bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermographic Selection of Effective Catalysts from an Encoded Polymer-Bound Library
Authors: Taylor Steven J. , Morken James P.
Published: July 2002

A general method is introduced for the rapid and simultaneous evaluation of each member of large encoded catalyst libraries for the ability to catalyze a reaction in solution. The procedure was used to select active catalysts from a library of potential polymer-bound multifunctional catalysts. From ∼7000 beads screened (3150 distinct catalysts), 23 beads were selected for catalysis of an acylation reaction. Kinetic experiments indicate that the most strongly selected beads are also the most efficient catalysts.
Enzyme Structure with Two Catalytic Sites for Double-Sieve Selection of Substrate
Authors: Nureki Osamu , Vassylyev Dmitry G. , Tateno Masaru , Shimada Atsushi , Nakama Takashi , Fukai Shuya , Konno Mitiko , Hendrickson Tamara L. , Schimmel Paul , Yokoyama Shigeyuki
Published: July 2002

High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl–transfer RNA synthetase, activates not only the cognate substrate
l
-isoleucine but also the minimally distinct
l
-valine in the first, aminoacylation step. Then, in a second, “editing” step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a “double-sieve” mechanism has already been proposed. The present crystal structures of the synthetase in complexes with
l
-isoleucine and
l
-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular β-barrel domain that protrudes from the aminoacylation domain.
Proteolytic Inactivation of MAP-Kinase-Kinase by Anthrax Lethal Factor
Authors: Duesbery Nicholas S. , Webb Craig P. , Leppla Stephen H. , Gordon Valery M. , Klimpel Kurt R. , Copeland Terry D. , Ahn Natalie G. , Oskarsson Marianne K. , Fukasawa Kenji , Paull Ken D. , Vande Woude George F.
Published: July 2002

Anthrax lethal toxin, produced by the bacterium
Bacillus anthracis,
is the major cause of death in animals infected with anthrax. One component of this toxin, lethal factor (LF), is suspected to be a metalloprotease, but no physiological substrates have been identified. Here it is shown that LF is a protease that cleaves the amino terminus of mitogen-activated protein kinase kinases 1 and 2 (MAPKK1 and MAPKK2) and that this cleavage inactivates MAPKK1 and inhibits the MAPK signal transduction pathway. The identification of a cleavage site for LF may facilitate the development of LF inhibitors.
Neptune's Eccentricity and the Nature of the Kuiper Belt
Authors: Ward William R. , Hahn Joseph M.
Published: July 2002

The small eccentricity of Neptune may be a direct consequence of apsidal wave interaction with the trans-Neptune population of debris called the Kuiper belt. The Kuiper belt is subject to resonant perturbations from Neptune, so that the transport of angular momentum by density waves can result in orbital evolution of Neptune as well as changes in the structure of the Kuiper belt. In particular, for a belt eroded out to the vicinity of Neptune's 2:1 resonance at about 48 astronomical units, Neptune's eccentricity can damp to its current value over the age of the solar system if the belt contains slightly more than an earth mass of material out to about 75 astronomical units.
IEX
-1L, an Apoptosis Inhibitor Involved in NF-κB-Mediated Cell Survival
Authors: Wu Mei X. , Ao Zhaohui , Prasad K. V. S. , Wu Ruilian , Schlossman Stuart F.
Published: July 2002

Transcription factors of the nuclear factor–κB/rel (NF-κB) family may be important in cell survival by regulating unidentified, anti-apoptotic genes. One such gene that protects cells from apoptosis induced by Fas or tumor necrosis factor type α (TNF),
IEX-
1L, is described here. Its transcription induced by TNF was decreased in cells with defective NF-κB activation, rendering them sensitive to TNF-induced apoptosis, which was abolished by transfection with
IEX-
1L. In support, overexpression of antisense
IEX-
1L partially blocked TNF-induced expression of
IEX
-1L and sensitized normal cells to killing. This study demonstrates a key role of
IEX-
1L in cellular resistance to TNF-induced apoptosis.
Grain Feeding and the Dissemination of Acid-Resistant
Escherichia coli
from Cattle
Authors: Diez-Gonzalez Francisco , Callaway Todd R. , Kizoulis Menas G. , Russell James B.
Published: July 2002

The gastric stomach of humans is a barrier to food-borne pathogens, but
Escherichia coli
can survive at pH 2.0 if it is grown under mildly acidic conditions. Cattle are a natural reservoir for pathogenic
E. coli
, and cattle fed mostly grain had lower colonic pH and more acid-resistant
E. coli
than cattle fed only hay. On the basis of numbers and survival after acid shock, cattle that were fed grain had 10
6
-fold more acid-resistant
E. coli
than cattle fed hay, but a brief period of hay feeding decreased the acid-resistant count substantially.
Controlling Gene Expression in Living Cells Through Small Molecule-RNA Interactions
Authors: Werstuck Geoffrey , Green Michael R.
Published: July 2002

Short RNA aptamers that specifically bind to a wide variety of ligands in vitro can be isolated from randomized pools of RNA. Here it is shown that small molecule aptamers also bound their ligand in vivo, enabling development of a method for controlling gene expression in living cells. Insertion of a small molecule aptamer into the 5′ untranslated region of a messenger RNA allowed its translation to be repressible by ligand addition in vitro as well as in mammalian cells. The ability of small molecules to control expression of specific genes could facilitate studies in many areas of biology and medicine.
Two-Dimensional Magnetic Particles
Authors: Stamm C. , Marty F. , Vaterlaus A. , Weich V. , Egger S. , Maier U. , Ramsperger U. , Fuhrmann H. , Pescia D.
Published: July 2002

