab scientists are devising practical solutions to everything from global warming to how you get to work. On May 11, 2009, five Berkeley Lab scientists participated in a roundtable dicussion moderated by KTVU's John Fowler on their leading-edge research. This "Science at the Theater" event, held at the Berkeley Repertory Theatre, featured technologies such as cool roofs, battery-driven transportation, a pocket-sized DNA probe, green supercomputing, and a noncontact method for restoring damaged and fragile mechanical recordings.

BEARS: Radioactive Ion Beams at Berkeley

DOE Office of Scientific and Technical Information (OSTI.GOV)

Powell, J.; Joosten, R.; Donahue, C.A.

2000-03-14

A light-isotope radioactive ion beam capability has been added to the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory by coupling to the production cyclotron of the Berkeley Isotope Facility. The connection required the development and construction of a 350 m gas transport system between the two accelerators as well as automated cryogenic separation of the produced activity. The first beam developed, {sup 11}C, has been successfully accelerated with an on-target intensity of 1 x 10{sup 8} ions/sec at energies of around 10 MeV/u.

Water and organics in interplanetary dust particles

NASA Astrophysics Data System (ADS)

Bradley, John P.

2015-08-01

Interplanetary dust particles (IDPs) and larger micrometeorites (MMs) impinge on the upper atmosphere where they decelerate at ~90 km altitude and settle to the Earth’s surface. Comets and asteroids are the major sources and the flux, 30,000-40,000 tons/yr, is comparable to the mass of larger meteorites impacting the Earth’s surface. The sedimentary record suggests that the flux was much higher on the early Earth. The chondritic porous (CP) subset of IDPs together with their larger counterparts, ultracarbonaceous micrometeorites (UCMMs), appear to be unique among known meteoritic materials in that they are composed almost exclusively of anhydrous minerals, some of them contain >> 50% organic carbon by volume as well as the highest abundances of presolar silicate grains including GEMS. D/H and 15N abundances implicate the Oort Cloud or presolar molecular cloud as likely sources of the organic carbon. Prior to atmospheric entry, IDPs and MMs spend ~104-105 year lifetimes in solar orbit where their surfaces develop amorphous space weathered rims from exposure to the solar wind (SW). Similar rims are observed on lunar soil grains and on asteroid Itokawa regolith grains. Using valence electron energy-loss spectroscopy (VEELS) we have detected radiolytic water in the rims on IDPs formed by the interaction of solar wind protons with oxygen in silicate minerals. Therefore, IDPs and MMs continuously deliver both water and organics to the earth and other terrestrial planets. The interaction of protons with oxygen-rich minerals to form water is a universal process.Affiliations:a University of Hawaii at Manoa, Hawaii Institute of Geophysics and Planetology, 1680 East-West Road, Honolulu, HI 96822, USA.b National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.c Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.d Department of Materials Science & Engineering, University of California, Berkeley, CA 94720, USA.e Advanced Light Source Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Beyond SWEAT: Developing Infrastructure in Stability and COIN Operations

DTIC Science & Technology

2011-10-05

respecting their desire for self-determination. See Pressman , Jeffrey L. and Wildavsky, Aaron. Implementation. (Berkeley: University of California Press... Pressman , Jeffrey L. and Wildavsky, Aaron. Implementation. (Berkeley: University of California Press 1971). Sablan, Gregory. Developing

Summer Series 2012 - Conversation with Kathy Yelick

ScienceCinema

Yelick, Kathy, Miller, Jeff

2018-05-11

Jeff Miller, head of Public Affairs, sat down in conversation with Kathy Yelick, Associate Berkeley Lab Director, Computing Sciences, in the second of a series of powerpoint-free talks on July 18th 2012, at Berkeley Lab.

Theory-based Bayesian Models of Inductive Inference

DTIC Science & Technology

2010-07-19

Subjective randomness and natural scene statistics. Psychonomic Bulletin & Review . http://cocosci.berkeley.edu/tom/papers/randscenes.pdf Page 1...in press). Exemplar models as a mechanism for performing Bayesian inference. Psychonomic Bulletin & Review . http://cocosci.berkeley.edu/tom

Summer Series 2012 - Conversation with Kathy Yelick

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yelick, Kathy, Miller, Jeff

2012-07-23

Jeff Miller, head of Public Affairs, sat down in conversation with Kathy Yelick, Associate Berkeley Lab Director, Computing Sciences, in the second of a series of powerpoint-free talks on July 18th 2012, at Berkeley Lab.

Berkeley bicycle plan : draft for inclusion in the general plan

DOT National Transportation Integrated Search

1998-12-31

The City of Berkeley has long supported bicycling as an environmentally friendly, healthy, lowcost method of transportation and recreation. Frequently, roadway facility and funding decisions are made with little consideration for bicycling as a serio...

Berkeley Lab 2nd Grader Outreach

ScienceCinema

Scoggins, Jackie; Louie, Virginia

2017-12-11

The Berkeley Lab IT Department sponsored a community outreach program aimed at teaching young children about computers and networks. Second graders from LeConte Elementary School joined Lab IT Staff for a day of in-depth exercises and fun.

Analysis, tuning and comparison of two general sparse solvers for distributed memory computers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amestoy, P.R.; Duff, I.S.; L'Excellent, J.-Y.

2000-06-30

We describe the work performed in the context of a Franco-Berkeley funded project between NERSC-LBNL located in Berkeley (USA) and CERFACS-ENSEEIHT located in Toulouse (France). We discuss both the tuning and performance analysis of two distributed memory sparse solvers (superlu from Berkeley and mumps from Toulouse) on the 512 processor Cray T3E from NERSC (Lawrence Berkeley National Laboratory). This project gave us the opportunity to improve the algorithms and add new features to the codes. We then quite extensively analyze and compare the two approaches on a set of large problems from real applications. We further explain the main differencesmore » in the behavior of the approaches on artificial regular grid problems. As a conclusion to this activity report, we mention a set of parallel sparse solvers on which this type of study should be extended.« less

Site Environmental Report for 2011, Volumes 1& 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baskin, David; Bauters, Tim; Borglin, Ned

2012-09-12

The Site Environmental Report for 2011 summarizes Berkeley Lab’s environmental management performance, presents environmental monitoring results, and describes significant programs for calendar year (CY) 2011. Throughout this report, “Berkeley Lab” or “LBNL” refers both to (1) the multiprogram scientific facility the UC manages and operates on the 202-acre university-owned site located in the hills above the UC Berkeley campus, and the site itself, and (2) the UC as managing and operating contractor for Ernest Orlando Lawrence Berkeley National Laboratory. The report is separated into two volumes. Volume I is organized into an executive summary followed by six chapters that includemore » an overview of LBNL, a discussion of its Environmental Management System (EMS), the status of environmental programs, summarized results from surveillance and monitoring activities, and quality assurance (QA) measures. Volume II contains individual data results from surveillance and monitoring activities.« less

A Provost for Professional Schools and Colleges. Research & Occasional Paper Series: CSHE.3.13

ERIC Educational Resources Information Center

King, C. Judson

2013-01-01

From 1972 to 1994, the academic administrative structure of the Berkeley campus of the University of California was unusual, in that it involved two Provosts, one who was also Dean of the College of Letters and Science, and another who was responsible for the remainder of the academic units, which were for the most part professional schools and…

Complementary Metal-Oxide-Silicon (CMOS)-Memristor Hybrid Nanoelectronics for Advanced Encryption Standard (AES) Encryption

DTIC Science & Technology

2016-04-01

with Al top electrodes and Cu bottom electrodes. ................... 9 Figure 4. SPICE netlist structure...memory elements play a part in logic gate. 4.4.2 Simulation SPICE Simulation Program for Integrated Circuits Emphasis ( SPICE ) is a general-purpose...analog circuit simulator that was developed at the Electronics Research Laboratory of the University of California, Berkeley [6]. In 1975, SPICE

Material Modeling for Terminal Ballistic Simulation

DTIC Science & Technology

1992-09-01

DYNA-3D-a nonlinear, explicit, three-dimensional finite element code for solid and structural mechanics- user manual. Technical Report UCRL -MA...Rep. UCRL -50108, Rev. 1, Lawrence Livermore Laboratory, 1977. [34] S. P. Marsh. LASL Shock Hugoniot Data. University of California Press, Berkeley, CA...Steinberg. Equation of state and strength properties of selected ma- teriaJs. Tech. Rep. UCRL -MA-106439, Lawrence Livermore National Labo- ratory, 1991. [371

In Conversation With Materials Scientist Ron Zuckermann

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ron Zuckerman

2009-11-18

Nov. 11, 2009: Host Alice Egan of Berkeley Lab's Materials Sciences Division interviews scientists about their lives and work in language everyone can understand. Her guest Berkeley Lab's Ron Zuckerman, who discusses biological nanostructures and the world of peptoids.

Early Geologic Education in California--Berkeley and Stanford Show the Way.

ERIC Educational Resources Information Center

Norris, Robert M.

1981-01-01

Traces the early history of geological education in California universities, with emphasis upon programs at Berkeley and Stanford. Among the pioneers in the field were Joseph LeConte, Andrew C. Lawson, and John C. Branner. (WB)

In Conversation With Materials Scientist Ron Zuckermann

ScienceCinema

Ron Zuckerman

2017-12-09

Nov. 11, 2009: Host Alice Egan of Berkeley Lab's Materials Sciences Division interviews scientists about their lives and work in language everyone can understand. Her guest Berkeley Lab's Ron Zuckerman, who discusses biological nanostructures and the world of peptoids.

1985 VGP Awards

NASA Astrophysics Data System (ADS)

Carmichael, I. S. E.; Hildreth, Wes; Peterson, Donald W.; Fisher, Richard; Schmincke, Hans-Ulrich

We are here to acknowledge Wes Hildreth's researches on silicic magmatism. His celebrated account of the Bishop Tuff, now eponymous, is the most extensively analyzed and influential rock mass since the Skaergaard intrusion and, for its detail and significance, has become the yardstick of silicic petrology; yet his study is less than 7 years old.Edward Wesley Hildreth III was born in 1938, and as the English would say, attended Harvard College in 1956. In 1961, he graduated cum laude with a major in geology, a minor in government, and a travelling scholarship to see the world. For the next 10 years he did so and became a naturalist in the U.S. National Park Service, with periods in Death Valley and in the Olympics. His “Death Valley Days” were to return, forthrough his love of the Panamint Ranges he met Mitch Reynolds, then an assistant professor at [the University of California] Berkeley, and in 1971 he arrived in Berkeley as a new graduate student, anxious and impatient to unravel the structure of the Panamints.

What is Supercomputing? A Conversation with Kathy Yelick

ScienceCinema

Yelick, Kathy

2017-12-11

In this highlight video, Jeff Miller, head of Public Affairs, sat down in conversation with Kathy Yelick, Associate Berkeley Lab Director, Computing Sciences, in the second of a series of "powerpoint-free" talks on July 18th 2012, at Berkeley Lab.

What is Supercomputing? A Conversation with Kathy Yelick

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yelick, Kathy

2012-07-23

In this highlight video, Jeff Miller, head of Public Affairs, sat down in conversation with Kathy Yelick, Associate Berkeley Lab Director, Computing Sciences, in the second of a series of "powerpoint-free" talks on July 18th 2012, at Berkeley Lab.

LBNL Computational ResearchTheory Facility Groundbreaking - Full Press Conference. Feb 1st, 2012

ScienceCinema

Yelick, Kathy

2018-01-24

Energy Secretary Steven Chu, along with Berkeley Lab and UC leaders, broke ground on the Lab's Computational Research and Theory (CRT) facility yesterday. The CRT will be at the forefront of high-performance supercomputing research and be DOE's most efficient facility of its kind. Joining Secretary Chu as speakers were Lab Director Paul Alivisatos, UC President Mark Yudof, Office of Science Director Bill Brinkman, and UC Berkeley Chancellor Robert Birgeneau. The festivities were emceed by Associate Lab Director for Computing Sciences, Kathy Yelick, and Berkeley Mayor Tom Bates joined in the shovel ceremony.

LBNL Computational Research and Theory Facility Groundbreaking. February 1st, 2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yelick, Kathy

2012-02-02

Energy Secretary Steven Chu, along with Berkeley Lab and UC leaders, broke ground on the Lab's Computational Research and Theory (CRT) facility yesterday. The CRT will be at the forefront of high-performance supercomputing research and be DOE's most efficient facility of its kind. Joining Secretary Chu as speakers were Lab Director Paul Alivisatos, UC President Mark Yudof, Office of Science Director Bill Brinkman, and UC Berkeley Chancellor Robert Birgeneau. The festivities were emceed by Associate Lab Director for Computing Sciences, Kathy Yelick, and Berkeley Mayor Tom Bates joined in the shovel ceremony.

LBNL Computational Research and Theory Facility Groundbreaking. February 1st, 2012

ScienceCinema

Yelick, Kathy

2017-12-09

Energy Secretary Steven Chu, along with Berkeley Lab and UC leaders, broke ground on the Lab's Computational Research and Theory (CRT) facility yesterday. The CRT will be at the forefront of high-performance supercomputing research and be DOE's most efficient facility of its kind. Joining Secretary Chu as speakers were Lab Director Paul Alivisatos, UC President Mark Yudof, Office of Science Director Bill Brinkman, and UC Berkeley Chancellor Robert Birgeneau. The festivities were emceed by Associate Lab Director for Computing Sciences, Kathy Yelick, and Berkeley Mayor Tom Bates joined in the shovel ceremony.

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeSantis, Todd

Scientists at Berkeley Lab and the University of California, Merced are using an innovative DNA array developed at Berkeley Lab to catalog the microbes that live among coral in the tropical waters off the coast of Puerto Rico. More info: http://newscenter.lbl.gov/feature-stories/2009/02/02/coral-reefs/

Smart parking Value Pricing Pilot Project (VPPP) on the COASTER commuter rail line in San Diego, California.

DOT National Transportation Integrated Search

2012-03-01

This study provides a report on the Smart Parking Pilot, which was a partnership among the California Department of Transportation (Caltrans); the Institute of Transportation Studies- Berkeley's (ITS-Berkeley) Transportation Sustainability Research C...

77 FR 75639 - National Cancer Institute Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-21

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Cancer Institute... Proposed Frederick National Laboratory for Cancer Research Strategic Plan. Place: The Lawrence Berkeley..., Berkeley, CA 94720. Contact Person: Thomas M. Vollberg, Sr., Ph.D., Executive Secretary, National Cancer...

Carbon Smackdown: Smart Windows (LBNL Summer Lecture Series)

ScienceCinema

Milliron, Delia; Selkowitz, Stephen

2017-12-09

August 3, 2010 Berkeley Lab talk: In the fourth of five Carbon Smackdown matches, Berkeley Lab researchers Delia Milliron of the Materials Sciences Division and Stephen Selkowitz of the Environmental Energy Technologies Division talk about their work on energy-saving smart windows.

Hand-Held UXO Discriminator

DTIC Science & Technology

2010-04-01

structure design showed that we could achieve both of these goals with a 14-in (0.35 m) sensor cube. To avoid the reliance on accurate multiple...differenced pair receiver. 4. Conclusions We have designed and built a sensor package of a 14-in (0.35 m) cube based on the...funding (UX-1225, MM-0437, and MM-0838), we have successfully designed and built a cart-mounted Berkeley UXO Discriminator (BUD) and demonstrated its

Earphone English.

ERIC Educational Resources Information Center

Goldsmith, Francisca

2002-01-01

Describes Earphone English, a student club sponsored through a partnership between Berkeley High School and the Berkeley Public Library that offers students whose primary language is not English to practice their spoken and aural English skills. Discusses the audiobooks used in the program and the importance of multicultural content and age…

The Universe Adventure - Credits

Science.gov Websites

Basel), and George Smoot (LBNL) Content, Graphic/Web Design Artie Konrad (student, UC Berkeley) 2004 Berkeley) Laurie Kerrigan (teacher, Mercy High School) Graphic/Web Design Melissa McClure (student ) Graphic/Web Design Paul Higgins (student, Contra Costa College) Other Gordon Aubrecht (Ohio State

Reimagining Educational Research: A Conversation

ERIC Educational Resources Information Center

Carter, Prudence L.; Nasir, Na'ilah Suad

2017-01-01

The following is a transcript of an interview between the Dean of the University of California (UC) Berkeley's Graduate School of Education, Prudence Carter, and UC Berkeley's outgoing Vice Chancellor for Equity and Inclusion, Na'ilah Suad Nasir, recorded at the 2017 Graduate School of Education Research Day.

Alessandra Lanzara

Science.gov Websites

Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Search MSD Go MSD - Materials Investigators Division Staff Facilities and Centers Staff Jobs Safety Personnel Resources Committees In Case of ; Finance Templates Travel One-Stop Investigators Division Staff Facilities and Centers Staff Jobs

Obtaining Parts

Science.gov Websites

The Cosmic Connection Parts for the Berkeley Detector Suppliers: Scintillator Eljen Technology 1 obtain the components needed to build the Berkeley Detector. These companies have helped previous the last update. He estimates that the cost to build a detector varies from $1500 to $2700 depending

NIEHS/EPA CEHCs: Berkeley/Stanford Children's Environment Health Center - UC Berkeley

EPA Pesticide Factsheets

The goal of this Center is to better understand the effects of exposure in the womb to air pollutants and airborne bacteria on newborn health, immune system health during childhood, and to understand the relationship of these early-life exposures to asthma

Berkeley Lab's Saul Perlmutter Wins the Einstein Medal | Berkeley Lab

Science.gov Websites

TAGS: awards, cosmology and astrophysics, physics Connect twitter instagram LinkedIn facebook youtube Physics + Cosmology Chemistry + Materials Sciences twitter instagram LinkedIn facebook youtube A U.S Privacy & Security Notice twitter instagram LinkedIn facebook youtube

Taxi Regulatory Revision in Oakland and Berkeley, California : Two Case Studies

DOT National Transportation Integrated Search

1983-06-01

A case study was performed of regulatory changes pertaining to taxicabs in Oakland and neighboring Berkeley, CA. In Oakland rates were approximately doubled and limits on the number of taxi permits removed. Companies were allowed to levy a per-trip s...

40 CFR 81.341 - South Carolina.

Code of Federal Regulations, 2012 CFR

2012-07-01

... County X Anderson County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun... County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun County X... Calhoun County Charleston County Cherokee County Chester County Chesterfield County Clarendon County...

40 CFR 81.341 - South Carolina.

Code of Federal Regulations, 2013 CFR

2013-07-01

... County X Anderson County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun... County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun County X... Calhoun County Charleston County Cherokee County Chester County Chesterfield County Clarendon County...

Comprehensive facilities plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1997-09-01

The Ernest Orlando Lawrence Berkeley National Laboratory`s Comprehensive Facilities Plan (CFP) document provides analysis and policy guidance for the effective use and orderly future development of land and capital assets at the Berkeley Lab site. The CFP directly supports Berkeley Lab`s role as a multiprogram national laboratory operated by the University of California (UC) for the Department of Energy (DOE). The CFP is revised annually on Berkeley Lab`s Facilities Planning Website. Major revisions are consistent with DOE policy and review guidance. Facilities planing is motivated by the need to develop facilities for DOE programmatic needs; to maintain, replace and rehabilitatemore » existing obsolete facilities; to identify sites for anticipated programmatic growth; and to establish a planning framework in recognition of site amenities and the surrounding community. The CFP presents a concise expression of the policy for the future physical development of the Laboratory, based upon anticipated operational needs of research programs and the environmental setting. It is a product of the ongoing planning processes and is a dynamic information source.« less

A QUANTITATIVE ANALYSIS OF DISTANT OPEN CLUSTERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janes, Kenneth A.; Hoq, Sadia

2011-03-15

The oldest open star clusters are important for tracing the history of the Galactic disk, but many of the more distant clusters are heavily reddened and projected against the rich stellar background of the Galaxy. We have undertaken an investigation of several distant clusters (Berkeley 19, Berkeley 44, King 25, NGC 6802, NGC 6827, Berkeley 52, Berkeley 56, NGC 7142, NGC 7245, and King 9) to develop procedures for separating probable cluster members from the background field. We next created a simple quantitative approach for finding approximate cluster distances, reddenings, and ages. We first conclude that with the possible exceptionmore » of King 25 they are probably all physical clusters. We also find that for these distant clusters our typical errors are about {+-}0.07 in E(B - V), {+-}0.15 in log(age), and {+-}0.25 in (m - M){sub o}. The clusters range in age from 470 Myr to 7 Gyr and range from 7.1 to 16.4 kpc from the Galactic center.« less

What's Right with Kansas? (LBNL Science at the Theater)

ScienceCinema

Fuller, Merrian; Jackson, Nancy

2018-06-20

On Monday, Oct. 3 at 7 p.m. in Berkeley's Repertory Theater, the Lab presented "What's Right with Kansas," an evening of conversation with the Kansas-based Climate and Energy Project's founder and board chair, Nancy Jackson, and Berkeley Lab scientist Merrian Fuller, an electricity-market, policy and consumer behavior expert. Berkeley Lab will also debut its video "Common Ground," which showcases how CEP has become a Kansas mainstay and an inspiration to environmental organizations across the country. In a state rife with climate-change skepticism, CEP has changed behavior, and some minds, by employing rural values of thrift, independence, conservation, and friendly competition to promote energy efficiency.

A Window into Longer Lasting Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2016-11-29

There’s a new tool in the push to engineer rechargeable batteries that last longer and charge more quickly. An X-ray microscopy technique recently developed at Berkeley Lab has given scientists the ability to image nanoscale changes inside lithium-ion battery particles as they charge and discharge. The real-time images provide a new way to learn how batteries work, and how to improve them. The method was developed at Berkeley Lab’s Advanced Light Source, a DOE Office of Science User Facility, by a team of researchers from the Department of Energy’s SLAC National Accelerator Laboratory, Berkeley Lab, Stanford University, and other institutions.

Maria Lucia Ghirardi | NREL

Science.gov Websites

/pathways Education University of California, Berkeley: Ph.D. in Comparative Biochemistry, 1988. Graduate advisor: Dr. Anastasios Melis University of California, Berkeley: M.A. in Comparative Biochemistry, 1983 ); pp. 35192-35209. Wecker, M., Meuser, J., Posewitz, M. and Ghirardi, M. (2011). "Design of a new

Interviews with Exemplary Teachers: Leon F. Litwack.

ERIC Educational Resources Information Center

Rosenzweig, Roy

2001-01-01

Presents an interview with Leon F. Litwack, a professor of U.S. history at the University of California, Berkeley. Covers topics such as what led him to teaching history, his lectures at Berkeley, themes covered in his U.S. history surveys, and his perception of good teaching. (CMK)

New Tech Measures Artery Health: Engevity Cuff

ScienceCinema

Maltz, Jonathan

2018-05-22

Jonathan Maltz, a Berkeley Lab scientist in the Molecular Biophysics and Integrated Bioimaging division, explains a new technology developed at Berkeley Lab that could soon make detecting the process of plaque buildup in vessels a routine part of a visit to the doctor and, perhaps, home healthcare settings.

Free Speech Advocates at Berkeley.

ERIC Educational Resources Information Center

Watts, William A.; Whittaker, David

1966-01-01

This study compares highly committed members of the Free Speech Movement (FSM) at Berkeley with the student population at large on 3 sociopsychological foci: general biographical data, religious orientation, and rigidity-flexibility. Questionnaires were administered to 172 FSM members selected by chance from the 10 to 1200 who entered and…

Berkeley Bravado: Rochdale Village, University of California, Berkeley

ERIC Educational Resources Information Center

Woodbridge, Sally

1975-01-01

Rochdale Village is a successful example of active student participation in the design and construction of student housing. The apartment complex reflects students' desire for a village of lowrise, wood-shingled buildings, while meeting the University of California's density requirement of 250 units per acre. (JG)

New Tech Measures Artery Health: Engevity Cuff

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maltz, Jonathan

2016-05-19

Jonathan Maltz, a Berkeley Lab scientist in the Molecular Biophysics and Integrated Bioimaging division, explains a new technology developed at Berkeley Lab that could soon make detecting the process of plaque buildup in vessels a routine part of a visit to the doctor and, perhaps, home healthcare settings.

Next Generation Lighting Technologies (LBNL Summer Lecture Series)

ScienceCinema

Siminovittch, Micheal

2018-04-27

For the past several years, Michael Siminovittch, a researcher in the Environmental Energy Technologies Division of Lawrence Berkeley National Laboratory, has worked to package efficient lighting in an easy-to-use and good-looking lamp. His immensely popular "Berkeley Lamp" has redefined how America lights its offices.

Multiple Landslide-Hazard Scenarios Modeled for the Oakland-Berkeley Area, Northern California

USGS Publications Warehouse

Pike, Richard J.; Graymer, Russell W.

2008-01-01

With the exception of Los Angeles, perhaps no urban area in the United States is more at risk from landsliding, triggered by either precipitation or earthquake, than the San Francisco Bay region of northern California. By January each year, seasonal winter storms usually bring moisture levels of San Francisco Bay region hillsides to the point of saturation, after which additional heavy rainfall may induce landslides of various types and levels of severity. In addition, movement at any time along one of several active faults in the area may generate an earthquake large enough to trigger landslides. The danger to life and property rises each year as local populations continue to expand and more hillsides are graded for development of residential housing and its supporting infrastructure. The chapters in the text consist of: *Introduction by Russell W. Graymer *Chapter 1 Rainfall Thresholds for Landslide Activity, San Francisco Bay Region, Northern California by Raymond C. Wilson *Chapter 2 Susceptibility to Deep-Seated Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Richard J. Pike and Steven Sobieszczyk *Chapter 3 Susceptibility to Shallow Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Kevin M. Schmidt and Steven Sobieszczyk *Chapter 4 Landslide Hazard Modeled for the Cities of Oakland, Piedmont, and Berkeley, Northern California, from a M=7.1 Scenario Earthquake on the Hayward Fault Zone by Scott B. Miles and David K. Keefer *Chapter 5 Synthesis of Landslide-Hazard Scenarios Modeled for the Oakland-Berkeley Area, Northern California by Richard J. Pike The plates consist of: *Plate 1 Susceptibility to Deep-Seated Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Richard J. Pike, Russell W. Graymer, Sebastian Roberts, Naomi B. Kalman, and Steven Sobieszczyk *Plate 2 Susceptibility to Shallow Landsliding Modeled for the Oakland-Berkeley Area, Northern California by Kevin M. Schmidt and Steven Sobieszczyk *Plate 3 Susceptibility to Shallow Landsliding Modeled for the Cities of Oakland and Piedmont Northern California by Kevin M. Schmidt and Steven Sobieszczyk *Plate 4 Seismic Landslide Hazard Modeled for the Cities of Oakland, Piedmont, and Berkeley, Northern California by Scott B. Miles and David K. Keefer III The relative hazard for each of several landslide scenarios is presented as a geospatial database. This publication includes ARC/INFO (Environmental Systems Research Institute, http://www.esri.com) version 8.1.2 grids and associated tables and four text files of FGDC-compliant metadata for each grid.

Higher Retail Prices of Sugar-Sweetened Beverages 3 Months After Implementation of an Excise Tax in Berkeley, California

PubMed Central

Rojas, Nadia; Grummon, Anna H.; Madsen, Kristine A.

