bluuebunny/crossref_metadata_2025 huggingface dataset:
Similarity Between the Transcriptional Silencer Binding Proteins ABF1 and RAP1
Authors: Diffley John F. X. , Stillman Bruce
Published: October 2006

The yeast ARS binding factor 1 (ABF1)—where ARS is an autonomously replicating sequence—and repressor/activator protein 1 (RAP1) have been implicated in DNA replication, transcriptional activation, and transcriptional silencing. The
ABF1
gene was cloned and sequenced and shown to be essential for viability. The predicted amino acid sequence contains a novel sequence motif related to the zinc finger, and the ABF1 protein requires zinc and unmodified cysteine residues for sequence-specific DNA binding. Interestingly, ABF1 is extensively related to its counterpart, RAP1, and both proteins share a region of similarity with SAN1, a suppressor of certain
SIR4
mutations, suggesting that this region may be involved in mediating SIR function at the silent mating type loci.
The Response of Electrons to Structural Changes
Authors: Wiberg Kenneth B. , Hadad Christopher M. , Breneman Curt M. , Laidig Keith E. , Murcko Mark A. , LePage Teresa J.
Published: October 2006

The properties of a molecule are determined by the distribution of its electrons. This distribution can be described by the charge density, which is readily obtained from the wave functions derived by ab initio molecular orbital calculations. The charge density may be analyzed in a number of different fashions to give information about the effects of substituents, structural changes, and electronic excitation on the properties of molecules; one common procedure makes use of projection density or charge difference plots. Charge density also may be partitioned among atoms, and by numerical integration over appropriate volume elements one may obtain atomic charges, dipoles, kinetic energies, and other properties of the atoms in a molecule. Many chemical phenomena have been analyzed in terms of charge densities.
Asteroid 1986 DA: Radar Evidence for a Metallic Composition
Authors: Ostro S. J. , Campbell D. B. , Chandler J. F. , Hine A. A. , Hudson R. S. , Rosema K. D. , Shapiro I. I.
Published: October 2006

Echoes from the near-Earth object 1986 DA show it to be significantly more reflective than other radar-detected asteroids. This result supports the hypothesis that 1986 DA is a piece of NiFe metal derived from the interior of a much larger object that melted, differentiated, cooled, and subsequently was disrupted in a catastrophic collision. This 2-kilometer asteroid, which appears smooth at centimeter to meter scales but extremely irregular at 10- to 100-meter scales, might be (or have been a part of) the parent body of some iron meteorites.
Pressure Dependence of Superconductivity in Single-Phase K
3
C
60
Authors: Sparn G. , Thompson J. D. , Huang S.-M. , Kaner R. B. , Diederich F. , Whetten R. L. , Grüner G. , Holczer K.
Published: October 2006

The superconducting compound K
3
C
60
(with transition temperature
T
c
= 19.3 kelvin at ambient pressure), formed as a single phase by reaction of alkali vapor with solids of the icosahedral C
60
molecule (buckminsterfullerene), shows a very large decrease of
T
c
with increasing pressure. Susceptibility measurements on sintered pellets showing bulk superconductivity are reported up to 21 kilobars of pressure, where
T
c
is already less than 8 kelvin. The results are consistent with a piling up of the density of states at the Fermi level.
Heat Conductivity of Amorphous Solids: Simulation Results on Model Structures
Authors: Sheng Ping , Zhou Minyao
Published: October 2006

Through numerical simulation and consideration of phonon scattering by two-level states, the heat conductivity κ(
T
), where
T
is temperature, has been calculated on model structures. The values obtained are in good quantitative agreement with measured data on polymethylmethacrylate, epoxy, amorphous selenium, and amorphous silicon dioxide over the temperature range 0.1 to 100 K. The calculated results reproduce the plateau feature, in the range of 5 to 20 K, that is generic to the heat conductivity of amorphous solids. Two model parameters, one characterizing the degree of structural disorder and the other related to the relaxational absorption of two-level states, are identified as being responsible for the behavior of κ(
T
) at
T
≳ 5 K. The simulation results indicate the existence of a frequency-independent phonon diffusion regime that is consistent with the minimum phonon mean-free-path hypothesis. The magnitude of the phonon diffusion constant in this regime is shown to give a reasonable quantitative account of high-temperature κ(
T
) in amorphous systems.
Second Cytotoxic Pathway of Diphtheria Toxin Suggested by Nuclease Activity
Authors: Chang Michael P. , Baldwin Rae Lynn , Bruce Can , Wisnieski Bernadine J.
Published: October 2006

Diphtheria toxin (DTx) provokes extensive internucleosomal degradation of DNA before cell lysis. The possibility that DNA cleavage stems from direct chromosomal attack by intracellular toxin molecules was tested by in vitro assays for a DTx-associated nuclease activity. DTx incubated with DNA in solution or in a DNA-gel assay showed Ca
2+
- and Mg
2+
-stimulated nuclease activity. This activity proved susceptible to inhibition by specific antitoxin and migrated with fragment A of the toxin. Assays in which supercoiled double-stranded DNA was used revealed rapid endonucleolytic attack. Discovery of a DTx-associated nuclease activity lends support to the model that DTx-induced cell lysis is not a simple consequence of protein synthesis inhibition.
X-Ray Diffraction Evidence for Nonstoichiometric Rubidium-C
60
Intercalation Compounds
Authors: Zhu Qing , Zhou Otto , Coustel Nicole , Vaughan Gavin B. M. , McCauley John P. , Romanow William J. , Fischer John E. , Smith Amos B.
Published: October 2006

