Showing papers by "Lawrence Berkeley National Laboratory published in 1998"

Semiconductor Nanocrystals as Fluorescent Biological Labels

Abstract: Semiconductor nanocrystals were prepared for use as fluorescent probes in biological staining and diagnostics. Compared with conventional fluorophores, the nanocrystals have a narrow, tunable, symmetric emission spectrum and are photochemically stable. The advantages of the broad, continuous excitation spectrum were demonstrated in a dual-emission, single-excitation labeling experiment on mouse fibroblasts. These nanocrystal probes are thus complementary and in some cases may be superior to existing fluorophores.

Bro: a system for detecting network intruders in real-time

Abstract: We describe Bro, a stand-alone system for detecting network intruders in real-time by passively monitoring a network link over which the intruder's traffic transits. We give an overview of the system's design, which emphasizes high-speed (FDDI-rate) monitoring, real-time notification, clear separation between mechanism and policy, and extensibility. To achieve these ends, Bro is divided into an "event engine" that reduces a kernel-filtered network traffic stream into a series of higher-level events, and a "policy script interpreter" that interprets event handlers written in a specialized language used to express a site's security policy. Event handlers can update state information, synthesize new events, record information to disk, and generate real-time notifications via syslog. We also discuss a number of attacks that attempt to subvert passive monitoring systems and defenses against these, and give particulars of how Bro analyzes the four applications integrated into it so far: Finger, FTP, Portmapper and Telnet. The system is publicly available in source code form.

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays

Abstract: Gene dosage variations occur in many diseases. In cancer, deletions and copy number increases contribute to alterations in the expression of tumour-suppressor genes and oncogenes, respectively. Developmental abnormalities, such as Down, Prader Willi, Angelman and Cri du Chat syndromes, result from gain or loss of one copy of a chromosome or chromosomal region. Thus, detection and mapping of copy number abnormalities provide an approach for associating aberrations with disease phenotype and for localizing critical genes. Comparative genomic hybridization3(CGH) was developed for genome-wide analysis of DNA sequence copy number in a single experiment. In CGH, differentially labelled total genomic DNA from a 'test' and a 'reference' cell population are cohybridized to normal metaphase chromosomes, using blocking DNA to suppress signals from repetitive sequences. The resulting ratio of the fluorescence intensities at a location on the 'cytogenetic map', provided by the chromosomes, is approximately proportional to the ratio of the copy numbers of the corresponding DNA sequences in the test and reference genomes. CGH has been broadly applied to human and mouse malignancies. The use of metaphase chromosomes, however, limits detection of events involving small regions (of less than 20 Mb) of the genome, resolution of closely spaced aberrations and linking ratio changes to genomic/genetic markers. Therefore, more laborious locus-by-locus techniques have been required for higher resolution studies2,3,4,5. Hybridization to an array of mapped sequences instead of metaphase chromosomes could overcome the limitations of conventional CGH (ref. 6) if adequate performance could be achieved. Copy number would be related to the test/reference fluorescence ratio on the array targets, and genomic resolution could be determined by the map distance between the targets, or by the length of the cloned DNA segments. We describe here our implementation of array CGH. We demonstrate its ability to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer.

Discovery of a supernova explosion at half the age of the Universe

Abstract: The ultimate fate of the Universe, infinite expansion or a big crunch, can be determined by using the redshifts and distances of very distant supernovae to monitor changes in the expansion rate. We can now find1 large numbers of these distant supernovae, and measure their redshifts and apparent brightnesses; moreover, recent studies of nearby type Ia supernovae have shown how to determine their intrinsic luminosities2,3,4—and therefore with their apparent brightnesses obtain their distances. The >50 distant supernovae discovered so far provide a record of changes in the expansion rate over the past several billion years5,6,7. However, it is necessary to extend this expansion history still farther away (hence further back in time) in order to begin to distinguish the causes of the expansion-rate changes—such as the slowing caused by the gravitational attraction of the Universe's mass density, and the possibly counteracting effect of the cosmological constant8. Here we report the most distant spectroscopically confirmed supernova. Spectra and photometry from the largest telescopes on the ground and in space show that this ancient supernova is strikingly similar to nearby, recent type Ia supernovae. When combined with previous measurements of nearer supernovae2,5, these new measurements suggest that we may live in a low-mass-density universe.

