bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient Ne-like Cr x-ray lasers driven by picosecond laser pulses
Authors: Zhang Ying , Zhang Jie , Liu Shi-bing , Zhang Dao-zhong , Nie Yu-xin
Published: July 2002

In this paper we model transient Ne-like Cr x-ray lasers produced by picosecond laser heating of a nanosecond pulse preformed plasma. The model calculation shows that transient high gain can be generated on (2p1/2,3p1/2)J=0→(2p1/2,3s1/2)J=1 transition at 27.5 nm with only a few joules of drive energy.
Stimulated Brillouin scattering of an electromagnetic wave in a strongly magnetized plasma
Authors: Jaiman N. K. , Tripathi V. K.
Published: July 2002

In a strongly magnetized nonisothermal plasma, a large amplitude electromagnetic wave propagating at an angle θ0 to a strong magnetic field undergoes stimulated Brillouin scattering off the ion mode. In an isothermal plasma the process goes over to stimulated Compton scattering with considerably lower growth rate. In both cases the growth rate is sensitive to the angle θ=(θ1−θ0), where θ0 is the angle of the pump wave vector k0 with the dc magnetic field, Bsẑ, and θ1 is the angle of the sideband wave vector k1 with Bsẑ.
Particle trajectories in a sheath in a strongly tilted magnetic field
Authors: Cohen R. H. , Ryutov D. D.
Published: July 2002

In this paper we provide a systematic analysis of particle motion in a sheath under the condition that the magnetic field intersects the wall at a small angle. A general qualitative classification of particle trajectories is presented. It is shown that the ion motion in the ion subsheath can be described in terms of an adiabatic invariant, despite the fact that the electrostatic potential varies on a scale comparable with the ion gyroradius. Trajectories of heavy impurity ions for the cases of both low and high ionization states have been found. Electron motion is considered, and it is shown that, if the electron gyroradius is much less than the electron Debye radius, electrons hit the wall at shallow angles. The possible role of an electrostatic field directed along the wall is briefly discussed. The results obtained in the paper can be used for evaluating the sputtering rate and the secondary emission coefficient, as well as for analyzing sheath stability and for formulating the boundary conditions for the bulk of the plasma.
Effects of Er shear on edge turbulence of the China Tokamak-6B
Authors: Wang Guiding , Yang Xuanzong , Feng Chunhua , Jiang Diming , Zhou Baosuo , Qi Xiazhi , Wang Long
Published: July 2002

On the China Tokamak (CT-6B) [Nucl. Fusion 36, 1669 (1996)], application of negative limiter bias resulted in enhanced Er shear in the naturally occurring Er shear layer near the fixed limiter radius with negligible change of plasma density, electron temperature, the parallel plasma flow, and the impurity ion radiation power. In the layer, decreased turbulent fluctuation, reduced poloidal correlation and increased nonlinear coupling of the turbulence were observed to be very possibly correlated with enhanced Er shear. The results suggest that there exists interaction of Er shear with turbulence, and an Er shear-induced shift in the phase angle between density and poloidal electric field fluctuations and nonlinear three-wave coupling may play an important role in suppressing edge turbulence.
Analytic and numerical study of magnetic fields in the plasma wake of an intense laser pulse
Authors: Sheng Z. M. , Meyer-ter-Vehn J. , Pukhov A.
Published: July 2002

Magnetic field generation by a laser-induced wakefield is studied in two-dimensional (2D) planar geometry, both analytically and numerically via particle-in-cell (PIC) code simulations. Generally, the magnetic field in the wake is perpendicular to the 2D plane and can be separated into two components: one is independent of time and uniform in the longitudinal (laser propagation) direction; the other depends on time and varies longitudinally. The scaling of magnetic field strength changes from dIL2/dr⊥ at low light intensities to dIL/dr⊥ at high intensities, where IL is the laser intensity and r⊥ the transverse coordinate. Furthermore, the varying component changes from a periodic to a rather complicated structure and tends to increase with the distance from the pulse front. In addition to the quasistatic component, the magnetic field contains a transient component radiating at nearly twice the plasma frequency during the early stage of wakefield buildup. Phase velocities of the wakefield equal to and less than the vacuum speed of light are considered.
Fast particle destabilization of toroidicity-induced Alfvén eigenmodes in the National Spherical Torus Experiment
Authors: Gorelenkov N. N. , Cheng C. Z. , Fu G. Y. , Kaye S. , White R. , Gorelenkova M. V.
Published: July 2002

Toroidicity-induced Alfvén eigenmode (TAE) stability in the National Spherical Torus Experiment (NSTX) [S. M. Kaye, M. Ono, Y.-K. M. Peng et al., Fusion Technol. 36, 16 (1999)] is analyzed using the improved NOVA-K code [N. N. Gorelenkov, C. Z. Cheng, and G. Y. Fu, Phys. Plasmas 6, 2802 (1999)], which includes finite orbit width and Larmor radius effects and is able to predict the saturation amplitude for the mode using the quasilinear theory. A broad spectrum of unstable global TAEs with different toroidal mode numbers is predicted. Due to the strong poloidal field and the presence of the magnetic well in NSTX, better particle confinement in the presence of TAEs in comparison with tokamaks is illustrated making use of the ORBIT code [R. B. White and M. S. Chance, Phys. Fluids 27, 2455 (1984)].
Atomic layer epitaxy of III-V binary compounds
Authors: Bedair S. M. , Tischler M. A. , Katsuyama T. , El-Masry N. A.
Published: July 2002