Powder x-ray diffraction at 300 K on equilibrated samples of several nominal compositions
x
in Rb

x

C
60
is reported. In addition to the face-centered cubic (fcc) (
x
= 3, superconducting), body-centered tetragonal (
x
= 4), and body-centered cubic (bcc) (
x
= 6) stoichiometric phases, direct evidence for a dilute fcc doped phase, 0 <
x
≤ 1, and for a substoichiometric bcc phase,
x
∼ 5, is presented. In contrast,
x
= 3 and
x
= 4 appear to be line phases with nearly zero solubility of Rb vacancies and interstitials at 300 K. These results are summarized in a provisional binary phase diagram.
Stress Fields of the Overriding Plate at Convergent Margins and Beneath Active Volcanic Arcs
Authors: Apperson K. Denise
Published: October 2006

Tectonic stress fields in the overriding plate at convergent plate margins are complex and vary on local to regional scales. Volcanic arcs are a common element of overriding plates. Stress fields in the volcanic arc region are related to deformation generated by subduction and to magma generation and ascent processes. Analysis of moment tensors of shallow and intermediate depth earthquakes in volcanic arcs indicates that the seismic strain field in the arc region of many convergent margins is subhorizontal extension oriented nearly perpendicular to the arc. A process capable of generating such a globally consistent strain field is induced asthenospheric corner flow below the arc region.
Hydrogen as a Probe of Semiconductor Surface Structure: The Ge(111)-c(2 × 8) Surface
Authors: Boland John J.
Published: October 2006

Hydrogen can be used as an effective probe of the structure of semiconductor surfaces. Such surfaces consist of bonds with varying degrees of bond strain, and hydrogen can react with each selectively depending on the reaction conditions. This selectivity is derived from a reduced barrier to reaction associated with strained bonds. In this manner, hydrogen can be used to pick apart the surface one bond type at a time, thereby revealing the structure of even complex multilayer reconstructions. This method is used to directly show that the rest-layer of the Ge(111)-c(2 × 8) surface has a bulk structure.
Late Holocene Tectonics and Paleoseismicity, Southern Cascadia Subduction Zone
Authors: Clarke Samuel H. , Carver Gary A.
Published: October 2006

Holocene deformation indicative of large subduction-zone earthquakes has occurred on two large thrust fault systems in the Humboldt Bay region of northern California. Displaced stratigraphic markers record three offsets of 5 to 7 meters each on the Little Salmon fault during the past 1700 years. Smaller and less frequent Holocene displacements have occurred in the Mad River fault zone. Elsewhere, as many as five episodes of sudden subsidence of marsh peats and fossil forests and uplift of marine terraces are recorded. Carbon-14 dates suggest that the faulting, subsidence, and uplift events were synchronous. Relations between magnitude and various fault-offset parameters indicate that earthquakes accompanying displacements on the Little Salmon fault had magnitudes of at least 7.6 to 7.8. More likely this faulting accompanied rupture of the boundary between the Gorda and North American plates, and magnitudes were about 8.4 or greater.
Sibling Species in
Montastraea annularis
, Coral Bleaching, and the Coral Climate Record
Authors: Knowlton Nancy , Weil Ernesto , Weigt Lee A. , Guzmán Héctor M.
Published: October 2006

Measures of growth and skeletal isotopic ratios in the Caribbean coral
Montastraea annularis
are fundamental to many studies of paleoceanography, environmental degradation, and global climate change. This taxon is shown to consist of at least three sibling species in shallow waters. The two most commonly studied of these show highly significant differences in growth rate and oxygen isotopic ratios, parameters routinely used to estimate past climatic conditions; unusual coloration in the third may have confused research on coral bleaching. Interpretation or comparison of past and current studies can be jeopardized by ignoring these species boundaries.
Experimental Constraints on the Theory of High-
T
c
Superconductivity
Authors: Anderson P. W.
Published: October 2006

Analysis of the many experiments on high-temperature superconductivity indicate several essential aspects of any theory. The conductivity and other transport properties as a function of disorder, temperature, and frequency point to a non-Fermi liquid-like behavior, whereas photoemission experiments and magnetic properties indicate the presence of a Fermi surface in momentum space. To reconcile this apparent contradiction, a new type of electron liquid, called a Luttinger liquid, has been postulated, and the present article aims to show the need for this postulate. Theory and experiment indicate that the suitable phenomenological electronic structure model of the CuO layers is that of the one-band Hubbard model. It is also argued that experiment clearly indicates that interlayer interactions strongly affect the superconducting transition temperature,
T
c
, consistent with the fact that no theoretical calculations on two-dimensional Hubbard models have resulted in the prediction of high transition temperatures, and that anyon models are not favored by experiment.
Purification of Growth Hormone-Specific Transcription Factor GHF-1 Containing Homeobox
Authors: Castrillo José-Luis , Bodner Mordechai , Karin Michael
Published: October 2006

Pituitary-specific expression of the growth hormone (GH) gene is governed by a transcription factor, GHF-1, that binds to two sites within its promoter. Recently, GHF-1 was shown to be a member of the homeobox family of DNA-binding proteins. An important question is whether GHF-1 controls the expression of other pituitary specific genes, such as prolactin (Prl), expressed in closely related cell types. To this end, GHF-1 was purified from extracts of GH- and Prl-expressing pituitary tumor cells and identified as a 33-kilodalton polypeptide. Although GHF-1 bound to and activated the GH promoter, it did not recognize the Prl promoter. However, at least one other factor in the same extracts, which was easily separated from GHF-1, bound to several sites within the Prl but not the GH promoter. Antibodies to GHF-1 did not react with the Prl binding activity. These results imply that the pituitary-specific expression of GH and Prl is governed by two distinct trans-acting factors.
Surface and Bulk Charge Density Wave Structure in 1 T-TaS
2
Authors: Burk B. , Thomson R. E. , Clarke John , Zettl A.
Published: October 2006

