bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of cluster shape upon its growth in a two-dimensional Ising model
Authors: Berim Gersh O. , Ruckenstein Eli
Published: September 2002

The formalism of the kinetic Ising model was used to investigate the initial growth of clusters with various number of spins and shapes in the two-dimensional Ising model on a square lattice. A general expression which provides the initial growth rate of a cluster was derived and applied to clusters of various shapes. For the simple shapes, such as rectangular, triangular, etc., the problem was treated analytically for any cluster size and expressions for the shape dependent critical size above which clusters of given shape initially grow derived. To analyze the case of arbitrary shapes, all possible configurations of clusters with up to 10 spins were generated by computer and their initial growth rate was investigated numerically. It was shown that the initial growth rate of a cluster depends not only on its size but also on the cluster shape. For a given shape there is a critical size above which the cluster initially grows. Because of this initial growth, the cluster can change its shape and will continue to grow only if its size is greater than the critical size for the new shape, and so on.
Study of surface recombination velocity of Cd1−xZnxTe radiation detectors by direct current photoconductivity
Authors: Cui Y. , Groza M. , Hillman D. , Burger A. , James R. B.
Published: September 2002

The surface recombination velocity of a Cd1−xZnxTe (CZT) radiation detector treated by mechanical polishing and by a standard 5% bromine in methanol chemical etch is reported. The light power dependence of the surface recombination velocity was measured using dc photoconductivity. The results reveal that the surface recombination velocity is a function of the electron generation rate, which can be described by a Shockley–Read one-center model. It was observed that the surface recombination velocity of the CZT detector treated by polishing only is much larger than that treated with polishing followed by chemical etching. The correlation of dc photoconductivity and low-temperature photoluminescence measurements of the CZT detector is also discussed.
Inequalities for quantum entropy: A review with conditions for equality
Authors: Ruskai Mary Beth
Published: September 2002

This article presents self-contained proofs of the strong subadditivity inequality for von Neumann’s quantum entropy, S(ρ), and some related inequalities for the quantum relative entropy, most notably its convexity and its monotonicity under stochastic maps. Moreover, the approach presented here, which is based on Klein’s inequality and Lieb’s theorem that the function A→Tr eK+log A is concave, allows one to obtain conditions for equality. In the case of strong subadditivity, which states that S(ρ123)+S(ρ2)⩽S(ρ12)+S(ρ23) where the subscripts denote subsystems of a composite system, equality holds if and only if log ρ123=log ρ12−log ρ2+log ρ23. Using the fact that the Holevo bound on the accessible information in a quantum ensemble can be obtained as a consequence of the monotonicity of relative entropy, we show that equality can be attained for that bound only when the states in the ensemble commute. The article concludes with an Appendix giving a short description of Epstein’s elegant proof of Lieb’s theorem.
Thermal conductivity of GaN films: Effects of impurities and dislocations
Authors: Zou J. , Kotchetkov D. , Balandin A. A. , Florescu D. I. , Pollak Fred H.
Published: September 2002

We report details of the calculation of the lattice thermal conductivity κ in wurtzite GaN. Numerical simulations are performed for n-type wurtzite GaN with different density of silicon dopants, point defects and threading dislocations. Using the material specific model we verified the experimentally observed linear decrease of the room-temperature thermal conductivity with the logarithm of the carrier density n. The decrease was attributed mostly to the increased phonon relaxation on dopants. Our calculations show that the increase in the doping density from 1017 to 1018 cm−3 leads to about a factor of 2 decrease in thermal conductivity from 1.77 W/cm K to 0.86 W/cm K. We have also established that the room-temperature thermal conductivity in GaN can be limited by dislocations when their density is high, e.g., ND>1010 cm−2. The obtained results are in good agreement with experimental data. The developed calculation procedure can be used for accurate simulation of self-heating effects in GaN-based devices.
Gas–solid coexistence of the Lennard-Jones system
Authors: van der Hoef Martin A.
Published: September 2002

Recently, the absolute free energies of the Lennard-Jones system at solid–liquid and solid–gas coexistence were computed from Monte Carlo simulations [J. Chem. Phys. 116, 7145 (2002)]. In this note, we show that the values along the sublimation line are in good agreement with the results from an equation of state published earlier [J. Chem. Phys. 113, 8142 (2000)]. The present values for the thermodynamic properties along the sublimation line are the most accurate reported to date.
Photocurrent multiplication in organic single crystals
Authors: Hiramoto Masahiro , Miki Ayako , Yoshida Manabu , Yokoyama Masaaki
Published: September 2002

A photocurrent multiplication of up to 200 times has been observed in single crystals of naphthalene tetracarboxylic anhydride sandwiched between metal electrodes. Photocurrent multiplication arises from photoinduced electron injection occurring at the crystal/metal interface. The high-speed response of the multiplied photocurrent reached 500 ms.
Thermal stability of rhenium Schottky contacts on n-type AlxGa1−xN
Authors: Zhou L. , Khan F. A. , Cueva G. , Kumar V. , Adesida I. , Sardela M. R. , Auret F. D.
Published: September 2002