Structure of the alpha beta tubulin dimer by electron crystallography.

Abstract: The αβ tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. Each tubulin monomer binds a guanine nucleotide, which is non-exchangeable when it is bound in the α subunit, or N site, and exchangeable when bound in the β subunit, or E site. The α- and β-tubulins share 40% amino-acid sequence identity, both exist in several isotype forms, and both undergo a variety of post-translational modifications1. Limited sequence homology has been found with the proteins FtsZ2 and Misato3, which are involved in cell division in bacteria and Drosophila, respectively. Here we present an atomic model of the αβ tubulin dimer fitted to a 3.7-A density map obtained by electron crystallography of zinc-induced tubulin sheets. The structures of α- and β-tubulin are basically identical: each monomer is formed by a core of two β-sheets surrounded by α-helices. The monomer structure is very compact, but can be divided into three functional domains: the amino-terminal domain containing the nucleotide-binding region, an intermediate domain containing the Taxol-binding site, and the carboxy-terminal domain, which probably constitutes the binding surface for motor proteins.

Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex.

Abstract: Mitochondrial cytochrome bc1 complex performs two functions: It is a respiratory multienzyme complex and it recognizes a mitochondrial targeting presequence. Refined crystal structures of the 11-subunit bc1 complex from bovine heart reveal full views of this bifunctional enzyme. The "Rieske" iron-sulfur protein subunit shows significant conformational changes in different crystal forms, suggesting a new electron transport mechanism of the enzyme. The mitochondrial targeting presequence of the "Rieske" protein (subunit 9) is lodged between the two "core" subunits at the matrix side of the complex. These "core" subunits are related to the matrix processing peptidase, and the structure unveils how mitochondrial targeting presequences are recognized.

Computing geodesic paths on manifolds

Abstract: The Fast Marching Method is a numerical algorithm for solving the Eikonal equation on a rectangular orthogonal mesh in O(M log M) steps, where M is the total number of grid points. In this paper we extend the Fast Marching Method to triangulated domains with the same computational complexity. As an application, we provide an optimal time algorithm for computing the geodesic distances and thereby extracting shortest paths on triangulated manifolds.

Electron transfer by domain movement in cytochrome bc1.

Abstract: The cytochrome bc1 is one of the three major respiratory enzyme complexes residing in the inner mitochondrial membrane. Cytochrome bc1 transfers electrons from ubiquinol to cytochrome c and uses the energy thus released to form an electrochemical gradient across the inner membrane. Our X-ray crystal structures of the complex from chicken, cow and rabbit in both the presence and absence of inhibitors of quinone oxidation, reveal two different locations for the extrinsic domain of one component of the enzyme, an iron-sulphur protein. One location is close enough to the supposed quinol oxidation site to allow reduction of the Fe-S protein by ubiquinol. The other site is close enough to cytochrome c1 to allow oxidation of the Fe-S protein by the cytochrome. As neither location will allow both reactions to proceed at a suitable rate, the reaction mechanism must involve movement of the extrinsic domain of the Fe-S component in order to shuttle electrons from ubiquinol to cytochrome c1. Such a mechanism has not previously been observed in redox protein complexes.

Methods for analyzing anisotropic flow in relativistic nuclear collisions

Abstract: The strategy and techniques for analyzing anisotropic flow (directed, elliptic, etc.) in relativistic nuclear collisions are presented. The emphasis is on the use of the Fourier expansion of azimuthal distributions. We present formulas relevant for this approach, and in particular, show how the event multiplicity enters into the event plane resolution. We also discuss the role of nonflow correlations and a method for introducing flow into a simulation.