Incommensurate charge density waves (CDWs) in some materials form domains within which the CDWs may be commensurate. However, two questions have remained controversial: What is the geometrical structure of these domains, and are they or are they not identical on the surface and in the bulk? To address these issues in the triclinic (T) phase of tantalum disulfide (1T-TaS
2
) the CDW domain structure has been accurately determined for both the crystal surface and the crystal bulk. By analyzing the bulk CDW wave vectors and associated satellites by x-ray diffraction, it is found that the bulk contains three dimensionally ordered striped domains that have previously been misidentified. Scanning tunneling microscope images show that the striped domain configuration propagates unaltered to the crystal surface, and their Fourier transforms yield the same satellite positions as the x-rays. These observations demonstrate that the surface and bulk CDW domain structures in 1T-TaS
2
are identical.
Maintenance of in Vivo Tolerance by Persistence of Antigen
Authors: Ramsdell Fred , Fowlkes B. J.
Published: October 2006

T cells of the immune system respond only to foreign antigens because those cells with reactivity for self proteins are either deleted during their development or rendered nonresponsive (anergic). The maintenance of the nonresponsive state was found to require the continual exposure of the anergic T cells to antigen. When anergic T cells were removed from the self antigen by adoptive transfer to a mouse strain lacking the antigen or by in vitro culture, nonresponsiveness was reversed and the anergic cells returned to normal functional status.
Effect of Carboxylic Acid Side Chains on the Absorption Maximum of Visual Pigments
Authors: Zhukovsky Eugene A. , Oprian Daniel D.
Published: October 2006

The proposal that the absorption maximum of the visual pigments is governed by interaction of the 11-
cis
-retinal chromophore with charged carboxylic acid side chains in the membrane-embedded regions of the proteins has been tested by mutating five Asp and Glu residues thought to be buried in rhodopsin. Changing Glu
113
to Gln causes a dramatic shift in the absorption maximum from 500 nanometers to 380 nanometers, a decrease in the p
K
a
(acidity constant) of the protonated Schiff base of the chromophore to about 6, and a greatly increased reactivity with hydroxylamine. Thus Glu
113
appears to be the counterion to the protonated Schiff base. Wavelength modulation in visual pigments apparently is not governed by electrostatic interaction with carboxylate residues, other than the counterion.
Changes in State of Stress on the Southern San Andreas Fault Resulting from the California Earthquake Sequence of April to June 1992
Authors: Jaumé Steven C. , Sykes Lynn R.
Published: October 2006

The April to June 1992 Landers earthquake sequence in southern California modified the state of stress along nearby segments of the San Andreas fault, causing a 50-kilometer segment of the fault to move significantly closer to failure where it passes through a compressional bend near San Gorgonio Pass. The decrease in compressive normal stress may also have reduced fluid pressures along that fault segment. As pressures are reequilibrated by diffusion, that fault segment should move closer to failure with time. That fault segment and another to the southeast probably have not ruptured in a great earthquake in about 300 years.
X-ray Detection of the Period-Four Cycling of the Manganese Cluster in Photosynthetic Water Oxidizing Enzyme
Authors: Ono Taka-aki , Noguchi Takumi , Inoue Yorinao , Kusunoki Masami , Matsushita Tadashi , Oyanagi Hiroyuki
Published: October 2006

X-ray absorption near-edge structure spectra of the manganese (Mn) cluster in physiologically native intermediate states of photosynthetic water oxidation induced by short laser flash were measured with a compact heat-insulated chamber equipped with an x-ray detector near the sample surface. The half-height energy of the Mn K-edge showed a period-four oscillation dependent on cycling of the Joliot-Kok's oxygen clock. The flash number-dependent shift in the Mn K-edge suggests that the Mn cluster is oxidized by one electron upon the S
0
-to-S
1
, S
1
-to-S
2
, and S
2
-to-S
3
transitions and then reduced upon the S
3
-to-S
0
transition that releases molecular oxygen.
Direct Detection of C
4
H
2
Photochemical Products: Possible Routes to Complex Hydrocarbons in Planetary Atmospheres
Authors: Bandy Ralph E. , Lakshminarayan Chitra , Frost Rex K. , Zwier Timothy S.
Published: October 2006

The photochemistry of diacetylene (C
4
H
2
), the largest hydrocarbon to be unambiguously identified in planetary atmospheres, is of considerable importance to understanding the mechanisms by which complex molecules are formed in the solar system. In this work, the primary products of C
4
H
2
's ultraviolet photochemistry were determined in a two-laser pump-probe scheme in which the products of C
4
H
2
photoexcitation are detected by vacuum ultraviolet photoionization in a time-of-flight mass spectrometer. Three larger hydrocarbon primary products were observed with good yield in the C
4
H
2
* + C
4
H
2
reaction: C
6
H
2
, C
8
H
2
, and C
8
H
3
. Neither C
6
H
2
nor C
8
H
3
is anticipated by current photochemical models of the atmospheres of Titan, Uranus, Neptune, Pluto, and Triton. The free hydrogen atoms that are released during the formation of the C
8
H
3
and C
8
H
2
products also may partially offset the role of C
4
H
2
in catalyzing the recombination of free hydrogen atoms in the planetary atmospheres.
Charge Donation by Calcium into the
t
1g
Band of C
60
Authors: Wertheim G. K. , Buchanan D. N. E. , Rowe J. E.
Published: October 2006