2015-01-01

Objectives. We assessed the short-term ability to increase retail prices of the first US 1-cent-per-ounce excise tax on the distribution of sugar-sweetened beverages (SSBs), which was implemented in March 2015 by Berkeley, California. Methods. In 2014 and 2015, we examined pre- to posttax price changes of SSBs and non-SSBs in a variety of retailers in Berkeley and in the comparison cities Oakland and San Francisco, California. We examined price changes by beverage, brand, size, and retailer type. Results. For smaller beverages (≤ 33.8 oz), price increases (cents/oz) in Berkeley relative to those in comparison cities were 0.69 (95% confidence interval [CI] = 0.36, 1.03) for soda, 0.47 (95% CI = 0.08, 0.87) for fruit-flavored beverages, and 0.47 (95% CI = 0.25, 0.69) for SSBs overall. For 2-liter bottles and multipacks of soda, relative price increases were 0.46 (95% CI = 0.03, 0.89) and 0.49 (95% CI = 0.21, 0.77). We observed no relative price increases for nontaxed beverages overall. Conclusions. Approximately 3 months after the tax was implemented, SSB retail prices increased more in Berkeley than in nearby cities, marking a step in the causal pathway between the tax and reduced SSB consumption. PMID:26444622

Documentation for a web site to serve ULF-EM (Ultra-Low Frequency Electromagnetic) data to the public

USGS Publications Warehouse

Neumann, Danny A.; McPherson, Selwyn; Klemperer, Simon L.; Glen, Jonathan M.G.; McPhee, Darcy K.; Kappler, Karl

2011-01-01

The Stanford Ultra-Low Frequency Electromagnetic (ULF-EM) Monitoring Project is recording naturally varying electromagnetic signals adjacent to active earthquake faults, in an attempt to establish whether there is any variation in these signals associated with earthquakes. Our project is collaborative between Stanford University, the U.S. Geological Survey (USGS), and UC Berkeley. Lead scientists are Simon Klemperer (Stanford University), Jonathan Glen (USGS) and Darcy Karakelian McPhee (USGS). Our initial sites are in the San Francisco Bay Area, monitoring different strands of the San Andreas fault system, at Stanford University's Jasper Ridge Biological Preserve (JRSC), Marin Headlands of the Golden Gate National Recreation Area (MHDL), and the UC Berkeley's Russell Reservation Field Station adjacent to Briones Regional Park (BRIB). In addition, we maintain in conjunction with the Berkeley Seismological Laboratory (BSL) two remote reference stations at the Bear Valley Ranch in Parkfield, Calif., (PKD) and the San Andreas Geophysical Observatory at Hollister, Calif., (SAO). Metadata about our site can be found at http://ulfem-data.stanford.edu/info.html. Site descriptions can be found at the BSL at http://seismo.berkeley.edu/, and seismic data can be obtained from the Northern California Earthquake Data Center at http://www.ncedc.org/. The site http://ulfem-data.stanford.edu/ allows access to data from the Stanford-USGS sites JRSC, MHDL and BRIB, as well as UC Berkeley sites PKD and SAO.

Higher Retail Prices of Sugar-Sweetened Beverages 3 Months After Implementation of an Excise Tax in Berkeley, California.

PubMed

Falbe, Jennifer; Rojas, Nadia; Grummon, Anna H; Madsen, Kristine A

2015-11-01

We assessed the short-term ability to increase retail prices of the first US 1-cent-per-ounce excise tax on the distribution of sugar-sweetened beverages (SSBs), which was implemented in March 2015 by Berkeley, California. In 2014 and 2015, we examined pre- to posttax price changes of SSBs and non-SSBs in a variety of retailers in Berkeley and in the comparison cities Oakland and San Francisco, California. We examined price changes by beverage, brand, size, and retailer type. For smaller beverages (≤ 33.8 oz), price increases (cents/oz) in Berkeley relative to those in comparison cities were 0.69 (95% confidence interval [CI] = 0.36, 1.03) for soda, 0.47 (95% CI = 0.08, 0.87) for fruit-flavored beverages, and 0.47 (95% CI = 0.25, 0.69) for SSBs overall. For 2-liter bottles and multipacks of soda, relative price increases were 0.46 (95% CI = 0.03, 0.89) and 0.49 (95% CI = 0.21, 0.77). We observed no relative price increases for nontaxed beverages overall. Approximately 3 months after the tax was implemented, SSB retail prices increased more in Berkeley than in nearby cities, marking a step in the causal pathway between the tax and reduced SSB consumption.

Berkeley Lab Wins Seven 2015 R&D 100 Awards | Berkeley Lab

Science.gov Websites

products from industry, academia, and government-sponsored research, ranging from chemistry to materials to problems in metrology techniques: the quantitative characterization of the imaging instrumentation Computational Research Division led the development of the technology. Sensor Integrated with Recombinant and

PhyloChip Tackles Coral Disease

ScienceCinema

DeSantis, Todd

2017-12-13

Scientists at Berkeley Lab and the University of California, Merced are using an innovative DNA array developed at Berkeley Lab to catalog the microbes that live among coral in the tropical waters off the coast of Puerto Rico. More info: http://newscenter.lbl.gov/feature-stories/2009/02/02/coral-reefs/

Teaching at Berkeley: A Guide for Foreign Teaching Assistants.

ERIC Educational Resources Information Center

Cohen, Robby, Ed.; Robin, Ron, Ed.

A handbook for foreign teaching assistants (TAs) is presented by foreign graduate students with teaching experience and other educators who have worked closely with them. Language skills, teaching strategies, cultural issues, resources, and the environment at the University of California, Berkeley, are addressed in 16 articles. Article titles and…

Improved Cosmological Constraints from New, Old, and Combined Supernova

Science.gov Websites

Data Set SAO/NASA ADS Astronomy Abstract Service Title: Improved Cosmological Constraints from , Harvard University, 60 Garden Street, Cambridge, MA 02138), AK(Department of Astronomy and Astrophysics Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720), BI(Department of Physics and Astronomy

Computerized Serial Processing System at the University of California, Berkeley

ERIC Educational Resources Information Center

Silberstein, Stephen M.

1975-01-01

The extreme flexibility of the MARC format coupled with the simplicity of a batch-oriented processing system centered around a sequential master file has enabled the University of California, Berkeley, library to gradually build an unusually large serials data base in support of both technical and public services. (Author)

The Universe Adventure - Help

Science.gov Websites

teachers introduce the material to their students. Clicking the link will open another window with activity ideas or worksheets to download. The number of stars next to the activity name indicates how difficult . Bechtel, Jr. Foundation [ Site Map ] optimized for Firefox [ UC Berkeley ] [ UC Berkeley Physics

The Berkeley Environmental Simulation Laboratory: Its Use In Environmental Impact Assessment.

ERIC Educational Resources Information Center

Appleyard, Donald; And Others

An environmental simulation laboratory at the University of California, Berkeley, is testing the adequacy of different techniques for simulating environmental experiences. Various levels of realism, with various costs, are available in different presentation modes. The simulations can aid in communication about and the resolution of environmental…

The Ph.D. Production Function: The Case at Berkeley.

ERIC Educational Resources Information Center

Breneman, David W.

This report analyzes departmental variations in time to degree and attrition in Ph.D. programs at Berkeley. An alternative hypothesis, the Ph.D. production function, is examined by cross-section econometric analysis of 28 departments. The inputs included in the production function were student variables--quality and percent males; faculty…

Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization.

PubMed

Sugita, Chieko; Ogata, Koretsugu; Shikata, Masamitsu; Jikuya, Hiroyuki; Takano, Jun; Furumichi, Miho; Kanehisa, Minoru; Omata, Tatsuo; Sugiura, Masahiro; Sugita, Mamoru

2007-01-01

The entire genome of the unicellular cyanobacterium Synechococcus elongatus PCC 6301 (formerly Anacystis nidulans Berkeley strain 6301) was sequenced. The genome consisted of a circular chromosome 2,696,255 bp long. A total of 2,525 potential protein-coding genes, two sets of rRNA genes, 45 tRNA genes representing 42 tRNA species, and several genes for small stable RNAs were assigned to the chromosome by similarity searches and computer predictions. The translated products of 56% of the potential protein-coding genes showed sequence similarities to experimentally identified and predicted proteins of known function, and the products of 35% of the genes showed sequence similarities to the translated products of hypothetical genes. The remaining 9% of genes lacked significant similarities to genes for predicted proteins in the public DNA databases. Some 139 genes coding for photosynthesis-related components were identified. Thirty-seven genes for two-component signal transduction systems were also identified. This is the smallest number of such genes identified in cyanobacteria, except for marine cyanobacteria, suggesting that only simple signal transduction systems are found in this strain. The gene arrangement and nucleotide sequence of Synechococcus elongatus PCC 6301 were nearly identical to those of a closely related strain Synechococcus elongatus PCC 7942, except for the presence of a 188.6 kb inversion. The sequences as well as the gene information shown in this paper are available in the Web database, CYORF (http://www.cyano.genome.jp/).

Dynamic Geometry Capture with a Multi-View Structured-Light System

DTIC Science & Technology

2014-12-19

funding was never a problem during my studies . One of the best parts of my time at UC Berkeley has been working with colleagues within the Video and...scientific and medical applications such as quantifying improvement in physical therapy and measuring unnatural poses in ergonomic studies . Specifically... cases with limited scene texture. This direct generation of surface geometry provides us with a distinct advantage over multi-camera based systems. For

Blasting Rocks and Blasting Cars: Applied Engineering (LBNL Summer Lecture Series)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hopkins, Deborah

2004-06-30

Summer Lecture Series 2004: Deb Hopkins works with industries like automobile, mining and paper to improve their evaluation and measuring techniques. For several years, she has coordinated a program at Berkeley Lab funded under the Partnership for a New Generation of Vehicles, a collaboration between the federal government and the U.S. Council for Automotive Research. Nondestructive evaluation techniques to test a car's structural integrity are being developed for auto assembly lines.

Blasting Rocks and Blasting Cars: Applied Engineering (LBNL Summer Lecture Series)

ScienceCinema

Hopkins, Deborah [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Engineering Division

2017-12-09

Summer Lecture Series 2004: Deb Hopkins works with industries like automobile, mining and paper to improve their evaluation and measuring techniques. For several years, she has coordinated a program at Berkeley Lab funded under the Partnership for a New Generation of Vehicles, a collaboration between the federal government and the U.S. Council for Automotive Research. Nondestructive evaluation techniques to test a car's structural integrity are being developed for auto assembly lines.

Accessing northern California earthquake data via Internet

NASA Astrophysics Data System (ADS)

Romanowicz, Barbara; Neuhauser, Douglas; Bogaert, Barbara; Oppenheimer, David

The Northern California Earthquake Data Center (NCEDC) provides easy access to central and northern California digital earthquake data. It is located at the University of California, Berkeley, and is operated jointly with the U.S. Geological Survey (USGS) in Menlo Park, Calif., and funded by the University of California and the National Earthquake Hazard Reduction Program. It has been accessible to users in the scientific community through Internet since mid-1992.The data center provides an on-line archive for parametric and waveform data from two regional networks: the Northern California Seismic Network (NCSN) operated by the USGS and the Berkeley Digital Seismic Network (BDSN) operated by the Seismographic Station at the University of California, Berkeley.

Fracture trace map and single-well aquifer test results in a carbonate aquifer in Berkeley County, West Virginia

USGS Publications Warehouse

McCoy, Kurt J.; Podwysocki, Melvin H.; Crider, E. Allen; Weary, David J.

2005-01-01

These data contain information on the results of single-well aquifer tests, lineament analysis, and a bedrock geologic map compilation for the low-lying carbonate and shale areas of eastern Berkeley County, West Virginia. Efforts have been initiated by management agencies of Berkeley County in cooperation with the U.S. Geological Survey to further the understanding of the spatial distribution of fractures in the carbonate regions and their correlation with aquifer properties. This report presents transmissivity values from about 200 single-well aquifer tests and a map of fracture-traces determined from aerial photos and field investigations. Transmissivity values were compared to geologic factors possibly affecting its magnitude.

A community of scientists: cultivating scientific identity among undergraduates within the Berkeley Compass Project

NASA Astrophysics Data System (ADS)

Aceves, Ana V.; Berkeley Compass Project

2015-01-01

The Berkeley Compass Project is a self-formed group of graduate and undergraduate students in the physical sciences at UC Berkeley. Our goals are to improve undergraduate physics education, provide opportunities for professional development, and increase retention of students from populations typically underrepresented in the physical sciences. For students who enter as freshmen, the core Compass experience consists of a summer program and several seminar courses. These programs are designed to foster a diverse, collaborative student community in which students engage in authentic research practices and regular self-reflection. Compass encourages undergraduates to develop an identity as a scientist from the beginning of their university experience.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Eric Cornell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cornell, Eric

2008-08-30

Eric Cornell presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Kurt Gibble

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibble, Kurt

2008-08-30

Kurt Gibble presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Jay Keasling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keasling, Jay

2008-08-30

Jay Keasling presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman

ScienceCinema

Wieman, Carl

2017-12-09

Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Berkeley Lab - Materials Sciences Division

Science.gov Websites

; Finance Templates Travel One-Stop Personnel Resources Committees In Case of Emergency Looking for MSD0010 Officer Mary Gross MCGross@lbl.gov Research Group Representatives Group Rep Ager Rachel Woods-Robinson Somorjai (see Salmeron Group) Yaghi Xiaokun Pei xiaokun_pei@berkeley.edu Zhang Sui Yang SuiYang@lbl.gov

Carbon Flux Explorers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bishop, Jim

Jim Bishop, senior scientist at Berkeley Lab and professor at UC Berkeley, is leading a project to deploy robotic floats that provide data on how microorganisms sequester carbon in the ocean. He recently led a research team on a 10-day voyage, funded by the National Science Foundation, to put the Carbon Flux Explorers to the test.

Care for Our Children: A Comprehensive Plan for Child Care Services in Berkeley.

ERIC Educational Resources Information Center

Pacific Training and Technical Assistance Corp., Berkeley, CA.

This document reports research and recommendations made by the Pacific Training and Technical Assistance Corporation for a comprehensive child-care program in Berkeley. The report is divided into two sections. Section I, "Research and Planning," describes research methodology and findings and includes demographic information on the city…

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Eric Cornell

ScienceCinema

Cornell, Eric

2018-02-05

Eric Cornell presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Neighborhood organization activities: evacuation drills, clusters, and fire safety awareness

Treesearch

Dick White

1995-01-01

Emergency preparedness activities of one Berkeley-Oakland Hills neighborhood at the wildland/urban interface include establishing clusters that reduce fire hazards and fuel loads, setting aside emergency supplies, and identifying evacuation routes; taking emergency preparedness courses from the Offices of Emergency Services of Berkeley and Oakland (the CERT and CORE...

Ting Xu

Science.gov Websites

California, Berkeley tingxu@berkeley.edu 510-642-1632 Research profile » A U.S. Department of Energy National Laboratory Operated by the University of California UC logo Questions & Comments * Privacy Computational Study of Excited-State Phenomena in Energy Materials Center for X-ray Optics MSD Facilities Ion

Electron Microscope Center Opens at Berkeley.

ERIC Educational Resources Information Center

Robinson, Arthur L.

1981-01-01

A 1.5-MeV High Voltage Electron Microscope has been installed at the Lawrence Berkeley Laboratory which will help materials scientists and biologists study samples in more true-to-life situations. A 1-MeV Atomic Resolution Microscope will be installed at the same location in two years which will allow scientists to distinguish atoms. (DS)

Energy Efficient Buildings and Appliances: From Berkeley Lab to the Marketplace (LBNL Summer Lecture Series)

ScienceCinema

Rosenfeld, Art [California Energy Commission, Sacramento, CA (United States)

2018-02-16

Summer Lecture Series 2006: Art Rosenfeld, an appointee to the California Energy Commission and one of the architects of energy efficiency research at Berkeley Lab in the 1970s, discusses what it takes to shepherd innovative energy efficiency research from the lab to the real world.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Jay Keasling

ScienceCinema

Keasling, Jay

2018-02-14

Jay Keasling presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

A CAT scan for cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2009-01-01

Recently, a team of scientists from Berkeley Lab, Stanford University, and the University of California, San Francisco used Berkeley Lab's National Center for X-ray Tomography to capture the changes that occur when Candida albicans is exposed to a new and promising antifungal therapy. http://newscenter.lbl.gov/feature-stories/2009/12/10/cat-scan-cells/

Carbon Smackdown: Cookstoves for the developing world

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ashok Gadgil, Kayje Booker, and Adam Rausch

2010-07-07

In this June 30, 2010 Berkeley Lab summer lecture, learn how efficient cookstoves for the developing world — from Darfur to Ethiopia and beyond — are reducing carbon dioxide emissions, saving forests, and improving health. Berkeley Lab's Ashok Gadgil, Kayje Booker, and Adam Rausch discuss why they got started in this great challenge and what's next.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wieman, Carl

Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

In Search of Good Governance

ERIC Educational Resources Information Center

Grush, Mary

2007-01-01

Since his retirement in 2005, UC-Berkeley's Associate Vice Chancellor and CIO Emeritus and current ECAR fellow John (Jack) McCredie has devoted much of his professional energy to studying and writing/speaking about IT governance and leadership in higher education. In his role at UC-Berkeley, he was responsible for leading central IT support for…

Carbon Flux Explorers

ScienceCinema

Bishop, Jim

2018-06-12

Jim Bishop, senior scientist at Berkeley Lab and professor at UC Berkeley, is leading a project to deploy robotic floats that provide data on how microorganisms sequester carbon in the ocean. He recently led a research team on a 10-day voyage, funded by the National Science Foundation, to put the Carbon Flux Explorers to the test.

Undergraduate Research Participation at the University of California, Berkeley. Research & Occasional Paper Series: CSHE.17.08

ERIC Educational Resources Information Center

Berkes, Elizabeth

2008-01-01

Although the University of California, Berkeley has increased efforts to involve undergraduates in scientific research, little data exists regarding the number of undergraduate researchers. The University of California Undergraduate Experience Survey (UCUES) presents an opportunity to investigate the extent of undergraduate research involvement at…

The Berkeley Puppet Interview: A Screening Instrument for Measuring Psychopathology in Young Children

ERIC Educational Resources Information Center

Stone, Lisanne L.; van Daal, Carlijn; van der Maten, Marloes; Engels, Rutger C. M. E.; Janssens, Jan M. A. M.; Otten, Roy

2014-01-01

Background: While child self-reports of psychopathology are increasingly accepted, little standardized instruments are utilized for these practices. The Berkeley Puppet Interview (BPI) is an age-appropriate instrument for self-reports of problem behavior by young children. Objective: Psychometric properties of the Dutch version of the BPI will be…

"A Woman's World": The University of California, Berkeley, during the Second World War

ERIC Educational Resources Information Center

Dorn, Charles

2008-01-01

During World War II, female students at the University of California, Berkeley--then the most populous undergraduate campus in American higher education--made significant advances in collegiate life. In growing numbers, women enrolled in male-dominated academic programs, including mathematics, chemistry, and engineering, as they prepared for…

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Kurt Gibble

ScienceCinema

Gibble, Kurt

2018-02-05

Kurt Gibble presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

A Radiation Homeland Security Workshop Presented to the City of Berkeley Fire Department

NASA Astrophysics Data System (ADS)

Matis, Howard

2005-04-01

A radiation incident in a community, ranging from a transportation accident to a dirty bomb, is expected to be rare, but still can occur. First responders to such an incident must be prepared. City of Berkeley officials met with members of the Lawrence Berkeley National Laboratory staff and agreed that the laboratory participants would create material and teach it to all of their fire fighting staff. To design such a course, nuclear physicists, biologists and health physicists merged some of their existing teaching material together with previous homeland security efforts to produce a course that lasted one full day. The material was designed to help alleviate the myths and fear of radiation experienced by many first responders. It included basic nuclear physics information, biological effects, and methods that health physicists use to detect and handle radiation. The curriculum included several hands on activities which involved working directly with the meters the Berkeley Fire Department possessed. In addition, I will discuss some observations from teaching this course material plus some unusual problems that we encountered, such as suddenly the whole class responding to a fire.

Site Environmental Report for 2002, Volume 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pauer, Ron

2003-07-01

Each year, Ernest Orlando Lawrence Berkeley National Laboratory prepares an integrated report on its environmental programs to satisfy the requirements of United States Department of Energy Order 231.1. The ''Site Environmental Report for 2002'' summarizes Berkeley Lab's compliance with environmental standards and requirements, characterizes environmental management efforts through surveillance and monitoring activities, and highlights significant programs and efforts for calendar year 2002. Throughout this report, Ernest Orlando Lawrence Berkeley National Laboratory is referred to as ''Berkeley Lab,'' ''the Laboratory,'' ''Lawrence Berkeley National Laboratory,'' and ''LBNL.'' The report is separated into two volumes. Volume I contains a general overview of themore » Laboratory, the status of environmental programs, and summarized results from surveillance and monitoring activities. Volume II contains individual data results from the monitoring programs. This year, the ''Site Environmental Report'' was distributed on a CD in PDF format that includes Volume I, Volume II, and related documents. The report is also available on the Web at http://www.lbl.gov/ehs/esg/. The report follows the Laboratory's policy of using the International System of Units (SI), also known as the metric system of measurements. Whenever possible, results are additionally reported using the more conventional (non-SI) system of measurements because this system is referenced by some current regulatory standards and is more familiar to some readers. The tables included at the end of the Glossary are intended to help readers understand the various prefixes used with SI units of measurement and convert these units from one system to the other.« less

Site Environmental Report for 2002, Volume 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pauer, Ron

2003-07-01

Each year, Ernest Orlando Lawrence Berkeley National Laboratory prepares an integrated report on its environmental programs to satisfy the requirements of United States Department of Energy Order 231.1. The ''Site Environmental Report for 2002'' summarizes Berkeley Lab's compliance with environmental standards and requirements, characterizes environmental management efforts through surveillance and monitoring activities, and highlights significant programs and efforts for calendar year 2002. Throughout this report, Ernest Orlando Lawrence Berkeley National Laboratory is referred to as ''Berkeley Lab,'' ''the Laboratory,'' ''Lawrence Berkeley National Laboratory,'' and ''LBNL.'' The report is separated into two volumes. Volume I contains a general overview of themore » Laboratory, the status of environmental programs, and summarized results from surveillance and monitoring activities. Volume II contains individual data results from the monitoring programs. This year, the ''Site Environmental Report'' was distributed on a CD in PDF format that includes Volume I, Volume II, and related documents. The report is also available on the Web at http://www.lbl.gov/ehs/esg/. The report follows the Laboratory's policy of using the International System of Units (SI), also known as the metric system of measurements. Whenever possible, results are additionally reported using the more conventional (non-SI) system of measurements because this system is referenced by some current regulatory standards and is more familiar to some readers. The tables included at the end of the Glossary are intended to help readers understand the various prefixes used with SI units of measurement and convert these units from one system to the other.« less

VLA observations of unidentified Leiden-Berkeley Deep-Survey sources - Luminosity and redshift dependence of spectral properties

NASA Technical Reports Server (NTRS)

Kapahi, Vijay K.; Kulkarni, Vasant K.

1990-01-01

VLA observations of a complete subset of the Leiden-Berkeley Deep Survey sources that have S(1.4 GHz) greater than 10 mJy and are not optically identified down to F=22 mag are reported. By comparing the spectral and structural properties of the sources with samples from the literature, an attempt was made to disentangle the luminosity and redshift dependence of the spectral indices of extended emission in radio galaxies and of the incidence of compact steep-spectrum sources. It is found that the fraction of compact sources among those with a steep spectrum is related primarily to redshift, being much larger at high redshifts for sources of similar radio luminosity. Only a weak and marginally significant dependence of spectral indices of the extended sources on luminosity and redshift is found in samples selected at 1.4 and 2.7 GHz. It is pointed out that the much stronger correlation of spectral indices with luminosity may be arising partly from spectral curvature, and partly due to the preferential inclusion of very steep-spectrum sources from high redshift in low-frequency surveys.

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

PubMed

Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

2010-07-01

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

Balancing Power Absorption and Structural Loading for an Asymmetric Heave Wave-Energy Converter in Regular Waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tom, Nathan M.; Madhi, Farshad; Yeung, Ronald W.

2016-06-24

The aim of this paper is to maximize the power-to-load ratio of the Berkeley Wedge: a one-degree-of-freedom, asymmetrical, energy-capturing, floating breakwater of high performance that is relatively free of viscosity effects. Linear hydrodynamic theory was used to calculate bounds on the expected time-averaged power (TAP) and corresponding surge restraining force, pitch restraining torque, and power take-off (PTO) control force when assuming that the heave motion of the wave energy converter remains sinusoidal. This particular device was documented to be an almost-perfect absorber if one-degree-of-freedom motion is maintained. The success of such or similar future wave energy converter technologies would requiremore » the development of control strategies that can adapt device performance to maximize energy generation in operational conditions while mitigating hydrodynamic loads in extreme waves to reduce the structural mass and overall cost. This paper formulates the optimal control problem to incorporate metrics that provide a measure of the surge restraining force, pitch restraining torque, and PTO control force. The optimizer must now handle an objective function with competing terms in an attempt to maximize power capture while minimizing structural and actuator loads. A penalty weight is placed on the surge restraining force, pitch restraining torque, and PTO actuation force, thereby allowing the control focus to be placed either on power absorption or load mitigation. Thus, in achieving these goals, a per-unit gain in TAP would not lead to a greater per-unit demand in structural strength, hence yielding a favorable benefit-to-cost ratio. Demonstrative results in the form of TAP, reactive TAP, and the amplitudes of the surge restraining force, pitch restraining torque, and PTO control force are shown for the Berkeley Wedge example.« less

Laboratory directed research and development program FY 1997

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-03-01

This report compiles the annual reports of Laboratory Directed Research and Development projects supported by the Berkeley Lab. Projects are arranged under the following topical sections: (1) Accelerator and fusion research division; (2) Chemical sciences division; (3) Computing Sciences; (4) Earth sciences division; (5) Environmental energy technologies division; (6) life sciences division; (7) Materials sciences division; (8) Nuclear science division; (9) Physics division; (10) Structural biology division; and (11) Cross-divisional. A total of 66 projects are summarized.

Accelerating Exploitation of Low-grade Intelligence through Semantic Text Processing of Social Media

DTIC Science & Technology

2013-06-01

importance as an information source. The brevity of social media content (e.g., 140 characters per tweet) combined with the increasing usage of mobile...platform imports unstructured text from a variety of sources and then maps the text to an existing ontology of frames (FrameNet, https...framenet.icsi.berkeley.edu/fndrupal/) during a process of Semantic Role Labeling ( SRL ). FrameNet is a structured language model grounded in the theory of Frame

Nanofiber-Based Bulk-Heterojunction Organic Solar Cells Using Coaxial Electrospinning

DTIC Science & Technology

2012-01-01

chains are likely oriented with the [010] direction, perpendicular to the substrate, in the fi lm device. Glancing incidence X - ray diffraction (GIXD...Electron and X - ray diffraction measurements were per- formed in order to study the structural order in annealed fi bers and devices. For reference... angle X - ray scattering (SAXS/WAXS) beamline 7.3.3 of the Advanced Light Source at Lawrence Berkeley National Laboratory at 10 keV (1.24 Å) from a bend

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: Remarks from Steve Chu at the Scientific Symposium Held in his Honor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu, Steve

2008-08-30

Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize, presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium in his honor. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk from Leo Holberg and Allen Mills

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holberg, Leo; Mills, Allen

2008-08-30

Leo Holberg and Allen Mills present a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Carbon Smackdown: Cookstoves for the developing world

ScienceCinema

Ashok Gadgil, Kayje Booker, and Adam Rausch

2017-12-09

In this June 30, 2010 Berkeley Lab summer lecture, learn how efficient cookstoves for the developing world — from Darfur to Ethiopia and beyond — are reducing carbon dioxide emissions, saving forests, and improving health. Berkeley Lab's Ashok Gadgil, Kayje Booker, and Adam Rausch discuss why they got started in this great challenge and what's next.