The impact of rapid thermal annealing on the electrical and materials characteristics of Re Schottky contacts on n-type GaN and AlxGa1−xN (x=0.10 and 0.26) was investigated. Effective barrier heights were obtained from current–voltage and modified Norde measurements on diodes annealed at up to 800 °C. For AlxGa1−xN with x>0, Schottky barrier heights were found to increase upon annealing from the as-deposited state, but decreased sharply after annealing at 600 °C. Modified Norde measurements indicate that this degradation could be explained by the existence of a shunt conduction path with an associated barrier height below 0.46 V, possibly a consequence of an inhomogeneous interface after annealing at temperatures above 600 °C. A new defect lying at 0.34 eV below the conduction band edge was also detected by deep level transient spectroscopy after contact degradation.
Last but Not Least
Authors: Ditzinger Thomas , Billock Vincent A , Kelso J A Scott , Holtz Jochen
Published: September 2002

We report a novel, easily observed, and extraordinarily striking optical illusion mediated by interactions of colour, brightness, form, and motion perception—the Leaning Tower of Pisa (LTOP) illusion. Under some circumstances, the perception of orientation of coloured forms is radically altered by rotary movement. We demonstrate that this kinetic effect—easily reproduced with a common record turntable—is optimised by particular colour and brightness differences between foreground and background with an illusory tilt of 8° and more. The described illusions can be easily studied at home by downloading the colour figures from www.perceptionweb.com/perc1000/ditzinger , printing them on a common colour printer and placing them on a rotating record turntable.
Genetic variation for disease resistance and tolerance among
Arabidopsis thaliana
accessions
Authors: Kover Paula X. , Schaal Barbara A.
Published: September 2002

Pathogens can be an important selective agent in plant evolution because they can severely reduce plant fitness and growth. However, the role of pathogen selection on plant evolution depends on the extent of genetic variation for resistance traits and their covariance with host fitness. Although it is usually assumed that resistance traits will covary with plant fitness, this assumption has not been tested rigorously in plant–pathogen interactions. Many plant species are tolerant to herbivores, decoupling the relationship between resistance and fitness. Tolerance to pathogens can reduce selection for resistance and alter the effect of pathogens on plant evolution. In this study, we measured three components of
Arabidopsis thaliana
resistance (pathogen growth, disease symptoms, and host fitness) to the bacteria
Pseudomonas
syringae
and investigated their covariation to determine the relative importance of resistance and tolerance. We observed extensive quantitative variation in the severity of disease symptoms, the bacterial population size, and the effect of infection on host fitness among 19 accessions of
A. thaliana
infected with
P. syringae
. The severity of disease symptoms was strongly and positively correlated with bacterial population size. Although the average fitness of infected plants was smaller than noninfected plants, we found no correlation between the bacterial growth or symptoms expressed by different accessions of
A. thaliana
and their relative fitness after infection. These results indicate that the accessions studied vary in tolerance to
P. syringae
, reducing the strength of selection on resistance traits, and that symptoms and bacterial growth are not good predictors of host fitness.
Arizona porphyry copper/hydrothermal deposits II: Crystal structure of ajoite, (K + Na)
3
Cu
20
Al
3
Si
29
O
76
(OH)
16
⋅∼8H
2
O
Authors: Pluth Joseph J. , Smith Joseph V.
Published: September 2002

A crystal from the type locality Ajo, AZ, yielded just enough intensity from streaked diffractions using synchrotron x-rays at the Advanced Photon Source to solve the crystal structure with composition (K + Na)
3
Cu
20
Al
3
Si
29
O
76
(OH)
16
⋅∼8H
2
O; triclinic, P1̄,
a
= 13.634(5) Å,
b
= 13.687(7),
c
= 14.522(7), α = 110.83(1)°, β = 107.21(1), γ = 105.68(1); refined to a final
R
= 12.5%. Electron microprobe analysis yielded a similar chemical composition that is slightly different from the combined chemical and electron microprobe analyses in the literature. The ajoite structure can be described as a zeolitic octahedral-tetrahedral framework that combines the alternate stacking of edge-sharing octahedral CuO
6
layers and curved aluminosilicate layers and strings. Channels bounded by elliptical 12-rings and circular 8-rings of tetrahedra contain (K and Na) ions and water. The Al atoms occupy some of the Si tetrahedral sites. Each Cu atom has near-planar bonds to four oxygen atoms plus two longer distances that generate a distorted octahedron. Valence bond estimates indicate that 8 oxygen atoms of 46 are hydroxyl. Only one alkali atom was located in distorted octahedral coordination, and electron microprobe analyses indicate K and Na as major substituents. The water from chemical analysis presumably occurs as disordered molecules of zeolitic type not giving electron density from diffraction. The high
R
factor results from structural disorder and many weak intensities close to detection level. The crystal chemistry is compared with shattuckite, Cu
5
(SiO
3
)
4
(OH)
2
, and planchéite, Cu
8
Si
8
O
22
(OH)
4
⋅H
2
O, both found in oxidized copper deposits of Arizona but only the former directly with ajoite.
CRINEPT-TROSY NMR reveals p53 core domain bound in an unfolded form to the chaperone Hsp90
Authors: Rüdiger Stefan , Freund Stefan M. V. , Veprintsev Dmitry B. , Fersht Alan R.
Published: September 2002