Photoemission spectra of compounds prepared by the reaction of C
60
films with calcium show two distinct metallic phases, whereas alkali-doped C
60
films have only one. In the first phase the bulk
t
1u
band, derived from the lowest unoccupied molecular orbital of C
60
, is partially occupied. This is followed by an insulating phase that has the composition Ca
3
C
60
in which the
t
1u
band is filled and has properties analogous to those of K
6
C
60
. Continued exposure to calcium produces a second metallic phase in which electrons are donated into the
t
1g
band. The superconductivity of Ca
5
C
60
is associated with the
t
1g
band.
Evidence from the Lamarck Granodiorite for Rapid Late Cretaceous Crust Formation in California
Authors: Coleman Drew S. , Glazner Allen F. , Frost Thomas P.
Published: October 2006

Strontium and neodymium isotopic data for rocks from the voluminous 90-million-year-old Lamarck intrusive suite in the Sierra Nevada batholith, California, show little variation across a compositional range from gabbro to granite. Data for three different gabbro intrusions within the suite are identical within analytical error and are consistent with derivation from an enriched mantle source. Recognition of local involvement of enriched mantle during generation of the Sierran batholith modifies estimates of crustal growth rates in the United States. These data indicate that parts of the Sierra Nevada batholith may consist almost entirely of juvenile crust added during Cretaceous magmatism.
Homology of β-Lactoglobulin, Serum Retinol-Binding Protein, and Protein HC
Authors: Pervaiz Syed , Brew Keith
Published: October 2006

The milk protein β-lactoglobulin has been extensively studied but its function has not been identified. A clue regarding the function of a protein can be obtained by discovering a genetic relationship with a protein of known function through comparisons of amino acid sequence. Such comparisons revealed that β-lactoglobulin is similar to human serum retinol-binding protein and to another human protein of unknown function known as complex-forming glycoprotein heterogeneous in charge (protein HC). β-Lactoglobulins from several species have been found to bind retinol, while the absorption and fluorescence properties reported for the unidentified heterogeneous prosthetic group of protein HC are retinoid-like. The role of serum retinol-binding protein in vitamin A transport in the circulation suggests that the other two homologous proteins may function in the binding and transport of retinoids; β-lactoglobulin may facilitate the absorption of vitamin A from milk and protein HC may mediate the excretion of retinol-derived metabolites.
Selective Extraction of Small and Large Molecules from the Cerebrospinal Fluid by Purkinje Neurons
Authors: Borges Lawrence F. , Elliott Peter J. , Gill Ramanjit , Iversen Susan D. , Iversen Leslie L.
Published: October 2006

Cerebellar Purkinje neurons accumulated propidium iodide, granular blue, and horseradish peroxidase conjugated to wheat germ agglutinin but not unconjugated horseradish peroxidase, bisbenzimide, or Evans blue when these compounds were infused into the lateral cerebral ventricles of awake, unrestrained rats. Accumulation of propidium iodide by Purkinje neurons of the vermis was associated with a reproducible behavioral abnormality characterized by truncal tremor, ataxia, and nystagmus. Both the accumulation of propidium iodide in Purkinje cells and the behavioral abnormality were prevented by prior intracerebroventricular administration of ouabain or colchicine, drugs that block neuronal transport processes. The ability of cerebellar Purkinje neurons to extract small and large molecules from the cerebrospinal fluid has important implications for their physiology and pathology.
Fabrication and Properties of Free-Standing C
60
Membranes
Authors: Eom C. B. , Hebard A. F. , Trimble L. E. , Celler G. K. , Haddon R. C.
Published: October 2006

Van der Waals forces that bind C
60
molecular solids are found to be sufficiently strong to allow the reproducible fabrication of free-standing C
60
membranes on (100) silicon wafers. Membranes, 2000 to 6000 angstroms thick, were fabricated by a modified silicon micromachining process and were found to be smooth, flat, and mechanically robust. An important aspect of the silicon-compatible fabrication procedure is the demonstration that C
60
films can be uniformly and nondestructively thinned in a CF
4
plasma. Young's modulus and fracture strength measurements were made on membranes with areas larger than 6 millimeters by 6 millimeters. It may be possible to use C
60
membranes for physical property measurements and applications.
Oxygen Diffusion in Perovskite: Implications for Electrical Conductivity in the Lower Mantle
Authors: Gautason Bjarni , Muehlenbachs Karlis
Published: October 2006

Experimental determination of oxygen self-diffusion in CaTiO
3
perovskite, a structural analog of (Mg,Fe)SiO
3
perovskite, confirms a theoretical relation between diffusion constants and anion porosity. Oxygen diffusion rates in (Mg,Fe)SiO
3
perovskite calculated with this relation increase by about eight orders of magnitude through the lower mantle. Electrical conductivity values calculated from these diffusion rates are consistent with inferred conductivity values for the lower mantle. This result suggests that the dominant conductivity mechanism in the deep mantle is ionic.
Poly(phenylcarbyne): A Polymer Precursor to Diamond-Like Carbon
Authors: Visscher Glenn T. , Nesting David C. , Badding John V. , Bianconi Patricia A.
Published: October 2006

The synthesis of poly(phenylcarbyne), one of a class of carbon-based random network polymers, is reported. The network backbone of this polymer is composed of tetrahedrally hybridized carbon atoms, each bearing one phenyl substituent and linking, by means of three carbon-carbon single bonds, into a three-dimensional random network of fused rings. This atomic-level carbon network backbone confers unusual properties on the polymer, including facile thermal decomposition, which yields diamond or diamond-like carbon phases at atmospheric pressure.
Detection of a Meteoritic Component in Ivory Coast Tektites with Rhenium-Osmium Isotopes
Authors: Koeberl Christian , Shirey Steven B.
Published: October 2006