Atomic layer epitaxy (ALE) of III-V semiconductors is reported for the first time using metalorganic and hydride sources. This is achieved by using a new growth chamber and susceptor design which incorporates a shuttering mechanism to allow successive exposure to streams of gases from the two sources. Also, most of the gaseous boundary layer is sheared off after exposure to the gas streams. GaAs and AlAs deposited by ALE are single crystal and show good optical properties.
Wafer bonding for silicon-on-insulator technologies
Authors: Lasky J. B.
Published: July 2002

A silicon wafer bonding process is described in which only thermally grown oxide is present between wafer pairs. Bonding occurs after insertion into an oxidizing ambient. It is proposed the wafers are drawn into intimate contact as a result of the gaseous oxygen between them being consumed by oxidation, thus producing a partial vacuum. The proposed bonding mechanism is polymerization of silanol bonds between wafer pairs. Silicon on insulator (SOI) is produced by etching away all but a few microns of one of the bonded pair. Capacitor measurements show a 27 μs minority-carrier lifetime and no degradation of the SOI-insulator interface. In addition, there is negligible charge at the bonding interface making the technique attractive for three-dimensional as well as planar SOI applications.
Growth of GaN films using trimethylgallium and hydrazine
Authors: Gaskill D. K. , Bottka N. , Lin M. C.
Published: July 2002

Hydrazine has been used as a nitrogen source for the organometallic vapor phase deposition of GaN using trimethylgallium and a nitrogen carrier gas in the temperature range 425–960 °C. Hydrazine and trimethylgallium form an adduct at room temperature which decomposes over the substrate with an activation energy of 1 eV for temperatures below 650 °C. No carbon has been detected by Auger spectroscopy in the films. The electrical properties are dominated by oxygen impurities, probably originating from the hydrazine. Since hydrazine readily decomposes above 400 °C, it is a better source of nitrogen for low-temperature depositions than other, more stable nitrogen sources.
Cesium migration and equilibrium in a strong electric field on the surface of silicon
Authors: van Gorkom G. G. P. , van Oostrom A. , Crombeen J. E. , Hoeberechts A. M. E.
Published: July 2002

It is found experimentally that a balance between the chemical force and the force due to an applied electric field acting on fractionally charged cesium particles on the surface of silicon leads to an equilibrium state. Measurements of the coverage gradient (∂θ/∂x) in this equilibrium state give a relation between the gradient of the chemical potential (mainly the binding energy Ub) and the fractional charge of the cesium particles. For cesium atoms on silicon this relation is found to be f=0.16∂Ub/∂θ+0.03.
Electron spin resonance study of hydrogenation effects in polycrystalline silicon
Authors: Ballutaud Dominique , Aucouturier Marc , Babonneau Florence
Published: July 2002

Electron spin resonance spectra obtained on polycrystalline silicon produced by annealing of chemical vapor deposition silicon are investigated before and after plasma hydrogenation of the material. Before hydrogenation, two paramagnetic defects are observed, one of them remaining unidentified (g=2.0084). Hydrogenation decreases the total spin density, but the two defects are affected differently; the defect with g=2.0084 is more efficiently passivated. The results are discussed in terms of the inter- and intragranular nature of the paramagnetic defects and of hydrogen diffusivity in the polycrystal.
Investigation by Raman scattering of the properties of III-V compound semiconductors at high temperature
Authors: Shealy J. R. , Wicks G. W.
Published: July 2002

The properties of several III-V compound semiconductor alloys, namely, GaAs, AlGaAs, and GaInP, have been studied at high temperatures using Raman spectroscopy. The temperature range used for these measurements includes the thermal dissociation temperatures for GaAs and GaInP in vacuum. The Raman spectra taken from the thermally dissociated surface yield information on the crystallinity (or lack of it) after decomposition in vacuum occurs. These data establish the feasibility to acquire Raman spectra of these materials and deduce their alloy composition and layer thickness during epitaxial growth. We have determined the phonon frequency shifts with temperature, and found that the linewidth broadening of the Raman peaks at high temperatures (700 °C) is minimal.
Proximity gettering with mega-electron-volt carbon and oxygen implantations
Authors: Wong H. , Cheung N. W , Chu P. K. , Liu J. , Mayer J. W.
Published: July 2002

We have demonstrated that a buried gettering layer can be formed with a single MeV ion implantation without damaging the top device region. The strong gettering efficiency of carbon implant and its linear dependence on dose are confirmed. A surprising feature of the carbon implanted layers is that no extended defects are formed after annealing for implant doses up to 2×1016 cm−2 at 3 MeV, compared to a layer of small precipitates and dislocations in the case of oxygen implantation. It is suggested that the carbon-related gettering centers are point defects or their clusters.
Soft mode behavior in the orthorhombic to tetragonal transition in the high T
c superconductor YBa2Cu3O7−δ
Authors: Tallon J. L. , Schuitema A. H. , Tapp N. E.
Published: July 2002

The Young’s modulus and rigidity modulus of the high Tc superconductor YBa2Cu3O7−δ is measured from 300 to 1125 K using a 40-kHz ultrasonic resonant composite oscillator. Marked soft mode behavior occurs in both moduli in the vicinity of the orthorhombic to tetragonal transition, the softening being associated with orthorhombic shear fluctuations. The deep soft mode cusp allows the transition to be precisely determined as a function of oxygen partial pressure. A mechanical damping peak similar to that in Y-ZrO2 occurs at 800 K presumably arising from oxygen ion hopping.
Negative differential photoconductance in an alternately doped multiple quantum well structure
Authors: Choi K. K. , Levine B. F. , Bethea C. G. , Walker J. , Malik R. J.
Published: July 2002

