bluuebunny/crossref_metadata_2025 huggingface dataset:
High-power operation of InP/InGaAsP double-channel planar buried-heterostructure lasers with asymmetric facet coatings
Authors: Koszi L. A. , Temkin H. , Pryzbylek G. J. , Segner B. P. , Napholtz S. G. , Bogdanowicz C. M. , Dutta N. K.
Published: July 2002

We report the high-power operation of λ=1.3 μm InGaAsP double-channel planar buried-heterostructure lasers with asymmetric mirror coatings. A stack of four dielectric layers is used to raise the reflectivity of one facet to over 80%, and the thickness of a single layer coating on the output facet is chosen to reduce the reflectivity to about 4%. The resulting lasers are characterized by a low threshold current of 25 mA, slope efficiency as high as 50%, and a power output of as much as 150 mW (at 5 °C) at a current of less than 300 mA. The lasers operate in a single transverse mode over the entire current range and as much as 45 mW of power could be coupled into a lensed single-mode fiber. Preliminary high-power aging data show excellent device reliability.
Improved optical switching extinction in three-electrode Ti:LiNbO3 directional couplers
Authors: Choquette K. D. , McCaughan L. , Smith Wiley K.
Published: July 2002

Utilizing three electrodes and three independent voltages in Ti:LiNbO3 directional coupler optical switches, we have achieved significant improvements in switching extinction over the standard uniform Δβ configuration. The reductions in optical crosstalk vary from 3 to 24 dB for both switching states of several fabricated devices. We have observed a bar state extinction of −47.8 dB, which is the largest extinction ratio reported to date. We find that switching measurements are limited by the largest contrast ratio which can be obtained in the optical waveguides.
Solid phase doping of silicon with boron by surface scanning with cw CO2 laser radiation
Authors: Ursu I. , Crăciun V. , Mihăilescu I. N. , Medianu R. , Popa Al. , Prokhorov A. M. , Kiyak S. G. , Manenkov A. A. , Mikhailova G. N.
Published: July 2002

Silicon doping with boron was achieved by cw CO2 laser radiation surface scanning of n-Si wafers (≊10 Ω cm) vacuum coated with a thin (∼100 Å) film of boron, both from the boron-coated and from the uncoated sides. Electrical and secondary ion mass spectrometry measurements indicate that the dopant is electrically active and the p-n junctions which are formed are very shallow (<500 Å). The values of sheet resistance versus junction depth are below any results reported in the literature.
Remote gate capacitance-voltage studies for noninvasive surface characterization
Authors: Chang R. R. , Lile D. L. , Gann R.
Published: July 2002

A measurement technique has been developed which allows noncontact capacitance-voltage measurements to be made using a gate electrode located remote from the semiconductor surface under study. With gate electrodes ∼0.5 mm in diameter and gate to semiconductor separations ∼1500 Å we have been able to generate data entirely comparable to that obtained with integrated metal-insulator-semiconductor structures but with the advantage that we have access directly to the free-semiconductor surface. We have applied this technique to bulk single-crystal Si and InP samples and have been able to determine the effects of varying chemical treatments on the surface trap densities of the free surface. H2O2, for example, has been shown to create a poor InP surface whereas NRL etchant has yielded a surface seemingly quite close to the ideal.
Unidirectional anisotropy in surface magnetism of amorphous GdCo
Authors: Bona G. L. , Meier F. , Siegmann H. C. , Gambino R. J.
Published: July 2002

Surface magnetization curves measured by spin-polarized photoemission show the presence of unidirectional anisotropy at low temperatures causing a displacement of the hysteresis loops along the external field axis. In addition, wall pinning has been observed which also depends on the direction of the applied field.
Comment on ‘‘New evidence of small lattice relaxation for the D
X center in AlxGa1−xAs’’ [Appl. Phys. Lett. 5
1, 1358 (1987)]
Authors: Yu Peter Y. , Li Ming-fu
Published: July 2002

Deep level transient spectroscopy has been performed on the DX center in the Ga0.65Al0.35As:Te as a function of pressure. The lattice relaxation we observed showed that the results of Talwar et al. (small lattice relaxation) are inconsistent and inconclusive. Our results significantly weaken their evidence in favor of small lattice relaxation. (AIP)
Optoelectronic bistability in gallium phosphide
Authors: Choi Mun S. , Hur J. H. , Gundersen Martin A.
Published: July 2002

An optoelectronic bistability in GaP is reported. The bistable mechanism which is based on trap filling is discussed, and possible applications are described. This simple bistable device can be realized using a commercial light-emitting diode.
Dual wavelength CO2-N2-CS2 gasdynamic laser
Authors: Reddy K. P. J.
Published: July 2002

A new method for producing simultaneous lasing at 10.6 μm and 38.3 μm in a CO2-N2-CS2 gasdynamic laser is presented. The theoretical analysis predicts small-signal gain values of the order 0.21 m−1 for 10.6 μm lasing in CO2 molecules and 0.085 m−1 for 38.3 μm lasing in CS2 molecules, indicating the possibility of dual wave lasing.
Thickness dependence of strains in strained-layer superlattices
Authors: Shahzad K. , Olego D. J. , Cammack D. A.
Published: July 2002