The molecular chaperone Hsp90 sequesters oncogenic mutants of the tumor suppressor p53 that have unstable core domains. It is not known whether p53 is bound in an unfolded, partly folded, or distorted structure, as is unknown for the structure of any bound substrate of Hsp90. It is a particularly difficult problem to analyze in detail the structures of large complexes in which one component is (partly) unfolded. We have shown by transverse relaxation-optimized NMR spectroscopy combined with cross-correlated relaxation-enhanced polarization transfer (CRINEPT-TROSY) that p53 core domain bound in an ≈200-kDa complex with Hsp90 was predominantly unfolded lacking helical or sheet secondary structure. This mode of binding might be a general feature of substrates of Hsp90.
Reduced fear expression after lesions of the ventral hippocampus
Authors: Kjelstrup Kirsten G. , Tuvnes Frode A. , Steffenach Hill-Aina , Murison Robert , Moser Edvard I. , Moser May-Britt
Published: September 2002

The hippocampus has a critical role in several fundamental memory operations, including the conditioning of fear to contextual information. We show that the hippocampus is necessary also for unconditioned fear, and that the involved circuitry is at the ventral pole of the hippocampus. Rats with selective hippocampal lesions failed to avoid open arms in an elevated plus-maze and had decreased neuroendocrine stress responses during confinement to a brightly lit chamber. These effects were reproduced by lesions of the ventral half of the hippocampus, but not by damage to the dorsal three-quarters of the hippocampus or the amygdala. Ventral lesions failed to impair contextual fear conditioning or spatial navigation, suggesting that the ventral hippocampus may specifically influence some types of defensive fear-related behavior.
Evidence for the control of phytolith formation in
Cucurbita
fruits by the hard rind (
Hr
) genetic locus: Archaeological and ecological implications
Authors: Piperno Dolores R. , Holst Irene , Wessel-Beaver Linda , Andres Thomas C.
Published: September 2002

Many angiosperms, both monocotyledons and dicotyledons, heavily impregnate their vegetative and reproductive organs with solid particles of silicon dioxide (SiO
2
) known as opaline phytoliths. The underlying mechanisms accounting for the formation of phytoliths in plants are poorly understood, however. Using wild and domesticated species in the genus
Cucurbita
along with their F
1
and F
2
progeny, we have demonstrated that the production of large diagnostic phytoliths in fruit rinds exhibits a one-to-one correspondence to the lignification of these structures. We propose that phytolith formation in
Cucurbita
fruits is primarily determined by a dominant genetic locus, called hard rind (
Hr)
, previously shown to code for lignin deposition. If true, this evidence represents a demonstration of genetic control over phytolith production in a dicotyledon and provides considerable support to hypotheses that silica phytoliths constitute another important system of mechanical defense in plants. Our research also identifies
Hr
as another single locus controlling more than one important phenotypic difference between wild and domesticated plants, and establishes rind tissue cell structure and hardness under the effects of
Hr
as an important determinant of phytolith morphology. When recovered from pre-Columbian archaeological sites,
Cucurbita
phytoliths represent genetically controlled fossil markers of exploitation and domestication in this important economic genus.
Drops: The collapse of capillary jets
Authors: Cordoba Antonio , Cordoba Diego , Fefferman Charles , Fontelos Marco A.
Published: September 2002

The appearance of fluid filaments during the evolution of a viscous fluid jet is a commonly observed phenomenon. It is shown here that the break-up of such a jet subject to capillary forces is impossible through the collapse of a uniform filament.
Erythropoietin administration protects retinal neurons from acute ischemia-reperfusion injury
Authors: Junk Anna K. , Mammis Antonios , Savitz Sean I. , Singh Manjeet , Roth Steven , Malhotra Samit , Rosenbaum Pearl S. , Cerami Anthony , Brines Michael , Rosenbaum Daniel M.
Published: September 2002

Erythropoietin (EPO) plays an important role in the brain's response to neuronal injury. Systemic administration of recombinant human EPO (rhEPO) protects neurons from injury after middle cerebral artery occlusion, traumatic brain injury, neuroinflammation, and excitotoxicity. Protection is in part mediated by antiapoptotic mechanisms. We conducted parallel studies of rhEPO in a model of transient global retinal ischemia induced by raising intraocular pressure, which is a clinically relevant model for retinal diseases. We observed abundant expression of EPO receptor (EPO-R) throughout the ischemic retina. Neutralization of endogenous EPO with soluble EPO-R exacerbated ischemic injury, which supports a crucial role for an endogenous EPO/EPO-R system in the survival and recovery of neurons after an ischemic insult. Systemic administration of rhEPO before or immediately after retinal ischemia not only reduced histopathological damage but also promoted functional recovery as assessed by electroretinography. Exogenous EPO also significantly diminished terminal deoxynucleotidyltransferase-mediated dUTP end labeling labeling of neurons in the ischemic retina, implying an antiapoptotic mechanism of action. These results further establish EPO as a neuroprotective agent in acute neuronal ischemic injury.
Tracing the LINEs of human evolution
Authors: Ovchinnikov Igor , Rubin Adrienne , Swergold Gary D.
Published: September 2002