Measurement of rhenium (Re) and osmium (Os) concentrations and Os isotopic compositions in Ivory Coast tektites (natural glasses with upper crustal compositions that are ejected great distances during meteorite impact) and rocks from the inferred source crater, Lake Bosumtwi, Ghana, show that these tektites incorporate about 0.6 percent of a meteoritic component. Analysis of elemental abundances of noble metals alone gives equivocal results in the detection of meteoritic components because the target rocks already have relatively large amounts of noble metals. The Re-Os system is ideally suited for the study of meteorite impacts on old continental crust for three reasons. (i) The isotopic compositions of the target rocks and the meteoritic impactor are significantly different. (ii) Closed-system mixing of target rocks and meteorites is linear on Re-Os isochron diagrams, which thus permits identification of the loss of Re or Os. (iii) Osmium isotopic compositions are not likely to be altered during meteorite impact even if Re and Os are lost.
Electron Localization in Metallic Quasicrystals
Authors: Pierce F. S. , Poon S. J. , Guo Q.
Published: October 2006

Bulk icosahedral-quasicrystalline aluminum-palladium-rhenium alloys of high structural quality and thermal stability are found to exhibit low-temperature electrical resistivities that are four orders of magnitude larger than those found in disordered metals and metallic glasses. Experiments suggest that these quasiperiodic alloys, which have a semimetallic electron density, are insulators at low temperature. The findings are discussed in light of theories on electron localization and band-gap formation in ordered metallic systems.
The Phase Composition of Triton's Polar Caps
Authors: Duxbury N. S. , Brown R. H.
Published: October 2006

Triton's polar caps are modeled as permanent nitrogen deposits hundreds of meters thick. Complex temperature variations on Triton's surface induce reversible transitions between the cubic and hexagonal phases of solid nitrogen, often with two coexisting propagating transition fronts. Subsurface temperature distributions are calculated using a two-dimensional thermal model with phase changes. The phase changes fracture the upper nitrogen layer, increasing its reflectivity and thus offering an explanation for the surprisingly high southern polar cap albedo (approximately 0.8) seen during the Voyager 2 flyby. The model has other implications for the phase transition phenomena on Triton, such as a plausible mechanism for the origin of geyser-like plume vent areas and a mechanism of energy transport toward them.
On the Thermodynamic Stability of Confined Thin Films Under Shear
Authors: Diestler Dennis J. , Schoen Martin , Cushman John H.
Published: October 2006

Thin films of monatomic fluid constrained between two plane-parallel structured solid walls have been modeled by Monte Carlo simulation under conditions (fixed temperature, chemical potential, and normal stress or load) prevailing in high-precision measurements of surface forces. Several states of the film, corresponding to different numbers of layers of fluid parallel with the walls, are generally consistent with these conditions, but only one is thermodynamically stable; the others are metastable. When the walls are properly aligned, epitaxial solid phases are stable. These melt under shear, eventually becoming metastable, whereupon a drainage (or imbibition) transition occurs, leading to a stable phase with fewer (or more) layers.
Melting of (Mg, Fe)SiO
3
-Perovskite to 625 Kilobars: Indication of a High Melting Temperature in the Lower Mantle
Authors: Zerr A. , Boehier R.
Published: October 2006

The melting curves of two compositions of (Mg,Fe)SiO
3
-perovskite, the likely dominant mineral phase in the lower mantle, have been measured in a CO
2
laser-heated diamond cell with direct temperature measurements and in situ detection of melting. At 625 kilobars, the melting temperature is 5000 ± 200 kelvin, independent of composition. Extrapolation to the core-mantle boundary pressure of 1.35 megabar with three different melting relations yields melting temperatures between 7000 and 8500 kelvin. Thus, the temperature at the base of the lower mantle, accepted to lie between 2550 and 2750 kelvin, is only at about one-third of the melting temperature. The large difference between mantle temperature and corresponding melting temperature has several important implications; particularly the temperature sensitivity of the viscosity is reduced thus allowing large lateral temperature variations inferred from seismic tomographic velocity anomalies and systematics found in measured velocity-density functions. Extensive melting of the lower mantle can be ruled out throughout the history of the Earth.
Protein-RNA Interactions in an Icosahedral Virus at 3.0 Å Resolution
Authors: Chen Zhongguo , Stauffacher Cynthia , Li Yunge , Schmidt Tim , Bomu Wu , Kamer Greg , Shanks Michael , Lomonossoff George , Johnson John E.
Published: October 2006

Nearly 20 percent of the packaged RNA in bean-pod mottle virus (BPMV) binds to the capsid interior in a symmetric fashion and is clearly visible in the electron density map. The RNA displaying icosahedral symmetry is single-stranded with well-defined polarity and stereochemical properties. Interactions with protein are dominated by nonbonding forces with few specific contacts. The tertiary and quaternary structures of the BPMV capsid proteins are similar to those observed in animal picornaviruses, supporting the close relation between plant comoviruses and animal picornaviruses established by previous biological studies.
Understanding the Anomalous Electrophoresis of Bent DNA Molecules: a Reptation Model
Authors: Levene Stephen D. , Zimm Bruno H.
Published: October 2006