We present a photoluminescence study of ZnSe-ZnSxSe1−x strained-layer superlattices (SLS’s) grown on 1-μm-thick ZnSe buffer layers using GaAs substrates. The total thickness D of SLS was varied from ∼0.1 to ∼4.6 μm to monitor the behavior of the planar biaxially compressive strains in the ZnSe well layers. We find that SLS’s can exist in a continuous range from a perfectly coherent state to a totally free-standing state as D increases, with these planar strains in the ZnSe layers increasing from almost zero to ∼0.4%. In addition, we also observe clear strain effects produced by the SLS’s on the buffer layers.
Spatial light modulators using charge-coupled-device addressing and electroabsorption effects in GaAs/AlGaAs multiple quantum wells
Authors: Nichols K. B. , Burke B. E. , Aull B. F. , Goodhue W. D. , Gramstorff B. F. , Hoyt C. D. , Vera A.
Published: July 2002

We describe the fabrication and performance of the first spatial light modulators (SLM’s) which combine addressing in AlGaAs charge-coupled devices (CCD’s) and electroabsorption effects in GaAs/AlGaAs multiple quantum wells (MQW’s). One-dimensional, sixteen-stage, three-phase AlGaAs CCD’s with semitransparent gates were fabricated on the surface of the SLM. The optical signal propagates normal to the surface and enters the SLM through the gates. The transmission of this signal through the MQW is then modulated according to the channel voltage of the CCD’s. The maximum contrast ratio at 847 nm was measured to be 1.45:1 for these GaAs/AlGaAs -based SLM’s.
Signal and white noise properties of edge junction dc SQUID’s
Authors: Wakai R. T. , Van Harlingen D. J.
Published: July 2002

We have fabricated and characterized the noise performance of submicron edge junction dc superconducting quantum interference devices (SQUID’s) which exhibit excellent signal properties and extremely high flux sensitivity. At frequencies above about 3 MHz, the SQUID noise is white and is in reasonable agreement with computer simulations for a thermal noise-limited detector. In one device the measured flux energy resolution is 1.6±0.5ℏ at 1.5 K, within a factor of 2 of the quantum-limited value suggested by theoretical modeling.
Time-resolved measurement of space charge in polymeric material under prebreakdown ac field
Authors: Lebey T. , Laurent C. , Sarlaboux J.
Published: July 2002

The buildup of space charge following carrier injection under a prebreakdown field is often considered as a possible degradation process of a polymeric material. The energy released during trapping (phonons and photons) might be at the origin of bond breaking, even if the details of this process are not completely elucidated. Space-charge formation is of particular importance during ac stressing, since the nature of the trapped charge depends on stress polarity. We present in the following a very sensitive and new experimental setup that allows for the first time the analog, time-resolved measurement of trapped charge during ac polarization at high field in a dielectric material.
High-power seven-element grating surface emitting diode laser array with 0.012° far-field angle
Authors: Carlson N. W. , Evans G. A. , Hammer J. M. , Lurie M. , Carr L. A. , Hawrylo F. Z. , James E. A. , Kaiser C. J. , Kirk J. B. , Reichert W. F. , Truxal D. A. , Shealy J. R. , Chinn S. R. , Zory P. S.
Published: July 2002

A coherent seven-element grating surface emitting diode laser array with a predominant single-lobe far-field pattern having an angular divergence of 0.012° has been demonstrated. The extent of the emitting aperture was 4 mm, and the beam divergence was within 10% of the diffraction limit. Under pulsed operation the array had a peak output power of over 400 mW and a differential quantum efficiency of 15%.
Reduced photoinduced degradation in chemical vapor deposited hydrogenated amorphous silicon films
Authors: Chu T. L. , Chu Shirley S. , Bylander E. G. , Ang S. T.
Published: July 2002

Hydrogenated amorphous silicon (a-Si:H) films prepared by the thermal decomposition of disilane in a He atmosphere [chemical vapor deposition (CVD)] contain 3–4% hydrogen, considerably less than the hydrogen content in a-Si:H films prepared by glow discharge (GD). The CVD a-Si:H films have been irradiated for up to 175 h at 500 and 600 mW/cm2 using a quartz-halogen lamp. The defect density in CVD a-Si:H films is estimated to approach saturation at mid 1016 cm−3 from an initial defect density of less than 6×1015 cm−3, whereas the typical defect density at saturation is greater than 1018 cm−3 for GD a-Si:H films. The significantly reduced Staebler–Wronski effect in CVD a-Si:H films is attributed to the lower concentration of clustered hydrogen atoms or silicon–hydrogen bonds.
Chemically etched micromirrors in silicon
Authors: Kendall D. L. , de Guel G. R. , Guel-Sandoval S. , Garcia E. J. , Allen T. A.
Published: July 2002