The amplification of DNA by LINE-1 (L1) retrotransposons has created a large fraction of the human genome. To better understand their role in human evolution we endeavored to delineate the L1 elements that have amplified since the emergence of the hominid lineage. We used an approach based on shared sequence variants to trace backwards from the currently amplifying Ta subfamily. The newly identified groups of insertions account for much of the molecular evolution of human L1s. We report the identification of a L1 subfamily that amplified both before and after the divergence of humans from our closest extant relatives. Progressively more modern groups of L1s include greater numbers of insertions. Our data are consistent with the hypothesis that the rate of L1 amplification has been increasing during recent human evolution.
MHC heterozygosity confers a selective advantage against multiple-strain infections
Authors: Penn Dustin J. , Damjanovich Kristy , Potts Wayne K.
Published: September 2002

Genetic heterozygosity is thought to enhance resistance of hosts to infectious diseases, but few tests of this idea exist. In particular, heterozygosity at the MHC, the highly polymorphic loci that control immunological recognition of pathogens, is suspected to confer a selective advantage by enhancing resistance to infectious diseases (the “heterozygote advantage” hypothesis). To test this hypothesis, we released mice into large population enclosures and challenged them with multiple strains ofSalmonellaand one ofListeria. We found that duringSalmonellainfections with three avirulent strains, MHC heterozygotes had greater survival and weight than homozygotes (unlike sham controls), and they were more likely to clear chronicSalmonellainfection than homozygotes. In laboratory experiments, we found that MHC heterozygosity enhanced the clearance of multiple-strainSalmonellainfections. Yet, contrary to what is widely assumed, the benefits of heterozygosity were due to resistance being dominant rather than overdominant, i.e., heterozygotes were more resistant than the average of parental homozygotes, but they were not more resistant than both. The fact that MHC heterozygotes were more resistant to infection and had higher fitness than homozygotes provides a functional explanation for MHC-disassortative mating preferences.
A strong signature of balancing selection in the 5′
cis
-regulatory region of
CCR5
Authors: Bamshad Michael J. , Mummidi Srinivas , Gonzalez Enrique , Ahuja Seema S. , Dunn Diane M. , Watkins W. Scott , Wooding Stephen , Stone Anne C. , Jorde Lynn B. , Weiss Robert B. , Ahuja Sunil K.
Published: September 2002

CCR5
encodes a cell surface chemokine receptor molecule that serves as the principal coreceptor, with CD4, for HIV-type 1 (HIV-1). Varied HIV-1 susceptibility and time to progression to AIDS have been associated with polymorphisms in
CCR5
. Many of these polymorphisms are located in the 5′
cis
-regulatory region of
CCR5
, suggesting that it may have been a target of natural selection. We characterized
CCR5
sequence variation in this region in 400 chromosomes from worldwide populations and compared it to a genome-wide analysis of 100
Alu
polymorphisms typed in the same populations. Variation was substantially higher than expected and characterized by an excess of intermediate-frequency alleles. A genealogy of
CCR5
haplotypes had deep branch lengths despite markedly little differentiation among populations. This finding suggested a deviation from neutrality not accounted for by population structure, which was confirmed by tests for natural selection. These results are strong evidence that balancing selection has shaped the pattern of variation in
CCR5
and suggest that HIV-1 resistance afforded by
CCR5
5′
cis
-regulatory region haplotypes may be the consequence of adaptive changes to older pathogens.
Dynamic trafficking and delivery of connexons to the plasma membrane and accretion to gap junctions in living cells
Authors: Lauf Undine , Giepmans Ben N. G. , Lopez Patricia , Braconnot Sébastien , Chen Shu-Chih , Falk Matthias M.
Published: September 2002

Certain membrane channels including acetylcholine receptors, gap junction (GJ) channels, and aquaporins arrange into large clusters in the plasma membrane (PM). However, how these channels are recruited to the clusters is unknown. To address this question, we have investigated delivery of GJ channel subunits (connexons) assembled from green fluorescent protein (GFP)-tagged connexin 43 (Cx43) to the PM and GJs in living cells. Fluorescence-photobleaching of distinct areas of Cx43-GFP GJs demonstrated that newly synthesized channels were accrued to the outer margins of channel clusters. Time-lapse microscopy further revealed that connexons were delivered in vesicular carriers traveling along microtubules from the Golgi to the PM. Routing and insertion of connexons occurred predominantly into the nonjunctional PM. These PM connexons can move laterally as shown by photo-bleaching and thus, can reach the margins of channel clusters. There, the apposing PMs are close enough to allow connexons to dock into complete GJ channels. When connexon delivery to the PM was inhibited by brefeldin A, or nocodazole pretreatment, the PM pool initially enabled connexon accrual to the clusters but further accrual was inhibited upon depletion. Taken together, our results indicate that GJ channel clusters grow by accretion at their outer margins from connexon subunits that were delivered to the nonjunctional PM, and explain how connexons in the PM can function in intra-/extracellular signaling before GJ channel formation and direct cell–cell communication.
Biomaterial adherent macrophage apoptosis is increased by hydrophilic and anionic substratesinvivo
Authors: Brodbeck William G. , Patel Jasmine , Voskerician Gabriela , Christenson Elizabeth , Shive Matthew S. , Nakayama Yasuhide , Matsuda Takehisa , Ziats Nicholas P. , Anderson James M.
Published: September 2002