In polyacrylamide gel electrophoresis, the retardation of DNA molecules containing regions of intrinsic curvature can be explained by a novel reptation model that includes the elastic free energy of the DNA chain. Computer simulations based on this model give results that reproduce the dependence of anomalous mobility on gel concentration, which is quantified by new experimental data on the mobilities of circularly permuted isomers of kinetoplast DNA fragments. Fitting of the data required allowing for the elasticity of the gel.
The Mechanism of DNA Transfer in the Mating System of an Archaebacterium
Authors: Rosenshine Ilan , Tchelet Ronen , Mevarech Moshe
Published: October 2006

The genetic transfer system in the extremely halophilic archaebacterium
Halobacterium volcanii
is the only archaebacterial mating system known. The mechanism of genetic transfer of this archaebacterium was studied by using the immobile plasmids pHV2 and pHV11 as cytoplasmic markers. It was found that the cytoplasms of the parental types do not mix during the mating process, that each parental type can serve both as a donor and as a recipient, and that cytoplasmic bridges, with dimensions of up to 2 micrometers long and 0.1 micrometer in diameter, were formed between the parental types. These bridges appear to be used for the transfer of DNA from one cell to another. If so, this archaebacterial mating system is different from both eubacterial conjugation and eukaryotic sexual cell fusion.
Global Flexibility in a Sensory Receptor: a Site-Directed Cross-Linking Approach
Authors: Falke Joseph J. , Koshland Daniel E.
Published: October 2006

The aspartate receptor of
Escherichia coli
and
Salmonella typhimurium
is a cell surface sensory transducer that binds extracellular aspartate and sends a transmembrane signal to the inside of the bacterium. The flexibility and allostery of this receptor was examined by placing sulfhydryl groups as potential cross-linking sites at targeted locations in the protein. Seven different mutant receptors were constructed, each containing a single cysteine residue at a different position in the primary structure. Intramolecular disulfide bond formation within oligomers of these mutant receptors is shown to trap structural fluctuations and to detect ligand-induced changes in structure. The results indicate that the receptor oligomer has a flexible, dynamic structure which undergoes a global change upon aspartate binding.
Selection of Amino Acid Sequences in the Beta Chain of the T Cell Antigen Receptor
Authors: Hedrick Stephen M. , Engel Isaac , McElligott David L. , Fink Pamela J. , Hsu Mei-Ling , Hansburg Daniel , Matis Louis A.
Published: October 2006

The induction of an immune response in mammals is initiated by specifically reactive T lymphocytes. The specificity of the reaction is mediated by a complex receptor, part of which is highly variable in sequence and analogous to immunoglobulin heavy- and light-chain variable domains. The functional specificity of the T cell antigen receptor is, however, markedly different from immunoglobulins in that it mediates cell-cell interactions via the simultaneous recognition of foreign antigens and major histocompatibility complex-encoded molecules expressed on the surface of various lymphoid and nonlymphoid cells. The relation between the structure of the receptor and its functional specificity was investigated by analyzing the primary sequences of the receptors expressed by a series of T lymphocyte clones specific for a model antigen, pigeon cytochrome c. Within this set of T lymphocyte clones there was a striking selection for amino acid sequences in the receptor β-chain in the region analogous to the third complementarity-determining region of immunoglobulins. Thus, despite the functional differences between T cell antigen receptors and immunoglobulin molecules, analogous regions appear to be important in determining ligand specificity.
RNA Processing Generates the Mature 3′ End of Yeast
CYC1
Messenger RNA in Vitro
Authors: Butler J. Scott , Platt Terry
Published: October 2006

In whole cell extracts of
Saccharomyces cerevisiae
, incubation of precursor mRNA transcripts encoding the sequences essential in vivo for forming the 3′ end of the iso-1-cytochrome c mRNA (
CYC1
) revealed an endonuclease activity with the characteristics required for producing the mature mRNA 3′ end. The observed cleavage in vitro is (i) accurate, occurring at or near the polyadenylation site of
CYC1
RNA, (ii) 30 to 50 percent efficient, (iii) adenosine triphosphate dependent, (iv) specific for the 3′ ends of at least two yeast pre-mRNA's, and (v) absent with related pre-mRNA's carrying mutations that abolish correct 3′ end formation in vivo. In addition, a second activity in the extract polyadenylates the product under appropriate conditions. Thus, the mature 3′ ends of yeast mRNA's may be generated by endonucleolytic cleavage and polyadenylation rather than by transcription termination.
Transient Expression Shows Ligand Gating and Allosteric Potentiation of GABA
A
Receptor Subunits
Authors: Pritchett Dolan B. , Sontheimer Harald , Gorman Cornelia M. , Kettenmann Helmut , Seeburg Peter H. , Schofield Peter R.
Published: October 2006

Human γ-aminobutyric acid A (GABA
A
) receptor subunits were expressed transiently in cultured mammalian cells. This expression system allows the simultaneous characterization of ligand-gated ion channels by electrophysiology and by pharmacology. Thus, coexpression of the α and β subunits of the GABA
A
receptor generated GABA-gated chloride channels and binding sites for GABA
A
receptor ligands. Channels consisting of only α or β subunits could also be detected. These homomeric channels formed with reduced efficiencies compared to the heteromeric receptors. Both of these homomeric GABA-responsive channels were potentiated by barbiturate, indicating that sites for both ligand-gating and allosteric potentiation are present on receptors assembled from either subunit.
Mechanisms of Coenzyme B
12
-Dependent Rearrangements
Authors: Halpern Jack
Published: October 2006