4D Conformal Field Theories and Strings on Orbifolds

Abstract: We propose and test correspondences between 4D quantum field theories (QFTs) with N=2,thinsp1,thinsp0 (super)conformal invariance and type IIB string theory on various orbifolds of AdS{sub 5}{times} S{sup 5} . This allows us to translate the problem of finding stable nontrivial nonsupersymmetric string backgrounds into the problem of realizing nontrivial renormalization group (RG) fixed point QFTs on branes. RG fixed lines in this context correspond to string theories in which no vacuum energy is generated quantum mechanically. {copyright} {ital 1998} {ital The American Physical Society}

The COBE Diffuse Infrared Background Experiment Search for the Cosmic Infrared Background. I. Limits and Detections

Abstract: The Diffuse Infrared Background Experiment (DIRBE) on the Cosmic Background Explorer (COBE) spacecraft was designed primarily to conduct a systematic search for an isotropic cosmic infrared background (CIB) in 10 photometric bands from 1.25 to 240 μm. The results of that search are presented here. Conservative limits on the CIB are obtained from the minimum observed brightness in all-sky maps at each wavelength, with the faintest limits in the DIRBE spectral range being at 3.5 μm (νIν < 64 nW m-2 sr-1, 95% confidence level) and at 240 μm (νIν < 28 nW m-2 sr-1, 95% confidence level). The bright foregrounds from interplanetary dust scattering and emission, stars, and interstellar dust emission are the principal impediments to the DIRBE measurements of the CIB. These foregrounds have been modeled and removed from the sky maps. Assessment of the random and systematic uncertainties in the residuals and tests for isotropy show that only the 140 and 240 μm data provide candidate detections of the CIB. The residuals and their uncertainties provide CIB upper limits more restrictive than the dark sky limits at wavelengths from 1.25 to 100 μm. No plausible solar system or Galactic source of the observed 140 and 240 μm residuals can be identified, leading to the conclusion that the CIB has been detected at levels of νIν = 25 ± 7 and 14 ± 3 nW m-2 sr-1 at 140 and 240 μm, respectively. The integrated energy from 140 to 240 μm, 10.3 nW m-2 sr-1, is about twice the integrated optical light from the galaxies in the Hubble Deep Field, suggesting that star formation might have been heavily enshrouded by dust at high redshift. The detections and upper limits reported here provide new constraints on models of the history of energy-releasing processes and dust production since the decoupling of the cosmic microwave background from matter.

Crystal structure of botulinum neurotoxin type A and implications for toxicity.

Abstract: Botulinum neurotoxin type A (BoNT/A) is the potent disease agent in botulism, a potential biological weapon and an effective therapeutic drug for involuntary muscle disorders. The crystal structure of the entire 1,285 amino acid di-chain neurotoxin was determined at 3.3 A resolution. The structure reveals that the translocation domain contains a central pair of alpha-helices 105 A long and a approximately 50 residue loop or belt that wraps around the catalytic domain. This belt partially occludes a large channel leading to a buried, negative active site--a feature that calls for radically different inhibitor design strategies from those currently used. The fold of the translocation domain suggests a mechanism of pore formation different from other toxins. Lastly, the toxin appears as a hybrid of varied structural motifs and suggests a modular assembly of functional subunits to yield pathogenesis.

Electron-Hole Excitations in Semiconductors and Insulators

Abstract: We present a new {ital abthinspthinspinitio} approach to calculate the interaction between electrons and holes in periodic crystals and to evaluate the resulting coupled electron-hole excitations. This involves a novel interpolation scheme in reciprocal space in solving the Bethe-Salpeter equation for the two-particle Green{close_quote}s function. We apply this approach to the calculation of the entire optical absorption spectrum, as well as of the energies and wave functions of bound exciton states in GaAs and LiF. Very good agreement with experiment is observed. {copyright} {ital 1998} {ital The American Physical Society}

Reciprocal interactions between β1-integrin and epidermal growth factor receptor in three-dimensional basement membrane breast cultures: A different perspective in epithelial biology