Anin vivorat cage implant system was used to identify potential surface chemistries that prevent failure of implanted biomedical devices and prostheses by limiting monocyte adhesion and macrophage fusion into foreign-body giant cells while inducing adherent-macrophage apoptosis. Hydrophobic, hydrophilic, anionic, and cationic surfaces were used for implantation. Analysis of the exudate surrounding the materials revealed no differences between surfaces in the types or levels of cells present. Conversely, the proportion of adherent cells undergoing apoptosis was increased significantly on anionic and hydrophilic surfaces (46 ± 3.7 and 57 ± 5.0%, respectively) when compared with the polyethylene terephthalate base surface. Additionally, hydrophilic and anionic substrates provided decreased rates of monocyte/macrophage adhesion and fusion. These studies demonstrate that biomaterial-adherent cells undergo material-dependent apoptosisin vivo, rendering potentially harmful macrophages nonfunctional while the surrounding environment of the implant remains unaffected.
Supply–demand balance and metabolic scaling
Authors: Banavar Jayanth R. , Damuth John , Maritan Amos , Rinaldo Andrea
Published: September 2002

It is widely accepted that metabolic rates scale across species approximately as the 3/4 power of mass in most if not all groups of organisms. Metabolic demand per unit mass thus decreases as body mass increases. Metabolic rates reflect both the ability of the organism's transport system to deliver metabolites to the tissues and the rate at which the tissues use them. We show that the ubiquitous 3/4 power law for interspecific metabolic scaling arises from simple, general geometric properties of transportation networks constrained to function in biological organisms. The 3/4 exponent and other observed scaling relationships follow when mass-specific metabolic demands match the changing delivery capacities of the network at different body sizes. Deviation from the 3/4 exponent suggests either inefficiency or compensating physiological mechanisms. Our conclusions are based on general arguments incorporating the minimum of biological detail and should therefore apply to the widest range of organisms.
A genotyping strategy based on incorporation and cleavage of chemically modified nucleotides
Authors: Wolfe Jia Liu , Kawate Tomohiko , Sarracino David A. , Zillmann Martin , Olson Jeffrey , Stanton Vincent P. , Verdine Gregory L.
Published: September 2002

Aiming to facilitate the analysis of human genetic variations in the context of disease susceptibility and varied drug response, we have developed a genotyping method that entails incorporation of a chemically labile nucleotide by PCR followed by specific chemical cleavage of the resulting amplicon at the modified bases. The identity of the cleaved fragments determines the genotype of the DNA. This method, termed Incorporation and Complete Chemical Cleavage, utilizes modified nucleotides 7-deaza-7-nitro-dATP, 7-deaza-7-nitro-dGTP, 5-hydroxy-dCTP, and 5-hydroxy-dUTP, which have increased chemical reactivity but are able to form standard Watson–Crick base pairs. Thus one analog is substituted for the corresponding nucleotide during PCR, generating amplicons that contain nucleotide analogs at each occurrence of the selected base throughout the target DNA except for the primer sequences. Subsequent treatment with an oxidant followed by an organic base results in chemical cleavage at each site of modification, which produces fragments of different lengths and/or molecular weights that reflect the genotype of the original DNA sample at the site of interest. This incorporation and cleavage chemistry are widely applicable to many existing nucleic acid analysis platforms, including gel electrophoresis and mass spectrometry. By combining DNA amplification and analog incorporation into one step, this strategy eliminates preamplification, DNA-strand separation, primer extension, and purification procedures associated with traditional chain-termination chemistry and therefore presents significant advantages in terms of speed, cost, and simplicity of genotyping.
Adipose tissue mass can be regulated through the vasculature
Authors: Rupnick Maria A. , Panigrahy Dipak , Zhang Chen-Yu , Dallabrida Susan M. , Lowell Bradford B. , Langer Robert , Folkman M. Judah
Published: September 2002

Tumor growth is angiogenesis dependent. We hypothesized that nonneoplastic tissue growth also depends on neovascularization. We chose adipose tissue as an experimental system because of its remodeling capacity. Mice from different obesity models received anti-angiogenic agents. Treatment resulted in dose-dependent, reversible weight reduction and adipose tissue loss. Marked vascular remodeling was evident in adipose tissue sections, which revealed decreased endothelial proliferation and increased apoptosis in treated mice compared with controls. Continuous treatment maintained mice near normal body weights for age without adverse effects. Metabolic adaptations in food intake, metabolic rate, and energy substrate utilization were associated with anti-angiogenic weight loss. We conclude that adipose tissue mass is sensitive to angiogenesis inhibitors and can be regulated by its vasculature.
Nitric oxide-induced genotoxicity, mitochondrial damage, and apoptosis in human lymphoblastoid cells expressing wild-type and mutant p53
Authors: Li Chun-Qi , Trudel Laura J. , Wogan Gerald N.
Published: September 2002