Integration Defended: Berkeley Unified's Strategy to Maintain School Diversity

ERIC Educational Resources Information Center

Chavez, Lisa; Frankenberg, Erica

2009-01-01

In June 2007, the Supreme Court limited the tools that school districts could use to voluntarily integrate schools. In the aftermath of the decision, educators around the country have sought models of successful plans that would also be legal. One such model may be Berkeley Unified School District's (BUSD) plan. Earlier this year, the California…

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk from Leo Holberg and Allen Mills

ScienceCinema

Holberg, Leo; Mills, Allen

2018-05-07

Leo Holberg and Allen Mills present a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

A Proposal to Eliminate the SAT in Berkeley Admissions. Research & Occasional Paper Series: CSHE.4.16

ERIC Educational Resources Information Center

Geiser, Saul

2016-01-01

The SAT is used for two purposes at the University of California. First is "eligibility": Determining whether applicants meet the minimum requirements for admission to the UC system. Second is "admissions selection": At high-demand campuses such as Berkeley, with many more eligible applicants than places available, test scores…

For Berkeley's Sports Endowment, a Goal of $1-Billion

ERIC Educational Resources Information Center

Keller, Josh

2009-01-01

Most athletics programs, if forced to raise $300-million to renovate a football stadium, would not set an ambitious endowment goal at the same time. The University of California at Berkeley is trying to do both. The university's California Memorial Stadium sits directly over an earthquake fault: it needs a major seismic retrofit that will take…

The principle of phase stability and the accelerator program at Berkeley, 1945--1954

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lofgren, E.J.

1994-07-01

The discovery of the Principle of Phase Stability by Vladimir Veksler and Edwin McMillian and the end of the war released a surge of accelerator activity at the Lawrence Berkeley Laboratory (then The University of California Radiation Laboratory). Six accelerators incorporating the Principle of Phase Stability were built in the period 1945--1954.

VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF CHANNING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF CHANNING WAY VIEW OF 2401 PIEDMONT, ALPHA EPSILON PHI HOUSE BY RATCLIFF & RATCLIFF, 1958. SEEN FROM NW CORNER LOOKING SE. Photograph by Brian Grogan, July 8, 2007 - Piedmont Way & the Berkeley Property Tract, East of College Avenue between Dwight Way & U.C. Memorial Stadium, Berkeley, Alameda County, CA

Social Integration and School Violence in a Multiracial Northern High School.

ERIC Educational Resources Information Center

Marascuilo, Leonard A.; Dagenais, Fred

This study, conducted in Berkeley, California, was designed to test the hypothesis that socially integrated high school students would not be involved in interracial violence and conflict, while students who were socially isolated would. Data were collected by means of a questionnaire, sent to the 1970 graduating class of Berkeley High School,…

Berkeley Foundation for Opportunities in Information Technology: A Decade of Broadening Participation

ERIC Educational Resources Information Center

Crutchfield, Orpheus S. L.; Harrison, Christopher D.; Haas, Guy; Garcia, Daniel D.; Humphreys, Sheila M.; Lewis, Colleen M.; Khooshabeh, Peter

2011-01-01

The Berkeley Foundation for Opportunities in Information Technology is a decade-old endeavor to expose pre-college young women and underrepresented racial and ethnic minorities to the fields of computer science and engineering, and prepare them for rigorous, university-level study. We have served more than 150 students, and graduated more than 65…

VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF CHANNING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF CHANNING WAY. SEEN FROM SW CORNER TOWARDS 2395 PIEDMONT, SIGMA PI HOUSE BY FREDERICK H. REIMERS, 1928. LOOKING NORTH. Photograph by Brian Grogan, July 8, 2007 - Piedmont Way & the Berkeley Property Tract, East of College Avenue between Dwight Way & U.C. Memorial Stadium, Berkeley, Alameda County, CA

Martinsburg-Berkeley County Public Library, Final Performance Report for Library Services and Construction Act (LSCA) Title VI, Library Literacy Program.

ERIC Educational Resources Information Center

Hess, Therese M.

The Martinsburg-Berkeley County Public Library (West Virginia) conducted a project that involved recruitment, retention, coalition building, public awareness, training, basic literacy, collection development, tutoring, computer assisted, other technology, and English as a Second Language (ESL) programs. The project served a three-county community…

Berkeley Pact with a Swiss Company Takes Technology Transfer to a New Level.

ERIC Educational Resources Information Center

Blumenstyk, Goldie

1998-01-01

In search of increased support for graduate students in plant science and upgraded laboratories, the College of Plant and Microbial Biology, University of California Berkeley, offered the college's expertise in exchange for major financial backing from the single company making the best offer. The resulting five-year, $25-million alliance with one…

Berkeley Lab Scientist Co-Leads Breast Cancer Dream Team

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gray, Joe

2009-05-19

An $16.5 million, three-year grant to develop new and more effective therapies to fight breast cancer was awarded today to a multi-institutional Dream Team of scientists and clinicians that is co-led by Joe Gray, a renowned cancer researcher with the U.S. Department of Energys Lawrence Berkeley National Laboratory. http://newscenter.lbl.gov/

76 FR 28066 - Notice of Intent To Repatriate a Cultural Item: Phoebe A. Hearst Museum of Anthropology...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-13

... California, Berkeley, Berkeley, CA, that meets the definition of sacred object under 25 U.S.C. 3001. This... sacred object, and the museum agrees with all the evidence presented and will repatriate the object... object needed by traditional Native American religious leaders for the practice of traditional Native...

The University of California at Berkeley: An Emerging Global Research University

ERIC Educational Resources Information Center

Ma, Wanhua

2008-01-01

Federal government science policy and R&D investment are two major factors for the success of research universities in the United States. This case analysis examines how the University of California at Berkeley shifted from a regional to a globally oriented research university by the influence of federal government science policy and R&D…

Berkeley Lab Scientist Co-Leads Breast Cancer Dream Team

ScienceCinema

Gray, Joe

2017-12-27

An $16.5 million, three-year grant to develop new and more effective therapies to fight breast cancer was awarded today to a multi-institutional Dream Team of scientists and clinicians that is co-led by Joe Gray, a renowned cancer researcher with the U.S. Department of Energys Lawrence Berkeley National Laboratory. http://newscenter.lbl.gov/

Doing Much More with Less: Implementing Operational Excellence at UC Berkeley. Research & Occasional Paper Series: CSHE.10.13

ERIC Educational Resources Information Center

Szeri, Andrew J.; Lyons, Richard; Huston, Peggy; Wilton, John

2013-01-01

Universities are undergoing historic change, from the sharp downward shift in government funding to widespread demands to document performance. At the University of California Berkeley, this led to an operational change effort unlike any the university had ever attempted, dubbed Operational Excellence. The authors describe their experiences…

The University of California, Berkeley, and the Government. An Institutional Self Study.

ERIC Educational Resources Information Center

Bowker, Albert H.; Morgan, Patrick M.

The relationship between the University of California at Berkeley and the government is examined. Interviews with over 150 people on campus, ranging from leading administrators to a sample of faculty researchers to section heads in departments such as Personnel and Purchasing, as well as written reports by numerous offices supplied the data of…

ALTERNATE VIEW OF SIDEWALK AND WALL OF INDIGENOUS VOLCANIC RYOLITE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

ALTERNATE VIEW OF SIDEWALK AND WALL OF INDIGENOUS VOLCANIC RYOLITE EASTSIDE OF PIEDMONT AVENUE ADJACENT TO OAK GROVE AND CALIFORNIA MEMORIAL STADIUM. LOOKING NORTH. Photograph by Fredrica Drotos and Michael Kelly, June 29, 2006 - Piedmont Way & the Berkeley Property Tract, East of College Avenue between Dwight Way & U.C. Memorial Stadium, Berkeley, Alameda County, CA

Berkeley Lab's Cool Your School Program

ScienceCinema

Brady, Susan; Gilbert, Haley; McCarthy, Robert

2018-02-02

Cool Your School is a series of 6th-grade, classroom-based, science activities rooted in Berkeley Lab's cool-surface and cool materials research and aligned with California science content standards. The activities are designed to build knowledge, stimulate curiosity, and carry the conversation about human-induced climate change, and what can be done about it, into the community.

Requirements Analysis and Course Improvements for EO3502 Telecommunications Systems Engineering

DTIC Science & Technology

2005-03-01

California, Berkeley, School of Information Management and Systems The University of California, Berkeley (Cal) is a public, coeducational university...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS REQUIREMENTS ANALYSIS AND COURSE IMPROVEMENTS FOR E03502 TELECOMMUNICATIONS SYSTEMS ENGINEERING...Postgraduate School ORGANIZATION REPORT Monterey, CA 93943-5000 NUMBER 9. SPONSORING /MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSORING

An Evaluation of the New Curriculum at the University of California, Berkeley, School of Optometry.

ERIC Educational Resources Information Center

Harris, Michael G.; Kashani, Sandy; Saroj, Namrata

2001-01-01

Evaluated the new curriculum at the University of California, Berkeley, School of Optometry by comparing the content of the new curriculum to the old curriculum and by surveying faculty and students regarding their opinion of the new curriculum. Findings indicated that the curriculum is successful in implementing desired changes, including reduced…

Reducing Our Carbon Footprint: A Low-Energy House in Berkeley, Kabul, and Washington DC (LBNL Science at the Theater)

ScienceCinema

Diamond, Rick [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2018-05-14

How well can we assess and improve building energy performance in California homes? How much energy-and carbon-do homes use in other parts of the world? Rick Diamond, deputy group leader of the Berkeley Lab Energy Performance of Buildings Group, discusses change, global solutions, and the stories of three houses in Berkeley, Kabul (Afghanistan), and Washington, D.C. Diamond, who is also a senior advisor at the California Institute for Energy and Environment, investigates user interactions with the built environment for improved building energy performance. The group has studied a wide range of issues related to energy use in housing, including duct system efficiency, user behavior, and infiltration and ventilation measurements.

A community of educators: professional development for graduate students within the Berkeley Compass Project

NASA Astrophysics Data System (ADS)

Schwab, Josiah; Roth, Nathaniel; Berkeley Compass Project

2015-01-01

The Berkeley Compass Project is a self-formed group of graduate and undergraduate students in the physical sciences at UC Berkeley. Our goals are to improve undergraduate physics education, provide opportunities for professional development, and increase retention of students from populations typically underrepresented in the physical sciences. Graduate students, together with upper-level undergraduates, design and run all Compass programs. We strive to create a community of educators that incorporates best practices from the science education literature. Along the way, we develop experience in curriculum development, fundraising, grant writing, interfacing with university administration, and other aspects of running an effective organization. Our experience in Compass leaves us better poised to be successful researchers, teachers, and mentors.

A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model

PubMed Central

Pinthong, Watthanai; Muangruen, Panya

2016-01-01

Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software. PMID:27547555

C. Judson King of UC Berkeley

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prausnitz, John

2005-06-01

In the middle of the UC Berkeley campus, next to the Main Library, South Hall is the last surviving building from the original campus, founded about 135 years ago. A tiny tree-shaded appendix to this venerated classical building houses Berkeley's Center for Studies in Higher Education, directed by C. Judson King, former Provost and Senior Vice President--Academic Affairs of the ten-campus University of California and long-time Professor of Chemical Engineering at Berkeley. Jud came to Berkeley in 1963 as assistant professor of chemical engineering, following receipt of a doctor's degree from MIT and a subsequent short appointment as director ofmore » the MIT chemical engineering practice school station at what was then Esso (now Exxon) in New Jersey. His undergraduate degree is from Yale. Starting with his MIT doctoral dissertation on gas absorption, Jud has devoted much of his professional career to separation processes. His teaching and research activities have been primarily concerned with separation of mixtures with emphasis on liquid-liquid extraction and drying. As a consultant to Procter and Gamble, he contributed to the technology of making instant coffee. His life-long activities in hiking and camping stimulated Jud's interest in the manufacture of freeze-dried foods (e.g. turkey meat) to minimize the weight of his hiking back-pack. Jud is internationally known not only for his many research publications but even more, for his acclaimed textbook ''Separation Processses'' (McGraw-Hill, second edition 1980) that is used in standard chemical engineering courses in the US and abroad.« less

A Report on the Status of Women Employed in the Library of the University of California, Berkeley, with Recommendations for Affirmative Action.

ERIC Educational Resources Information Center

Lipow, Anne; And Others

This report deals with discrimination against women employed as librarians and library assistants at the University of California, Berkeley Library. The report demonstrates that (1) library professional, technical and clerical personnel--both women and men--work in "women's occupations," and, therefore, are underpaid when compared to…

Reduced Chemical Kinetic Mechanisms for Hydrocarbon Fuels

DTIC Science & Technology

2006-01-01

Technologies Reaction Engineering International 77 West 200 South, Suite # 210 Salt Lake City, UT 84101 3Professor Department of Mechanical ... Engineering University of California, Berkeley Berkeley, CA 94720 4Program Leader for Computational Chemistry Lawrence Livermore National Laboratory...species by the error introduced by assuming they are in quasi-steady state. The reduced mechanisms have been compared to detailed chemistry calculations

THE "FREE SPEECH" CRISES AT BERKELEY, 1964-1965--SOME ISSUES FOR SOCIAL AND LEGAL RESEARCH.

ERIC Educational Resources Information Center

LUNSFORD, TERRY F.

AN EXAMINATION WAS MADE OF THE ISSUES AND EVENTS OF THE "FREE SPEECH" CRISES ON THE BERKELEY CAMPUS OF THE UNIVERSITY OF CALIFORNIA IN AN ATTEMPT TO PROVIDE THE BASIS FOR MORE SYSTEMATIC AND DISPASSIONATE STUDY OF CERTAIN ISSUES BEHIND THE STUDENT PROTESTS, AND TO STIMULATE SOCIAL AND LEGAL RESEARCH ON THESE ISSUES. FOLLOWING AN…

The East Bay Vegetation Management Consortium:\\ta subregional approach to resource management and planning

Treesearch

Tony Acosta

1995-01-01

Formed in response to the October 20, 1991, Oakland/Berkeley hills firestorm, the East Bay Vegetation Management Consortium (EBVMC) is a voluntary association of public agencies concerned with vegetation management and planning related to fire hazard reduction in the Oakland/ Berkeley hills. To date, a total of nine agencies are participating in the EBVMC, including...

Follow the Money: Engineering at Stanford and UC Berkeley during the Rise of Silicon Valley

ERIC Educational Resources Information Center

Adams, Stephen B.

2009-01-01

A comparison of the engineering schools at UC Berkeley and Stanford during the 1940s and 1950s shows that having an excellent academic program is necessary but not sufficient to make a university entrepreneurial (an engine of economic development). Key factors that made Stanford more entrepreneurial than Cal during this period were superior…

DETAIL VIEW OF SIDEWALKS AND TREES ON CHANNING WAY AT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

DETAIL VIEW OF SIDEWALKS AND TREES ON CHANNING WAY AT INTERSECTION OF PIEDMONT AVENUE WITH 2395 PIEDMONT, SIGMA PI HOUSE BY FREDERICK H. REIMERS, 1928, LOOKING NW. Photograph by Fredrica Drotos and Michael Kelly, July 9, 2006 - Piedmont Way & the Berkeley Property Tract, East of College Avenue between Dwight Way & U.C. Memorial Stadium, Berkeley, Alameda County, CA

DETAIL VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

DETAIL VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF CHANNING WAY. SEEN FROM EAST SIDE OF CIRCLE LOOKING NORTH AT 2395 PIEDMONT, SIGMA PI HOUSE BY FREDERICK H. REIMERS, 1928. Photograph by Brian Grogan, July 8, 2007 - Piedmont Way & the Berkeley Property Tract, East of College Avenue between Dwight Way & U.C. Memorial Stadium, Berkeley, Alameda County, CA

A Tale of Three Campuses: Planning and Design in Response to the Cultural Heritages at Mills College, the University of California, Berkeley, and Stanford University

ERIC Educational Resources Information Center

Fiene, Karen; Sabbatini, Robert

2011-01-01

How do forward-looking institutions with rich landscape and architectural heritages integrate contemporary programming and design? This article explores the evolution of the Mills College campus and compares it with two larger western universities: the University of California, Berkeley (UCB) and Leland Stanford, Jr., University (Stanford…

Berkeley extreme-ultraviolet airglow rocket spectrometer - BEARS

NASA Technical Reports Server (NTRS)

Cotton, D. M.; Chakrabarti, S.

1992-01-01

The Berkeley EUV airglow rocket spectrometer (BEARS) instrument is described. The instrument was designed in particular to measure the dominant lines of atomic oxygen in the FUV and EUV dayglow at 1356, 1304, 1027, and 989 A, which is the ultimate source of airglow emissions. The optical and mechanical design of the instrument, the detector, electronics, calibration, flight operations, and results are examined.

Survey of Spring 1982 Graduating Seniors in the College of Engineering, University of California, Berkeley.

ERIC Educational Resources Information Center

Thomson, Gregg E.

Opinions and experiences of college seniors majoring in engineering at the University of California, Berkeley, were studied in spring 1982. Specific attention was focused on the unequal distribution of interest in the various engineering programs. Data were analyzed by program, year of entry, and commitment to engineering in general and/or one's…

Behind the Scenes at Berkeley Lab - The Mechanical Fabrication Facility

ScienceCinema

Wells, Russell; Chavez, Pete; Davis, Curtis; Bentley, Brian

2018-04-16

Part of the Behind the Scenes series at Berkeley Lab, this video highlights the lab's mechanical fabrication facility and its exceptional ability to produce unique tools essential to the lab's scientific mission. Through a combination of skilled craftsmanship and precision equipment, machinists and engineers work with scientists to create exactly what's needed - whether it's measured in microns or meters.

Projects made with the Berkeley Lab Circuit Board

Science.gov Websites

dependence of cosmic rays. Greg Poe, a student at Travis High School in Richmond, Texas, received an the journal Physics Education. He used the Berkeley Lab circuit board together with spare parts from New York Schools Cosmic Particle Telescope workshop. Ken Cecire has created a web page which describes

Solar Fridges and Personal Power Grids: How Berkeley Lab is Fighting Global Poverty (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buluswar, Shashi; Gadgil, Ashok

At this November 26, 2012 Science at the Theater, scientists discussed the recently launched LBNL Institute for Globally Transformative Technologies (LIGTT) at Berkeley Lab. LIGTT is an ambitious mandate to discover and develop breakthrough technologies for combating global poverty. It was created with the belief that solutions will require more advanced R&D and a deep understanding of market needs in the developing world. Berkeley Lab's Ashok Gadgil, Shashi Buluswar and seven other LIGTT scientists discussed what it takes to develop technologies that will impact millions of people. These include: 1) Fuel efficient stoves for clean cooking: Our scientists are improvingmore » the Berkeley Darfur Stove, a high efficiency stove used by over 20,000 households in Darfur; 2) The ultra-low energy refrigerator: A lightweight, low-energy refrigerator that can be mounted on a bike so crops can survive the trip from the farm to the market; 3) The solar OB suitcase: A low-cost package of the five most critical biomedical devices for maternal and neonatal clinics; 4) UV Waterworks: A device for quickly, safely and inexpensively disinfecting water of harmful microorganisms.« less

Fast and accurate inference of local ancestry in Latino populations

PubMed Central

Baran, Yael; Pasaniuc, Bogdan; Sankararaman, Sriram; Torgerson, Dara G.; Gignoux, Christopher; Eng, Celeste; Rodriguez-Cintron, William; Chapela, Rocio; Ford, Jean G.; Avila, Pedro C.; Rodriguez-Santana, Jose; Burchard, Esteban Gonzàlez; Halperin, Eran

2012-01-01

Motivation: It is becoming increasingly evident that the analysis of genotype data from recently admixed populations is providing important insights into medical genetics and population history. Such analyses have been used to identify novel disease loci, to understand recombination rate variation and to detect recent selection events. The utility of such studies crucially depends on accurate and unbiased estimation of the ancestry at every genomic locus in recently admixed populations. Although various methods have been proposed and shown to be extremely accurate in two-way admixtures (e.g. African Americans), only a few approaches have been proposed and thoroughly benchmarked on multi-way admixtures (e.g. Latino populations of the Americas). Results: To address these challenges we introduce here methods for local ancestry inference which leverage the structure of linkage disequilibrium in the ancestral population (LAMP-LD), and incorporate the constraint of Mendelian segregation when inferring local ancestry in nuclear family trios (LAMP-HAP). Our algorithms uniquely combine hidden Markov models (HMMs) of haplotype diversity within a novel window-based framework to achieve superior accuracy as compared with published methods. Further, unlike previous methods, the structure of our HMM does not depend on the number of reference haplotypes but on a fixed constant, and it is thereby capable of utilizing large datasets while remaining highly efficient and robust to over-fitting. Through simulations and analysis of real data from 489 nuclear trio families from the mainland US, Puerto Rico and Mexico, we demonstrate that our methods achieve superior accuracy compared with published methods for local ancestry inference in Latinos. Availability: http://lamp.icsi.berkeley.edu/lamp/lampld/ Contact: bpasaniu@hsph.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22495753

Barriers to communication and cooperation in addressing community impacts of radioactive releases from research facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrach, Robert J.; Peterson, S. Ring

1999-05-05

Two instances of research facilities responding to public scrutiny will be discussed. The first concerns emissions from a "tritium labeling facility" operated at Lawrence Berkeley National Laboratory (LBNL); the second deals with releases of plutonium from Lawrence Livermore National Laboratory (LLNL). There are many parallels between these two cases, both of which are still ongoing. In both, the national laboratory is the acknowledged source of low-level (by regulatory standards) radioactive contamination in the community. A major purpose of both investigations is to determine the degree of the contamination and the threat it poses to public health and the environment. Themore » examining panel or committee is similarly constituted in the two cases, including representatives from all four categories of stakeholders: decision makers; scientists and other professionals doing the analysis/assessment; environmental activist or public interest groups; and "ordinary" citizens (nearly everyone else not in one or more of the first three camps). Both involved community participation from the beginning. The levels of outrage over the events triggering the assessment are comparable; though "discovered" or "appreciated" only a few years ago, the release of radiation in both cases occurred or began occurring more than a decade ago. The meetings have been conducted in a similar manner, with comparable frequency, often utilizing the services of professional facilitators. In both cases, the sharply contrasting perceptions of risk commonly seen between scientists and activists were present from the beginning, though the contrast was sharper and more problematical in the Berkeley case. Yet, the Livermore case seems to be progressing towards a satisfactory resolution, while the Berkeley case remains mired in ill-will, with few tangible results after two years of effort. We perceive a wide gap in negotiation skills (at the very least), and a considerable difference in willingness to compromise, between the environmental activist groups participating in the two cases. A degree of contentiousness existed from the start among the participants in the Berkeley case particularly between the environmental activists and the scientists/regulators that was not approached in the Livermore case, and which was and still is severe enough to stifle meaningful progress. The Berkeley activists are considerably more aggressive, we believe, in arguing their points of view, making demands about what should be done, and verbally assailing the scientists and government regulators. We offer the following comments on the barriers to communication and cooperation that distinguish the Berkeley and Livermore cases. In no particular order, they are (a) the presence of a higher degree of polarization between the Berkeley activists and the "establishment," as represented by government scientists and regulators, (b) the absence, in the Berkeley case, of an activist leader with skills and effectiveness comparable to a well-known leader in Livermore, (c) frequent displays by several of the Berkeley activists of incivility, distrust, and disrespect for the regulators and scientists, (d) extraordinary difficulties in reaching consensus in the Tritium Issues Work Group meetings, perhaps because goals diverged among the factions, (e) a considerable degree of resentment by the Berkeley activists over the imbalance in conditions of participation, pitting well-paid, tax-supported professionals against "citizen volunteers," (f) the brick wall that divides the perspectives of "no safe dose" and "levels below regulatory concern" when trying to reach conclusions about radiation dangers to the community, and (g) unwillingness to consider both sides of the risk-reward coin: benefits to the community and society at large of the tritium labeling activity, vs. the health risk from small quantities of tritium released to the environment.« less

THE YOUNG OPEN CLUSTER BERKELEY 55

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negueruela, Ignacio; Marco, Amparo, E-mail: ignacio.negueruela@ua.es, E-mail: amparo.marco@ua.es

We present UBV photometry of the highly reddened and poorly studied open cluster Berkeley 55, revealing an important population of B-type stars and several evolved stars of high luminosity. Intermediate-resolution far-red spectra of several candidate members confirm the presence of one F-type supergiant and six late supergiants or bright giants. The brightest blue stars are mid-B giants. Spectroscopic and photometric analyses indicate an age 50 {+-} 10 Myr. The cluster is located at a distance d Almost-Equal-To 4 kpc, consistent with other tracers of the Perseus Arm in this direction. Berkeley 55 is thus a moderately young open cluster withmore » a sizable population of candidate red (super)giant members, which can provide valuable information about the evolution of intermediate-mass stars.« less

A Community of Scientists and Educators: The Compass Project at UC Berkeley

NASA Astrophysics Data System (ADS)

Roth, Nathaniel; Schwab, Josiah

2016-01-01

The Berkeley Compass Project is a self-formed group of graduate and undergraduate students in the physical sciences at the University of California, Berkeley. Its goals are to improve undergraduate physics education, provide opportunities for professional development, and increase retention of students from populations underrepresented in the physical sciences. For undergraduate students, the core Compass experience consists of a summer program and several seminar courses. These programs are designed to foster a diverse, collaborative student community in which students engage in authentic research practices and regular self-reflection. Graduate students, together with upper-level undergraduates, design and run all Compass programs. Compass strives to incorporate best practices from the science education literature. Experiences in Compass leave participants poised to be successful students researchers, teachers, and mentors.

Laboratory Directed Research and Development Program FY 2008 Annual Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

editor, Todd C Hansen

2009-02-23

The Ernest Orlando Lawrence Berkeley National Laboratory (Berkeley Lab or LBNL) is a multi-program national research facility operated by the University of California for the Department of Energy (DOE). As an integral element of DOE's National Laboratory System, Berkeley Lab supports DOE's missions in fundamental science, energy resources, and environmental quality. Berkeley Lab programs advance four distinct goals for DOE and the nation: (1) To perform leading multidisciplinary research in the computing sciences, physical sciences, energy sciences, biosciences, and general sciences in a manner that ensures employee and public safety and protection of the environment. (2) To develop and operatemore » unique national experimental facilities for qualified investigators. (3) To educate and train future generations of scientists and engineers to promote national science and education goals. (4) To transfer knowledge and technological innovations and to foster productive relationships among Berkeley Lab's research programs, universities, and industry in order to promote national economic competitiveness. Berkeley Lab's research and the Laboratory Directed Research and Development (LDRD) program support DOE's Strategic Themes that are codified in DOE's 2006 Strategic Plan (DOE/CF-0010), with a primary focus on Scientific Discovery and Innovation. For that strategic theme, the Fiscal Year (FY) 2008 LDRD projects support each one of the three goals through multiple strategies described in the plan. In addition, LDRD efforts support the four goals of Energy Security, the two goals of Environmental Responsibility, and Nuclear Security (unclassified fundamental research that supports stockpile safety and nonproliferation programs). The LDRD program supports Office of Science strategic plans, including the 20-year Scientific Facilities Plan and the Office of Science Strategic Plan. The research also supports the strategic directions periodically under consideration and review by the Office of Science Program Offices, such as LDRD projects germane to new research facility concepts and new fundamental science directions. Berkeley Lab LDRD program also play an important role in leveraging DOE capabilities for national needs. The fundamental scientific research and development conducted in the program advances the skills and technologies of importance to our Work For Others (WFO) sponsors. Among many directions, these include a broad range of health-related science and technology of interest to the National Institutes of Health, breast cancer and accelerator research supported by the Department of Defense, detector technologies that should be useful to the Department of Homeland Security, and particle detection that will be valuable to the Environmental Protection Agency. The Berkeley Lab Laboratory Directed Research and Development Program FY2008 report is compiled from annual reports submitted by principal investigators following the close of the fiscal year. This report describes the supported projects and summarizes their accomplishments. It constitutes a part of the LDRD program planning and documentation process that includes an annual planning cycle, project selection, implementation, and review.« less

The three-dimensional genome organization of Drosophila melanogaster through data integration.