Single two-dimensional (2D) atomically thick magnetic particles of cobalt and iron with variable size and shape were fabricated by combining a mask technique with standard molecular beam epitaxy. Reduction of the lateral size of in-plane magnetized 2D cobalt films down to about 100 nanometers did not essentially modify their magnetic properties; although the separation of boundaries decreased greatly, neither domain penetrated the particle, nor was any sizable shape anisotropy observed. The mutual interaction of 2D cobalt particles was negligible, and the magnetic state of a single particle could be switched without modifying the state of the neighbors. Perpendicularly magnetized iron particles did not exhibit such responses. These results suggest that only a few atoms forming a 2D in-plane magnetized dot may provide a stable elementary bit for nanorecording.
Databases in Genomic Research
Authors: Gelbart William M.
Published: July 2002

Genome-related databases have already become an invaluable part of the scientific landscape. The role played by these databases will only increase as the volume and complexity of relevant biology data rapidly expand. We are far enough into the genome project and into the development of these databases to assess their attributes and to reexamine some of the conceptual organizations and approaches they are taking. It is clear that there are needs for both highly detailed and simplified database views, the latter being especially needed to make expert domain data more accessible to nonspecialists.
The Transcriptional Program of Sporulation in Budding Yeast
Authors: Chu S. , DeRisi J. , Eisen M. , Mulholland J. , Botstein D. , Brown P. O. , Herskowitz I.
Published: July 2002

Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis. DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation. At least seven distinct temporal patterns of induction were observed. The transcription factor Ndt80 appeared to be important for induction of a large group of genes at the end of meiotic prophase. Consensus sequences known or proposed to be responsible for temporal regulation could be identified solely from analysis of sequences of coordinately expressed genes. The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis.
Genome Sequence of an Obligate Intracellular Pathogen of Humans:
Chlamydia trachomatis
Authors: Stephens Richard S. , Kalman Sue , Lammel Claudia , Fan Jun , Marathe Rekha , Aravind L. , Mitchell Wayne , Olinger Lynn , Tatusov Roman L. , Zhao Qixun , Koonin Eugene V. , Davis Ronald W.
Published: July 2002

Analysis of the 1,042,519–base pair
Chlamydia trachomatis
genome revealed unexpected features related to the complex biology of chlamydiae. Although chlamydiae lack many biosynthetic capabilities, they retain functions for performing key steps and interconversions of metabolites obtained from their mammalian host cells. Numerous potential virulence-associated proteins also were characterized. Several eukaryotic chromatin-associated domain proteins were identified, suggesting a eukaryotic-like mechanism for chlamydial nucleoid condensation and decondensation. The phylogenetic mosaic of chlamydial genes, including a large number of genes with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to obligate intracellular parasitism.
Haldane's Rule in Taxa Lacking a Hemizygous X
Authors: Presgraves Daven C. , Orr H. Allen
Published: July 2002

Haldane's rule states that species hybrids of the XY sex are preferentially sterile or inviable. In all taxa known to obey this rule, the Y is inert and X-linked genes show full expression in XY individuals. Until recently, all theories of Haldane's rule depended on this hemizygosity. A test of Haldane's rule in animals lacking a hemizygous sex—mosquitoes having two functional sex chromosomes in both sexes—reveals that these species show Haldane's rule for sterility but not inviability. A related group having a “normal” hemizygous X obeys Haldane's rule for both sterility and inviability. These results support the faster male and dominance theories of Haldane's rule.
Genetic Classification of Primary Neurodegenerative Disease
Authors: Hardy John , Gwinn-Hardy Katrina
Published: July 2002

During the past 10 years (the “decade of the brain”), some of the genetic causes of many of the primary neurodegenerative diseases, which include Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, prion disease, and many ataxic syndromes, have been found. These breakthroughs mean that for many of these diseases we now know the initiating trigger as well as the final outcome. These diseases have many pathological mechanisms in common, and there may be relatively few pathways to neuronal death seen in these disorders. Thus, treatment strategies developed for a particular disease may be found to have efficacy in more than one disorder.
Transformation of Tooth Type Induced by Inhibition of BMP Signaling
Authors: Tucker Abigail S. , Matthews Karen L. , Sharpe Paul T.
Published: July 2002

Mammalian dentitions are highly patterned, with different types of teeth positioned in different regions of the jaws. BMP4 is an early oral epithelial protein signal that directs odontogenic gene expression in mesenchyme cells of the developing mandibular arch. BMP4 was shown to inhibit expression of the homeobox gene
Barx-1
and to restrict expression to the proximal, presumptive molar mesenchyme of mouse embryos at embryonic day 10. The inhibition of BMP signaling early in mandible development by the action of exogenous Noggin protein resulted in ectopic
Barx-1
expression in the distal, presumptive incisor mesenchyme and a transformation of tooth identity from incisor to molar.
A Rapidly Evolving Homeobox at the Site of a Hybrid Sterility Gene
Authors: Ting Chau-Ti , Tsaur Shun-Chern , Wu Mao-Lien , Wu Chung-I
Published: July 2002

