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At least 487 records · Page 27Linked to original sources
PubMed2006

Laser guiding for GeV laser-plasma accelerators.

Guiding of relativistically intense laser beams in preformed plasma channels is discussed for development of GeV-class laser accelerators. Experiments using a channel guided laser wakefield accelerator at Lawrence Berkeley National Laboratory (LBNL) have demonstrated that near mono-energetic 100 MeV-class electron beams can be produced with a 10 TW laser system. Analysis, aided by particle-in-cell simulations, as well as experiments with various plasma lengths and densities, indicate that tailoring the length of the accelerator, together with loading of the accelerating structure with beam, is the key to production of mono-energetic electron beams. Increasing the energy towards a GeV and beyond will require reducing the plasma density and design criteria are discussed for an optimized accelerator module. The current progress and future directions are summarized through comparison with conventional accelerators, highlighting the unique short-term prospects for intense radiation sources based on laser-driven plasma accelerators.

Journal Article↗
PubMed2003

Prokaryote taxonomy of the 20th century and the impact of studies on the genus Pseudomonas: a personal view.

The taxonomic studies on the genus Pseudomonas performed in the Department of Bacteriology of the University of California at Berkeley played a significant rôle in the development of modern prokaryote taxonomy, which started in the 1960s. This impact was due to a revival of the method of den Dooren de Jong for the nutritional analysis of chemoorganotrophic organisms and, mostly, to the introduction of the determination of rRNA as a method of taxonomic analysis. While the introduction of the nutritional studies facilitated the characterization of Pseudomonas and other chemoorganotrophs, the applicability of the rRNA studies extended to all prokaryotes.

Bacteria↗
PubMed2000

Molecular cloning, genomic organization, developmental regulation, and a knock-out mutant of a novel leu-rich repeats-containing G protein-coupled receptor (DLGR-2) from Drosophila melanogaster.

After screening the Berkeley Drosophila Genome Project database with sequences from a recently characterized Leu-rich repeats-containing G protein-coupled receptor (LGR) from Drosophila (DLGR-1), we identified a second gene for a different LGR (DLGR-2) and cloned its cDNA. DLGR-2 is 1360 amino acid residues long and shows a striking structural homology with members of the glycoprotein hormone [thyroid-stimulating hormone (TSH); follicle-stimulating hormone (FSH); luteinizing hormone/choriogonadotropin (LH/CG)] receptor family from mammals and with two additional, recently identified mammalian orphan LGRs (LGR-4 and LGR-5). This homology includes the seven transmembrane region (e.g., 49% amino acid identity with the human TSH receptor) and the very large extracellular amino terminus. This amino terminus contains 18 Leu-rich repeats-in contrast with the 3 mammalian glycoprotein hormone receptors and DLGR-1 that contain 9 Leu-rich repeats, but resembling the mammalian LGR-4 and LGR-5 that each have 17 Leu-rich repeats in their amino termini. The DLGR-2 gene is >18.6 kb pairs long and contains 15 exons and 14 introns. Four intron positions coincide with the intron positions of the three mammalian glycoprotein hormone receptors and have the same intron phasing, showing that DLGR-2 is evolutionarily related to these mammalian receptors. The DLGR-2 gene is located at position 34E-F on the left arm of the second chromosome and is expressed in embryos and pupae but not in larvae and adult flies. Homozygous knock-out mutants, where the DLGR-2 gene is interrupted by a P element insertion, die around the time of hatching. This finding, together with the expression data, strongly suggests that DLGR-2 is exclusively involved in development.

Alternative Splicing↗
PubMed2004

Ordered partitioning reveals extended splice-site consensus information.

Using recently available cDNA and genomic data (Berkeley Drosophila Genome Project; http://www.fruitfly.org), we computed a large sample of 10,057 Drosophila splice sites. An information-theoretic analysis of the nucleotide sequences adjacent to these splice sites showed a strong correlation between the sizes of introns and exons and the levels of information, which is a measure of sequence conservation. The strong correlation permitted us to determine extensive consensus sequences at the donor and acceptor sites of longer introns. These sequences were further refined and extended by examining the information in regions around splice sites that only partially matched the consensus. The correlation between length and information provided the basis for determining alternative consensus arrangements associated with shorter introns, as well as general base-composition preferences that likely promote spliceosome function. We also observed a correlation between information near splice sites and the lengths of nonadjacent introns, indicating that there are long-range effects spanning multiple introns. The ordered partitioning approach used in this analysis may become increasingly useful as large genomic data sets become available.

Animals↗
PubMed2004

Automated whole-genome multiple alignment of rat, mouse, and human.

We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment and consists of two main steps: (1) alignment of the mouse and rat genomes, and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human, and 97% of all alignments with human sequence >100 kb agree with a three-way synteny map built independently, using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment, and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.

Animals↗
PubMed2005

Drosophila melanogaster: a case study of a model genomic sequence and its consequences.