PubMed

Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

2017-07-31

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

Fast Surface Reconstruction and Segmentation with Terrestrial LiDAR Range Data

DTIC Science & Technology

2009-05-18

UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) University of California at Berkeley,Department of Electrical Engineering and Computer...Sciences,Berkeley,CA,94720 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S...ACRONYM(S) 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 12. DISTRIBUTION /AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13

The Vicious Cycle of Gender and Status at the University of California at Berkeley, 1918-1954. ASHE 1988 Annual Meeting Paper.

ERIC Educational Resources Information Center

Nerad, Maresi

The way in which an all-women's department, the Department of Home Economics at the University of California (Berkeley), tried to raise its status and adhere to academic values of a research university after starting out as a low prestige undergraduate program is analyzed. Some of the related research questions are: whether academic departments…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haber, Carl

Summer Lecture Series 2006: Physicist Carl Haber and colleagues have found a way to digitize century-old recordings believed to be unplayable, and as a result, some of the music and spoken word recordings in the Library of Congress collection may spring back to life. Learn how basic scientific research done at Berkeley Lab may yield results of benefit in other areas of science and culture. Series: "Lawrence Berkeley National Laboratory Summer Lecture Series"

Shut out of the System: As Competition Increases for Slots at UC-Berkeley, Admission Offers to Minority Students Continue to Decline

ERIC Educational Resources Information Center

Burdman, Pamela

2004-01-01

As University of California officials announced admissions results for the fall, it appeared that increasing competition for seats at the university, rising tuition costs, and continued controversy over the role of race in admissions were conspiring to reduce the slots offered to African American students at UC-Berkeley. At the same time, the…

Pump for spawning channels includes a turbine and motor. Turbine ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Pump for spawning channels includes a turbine and motor. Turbine is Berkeley H-17500, model 8C2PH, Serial No. 2889, B.M. No. 4886 - Berkeley Pump Co. The Motor is G.E. Induction Motor, model 5K4256XA3YI, serial no. GAJ728337, Tri-Clad. View looking northeast. - Prairie Creek Fish Hatchery, Hwy. 101, Orick, Humboldt County, CA

Map showing bottom topography of the Pacific Continental Margin, Cape Mendocino to Point Conception

USGS Publications Warehouse

Chase, T.E.; Wilde, Pat; Normark, W.R.; Evenden, G.I.; Miller, C.P.; Seekins, B.A.; Young, J. D.; Grim, M.S.; Lief, C.J.

1992-01-01

Wilde, Pat, Chase, T.E., Holmes, M.L., Normark, W.R., Thomas, J.A., McCulloch, D.S., and Kulm, L.D., 1978, Oceanographic data off northern California-southern Oregon 40° to 43° North including the Gorda Deep Sea Fan: Berkeley, University of California, Lawrence Berkeley Laboratory Publication 251, scale 1:815,482 at 42° latitude.

Peacebook: A Resource Guide for Peace Studies at U.C. Berkeley, 1982-83 [and] 1983-84.

ERIC Educational Resources Information Center

Peace Studies Student Association.

A series of essays and lists of resource materials as well as courses relevant to peace studies at the University of California Berkeley are presented in the two guides. Topics of the 1982-83 guide include the undergraduate major in Peace and Conflict Studies (PACS), a proposed curriculum, core courses, concentration area courses (social systems,…

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

PubMed

Butler, J B; Vaillancourt, R E; Potts, B M; Lee, D J; King, G J; Baten, A; Shepherd, M; Freeman, J S

2017-05-22

Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

Dark Secrets: What Science Tells Us About the Hidden Universe (LBNL Science at the Theater)

ScienceCinema

Permutter, Saul [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)] (ORCID:0000000244364661); Schlegel, David [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Leauthaud, Alexie [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2018-06-12

No mystery is bigger than dark energy - the elusive force that makes up three-quarters of the Universe and is causing it to expand at an accelerating rate. KTVU Channel 2 health and science editor John Fowler will moderate a panel of Lawrence Berkeley National Laboratory scientists who use phenomena such as exploding stars and gravitational lenses to explore the dark cosmos. Saul Perlmutter heads the Supernova Cosmology Project, which pioneered the use of precise observations of exploding stars to study the expansion of the Universe. His international team was one of two groups who independently discovered the amazing phenomenon known as dark energy, and he led a collaboration that designed a satellite to study the nature of this dark force. He is an astrophysicist at Berkeley Lab and a professor of physics at UC Berkeley. David Schlegel is a Berkeley Lab astrophysicist and the principal investigator of Baryon Oscillation Spectroscopic Survey (BOSS), the largest of four night-sky surveys being conducted in the third phase of the Sloan Digital Sky Survey, known as SDSS-III. BOSS will generate a 3-D map of two million galaxies and quasars, using a specially built instrument outfitted with 1,000 optical fibers and mounted on the SDSS telescope in New Mexico. Alexie Leauthaud is Chamberlain Fellow at Berkeley Lab. Her work probes dark matter in the Universe using a technique called gravitational lensing. When gravity from a massive object such as a cluster of galaxies warps space around it, this can distort our view of the light from an even more distant object. The scale and direction of this distortion allows astronomers to directly measure the properties of both dark matter and dark energy.

The Berkeley Instrumental Neutron Generator (BINGE) for 40Ar/39Ar geochronology

NASA Astrophysics Data System (ADS)

Renne, P. R.; Becker, T. A.; Bernstein, L.; Firestone, R. B.; Kirsch, L.; Leung, K. N.; Rogers, A.; Van Bibber, K.; Waltz, C.

2014-12-01

The Berkeley Instrumental Neutron Generator (BINGE) facility is the product of a consortium involving the Berkeley Geochronology Center (BGC), the U.C. Berkeley Nuclear Engineering Dept. (UCB/NE), and Lawrence Berkeley (LBNL) and Lawrence Livermore (LLNL) National Labs. BINGE was initially designed (and funded by NSF) for 40Ar/39Ar geochronology. BINGE uses a plasma-based deuteron ion source and a self-loading Ti-surfaced target to induce deuteron-deuterium (DD) fusion via the reaction 2H(d,n)3He, producing 2.45 MeV neutrons. The limited neutron energy spectrum is aimed at reducing recoil effects, interfering nuclear reactions, and unwanted radioactive byproducts, all of which are undesirable consequences of conventional irradiation with 235U fission spectrum neutrons. Minimization of interfering reactions such as 40Ca(n,na)36Ar greatly reduces penalties for over-irradiation, enabling improved signal/background measurement of e.g. 39Ar. BINGE will also be used for a variety of nuclear physics and engineering experiments that require a high flux of monoenergetic neutrons. Neutron energies lower than 2.45 MeV can be obtained via irradiation ports within and external to polyethylene shielding. Initial commissioning produced a neutron flux of 108 n/sec/cm2 at 1 mA source current and 100 kV anode voltage, as expected. When scaled up to the 1 A source current as planned, this indicates that BINGE will achieve the design objective neutron flux of 1011 n/sec/cm2. Further progress towards this goal will be reported. Supported by NSF (grant #EAR-0960138), BGC, UCB/NE, University of California Office of the President, and DOE through LLNL under contract #DE-AC52-07NA27344 and LBNL under contract #DE-AC02-05CH11231.

Multi-sensor radiation detection, imaging, and fusion

NASA Astrophysics Data System (ADS)

Vetter, Kai

2016-01-01

Glenn Knoll was one of the leaders in the field of radiation detection and measurements and shaped this field through his outstanding scientific and technical contributions, as a teacher, his personality, and his textbook. His Radiation Detection and Measurement book guided me in my studies and is now the textbook in my classes in the Department of Nuclear Engineering at UC Berkeley. In the spirit of Glenn, I will provide an overview of our activities at the Berkeley Applied Nuclear Physics program reflecting some of the breadth of radiation detection technologies and their applications ranging from fundamental studies in physics to biomedical imaging and to nuclear security. I will conclude with a discussion of our Berkeley Radwatch and Resilient Communities activities as a result of the events at the Dai-ichi nuclear power plant in Fukushima, Japan more than 4 years ago.

Disintegration of the Aged Open Cluster Berkeley 17

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacharya, Souradeep; Vaidya, Kaushar; Mishra, Ishan

We present the analysis of the morphological shape of Berkeley 17, the oldest known open cluster (∼10 Gyr), using the probabilistic star counting of Pan-STARRS point sources, and confirm its core-tail shape, plus an antitail, previously detected with the 2MASS data. The stellar population, as diagnosed by the color–magnitude diagram and theoretical isochrones, shows many massive members in the clusters core, whereas there is a paucity of such members in both of the tails. This manifests mass segregation in this aged star cluster with the low-mass members being stripped away from the system. It has been claimed that Berkeley 17more » is associated with an excessive number of blue straggler candidates. A comparison of nearby reference fields indicates that about half of these may be field contamination.« less

Solar + Storage Synergies for Managing Commercial-Customer Demand Charges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gagnon, P.; Govindarajan, A.; Bird, L.

Demand charges, which are based on a customer’s maximum demand in kilowatts (kW), are a common element of electricity rate structures for commercial customers. Customer-sited solar photovoltaic (PV) systems can potentially reduce demand charges, but the level of savings is difficult to predict, given variations in demand charge designs, customer loads, and PV generation profiles. Lawrence Berkeley National Laboratory (Berkeley Lab) and the National Renewable Energy Laboratory (NREL) are collaborating on a series of studies to understand how solar PV can impact demand charges. Prior studies in the series examined demand charge reductions from solar on a stand-alone basis formore » residential and commercial customers. Those earlier analyses found that solar, alone, has limited ability to reduce demand charges depending on the specific design of the demand charge and on the shape of the customer’s load profile. This latest analysis estimates demand charge savings from solar in commercial buildings when co-deployed with behind-the-meter storage, highlighting the complementary roles of the two technologies. The analysis is based on simulated loads, solar generation, and storage dispatch across a wide variety of building types, locations, system configurations, and demand charge designs.« less

VLA observations of unidentified Leiden-Berkeley Deep-Survey sources - Luminosity and redshift dependence of spectral properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kapahi, V.K.; Kulkarni, V.K.

1990-05-01

VLA observations of a complete subset of the Leiden-Berkeley Deep Survey sources that have S(1.4 GHz) greater than 10 mJy and are not optically identified down to F=22 mag are reported. By comparing the spectral and structural properties of the sources with samples from the literature, an attempt was made to disentangle the luminosity and redshift dependence of the spectral indices of extended emission in radio galaxies and of the incidence of compact steep-spectrum sources. It is found that the fraction of compact sources among those with a steep spectrum is related primarily to redshift, being much larger at highmore » redshifts for sources of similar radio luminosity. Only a weak and marginally significant dependence of spectral indices of the extended sources on luminosity and redshift is found in samples selected at 1.4 and 2.7 GHz. It is pointed out that the much stronger correlation of spectral indices with luminosity may be arising partly from spectral curvature, and partly due to the preferential inclusion of very steep-spectrum sources from high redshift in low-frequency surveys. 54 refs.« less

Map showing bottom topography of the Pacific Continental Margin, Strait of Juan de Fuca to Cape Mendocino

USGS Publications Warehouse

Grim, M.S.; Chase, T.E.; Evenden, G.I.; Holmes, M.L.; Normark, W.R.; Wilde, Pat; Fox, C.J.; Lief, C.J.; Seekins, B.A.

1992-01-01

Wilde, Pat, Chase, T.E., Holmes, M.L., Normark, W.R., Thomas, J.A., McCulloch, D.S., and Kulm, L.D., 1978, Oceanographic data off northern California-southern Oregon 40° to 43° North including the Gorda Deep Sea Fan: Berkeley, University of California, Lawrence Berkeley Laboratory Publication 251, scale 1:815,482 at 42° latitude.

Collection Conservation Treatment: A Resource Manual for Program Development and Conservation Technician Training, Including "Report on Training the Trainers: A Conference on Training in Collection Conservation, Berkeley, California, April 28-May 2, 1992."

ERIC Educational Resources Information Center

Jones, Maralyn, Comp.

The documentation of collection conservation treatments and program management information compiled in this publication are the result of the "Training the Trainers" conference in April 1992 at the University of California, Berkeley. Only treatments appropriate for general, usually circulating, collections have been included, emphasizing…

What is Gravitational Lensing?(LBNL Summer Lecture Series)

ScienceCinema

Alexie, Leauthaud; Reiko, Nakajima [Berkeley Center for Cosmological Physics, Berkely, California, United States

2017-12-09

July 28, 2009 Berkeley Lab summer lecture: Gravitational lensing is explained by Einstein's general theory of relativity: galaxies and clusters of galaxies, which are very massive objects, act on spacetime by causing it to become curved. Alexie Leauthaud and Reiko Nakajima, astrophysicists with the Berkeley Center for Cosmological Physics, will discuss how scientists use gravitational lensing to investigate the nature of dark energy and dark matter in the universe.

First Light for BOSS - A New Kind of Search for Dark Energy | Berkeley

Science.gov Websites

in the clumping of invisible dark matter. Comparing these scales at different eras makes it possible Web People Close About the Lab Leadership/Organization Calendar News Center Today At Berkeley Lab News Preuss, (510) 486-6249 On the night of September 14 the largest program in the Sloan Digital Sky Survey

Nanoscience at Work: Creating Energy from Sunlight (LBNL Science at the Theater)

ScienceCinema

Alivisatos, Paul [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2018-02-26

Paul Alivisatos, co-leader of Berkeley Lab's Helios Project, is the Associate Director for Physical Sciences and director of the Materials Sciences Division at Berkeley Lab. In the Helios Project, Alivisatos will use nanotechnology in the efficient capture of sunlight and its conversion to electricity to drive economical fuel production processes. He is an authority on artificial nanostructure synthesis and inventor of the quantum dot technology.

Berkeley's New Approach to Global Engagement: Early and Current Efforts to Become More International. Research & Occasional Paper Series: CSHE.12.15

ERIC Educational Resources Information Center

Dirks, Nicholas B.; Gilman, Nils

2015-01-01

This essay discusses past and current thinking about the globalization of higher education (from a U.S. point of view in particular) and a new model we are attempting to develop at the University of California, Berkeley. This essay begins with a brief narrative of the historical evolution of efforts to internationalize education, from the…

Expanding Off-Campus Enrollment Capacity at Berkeley: A Concept Paper. Research & Occasional Paper Series: CSHE.2.17

ERIC Educational Resources Information Center

Geiser, Saul

2017-01-01

Like Berkeley, the UC system as a whole is quickly running out of space to accommodate the next generation of Californians who will be reaching college age by mid-century. Even with the added capacity at UC Merced, the UC system will run out of space on existing campuses in the next decade. In the normal course of events, this would trigger…

Better Batteries for Transportation: Behind the Scenes @ Berkeley Lab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Battaglia, Vince

Vince Battaglia leads a behind-the-scenes tour of Berkeley Lab's BATT, the Batteries for Advanced Transportation Technologies Program he leads, where researchers aim to improve batteries upon which the range, efficiency, and power of tomorrow's electric cars will depend. This is the first in a forthcoming series of videos taking viewers into the laboratories and research facilities that members of the public rarely get to see.

PART 2 OF 2 PART PANORAMA WITH NO. CA212 VIEW ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

PART 2 OF 2 PART PANORAMA WITH NO. CA-2-12 VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF CHANNING WAY WITH 2395 PIEDMONT, SIGMA PI HOUSE BY FREDERICK H. REIMERS, 1928. SEEN FROM SE CORNER LOOKING NW. Photograph by Brian Grogan, July 8, 2007 - Piedmont Way & the Berkeley Property Tract, East of College Avenue between Dwight Way & U.C. Memorial Stadium, Berkeley, Alameda County, CA

How Bilayer Graphene Got a Bandgap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng Wang

2009-06-02

Graphene is the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. But theres a catch: graphene has no bandgap. Now Feng Wang and his colleagues at Berkeley Lab and UC Berkeley have engineered a bandgap in bilayer graphene that can be precisely controlled from 0 to 250 milli-electron volts, which is the energy of infrared radiation.

Better Batteries for Transportation: Behind the Scenes @ Berkeley Lab

ScienceCinema

Battaglia, Vince

2018-02-06

Vince Battaglia leads a behind-the-scenes tour of Berkeley Lab's BATT, the Batteries for Advanced Transportation Technologies Program he leads, where researchers aim to improve batteries upon which the range, efficiency, and power of tomorrow's electric cars will depend. This is the first in a forthcoming series of videos taking viewers into the laboratories and research facilities that members of the public rarely get to see.

Progress Report on the Berkeley/Anglo-Australian Observatory High-redshift Supernova Search

DOE R&D Accomplishments Database

Goldhaber, G.; Perlmutter, S.; Pennypacker, C.; Marvin, H.; Muller, R. A.; Couch, W.; Boyle, B.

1990-11-01

There are two main efforts related to supernovae in progress at Berkeley. The first is an automated supernova search for nearby supernovae, which was already discussed by Carl Pennypacker at this conference. The second is a search for distant supernovae, in the z = 0.3 to 0.5 region, aimed at measuring {Omega}. It is the latter that I want to discuss in this paper.

How Bilayer Graphene Got a Bandgap

ScienceCinema

Feng Wang

2017-12-09

Graphene is the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. But theres a catch: graphene has no bandgap. Now Feng Wang and his colleagues at Berkeley Lab and UC Berkeley have engineered a bandgap in bilayer graphene that can be precisely controlled from 0 to 250 milli-electron volts, which is the energy of infrared radiation.

How Bilayer Graphene Got a Bandgap

ScienceCinema

Wang, Feng

2018-01-08

Graphene is the two-dimensional crystalline form of carbon, whose extraordinary electron mobility and other unique features hold great promise for nanoscale electronics and photonics. But theres a catch: graphene has no bandgap. Now Feng Wang and his colleagues at Berkeley Lab and UC Berkeley have engineered a bandgap in bilayer graphene that can be precisely controlled from 0 to 250 milli-electron volts, which is the energy of infrared radiation.

Laboratory directed research and development program, FY 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1997-02-01

The Ernest Orlando Lawrence Berkeley National Laboratory (Berkeley Lab) Laboratory Directed Research and Development Program FY 1996 report is compiled from annual reports submitted by principal investigators following the close of the fiscal year. This report describes the projects supported and summarizes their accomplishments. It constitutes a part of the Laboratory Directed Research and Development (LDRD) program planning and documentation process that includes an annual planning cycle, projection selection, implementation, and review. The Berkeley Lab LDRD program is a critical tool for directing the Laboratory`s forefront scientific research capabilities toward vital, excellent, and emerging scientific challenges. The program provides themore » resources for Berkeley Lab scientists to make rapid and significant contributions to critical national science and technology problems. The LDRD program also advances the Laboratory`s core competencies, foundations, and scientific capability, and permits exploration of exciting new opportunities. Areas eligible for support include: (1) Work in forefront areas of science and technology that enrich Laboratory research and development capability; (2) Advanced study of new hypotheses, new experiments, and innovative approaches to develop new concepts or knowledge; (3) Experiments directed toward proof of principle for initial hypothesis testing or verification; and (4) Conception and preliminary technical analysis to explore possible instrumentation, experimental facilities, or new devices.« less

Economic impact

DOE Office of Scientific and Technical Information (OSTI.GOV)

Technology Transfer Department

2001-06-01

In federal fiscal year 2000 (FY00), Berkeley Lab had 4,347 full- and part-time employees. In addition, at any given time of the year, there were more than 1,000 Laboratory guests. These guests, who also reside locally, have an important economic impact on the nine-county Bay Area. However, Berkeley Lab's total economic impact transcends the direct effects of payroll and purchasing. The direct dollars paid to the Lab's employees in the form of wages, salaries, and benefits, and payments made to contractors for goods and services, are respent by employees and contractors again and again in the local and greater economy.more » Further, while Berkeley Lab has a strong reputation for basic scientific research, many of the Lab's scientific discoveries and inventions have had direct application in industry, spawning new businesses and creating new opportunities for existing firms. This analysis updates the Economic Impact Analysis done in 1996, and its purpose is to describe the economic and geographic impact of Laboratory expenditures and to provide a qualitative understanding of how Berkeley Lab impacts and supports the local community. It is intended as a guide for state, local, and national policy makers as well as local community members. Unless otherwise noted, this analysis uses data from FY00, the most recent year for which full data are available.« less

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

PubMed

Mak, Angel C Y; Lai, Yvonne Y Y; Lam, Ernest T; Kwok, Tsz-Piu; Leung, Alden K Y; Poon, Annie; Mostovoy, Yulia; Hastie, Alex R; Stedman, William; Anantharaman, Thomas; Andrews, Warren; Zhou, Xiang; Pang, Andy W C; Dai, Heng; Chu, Catherine; Lin, Chin; Wu, Jacob J K; Li, Catherine M L; Li, Jing-Woei; Yim, Aldrin K Y; Chan, Saki; Sibert, Justin; Džakula, Željko; Cao, Han; Yiu, Siu-Ming; Chan, Ting-Fung; Yip, Kevin Y; Xiao, Ming; Kwok, Pui-Yan

2016-01-01

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation. Copyright © 2016 by the Genetics Society of America.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tom, Nathan M.; Madhi, Farshad; Yeung, Ronald W.

The aim of this paper is to maximize the power-to-load ratio of the Berkeley Wedge: a one-degree-of-freedom, asymmetrical, energy-capturing, floating breakwater of high performance that is relatively free of viscosity effects. Linear hydrodynamic theory was used to calculate bounds on the expected time-averaged power (TAP) and corresponding surge restraining force, pitch restraining torque, and power take-off (PTO) control force when assuming that the heave motion of the wave energy converter remains sinusoidal. This particular device was documented to be an almost-perfect absorber if one-degree-of-freedom motion is maintained. The success of such or similar future wave energy converter technologies would requiremore » the development of control strategies that can adapt device performance to maximize energy generation in operational conditions while mitigating hydrodynamic loads in extreme waves to reduce the structural mass and overall cost. This paper formulates the optimal control problem to incorporate metrics that provide a measure of the surge restraining force, pitch restraining torque, and PTO control force. The optimizer must now handle an objective function with competing terms in an attempt to maximize power capture while minimizing structural and actuator loads. A penalty weight is placed on the surge restraining force, pitch restraining torque, and PTO actuation force, thereby allowing the control focus to be placed either on power absorption or load mitigation. Thus, in achieving these goals, a per-unit gain in TAP would not lead to a greater per-unit demand in structural strength, hence yielding a favorable benefit-to-cost ratio. Demonstrative results in the form of TAP, reactive TAP, and the amplitudes of the surge restraining force, pitch restraining torque, and PTO control force are shown for the Berkeley Wedge example.« less

Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome

PubMed Central

Li, Jian; Harris, R. Alan; Cheung, Sau Wai; Coarfa, Cristian; Jeong, Mira; Goodell, Margaret A.; White, Lisa D.; Patel, Ankita; Kang, Sung-Hae; Shaw, Chad; Chinault, A. Craig; Gambin, Tomasz; Gambin, Anna; Lupski, James R.; Milosavljevic, Aleksandar

2012-01-01

The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ∼1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH) chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR–mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease. PMID:22615578

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somerville, Chris

Berkeley Lab's Chris Somerville is a leading authority on the structure and function of plant cell walls, which comprise most of the body mass of higher plants. He views the knowledge of cell wall structure and function as furthering the development of plants with improved usefulness: these plants are strong potential sources of renewable materials and biofuel feedstocks. His scientific expertise defines an ideal match of his interest - in the development of cellulosic and other solar-to-fuel science - with his recent appointment as Director of the Energy Biosciences Institute (EBI). With colleagues in biology, physical sciences, engineering, and environmentalmore » and the social sciences, he now leads the EBI multidisciplinary teams' research efforts to develop next-generation, carbon-neutral transportation fuels.« less

Configuration interaction in charge exchange spectra of tin and xenon

NASA Astrophysics Data System (ADS)

D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

2011-06-01

Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

AIDS and Young Children: Emerging Issues. Hearing before the Select Committee on Children, Youth, and Families. House of Representatives, One Hundredth Congress, First Session. Hearing Held in Berkeley, California.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. House Select Committee on Children, Youth, and Families.

This field hearing in Berkeley, California examined: (1) the increasing incidence of babies born with, or at risk of contracting, Acquired Immune Deficiency Syndrome (AIDS); (2) the ability of health and social service systems to care for AIDS-infected infants and children and their families; and (3) prevention efforts to reduce the spread of…

New Insights on Visual Cortex. Abstracts. Center for Visual Science Symposium (16th) Held in Rochester, New York on June 16-18, 1988

DTIC Science & Technology

1988-06-01

Cortex of the Cat John G. Robson Craik Physiological Laboratory Cambridge University Cambridge, England When tested with spatially-localized stimuli...University, New York, NY Stanley Klein - School of Optometry, University Berkeley, Berkeley, CA Jennifer Knight - Neurobiology & Behavior, Cornell University...Village, Poughkeepsie, NY Jeffrcy Lubin - Psychology Department, University of PA, Philadelphia, PA Jennifer S. Lund - University of Pittsburgh

Berkeley Lab Answers Your Home Energy Efficiency Questions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, Iain

2013-02-14

In this follow-up "Ask Berkeley Lab" video, energy efficiency expert Iain Walker answers some of your questions about home energy efficiency. How do you monitor which appliances use the most energy? Should you replace your old windows? Are photovoltaic systems worth the cost? What to do about a leaky house? And what's the single biggest energy user in your home? Watch the video to get the answers to these and more questions.

Berkeley Lab Answers Your Home Energy Efficiency Questions

ScienceCinema

Walker, Iain

2018-01-16

In this follow-up "Ask Berkeley Lab" video, energy efficiency expert Iain Walker answers some of your questions about home energy efficiency. How do you monitor which appliances use the most energy? Should you replace your old windows? Are photovoltaic systems worth the cost? What to do about a leaky house? And what's the single biggest energy user in your home? Watch the video to get the answers to these and more questions.