Nitric oxide (NO
•
) is mutagenic and, under appropriate conditions of exposure, also induces apoptosis in many
in vitro
and
in vivo
experimental models. Biochemical and cellular mechanisms through which NO
•
induces apoptosis are incompletely understood, but involve p53/mitochondria-dependent signaling pathways. In this study, we exposed human lymphoblastoid cells harboring either wild-type (TK6 cells) or mutant p53 (WTK-1 cells) to NO
•
, delivered by diffusion through Silastic tubing. Cells were exposed for 2 h at constant rates of 100–533 nM/s, similar to levels estimated to occur
in vivo
in inflamed tissues. DNA double-strand breaks and fragmentation detected 8–48 h after NO
•
treatment were more extensive in TK6 cells than in WTK-1 cells, whereas NO
•
-induced mutant fractions in both
HPRT
and
TK1
genes were significantly lower in TK6 cells than in WTK-1 cells (
P
< 0.01–0.05)
.
Treatment of TK6 cells with NO
•
caused extensive apoptosis, but this response was delayed and greatly reduced in magnitude in WTK-1 cells. Mitochondrial membrane depolarization and cytochrome
c
release were induced in both cell types. However, elevation of apoptotic protease-activating factor-1 (Apaf-1) protein and reduction of X-chromosome-linked inhibitor of apoptosis (XIAP) protein were observed only in TK6 cells. These results indicate that p53 status is an important modulator of NO
•
-induced mutagenesis and apoptosis, and suggest that levels of the Apaf-1 and XIAP proteins, but not mitochondrial depolarization and cytochrome
c
release, are regulated by p53 in these human lymphoblastoid cells. Thus, Apaf-1 and XIAP may play important roles in the regulation of p53-mediated apoptotic responses.
Targeted mutagenesis of the murine transferrin receptor-2 gene produces hemochromatosis
Authors: Fleming Robert E. , Ahmann John R. , Migas Mary C. , Waheed Abdul , Koeffler H. Phillip , Kawabata Hiroshi , Britton Robert S. , Bacon Bruce R. , Sly William S.
Published: September 2002

Hereditary hemochromatosis (HH) is a common genetic disorder characterized by excess absorption of dietary iron and progressive iron deposition in several tissues, particularly liver. The vast majority of individuals with HH are homozygous for mutations in the
HFE
gene. Recently a second transferrin receptor (TFR2) was discovered, and a previously uncharacterized type of hemochromatosis (HH type 3) was identified in humans carrying mutations in the
TFR2
gene. To characterize the role for TFR2 in iron homeostasis, we generated mice in which a premature stop codon (Y245X) was introduced by targeted mutagenesis in the murine
Tfr2
coding sequence. This mutation is orthologous to the Y250X mutation identified in some patients with HH type 3. The homozygous

Tfr2
Y245X

mutant mice showed profound abnormalities in parameters of iron homeostasis. Even on a standard diet, hepatic iron concentration was several-fold higher in the homozygous

Tfr2
Y245X

mutant mice than in wild-type littermates by 4 weeks of age. The iron deposition in the mutant mice was predominantly hepatocellular and periportal. The mean splenic iron concentration in the homozygous

Tfr2
Y245X

mutant mice was significantly less than that observed in the wild-type mice. The homozygous

Tfr2
Y245X

mutant mice also demonstrated elevated transferrin saturations. There were no significant differences in parameters of erythrocyte production including hemoglobin levels, hematocrits, erythrocyte indices, and reticulocyte counts. Heterozygous

Tfr2
Y245X

mice did not differ in any measured parameter from wild-type mice. This study confirms the important role for TFR2 in iron homeostasis and provides a tool for investigating the excess iron absorption and abnormal iron distribution in iron-overload disorders.
Riboflavin is a component of the Na
+
-pumping NADH–quinone oxidoreductase from
Vibrio
cholerae
Authors: Barquera Blanca , Zhou Weidong , Morgan Joel E. , Gennis Robert B.
Published: September 2002

Flavins are cofactors in many electron-transfer enzymes. Typically, two types of flavins perform this role: 5′-phosphoriboflavin (FMN) and flavin-adenine dinucleotide (FAD). Both of these are riboflavin derivatives, but riboflavin itself has never been reported to be an enzyme-bound component. We now report that tightly bound riboflavin is a component of the NADH-driven sodium pump from
Vibrio cholerae.
tRNA-mediated transcription antitermination
in vitro
: Codon–anticodon pairing independent of the ribosome
Authors: Grundy Frank J. , Winkler Wade C. , Henkin Tina M.
Published: September 2002

Uncharged tRNA acts as the effector for transcription antitermination of genes in the T box family in
Bacillus subtilis
and other Gram-positive bacteria. Genetic studies suggested that expression of these genes is induced by stabilization of an antiterminator element in the leader RNA of each target gene by the cognate uncharged tRNA. The specificity of the tRNA response is dependent on a single codon in the leader, which was postulated to pair with the anticodon of the corresponding tRNA. It was not known whether the leader RNA–tRNA interaction requires additional factors. We show here that tRNA-dependent antitermination occurs
in vitro
in a purified transcription system, in the absence of ribosomes or accessory factors, demonstrating that the RNA–RNA interaction is sufficient to control gene expression by antitermination. The tRNA response exhibits similar specificity
in vivo
and
in vitro
, and the antitermination reaction
in vitro
is independent of NusA and functions with either
B. subtilis
or
Escherichia coli
RNA polymerase.
Interactions between lipids and bacterial reaction centers determined by protein crystallography
Authors: Camara-Artigas A. , Brune D. , Allen J. P.
Published: September 2002