We have measured the infrared photoconductivity of an alternately doped multiple quantum well structure. From this measurement, the density of the electrons dynamically stored in the undoped wells, which is critically important in the theory of tunneling, can be deduced at different external biases. A striking negative differential photoconductance feature is observed which is fully consistent with the theory of sequential tunneling.
High levels of Y-chromosome nucleotide diversity in the genusPan
Authors: Stone Anne C. , Griffiths Robert C. , Zegura Stephen L. , Hammer Michael F.
Published: July 2002

Although some mitochondrial, X chromosome, and autosomal sequence diversity data are available for our closest relatives,Pan troglodytesandPan paniscus, data from the nonrecombining portion of the Y chromosome (NRY) are more limited. We examined ≈3 kb of NRY DNA from 101 chimpanzees, seven bonobos, and 42 humans to investigate: (i) relative levels of intraspecific diversity; (ii) the degree of paternal lineage sorting among species and subspecies of the genusPan; and (iii) the date of the chimpanzee/bonobo divergence. We identified 10 informative sequence-tagged sites associated with 23 polymorphisms on the NRY from the genusPan. Nucleotide diversity was significantly higher on the NRY of chimpanzees and bonobos than on the human NRY. Similar to mtDNA, but unlike X-linked and autosomal loci, lineages defined by mutations on the NRY were not shared among subspecies ofP. troglodytes. Comparisons with mtDNAND2sequences from some of the same individuals revealed a larger female versus male effective population size for chimpanzees. The NRY-based divergence time between chimpanzees and bonobos was estimated at ≈1.8 million years ago. In contrast to human populations who appear to have had a low effective size and a recent origin with subsequent population growth, some taxa within the genusPanmay be characterized by large populations of relatively constant size, more ancient origins, and high levels of subdivision.
Functional p53 chimeras containing the Epstein–Barr virus Gly-Ala repeat are protected from Mdm2- and HPV-E6-induced proteolysis
Authors: Heessen Stijn , Leonchiks Ainars , Issaeva Natalia , Sharipo Anatoly , Selivanova Galina , Masucci Maria G. , Dantuma Nico P.
Published: July 2002

Functional inactivation of the tumor suppressor protein p53 by accelerated ubiquitin/proteasome-dependent proteolysis is a common event in tumor progression. Proteasomal degradation is inhibited by the Gly-Ala repeat (GAr) of the Epstein–Barr virus nuclear antigen-1, which acts as a transferable element on a variety of proteasomal substrates. We demonstrate that p53 chimeras containing GAr domains of different lengths and positions within the protein are protected from proteolysis induced by the ubiquitin ligases murine double minute 2 and E6-associated protein but are still ubiquitinated and retain the capacity to interact with the S5a ubiquitin-binding subunit of the proteasome. The GAr chimeras transactivate p53 target genes, induce cell cycle arrest and apoptosis, and exhibit improved growth inhibitory activity in tumor cells with impaired endogenous p53 activity.
Embryonic stem cells develop into functional dopaminergic neurons after transplantation in a Parkinson rat model
Authors: Björklund Lars M. , Sánchez-Pernaute Rosario , Chung Sangmi , Andersson Therese , Chen Iris Yin Ching , McNaught Kevin St. P. , Brownell Anna-Liisa , Jenkins Bruce G. , Wahlestedt Claes , Kim Kwang-Soo , Isacson Ole
Published: July 2002

Although implantation of fetal dopamine (DA) neurons can reduce parkinsonism in patients, current methods are rudimentary, and a reliable donor cell source is lacking. We show that transplanting low doses of undifferentiated mouse embryonic stem (ES) cells into the rat striatum results in a proliferation of ES cells into fully differentiated DA neurons. ES cell-derived DA neurons caused gradual and sustained behavioral restoration of DA-mediated motor asymmetry. Behavioral recovery paralleled
in vivo
positron emission tomography and functional magnetic resonance imaging data demonstrating DA-mediated hemodynamic changes in the striatum and associated brain circuitry. These results demonstrate that transplanted ES cells can develop spontaneously into DA neurons. Such DA neurons can restore cerebral function and behavior in an animal model of Parkinson's disease.
Locking in alternate conformations of the integrin αLβ2 I domain with disulfide bonds reveals functional relationships among integrin domains
Authors: Lu Chafen , Shimaoka Motomu , Zang Qun , Takagi Junichi , Springer Timothy A.
Published: July 2002