Coenzyme B
12
serves as a cofactor in various enzymatic reactions in which a hydrogen atom is interchanged with a substituent on an adjacent carbon atom. Measurement of the dissociation energy of the coenzyme's cobalt-carbon bond and studies of the rearrangement of model free radicals related to those derived from methylmalonyl-coenzyme A suggest that these enzymatic reactions occur through homolytic dissociation of the coenzyme's cobalt-carbon bond, abstraction of a hydrogen atom from the substrate by the coenzyme-derived 5′-deoxyadenosyl radical, and rearrangement of the resulting substrate radical. The only role thus far identified for coenzyme B
12
in these reactions—namely, that of a free radical precursor—reflects the weakness, and facile dissociation, of the cobalt-carbon bond.
Antigenic and Genetic Properties of Viruses Linked to Hemorrhagic Fever with Renal Syndrome
Authors: Schmaljohn C. S. , Hasty S. E. , Dalrymple J. M. , LeDuc J. W. , Lee H. W. , von Bonsdorff C.-H. , Brummer-Korvenkontio M. , Vaheri A. , Tsai T. F. , Regnery H. L. , Goldgaber D. , Lee P. W.
Published: October 2006

Hemorrhagic fever with renal syndrome (HFRS) comprises a variety of clinically similar diseases of viral etiology that are endemic to and sporadically epidemic throughout the Eurasian continent and Japan. Although HFRS has not been reported in North America, viruses that are antigenically similar to HFRS agents were recently isolated from rodents in the United States. Examination and comparison of eight representative isolates from endemic disease areas and from regions with no known associated HFRS indicate that these viruses represent a new and unique group that constitutes a separate genus in the Bunyaviridae family of animal viruses.
A Glycophospholipid Tail at the Carboxyl Terminus of the Thy-1 Glycoprotein of Neurons and Thymocytes
Authors: Tse Albert G. D. , Barclay A. Neil , Watts Anthony , Williams Alan F.
Published: October 2006

Cell surface molecules of eukaryotic cells have been considered to be integrated into the membrane bilayer by a transmembrane protein sequence. The Thy-1 antigen of rodent thymocytes and brain was the first eukaryotic membrane molecule for which biochemical data clearly suggested membrane integration via a nonprotein tail. Direct evidence is now presented showing that a glycophospholipid structure is attached to the carboxyl-terminal cysteine residue and that 31 carboxyl-terminal amino acids predicted from the Thy-1 complementary DNA sequence are not present in the mature glycoprotein. These experimental results raise questions concerning signaling across a cell membrane since antibodies to Thy-1 can stimulate T lymphocytes to release lymphokines and undergo cell division.
Contributions of Quisqualate and NMDA Receptors to the Induction and Expression of LTP
Authors: Muller Dominique , Joly Michel , Lynch Gary
Published: October 2006

The contributions of two subclasses of excitatory amino acid transmitter receptors to the induction and expression of long-term potentiation (LTP) were analyzed in hippocampal slices. The quisqualate/kainate receptor antagonist DNQX (6,7-dinitroquinoxaline-2,3-dione) blocked 85% of the evoked field potential, leaving a small response that was sensitive to D-AP5 (D-2-amino-5-phosphonopentanoate), an
N
-methyl-D-aspartate (NMDA) receptor blocker. This residual D-AP5-sensitive response was of comparable size in control and previously potentiated inputs. High-frequency stimulation in the presence of DNQX did not result in the development of robust LTP. Washout of the drug, however, revealed the potentiation effect. Thus NMDA-mediated responses can induce, but are not greatly affected by, LTP; non-NMDA receptors, conversely, mediate responses that are not needed to elicit LTP but that are required for its expression.
Chromatin Structure and de Novo Methylation of Sperm DNA: Implications for Activation of the Paternal Genome
Authors: Groudine Mark , Conklin Kathleen F.
Published: October 2006

The chromatin structure characteristic of constitutively expressed genes, tissue-specific genes, and inactive genes is absent in chicken sperm chromatin. However, point sites of undermethylation in sperm DNA within constitutively expressed genes, but not within globin genes or an inactive gene, correspond to the location of regions of altered chromatin structure (hypersensitive sites) in somatic tissue and spermatogonial cells. A de novo methylation process whereby regions within and flanking these genes become methylated, but which excludes the methylation of sequences within hypersensitive sites, occurs between the spermatogonial stage and the first meiotic prophase. These undermethylated regions may play a role in the activation of the paternal genome during embryogenesis.
Trans
-Activator Gene of Human T-Lymphotropic Virus Type III (HTLV-III)
Authors: Arya Suresh K. , Guo Chan , Josephs Steven F. , Wong-Staal Flossie
Published: October 2006

Human T-lymphotropic virus type III (HTLV-III) encodes a trans-acting factor that activates the expression of genes linked to the HTLV-III long terminal repeat. By functional mapping of complementary DNA transcripts of viral messenger RNA's the major functional domain of the gene encoding this factor was localized to a region immediately before the
env
gene of the virus, a region previously thought to be noncoding. This newly identified gene consists of three exons, and its transcription into messenger RNA involves two splicing events bringing together sequences from the 5′ part (287 base pairs), middle (268 base pairs), and 3′ part (1258 base pairs) of the HTLV-III genome. A similar messenger RNA with a truncated second exon (70 base pairs) does not encode a
trans
-acting function. It is proposed that this second messenger RNA is the transcript of a gene (3′-
orf
) located after the
env
gene. Messenger RNA′s were also identified for the
env
and
gag
-
pol
genes of HTLV-III.
Isolation and Propagation of a Human Enteric Coronavirus
Authors: Resta Silvia , Luby James P. , Rosenfeld Charles R. , Siegel Jane D.
Published: October 2006