Joint Services Electronics Program

DTIC Science & Technology

1982-09-30

and angle both within the wafer and in the backscattered signal have been published by Y. C. Lin (Ph.D. thesis ). As an extension of that work, Albert...zositive photoresist," Ř.S. thesis , Department of Flectrical Engineering and Computer Sciences, University of California, Berkeley. Kim, W. 3. Oldham and A...Mehotra, "’Tnaracteriza :on of ?ositive Phcoresist," .!. S Thesis University of California, Berkeley, 1980. [31 d. 3. Oldham, "In Situ Characterization of

Genes and the Microenvironment: Two Faces of Breast Cancer (LBNL Science at the Theater)

ScienceCinema

Gray, Joe; Love, Susan M.; Bissell, Min; Barcellos-Hoff, Mary Helen

2018-05-24

In this April 21, 2008 Berkeley Lab event, a dynamic panel of Berkeley Lab scientists highlight breast cancer research advances related to susceptibility, early detection, prevention, and therapy - a biological systems approach to tackling the disease from the molecular and cellular levels, to tissues and organs, and ultimately the whole individual. Joe Gray, Berkeley Lab Life Sciences Division Director, explores how chromosomal abnormalities contribute to cancer and respond to gene-targeted therapies. Mina Bissell, former Life Sciences Division Director, approaches the challenge of breast cancer from the breast's three dimensional tissue microenvironment and how the intracellular ''conversation'' triggers malignancies. Mary Helen Barcellos-Hoff, Deputy Director, Life Sciences Division, identifies what exposure to ionizing radiation can tell us about how normal tissues suppress carcinogenesis. The panel is moderated by Susan M. Love, breast cancer research pioneer, author, President and Medical Director of the Dr. Susan Love Research Foundation.

Supernovae, Dark Energy and the Accelerating Universe: How DOE Helped to Win (yet another) Nobel Prize

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perlmutter, Saul

2012-01-13

The Department of Energy (DOE) hosted an event Friday, January 13, with 2011 Physics Nobel Laureate Saul Perlmutter. Dr. Perlmutter, a physicist at the Department’s Lawrence Berkeley National Laboratory and a professor of physics at the University of California at Berkeley, won the 2011 Nobel Prize in Physics “for the discovery of the accelerating expansion of the Universe through observations of distant supernovae.” DOE’s Office of Science has supported Dr. Perlmutter’s research at Berkeley Lab since 1983. After the introduction from Secretary of Energy Steven Chu, Dr. Perlmutter delivered a presentation entitled "Supernovae, Dark Energy and the Accelerating Universe: Howmore » DOE Helped to Win (yet another) Nobel Prize." [Copied with editing from DOE Media Advisory issued January 10th, found at http://energy.gov/articles/energy-department-host-event-2011-physics-nobel-laureate-saul-perlmutter]« less

Professional Conduct: What can we learn from recent events?

NASA Astrophysics Data System (ADS)

2003-03-01

Recent evidence of professional misconduct in two different areas of physics has caused the community to think deeply about such issues. In November, the APS Council approved two new statements on professional ethics and a revised ``Guidelines for Professional Conduct." The panelists have all been involved in dealing with these issues; in particular, one served on the Berkeley review committee and another on the Lucent review committee. APS leadership is anxious to hear the views of the physics community and there will be considerable time for discussion. Moderator: Miriam Sarachik, CCNY-CUNY, APS President Panelists: Pierre Hohenberg, Yale University (2003 Lars Onsager Prize Recipient) ``What can we learn from other sciences?" Arthur Bienenstock, Stanford University ``APS response to recent events" George Trilling, Lawrence Berkeley National Laboratory ``What can we learn from the Berkeley experience?" Malcolm Beasley, Stanford University ``What can we learn from the Lucent experience?"

Genes and the Microenvironment: Two Faces of Breast Cancer (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gray, Joe; Love, Susan M.; Bissell, Min

In this April 21, 2008 Berkeley Lab event, a dynamic panel of Berkeley Lab scientists highlight breast cancer research advances related to susceptibility, early detection, prevention, and therapy - a biological systems approach to tackling the disease from the molecular and cellular levels, to tissues and organs, and ultimately the whole individual. Joe Gray, Berkeley Lab Life Sciences Division Director, explores how chromosomal abnormalities contribute to cancer and respond to gene-targeted therapies. Mina Bissell, former Life Sciences Division Director, approaches the challenge of breast cancer from the breast's three dimensional tissue microenvironment and how the intracellular ''conversation'' triggers malignancies. Marymore » Helen Barcellos-Hoff, Deputy Director, Life Sciences Division, identifies what exposure to ionizing radiation can tell us about how normal tissues suppress carcinogenesis. The panel is moderated by Susan M. Love, breast cancer research pioneer, author, President and Medical Director of the Dr. Susan Love Research Foundation.« less

Guidelines for generators to meet HWHF acceptance requirements for hazardous, radioactive, and mixed wastes at Berkeley Lab. Revision 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albert, R.

1996-06-01

This document provides performance standards that one, as a generator of hazardous chemical, radioactive, or mixed wastes at the Berkeley Lab, must meet to manage their waste to protect Berkeley Lab staff and the environment, comply with waste regulations and ensure the continued safe operation of the workplace, have the waste transferred to the correct Waste Handling Facility, and enable the Environment, Health and Safety (EH and S) Division to properly pick up, manage, and ultimately send the waste off site for recycling, treatment, or disposal. If one uses and generates any of these wastes, one must establish a Satellitemore » Accumulation Area and follow the guidelines in the appropriate section of this document. Topics include minimization of wastes, characterization of the wastes, containers, segregation, labeling, empty containers, and spill cleanup and reporting.« less

Quantification of Black Carbon and Other Pollutant Emissions from a Traditional and an Improved Cookstove

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirchstetter, Thomas; Preble, Chelsea; Hadley, Odelle

2010-11-05

Traditional methods of cooking in developing regions of the world emit pollutants that endanger the lives of billions of people and contribute to climate change. This study quantifies the emission of pollutants from the Berkeley-Darfur Stove and the traditional three-stone fire at the Lawrence Berkeley National Laboratory cookstove testing facility. The Berkeley-Darfur Stove was designed as a fuel efficient alternative to the three-stone fire to aid refugees in Darfur, who walk long distances from their camps and risk bodily harm in search of wood for cooking. A potential co-benefit of the more fuel efficient stove may be reduced pollutant emissions.more » This study measured emissions of carbon dioxide, carbon monoxide, particulate matter, and sunlight-absorbing black carbon. It also measured climate-relevant optical properties of the emitted particulate matter. Pollutant monitors were calibrated specifically for measuring cookstove smoke.« less

Distributed Energy Resource Optimization Using a Software as Service (SaaS) Approach at the University of California, Davis Campus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stadler, Michael; Marnay, Chris; Donadee, Jon

2011-02-06

Together with OSIsoft LLC as its private sector partner and matching sponsor, the Lawrence Berkeley National Laboratory (Berkeley Lab) won an FY09 Technology Commercialization Fund (TCF) grant from the U.S. Department of Energy. The goal of the project is to commercialize Berkeley Lab's optimizing program, the Distributed Energy Resources Customer Adoption Model (DER-CAM) using a software as a service (SaaS) model with OSIsoft as its first non-scientific user. OSIsoft could in turn provide optimization capability to its software clients. In this way, energy efficiency and/or carbon minimizing strategies could be made readily available to commercial and industrial facilities. Specialized versionsmore » of DER-CAM dedicated to solving OSIsoft's customer problems have been set up on a server at Berkeley Lab. The objective of DER-CAM is to minimize the cost of technology adoption and operation or carbon emissions, or combinations thereof. DER-CAM determines which technologies should be installed and operated based on specific site load, price information, and performance data for available equipment options. An established user of OSIsoft's PI software suite, the University of California, Davis (UCD), was selected as a demonstration site for this project. UCD's participation in the project is driven by its motivation to reduce its carbon emissions. The campus currently buys electricity economically through the Western Area Power Administration (WAPA). The campus does not therefore face compelling cost incentives to improve the efficiency of its operations, but is nonetheless motivated to lower the carbon footprint of its buildings. Berkeley Lab attempted to demonstrate a scenario wherein UCD is forced to purchase electricity on a standard time-of-use tariff from Pacific Gas and Electric (PG&E), which is a concern to Facilities staff. Additionally, DER-CAM has been set up to consider the variability of carbon emissions throughout the day and seasons. Two distinct analyses of value to UCD are possible using this approach. First, optimal investment choices for buildings under the two alternative objectives can be derived. Second, a week-ahead building operations forecaster has been written that executes DER-CAM to find an optimal operating schedule for buildings given their expected building energy services requirements, electricity prices, and local weather. As part of its matching contribution, OSIsoft provided a full implementation of PI and a server to install it on at Berkeley Lab. Using the PItoPI protocol, this gives Berkeley Lab researchers direct access to UCD's PI data base. However, this arrangement is in itself inadequate for performing optimizations. Additional data not included in UCD's PI database would be needed and the campus was not able to provide this information. This report details the process, results, and lessons learned of this commercialization project.« less

Obituary: Sumner P. Davis (1924-2008)

NASA Astrophysics Data System (ADS)

Feinberg, Jack

2011-12-01

University of California, Berkeley physicist Sumner P. Davis, a beloved teacher whose research centered on the optical spectroscopy of diatomic molecules found in the sun and other stars, died Dec. 31, 2008 in El Cerrito, CA after a brief illness. He was 84. After his military service during WWII, Davis finished his undergraduate work at UCLA in 1947, pursuing spectroscopy under the guidance of Joseph Ellis. Davis trained as a graduate student under molecular spectroscopist Francis Jenkins at UC Berkeley, where Davis used his ham radio expertise to construct an RF discharge to excite isotopes of diatomic selenium for his thesis. After receiving his Ph.D. from UC Berkeley, Davis went to MIT to postdoc under George Harrison, the premier artisan of finely-ruled diffraction gratings. In 1959, Jenkins invited Davis back to UC Berkeley to join the physics faculty, and Davis brought with him a highly prized gift - a diffraction grating presented to him by Harrison which Davis used for years to measure molecular spectra. At UC Berkeley Davis constructed a walk-in 15-foot-long spectrometer to produce detailed spectra of diatomic molecules of interest to astrophysics. With John G. Phillips he measured with high-precision the molecular constants of CN, C2, FeH, CS, SH and SiC2, TiO and others. Davis also studied the effect of the nuclear structure of Hg and Se on their optical spectra. He authored a book, Diffraction Grating Spectographs (1970), as well as monographs on CN and C2 spectra. Davis frequently traveled to the National Solar Observatory at Kitt Peak, to collect laboratory data using their Fourier transform spectrometer. He coauthored the book Fourier Transform Spectrometry (2001) with Mark C. Abrams and James Brault. In 1989, while returning to California after a long session on the spectrometer, his car, driven by Grace, his wife of 42 years, went off the road. Grace was killed but Sumner survived. Sumner Davis was, first and foremost, a consummate teacher: articulate and insightful, patient and empathetic. Joe Reader, a former student of Davis and now a director of the Atomic Spectroscopy Data Center at NIST in Gaithersburg, Maryland recalls: "Sumner always had an extremely positive attitude. When I told him that a vacuum pump I had built had exploded in the laboratory, he replied: "Well, now, we have to ask ourselves, what can we learn from this explosion?" Restless after his retirement in 1993, Davis returned to UC Berkeley for another decade to direct the upper division physics teaching laboratory. He created dozens of videos explaining the various laboratory experiments, ranging from Zeeman spectroscopy to Josephson junctions. Davis supervised 36 Ph.D.s during his career, many of whom became his lifelong friends. He would take his students bicycling through the Berkeley hills, and invite them to his home each Sunday evening to play music with other amateur musicians, with Davis playing (fairly respectable) oboe. Davis learned to fly as a young man while in the Army Air Corps, and he remained an avid glider pilot into his 80s. As recently as 2000, Davis served as president of the Pacific Soaring Council, Inc. He always offered his graduate students a ride in his glider, and Davis and his glider were pictured in National Geographic magazine after achieving an altitude record of 10,000+ feet over Arizona. He was a fellow of the American Physical Society and the Optical Society of America, and a member of the American Astronomical Society and the American Association of Physics Teachers. Upon his retirement, he received the Berkeley Citation. He was a NATO Senior Fellow in Science in 1967 and twice a visiting astronomer at the National Solar Observatory in Kitt Peak. Davis is survived by his wife, Robin Free, of El Cerrito, CA, who remarked, "He was like a 10-year-old boy. Every morning he would wake up and think, what adventures am I going to have today?" His recent e-mail sums up his spirit: "My desktop has been down for a week, and I am snowed with e-mail and behind on a few other things. Otherwise, all is well. We had 11 Chinese educators visit us, to look over all the labs. As I started to introduce our advanced lab, I put on my academic gown and a large conical wizard's cap, and told them how wizardry is necessary even in scientific Physics laboratories. I then made a pass through the lab rooms in my tie-dyed lab coat and the cat's hat from Dr. Seuss's Cat in the Hat. Got a few high fives from the students. The hat is now resting on the head of large giraffe in my office."

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

PubMed

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

2013-01-01

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

Hayward Fault rate constraints at Berkeley: Evaluation of the 335-meter Strawberry Creek offset

NASA Astrophysics Data System (ADS)

Williams, P. L.

2007-12-01

At UC Berkeley the active channel of Strawberry Creek is offset 335 meters by the Hayward fault and two abandoned channels of Strawberry Creek are laterally offset 580 and 730 meters. These relationships record the displacement of the northern Hayward fault at Berkeley over a period of tens of millennia. The Strawberry Creek site has a similar geometry to the central San Andreas fault's Wallace Creek site, which arguably provides the best geological evidence of "millennial" fault kinematics in California (Sieh and Jahns, 1984). Slip rate determinations are an essential component of overall hazard evaluation for the Hayward fault, and this site is ripe to disclose a long-term form of this parameter, to contrast with geodetic and other geological rate evidence. Large offsets at the site may lower uncertainty in the rate equation relative to younger sites, as the affect of stream abandonment age, generally the greatest source of rate uncertainty, is greatly reduced. This is helpful here because it more-than-offsets uncertainties resulting from piercing projections to the fault. Strawberry Creek and its ancestral channels suggest west-side-up vertical deformation across the Hayward fault at this location. The development of the vertical deformation parameter will complement ongoing geodetic measurements, particularly InSAR, and motivate testing of other geological constraints. Up-to-the-west motion across the Hayward fault at Berkeley has important implications for the partitioning of strain and kinematics of the northern Hayward fault, and may explain anomalous up-on-the-west landforms elsewhere along the fault. For example, geological features of the western Berkeley Hills are consistent with rapid and recent uplift to the west of the fault. On the basis of a preliminary analysis of the offset channels of Strawberry Creek, up-to-the-west uplift is about 0.5mm/yr across the Hayward fault at Berkeley. If this is in fact the long-term rate, the 150 m height of the Hills to the northwest of the Strawberry Creek site was produced during the past about 300,000 years by a significant dip- slip (thrust) component of Hayward fault motion. Rapid and recent uplift of some portions of the East Bay Hills has important implications for fault geometries and slope stability, and should strongly influence the investigation fault hazards in areas that are more complexly deformed.

Global Organization of a Positive-strand RNA Virus Genome

PubMed Central

Wu, Baodong; Grigull, Jörg; Ore, Moriam O.; Morin, Sylvie; White, K. Andrew

2013-01-01

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2′-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context. PMID:23717202

Fast Surface Reconstruction and Segmentation with Ground-Based and Airborne LIDAR Range Data

DTIC Science & Technology

2009-01-14

to perform a union find on the ground mesh vertices to calculate the sizes of ground mesh segments, 462 seconds to read the airborne data in to a...NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) University of...California at Berkeley,Department of Electrical Engineering and Computer Sciences,Berkeley,CA,94720 8. PERFORMING ORGANIZATION REPORT NUMBER 9

Carbon Cycle 2.0: Paul Alivisatos: Introduction

ScienceCinema

Paul Alivisatos

2017-12-09

Berkeley Lab Director Paul Alivisatos speaks at the Carbon Cycle 2.0 kick-off symposium Feb. 1, 2010. Humanity emits more carbon into the atmosphere than natural processes are able to remove - an imbalance with negative consequences.Carbon Cycle 2.0 is a Berkeley Lab initiative to provide the science needed to restore this balance by integrating the Labs diverse research activities and delivering creative solutions toward a carbon-neutral energy future. http://carboncycle2.lbl.gov/

Rational Arithmetic in Floating-Point.

DTIC Science & Technology

1986-09-01

RD-RI75 190 RATIONAL ARITHMETIC IN FLOTING-POINT(U) CALIFORNIA~UNIY BERKELEY CENTER FOR PURE AND APPLIED MATHEMATICS USI FE N KAHAN SEP 86 PRM-343...8217 ," .’,.-.’ .- " .- . ,,,.". ".. .. ". CENTER FOR PURE AND APPLIED MATHEMATICS UNIVERSITY OF CALIFORNIA, BERKELEY PAf4343 0l RATIONAL ARITHMIETIC IN FLOATING-POINT W. KAHAN SETMER18 SEPTEMBE...delicate balance between, on the one hand, the simplicity and aesthetic appeal of the specifications and, on the other hand, the complexity and

Access Point Selection for Multi-Rate IEEE 802.11 Wireless LANs

DTIC Science & Technology

2014-05-16

Mobile Systems, Applications and Services, 2006. [2] S . Vasudevan, K. Papagiannaki, C . Diot, J. Kurose, and D. Towsley, “Facilitating Access Point...LANs 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7...PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) University of California at Berkeley,Electrical Engineering and Computer Sciences,Berkeley,CA,94720 8

(NII) Novel Catalytic, Synthesis Methods for Main Group

DTIC Science & Technology

2014-12-23

Hydride Complex.” Dalt. Trans. 2014, 43, 10046–10056. 7. Johnson, M. W.; Bagley , S . W.; Mankad, N. P.; Bergman, R. G.; Mascitti, V.; Toste, F. D...6. AUTHOR( S ) Bergman, Robert G. Arnold, John Toste, F. Dean 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION...NAME( S ) AND ADDRESS(ES) Regents of the University of California, Berkeley 2220 Piedmont Ave, Berkeley, CA 94720 8. PERFORMING ORGANIZATION REPORT

PART 1 OF 2 PART PANORAMA WITH NO. CA213 VIEW ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

PART 1 OF 2 PART PANORAMA WITH NO. CA-2-13 VIEW OF PIEDMONT AVENUE TRAFFIC CIRCLE AT INTERSECTION OF CHANNING WAY WITH VIW AT REAR OF ALPHA SIGMA PHI HOUSE BY WILLIAM C. HAYS, 1920, AT 2739 CHANNING. SEEN FROM SE CORNER LOOKING WEST. Photograph by Brian Grogan, July 8, 2007 - Piedmont Way & the Berkeley Property Tract, East of College Avenue between Dwight Way & U.C. Memorial Stadium, Berkeley, Alameda County, CA

Single-Event Effect Testing of the Linear Technology LTC6103HMS8#PBF Current Sense Amplifier

NASA Technical Reports Server (NTRS)

Yau, Ka-Yen; Campola, Michael J.; Wilcox, Edward

2016-01-01

The LTC6103HMS8#PBF (henceforth abbreviated as LTC6103) current sense amplifier from Linear Technology was tested for both destructive and non-destructive single-event effects (SEE) using the heavy-ion cyclotron accelerator beam at Lawrence Berkeley National Laboratory (LBNL) Berkeley Accelerator Effects (BASE) facility. During testing, the input voltages and output currents were monitored to detect single event latch-up (SEL) and single-event transients (SETs).

Multicore: Fallout from a Computing Evolution

ScienceCinema

Yelick, Kathy [Director, NERSC

2017-12-09

July 22, 2008 Berkeley Lab lecture: Parallel computing used to be reserved for big science and engineering projects, but in two years that's all changed. Even laptops and hand-helds use parallel processors. Unfortunately, the software hasn't kept pace. Kathy Yelick, Director of the National Energy Research Scientific Computing Center at Berkeley Lab, describes the resulting chaos and the computing community's efforts to develop exciting applications that take advantage of tens or hundreds of processors on a single chip.

Queries and Views of Programs Using a Relational Database System

DTIC Science & Technology

1983-12-01

look different but you have changed. I’m looking through you, you’re not the same! - from the song I’m looking through you by the Beatles Seeing...Berkeley, CA 94720 December 1983 Submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Computer Science...in the Graduate Division of the University of California, Berkeley. Copyright© 1983 by Mark A. Linton Research supported by NSF grant MCS-8010686

Carbon Cycle 2.0: Paul Alivisatos: Introduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paul Alivisatos

2010-02-09

Berkeley Lab Director Paul Alivisatos speaks at the Carbon Cycle 2.0 kick-off symposium Feb. 1, 2010. Humanity emits more carbon into the atmosphere than natural processes are able to remove - an imbalance with negative consequences.Carbon Cycle 2.0 is a Berkeley Lab initiative to provide the science needed to restore this balance by integrating the Labs diverse research activities and delivering creative solutions toward a carbon-neutral energy future. http://carboncycle2.lbl.gov/

Secrets of the Soil (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brodie, Eoin; Northen, Trent; Jansson, Janet

2011-11-07

Four Berkeley Lab scientists unveil the "Secrets of the Soil"at this Nov. 7, 2011 Science at the Theater event. Eoin Brodie, Janet Jansson, Margaret Torn and Trent Northen talk about their research and how soil could hold the key to our climate and energy future.The discussion was moderated by John Harte, who holds a joint professorship in the Energy and Resources Group and the Ecosystem Sciences Division of UC Berkeley's College of Natural Resources

Defense Planning in the Ministry of Defense of Ukraine: Decade of Attempts and Mistakes

DTIC Science & Technology

2015-06-01

Defense. (University of California Press, Berkeley and Los Angeles , 1967). 22 but due to the Soviet Union basis system, it is not as efficient in...Making for Defense. University of California Press, Berkeley and Los Angeles , 1967. Hitch, Charles Johnston and Roland N. McKean. The Economics of...loss of defense is not an instantaneous phenomenon. This phenomenon has led to human disorder, blind and continuous personnel downsizing, reform of the

Ernest Orlando Berkeley National Laboratory - Fundamental and applied research on lean premixed combustion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Robert K.

Ernest Orland Lawrence Berkeley National Laboratory (Berkeley Lab) is the oldest of America's national laboratories and has been a leader in science and engineering technology for more than 65 years, serving as a powerful resource to meet Us national needs. As a multi-program Department of Energy laboratory, Berkeley Lab is dedicated to performing leading edge research in the biological, physical, materials, chemical, energy, environmental and computing sciences. Ernest Orlando Lawrence, the Lab's founder and the first of its nine Nobel prize winners, invented the cyclotron, which led to a Golden Age of particle physics and revolutionary discoveries about the naturemore » of the universe. To this day, the Lab remains a world center for accelerator and detector innovation and design. The Lab is the birthplace of nuclear medicine and the cradle of invention for medical imaging. In the field of heart disease, Lab researchers were the first to isolate lipoproteins and the first to determine that the ratio of high density to low density lipoproteins is a strong indicator of heart disease risk. The demise of the dinosaurs--the revelation that they had been killed off by a massive comet or asteroid that had slammed into the Earth--was a theory developed here. The invention of the chemical laser, the unlocking of the secrets of photosynthesis--this is a short preview of the legacy of this Laboratory.« less

Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

PubMed Central

Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

2011-01-01

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

Site Environmental Report for 2009, Volume I

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lackner, Regina

2010-08-17

Each year, the University of California (UC), as the managing and operating contractor of the Ernest Orlando Lawrence Berkeley National Laboratory, prepares an integrated report regarding its environmental programs to satisfy the requirements of United States Department of Energy (DOE) Order 231.1A, Environment, Safety, and Health Reporting.1 The Site Environmental Report for 2009 summarizes Berkeley Lab's environmental management performance, presents environmental monitoring results, and describes significant programs for calendar year (CY) 2009. Throughout this report, 'Berkeley Lab' or 'LBNL' refers both to (1) the multiprogram scientific facility the UC manages and operates on the 202-acre university-owned site located in themore » hills above the UC Berkeley campus, and the site itself, and (2) the UC as managing and operating contractor for Ernest Orlando Lawrence Berkeley National Laboratory. The report is separated into two volumes. Volume I is organized into an executive summary followed by six chapters that contain an overview of LBNL, a discussion of its environmental management system (EMS), the status of environmental programs, summarized results from surveillance and monitoring activities, and quality assurance (QA) measures. Volume II contains individual data results from surveillance and monitoring activities. The Site Environmental Report is distributed by releasing it on the World Wide Web (Web) from the Berkeley Lab Environmental Services Group (ESG) home page, which is located at www.lbl.gov/ehs/esg/. Many of the documents cited in this report also are accessible from the ESG Web page. Links to documents available on the Web are given with the citations in the References section. CD and printed copies of this Site Environmental Report are available upon request. The report follows Berkeley Lab's policy of using the International System of Units (SI), also known as the metric system of measurements. Whenever possible, results are also reported using the more conventional (non-SI) system of measurements, because the non-SI system is referenced by several current regulatory standards and is more familiar to some readers. Two tables are provided at the end of the Glossary to help readers: Table G-1 defines the prefixes used with SI units of measurement, and Table G-2 provides conversions to non-SI units. Years mentioned in this report refer to calendar years unless specified as fiscal year(s). Berkeley Lab's fiscal year (FY) is October 1 to September 30, and begins in the year previous to its name, i.e., FY 2009 was from October 1, 2008, to September 30, 2009. For ease of reference, a key to acronyms and abbreviations used in this report can be found directly after the text, at the end of Chapter 6. Following that is also a glossary for readers who may be unfamiliar with some of the terms used in this report. This report was prepared under the direction of Ron Pauer of ESG. Please address any questions regarding this report to him by telephone at 510-486-7614, or by e-mail at ropauer@lbl.gov. The primary contributors were David Baskin, Tim Bauters, Ned Borglin, Robert Fox, John Jelinski, Ginny Lackner, Patrick Thorson, Linnea Wahl, and Suying Xu (Volume II). Readers are encouraged to comment on this report by completing the survey form found at the ESG Web page where this report is available.« less

Earth Observations taken by the Expedition 13 crew

NASA Image and Video Library

2006-08-02

ISS013-E-63766 (2 Aug. 2006) --- Berkeley Pit and Butte, Montana are featured in this image photographed by an Expedition 13 crewmember on the International Space Station. The city of Butte, Montana has long been a center of mining activity. Underground mining of copper began in Butte in the 1870s, and by 1901 underground workings had extended to the groundwater table. Thus began the creation of an intricate complex of underground drains and pumps to lower the groundwater level and continue the extraction of copper. Water extracted from the mines was so rich in dissolved copper sulfate that it was also "mined" (by chemical precipitation) for the copper it contained. In 1955, the Anaconda Copper Mining Company began open-pit mining for copper in what is now know as the Berkeley Pit (dark oblong area in center). The mine took advantage of the existing subterranean drainage and pump network to lower groundwater until 1982, when the new owner ARCO suspended operations at the mine. The groundwater level swiftly rose, and today water in the Pit is more than 900 feet deep. Many features of the mine workings are visible in this image such as the many terraced levels and access roadways of the open mine pits (gray and tan sculptured surfaces). A large gray tailings pile of waste rock and an adjacent tailings pond are visible to the north of the Berkeley Pit. Color changes in the tailings pond are due primarily to changing water depth. The Berkeley Pit is listed as a federal Superfund site due to its highly acidic water, which contains high concentrations of metals such as copper and zinc. The Berkeley Pit receives groundwater flowing through the surrounding bedrock and acts as a "terminal pit" or sink for these heavy metal-laden waters. Ongoing efforts include regulation of water flow into the pit to reduce filling of the Pit and potential release of contaminated water into local aquifers or surface streams.