We used integrin αLβ2 heterodimers containing I domains locked open (active) or closed (inactive) with disulfide bonds to investigate regulatory interactions among domains in integrins. mAbs to the αL I domain and β2 I-like domain inhibit adhesion of wild-type αLβ2 to intercellular adhesion molecule-1. However, with αLβ2 containing a locked open I domain, mAbs to the I domain were subdivided into subsets (i) that did not inhibit, and thus appear to inhibit by favoring the closed conformation, and (ii) that did inhibit, and thus appear to bind to the ligand binding site. Furthermore, αLβ2 containing a locked open I domain was completely resistant to inhibition by mAbs to the β2 I-like domain, but became fully susceptible to inhibition after disulfide reduction with DTT. This finding suggests that the I-like domain indirectly contributes to ligand binding by regulating opening of the I domain in wild-type αLβ2. Conversely, locking the I domain closed partially restrained conformational change of the I-like domain by Mn2+, as measured with mAb m24, which we map here to the β2 I-like domain. By contrast, locking the I domain closed or open did not affect constitutive or Mn2+-induced exposure of the KIM127 epitope in the β2 stalk region. Furthermore, locked open I domains, in αLβ2 complexes or expressed in isolation on the cell surface, bound to intercellular adhesion molecule-1 equivalently in Mg2+and Mn2+. These results suggest that Mn2+activates αLβ2 by binding to a site other than the I domain, most likely the I-like domain of β2.
Analysis of MADS box protein–protein interactions in living plant cells
Authors: Immink Richard G. H. , Gadella Theodorus W. J. , Ferrario Silvia , Busscher Marco , Angenent Gerco C.
Published: July 2002

Over the last decade, the yeast two-hybrid system has become the tool to use for the identification of protein–protein interactions and recently, even complete interactomes were elucidated by this method. Nevertheless, it is an artificial system that is sensitive to errors resulting in the identification of false-positive and false-negative interactions. In this study, plant MADS box transcription factor interactions identified by yeast two-hybrid systems where studied in living plant cells by a technique based on fluorescence resonance energy transfer (FRET). Petunia MADS box proteins were fused to either cyan fluorescent protein or yellow fluorescent protein and transiently expressed in protoplasts followed by FRET-spectral imaging microscopy and FRET-fluorescence lifetime imaging microscopy to detect FRET and hence protein–protein interactions. All petunia MADS box heterodimers identified in yeast were confirmed in protoplasts. However, in contrast to the yeast two-hybrid results, homodimerization was demonstrated in plant cells for three petunia MADS box proteins. Heterodimers were identified between the ovule-specific MADS box protein FLORAL BINDING PROTEIN 11 and members of the petunia FLORAL BINDING PROTEIN 2 subfamily, which are also expressed in ovules, suggesting that these dimers play a role in ovule development. Furthermore, the role of dimerization in translocation of MADS box protein dimers to the nucleus is demonstrated, and the nuclear localization signal of MADS box proteins has been mapped to the N-terminal region of the MADS domain by means of mutant analyses.
HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors
Authors: Migueles Stephen A. , Sabbaghian M. Shirin , Shupert W. Lesley , Bettinotti Maria P. , Marincola Francesco M. , Martino Lisa , Hallahan Clair W. , Selig Sara M. , Schwartz David , Sullivan John , Connors Mark
Published: July 2002

A unique cohort of HIV-1-infected long term nonprogressors (LTNP) with normal CD4+T cell counts and <50 copies/ml of plasma were prospectively recruited for study. HLA typing revealed a dramatic association between the HLA B*5701 class I allele and nonprogressive infection [85% (11 of 13) vs. 9.5% (19 of 200) in progressors;P< 0.001]. Antigen-specific CD8+T cells were enumerated by flow cytometric detection of intracellular IFN-γ in response to HIV antigens and HLA B*57-gagtetramer staining. No quantitative differences in the total HIV-specific CD8+T cell responses were observed between B*57+LTNP and five B*57+progressors (P= 0.4). Although similar frequencies of peptide specific CD8+T cells were also found, thegag-specific CD8+T cell response in the LTNP group was highly focused on peptides previously shown to be B*57-restricted. These findings indicate that, within this phenotypically and genotypically distinct cohort, a host immune factor is highly associated with restriction of virus replication and nonprogressive disease. They also strongly suggest a mechanism of virus specific immunity that directly operates through the B*5701 molecule. Further characterization of qualitative differences in the virus-specific responses that distinguish HLA B*57+LTNP from progressors may ultimately define mechanisms of effective immune mediated restriction of virus replication.
Effects of elevated atmospheric CO
2
concentration on leaf dark respiration of
Xanthium strumarium
in light and in darkness
Authors: Wang Xianzhong , Lewis James D. , Tissue David T. , Seemann Jeffrey R. , Griffin Kevin L.
Published: July 2002

Leaf dark respiration (
R
) is an important component
of plant carbon balance, but the effects of rising atmospheric
CO
2
on leaf
R
during illumination are
largely unknown. We studied the effects of elevated CO
2
on
leaf
R
in light (
R
L
) and in
darkness (
R
D
) in
Xanthium
strumarium
at different developmental stages. Leaf
R
L
was estimated by using the Kok method,
whereas leaf
R
D
was measured as the rate of
CO
2
efflux at zero light. Leaf
R
L
and
R
D
were
significantly higher at elevated than at ambient CO
2
throughout the growing period. Elevated CO
2
increased the
ratio of leaf
R
L
to net photosynthesis at
saturated light (
A
max
) when plants were
young and also after flowering, but the ratio of leaf
R
D
to
A
max
was
unaffected by CO
2
levels. Leaf
R
N
was significantly higher at the beginning
but significantly lower at the end of the growing period in elevated
CO
2
-grown plants. The ratio of leaf
R
L
to
R
D
was used
to estimate the effect of light on leaf
R
during the
day. We found that light inhibited leaf
R
at both
CO
2
concentrations but to a lesser degree for elevated
(17–24%) than for ambient (29–35%) CO
2
-grown plants,
presumably because elevated CO
2
-grown plants had a higher
demand for energy and carbon skeletons than ambient
CO
2
-grown plants in light. Our results suggest that using
the CO
2
efflux rate, determined by shading leaves during
the day, as a measure for leaf
R
is likely to
underestimate carbon loss from elevated CO
2
-grown plants.
Estrogen increases synaptic connectivity between single presynaptic inputs and multiple postsynaptic CA1 pyramidal cells: A serial electron-microscopic study
Authors: Yankova Maya , Hart Sharron A. , Woolley Catherine S.
Published: July 2002