The homeodomain is a DNA binding motif that is usually conserved among diverse taxa. Rapidly evolving homeodomains are thus of interest because their divergence may be associated with speciation. The exact site of the Odysseus (
Ods
) locus of hybrid male sterility in
Drosophila
contains such a homeobox gene. In the past half million years, this homeodomain has experienced more amino acid substitutions than it did in the preceding 700 million years; during this period, it has also evolved faster than other parts of the protein or even the introns. Such rapid sequence divergence is driven by positive selection and may contribute to reproductive isolation.
Structure of a Covalently Trapped Catalytic Complex of HIV-1 Reverse Transcriptase: Implications for Drug Resistance
Authors: Huang Huifang , Chopra Rajiv , Verdine Gregory L. , Harrison Stephen C.
Published: July 2002

A combinatorial disulfide cross-linking strategy was used to prepare a stalled complex of human immunodeficiency virus–type 1 (HIV-1) reverse transcriptase with a DNA template:primer and a deoxynucleoside triphosphate (dNTP), and the crystal structure of the complex was determined at a resolution of 3.2 angstroms. The presence of a dideoxynucleotide at the 3′-primer terminus allows capture of a state in which the substrates are poised for attack on the dNTP. Conformational changes that accompany formation of the catalytic complex produce distinct clusters of the residues that are altered in viruses resistant to nucleoside analog drugs. The positioning of these residues in the neighborhood of the dNTP helps to resolve some long-standing puzzles about the molecular basis of resistance. The resistance mutations are likely to influence binding or reactivity of the inhibitors, relative to normal dNTPs, and the clustering of the mutations correlates with the chemical structure of the drug.
To Emerge or Not to Emerge
Authors: Mazer Susan J.
Published: July 2002

Seeds
Ecology, Biogeography, and Evolution of Dormancy and Germination. Carol C. Baskin and Jerry M. Baskin. Academic, San Diego, 1998. 680 pp. $99.95. ISBN 0-12-080260-0.

This is a comprehensive consideration of the phase in the life cycle of seed plants that extends from seed maturity to germination. It reflects Baskins' three decades of detailed studies on the topic.
Electron Transfer Between Bases in Double Helical DNA
Authors: Kelley Shana O. , Barton Jacqueline K.
Published: July 2002

Fluorescent analogs of adenine that selectively oxidize guanine were used to investigate photoinduced electron transfer through the DNA π-stack as a function of reactant stacking and energetics. Small variations in these factors led to profound changes in the kinetics and distance dependences of DNA-mediated electron-transfer reactions. Values of β, a parameter reflecting the dependence of electron transfer on distance, ranged from 0.1 to 1.0 per angstrom. Strong stacking interactions result in the fastest electron-transfer kinetics. Electrons are thus transported preferentially through an intrastrand rather than interstrand pathway. Reactant energetics also modulate the distance dependence of DNA-mediated charge transport. These studies may resolve the range of disparate results previously reported, and paradigms must now be developed to describe these properties of the DNA π-stack, which can range from insulator- to “wire”-like.
Dislocations Faster than the Speed of Sound
Authors: Gumbsch Peter , Gao Huajian
Published: July 2002

It is thought that dislocations cannot surpass the sound barrier at the shear wave velocity because the energy spent in radiation has a singularity there. Atomistic simulations show that dislocations can move faster than the speed of sound if they are created as supersonic dislocations at a strong stress concentration and are subjected to high shear stresses. This behavior is important for the understanding of low-temperature deformation processes such as mechanical twinning and may be relevant for the dynamics of tectonic faults. The motion of the dislocations at a speed of

2

times the shear wave velocity can be understood from a linear elastic analysis, but many of the peculiarities of the supersonic dislocations are dominated by nonlinear effects that require a realistic atomistic description.
Crystal Structure of Human ZAG, a Fat-Depleting Factor Related to MHC Molecules
Authors: Sánchez Luis M. , Chirino Arthur J. , Bjorkman Pamela J.
Published: July 2002

Zn-α
2
-glycoprotein (ZAG) is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain β
2
-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions.
Complexity and Climate
Authors: Rind D.
Published: July 2002

The climate that we experience results from both ordered forcing and chaotic behavior; the result is a system with characteristics of each. In forecasting prospective climate changes for the next century, the focus has been on the ordered system's responses to anthropogenic forcing. The chaotic component may be much harder to predict, but at this point it is not known how important it will be.
The Human Genus
Authors: Wood Bernard , Collard Mark
Published: July 2002

A general problem in biology is how to incorporate information about evolutionary history and adaptation into taxonomy. The problem is exemplified in attempts to define our own genus,
Homo
. Here conventional criteria for allocating fossil species to
Homo
are reviewed and are found to be either inappropriate or inoperable. We present a revised definition, based on verifiable criteria, for
Homo
and conclude that two species,
Homo habilis
and
Homo rudolfensis
, do not belong in the genus. The earliest taxon to satisfy the criteria is
Homo ergaster
, or early African
Homo erectus
, which currently appears in the fossil record at about 1.9 million years ago.
Viscosity Near Earth's Solid Inner Core
Authors: Smylie D. E.
Published: July 2002