The structure of the reaction center from
Rhodobacter sphaeroides
has been solved by using x-ray diffraction at a 2.55-Å resolution limit. Three lipid molecules that lie on the surface of the protein are resolved in the electron density maps. In addition to a cardiolipin that has previously been reported [McAuley, K. E., Fyfe, P. K., Ridge, J. P., Isaacs, N. W., Cogdell, R. J. & Jones, M. R. (1999)
Proc. Natl. Acad. Sci. USA
96, 14706–14711], two other major lipids of the cell membrane are found, a phosphatidylcholine and a glucosylgalactosyl diacylglycerol. The presence of these three lipids has been confirmed by laser mass spectroscopy. The lipids are located in the hydrophobic region of the protein surface and interact predominately with hydrophobic amino acids, in particular aromatic residues. Although the cardiolipin is over 15 Å from the cofactors, the other two lipids are in close contact with the cofactors and may contribute to the difference in energetics for the two branches of cofactors that is primarily responsible for the asymmetry of electron transfer. The glycolipid is 3.5 Å from the active bacteriochlorophyll monomer and shields this cofactor from the solvent in contrast to a much greater exposed surface evident for the inactive bacteriochlorophyll monomer. The phosphate atom of phosphatidylcholine is 6.5 Å from the inactive bacteriopheophytin, and the associated electrostatic interactions may contribute to electron transfer rates involving this cofactor. Overall, the lipids span a distance of ≈30 Å, which is consistent with a bilayer-like arrangement suggesting the presence of an “inner shell” of lipids around membrane proteins that is critical for membrane function.
Myc and Mad bHLHZ domains possess identical DNA-binding specificities but only partially overlapping functions
in
vivo
Authors: James Leonard , Eisenman Robert N.
Published: September 2002

The opposing transcriptional activities of the basic-helix–loop–helix-leucine zipper proteins Myc and Mad, taken together with information related to their expression patterns and biological effects, have led to a model of the Myc/Max/Mad network in which Myc and Mad proteins function as antagonists. This antagonism is presumed to operate at the level of genes targeted by these complexes, where Myc:Max activates and Mad:Max represses expression of the same set of genes. However, a detailed analysis of the DNA-binding preferences for Mad proteins has not been performed. Furthermore, the model does not address the findings that Myc:Max indirectly represses transcription of several regulatory genes. To examine these issues relating to DNA-binding specificity and biological responses, we have determined the DNA-binding preferences of Mad1 by using selection and amplification of randomized oligonucleotides and demonstrated that its intrinsic specificity is identical with that of c-Myc. We have also used a chimeric Myc protein, containing a substitution of the entire Mad basic-helix–loop–helix-leucine zipper motif, and shown that it can reproduce the growth-promoting activities of Myc, but not its apoptotic function. Our results suggest that Myc and Mad, although possessing identical
in vitro
DNA-binding specificities, do not have an identical set of target genes
in vivo
, and that apoptosis is one biological outcome in which the transcriptional effects of Myc are not directly antagonized by those of Mad.
The gene expression fingerprint of human heart failure
Authors: Tan Fen-Lai , Moravec Christine S. , Li Jianbo , Apperson-Hansen Carolyn , McCarthy Patrick M. , Young James B. , Bond Meredith
Published: September 2002

Multiple pathways are responsible for transducing mechanical and hormonal stimuli into changes in gene expression during heart failure. In this study our goals were (
i
) to develop a sound statistical method to establish a comprehensive cutoff point for identification of differentially expressed genes, (
ii
) to identify a gene expression fingerprint for heart failure, (
iii
) to attempt to distinguish different etiologies of heart failure by their gene expression fingerprint, and (
iv
) to identify gene clusters that show coordinated up- or down-regulation in human heart failure. We used oligonucleotide microarrays to profile seven nonfailing (NF) and eight failing (F) human hearts with a diagnosis of end-stage dilated cardiomyopathy. Biological and experimental variability of the hybridization data were analyzed, and then a statistical analysis procedure was developed, including Student's
t
test after log-transformation and Wilcoxon Mann–Whitney test. A comprehensive cutoff point composed of fold change, average difference, and absolute call was then established and validated by TaqMan PCR. Of 6,606 genes on the GeneChip, 103 genes in 10 functional groups were differentially expressed between F and NF hearts. A dendrogram identified a gene expression fingerprint of F and NF hearts and also distinguished two F hearts with distinct etiologies (familial and alcoholic cardiomyopathy, respectively) with different expression patterns. K means clustering also revealed two potentially novel pathways associated with up-regulation of atrial natriuretic factor and brain natriuretic peptide and with increased expression of extracellular matrix proteins. Gene expression fingerprints may be useful indicators of heart failure etiologies.
Toward predicting protein topology: An approach to identifying β hairpins
Authors: de la Cruz Xavier , Hutchinson E. Gail , Shepherd Adrian , Thornton Janet M.
Published: September 2002