The sequencing and annotation of the Drosophila melanogaster genome, first published in 2000 through collaboration between Celera Genomics and the Drosophila Genome Projects, has provided a number of important contributions to genome research. By demonstrating the utility of methods such as whole-genome shotgun sequencing and genome annotation by a community "jamboree," the Drosophila genome established the precedents for the current paradigm used by most genome projects. Subsequent releases of the initial genome sequence have been improved by the Berkeley Drosophila Genome Project and annotated by FlyBase, the Drosophila community database, providing one of the highest-quality genome sequences and annotations for any organism. We discuss the impact of the growing number of genome sequences now available in the genus on current Drosophila research, and some of the biological questions that these resources will enable to be solved in the future.

Animals↗
PubMed1993

Optical model analyses of 1.65 A GeV argon fragmentation: cross sections and momentum distributions.

An optical potential fragmentation model capable of predicting fragmentation cross sections and fragment momentum distributions is used to analyze recent measurements of 1.65 A GeV argon projectiles fragmenting in carbon and potassium-chloride targets obtained with the Heavy Ion Spectrometer System (HISS) at the Lawrence Berkeley Laboratory Bevalac. The theoretical model uses an abrasion-ablation-FSI (frictional spectator interaction) collision formalism to estimate elemental and isotopic production cross sections for comparison with the measured values. The collision momentum transfer model is incorporated into a Goldhaber formalism to analyze measured transverse and longitudinal distributions of the projectile fragments. Good agreement between theory and experiment is obtained for all observables.

Argon↗
PubMed2000

Evidence for new isotopes of element 107: 266Bh and 267Bh

New neutron rich isotopes 267107Bh and 266107Bh were produced in bombardments of a 249Bk target with 117-MeV and 123-MeV 22Ne ions at the Lawrence Berkeley National Laboratory 88-Inch Cyclotron. Identification was made by observation of correlated alpha-particle decays between the Bh isotopes and their Db and Lr daughters using a rotating wheel system. 267Bh was produced with a cross section of approximately 70 pb and decays with a 17(+14)(-6) s half life by emission of alpha particles with an average energy of 8.83+/-0.03 MeV. One atom of 266Bh was observed, decaying within 1 s by emission of a 9.29-MeV alpha particle.

Journal Article↗
PubMed2004

Measurement of the beta-nu correlation using magneto-optically trapped 21Na.

The beta-neutrino correlation coefficient, a(betanu), in 21Na is inferred from detecting the beta(+) and low-energy recoil daughter nucleus. 21Na is produced at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory and 800 000 atoms are maintained in a magneto-optical trap. From the measured time of flight of recoil ions in the presence of a drift electric field, we find a(betanu)=0.5243+/-0.0091. There may be a dependence on the trapped atom population. This and other systematic uncertainties are discussed.

Journal Article↗
PubMed2004

Development of an odd-Z-projectile reaction for heavy element synthesis: 208Pb(64Ni,n)271Ds and 208Pb(65Cu,n)(272)111.

Seven 271Ds decay chains were identified in the bombardment of 208Pb targets with 311.5 and 314.3 MeV 64Ni projectiles using the Berkeley Gas-filled Separator. These data, combined with previous results, provide an excitation function for this reaction. From these results, an optimum energy of 321 MeV was estimated for the production of (272)111 in the new reaction 208Pb(65Cu,n). One decay chain was observed, resulting in a cross section of 1.7(+3.9)(-1.4) pb. This experiment confirms the discovery of element 111 by the Darmstadt Group who used the 209Bi(64Ni,n)(272)111 reaction.

Journal Article↗
PubMed2002

The TB structural genomics consortium crystallization facility: towards automation from protein to electron density.

The crystallization facility of the TB (Tuberculosis) structural genomics consortium, one of nine NIH sponsored p50 structural genomic centres, provides TB consortium members with automated crystallization, data collection and basic molecular replacement (MR) structure solution up to bias minimized electron density maps. Crystallization setup of up to ten proteins per day follows the CRYSTOOL combinatorial screen protocol using a modular and affordable robotic design with an open architecture. Components include screen preparation, plate setup, automated image acquisition and analysis, and optimisation design. A new 96 well crystallization plate has been designed for optimal robotic handling while maintaining ease of manual crystal harvesting. Robotic crystal mounting, screening, and data collection are conducted in-house and at the Advanced Light Source (ALS) in Berkeley. A simple automated protocol based on MR and homology based structure prediction automatically solves modestly difficult problems. Multiple search models are evaluated in parallel MR and the best multi-segment rigid body refined MR solution is subjected to simulated annealing torsion angle molecular dynamics using CNS, bringing even marginal MR solutions within the convergence radius of the subsequent highly effective bias removal and map reconstruction protocol, Shake&wARP, used to generate electron density for initial rebuilding. Real space correlation plots allow rapid assessment of local structure quality. Modular design of robotics and automated scripts using publicly available programs for structure solution allow for efficient high throughput crystallography - at a reasonable cost.

Automation↗
PubMed2006

Advanced beamline automation for biological crystallography experiments.