Anomalous splitting of the two equatorial translational modes of oscillation of Earth's solid inner core is used to estimate the effective viscosity just outside its boundary. Superconducting gravimeter observations give periods of 3.5822 ± 0.0012 (retrograde) and 4.0150 ± 0.0010 (prograde) hours. With the use of Ekman layer theory to estimate viscous drag forces, an inferred single viscosity of 1.22 × 10
11
Pascal seconds gives calculated periods of 3.5839 and 4.0167 hours for the two modes, close to the observed values. The large effective viscosity is consistent with a fluid, solid-liquid mixture surrounding the inner core associated with the “compositional convection” that drives Earth's geodynamo.
Requirement for Tec Kinases Rlk and Itk in T Cell Receptor Signaling and Immunity
Authors: Schaeffer Edward M. , Debnath Jayanta , Yap George , McVicar Daniel , Liao X. Charlene , Littman Dan R. , Sher Alan , Varmus Harold E. , Lenardo Michael J. , Schwartzberg Pamela L.
Published: July 2002

T cell receptor (TCR) signaling requires activation of Zap-70 and Src family tyrosine kinases, but requirements for other tyrosine kinases are less clear. Combined deletion in mice of two Tec kinases, Rlk and Itk, caused marked defects in TCR responses including proliferation, cytokine production, and apoptosis in vitro and adaptive immune responses to
Toxoplasma gondii
in vivo. Molecular events immediately downstream from the TCR were intact in
rlk
−/−
itk
−/−
cells, but intermediate events including inositol trisphosphate production, calcium mobilization, and mitogen-activated protein kinase activation were impaired, establishing Tec kinases as critical regulators of TCR signaling required for phospholipase C–γ activation.
A Cell's Sense of Direction
Authors: Parent Carole A. , Devreotes Peter N.
Published: July 2002

In eukaryotic cells directional sensing is mediated by heterotrimeric guanine nucleotide–binding protein (G protein)–linked signaling pathways. In
Dictyostelium discoideum
amoebae and mammalian leukocytes, the receptors and G-protein subunits are uniformly distributed around the cell perimeter. Chemoattractants induce the transient appearance of binding sites for several pleckstrin homology domain–containing proteins on the inner face of the membrane. In gradients of attractant these sites are persistently present on the side of the cell facing the higher concentration, even in the absence of a functional actin cytoskeleton or cell movement. Thus, the cell senses direction by spatially regulating the activity of the signal transduction pathway.
Room-Temperature Deintercalation and Self-Extrusion of Ga from Cr
2
GaN
Authors: Barsoum M. W. , Farber L.
Published: July 2002

Bulk samples of the layered ternary nitride Cr
2
GaN were observed to extrude filaments of pure elemental gallium at room temperature. This self-extrusion phenomenon is best described as a room-temperature deintercalation of gallium from the basal planes of porous Cr
2
GaN samples. The extruded filaments are single crystals with 2- to 100-micrometer diameters and can be several centimeters long.
Electrostatic Modulation of Superconductivity in Ultrathin GdBa
2
Cu
3
O
7-x
Films
Authors: Ahn C. H. , Gariglio S. , Paruch P. , Tybell T. , Antognazza L. , Triscone J.-M.
Published: July 2002

The polarization field of the ferroelectric oxide lead zirconate titanate [Pb(Zr
x
Ti
1–x
)O
3
] was used to tune the critical temperature of the hightemperature superconducting cuprate gadolinium barium copper oxide (GdBa
2
Cu
3
O
7–x
) in a reversible, nonvolatile fashion. For slightly underdoped samples, a uniform shift of several Kelvin in the critical temperature was observed, whereas for more underdoped samples, an insulating state was induced. This transition from superconducting to insulating behavior does not involve chemical or crystalline modification of the material.
Estimation of Particulate Organic Carbon in the Ocean from Satellite Remote Sensing
Authors: Stramski Dariusz , Reynolds Rick A. , Kahru Mati , Mitchell B. Greg
Published: July 2002

Measurements from the Southern Ocean show that particulate organic carbon (POC) concentration is well correlated with the optical backscattering by particles suspended in seawater. This relation, in conjunction with retrieval of the backscattering coefficient from remote-sensing reflectance, provides an algorithm for estimating surface POC from satellite data of ocean color. Satellite imagery from SeaWiFS reveals the seasonal progression of POC, with a zonal band of elevated POC concentrations in December coinciding with the Antarctic Polar Front Zone. At that time, the POC pool within the top 100 meters of the entire Southern Ocean south of 40°S exceeded 0.8 gigatons.
Ceramic Fibers for Matrix Composites in High-Temperature Engine Applications
Authors: Baldus Peter , Jansen Martin , Sporn Dieter
Published: July 2002

High-temperature engine applications have been limited by the performance of metal alloys and carbide fiber composites at elevated temperatures. Random inorganic networks composed of silicon, boron, nitrogen, and carbon represent a novel class of ceramics with outstanding durability at elevated temperatures. SiBN
3
C was synthesized by pyrolysis of a preceramic
N
-methylpolyborosilazane made from the single-source precursor Cl
3
Si-NH-BCl
2
. The polymer can be processed to a green fiber by melt-spinning, which then undergoes an intermediate curing step and successive pyrolysis. The ceramic fibers, which are presently produced on a semitechnical scale, combine several desired properties relevant for an application in fiber-reinforced ceramic composites: thermal stability, mechanical strength, high-temperature creep resistivity, low density, and stability against oxidation or molten silicon.
Detection of Low-Temperature Hydrothermal Fluxes by Seawater Mg and Ca Anomalies
Authors: de Villiers Stephanie , Nelson Bruce K.
Published: July 2002