Abstract: Anchorage and growth factor independence are cardinal features of the transformed phenotype. Although it is logical that the two pathways must be coregulated in normal tissues to maintain homeostasis, this has not been demonstrated directly. We showed previously that down-modulation of β1-integrin signaling reverted the malignant behavior of a human breast tumor cell line (T4–2) derived from phenotypically normal cells (HMT-3522) and led to growth arrest in a three-dimensional (3D) basement membrane assay in which the cells formed tissue-like acini (14). Here, we show that there is a bidirectional cross-modulation of β1-integrin and epidermal growth factor receptor (EGFR) signaling via the mitogen-activated protein kinase (MAPK) pathway. The reciprocal modulation does not occur in monolayer (2D) cultures. Antibody-mediated inhibition of either of these receptors in the tumor cells, or inhibition of MAPK kinase, induced a concomitant down-regulation of both receptors, followed by growth-arrest and restoration of normal breast tissue morphogenesis. Cross-modulation and tissue morphogenesis were associated with attenuation of EGF-induced transient MAPK activation. To specifically test EGFR and β1-integrin interdependency, EGFR was overexpressed in nonmalignant cells, leading to disruption of morphogenesis and a compensatory up-regulation of β1-integrin expression, again only in 3D. Our results indicate that when breast cells are spatially organized as a result of contact with basement membrane, the signaling pathways become coupled and bidirectional. They further explain why breast cells fail to differentiate in monolayer cultures in which these events are mostly uncoupled. Moreover, in a subset of tumor cells in which these pathways are misregulated but functional, the cells could be “normalized” by manipulating either pathway.

Calculation of Couplings and Energy-Transfer Pathways between the Pigments of LH2 by the ab Initio Transition Density Cube Method

Abstract: A practical method for accurate evaluation of the Coulombic contribution to the electronic coupling for energy transfer at any donor−acceptor separation is reported. The method involves the exact interaction between transition densities of each chromophore which are calculated ab initio and may include electron correlation. The method is used to calculate coupling strengths between the pigments of the bacterial light-harvesting complex, LH2, and to compare with results using the ideal dipole approximation (IDA). The results suggest that the relatively symmetric transitions of bacteriochlorophyll a (Bchla) pigments are reasonably well described by the IDA for separations >15 A, although deviations are significant at smaller separations. The less symmetric transition of the twisted carotenoid pigment is rather poorly described by the IDA and shows significant deviation even at separations of well over 20 A. The calculated coupling strengths are combined with estimates of the spectral overlap integral to est...

A general framework for low level vision

Abstract: We introduce a new geometrical framework based on which natural flows for image scale space and enhancement are presented. We consider intensity images as surfaces in the (x,I) space. The image is, thereby, a two-dimensional (2-D) surface in three-dimensional (3-D) space for gray-level images, and 2-D surfaces in five dimensions for color images. The new formulation unifies many classical schemes and algorithms via a simple scaling of the intensity contrast, and results in new and efficient schemes. Extensions to multidimensional signals become natural and lead to powerful denoising and scale space algorithms.

Tubulin and FtsZ form a distinct family of GTPases.

Abstract: Tubulin and FtsZ share a common fold of two domains connected by a central helix. Structure-based sequence alignment shows that common residues localize in the nucleotide-binding site and a region that interacts with the nucleotide of the next tubulin subunit in the protofilament, suggesting that tubulin and FtsZ use similar contacts to form filaments. Surfaces that would make lateral interactions between protofilaments or interact with motor proteins are, however, different. The highly conserved nucleotide-binding sites of tubulin and FtsZ clearly differ from those of EF-Tu and other GTPases, while resembling the nucleotide site of glyceraldehyde-3-phosphate dehydrogenase. Thus, tubulin and FtsZ form a distinct family of GTP-hydrolyzing proteins.

Aspects of large N gauge theory dynamics as seen by string theory

Abstract: In this paper we explore some of the features of large N supersymmetric and nonsupersymmetric gauge theories using Maldacena’s duality conjectures. We show that the resulting strong coupling behavior of the gauge theories is consistent with our qualitative expectations of these theories. Some of these consistency checks are highly nontrivial and give additional evidence for the validity of the proposed dualities.