Berkeley Lab Sheds Light on Improving Solar Cell Efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lawrence Berkeley National Laboratory

2007-07-20

Typical manufacturing methods produce solar cells with an efficiency of 12-15%; and 14% efficiency is the bare minimum for achieving a profit. In work performed at the Ernest Orlando Lawrence Berkeley National Laboratory (Berkeley, CA, 5 10-486-577 1)--a US Department of Energy national laboratory that conducts unclassified scientific research and is managed by the University of California--scientist Scott McHugo has obtained keen insights into the impaired performance of solar cells manufactured from polycrystalline silicon. The solar cell market is potentially vast, according to Berkeley Lab. Lightweight solar panels are highly beneficial for providing electrical power to remote locations in developingmore » nations, since there is no need to build transmission lines or truck-in generator fuel. Moreover, industrial nations confronted with diminishing resources have active programs aimed at producing improved, less expensive solar cells. 'In a solar cell, there is a junction between p-type silicon and an n-type layer, such as diffused-in phosphorous', explained McHugo, who is now with Berkeley Lab's Accelerator and Fusion Research Division. 'When sunlight is absorbed, it frees electrons, which start migrating in a random-walk fashion toward that junction. If the electrons make it to the junction; they contribute to the cell's output of electric current. Often, however, before they reach the junction, they recombine at specific sites in the crystal' (and, therefore, cannot contribute to current output). McHugo scrutinized a map of a silicon wafer in which sites of high recombination appeared as dark regions. Previously, researchers had shown that such phenomena occurred not primarily at grain boundaries in the polycrystalline material, as might be expected, but more often at dislocations in the crystal. However, the dislocations themselves were not the problem. Using a unique heat treatment technique, McHugo performed electrical measurements to investigate the material at the dislocations. He was purportedly the first to show that they were 'decorated' with iron.« less

Physics 101: What Our Next President Needs to Know (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muller, Rich

2008-10-13

Rich Muller, author of Physics for Future Presidents, argues that the next president can't afford to be ignorant about the science behind terrorism, nuclear dangers, energy, space, and global warming. Muller, a MacArthur Fellow, Berkeley Lab physicist, and one of the most popular lecturers at UC Berkeley, discusses what it takes to survive in today's increasingly dangerous world -- information essential to the next commander-in-chief. He presented his talk Oct. 13, 2008.

A Call to Action: Carbon Cycle 2.0 (Carbon Cycle 2.0)

ScienceCinema

Alivisatos, Paul [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2018-05-21

Berkeley Lab Director Paul Alivisatos speaks at the Carbon Cycle 2.0 kick-off symposium Feb. 1, 2010. Humanity emits more carbon into the atmosphere than natural processes are able to remove - an imbalance with negative consequences.Carbon Cycle 2.0 is a Berkeley Lab initiative to provide the science needed to restore this balance by integrating the Labs diverse research activities and delivering creative solutions toward a carbon-neutral energy future. http://carboncycle2.lbl.gov/

Global Impacts (Carbon Cycle 2.0)

ScienceCinema

Gadgil, Ashok

2018-05-04

Ashok Gadgil, Faculty Senior Scientist and Acting Director, EETD, also Professor of Environmental Engineering, UC Berkeley, speaks at the Carbon Cycle 2.0 kick-off symposium Feb. 2, 2010. We emit more carbon into the atmosphere than natural processes are able to remove - an imbalance with negative consequences. Carbon Cycle 2.0 is a Berkeley Lab initiative to provide the science needed to restore this balance by integrating the Labs diverse research activities and delivering creative solutions toward a carbon-neutral energy future.

Berkeley Lab scientists develop criteria for $20 million energy challenge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, Iain

2009-08-26

Berkeley Labs Iain Walker and his colleagues in environmental energy research helped the Siebel Foundation develop the criteria for its Energy Free Home Challenge, which comes with a $20 million global incentive prize. The Challenge is a competition to create a new generation of systems and technologies for practical homes that realize a net-zero, non-renewable energy footprint without increasing the cost of ownership. It is open to everyone everywhere — university teams to handymen and hobbyists.

2nd CRISPR Research Conference Berkeley, CA, July 23-25 2009

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banfield, Jillian

The second meeting dedicated to the topic of clustered, regularly interspaced palindromic repeat (CRISPR)-based microbial immunity to viruses was held in Berkeley on July 23 and 25, 2009. The goal of this meeting was to stimulate discussion and advance understanding of the recently described acquired viral resistance system in bacteria and archaea and to explore its relevance in natural populations and communities. The meeting involved around X scientists with a range of backgrounds, with a program designed for extensive discussion.

Imaging the Voices of the Past: Using Physics to Restore Early Sound Recordings (LBNL Summer Lecture Series)

ScienceCinema

Haber, Carl [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2018-01-23

Summer Lecture Series 2006: Physicist Carl Haber and colleagues have found a way to digitize century-old recordings believed to be unplayable, and as a result, some of the music and spoken word recordings in the Library of Congress collection may spring back to life. Learn how basic scientific research done at Berkeley Lab may yield results of benefit in other areas of science and culture. Series: "Lawrence Berkeley National Laboratory Summer Lecture Series"

Popular Berkeley Lab X-ray Data Booklet reissued

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, Art

2001-03-02

X-ray scientists and synchrotron-radiation users who have been patiently waiting for an updated version of the popular X-Ray Data Booklet last published in 1986 by the Center for X-Ray Optics at the Lawrence Berkeley National Laboratory can breathe a sigh of relief. The venerable ''little orange book'' has now been reissued under the auspices of CXRO and the Advanced Light Source (ALS) with an April printing of 10,000 paper copies and the posting of a Web edition at http://xdb.lbl.gov.

Physics 101: What Our Next President Needs to Know (LBNL Science at the Theater)

ScienceCinema

Muller, Rich

2018-06-12

Rich Muller, author of Physics for Future Presidents, argues that the next president can't afford to be ignorant about the science behind terrorism, nuclear dangers, energy, space, and global warming. Muller, a MacArthur Fellow, Berkeley Lab physicist, and one of the most popular lecturers at UC Berkeley, discusses what it takes to survive in today's increasingly dangerous world -- information essential to the next commander-in-chief. He presented his talk Oct. 13, 2008.

Looking for Hazardous Pollutants in Your Kitchen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Brett

2013-07-22

For decades, teams of Berkeley Lab scientists have investigated the ways that indoor air quality affects human health. In Berkeley Lab's test kitchen scientist Brett Singer and his team are measuring the pollutants emitted by cooking foods and evaluating how effective various range hoods are in capturing the pollutants. In an unprecedented recent study, the scientists estimated that 60 percent of homes in California that cook at least once a week with a gas stove can reach pollutant levels that would be illegal if found outdoors.

Use of a krypton isotope for rapid ion changeover at the Lawrence Berkeley Laboratory 88-inch cyclotron

NASA Technical Reports Server (NTRS)

Soli, George A.; Nichols, Donald K.

1989-01-01

An isotope of krypton, Kr86, has been combined with a mix of Ar, Ne, and N ions at the electron cyclotron resonance (ECR) source, at the Lawrence Berkeley Laboratory cyclotron, to provide rapid ion changeover in Single Event Phenomena (SEP) testing. The new technique has been proved out successfully by a recent Jet Propulsion Laboratory (JPL) test in which it was found that there was no measurable contamination from other isotopes.

Berkeley Lab scientists develop criteria for $20 million energy challenge

ScienceCinema

Walker, Iain

2017-12-12

Berkeley Labs Iain Walker and his colleagues in environmental energy research helped the Siebel Foundation develop the criteria for its Energy Free Home Challenge, which comes with a $20 million global incentive prize. The Challenge is a competition to create a new generation of systems and technologies for practical homes that realize a net-zero, non-renewable energy footprint without increasing the cost of ownership. It is open to everyone everywhere — university teams to handymen and hobbyists.

Closing the Loop: Control and Robot Navigation in Wireless Sensor Networks

DTIC Science & Technology

2006-09-05

University of California at Berkeley Technical Report No. UCB/EECS- 2006 -112 http://www.eecs.berkeley.edu/Pubs/TechRpts/ 2006 /EECS- 2006 -112.html September 5... 2006 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to average 1...DATE 05 SEP 2006 2. REPORT TYPE 3. DATES COVERED 00-00- 2006 to 00-00- 2006 4. TITLE AND SUBTITLE Closing the Loop: Control and Robot Navigation in

Looking for Hazardous Pollutants in Your Kitchen

ScienceCinema

Singer, Brett

2018-02-14

For decades, teams of Berkeley Lab scientists have investigated the ways that indoor air quality affects human health. In Berkeley Lab's test kitchen scientist Brett Singer and his team are measuring the pollutants emitted by cooking foods and evaluating how effective various range hoods are in capturing the pollutants. In an unprecedented recent study, the scientists estimated that 60 percent of homes in California that cook at least once a week with a gas stove can reach pollutant levels that would be illegal if found outdoors.

Interfacing the VAX 11/780 Using Berkeley Unix 4.2.BSD and Ethernet Based Xerox Network Systems. Volume 1.

DTIC Science & Technology

1984-12-01

3Com Corporation ....... A-18 Ethernet Controller Support . . . . . . A-19 Host Systems Support . . . . . . . . . A-20 Personal Computers Support...A-23 VAX EtherSeries Software 0 * A-23 Network Research Corporation . o o o . o A-24 File Transfer Service . . . . o A-25 Virtual Terminal Service 0...Control office is planning to acquire a Digital Equipment Corporation VAX 11/780 mainframe computer with the Unix Berkeley 4.2BSD operating system. They

Challenges in NMR-based structural genomics

NASA Astrophysics Data System (ADS)

Sue, Shih-Che; Chang, Chi-Fon; Huang, Yao-Te; Chou, Ching-Yu; Huang, Tai-huang

2005-05-01

Understanding the functions of the vast number of proteins encoded in many genomes that have been completely sequenced recently is the main challenge for biologists in the post-genomics era. Since the function of a protein is determined by its exact three-dimensional structure it is paramount to determine the 3D structures of all proteins. This need has driven structural biologists to undertake the structural genomics project aimed at determining the structures of all known proteins. Several centers for structural genomics studies have been established throughout the world. Nuclear magnetic resonance (NMR) spectroscopy has played a major role in determining protein structures in atomic details and in a physiologically relevant solution state. Since the number of new genes being discovered daily far exceeds the number of structures determined by both NMR and X-ray crystallography, a high-throughput method for speeding up the process of protein structure determination is essential for the success of the structural genomics effort. In this article we will describe NMR methods currently being employed for protein structure determination. We will also describe methods under development which may drastically increase the throughput, as well as point out areas where opportunities exist for biophysicists to make significant contribution in this important field.

Reducing Our Carbon Footprint: Converting Plants to Fuel (LBNL Science at the Theater)

ScienceCinema

Somerville, Chris [Univ. of California, Berkeley, CA (United States)

2018-05-23

Berkeley Lab's Chris Somerville is a leading authority on the structure and function of plant cell walls, which comprise most of the body mass of higher plants. He views the knowledge of cell wall structure and function as furthering the development of plants with improved usefulness: these plants are strong potential sources of renewable materials and biofuel feedstocks. His scientific expertise defines an ideal match of his interest - in the development of cellulosic and other solar-to-fuel science - with his recent appointment as Director of the Energy Biosciences Institute (EBI). With colleagues in biology, physical sciences, engineering, and environmental and the social sciences, he now leads the EBI multidisciplinary teams' research efforts to develop next-generation, carbon-neutral transportation fuels.

Optimized guide RNA structure for genome editing via Cas9

PubMed Central

Xu, Jianyong; Lian, Wei; Jia, Yuning; Li, Lingyun; Huang, Zhong

2017-01-01

The genome editing tool Cas9-gRNA (guide RNA) has been successfully applied in different cell types and organisms with high efficiency. However, more efforts need to be made to enhance both efficiency and specificity. In the current study, we optimized the guide RNA structure of Streptococcus pyogenes CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system to improve its genome editing efficiency. Comparing with the original functional structure of guide RNA, which is composed of crRNA and tracrRNA, the widely used chimeric gRNA has shorter crRNA and tracrRNA sequence. The deleted RNA sequence could form extra loop structure, which might enhance the stability of the guide RNA structure and subsequently the genome editing efficiency. Thus the genome editing efficiency of different forms of guide RNA was tested. And we found that the chimeric structure of gRNA with original full length of crRNA and tracrRNA showed higher genome editing efficiency than the conventional chimeric structure or other types of gRNA we tested. Therefore our data here uncovered the new type of gRNA structure with higher genome editing efficiency. PMID:29212218

Hydraulic Conductivity Measurements Barrow 2014

DOE Data Explorer

Katie McKnight; Tim Kneafsey; Craig Ulrich; Jil Geller

2015-02-22

Six individual ice cores were collected from Barrow Environmental Observatory in Barrow, Alaska, in May of 2013 as part of the Next Generation Ecosystem Experiment (NGEE). Each core was drilled from a different location at varying depths. A few days after drilling, the cores were stored in coolers packed with dry ice and flown to Lawrence Berkeley National Laboratory (LBNL) in Berkeley, CA. 3-dimensional images of the cores were constructed using a medical X-ray computed tomography (CT) scanner at 120kV. Hydraulic conductivity samples were extracted from these cores at LBNL Richmond Field Station in Richmond, CA, in February 2014 by cutting 5 to 8 inch segments using a chop saw. Samples were packed individually and stored at freezing temperatures to minimize any changes in structure or loss of ice content prior to analysis. Hydraulic conductivity was determined through falling head tests using a permeameter [ELE International, Model #: K-770B]. After approximately 12 hours of thaw, initial falling head tests were performed. Two to four measurements were collected on each sample and collection stopped when the applied head load exceeded 25% change from the original load. Analyses were performed between 2 to 3 times for each sample. The final hydraulic conductivity calculations were computed using methodology of Das et al., 1985.

X-ray Micro-Tomography of Ablative Heat Shield Materials

NASA Technical Reports Server (NTRS)

Panerai, Francesco; Ferguson, Joseph; Borner, Arnaud; Mansour, Nagi N.; Barnard, Harold S.; MacDowell, Alastair A.; Parkinson, Dilworth Y.

2016-01-01

X-ray micro-tomography is a non-destructive characterization technique that allows imaging of materials structures with voxel sizes in the micrometer range. This level of resolution makes the technique very attractive for imaging porous ablators used in hypersonic entry systems. Besides providing a high fidelity description of the material architecture, micro-tomography enables computations of bulk material properties and simulations of micro-scale phenomena. This presentation provides an overview of a collaborative effort between NASA Ames Research Center and Lawrence Berkeley National Laboratory, aimed at developing micro-tomography experiments and simulations for porous ablative materials. Measurements are carried using x-rays from the Advanced Light Source at Berkeley Lab on different classes of ablative materials used in NASA entry systems. Challenges, strengths and limitations of the technique for imaging materials such as lightweight carbon-phenolic systems and woven textiles are discussed. Computational tools developed to perform numerical simulations based on micro-tomography are described. These enable computations of material properties such as permeability, thermal and radiative conductivity, tortuosity and other parameters that are used in ablator response models. Finally, we present the design of environmental cells that enable imaging materials under simulated operational conditions, such as high temperature, mechanical loads and oxidizing atmospheres.Keywords: Micro-tomography, Porous media, Ablation

Big Thinking: The Power of Nanoscience (LBNL Science at the Theater)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milliron, Delia; Sanili, Babak; Weber-Bargioni, Alex

2011-06-06

Science at the Theater, June 6th, 2011: Berkeley Lab scientists reveal how nanoscience will bring us cleaner energy, faster computers, and improved medicine. Alex Weber-Bargioni: How can we see things at the nanoscale? Alex is pioneering new methods that provide unprecedented insight into nanoscale materials and molecular interactions. The goal is to create rules for building nanoscale materials. Babak Sanii: Nature is an expert at making nanoscale devices such as proteins. Babak is developing ways to see these biological widgets, which could help scientists develop synthetic devices that mimic the best that nature has to offer. Ting Xu: How aremore » we going to make nanoscale devices? A future in which materials and devices are able to assemble themselves may not be that far down the road. Ting is finding ways to induce a wide range of nanoscopic building blocks to assemble into complex structures. Delia Milliron: The dividends of nanoscience could reshape the way we live, from smart windows and solar cells to artificial photosynthesis and improved medical diagnosis. Delia is at the forefront of converting fundamental research into nanotechnology. Moderated by Jim DeYoreo, interim director of the Molecular Foundry, a facility located at Berkeley Lab where scientists from around the world address the myriad challenges in nanoscience.« less

Producing genome structure populations with the dynamic and automated PGS software.

PubMed

Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

2018-05-01

Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

Berkeley extreme-ultraviolet airglow rocket spectrometer: BEARS.

PubMed

Cotton, D M; Chakrabarti, S

1992-09-20

We describe the Berkeley extreme-UV airglow rocket spectrometer, which is a payload designed to test several thermospheric remote-sensing concepts by measuring the terrestrial O I far-UV and extreme-UV dayglow and the solar extreme-UV spectrum simultaneously. The instrument consisted of two near-normal Rowland mount spectrometers and a Lyman-alpha photometer. The dayglow spectrometer covered two spectral regions from 980 to 1040 A and from 1300 to 1360 A with 1.5-A resolution. The solar spectrometer had a bandpass of 250-1150 A with an ~ 10-A resolution. All three spectra were accumulated by using a icrochannel-plate-intensified, two-dimensional imaging detector with three separate wedge-and strip anode readouts. The hydrogen Lyman-alpha photometer was included to monitor the solar Lyman-alpha irradiance and geocoronal Lyman-alpha emissions. The instrument was designed, fabricated, and calibrated at the University of California, Berkeley and was successfully launched on 30 September 1988 aboard the first test flight of a four-stage sounding rocket, Black Brant XII.

Higher transcription levels in ascorbic acid biosynthetic and recycling genes were associated with higher ascorbic acid accumulation in blueberry.

PubMed

Liu, Fenghong; Wang, Lei; Gu, Liang; Zhao, Wei; Su, Hongyan; Cheng, Xianhao

2015-12-01

In our preliminary study, the ripe fruits of two highbush blueberry (Vaccinium corymbosum L.) cultivars, cv 'Berkeley' and cv 'Bluecrop', were found to contain different levels of ascorbic acid. However, factors responsible for these differences are still unknown. In the present study, ascorbic acid content in fruits was compared with expression profiles of ascorbic acid biosynthetic and recycling genes between 'Bluecrop' and 'Berkeley' cultivars. The results indicated that the l-galactose pathway was the predominant route of ascorbic acid biosynthesis in blueberry fruits. Moreover, higher expression levels of the ascorbic acid biosynthetic genes GME, GGP, and GLDH, as well as the recycling genes MDHAR and DHAR, were associated with higher ascorbic acid content in 'Bluecrop' compared with 'Berkeley', which indicated that a higher efficiency ascorbic acid biosynthesis and regeneration was likely to be responsible for the higher ascorbic acid accumulation in 'Bluecrop'. Copyright © 2015 Elsevier Ltd. All rights reserved.

BErkeley Atmospheric CO2 Network (BEACON) - Bringing Measurements of CO2 Emissions to a School Near You

NASA Astrophysics Data System (ADS)

Teige, V. E.; Havel, E.; Patt, C.; Heber, E.; Cohen, R. C.

2011-12-01

The University of California at Berkeley in collaboration with the Chabot Space and Science Center describe a set of educational programs, workshops, and exhibits based on a multi-node greenhouse gas and air quality monitoring network being deployed over Oakland, California. Examining raw numerical data using highly engaging and effective geo-data visualization tools like Google Earth can make the science come alive for students, and provide a hook for drawing them into deeper investigations. The Climate Science Investigations teacher workshop at the Chabot Space and Science Center will make use of Google Earth, Excel, and other geo-data visualization tools to step students through the process from data acquisition to discovery. Using multiple data sources, including output from the BErkeley Atmospheric CO2 Network (BEACON) project, participants will be encouraged to explore a variety of different modes of data display toward producing a unique, and ideally insightful, illumination of the data.

Supernovae, Dark Energy and the Accelerating Universe: How DOE Helped to Win (yet another) Nobel Prize

ScienceCinema

Perlmutter, Saul; Chu, Steven

2018-05-31

The Department of Energy (DOE) hosted an event Friday, January 13, with 2011 Physics Nobel Laureate Saul Perlmutter. Dr. Perlmutter, a physicist at the Department’s Lawrence Berkeley National Laboratory and a professor of physics at the University of California at Berkeley, won the 2011 Nobel Prize in Physics “for the discovery of the accelerating expansion of the Universe through observations of distant supernovae.” DOE’s Office of Science has supported Dr. Perlmutter’s research at Berkeley Lab since 1983. After the introduction from Secretary of Energy Steven Chu, Dr. Perlmutter delivered a presentation entitled "Supernovae, Dark Energy and the Accelerating Universe: How DOE Helped to Win (yet another) Nobel Prize." [Copied with editing from DOE Media Advisory issued January 10th, found at http://energy.gov/articles/energy-department-host-event-2011-physics-nobel-laureate-saul-perlmutter

G2S: a web-service for annotating genomic variants on 3D protein structures.

PubMed

Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

2018-06-01

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online.

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.

PubMed

Liu, Siyang; Huang, Shujia; Rao, Junhua; Ye, Weijian; Krogh, Anders; Wang, Jun

2015-01-01

Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the de novo assembly strategy for definition of genome structure.

The Western Environmental Technology Office (WETO), Butte, Montana. Technology summary

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-03-01

The Western Environmental Technology Office (WETO) is a multi-purpose engineering test facility located in Butte, Montana, and is managed by MSE, Inc. WETO seeks to contribute to environmental research by emphasizing projects to develop heavy metals removal and recovery processes, thermal vitrification systems, and waste minimization/pollution prevention technologies. WETO`s environmental technology research and testing activities focus on the recovery of usable resources from waste. In one of WETO`s areas of focus, groundwater contamination, water from the Berkeley Pit, located near the WETO site, is being used in demonstrations directed toward the recovery of potable water and metal from the heavymore » metal-bearing water. The Berkeley Pit is part of an inactive copper mine near Butte that was once part of the nation`s largest open-pit mining operation. The Pit contains approximately 25 billion gallons of Berkeley Pit groundwater and surface water containing many dissolved minerals. As part of DOE/OST`s Resource Recovery Project (RRP), technologies are being demonstrated to not only clean the contaminated water but to recover metal values such as copper, zinc, and iron with an estimated gross value of more than $100 million. When recovered, the Berkeley Pit waters could benefit the entire Butte valley with new water resources for fisheries, irrigation, municipal, and industrial use. At WETO, the emphasis is on environmental technology development and commercialization activities, which will focus on mine cleanup, waste treatment, resource recovery, and water resource management.« less

The Paris-Sud yeast structural genomics pilot-project: from structure to function.

PubMed

Quevillon-Cheruel, Sophie; Liger, Dominique; Leulliot, Nicolas; Graille, Marc; Poupon, Anne; Li de La Sierra-Gallay, Inès; Zhou, Cong-Zhao; Collinet, Bruno; Janin, Joël; Van Tilbeurgh, Herman

2004-01-01

We present here the outlines and results from our yeast structural genomics (YSG) pilot-project. A lab-scale platform for the systematic production and structure determination is presented. In order to validate this approach, 250 non-membrane proteins of unknown structure were targeted. Strategies and final statistics are evaluated. We finally discuss the opportunity of structural genomics programs to contribute to functional biochemical annotation.

Exact Chiral Spin Liquid with Stable Spin Fermi Surface on the Kagome Lattice

DTIC Science & Technology

2011-05-17

REVIEW B 83, 180412(R) (2011) FIG. 3. (a) Band structure on a cylindrical geometry for J = J ′ = 1.0, J∇ = J ′∇ = 0.8, J5 = 0. There are two gapless...Grant No. DMR-0955778 (V.C. and G.A.F.) at Austin and DOE Grant No. DE -AC02- 05CH11231 (HY) at Berkeley. 1S. A. Kivelson, D. S. Rokhsar, and J. P...Helton et al., Phys. Rev. Lett. 98, 107204 (2007). 32D. F. Schroeter, E. Kapit , R. Thomale, and M. Greiter, Phys. Rev. Lett. 99, 97202 (2007). 33E. H

Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

PubMed

Uchiyama, Ikuo

2008-10-31

Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

Multiscale modeling of three-dimensional genome

NASA Astrophysics Data System (ADS)

Zhang, Bin; Wolynes, Peter

The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

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

PubMed

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

2016-08-26

Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates. We present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D . G23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

USDA-ARS?s Scientific Manuscript database

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identi...

The Energy Problem: What the Helios Project Can Do About it (LBNL Science at the Theater)

ScienceCinema

Chu, Steven

2018-06-15

The energy problem is one of the most important issues that science and technology has to solve. Nobel laureate and Berkeley Lab Director Steven Chu proposes an aggressive research program to transform the existing and future energy systems of the world away from technologies that emit greenhouse gases. Berkeley Lab's Helios Project concentrates on renewable fuels, such as biofuels, and solar technologies, including a new generation of solar photovoltaic cells and the conversion of electricity into chemical storage to meet future demand.

Scientific Visualization, Seeing the Unseeable

ScienceCinema

LBNL

2017-12-09

June 24, 2008 Berkeley Lab lecture: Scientific visualization transforms abstract data into readily comprehensible images, provide a vehicle for "seeing the unseeable," and play a central role in bo... June 24, 2008 Berkeley Lab lecture: Scientific visualization transforms abstract data into readily comprehensible images, provide a vehicle for "seeing the unseeable," and play a central role in both experimental and computational sciences. Wes Bethel, who heads the Scientific Visualization Group in the Computational Research Division, presents an overview of visualization and computer graphics, current research challenges, and future directions for the field.

Simulation and Mixed Integer Linear Programming Models for Analysis of Semi-Automated Mail Processing

DTIC Science & Technology

1989-12-01

Sincere appreciation is deserved by Geraldo Veiga , Department of Industrial Engineering and Operations Research, at the University of California, Berkeley...Convergence 124 Veiga , University of California, Berkeley, must be credited with applying the MINOS code to our GMF-A problems). MINOS is a FORTRAN...placed in cart ACT,O,,TS23; and if the cart is full, an ACT,O,LSN8l3CARr.GE.LSMBl3FULL,TS24; entity is sent to TS24 to ACr,O,,TT fl ; empty the cart

Secrets of the Soil: Promotion of the Nov. 7 Science at the Theater Event

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brodie, Eoin

2011-01-01

There are billions of microbes in a handful of soil, some of which could hold the key to our climate and energy future. Find out how at Secrets of the Soil, our next Science at the Theater Nov. 7 at the Berkeley Repertory Theatre. At the event, four Berkeley Lab scientists will reveal how our scientists travel the globe -- to deserts, rainforests, and the Arctic tundra -- to explore the secret world of soil microbes -- and what they mean to you. More info: http://www.lbl.gov/LBL-PID/fobl/

Secrets of the Soil: Promotion of the Nov. 7 Science at the Theater Event

ScienceCinema

Brodie, Eoin

2017-12-11

There are billions of microbes in a handful of soil, some of which could hold the key to our climate and energy future. Find out how at Secrets of the Soil, our next Science at the Theater Nov. 7 at the Berkeley Repertory Theatre. At the event, four Berkeley Lab scientists will reveal how our scientists travel the globe -- to deserts, rainforests, and the Arctic tundra -- to explore the secret world of soil microbes -- and what they mean to you. More info: http://www.lbl.gov/LBL-PID/fobl/

Core List of Astronomy and Physics Journals

NASA Astrophysics Data System (ADS)

Bryson, Liz; Fortner, Diane; Yorks, Pamela

This is a list of highly-used and highly-cited physics and astronomy journals. "Use" is measured largely on paper-journal counts from selective academic research-level libraries. Citation count titles are drawn from Institute for Scientific Information (ISI) data. Recognition is given to entrepreneurial electronic-only or new-style electronic journals. Selective news, magazine, and general science journals are omitted. The compilers welcome questions, suggestions for additions, or other advice. Comments may be sent c/o Diane Fortner, Physics Library, University of California, Berkeley. Dfortner@library.berkeley.edu

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.