Geochemical fluxes into and out of the ocean control its chemical composition. Measurements of the magnesium (Mg) content of seawater, an assumed “conservative” element in the ocean, reveal mid-depth Mg depletions in the vicinity of the East Pacific Rise. The magnitude of the anomalies suggests that fluxes associated with the low-temperature circulation of seawater through axial mid-ocean ridge systems are much larger than the high-temperature axial component. A higher total axial hydrothermal flux provides a mechanism that simultaneously satisfies the mass balance requirement of several major seawater constituents.
Alternative Dewetting Pathways of Thin Liquid Films
Authors: Yerushalmi-Rozen Rachel , Kerle Tobias , Klein Jacob
Published: July 2002

An alternative pathway for the initiation of dewetting in thin metastable films of partially miscible liquid mixtures is described. In this pathway, phase separation is followed by a dewetting process at the interface between the two phases. Dewetting proceeds (from the sample edges inward) as holes form. The initially smooth film breaks up into droplets at rates much faster than those allowed by classical rupture mechanisms. Marangoni flow appears to be responsible for the initiation of the flow of the dewetting front, and coupling between the flow in the two phases leads to accelerated hole formation.
Rapid Adaptation in Visual Cortex to the Structure of Images
Authors: Müller James R. , Metha Andrew B. , Krauskopf John , Lennie Peter
Published: July 2002

Complex cells in striate cortex of macaque showed a rapid pattern-specific adaptation. Adaptation made cells more sensitive to orientation change near the adapting orientation. It reduced correlations among the responses of populations of cells, thereby increasing the information transmitted by each action potential. These changes were brought about by brief exposures to stationary patterns, on the time scale of a single fixation. Thus, if successive fixations expose neurons' receptive fields to images with similar but not identical structure, adaptation will remove correlations and improve discriminability.
Imidazole Rescue of a Cytosine Mutation in a Self-Cleaving Ribozyme
Authors: Perrotta Anne T. , Shih I-hung , Been Michael D.
Published: July 2002

Ribozymes use a number of the same catalytic strategies as protein enzymes. However, general base catalysis by a ribozyme has not been demonstrated. In the hepatitis delta virus antigenomic ribozyme, imidazole buffer rescued activity of a mutant with a cytosine-76 (C76) to uracil substitution. In addition, a C76 to adenine substitution reduced the apparent p
K
a
(where
K
a
is the acid constant) of the self-cleavage reaction by an amount consistent with differences in the p
K
a
values of these two side chains. These results suggest that, in the wild-type ribozyme, C76 acts as a general base. This finding has implications for potential catalytic functions of conserved cytosines and adenines in other ribozymes and in ribonuclear proteins with enzymatic activity.
Structural Changes in Bacteriorhodopsin During Ion Transport at 2 Angstrom Resolution
Authors: Luecke Hartmut , Schobert Brigitte , Richter Hans-Thomas , Cartailler Jean-Philippe , Lanyi Janos K.
Published: July 2002

Crystal structures of the Asp
96
to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined to 1.8 and 2.0 angstroms resolution, respectively. The trapped photoproduct corresponds to the late M state in the transport cycle—that is, after proton transfer to Asp
85
and release of a proton to the extracellular membrane surface, but before reprotonation of the deprotonated retinal Schiff base. Its density map describes displacements of side chains near the retinal induced by its photoisomerization to 13-
cis
,15-
anti
and an extensive rearrangement of the three-dimensional network of hydrogen-bonded residues and bound water that accounts for the changed p
K
a
values (where
K
a
is the acid constant) of the Schiff base and Asp
85
. The structural changes detected suggest the means for conserving energy at the active site and for ensuring the directionality of proton translocation.
Tributaries of West Antarctic Ice Streams Revealed by RADARSAT Interferometry
Authors: Joughin Ian , Gray Laurence , Bindschadler Robert , Price Stephen , Morse David , Hulbe Christina , Mattar Karim , Werner Charles
Published: July 2002

Interferometric RADARSAT data are used to map ice motion in the source areas of four West Antarctic ice streams. The data reveal that tributaries, coincident with subglacial valleys, provide a spatially extensive transition between slow inland flow and rapid ice stream flow and that adjacent ice streams draw from shared source regions. Two tributaries flow into the stagnant ice stream C, creating an extensive region that is thickening at an average rate of 0.49 meters per year. This is one of the largest rates of thickening ever reported in Antarctica.
A Cyclic Antimicrobial Peptide Produced in Primate Leukocytes by the Ligation of Two Truncated α-Defensins
Authors: Tang Yi-Quan , Yuan Jun , Ösapay George , Ösapay Klara , Tran Dat , Miller Christopher J. , Ouellette Andre J. , Selsted Michael E.
Published: July 2002