Although secondary structure prediction methods have recently improved, progress from secondary to tertiary structure prediction has been limited. A promising but largely unexplored route to this goal is to predict structure motifs from secondary structure knowledge. Here we present a novel method for the recognition of β hairpins that combines secondary structure predictions and threading methods by using a database search and a neural network approach. The method successfully predicts 48 and 77%, respectively, of all of hairpin and nonhairpin β-coil-β motifs in a protein database. We find that the main contributors to motif recognition are predicted accessibility and turn propensities.
Global analysis of the
Deinococcus radiodurans
proteome by using accurate mass tags
Authors: Lipton Mary S. , Paša-Tolić Ljiljana , Anderson Gordon A. , Anderson David J. , Auberry Deanna L. , Battista John R. , Daly Michael J. , Fredrickson Jim , Hixson Kim K. , Kostandarithes Heather , Masselon Christophe , Markillie Lye Meng , Moore Ronald J. , Romine Margaret F. , Shen Yufeng , Stritmatter Eric , Tolić Nikola , Udseth Harold R. , Venkateswaran Amudhan , Wong Kwong-Kwok , Zhao Rui , Smith Richard D.
Published: September 2002

Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium
Deinococcus radiodurans
. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical.
A nonsense mutation in the gene encoding 2′-5′-oligoadenylate synthetase/L1 isoform is associated with West Nile virus susceptibility in laboratory mice
Authors: Mashimo Tomoji , Lucas Marianne , Simon-Chazottes Dominique , Frenkiel Marie-Pascale , Montagutelli Xavier , Ceccaldi Pierre-Emmanuel , Deubel Vincent , Guénet Jean-Louis , Desprès Philippe
Published: September 2002

A mouse model has been established to investigate the genetic determinism of host susceptibility to West Nile (WN) virus, a member of the genus flavivirus and family
Flaviviridae
. Whereas WN virus causes encephalitis and death in most laboratory inbred mouse strains after peripheral inoculation, most strains derived from recently trapped wild mice are completely resistant. The phenotype of resistance/susceptibility is determined by a major locus,
Wnv
, mapping to chromosome 5 within the 0.4-cM-wide interval defined by markers
D5Mit408
and
D5Mit242
. We constructed a high resolution composite/consensus map of the interval by merging the data from the mouse T31 Radiation Hybrid map and those from the homologous region of human chromosome 12q, and found the cluster of genes encoding 2′-5′-oligoadenylate synthetases (2′-5′-OAS) to be the most prominent candidate. This cluster encodes a multimember family of IFN-inducible proteins that is known to play an important role in the established endogenous antiviral pathway. Comparing the cDNA sequences of 2′-5′-OAS L1, L2, and L3 isoforms, between susceptible and resistant strains, we identified a STOP codon in exon 4 of the gene encoding the L1 isoform in susceptible strains that can lead to a truncated form with amputation of one domain, whereas all resistant mice tested so far have a normal copy of this gene. The observation that WN virus sensitivity of susceptible mice was completely correlated with the occurrence of a point mutation in 2′-5′-OAS L1 suggests that this isoform may play a critical role in WN pathogenesis.
Mechanism of caveolin filament assembly
Authors: Fernandez Imma , Ying Yunshu , Albanesi Joseph , Anderson Richard G. W.
Published: September 2002

Caveolin-1 was the first protein identified that colocalizes with the ≈10-nm filaments found on the inside surface of caveolae membranes. We have used a combination of electron microscopy (EM), circular dichroism, and analytical ultracentrifugation to determine the structure of the oligomers that form when the first 101 aa of caveolin-1 (Cav
1–101
) are allowed to associate. We determined that amino acids 79–96 in this caveolin-1 fragment are arranged in an α-helix. Cav
1–101
oligomers are ≈11 nm in diameter and contain seven molecules of Cav
1–101
. These subunits, in turn, are able to assemble into 50 nm long × 11 nm diameter filaments that closely match the morphology of the filaments in the caveolae filamentous coat. We propose that the heptameric subunit forms in part through lateral interactions between the α-helices of the seven Cav
1–101
units. Caveolin-1, therefore, appears to be the structural molecule of the caveolae filamentous coat.
Signature of balancing selection in
Arabidopsis
Authors: Tian Dacheng , Araki Hitoshi , Stahl Eli , Bergelson Joy , Kreitman Martin
Published: September 2002

Natural selection and genetic linkage cause DNA segments to have genealogical histories resembling those of the selected sites. When a polymorphism maintained by selection is old, it will have an island of enhanced sequence variability surrounding it, which represents a detectable “signature of selection.” We investigate the structure of single-nucleotide polymorphisms (SNPs) in a 20-kb interval containing the
Arabidopsis thaliana
disease resistance gene
RPS5
, a locus containing common alleles for the presence/absence of the entire locus. The alleles are considerably diverged at surrounding sites, indicative of an old polymorphism maintained by selection. The island of “enhanced” variability extends several kilobases to either side of the
RPS5
deletion junction, and these SNPs are in nearly complete linkage disequilibrium with the
RPS5
insertion/deletion. At a distance of 10 kb to either side of the locus, however, we find low levels of polymorphism and the absence of linkage disequilibrium between individual SNPs and
RPS5
alleles. Our results show that the interval of enhanced variability surrounding this balanced polymorphism in
Arabidopsis
is large enough to be readily detected, but small enough to span the focal gene and few others. For this species it should be possible to identify the complete set of genes with long-lived polymorphisms, a potentially important subset of genes segregating for functional variants.