PubMed

Hirao, Tomonori; Watanabe, Atsushi; Kurita, Manabu; Kondo, Teiji; Takata, Katsuhiko

2008-06-23

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

PubMed

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-09-18

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data

PubMed Central

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-01-01

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. PMID:25990738

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

PubMed Central

Marti-Renom, Marc A.; Mirny, Leonid A.

2011-01-01

Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. PMID:21779160

Scanning the human genome at kilobase resolution.

PubMed

Chen, Jun; Kim, Yeong C; Jung, Yong-Chul; Xuan, Zhenyu; Dworkin, Geoff; Zhang, Yanming; Zhang, Michael Q; Wang, San Ming

2008-05-01

Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ditag to represent the fragment; (3) application of the 454 sequencing system to reach a comprehensive ditag sequence collection; (4) determination of the genome origin of ditags by mapping to reference ditags from known genome sequences; (5) use of ditag sequences directly as the sense and antisense PCR primers to amplify the original DNA fragment. To study the relationship between ditags and genome structure, we performed a computational study by using the human genome reference sequences as a model, and analyzed the ditags experimentally collected from the well-characterized normal human DNA GM15510 and the leukemic human DNA of Kasumi-1 cells. Our studies show that DGS provides a kilobase resolution for studying genome structure with high specificity and high genome coverage. DGS can be applied to validate genome assembly, to compare genome similarity and variation in normal populations, and to identify genomic abnormality including insertion, inversion, deletion, translocation, and amplification in pathological genomes such as cancer genomes.

Visualization of RNA structure models within the Integrative Genomics Viewer.

PubMed

Busan, Steven; Weeks, Kevin M

2017-07-01

Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation

USDA-ARS?s Scientific Manuscript database

Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), contribute significantly to individual health and disease in primates and rodents. As a part of the bovine genome annotation effort, we performed the first genome-wide analysis of SD in cattle usin...

Resolving ultrafast exciton migration in organic solids at the nanoscale

NASA Astrophysics Data System (ADS)

Ginsberg, Naomi

The migration of Frenkel excitons, tightly-bound electron-hole pairs, in photosynthesis and in organic semiconducting films is critical to the efficiency of natural and artificial light harvesting. While these materials exhibit a high degree of structural heterogeneity on the nanoscale, traditional measurements of exciton migration lengths are performed on bulk samples. Since both the characteristic length scales of structural heterogeneity and the reported bulk diffusion lengths are smaller than the optical diffraction limit, we adapt far-field super-resolution fluorescence imaging to uncover the correlations between the structural and energetic landscapes that the excitons explore. By combining the ultrafast super-resolved measurements with exciton hopping simulations we furthermore specify the nature (in addition to the extent) of exciton migration as a function of the intrinsic and ensemble chromophore energy scales that determine a spatio-energetic landscape for migration. In collaboration with: Samuel Penwell, Lucas Ginsberg, University of California, Berkeley and Rodrigo Noriega University of Utah.

Simulations of carbon fiber composite delamination tests

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kay, G

2007-10-25

Simulations of mode I interlaminar fracture toughness tests of a carbon-reinforced composite material (BMS 8-212) were conducted with LSDYNA. The fracture toughness tests were performed by U.C. Berkeley. The simulations were performed to investigate the validity and practicality of employing decohesive elements to represent interlaminar bond failures that are prevalent in carbon-fiber composite structure penetration events. The simulations employed a decohesive element formulation that was verified on a simple two element model before being employed to perform the full model simulations. Care was required during the simulations to ensure that the explicit time integration of LSDYNA duplicate the near steady-statemore » testing conditions. In general, this study validated the use of employing decohesive elements to represent the interlaminar bond failures seen in carbon-fiber composite structures, but the practicality of employing the elements to represent the bond failures seen in carbon-fiber composite structures during penetration events was not established.« less

The structure and evolution of angiosperm nuclear genomes.

PubMed

Bennetzen, J L

1998-04-01

Despite several decades of investigation, the organization of angiosperm genomes remained largely unknown until very recently. Data describing the sequence composition of large segments of genomes, covering hundreds of kilobases of contiguous sequence, have only become available in the past two years. Recent results indicate commonalities in the characteristics of many plant genomes, including in the structure of chromosomal components like telomeres and centromeres, and in the order and content of genes. Major differences between angiosperms have been associated mainly with repetitive DNAs, both gene families and mobile elements. Intriguing new studies have begun to characterize the dynamic three-dimensional structures of chromosomes and chromatin, and the relationship between genome structure and co-ordinated gene function.

Reconstitution of wild type viral DNA in simian cells transfected with early and late SV40 defective genomes.

PubMed

O'Neill, F J; Gao, Y; Xu, X

1993-11-01

The DNAs of polyomaviruses ordinarily exist as a single circular molecule of approximately 5000 base pairs. Variants of SV40, BKV and JCV have been described which contain two complementing defective DNA molecules. These defectives, which form a bipartite genome structure, contain either the viral early region or the late region. The defectives have the unique property of being able to tolerate variable sized reiterations of regulatory and terminus region sequences, and portions of the coding region. They can also exchange coding region sequences with other polyomaviruses. It has been suggested that the bipartite genome structure might be a stage in the evolution of polyomaviruses which can uniquely sustain genome and sequence diversity. However, it is not known if the regulatory and terminus region sequences are highly mutable. Also, it is not known if the bipartite genome structure is reversible and what the conditions might be which would favor restoration of the monomolecular genome structure. We addressed the first question by sequencing the reiterated regulatory and terminus regions of E- and L-SV40 DNAs. This revealed a large number of mutations in the regulatory regions of the defective genomes, including deletions, insertions, rearrangements and base substitutions. We also detected insertions and base substitutions in the T-antigen gene. We addressed the second question by introducing into permissive simian cells, E- and L-SV40 genomes which had been engineered to contain only a single regulatory region. Analysis of viral DNA from transfected cells demonstrated recombined genomes containing a wild type monomolecular DNA structure. However, the complete defectives, containing reiterated regulatory regions, could often compete away the wild type genomes. The recombinant monomolecular genomes were isolated, cloned and found to be infectious. All of the DNA alterations identified in one of the regulatory regions of E-SV40 DNA were present in the recombinant monomolecular genomes. These and other findings indicate that the bipartite genome state can sustain many mutations which wtSV40 cannot directly sustain. However, the mutations can later be introduced into the wild type genomes when the E- and L-SV40 DNAs recombine to generate a new monomolecular genome structure.

Electronic Structure and Morphology of Graphene Layers on SiC

NASA Astrophysics Data System (ADS)

Ohta, Taisuke

2008-03-01

Recent years have witnessed the discovery and the unique electronic properties of graphene, a sheet of carbon atoms arranged in a honeycomb lattice. The unique linear dispersion relation of charge carriers near the Fermi level (``Dirac Fermions'') lead to exciting transport properties, such as an unusual quantum Hall effect, and have aroused scientific and technological interests. On the way towards graphene-based electronics, a knowledge of the electronic band structure and the morphology of epitaxial graphene films on silicon carbide substrates is imperative. We have studied the evolution of the occupied band structure and the morphology of graphene layers on silicon carbide by systematically increasing the layer thickness. Using angle-resolved photoemission spectroscopy (ARPES), we examine this unique 2D system in its development from single layer to multilayers, by characteristic changes in the π band, the highest occupied state, and the dispersion relation in the out-of-plane electron wave vector in particular. The evolution of the film morphology is evaluated by the combination of low-energy electron microscopy and ARPES. By exploiting the sensitivity of graphene's electronic states to the charge carrier concentration, changes in the on-site Coulomb potential leading to a change of π and π* bands can be examined using ARPES. We demonstrate that, in a graphene bilayer, the gap between π and π* bands can be controlled by selectively adjusting relative carrier concentrations, which suggests a possible application of the graphene bilayer for switching functions in electronic devices. This work was done in collaboration with A. Bostwick, J. L. McChesney, and E. Rotenberg at Advanced Light Source, Lawrence Berkeley National Laboratory, K. Horn at Fritz-Haber-Institut, K. V. Emtsev and Th. Seyller at Lehrstuhl für Technische Physik, Universität Erlangen-Nürnberg, and F. El Gabaly and A. K. Schmid at National Center for Electron Microscopy, Lawrence Berkeley National Laboratory.

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

Features and dimensions of the Hayward Fault Zone in the Strawberry and Blackberry Creek Area, Berkeley, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, P.L.

1995-03-01

This report presents an examination of the geometry of the Hayward fault adjacent to the Lawrence Berkeley Laboratory and University of California campuses in central Berkeley. The fault crosses inside the eastern border of the UC campus. Most subtle geomorphic (landform) expressions of the fault have been removed by development and by the natural processes of landsliding and erosion. Some clear expressions of the fault remain however, and these are key to mapping the main trace through the campus area. In addition, original geomorphic evidence of the fault`s location was recovered from large scale mapping of the site dating frommore » 1873 to 1897. Before construction obscured and removed natural landforms, the fault was expressed by a linear, northwest-tending zone of fault-related geomorphic features. There existed well-defined and subtle stream offsets and beheaded channels, fault scarps, and a prominent ``shutter ridge``. To improve our confidence in fault locations interpreted from landforms, we referred to clear fault exposures revealed in trenching, revealed during the construction of the Foothill Housing Complex, and revealed along the length of the Lawson Adit mining tunnel. Also utilized were the locations of offset cultural features. At several locations across the study area, distress features in buildings and streets have been used to precisely locate the fault. Recent published mapping of the fault (Lienkaemper, 1992) was principally used for reference to evidence of the fault`s location to the northwest and southeast of Lawrence Berkeley Laboratory.« less

Energy Landscapes of Folding Chromosomes

NASA Astrophysics Data System (ADS)

Zhang, Bin

The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

Predicted stem-loop structures and variation in nucleotide sequence of 3' noncoding regions among animal calicivirus genomes.

PubMed

Seal, B S; Neill, J D; Ridpath, J F

1994-07-01

Caliciviruses are nonenveloped with a polyadenylated genome of approximately 7.6 kb and a single capsid protein. The "RNA Fold" computer program was used to analyze 3'-terminal noncoding sequences of five feline calicivirus (FCV), rabbit hemorrhagic disease virus (RHDV), and two San Miguel sea lion virus (SMSV) isolates. The FCV 3'-terminal sequences are 40-46 nucleotides in length and 72-91% similar. The FCV sequences were predicted to contain two possible duplex structures and one stem-loop structure with free energies of -2.1 to -18.2 kcal/mole. The RHDV genomic 3'-terminal RNA sequences are 54 nucleotides in length and share 49% sequence similarity to homologous regions of the FCV genome. The RHDV sequence was predicted to form two duplex structures in the 3'-terminal noncoding region with a single stem-loop structure, resembling that of FCV. In contrast, the SMSV 1 and 4 genomic 3'-terminal noncoding sequences were 185 and 182 nucleotides in length, respectively. Ten possible duplex structures were predicted with an average structural free energy of -35 kcal/mole. Sequence similarity between the two SMSV isolates was 75%. Furthermore, extensive cloverleaflike structures are predicted in the 3' noncoding region of the SMSV genome, in contrast to the predicted single stem-loop structures of FCV or RHDV.

Editorial: Special issue dedicated to Gabor Somorjai's 80th birthday

NASA Astrophysics Data System (ADS)

2016-06-01

This special issue of Surface Science has been prepared to honor Professor Gabor A. Somorjai on the occasion of his 80th birthday. Professor Somorjai was born on May 4, 1935 in Budapest, Hungary. In 1953 he enrolled as a chemical engineering student at the Technical University of Budapest. Gabor was an active participant in the Hungarian Revolution of 1956. When the Soviet military crushed the revolution, he had to leave the country by walking across the border with his sister and his future wife. After immigrating to the USA in 1957, he applied to begin graduate studies and was accepted at the University of California, Berkeley. Gabor received a PhD in Chemistry in 1960, only three years later. Following a short sojourn at IBM, he returned to Berkeley in 1964 to take up a faculty position in the Department of Chemistry and the Lawrence Berkeley National Laboratory, which he still holds today. For the interested reader, more can be learned about Gabor's fascinating life in his autobiography, ;An American Scientist: The Autobiography of Gabor A. Somorjai.

New Implications on Genomic Adaptation Derived from the Helicobacter pylori Genome Comparison

PubMed Central

Lara-Ramírez, Edgar Eduardo; Segura-Cabrera, Aldo; Guo, Xianwu; Yu, Gongxin; García-Pérez, Carlos Armando; Rodríguez-Pérez, Mario A.

2011-01-01

Background Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. It evolved with its particular characteristics for biological adaptation. Because several H. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium. Principal Findings We analyzed nine H. pylori genomes with emphasis on microevolution from a different perspective. Inversion was an important factor to shape the genome structure. Illegitimate recombination not only led to genomic inversion but also inverted fragment duplication, both of which contributed to the creation of new genes and gene family, and further, homological recombination contributed to events of inversion. Based on the information of genomic rearrangement, the first genome scaffold structure of H. pylori last common ancestor was produced. The core genome consists of 1186 genes, of which 22 genes could particularly adapt to human stomach niche. H. pylori contains high proportion of pseudogenes whose genesis was principally caused by homopolynucleotide (HPN) mutations. Such mutations are reversible and facilitate the control of gene expression through the change of DNA structure. The reversible mutations and a quasi-panmictic feature could allow such genes or gene fragments frequently transferred within or between populations. Hence, pseudogenes could be a reservoir of adaptation materials and the HPN mutations could be favorable to H. pylori adaptation, leading to HPN accumulation on the genomes, which corresponds to a special feature of Helicobacter species: extremely high HPN composition of genome. Conclusion Our research demonstrated that both genome content and structure of H. pylori have been highly adapted to its particular life style. PMID:21387011

Mms1 is an assistant for regulating G-quadruplex DNA structures.

PubMed

Schwindt, Eike; Paeschke, Katrin

2018-06-01

The preservation of genome stability is fundamental for every cell. Genomic integrity is constantly challenged. Among those challenges are also non-canonical nucleic acid structures. In recent years, scientists became aware of the impact of G-quadruplex (G4) structures on genome stability. It has been shown that folded G4-DNA structures cause changes in the cell, such as transcriptional up/down-regulation, replication stalling, or enhanced genome instability. Multiple helicases have been identified to regulate G4 structures and by this preserve genome stability. Interestingly, although these helicases are mostly ubiquitous expressed, they show specificity for G4 regulation in certain cellular processes (e.g., DNA replication). To this date, it is not clear how this process and target specificity of helicases are achieved. Recently, Mms1, an ubiquitin ligase complex protein, was identified as a novel G4-DNA-binding protein that supports genome stability by aiding Pif1 helicase binding to these regions. In this perspective review, we discuss the question if G4-DNA interacting proteins are fundamental for helicase function and specificity at G4-DNA structures.

Multi-scale structural community organisation of the human genome.

PubMed

Boulos, Rasha E; Tremblay, Nicolas; Arneodo, Alain; Borgnat, Pierre; Audit, Benjamin

2017-04-11

Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines. We observed that there exist structural domains of all sizes up to chromosome length and demonstrated that the set of structural communities forms a hierarchy of chromosome segments. Hence, at all scales, chromosome folding predominantly involves interactions between neighbouring sites rather than the formation of links between distant loci. Multi-scale structural decomposition of human chromosomes provides an original framework to question structural organisation and its relationship to functional regulation across the scales. By construction the proposed methodology is independent of the precise assembly of the reference genome and is thus directly applicable to genomes whose assembly is not fully determined.

Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia.

PubMed

Campbell, Matthew A; Van Leuven, James T; Meister, Russell C; Carey, Kaitlin M; Simon, Chris; McCutcheon, John P

2015-08-18

Comparative genomics from mitochondria, plastids, and mutualistic endosymbiotic bacteria has shown that the stable establishment of a bacterium in a host cell results in genome reduction. Although many highly reduced genomes from endosymbiotic bacteria are stable in gene content and genome structure, organelle genomes are sometimes characterized by dramatic structural diversity. Previous results from Candidatus Hodgkinia cicadicola, an endosymbiont of cicadas, revealed that some lineages of this bacterium had split into two new cytologically distinct yet genetically interdependent species. It was hypothesized that the long life cycle of cicadas in part enabled this unusual lineage-splitting event. Here we test this hypothesis by investigating the structure of the Ca. Hodgkinia genome in one of the longest-lived cicadas, Magicicada tredecim. We show that the Ca. Hodgkinia genome from M. tredecim has fragmented into multiple new chromosomes or genomes, with at least some remaining partitioned into discrete cells. We also show that this lineage-splitting process has resulted in a complex of Ca. Hodgkinia genomes that are 1.1-Mb pairs in length when considered together, an almost 10-fold increase in size from the hypothetical single-genome ancestor. These results parallel some examples of genome fragmentation and expansion in organelles, although the mechanisms that give rise to these extreme genome instabilities are likely different.

A distributed system for fast alignment of next-generation sequencing data.

PubMed

Srimani, Jaydeep K; Wu, Po-Yen; Phan, John H; Wang, May D

2010-12-01

We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

Experimental and theoretical studies of metal vapor atoms

NASA Astrophysics Data System (ADS)

Whitfield, Scott B.; Wehlitz, Ralf; Martins, Michael

2004-05-01

Employing electron spectrometry in conjunction with tuneable synchrotron radiation, we will present a detailed examination of the photoionization dynamics of selected metal vapor atoms. In particular, this paper will focus on the relative partial cross sections of the atomic Li K-shell main and satellite (ionization with excitation) photoelectron lines in the region of the strong 1 snℓ n'ℓ' autoionizing transitions, the atomic Sc 3 d, 4 s main and satellite photoelectron lines in the region of the 3 p→3 d giant resonance, and also the atomic Fe 3 d, 4 s main and satellite photoelectron lines in the same resonance region. Our experimental data for Sc and Fe will be compared to our state-of-the-art calculations based on the superposition of configuration method developed by Cowan (The Theory of Atomic Structure and Spectra. University of California Berkeley Press, Berkeley and Los Angeles, 1981). Our partial cross section measurements for Li and Sc will be complemented with measurements of the angular distribution parameter, β. In addition, our Li data will also be compared with recent R-matrix calculations (Phys. Rev. 57 (1998) 1045). In the case of Fe, we will also address the term dependent behavior of the partial cross sections on resonance. These results will highlight what can be achieved with today's technology and point the way towards future endeavors in the study of the photoionization dynamics of open-shell metal vapor atoms.

Interaction Potentials for Br(2P) + Ar, Kr, Xe (1S) by the Crossed Molecular Beams Method.

DTIC Science & Technology

1981-03-01

recombination was significantly affected by eBr-RG" In their study, the interaction potential between Br and RG was assumed to be of the Lennard ... Jones (L-J) form with the following parameters: RG=Ar, c=1.0 kcal/mole, a=3.0 A; RG=Xe, e-1.0 kcal/mole, a=3.5 A. A slightly shallower Br-Ar potential ...AOA-A00 002 CALIFORNIA UNIV BERKELEY LAWRENCE BERKELEY LAB F/6 20/7 INTERACTION POTENTIALS FOR BR2P) + AR. KR. XE (IS) BY THE CROS--ETCfIU MAR 81 P

Annual environmental monitoring report of the Lawrence Berkeley Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schleimer, G.E.

1989-06-01

The Environmental Monitoring Program of the Lawrence Berkeley Laboratory (LBL) is described. Data for 1988 are presented and general trends are discussed. In order to establish whether LBL research activities produced any impact on the population surrounding the laboratory, a program of environmental air and water sampling and continuous radiation monitoring was carried on throughout the year. For 1988, as in the previous several years, dose equivalents attributable to LBL radiological operations were a small fraction of both the relevant radiation protection guidelines (RPG) and of the natural radiation background. 16 refs., 7 figs., 21 tabs.

VizieR Online Data Catalog: 42 millisecond pulsars high-precision timing (Desvignes+, 2016)

NASA Astrophysics Data System (ADS)

Desvignes, G.; Caballero, R. N.; Lentati, L.; Verbiest, J. P. W.; Champion, D. J.; Stappers, B. W.; Janssen, G. H.; Lazarus, P.; Oslowski, S.; Babak, S.; Bassa, C. G.; Brem, P.; Burgay, M.; Cognard, I.; Gair, J. R.; Graikou, E.; Guillemot, L.; Hessels, J. W. T.; Jessner, A.; Jordan, C.; Karuppusamy, R.; Kramer, M.; Lassus, A.; Lazaridis, K.; Lee, K. J.; Liu, K.; Lyne, A. G.; McKee, J.; Mingarelli, C. M. F.; Perrodin, D.; Petiteau, A.; Possenti, A.; Purver, M. B.; Rosado, P. A.; Sanidas, S.; Sesana, A.; Shaifullah, G.; Smits, R.; Taylor, S. R.; Theureau, G.; Tiburzi, C.; van Haasteren, R.; Vecchio, A.

2017-02-01

This paper presents the EPTA data set, up to mid-2014, that was gathered from the 'historical' pulsar instrumentations at EFF, JBO, NRT and WSRT with, respectively, the EBPP (Effelsberg-Berkeley Pulsar Processor), DFB (Digital FilterBank), BON (Berkeley-Orleans-Nancay) and PuMa (Pulsar Machine) backends. The data recorded with the newest generation of instrumentations, e.g. PSRIX at EFF (Lazarus et al., 2016MNRAS.458..868L) and PuMaII at WSRT (Karuppusamy, Stappers & van Straten 2008PASP..120..191K), will be part of a future EPTA data release. (8 data files).

Berkeley's moral philosophy.

PubMed Central

Warnock, G

1990-01-01

Berkeley held that the moral duty of mankind was to obey God's laws; that--since God was a benevolent Creator--the object of His laws must be to promote the welfare and flourishing of mankind; and that, accordingly, humans could identify their moral duties by asking what system of laws for conduct would in fact tend to promote that object. This position--which is akin to that of 'rule' Utilitarianism--is neither unfamiliar nor manifestly untenable. He was surely mistaken, however, in his further supposition that, if this theory were accepted, the resolution of all (or most) particular moral dilemmas would be simple and straightforward. PMID:2181141

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Child Development and Structural Variation in the Human Genome

ERIC Educational Resources Information Center

Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

2013-01-01

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

The Divided Bacterial Genome: Structure, Function, and Evolution.

PubMed

diCenzo, George C; Finan, Turlough M

2017-09-01

Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella , Vibrio , and Burkholderia . The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure. Copyright © 2017 American Society for Microbiology.

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

DOE PAGES

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; ...

2016-03-07

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

Vital Signs building work-up: The Museum of Anthropology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Millet, M.S.; Erwine, B.

The paper will present the structure and the results of an in depth study of the Museum of Anthropology, designed by Arthur Erickson Architects for the University of British Columbia in Vancouver and completed in 1976. Part of the Vital Signs Curriculum Project created by Cris Benton and administered through the University of California at Berkeley, this analytic project was designed and carried out by a faculty/student team in the Department of Architecture at the University of Washington. The significance of this study is the simultaneous presentation of qualitative and quantitative information about the thermal and luminous environment of thismore » building.« less

Astronomer to Data Scientist

NASA Astrophysics Data System (ADS)

Kirkpatrick, Jessica

2015-01-01

Jessica Kirkpatrick received her PhD in Astrophysics from Berkeley in 2012. After an exhaustive job search within academia and beyond, she accepted a job as a data scientist / analyst for the social network Yammer (acquired by Microsoft) and is now the Director of Data Science for Education Company InstaEDU. Now instead of spending her days finding patterns in the large scale structure of galaxies, she finds patterns in the behaviors of people. She'll talk about her transition from astrophysics to tech, compare and contrast the two fields, and give tips about how to land a tech job, and discuss useful tools which helped her with her transition.

Mutualism in museums: A model for engaging undergraduates in biodiversity science

PubMed Central

Cicero, Carla; Albe, Monica J.; Barclay, Theresa L. W.; Spencer, Carol L.; Koo, Michelle S.; Bowie, Rauri C. K.; Lacey, Eileen A.

2017-01-01

Museums have an untapped potential to engage students in hands-on learning. Here, we describe the development of a tiered museum-based program at the University of California, Berkeley as a model for engaging undergraduates in biodiversity science. This decade-long effort to increase student participation in collections demonstrates the mutual benefits of undergraduate involvement. Museums benefit from critical help in collections care and an increased intellectual vitality, while students simultaneously gain essential research skills and an unparalleled exposure to biodiversity. Five first steps to creating a program are: dedicate a coordinator, offer credit, diversify participation, create a tiered structure, and build community. PMID:29161253

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database.

PubMed

Chandonia, John-Marc; Fox, Naomi K; Brenner, Steven E

2017-02-03

SCOPe (Structural Classification of Proteins-extended, http://scop.berkeley.edu) is a database of relationships between protein structures that extends the Structural Classification of Proteins (SCOP) database. SCOP is an expert-curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. SCOPe classifies the majority of protein structures released since SCOP development concluded in 2009, using a combination of manual curation and highly precise automated tools, aiming to have the same accuracy as fully hand-curated SCOP releases. SCOPe also incorporates and updates the ASTRAL compendium, which provides several databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. SCOPe continues high-quality manual classification of new superfamilies, a key feature of SCOP. Artifacts such as expression tags are now separated into their own class, in order to distinguish them from the homology-based annotations in the remainder of the SCOPe hierarchy. SCOPe 2.06 contains 77,439 Protein Data Bank entries, double the 38,221 structures classified in SCOP. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

News from Online: More Spectroscopy

NASA Astrophysics Data System (ADS)

Sweeney Judd, Carolyn

1999-09-01

Absorption (one of three tools) (http://mc2.cchem.berkeley.edu/Chem1A/solar/applets/absorption/ index.html).