Analysis of rhesus macaque leukocytes disclosed the presence of an 18-residue macrocyclic, tridisulfide antibiotic peptide in granules of neutrophils and monocytes. The peptide, termed rhesus theta defensin-1 (RTD-1), is microbicidal for bacteria and fungi at low micromolar concentrations. Antibacterial activity of the cyclic peptide was threefold greater than that of an open-chain analog, and the cyclic conformation was required for antimicrobial activity in the presence of 150 millimolar sodium chloride. Biosynthesis of RTD-1 involves the head-to-tail ligation of two α-defensin–related nonapeptides, requiring the formation of two new peptide bonds. Thus, host defense cells possess mechanisms for synthesis and granular packaging of macrocyclic antibiotic peptides that are components of the phagocyte antimicrobial armamentarium.
First-Principles Determination of Elastic Anisotropy and Wave Velocities of MgO at Lower Mantle Conditions
Authors: Karki B. B. , Wentzcovitch R. M. , de Gironcoli S. , Baroni S.
Published: July 2002

The individual elastic constants of magnesium oxide (MgO) have been determined throughout Earth's lower mantle (LM) pressure-temperature regime with density functional perturbation theory. It is shown that temperature effects on seismic observables (density, velocities, and anisotropy) are monotonically suppressed with increasing pressure. Therefore, at realistic LM conditions, the isotropic wave velocities of MgO remain comparable to seismic velocities, as previously noticed in athermal high-pressure calculations. Also, the predicted strong pressure-induced anisotropy is preserved toward the bottom of the LM, so lattice-preferred orientations in MgO may contribute substantially to the observed seismic anisotropy in the D" layer.
Linking Spontaneous Activity of Single Cortical Neurons and the Underlying Functional Architecture
Authors: Tsodyks M. , Kenet T. , Grinvald A. , Arieli A.
Published: July 2002

The relation between the activity of a single neocortical neuron and the dynamics of the network in which it is embedded was explored by single-unit recordings and real-time optical imaging. The firing rate of a spontaneously active single neuron strongly depends on the instantaneous spatial pattern of ongoing population activity in a large cortical area. Very similar spatial patterns of population activity were observed both when the neuron fired spontaneously and when it was driven by its optimal stimulus. The evoked patterns could be used to reconstruct the spontaneous activity of single neurons.
Evolution of Shape Complementarity and Catalytic Efficiency from a Primordial Antibody Template
Authors: Xu Jian , Deng Qiaolin , Chen Jiangang , Houk Kendall N. , Bartek Johannes , Hilvert Donald , Wilson Ian A.
Published: July 2002

The crystal structure of an efficient Diels-Alder antibody catalyst at 1.9 angstrom resolution reveals almost perfect shape complementarity with its transition state analog. Comparison with highly related progesterone and Diels-Alderase antibodies that arose from the same primordial germ line template shows the relatively subtle mutational steps that were able to evolve both structural complementarity and catalytic efficiency.
Equilibrium Regained: From Nonequilibrium Chaos to Statistical Mechanics
Authors: Egolf David A.
Published: July 2002

Far-from-equilibrium, spatially extended chaotic systems have generally eluded analytical solution, leading researchers to consider theories based on a statistical rather than a detailed knowledge of the microscopic length scales. Building on the recent discovery of a separation of length scales between macroscopic behavior and microscopic chaos, a simple far-from-equilibrium spatially extended chaotic system has been studied computationally at intermediate, coarse-grained scales. Equilibrium properties such as Gibbs distributions and detailed balance are recovered at these scales, which suggests that the macroscopic behavior of some far-from-equilibrium systems might be understood in terms of equilibrium statistical mechanics.
Internal Structure and Early Thermal Evolution of Mars from Mars Global Surveyor Topography and Gravity
Authors: Zuber Maria T. , Solomon Sean C. , Phillips Roger J. , Smith David E. , Tyler G. Leonard , Aharonson Oded , Balmino Georges , Banerdt W. Bruce , Head James W. , Johnson Catherine L. , Lemoine Frank G. , McGovern Patrick J. , Neumann Gregory A. , Rowlands David D. , Zhong Shijie
Published: July 2002

Topography and gravity measured by the Mars Global Surveyor have enabled determination of the global crust and upper mantle structure of Mars. The planet displays two distinct crustal zones that do not correlate globally with the geologic dichotomy: a region of crust that thins progressively from south to north and encompasses much of the southern highlands and Tharsis province and a region of approximately uniform crustal thickness that includes the northern lowlands and Arabia Terra. The strength of the lithosphere beneath the ancient southern highlands suggests that the northern hemisphere was a locus of high heat flow early in martian history. The thickness of the elastic lithosphere increases with time of loading in the northern plains and Tharsis. The northern lowlands contain structures interpreted as large buried channels that are consistent with northward transport of water and sediment to the lowlands before the end of northern hemisphere resurfacing.
A Low-Operating-Temperature Solid Oxide Fuel Cell in Hydrocarbon-Air Mixtures
Authors: Hibino Takashi , Hashimoto Atsuko , Inoue Takao , Tokuno Jun-ichi , Yoshida Shin-ichiro , Sano Mitsuru
Published: July 2002

The performance of a single-chamber solid oxide fuel cell was studied using a ceria-based solid electrolyte at temperatures below 773 kelvin. Electromotive forces of ∼900 millivolts were generated from the cell in a flowing mixture of ethane or propane and air, where the solid electrolyte functioned as a purely ionic conductor. The electrode-reaction resistance was negligibly small in the total internal resistances of the cell. The resulting peak power density reached 403 and 101 milliwatts per square centimeter at 773 and 623 kelvin, respectively.
An Orientational Transition of Bent-Core Molecules in an Anisotropic Matrix
Authors: Pratibha R. , Madhusudana N. V. , Sadashiva B. K.
Published: July 2002