Dendritic spines are sites of the vast majority of excitatory
synaptic input to hippocampal CA1 pyramidal cells. Estrogen has been
shown to increase the density of dendritic spines on CA1 pyramidal cell
dendrites in adult female rats. In parallel with increased spine
density, estrogen has been shown also to increase the number of spine
synapses formed with multiple synapse boutons (MSBs). These findings
suggest that estrogen-induced dendritic spines form synaptic contacts
with preexisting presynaptic boutons, transforming some previously
single synapse boutons (SSBs) into MSBs. The goal of the current study
was to determine whether estrogen-induced MSBs form multiple synapses
with the same or different postsynaptic cells. To quantify same-cell
vs. different-cell MSBs, we filled individual CA1 pyramidal cells with
biocytin and serially reconstructed dendrites and dendritic spines of
the labeled cells, as well as presynaptic boutons in synaptic contact
with labeled and unlabeled (i.e., different-cell) spines. We found that
the overwhelming majority of MSBs in estrogen-treated animals form
synapses with more than one postsynaptic cell. Thus, in addition to
increasing the density of excitatory synaptic input to individual CA1
pyramidal cells, estrogen also increases the divergence of input from
individual presynaptic boutons to multiple postsynaptic CA1 pyramidal
cells. These findings suggest the formation of new synaptic connections
between previously unconnected hippocampal neurons.
Updating of the visual representation in monkey striate and extrastriate cortex during saccades
Authors: Nakamura Kae , Colby Carol L.
Published: July 2002

Neurons in the lateral intraparietal area, frontal eye field, and superior colliculus exhibit a pattern of activity known as remapping. When a salient visual stimulus is presented shortly before a saccade, the representation of that stimulus is updated, or remapped, at the time of the eye movement. This updating is presumably based on a corollary discharge of the eye movement command. To investigate whether visual areas also exhibit remapping, we recorded from single neurons in extrastriate and striate cortex while monkeys performed a saccade task. Around the time of the saccade, a visual stimulus was flashed either at the location occupied by the neuron's receptive field (RF) before the saccade (old RF) or at the location occupied by it after the saccade (new RF). More than half (52%) of V3A neurons responded to a stimulus flashed in the new RF even though the stimulus had already disappeared before the saccade. These neurons responded to a trace of the flashed stimulus brought into the RF by the saccade. In 16% of V3A neurons, remapped activity began even before saccade onset. Remapping also was observed at earlier stages of the visual hierarchy, including in areas V3 and V2. At these earlier stages, the proportion of neurons that exhibited remapping decreased, and the latency of remapped activity increased relative to saccade onset. Remapping was very rare in striate cortex. These results indicate that extrastriate visual areas are involved in the process of remapping.
Genome sequence and comparative microarray analysis of serotype M18 group A
Streptococcus
strains associated with acute rheumatic fever outbreaks
Authors: Smoot James C. , Barbian Kent D. , Van Gompel Jamie J. , Smoot Laura M. , Chaussee Michael S. , Sylva Gail L. , Sturdevant Daniel E. , Ricklefs Stacy M. , Porcella Stephen F. , Parkins Larye D. , Beres Stephen B. , Campbell David S. , Smith Todd M. , Zhang Qing , Kapur Vivek , Daly Judy A. , Veasy L. George , Musser James M.
Published: July 2002

Acute rheumatic fever (ARF), a sequelae of group A
Streptococcus
(GAS) infection, is the most common cause of preventable childhood heart disease worldwide. The molecular basis of ARF and the subsequent rheumatic heart disease are poorly understood. Serotype M18 GAS strains have been associated for decades with ARF outbreaks in the U.S. As a first step toward gaining new insight into ARF pathogenesis, we sequenced the genome of strain MGAS8232, a serotype M18 organism isolated from a patient with ARF. The genome is a circular chromosome of 1,895,017 bp, and it shares 1.7 Mb of closely related genetic material with strain SF370 (a sequenced serotype M1 strain). Strain MGAS8232 has 178 ORFs absent in SF370. Phages, phage-like elements, and insertion sequences are the major sources of variation between the genomes. The genomes of strain MGAS8232 and SF370 encode many of the same proven or putative virulence factors. Importantly, strain MGAS8232 has genes encoding many additional secreted proteins involved in human–GAS interactions, including streptococcal pyrogenic exotoxin A (scarlet fever toxin) and two uncharacterized pyrogenic exotoxin homologues, all phage-associated. DNA microarray analysis of 36 serotype M18 strains from diverse localities showed that most regions of variation were phages or phage-like elements. Two epidemics of ARF occurring 12 years apart in Salt Lake City, UT, were caused by serotype M18 strains that were genetically identical, or nearly so. Our analysis provides a critical foundation for accelerated research into ARF pathogenesis and a molecular framework to study the plasticity of GAS genomes.
Antigen polymorphism in
Borrelia hermsii
, a clonal pathogenic bacterium
Authors: Rich Stephen M. , Sawyer Stanley A. , Barbour Alan G.
Published: July 2002