Titanium: a high-performance Java dialect

Abstract: Titanium is a language and system for high-performance parallel scientific computing. Titanium uses Java as its base, thereby leveraging the advantages of that language and allowing us to focus attention on parallel computing issues. The main additions to Java are immutable classes, multidimensional arrays, an explicitly parallel SPMD model of computation with a global address space, and zone-based memory management. We discuss these features and our design approach, and report progress on the development of Titanium, including our current driving application: a three-dimensional adaptive mesh refinement parallel Poisson solver. © 1998 John Wiley & Sons, Ltd.

Defects in Semiconductors: Some Fatal, Some Vital

Abstract: REVIEW The role of defects as essential entities in semiconductor materials is reviewed. Early experiments with semiconductors were hampered by the extreme sensitivity of the electronic properties to minute concentrations of impurities. Semiconductors were viewed as a family of solids with irreproducible properties. Scientific efforts overcame this idiosyncrasy and turned the art of impurity doping into today9s exceedingly useful and reproducible technology that is used to control precisely electrical conductivity, composition, and minority-carrier lifetimes over wide ranges. Native defects such as vacancies and self-interstitials control basic processes, foremost self- and dopant diffusion. The structural properties of dislocations and higher dimensional defects have been studied with atomic resolution, but a thorough theoretical understanding of their electronic properties is incomplete. Reactions between defects within the host lattices are increasingly better understood and are used for gettering and electrical passivation of unwanted impurities. Metastable defects such as DX centers and the EL2-related arsenic antisite are briefly discussed. The recent development of isotopically controlled semiconductors has created new research opportunities in this field.