We report the discovery of an orientational transition of bent-core molecules in a background anisotropic medium, in this case a smectic liquid crystal made of rod-like molecules. The resulting director is apolar in nature, and the medium can be described as an orthogonal biaxial smectic. The detailed phase diagram of mixtures of the two types of compounds revealed the induction of two liquid crystalline phases that are specific to compounds with bent-core molecules. The chemical nature of the bounding surface had a marked influence on the observed textures.
Bacterial Mode of Replication with Eukaryotic-Like Machinery in a Hyperthermophilic Archaeon
Authors: Myllykallio Hannu , Lopez Philippe , López-Garcı́a Purificación , Heilig Roland , Saurin William , Zivanovic Yvan , Philippe Hervé , Forterre Patrick
Published: July 2002

Despite a rapid increase in the amount of available archaeal sequence information, little is known about the duplication of genetic material in the third domain of life. We identified a single origin of bidirectional replication in
Pyrococcus abyssi
by means of in silico analyses of cumulative oligomer skew and the identification of an early replicating chromosomal segment. The replication origin in three
Pyrococcus
species was found to be highly conserved, and several eukaryotic-like DNA replication genes were clustered around it. As in Bacteria, the chromosomal region containing the replication terminus was a hot spot of genome shuffling. Thus, although bacterial and archaeal replication proteins differ profoundly, they are used to replicate chromosomes in a similar manner in both prokaryotic domains.
An Inherited Functional Circadian Clock in Zebrafish Embryos
Authors: Delaunay Franck , Thisse Christine , Marchand Oriane , Laudet Vincent , Thisse Bernard
Published: July 2002

Circadian clocks are time-keeping systems found in most organisms. In zebrafish, expression of the clock gene
Period3
(
Per3
) oscillates throughout embryogenesis in the central nervous system and the retina.
Per3
rhythmic expression was free-running and was reset by light but not by the developmental delays caused by low temperature. The time of fertilization had no effect on
Per3
expression.
Per3
messenger RNA accumulates rhythmically in oocytes and persists in embryos. Our results establish that the circadian clock functions during early embryogenesis in zebrafish. Inheritance of maternal clock gene products suggests a mechanism of phase inheritance through ovogenesis.
Folds on Europa: Implications for Crustal Cycling and Accommodation of Extension
Authors: Prockter Louise M. , Pappalardo and Robert T.
Published: July 2002

Regional-scale undulations with associated small-scale secondary structures are inferred to be folds on Jupiter's moon Europa. Formation is consistent with stresses from tidal deformation, potentially triggering compressional instability of a region of locally high thermal gradient. Folds may compensate for extension elsewhere on Europa and then relax away over time.
Modulation of Human Visual Cortex by Crossmodal Spatial Attention
Authors: Macaluso Emiliano , Frith Chris D. , Driver Jon
Published: July 2002

A sudden touch on one hand can improve vision near that hand, revealing crossmodal links in spatial attention. It is often assumed that such links involve only multimodal neural structures, but unimodal brain areas may also be affected. We tested the effect of simultaneous visuo-tactile stimulation on the activity of the human visual cortex. Tactile stimulation enhanced activity in the visual cortex, but only when it was on the same side as a visual target. Analysis of effective connectivity between brain areas suggests that touch influences unimodal visual cortex via back-projections from multimodal parietal areas. This provides a neural explanation for crossmodal links in spatial attention.
Optically Induced Entanglement of Excitons in a Single Quantum Dot
Authors: Chen Gang , Bonadeo N. H. , Steel D. G. , Gammon † D. , Katzer D. S. , Park D. , Sham L. J.
Published: July 2002

Optically induced entanglement is identified by the spectrum of the phase-sensitive homodyne-detected coherent nonlinear optical response in a single gallium arsenide quantum dot. The electron-hole entanglement involves two magneto-excitonic states differing in transition energy and polarization. The strong coupling needed for entanglement is provided through the Coulomb interaction involving the electrons and holes. The result presents a first step toward the optical realization of quantum logic operations using two or more quantum dots.
Structural Mechanism for STI-571 Inhibition of Abelson Tyrosine Kinase
Authors: Schindler Thomas , Bornmann William , Pellicena Patricia , Miller W. Todd , Clarkson Bayard , Kuriyan John
Published: July 2002

The inadvertent activation of the Abelson tyrosine kinase (Abl) causes chronic myelogenous leukemia (CML). A small-molecule inhibitor of Abl (STI-571) is effective in the treatment of CML. We report the crystal structure of the catalytic domain of Abl, complexed to a variant of STI-571. Critical to the binding of STI-571 is the adoption by the kinase of an inactive conformation, in which a centrally located “activation loop” is not phosphorylated. The conformation of this loop is distinct from that in active protein kinases, as well as in the inactive form of the closely related Src kinases. These results suggest that compounds that exploit the distinctive inactivation mechanisms of individual protein kinases can achieve both high affinity and high specificity.
DNA Replication-Independent Silencing in
S. cerevisiae
Authors: Kirchmaier Ann L. , Rine Jasper
Published: July 2002