The relapsing fever spirochete,
Borrelia hermsii
,
escapes immune selection by alternating expression of surface
lipoprotein alleles. The switch results from a duplicative
transposition of one of several surface lipoprotein-encoding nucleotide
sequences into the singular expression site. These nucleotide sequences
constitute a large gene family whose diversity originated, in
some cases, before the major divergences of
Borrelia
species. We have examined the
B. hermsii vsp
subfamily
of alleles, which are carried on linear plasmids within each cell and
maintained in several diverse copies as an antigenic archive. Each
encodes a distinct serotype-specific protein. We sequenced more than
90% of the alleles within a single strain—
B. hermsii
strain HS1. A preponderance of allelic mosaicism suggests that
intragenic recombination, coupled with selection imposed by host immune
response, has driven diversification of the archived ensemble of
vsp
alleles. The recombinational diversification of
vsp
alleles generates change in the associated serotypes
of the magnitude (30–40% amino acid differentiation) necessary for
overcoming cross-reactivity of neutralizing antibodies. We conclude
that evolution of
vsp
has occurred by punctuated
occurrence of allelic differentiation, rather than by gradual selection
of incremental point mutations that do not meet the threshold for
antigenic diversity.
Interactions that determine the assembly of a retinoid X receptor/corepressor complex
Authors: Ghosh Jagadish C. , Yang Xiaofang , Zhang Aihua , Lambert Millard H. , Li Hui , Xu H. Eric , Chen J. Don
Published: July 2002

The retinoid X receptor (RXR) is a key regulator in multiple signaling pathways because it can form either a homodimer with itself or a heterodimer with members of the class I nuclear receptors. The RXR-containing dimers regulate transcription by recruiting coactivators or corepressors to the target promoters. The binding of coactivators to RXR is mediated through a hydrophobic pocket formed in part by the C-terminal activation helix (AF-2). However, little is known about interactions of corepressors with RXR and its roles in transcriptional repression. Here we show that the repression activity of RXR correlates with its binding to the corepressor silencing mediator for retinoid and thyroid hormone receptors (SMRT). This intrinsic repression activity is masked by the AF-2 helix, which antagonizes SMRT binding. Inhibition of SMRT binding by the AF-2 helix requires specific amino acid sequences and the helical structure. Furthermore, the SMRT-binding site on RXR is independent of helix 11 but overlaps with the coactivator-binding pocket. On the basis of these results, we propose a structural model to help understand the molecular mechanism of corepressor recruitment by RXR.
Loss of speciation rate will impoverish future diversity
Authors: Rosenzweig Michael L.
Published: July 2002

Human activities have greatly reduced the amount of the earth's area available to wild species. As the area they have left declines, so will their rates of speciation. This loss of speciation will occur for two reasons: species with larger geographical ranges speciate faster; and loss of area drives up extinction rates, thus reducing the number of species available for speciation. Theory predicts steady states in species diversity, and fossils suggest that these have typified life for most of the past 500 million years. Modern and fossil evidence indicates that, at the scale of the whole earth and its major biogeographical provinces, those steady states respond linearly, or nearly so, to available area. Hence, a loss ofx% of area will produce a loss of aboutx% of species. Local samples of habitats merely echo the diversity available in the whole province of which they are a part. So, conservation tactics that rely on remnant patches to preserve diversity cannot succeed for long. Instead, diversity will decay to a depauperate steady state in two phases. The first will involve deterministic extinctions, reflecting the loss of all areas in which a species can ordinarily sustain its demographics. The second will be stochastic, reflecting accidents brought on by global warming, new diseases, and commingling the species of the separate bio-provinces. A new kind of conservation effort, reconciliation ecology, can avoid this decay. Reconciliation ecology discovers how to modify and diversify anthropogenic habitats so that they harbor a wide variety of species. It develops management techniques that allow humans to share their geographical range with wild species.
Phosphorylation and microtubule association of the Opitz syndrome protein mid-1 is regulated by protein phosphatase 2A via binding to the regulatory subunit α4
Authors: Liu Jun , Prickett Todd D. , Elliott Elizabeth , Meroni Germana , Brautigan David L.
Published: July 2002

Opitz syndrome (OS) is a human genetic disease characterized by deformities such as cleft palate that are attributable to defects in embryonic development at the midline. Gene mapping has identified OS mutations within a protein called Mid1. Wild-type Mid1 predominantly colocalizes with microtubules, in contrast to mutant versions of Mid1 that appear clustered in the cytosol. Using yeast two-hybrid screening, we found that the α4-subunit of protein phosphatases 2A/4/6 binds Mid1. Epitope-tagged α4 coimmunoprecipitated endogenous or coexpressed Mid1 from COS7 cells, and this required only the conserved C-terminal region of α4. Localization of Mid1 and α4 was influenced by one another in transiently transfected cells. Mid1 could recruit α4 onto microtubules, and high levels of α4 could displace Mid1 into the cytosol. Metabolic32P labeling of cells showed that Mid1 is a phosphoprotein, and coexpression of full-length α4 decreased Mid1 phosphorylation, indicative of a functional interaction. Association of green fluorescent protein–Mid1 with microtubules in living cells was perturbed by inhibitors of MAP kinase activation. The conclusion is that Mid1 association with microtubules, which seems important for normal midline development, is regulated by dynamic phosphorylation involving MAP kinase and protein phosphatase that is targeted specifically to Mid1 by α4. Human birth defects may result from environmental or genetic disruption of this regulatory cycle.
p38 is essential for the assembly and stability of macromolecular tRNA synthetase complex: Implications for its physiological significance
Authors: Kim Jin Young , Kang Young-Sun , Lee Joong-Won , Kim Hyoung June , Ahn Young Ha , Park Heonyong , Ko Young-Gyu , Kim Sunghoon
Published: July 2002