Coronavirus-like particles were found by electron microscopy in stools from infants with necrotizing enterocolitis. Stool samples from these infants as well as control specimens were passaged in cultures of human fetal intestinal organs. Two samples yielded virus-like particles and these have now been passaged 14 times (HEC 14). Gradient-purified HEC 14 strains had typical coronavirus morphology on electron microscopy and contained five major proteins with molecular sizes ranging from 190 to 23 kilodaltons. Infants with necrotizing enterocolitis developed specific antibody to the viral antigens between the acute and convalescent stages of the disease, as shown by examining serum specimens by single radial hemolysis, immunoenzymatic assay, and Western immunoblotting. No cross-reactivity was shown with other coronavirus strains tested, or with the newly isolated viruses of the Breda-Berne group, responsible for calf or horse diarrhea.
Enhanced Transcription of c-
myc
in Bursal Lymphoma Cells Requires Continuous Protein Synthesis
Authors: Linial Maxine , Gunderson Nancy , Groudine Mark
Published: October 2006

In several bursal lymphoma cell lines in which c-
myc
transcription is regulated by avian leukosis virus (ALV) long terminal repeat (LTR) sequences, protein synthesis inhibition decreases the transcriptional activity of c-
myc
as well as other LTR driven viral genes. This decrease in transcription is associated with a change in the chromatin structure of c-
myc
, as measured by deoxyribonuclease I (DNase I) hypersensitivity, and a shift of transcription from the LTR to the normal c-
myc
promoter. In contrast, cycloheximide had little or no effect on the transcription of LTR driven genes in infected chicken embryo fibroblasts treated with the drug. These results suggest that a labile, cell type-specific protein may interact with the retroviral LTR and regulate transcription of genes under LTR control. Further, the results demonstrate that the increase in intracellular concentration of c-
myc
RNA induced by cycloheximide treatment of normal cells is the result of stabilization of this message.
Photoreceptor Outer Segments: Accelerated Membrane Renewal in Rods After Exposure to Light
Authors: Besharse Joseph C. , Hollyfield Joe G. , Rayborn Mary E.
Published: October 2006

The rate of rod outer segment renewal in
Rana pipiens
tadpoles under constant light and under diurnal conditions of 12 or 2 hours light per day is significantly increased compared to that in animals in darkness. Furthermore, during 24 hours in light after 6 days in darkness the rate of renewal is three to four times that in darkness. In
Xenopus laevis
tadpoles the rate of renewal is more than five times greater during the first 8 hours of a normal diurnal cycle than during the following 16 hours. These observations demonstrate that bursts of renewal activity occur as a response to light, and suggest that a normal pattern of light alternating with darkness plays a fundamental role in the regulation of rod outer segment turnover.
Tandem Duplication of D-Loop and Ribosomal RNA Sequences in Lizard Mitochondrial DNA
Authors: Moritz Craig , Brown Wesley M.
Published: October 2006

Some
Cnemidophorus exsanguis
have mitochondrial DNA's (mtDNA's) that are 22.2 kilobases (kb) in size, whereas most have mtDNA's of 17.4 kb. Restriction site mapping, DNA transfer hybridization experiments, and electron microscopy show that the size increment stems from the tandem duplication of a 4.8-kb region that includes regulatory sequences and transfer and ribosomal RNA genes. This observation is notable in that sequences outside of the control region are involved in major length variation. Besides revealing a novel form of mtDNA evolution in animals, these duplications provide a useful system for investigating the molecular and evolutionary biology of animal mtDNA.
Induction of B Cell Unresponsiveness to Noninherited Maternal HLA Antigens During Fetal Life
Authors: Claas Frans H. J. , Gijbels Yvonne , van der Velden-de Munck Jacqueline , van Rood Jon J.
Published: October 2006

Patients who have received many transfusions become highly sensitized and develop antibodies against almost all HLA alloantigens, so that finding a cross-match negative kidney donor is difficult. A survey of those patients showed that 50 percent did not form antibodies against the noninherited maternal HLA antigens. Apart from the obvious clinical implications, the data indicate that a human equivalent of murine neonatal or actively acquired tolerance has now been identified.
Automated Chemical Synthesis of a Protein Growth Factor for Hemopoietic Cells, Interleukin-3
Authors: Clark-Lewis Ian , Aebersold Ruedi , Ziltener Herman , Schrader John W. , Hood Leroy E. , Kent Stephen B. H.
Published: October 2006

Interleukin-3 (IL-3), a protein of 140 amino acids, was chemically synthesized by means of an automated peptide synthesizer and was shown to have the biological activities attributed to native IL-3. Assays of synthetic analogues established that an amino terminal fragment has detectable IL-3 activity, but that the stable tertiary structure of the complete molecule was required for full activity. The results demonstrate that automated peptide synthesis can be applied to the study of the structure and function of proteins.
Plant Phenolic Compounds Induce Expression of the
Agrobacterium tumefaciens
Loci Needed for Virulence
Authors: Bolton George W. , Nester Eugene W. , Gordon Milton P.
Published: October 2006

The virulence loci of
Agrobacterium tumefaciens
are a set of linked transcriptional units that play an essential role in the early stages of plant tumorigenesis. These loci are induced upon cocultivation of the bacteria with plant cells. Seven phenolic compounds that are widely distributed among the angiosperm plants—catechol, gallic acid, pyrogallic acid,
p
-hydroxybenzoic acid, protocatechuic acid, β-resorcylic acid, and vanillin—are able to induce the expression of the virulence loci. These phenolics in combination induce each transcriptional locus of the
vir
loci. Furthermore, this induction displays similar kinetics and genetic control to that observed during cocultivation of the bacteria with plant cells.