The premature ageing syndrome protein, WRN, is a 3′→5′ exonuclease

Abstract: Werner syndrome (WS) is a human autosomal recessive disorder that causes the premature appearance of a partial array of disorders characteristic of old age1,2. These disorders include atherosclerosis, cancer, type 2 diabetes, osteoporosis, cataracts, wrinkled skin and grey hair, among other ailments. Cells cultured from WS subjects have a shortened replicative life span3,4 and elevated rates of chromosome translocations, large deletions and homologous recombination5,6. The gene defective in WS, WRN, encodes a large RecQ-like DNA helicase7 of 1432 aa. Defects in another human RecQ-like helicase, BLM, result in Bloom’s syndrome8 (BS), a genetic disorder that is quite different from WS. BS is manifested by short stature, neoplasia, immunodeficiency and high risk of cancer. Cells from BS subjects show an increase in sister chromatid exchanges. DNA helicases can function in replication, repair, recombination, transcription or RNA processing. As WRN and BLM share no obvious homology outside the helicase domain, the non-helicase domains probably determine in which process each RecQ-like helicase participates, which provides the basis for the disparate cellular and organismal phenotypes that result from defects in these proteins. Statistical sequence analyses showed subtle but significant similarities between WRN and several 3′→5′ exonucleases9,10. To test the prediction that WRN is an exonuclease, we produced tagged recombinant wild-type and mutant WRN proteins. Two mutants had amino-acid substitutions at either position 82 (D82A) or 84 (E84A), two of the five residues predicted to be critical for exonuclease activity9,10. A third mutant had a substitution at position 577 (K577M), which abolished WRN helicase activity11. The fourth mutant was an N-terminal fragment (aa 1–333; N333) containing the putative exonuclease domain, but lacking the helicase domain. A tagged 36-aa vector-derived peptide served as a negative control (mock). Purified WRN and mock proteins were incubated with doubled-stranded DNA substrates. Wild-type WRN degraded a 5′ labelled substrate to a series of smaller, labelled products (Fig. 1a), and a 3′ labelled substrate to a single labelled product that migrated as a mononucleotide (Fig. 1b). Thus, WRN degraded DNA with 3′→5′ directionality. Although mock and full-length WRN preparations contained low levels of a contaminating 5′→3′ exonuclease, as shown by release of the 5′ label as a mononucleotide (Figs 1a,​,2b),2b), 3′→5′ degradation was entirely dependent on WRN. Fig. 1 Exonuclease activity of wild-type WRN and the N333 fragment. 6×his-tagged proteins were purified from baculovirus-infected insect cells using either nuclear (WRN, D82A, E84A, K577M, mock control) or cytosolic (N333, mock control) extracts. WRN, ... Fig. 2 Helicase and exonuclease activities of wild-type and mutant WRN proteins. a, WRN, K577M, E84A, D82A or mock proteins (10 ng) were assayed for helicase activity by incubating 5′ 32P-labelled DNA substrate (0.4 pmol; Fig. 1a) in helicase assay buffer ... WRN exonuclease activity resided in the N terminus. N333, which was essentially free of contaminating 5′→3′ exonuclease, degraded 5′ and 3′ labelled substrates similarly to full-length WRN (Fig. 1c,d). When incubated with a 374-bp DNA fragment labelled at the 3′ end with 32P, and internally with 3H, N333 released most of both labels (Fig. 1e). Thus, the WRN exonuclease is capable of substantial DNA degradation. Consistent with 3′→5′ directionality, N333 released 32P from 3′ ends more rapidly than 3H from internal residues. In addition, gel-purified N333, which lacked contaminating nuclease activities, efficiently removed the 3′, but not the 5′, label when incubated with DNA substrates labelled at either the 3′ or the 5′ end (Fig. 1f). Genetic evidence for WRN exonuclease activity was obtained by introducing point mutations at critical amino acids in the exonuclease domain (D82A and E84A). These mutants retained the wild-type level of helicase activity (Fig. 2a), but had little or no 3′→5′ exonuclease activity, using either a 5′ (Fig. 2b) or 3′ (Fig. 2c) 32P-labelled substrate, and were indistinguishable from mock protein in this regard (Fig. 2d). The K577M mutant, in contrast, was devoid of helicase activity (Fig. 2a), as expected, but had 3′→5′ exonuclease activity comparable to that of wild-type WRN (Fig. 2b–d). Our data indicate that WRN is indeed a 3′→5′ exonuclease. This activity resides in the N terminus, and is physically and functionally separable from the helicase activity. The identification of an exonuclease activity in WRN clearly distinguishes it from other human RecQ-like helicases, and may help explain the differences between WS and BS. What are the functions of the WRN exonuclease in vivo? It may participate in recombination and DNA repair. Exonucleases are integral components of some recombination pathways12, and WRN appears to have a role in recombination5,6,13. The finding that WS cells are hypersensitive to the DNA damaging agent 4-nitroquinoline-1-oxide14 suggests a role for WRN in DNA repair. Finally, WRN is homologous to FFA-1 (replication focus-forming activity 1) in Xenopus laevis15, raising the possibility that WRN may also be involved in DNA replication. In this context, the WRN exonuclease may provide 3′→5′ proofreading function to DNA polymerases that lack such activity. Whatever the case, an understanding of the functions of WRN exonuclease and their relationships to the other functions of WRN will lead to new insights into the molecular and cellular basis for WS and a subset of age-associated pathologies.

Fast, Approximate Synthesis of Fractional Gaussian Noise for Generating Self-Similar Network Traffic

Abstract: Recent network traffic studies argue that network arrival processes are much more faithfully modeled using statistically self-similar processes instead of traditional Poisson processes [LTWW94,PF95]. One difficulty in dealing with self-similar models is how to efficiently synthesize traces (sample paths) corresponding to self-similar traffic. We present a fast Fourier transform method for synthesizing approximate self-similar sample paths for one type of self-similar process, Fractional Gaussian Noise, and assess its performance and validity. We find that the method is as fast or faster than existing methods and appears to generate close approximations to true self-similar sample paths. We also discuss issues in using such synthesized sample paths for simulating network traffic, and how an approximation used by our method can dramatically speed up evaluation of Whittle's estimator for H, the Hurst parameter giving the strength of long-range dependence present in a self-similar time series.