Mammalian tRNA synthetases form a macromolecular complex with three nonenzyme factors: p43, p38, and p18. Here we introduced a mutation within the mouse p38 gene to understand its functional significance for the formation of the multi-tRNA synthetase complex. The complex was completely disintegrated by the deficiency of p38. In addition, the protein levels and catalytic activities of the component enzymes and cofactors were severely decreased. A partial truncation of the p38 polypeptide separated the associated components into different subdomains. The mutant mice showed lethality within 2 days of birth. Thus, this work provides the first evidence, to our knowledge, that p38 is essential for the structural integrity of the multi-tRNA synthetase complex and mouse viability.
Criteria for the control of drug-resistant tuberculosis
Authors: Dye Christopher , Williams Brian G.
Published: July 2002

Antibiotic resistance is a growing impediment to the control of infectious diseases worldwide, tuberculosis (TB) being among them. TB kills two million people each year and foci of multidrug-resistant TB (MDR-TB) have been identified in Eastern Europe, Africa, Asia, and Latin America. A critical question for health policy is whether standardized short-course chemotherapy for TB, based on cheap first-line drugs, can prevent and reverse the spread of drug resistance. Here we use mathematical modeling, in conjunction with treatment results from six countries, to show that best-practice short-course chemotherapy is highly likely to bring strains resistant to either of the two key drugs isoniazid and rifampicin under control and to prevent the emergence of MDR-TB. However, it is not certain to contain MDR-TB once it has emerged, partly because cure rates are too low. We estimate that approximately 70% of prevalent, infectious MDR-TB cases should be detected and treated each year, and at least 80% of these cases should be cured, in order to prevent outbreaks of MDR-TB. Poor control programs should aim to increase case detection and cure rates together for three reasons: (
i
) these variables act synergistically; (
ii
) when either is low, the other cannot succeed alone; and (
iii
) the second-line drugs needed to raise MDR-TB cure rates are few and extremely costly. We discuss the implications of these results for World Health Organization policy on the management of antibiotic resistance.
Cytochrome
c
′ folding triggered by electron transfer: Fast and slow formation of four-helix bundles
Authors: Lee Jennifer C. , Gray Harry B. , Winkler Jay R.
Published: July 2002

Reduced (Fe
II
)
Rhodopseudomonas palustris
cytochrome
c
′ (Cyt
c
′) is more stable toward unfolding ([GuHCl]
1/2
= 2.9(1) M) than the oxidized (Fe
III
) protein ([GuHCl]
1/2
= 1.9(1) M). The difference in folding free energies (ΔΔG
f
° = 70 meV) is less than half of the difference in reduction potentials of the folded protein (100 mV vs. NHE) and a free heme in aqueous solution (≈−150 mV). The spectroscopic features of unfolded Fe
II
–Cyt
c
′ indicate a low-spin heme that is axially coordinated to methionine sulfur (Met-15 or Met-25). Time-resolved absorption measurements after CO photodissociation from unfolded Fe
II
(CO)–Cyt
c
′ confirm that methionine can bind to the ferroheme on the microsecond time scale [
k
obs
= 5(2) × 10
4
s
−1
]. Protein folding was initiated by photoreduction (two-photon laser excitation of NADH) of unfolded Fe
III
–Cyt
c
′ ([GuHCl] = 2.02–2.54 M). Folding kinetics monitored by heme absorption span a wide time range and are highly heterogeneous; there are fast-folding (≈10
3
s
−1
), intermediate-folding (10
2
–10
1
s
−1
), and slow-folding (10
−1
s
−1
) populations, with the last two likely containing methionine-ligated (Met-15 or Met-25) ferrohemes. Kinetics after photoreduction of unfolded Fe
III
–Cyt
c
′ in the presence of CO are attributable to CO binding [1.4(6) × 10
3
s
−1
] and Fe
II
(CO)–Cyt
c
′ folding [2.8(9) s
−1
] processes; stopped-flow triggered folding of Fe
III
–Cyt
c
′ (which does not contain a protein-derived sixth ligand) is adequately described by a single kinetics phase with an estimated folding time constant of ≈4 ms [ΔG
f
° = −33(3) kJ mol
−1
] at zero denaturant.
Functional analysis of an olfactory receptor in
Drosophila melanogaster
Authors: Störtkuhl Klemens F. , Kettler Raffael
Published: July 2002

Fifty nine candidate olfactory receptor (Or) genes have recently been identified in
Drosophila melanogaster
, one of which is Or43a. In wild-type flies, Or43a is expressed at the distal edge of the third antennal segment in about 15 Or neurons. To identify ligands for the receptor we used the Gal4/UAS system to misexpress Or43a in the third antennal segment. Or43a mRNA expression in the antenna of transformed and wild-type flies was visualized by
in situ
hybridization with a digoxigenin-labeled probe. Electroantennogram recordings from transformed and wild-type flies were used to identify cyclohexanol, cyclohexanone, benzaldehyde, and benzyl alcohol as ligands for the Or43a. This
in vivo
analysis reveals functional properties of one member of the recently isolated Or family in
Drosophila
and will provide further insight into our understanding of olfactory coding.
Neurotrophin-3 promotes the cholinergic differentiation of sympathetic neurons
Authors: Brodski Claude , Schnürch Harald , Dechant Georg
Published: July 2002