An automated crystal-mounting/alignment system has been developed at Lawrence Berkeley National Laboratory and has been installed on three of the protein-crystallography experimental stations at the Advanced Light Source (ALS); it is currently being implemented at synchrotron crystallography beamlines at CHESS, NSLS and the APS. The benefits to using an automounter system include (i) optimization of the use of synchrotron beam time, (ii) facilitation of advanced data-collection techniques, (iii) collection of higher quality data, (iv) reduction of the risk to crystals and (v) exploration of systematic studies of experimental protocols. Developments on the next-generation automounter with improvements in robustness, automated alignment and sample tracking are under way, with an end-to-end data-flow process being developed to allow remote data collection and monitoring.

Automation↗
PubMed2005

Crystallization of a newly discovered histidine acid phosphatase from Francisella tularensis.

Francisella tularensis is a highly infectious bacterial pathogen that is considered by the Centers for Disease Control and Prevention to be a potential bioterrorism weapon. Here, the crystallization of a 37.2 kDa phosphatase encoded by the genome of F. tularensis subsp. holarctica live vaccine strain is reported. This enzyme shares 41% amino-acid sequence identity with Legionella pneumophila major acid phosphatase and contains the RHGXRXP motif that is characteristic of the histidine acid phosphatase family. Large diffraction-quality crystals were grown in the presence of Tacsimate, HEPES and PEG 3350. The crystals belong to space group P4(1)2(1)2, with unit-cell parameters a = 61.96, c = 210.78 A. The asymmetric unit is predicted to contain one protein molecule, with a solvent content of 53%. A 1.75 A resolution native data set was recorded at beamline 4.2.2 of the Lawrence Berkeley National Laboratory Advanced Light Source. Molecular-replacement trials using the human prostatic acid phosphatase structure as the search model (28% amino-acid sequence identity) did not produce a satisfactory solution. Therefore, the structure of F. tularensis histidine acid phosphatase will be determined by multiwavelength anomalous dispersion phasing using a selenomethionyl derivative.

Acid Phosphatase↗
PubMed2006

Cloning, expression, purification, crystallization and preliminary X-ray studies of epoxide hydrolases A and B from Mycobacterium tuberculosis.

Mycobacterium tuberculosis epoxide hydrolases A and B, corresponding to open reading frames Rv3617 and Rv1938, are detoxification enzymes against epoxides. The recombinant forms of these enzymes have been expressed in Escherichia coli and purified to homogeneity. Diffraction-quality crystals of Rv3617 and Rv1938 were obtained by the hanging-drop vapour-diffusion technique. Crystals of Rv3617 and Rv1938 diffracted to 3.0 and 2.1 A resolution, respectively, at the ALS synchrotron at Berkeley, CA, USA.

Bacterial Proteins↗
PubMed2006

Unsupervised multiscale color image segmentation based on MDL principle.

We present an unsupervised multiscale color image segmentation algorithm. The basic idea is to apply mean shift clustering to obtain an over-segmentation and then merge regions at multiple scales to minimize the minimum description length criterion. The performance on the Berkeley segmentation benchmark campares favorably with some existing approaches.

Algorithms↗
PubMedDate not supplied

The stability of attachment security from infancy to adolescence and early adulthood: general introduction.

Current attachment theory hypothesizes that attachment security during infancy influences individual differences in adult representations of attachment. We present three long-term longitudinal studies using three different samples relevant to this hypothesis. Each study assesses infant attachment by using the Ainsworth Strange Situation and adult attachment by using the Berkeley Adult Attachment Interview (AAI). Attachment security was significantly stable in the first two studies. Discontinuity in all three studies was related to negative life events and circumstances. Comparison of the results across these complementary studies affords a degree of replication and sheds light on alternative interpretations. Various mechanisms underlying the stability and instability of attachment security are discussed.

Adolescent↗
PubMedDate not supplied

Attachment security in infancy and early adulthood: a twenty-year longitudinal study.

Sixty White middle-class infants were seen in the Ainsworth Strange Situation at 12 months of age; 50 of these participants (21 males, 29 females) were recontacted 20 years later and interviewed by using the Berkeley Adult Attachment Interview (AAI). The interviewers were blind to the participants' Strange Situation classifications. Overall, 72% of the infants received the same secure versus insecure attachment classification in early adulthood, K = .44, p < .001. As predicted by attachment theory, negative life events-defined as (1) loss of a parent, (2) parental divorce, (3) life-threatening illness of parent or child (e.g., diabetes, cancer, heart attack), (4) parental psychiatric disorder, and (5) physical or sexual abuse by a family member-were an important factor in change. Forty-four percent (8 of 18) of the infants whose mothers reported negative life events changed attachment classifications from infancy to early adulthood. Only 22% (7 of 32) of the infants whose mothers reported no such events changed classification, p < .05. These results support Bowlby's hypothesis that individual differences in attachment security can be stable across significant portions of the lifespan and yet remain open to revision in light of experience. The task now is to use a variety of research designs, measurement strategies, and study intervals to clarify the mechanisms underlying stability and change.

Adult↗