Evaporative cooling in a Bose-Einstein condensation ( http://www.colorado.edu/physics/2000/applets/bec.html). Let's start with the spectrum--the electromagnetic spectrum, of course. Go to the EMSpectrum Explorer at http://mc2.cchem.berkeley.edu/chemcnx/light_energy/EMSpectrum /emspectrum.html. Not only do you get information about wavelength, frequency, and energy, but you also get a handy converter that will calculate frequency, wavelength, and energy when one value is entered. And there is more. For example, clicking on red light of 680 nanometers reveals that mitochondria, the power plants of cells, are about the same size as this wavelength, which is also used for photosynthesis. Interesting food for thought! From the EMSpectrum Explorer, go to the Light and Energy page at http://mc2.cchem.berkeley.edu/chemcnx/light_energy/index.html for three Colors of Light Tools. The Color from Emission tool ( http://mc2.cchem.berkeley.edu/chemcnx/light_energy/applets/emission/index.html) illustrates additive color by mixing differing amounts of Red, Blue, and Green light. Then look at the Color from Absorption tool at http://mc2.cchem.berkeley.edu/chemcnx/light_energy/applets/absorption/index.html. The image from the applet shows the white beam and three filters. Take out the blue, green, and red components by altering the scroll bars or text boxes. The third tool, Removing Color with a Single Filter from Colored Light at http://mc2.cchem.berkeley.edu/chemcnx/light_energy/applets/single/index.html, uses a single filter to take out various colors. Excellent for explaining the theory behind the operation of a basic spectrometer. The Light and Energy tools module, which received support from the National Science Foundation, has been developed under the direction of the ChemLinks Coalition--headed by Beloit College; and The ModularChem Consortium, MC2, headed by the University of California at Berkeley. The Project Director is Marco Molinaro from the University of California at Berkeley; the Project Manager is Susan Walden; Susan Ketchner and Leighanne McConnaughey are also members of the team for this excellent teaching site. For your information, all of the applets will soon be moving, along with the MC2 site, but the old addresses will still work. The next place to explore is Physics 2000 at http://www.colorado.edu/physics/2000/introduction.html. The introductory graphic is a harbinger of good things to come: move the negatively charged particle and see the water molecule spin in response to the position of the charged particle. One goal of the Physics 2000 Educational Initiative is to make physics more accessible to students and people of all ages. Sounds like a good goal for all sciences! One of the first sections is called Einstein's Legacy. Here you can find spectral lines explained in terms of team colors for rival football squads ( http://www.colorado.edu/physics/2000/quantumzone/index.html). Choose from 20 elements to see characteristic emission spectra. The cartoon teachers and students help explain emission spectra. Great applets compare the Bohr atom and the Schrödinger model as well as emission and absorption ( http://www.colorado.edu/physics/2000/quantumzone/schroedinger.html). Einstein's Legacy has many topics: X-rays and CAT Scans, Electromagnetic Waves and Particles, the Quantum Atom, Microwave Ovens, Lasers, and TV & Laptop Screens. Several topics also have sections for the advanced student. One of those advanced sections is part of the second major section of Physics 2000: The Atomic Lab. Two topics are Interference Experiments and Bose-Einstein Condensate. An applet illustrating Laser Cooling is at http://www.colorado.edu/physics/2000/bec/lascool1.html. Next go on to Evaporative Cooling at http://www.colorado.edu/physics/2000/bec/evap_cool.html. The cartoon professors begin the explanation with a picture of steam rising from a cup of hot coffee. Next is an applet with atoms in a parabolic magnetic trap at http://www.colorado.edu/physics/2000/applets/bec.html. The height of the magnetic trap can be changed in order to allow for escape of the most energetic atoms, resulting in cooling so that the Bose-Einstein Condensate is formed. Physics 2000 demands robust computing power. Check the system requirements on the introductory screen before venturing too far into this site. Martin V. Goldman, from the University of Colorado at Boulder, is the Director of Physics 2000, which received support from the Colorado Commission on Higher Education and the National Science Foundation. David Rea is the Technical Director, and many others help make this excellent site possible. Mark your calendars: October 31 through December 3, 1999! Bookmark this site-- http://www.ched-ccce.org/confchem/1999/d/index.html --and sign up. The Winter 1999 CONFCHEM Online Conference will focus on Developments in Spectroscopy and Innovative Strategies for Teaching Spectroscopy in the Undergraduate Curriculum. Scott Van Bramer of Widener University is the conference chair. Experts will present six papers, each to be followed by online discussions. CONFCHEM Online Conferences are sponsored by the American Chemical Society Division of Chemical Education's Committee on Computers in Chemical Education (CCCE). Several Online Conferences are held each year--all are well worth your time. World Wide Web Addresses EMSpectrum Explorer http://mc2.cchem.berkeley.edu/chemcnx/light_energy/EMSpectrum/emspectrum.html Light and Energy http://mc2.cchem.berkeley.edu/chemcnx/light_energy/index.html Emission Spectrum Java Applet http://mc2.cchem.berkeley.edu/chemcnx/light_energy/applets/emission/index.html Absorption Java Applet http://mc2.cchem.berkeley.edu/chemcnx/light_energy/applets/absorption/index.html Removing Color with a Single Filter from Colored Light http://mc2.cchem.berkeley.edu/chemcnx/light_energy/applets/single/index.html Physics 2000 http://www.colorado.edu/physics/2000/introduction.html Einstein's Legacy: Spectral lines http://www.colorado.edu/physics/2000/quantumzone/index.html Einstein's: Schrödinger's Atom http://www.colorado.edu/physics/2000/quantumzone /schroedinger.html The Atomic Lab: Laser Cooling http://www.colorado.edu/physics/2000/bec/lascool1.html The Atomic Lab: Evaporative Cooling in a Bose­Einstein Condensation http://www.colorado.edu/physics/2000/bec/evap_cool.html The Winter 1999 CONFCHEM Online Conference will focus on Developments in Spectroscopy and Innovative Strategies for Teaching Spectroscopy in the Undergraduate Curriculum http://www.ched-ccce.org/confchem/1999/d/index.html access date for all sites: July 1999

Phenetic Comparison of Prokaryotic Genomes Using k-mers

PubMed Central

Déraspe, Maxime; Raymond, Frédéric; Boisvert, Sébastien; Culley, Alexander; Roy, Paul H.; Laviolette, François; Corbeil, Jacques

2017-01-01

Abstract Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets. PMID:28957508

I-motif DNA structures are formed in the nuclei of human cells

NASA Astrophysics Data System (ADS)

Zeraati, Mahdi; Langley, David B.; Schofield, Peter; Moye, Aaron L.; Rouet, Romain; Hughes, William E.; Bryan, Tracy M.; Dinger, Marcel E.; Christ, Daniel

2018-06-01

Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

Molecular analysis of vector genome structures after liver transduction by conventional and self-complementary adeno-associated viral serotype vectors in murine and nonhuman primate models.

PubMed

Sun, Xun; Lu, You; Bish, Lawrence T; Calcedo, Roberto; Wilson, James M; Gao, Guangping

2010-06-01

Vectors based on several new adeno-associated viral (AAV) serotypes demonstrated strong hepatocyte tropism and transduction efficiency in both small- and large-animal models for liver-directed gene transfer. Efficiency of liver transduction by AAV vectors can be further improved in both murine and nonhuman primate (NHP) animals when the vector genomes are packaged in a self-complementary (sc) format. In an attempt to understand potential molecular mechanism(s) responsible for enhanced transduction efficiency of the sc vector in liver, we performed extensive molecular studies of genome structures of conventional single-stranded (ss) and sc AAV vectors from liver after AAV gene transfer in both mice and NHPs. These included treatment with exonucleases with specific substrate preferences, single-cutter restriction enzyme digestion and polarity-specific hybridization-based vector genome mapping, and bacteriophage phi29 DNA polymerase-mediated and double-stranded circular template-specific rescue of persisted circular genomes. In mouse liver, vector genomes of both genome formats seemed to persist primarily as episomal circular forms, but sc vectors converted into circular forms more rapidly and efficiently. However, the overall differences in vector genome abundance and structure in the liver between ss and sc vectors could not account for the remarkable differences in transduction. Molecular structures of persistent genomes of both ss and sc vectors were significantly more heterogeneous in macaque liver, with noticeable structural rearrangements that warrant further characterizations.

Molecular Analysis of Vector Genome Structures After Liver Transduction by Conventional and Self-Complementary Adeno-Associated Viral Serotype Vectors in Murine and Nonhuman Primate Models

PubMed Central

Sun, Xun; Lu, You; Bish, Lawrence T.; Calcedo, Roberto; Wilson, James M.

2010-01-01

Abstract Vectors based on several new adeno-associated viral (AAV) serotypes demonstrated strong hepatocyte tropism and transduction efficiency in both small- and large-animal models for liver-directed gene transfer. Efficiency of liver transduction by AAV vectors can be further improved in both murine and nonhuman primate (NHP) animals when the vector genomes are packaged in a self-complementary (sc) format. In an attempt to understand potential molecular mechanism(s) responsible for enhanced transduction efficiency of the sc vector in liver, we performed extensive molecular studies of genome structures of conventional single-stranded (ss) and sc AAV vectors from liver after AAV gene transfer in both mice and NHPs. These included treatment with exonucleases with specific substrate preferences, single-cutter restriction enzyme digestion and polarity-specific hybridization-based vector genome mapping, and bacteriophage ϕ29 DNA polymerase-mediated and double-stranded circular template-specific rescue of persisted circular genomes. In mouse liver, vector genomes of both genome formats seemed to persist primarily as episomal circular forms, but sc vectors converted into circular forms more rapidly and efficiently. However, the overall differences in vector genome abundance and structure in the liver between ss and sc vectors could not account for the remarkable differences in transduction. Molecular structures of persistent genomes of both ss and sc vectors were significantly more heterogeneous in macaque liver, with noticeable structural rearrangements that warrant further characterizations. PMID:20113166

Access to public drinking water fountains in Berkeley, California: a geospatial analysis.

PubMed

Avery, Dylan C; Smith, Charlotte D

2018-01-24

In January 2015, Berkeley, California became the first city in the Unites States to impose a tax on sugar-sweetened beverages. The tax is intended to discourage purchase of sugary beverages and promote consumption of healthier alternatives such as tap water. The goal of the study was to assess the condition of public drinking water fountains and determine if there is a difference in access to clean, functioning fountains based on race or socio-economic status. A mobile-GIS App was created to locate and collect data on existing drinking water fountains in Berkeley, CA. Demographic variables related to race and socio-economic status (SES) were acquired from the US Census - American Community Survey database. Disparities in access to, or condition of drinking water fountains relative to demographics was explored using spatial analyses. Spatial statistical-analysis was performed to estimate demographic characteristics of communities near the water fountains and logistic regression was used to examine the relationship between household median income or race and condition of fountain. Although most fountains were classified as functioning, some were dirty, clogged, or both dirty and clogged. No spatial relationships between demographic characteristics and fountain conditions were observed. All geo-located data and a series of maps were provided to the City of Berkeley and the public. The geo-database created as an outcome of this study is useful for prioritizing maintenance of existing fountains and planning the locations of future fountains. The methodologies used for this study could be applied to a wide variety of asset inventory and assessment projects such as clinics or pharmaceutical dispensaries, both in developed and developing countries.

New Cepheid variables in the young open clusters Berkeley 51 and Berkeley 55

NASA Astrophysics Data System (ADS)

Lohr, M. E.; Negueruela, I.; Tabernero, H. M.; Clark, J. S.; Lewis, F.; Roche, P.

2018-05-01

As part of a wider investigation of evolved massive stars in Galactic open clusters, we have spectroscopically identified three candidate classical Cepheids in the little-studied clusters Berkeley 51, Berkeley 55 and NGC 6603. Using new multi-epoch photometry, we confirm that Be 51 #162 and Be 55 #107 are bona fide Cepheids, with pulsation periods of 9.83±0.01 d and 5.850±0.005 d respectively, while NGC 6603 star W2249 does not show significant photometric variability. Using the period-luminosity relationship for Cepheid variables, we determine a distance to Be 51 of 5.3^{+1.0}_{-0.8} kpc and an age of 44^{+9}_{-8} Myr, placing it in a sparsely-attested region of the Perseus arm. For Be 55, we find a distance of 2.2±0.3 kpc and age of 63^{+12}_{-11} Myr, locating the cluster in the Local arm. Taken together with our recent discovery of a long-period Cepheid in the starburst cluster VdBH222, these represent an important increase in the number of young, massive Cepheids known in Galactic open clusters. We also consider new Gaia (data release 2) parallaxes and proper motions for members of Be 51 and Be 55; the uncertainties on the parallaxes do not allow us to refine our distance estimates to these clusters, but the well-constrained proper motion measurements furnish further confirmation of cluster membership. However, future final Gaia parallaxes for such objects should provide valuable independent distance measurements, improving the calibration of the period-luminosity relationship, with implications for the distance ladder out to cosmological scales.

Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture

PubMed Central

Matharu, Navneet K.; Ahanger, Sajad H.

2015-01-01

The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress. PMID:26340639

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

PubMed Central

Hamilton, Eileen P; Kapusta, Aurélie; Huvos, Piroska E; Bidwell, Shelby L; Zafar, Nikhat; Tang, Haibao; Hadjithomas, Michalis; Krishnakumar, Vivek; Badger, Jonathan H; Caler, Elisabet V; Russ, Carsten; Zeng, Qiandong; Fan, Lin; Levin, Joshua Z; Shea, Terrance; Young, Sarah K; Hegarty, Ryan; Daza, Riza; Gujja, Sharvari; Wortman, Jennifer R; Birren, Bruce W; Nusbaum, Chad; Thomas, Jainy; Carey, Clayton M; Pritham, Ellen J; Feschotte, Cédric; Noto, Tomoko; Mochizuki, Kazufumi; Papazyan, Romeo; Taverna, Sean D; Dear, Paul H; Cassidy-Hanley, Donna M; Xiong, Jie; Miao, Wei; Orias, Eduardo; Coyne, Robert S

2016-01-01

The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena’s germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum. DOI: http://dx.doi.org/10.7554/eLife.19090.001 PMID:27892853

Exploring the role of genome and structural ions in preventing viral capsid collapse during dehydration

NASA Astrophysics Data System (ADS)

Martín-González, Natalia; Guérin Darvas, Sofía M.; Durana, Aritz; Marti, Gerardo A.; Guérin, Diego M. A.; de Pablo, Pedro J.

2018-03-01

Even though viruses evolve mainly in liquid milieu, their horizontal transmission routes often include episodes of dry environment. Along their life cycle, some insect viruses, such as viruses from the Dicistroviridae family, withstand dehydrated conditions with presently unknown consequences to their structural stability. Here, we use atomic force microscopy to monitor the structural changes of viral particles of Triatoma virus (TrV) after desiccation. Our results demonstrate that TrV capsids preserve their genome inside, conserving their height after exposure to dehydrating conditions, which is in stark contrast with other viruses that expel their genome when desiccated. Moreover, empty capsids (without genome) resulted in collapsed particles after desiccation. We also explored the role of structural ions in the dehydration process of the virions (capsid containing genome) by chelating the accessible cations from the external solvent milieu. We observed that ion suppression helps to keep the virus height upon desiccation. Our results show that under drying conditions, the genome of TrV prevents the capsid from collapsing during dehydration, while the structural ions are responsible for promoting solvent exchange through the virion wall.

Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong Hongping; Zhang Bo; Shi Peiyong

2008-11-10

Genome cyclization is essential for flavivirus replication. We used RNases to probe the structures formed by the 5'-terminal 190 nucleotides and the 3'-terminal 111 nucleotides of the West Nile virus (WNV) genomic RNA. When analyzed individually, the two RNAs adopt stem-loop structures as predicted by the thermodynamic-folding program. However, when mixed together, the two RNAs form a duplex that is mediated through base-pairings of two sets of RNA elements (5'CS/3'CSI and 5'UAR/3'UAR). Formation of the RNA duplex facilitates a conformational change that leaves the 3'-terminal nucleotides of the genome (position - 8 to - 16) to be single-stranded. Viral NS5more » binds specifically to the 5'-terminal stem-loop (SL1) of the genomic RNA. The 5'SL1 RNA structure is essential for WNV replication. The study has provided further evidence to suggest that flavivirus genome cyclization and NS5/5'SL1 RNA interaction facilitate NS5 binding to the 3' end of the genome for the initiation of viral minus-strand RNA synthesis.« less

GAP Final Technical Report 12-14-04

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andrew J. Bordner, PhD, Senior Research Scientist

2004-12-14

The Genomics Annotation Platform (GAP) was designed to develop new tools for high throughput functional annotation and characterization of protein sequences and structures resulting from genomics and structural proteomics, benchmarking and application of those tools. Furthermore, this platform integrated the genomic scale sequence and structural analysis and prediction tools with the advanced structure prediction and bioinformatics environment of ICM. The development of GAP was primarily oriented towards the annotation of new biomolecular structures using both structural and sequence data. Even though the amount of protein X-ray crystal data is growing exponentially, the volume of sequence data is growing even moremore » rapidly. This trend was exploited by leveraging the wealth of sequence data to provide functional annotation for protein structures. The additional information provided by GAP is expected to assist the majority of the commercial users of ICM, who are involved in drug discovery, in identifying promising drug targets as well in devising strategies for the rational design of therapeutics directed at the protein of interest. The GAP also provided valuable tools for biochemistry education, and structural genomics centers. In addition, GAP incorporates many novel prediction and analysis methods not available in other molecular modeling packages. This development led to signing the first Molsoft agreement in the structural genomics annotation area with the University of oxford Structural Genomics Center. This commercial agreement validated the Molsoft efforts under the GAP project and provided the basis for further development of the large scale functional annotation platform.« less

Ras1 interacts with multiple new signaling and cytoskeletal loci in Drosophila eggshell patterning and morphogenesis.

PubMed Central

Schnorr, J D; Holdcraft, R; Chevalier, B; Berg, C A

2001-01-01

Little is known about the genes that interact with Ras signaling pathways to regulate morphogenesis. The synthesis of dorsal eggshell structures in Drosophila melanogaster requires multiple rounds of Ras signaling followed by dramatic epithelial sheet movements. We took advantage of this process to identify genes that link patterning and morphogenesis; we screened lethal mutations on the second chromosome for those that could enhance a weak Ras1 eggshell phenotype. Of 1618 lethal P-element mutations tested, 13 showed significant enhancement, resulting in forked and fused dorsal appendages. Our genetic and molecular analyses together with information from the Berkeley Drosophila Genome Project reveal that 11 of these lines carry mutations in previously characterized genes. Three mutations disrupt the known Ras1 cell signaling components Star, Egfr, and Blistered, while one mutation disrupts Sec61beta, implicated in ligand secretion. Seven lines represent cell signaling and cytoskeletal components that are new to the Ras1 pathway; these are Chickadee (Profilin), Tec29, Dreadlocks, POSH, Peanut, Smt3, and MESK2, a suppressor of dominant-negative Ksr. A twelfth insertion disrupts two genes, Nrk, a "neurospecific" receptor tyrosine kinase, and Tpp, which encodes a neuropeptidase. These results suggest that Ras1 signaling during oogenesis involves novel components that may be intimately associated with additional signaling processes and with the reorganization of the cytoskeleton. To determine whether these Ras1 Enhancers function upstream or downstream of the Egf receptor, four mutations were tested for their ability to suppress an activated Egfr construct (lambdatop) expressed in oogenesis exclusively in the follicle cells. Mutations in Star and l(2)43Bb had no significant effect upon the lambdatop eggshell defect whereas smt3 and dock alleles significantly suppressed the lambdatop phenotype. PMID:11606538

Ras1 interacts with multiple new signaling and cytoskeletal loci in Drosophila eggshell patterning and morphogenesis.

PubMed

Schnorr, J D; Holdcraft, R; Chevalier, B; Berg, C A

2001-10-01

Little is known about the genes that interact with Ras signaling pathways to regulate morphogenesis. The synthesis of dorsal eggshell structures in Drosophila melanogaster requires multiple rounds of Ras signaling followed by dramatic epithelial sheet movements. We took advantage of this process to identify genes that link patterning and morphogenesis; we screened lethal mutations on the second chromosome for those that could enhance a weak Ras1 eggshell phenotype. Of 1618 lethal P-element mutations tested, 13 showed significant enhancement, resulting in forked and fused dorsal appendages. Our genetic and molecular analyses together with information from the Berkeley Drosophila Genome Project reveal that 11 of these lines carry mutations in previously characterized genes. Three mutations disrupt the known Ras1 cell signaling components Star, Egfr, and Blistered, while one mutation disrupts Sec61beta, implicated in ligand secretion. Seven lines represent cell signaling and cytoskeletal components that are new to the Ras1 pathway; these are Chickadee (Profilin), Tec29, Dreadlocks, POSH, Peanut, Smt3, and MESK2, a suppressor of dominant-negative Ksr. A twelfth insertion disrupts two genes, Nrk, a "neurospecific" receptor tyrosine kinase, and Tpp, which encodes a neuropeptidase. These results suggest that Ras1 signaling during oogenesis involves novel components that may be intimately associated with additional signaling processes and with the reorganization of the cytoskeleton. To determine whether these Ras1 Enhancers function upstream or downstream of the Egf receptor, four mutations were tested for their ability to suppress an activated Egfr construct (lambdatop) expressed in oogenesis exclusively in the follicle cells. Mutations in Star and l(2)43Bb had no significant effect upon the lambdatop eggshell defect whereas smt3 and dock alleles significantly suppressed the lambdatop phenotype.

Self-similarity analysis of eubacteria genome based on weighted graph.

PubMed

Qi, Zhao-Hui; Li, Ling; Zhang, Zhi-Meng; Qi, Xiao-Qin

2011-07-07

We introduce a weighted graph model to investigate the self-similarity characteristics of eubacteria genomes. The regular treating in similarity comparison about genome is to discover the evolution distance among different genomes. Few people focus their attention on the overall statistical characteristics of each gene compared with other genes in the same genome. In our model, each genome is attributed to a weighted graph, whose topology describes the similarity relationship among genes in the same genome. Based on the related weighted graph theory, we extract some quantified statistical variables from the topology, and give the distribution of some variables derived from the largest social structure in the topology. The 23 eubacteria recently studied by Sorimachi and Okayasu are markedly classified into two different groups by their double logarithmic point-plots describing the similarity relationship among genes of the largest social structure in genome. The results show that the proposed model may provide us with some new sights to understand the structures and evolution patterns determined from the complete genomes. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

PubMed

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.

Differences in STEM doctoral publication by ethnicity, gender and academic field at a large public research university

PubMed Central

Patt, Colette; Fisher, Aaron; Eppig, Andrew; Young, Ira; Smith, Andrew; Richards, Mark A.

2017-01-01

Two independent surveys of PhD students in STEM fields at the University of California, Berkeley, indicate that underrepresented minorities (URMs) publish at significantly lower rates than non-URM males, placing the former at a significant disadvantage as they compete for postdoctoral and faculty positions. Differences as a function of gender reveal a similar, though less consistent, pattern. A conspicuous exception is Berkeley’s College of Chemistry, where publication rates are tightly clustered as a function of ethnicity and gender, and where PhD students experience a highly structured program that includes early and systematic involvement in research, as well as clear expectations for publishing. Social science research supports the hypothesis that this more structured environment hastens the successful induction of diverse groups into the high-performance STEM academic track. PMID:28380061

An Integrative Breakage Model of genome architecture, reshuffling and evolution: The Integrative Breakage Model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity.

PubMed

Farré, Marta; Robinson, Terence J; Ruiz-Herrera, Aurora

2015-05-01

Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the study of genome evolution. The analysis of the high-level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders. © 2015 WILEY Periodicals, Inc.

Coordinates and intervals in graph-based reference genomes.

PubMed

Rand, Knut D; Grytten, Ivar; Nederbragt, Alexander J; Storvik, Geir O; Glad, Ingrid K; Sandve, Geir K

2017-05-18

It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords .

Genome Pool Strategy for Structural Coverage of Protein Families

PubMed Central

Jaroszewski, Lukasz; Slabinski, Lukasz; Wooley, John; Deacon, Ashley M.; Lesley, Scott A.; Wilson, Ian. A.; Godzik, Adam

2010-01-01

As noticed by generations of structural biologists, closely homologous proteins may have substantially different crystallization properties and propensities. These observations can be used to systematically introduce additional dimensionality into crystallization trials by targeting homologous proteins from multiple genomes in a “genome pool” strategy. Through extensive use of our recently introduced “crystallization feasibility score” (Slabinski et al., 2007a), we can explain that the genome pool strategy works well because the crystallization feasibility scores are surprisingly broad within families of homologous proteins, with most families containing a range of optimal to very difficult targets. We also show that some families can be regarded as relatively “easy”, where a significant number of proteins are predicted to have optimal crystallization features, and others are “very difficult”, where almost none are predicted to result in a crystal structure. Thus, the outcome of such variable distributions of such crystallizability' preferences leads to uneven structural coverage of known families, with “easier” or “optimal” families having several times more solved structures than “very difficult” ones. Nevertheless, this latter category can be successfully targeted by increasing the number of genomes that are used to select targets from a given family. On average, adding 10 new genomes to the “genome pool” provides more promising targets for 7 “very difficult” families. In contrast, our crystallization feasibility score does not indicate that any specific microbial genomes can be readily classified as “easier” or “very difficult” with respect to providing suitable candidates for crystallization and structure determination. Finally, our analyses show that specific physicochemical properties of the protein sequence favor successful outcomes for structure determination and, hence, the group of proteins with known 3D structures is systematically different from the general pool of known proteins. We, therefore, assess the structural consequences of these differences in protein sequence and protein biophysical properties. PMID:19000818

Honey Bee Deformed Wing Virus Structures Reveal that Conformational Changes Accompany Genome Release.

PubMed

Organtini, Lindsey J; Shingler, Kristin L; Ashley, Robert E; Capaldi, Elizabeth A; Durrani, Kulsoom; Dryden, Kelly A; Makhov, Alexander M; Conway, James F; Pizzorno, Marie C; Hafenstein, Susan

2017-01-15

The picornavirus-like deformed wing virus (DWV) has been directly linked to colony collapse; however, little is known about the mechanisms of host attachment or entry for DWV or its molecular and structural details. Here we report the three-dimensional (3-D) structures of DWV capsids isolated from infected honey bees, including the immature procapsid, the genome-filled virion, the putative entry intermediate (A-particle), and the empty capsid that remains after genome release. The capsids are decorated by large spikes around the 5-fold vertices. The 5-fold spikes had an open flower-like conformation for the procapsid and genome-filled capsids, whereas the putative A-particle and empty capsids that had released the genome had a closed tube-like spike conformation. Between the two conformations, the spikes undergo a significant hinge-like movement that we predicted using a Robetta model of the structure comprising the spike. We conclude that the spike structures likely serve a function during host entry, changing conformation to release the genome, and that the genome may escape from a 5-fold vertex to initiate infection. Finally, the structures illustrate that, similarly to picornaviruses, DWV forms alternate particle conformations implicated in assembly, host attachment, and RNA release. Honey bees are critical for global agriculture, but dramatic losses of entire hives have been reported in numerous countries since 2006. Deformed wing virus (DWV) and infestation with the ectoparasitic mite Varroa destructor have been linked to colony collapse disorder. DWV was purified from infected adult worker bees to pursue biochemical and structural studies that allowed the first glimpse into the conformational changes that may be required during transmission and genome release for DWV. Copyright © 2017 American Society for Microbiology.

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

PubMed Central

Chambers, Emily V.; Bickmore, Wendy A.; Semple, Colin A.

2013-01-01

Several recent studies have examined different aspects of mammalian higher order chromatin structure – replication timing, lamina association and Hi-C inter-locus interactions — and have suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and until now little has been known about the characteristics of any divergent loci present. Here, we generate a dataset combining multiple measurements of chromatin structure and organisation over many embryonic cell types for both human and mouse that, for the first time, allows a comprehensive assessment of the extent of structural divergence between mammalian genomes. Comparison of orthologous regions confirms that all measurable facets of higher order structure are conserved between human and mouse, across the vast majority of the detectably orthologous genome. This broad similarity is observed in spite of many loci possessing cell type specific structures. However, we also identify hundreds of regions (from 100 Kb to 2.7 Mb in size) showing consistent evidence of divergence between these species, constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human and mouse genes. These regions show unusual shifts in human GC content, are unevenly distributed across both genomes, and are enriched in human subtelomeric regions. Divergent regions are also relatively enriched for genes showing divergent expression patterns between human and mouse ES cells, implying these regions cause divergent regulation. Particular divergent loci are strikingly enriched in genes implicated in vertebrate development, suggesting important roles for structural divergence in the evolution of mammalian developmental programmes. These data suggest that, though relatively rare in the mammalian genome, divergence in higher order chromatin structure has played important roles during evolution. PMID:23592965

Single cell Hi-C reveals cell-to-cell variability in chromosome structure

PubMed Central

Schoenfelder, Stefan; Yaffe, Eitan; Dean, Wendy; Laue, Ernest D.; Tanay, Amos; Fraser, Peter

2013-01-01

Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. PMID:24067610