Neurotrophins influence the epigenetic shaping of the vertebrate nervous system by regulating neuronal numbers during development and synaptic plasticity. Here we attempt to determine whether these growth factors can also regulate neurotransmitter plasticity. As a model system we used the selection between noradrenergic and cholinergic neurotransmission by paravertebral sympathetic neurons. Developing sympathetic neurons express the neurotrophin receptors TrkA and TrkC, two highly related receptor tyrosine kinases. Whereas the TrkA ligand nerve growth factor (NGF) has long been known to regulate both the survival and the expression of noradrenergic traits in sympathetic neurons, the role of TrkC and of its ligand neurotrophin-3 (NT3) has remained unclear. We found that TrkC expression in the avian sympathetic chain overlaps substantially with that of choline acetyltransferase. In sympathetic chain explants, transcripts of the cholinergic marker genes choline acetyltransferase and vasoactive intestinal polypeptide were strongly enriched in the presence of NT3 compared with NGF, whereas the noradrenergic markers tyrosine hydroxylase and norepinephrine transporter were reduced. The transcription factor chicken achaete scute homolog 1 was coexpressed with cholinergic markers. The effects of NT3 are reversed and antagonized by NGF. They are independent of neuronal survival and developmentally regulated. These results suggest a role for NT3 as a differentiation factor for cholinergic neurons and establish a link between neurotrophins and neurotransmitter plasticity.
Mechanism of termination of DNA replication of
Escherichia coli
involves helicase–contrahelicase interaction
Authors: Mulugu Sashidhar , Potnis Aardra , Shamsuzzaman  , Taylor Jeffery , Alexander Ken , Bastia Deepak
Published: July 2002

Using yeast forward and reverse two-hybrid analyses, we have
discovered that the replication terminator protein Tus of
Escherichia coli
physically interacts with DnaB helicase
in vivo
. We have confirmed this protein–protein
interaction
in vitro
. We show further that replication
termination involves protein–protein interaction between Tus and DnaB
at a critical region of Tus protein, called the L1 loop. Several
mutations located in the L1 loop region not only reduced the
protein–protein interaction but also eliminated or reduced the ability
of the mutant forms of Tus to arrest DnaB at a
Ter
site.
At least one mutation, E49K, significantly reduced Tus–DnaB
interaction and almost completely eliminated the contrahelicase
activity of Tus protein
in vitro
without significantly
reducing the affinity of the mutant form of Tus for
Ter
DNA, in comparison with the wild-type protein. The results, considered
along with the crystal structure of Tus–
Ter
complex,
not only elucidate further the mechanism of helicase arrest but also
explain the molecular basis of polarity of replication fork arrest at
Ter
sites.
Calcium-triggered acrosomal exocytosis in human spermatozoa requires the coordinated activation of Rab3A and
N
-ethylmaleimide-sensitive factor
Authors: Michaut M. , Tomes C. N. , De Blas G. , Yunes R. , Mayorga L. S.
Published: July 2002

The acrosome reaction of spermatozoa is a complex, calcium-dependent, regulated exocytosis. Fusion at multiple sites between the outer acrosomal membrane and the cell membrane causes the release of the acrosomal contents and the loss of the membranes surrounding the acrosome. However, very little is known about the molecules that mediate and regulate this unique fusion process. Here, we show that
N
-ethylmaleimide-sensitive factor (NSF), a protein essential for most fusion events, is present in the acrosome of several mammalian spermatozoa. Moreover, we demonstrate that calcium-dependent exocytosis of permeabilized sperm requires active NSF. Previously, we have shown that the addition of the active (GTP-bound) form of the small GTPase Rab3A triggers exocytosis in permeabilized spermatozoa. In the present report we show that Rab3A is necessary for calcium-dependent exocytosis. The activation of Rab3A protects NSF from
N
-ethylmaleimide inhibition and precludes the exchange of the endogenous protein with recombinant dominant negative mutants of NSF. Furthermore, Rab3A activation of acrosomal exocytosis requires active NSF. Our results suggest that, upon calcium stimulation, Rab3A switches to its active GTP-bound form, triggering the formation of a protein complex in which NSF is protected. This process is suggested to be an essential part of the molecular mechanism of membrane fusion leading to the release of the acrosomal contents.
Remotely sensed habitat diversity predicts butterfly species richness and community similarity in Canada
Authors: Kerr Jeremy T. , Southwood T. R. E. , Cihlar Josef
Published: July 2002

Although there is no shortage of potential explanations for the
large-scale patterns of biological diversity, the hypothesis that
energy-related factors are the primary determinants is perhaps most
extensively supported, especially in cold-temperate regions. By using
unusually high-resolution biodiversity and environmental data that have
not previously been available, we demonstrate that habitat
heterogeneity, as measured by remotely sensed land cover variation,
explains Canadian butterfly richness better than any energy-related
variable we measured across spatial scales. Although species-richness
predictability declines with progressively smaller quadrat sizes, as
expected, we demonstrate that most variability (>90%) in butterfly
richness may be explained by habitat heterogeneity with secondary
contributions from climatic energy. We also find that patterns of
community similarity across Canada are strongly related to patterns of
habitat composition but not to differences in energy-related factors.
Energy should still be considered significant but its main role may be
through its effects on within-habitat diversity and perhaps,
indirectly, on the sorts of habitats that may be found in a region.
Effects of sampling intensity and spatial autocorrelation do not alter
our findings.