In
Saccharomyces cerevisiae
, the silent mating loci are repressed by their assembly into heterochromatin. The formation of this heterochromatin requires a cell cycle event that occurs between early S phase and G
2
/M phase, which has been widely assumed to be DNA replication. To determine whether DNA replication through a silent mating-type locus,

HMR
a

, is required for silencing to be established, we monitored heterochromatin formation at

HMR
a

on a chromosome and on a nonreplicating extrachromosomal cassette as cells passed through S phase. Cells that passed through S phase established silencing at both the chromosomal

HMR
a

locus and the extrachromosomal

HMR
a

locus with equal efficiency. Thus, in contrast to the prevailing view, the establishment of silencing occurred in the absence of passage of the DNA replication fork through or near the
HMR
locus, but retained a cell cycle dependence.
Tropical Tropospheric Ozone and Biomass Burning
Authors: Thompson Anne M. , Witte Jacquelyn C. , Hudson Robert D. , Guo Hua , Herman Jay R. , Fujiwara Masatomo
Published: July 2002

New methods for retrieving tropospheric ozone column depth and absorbing aerosol (smoke and dust) from the Earth Probe–Total Ozone Mapping Spectrometer (EP/TOMS) are used to follow pollution and to determine interannual variability and trends. During intense fires over Indonesia (August to November 1997), ozone plumes, decoupled from the smoke below, extended as far as India. This ozone overlay a regional ozone increase triggered by atmospheric responses to the El Niño and Indian Ocean Dipole. Tropospheric ozone and smoke aerosol measurements from the Nimbus 7 TOMS instrument show El Niño signals but no tropospheric ozone trend in the 1980s. Offsets between smoke and ozone seasonal maxima point to multiple factors determining tropical tropospheric ozone variability.
A Functional Screen for the Type III (Hrp) Secretome of the Plant Pathogen
Pseudomonas syringae
Authors: Guttman David S. , Vinatzer Boris A. , Sarkar Sara F. , Ranall Max V. , Kettler Gregory , Greenberg Jean T.
Published: July 2002

Type III secreted “effector” proteins of bacterial pathogens play central roles in virulence, yet are notoriously difficult to identify. We used an in vivo genetic screen to identify 13 effectors secreted by the type III apparatus (called Hrp, for “hypersensitive response and pathogenicity”) of the plant pathogen
Pseudomonas syringae
. Although sharing little overall homology, the amino-terminal regions of these effectors had strikingly similar amino acid compositions. This feature facilitated the bioinformatic prediction of 38
P. syringae
effectors, including 15 previously unknown proteins. The secretion of two of these putative effectors was shown to be type III–dependent. Effectors showed high interstrain variation, supporting a role for some effectors in adaptation to different hosts.
Recognition and Rejection of Self in Plant Reproduction
Authors: Nasrallah June B.
Published: July 2002

Plant self-incompatibility (SI) systems are unique among self/nonself recognition systems in being based on the recognition of self rather than nonself. SI in crucifer species is controlled by highly polymorphic and co-evolving genes linked in a complex. Self recognition is based on allele-specific interactions between stigma receptors and pollen ligands that result in the arrest of pollen tube development. Commonalities and differences between SI and other self/nonself discrimination systems are discussed.
Evidence for an Efflux Pump Mediating Multiple Antibiotic Resistance in
Salmonella enterica
Serovar Typhimurium
Authors: Piddock Laura J. V. , White David G. , Gensberg Karl , Pumbwe Lilian , Griggs Deborah J.
Published: July 2002

The mechanism of multiple antibiotic resistance in six isolates of
Salmonella enterica
serovar Typhimurium recovered from a patient treated with ciprofloxacin was studied to investigate the role of efflux in the resistance phenotype. Compared to the patient's pretherapy isolate (L3), five of six isolates accumulated less ciprofloxacin, three of six isolates accumulated less chloramphenicol, and all six accumulated less tetracycline. The accumulation of one or more antibiotics was increased by carbonyl cyanide
m
-chlorophenylhydrazone to concentrations similar to those accumulated by L3 for all isolates except one, in which accumulation of all three agents remained approximately half that of L3. All isolates had the published wild-type sequences of
marO
and
marR
. No increased expression of
marA
,
tolC
, or
soxS
was observed by Northern blotting; however, three isolates showed increased expression of
acrB
, which was confirmed by quantitative competitive reverse transcription-PCR. However, there were no mutations within
acrR
or the promoter region of
acrAB
in any of the isolates.
Activities of an Intravenous Formulation of Itraconazole in Experimental DisseminatedAspergillus,Candida, andCryptococcusInfections
Authors: Odds Frank C. , Oris Michel , Van Dorsselaer Pascal , Van Gerven Frans
Published: July 2002

An intravenous (i.v.) formulation of itraconazole was evaluated in disseminated fungal infection models in guinea pigs. In acute disseminatedCandida albicansandAspergillus fumigatusinfections, treatment at 5 mg/kg of body weight twice a day (b.i.d.) significantly prolonged survival. In these models and in animals with chronic disseminated cryptococcosis, itraconazole given i.v. at 2.5 and 5 mg/kg b.i.d. greatly reduced the proportions of organs with culture-detectable fungal burdens. The efficacy of i.v. itraconazole in these animal models justifies its further investigation for the treatment of life-threatening mycoses in humans.