Purposely introduced pinholes can be processed so as to produce nearly spherical or paraboloidal depressions in (100) silicon by a two-step chemical etching procedure in KOH:water solutions. Regular arrays of f/1–f/10 specularly reflecting micromirrors can be fabricated.
30 ps cavity-dumped pulses from an argon laser
Authors: Harvey J. D. , Proctor M. J. , Steed C. A.
Published: July 2002

The pulse characteristics of a mode-locked cavity-dumped argon laser have been investigated by autocorrelation of the pulses using two photon fluorescence, and (when operating at a 13 ns repetition rate) by cross correlation with a synchronously pumped dye laser. The system has been found to yield remarkably short duration pulses. In cavity-dumped operation at a repetition rate of 3.8 MHz, the laser generates pulses of approximately 30 ps duration and 2.5 kW peak power. It is suggested that the increased bandwidth of this laser compared with that of conventional mode-locked systems derives from self-phase modulation in the silica block of the cavity dumper.
Universal presence of saturable nonradiative currents in six types of 1.3 μm buried heterostructure lasers
Authors: LaCourse Joanne , Olshansky Robert
Published: July 2002

Measurement of the carrier lifetime below threshold reveals that the saturable nonradiative current reported previously for 1.3 μm vapor-phase-regrowth buried heterostructure lasers is a widespread problem in 1.3 μm InGaAsP buried heterostructure lasers. The saturable nonradiative current represents 10%–30% of the threshold current for most geometries and about 6% for buried crescent lasers. This nonradiative current is also responsible for low spontaneous output at very low currents.
Ion-induced epitaxial growth of chemical vapor deposited Si layers
Authors: La Ferla A. , Rimini E. , Ferla G.
Published: July 2002

Thin layers of Si were chemical vapor deposited onto as-received 〈100〉 p-type Si wafers. The samples were subsequently implanted with 1×1015/cm2, 80 keV As. The native oxide film impedes the growth even at 800 °C, 1 h; instead irradiation with 600 keV Kr++ at 450 °C causes the epitaxial growth of the entire deposited and amorphized Si layer. The sheet resistance of these As-doped layers (130 Ω/⧠) coincides with that of samples in which the amorphous layer was obtained by As ion implantation only. The value is at least ten times lower than that of the polycrystalline layer doped with the same amount of As.
High-efficiency, laser grooved, buried contact silicon solar cells
Authors: Chong Chee Mun , Wenham Stuart R. , Green Martin A.
Published: July 2002

Improvements in the performance of silicon solar cells based on a novel, laser grooved, buried contact approach are described. Independently confirmed energy conversion efficiencies as high as 19.8% are reported for cells of 12 cm2 area, as are the resistivity dependence of efficiency, spectral response data, and the results of laser beam induced current scans. The potential for further improvement is also discussed.
Determination of pairwise interaction potential parameters from a double scattering experiment
Authors: Hetterich W. , Derks H. , Heiland W.
Published: July 2002

The backscattering of K+ from an Ir(110) surface is used to determine the parameters of the screening function of the interaction potential. The energy range used (from 0.3 to 6 keV) corresponds to a potential range from 10 to 4000 eV. In the case studied the J. F. Ziegler, J. P. Biersack, U. Littmark [Stopping Powers and Ranges of Ions in Matter, edited by J. F. Ziegler (Pergamon, New York, 1985)] (ZBL) universal screening function gives a better fit to the experiment than the G. Molière [Z. Naturf. 2a, 133 (1947)] screening function.
Structure and electrical properties of TiN/GaAs Schottky contacts
Authors: Ding J. , Liliental-Weber Z. , Weber E. R. , Washburn J. , Fourkas R. M. , Cheung N. W.
Published: July 2002

The interface structure and morphology of TiN/GaAs contacts before and after annealing at 500, 700, and 850 °C have been investigated by transmission electron microscopy. Results reveal that pocket-like protrusions are formed beneath the interface after annealing at 500 °C. These pockets increased in number and maximum size with increased annealing temperature. Outdiffusion of Ga and/or As along high angle grain boundaries between columnar structure of the as-deposited TiN thin film has been proposed as being responsible for the pocket formation. The changes of electrical characteristics of these materials after annealing have been related to the formation of these pockets.
Stationary chaotic states in linear magnetohydrodynamic generators
Authors: Simpson S. W. , Schmidt-Harms C. A.
Published: July 2002

In linear magnetohydrodynamic generators operating with a slag layer coating the electrode walls, highly nonuniform electrical characteristics are often observed. It is proposed that the voltage patterns in these channels are an example of chaos in a discrete spatial system. An idealized model is presented, based on the Hall effect and nonlinear resistance in the slag layer. The model, which correctly predicts observed features, exhibits complex chaotic behavior.
Charge state controlled short- and long-range defect motions in GaAs
Authors: Kamada H. , Ando K.
Published: July 2002

We report the charge state dependent annealing reactions for a defect (H2, 0.4 eV) in p-type GaAs following room-temperature electron irradiation. Using deep level transient spectroscopy, it is shown that one of two absolutely different defect reaction branches is chosen depending on the junction bias condition. The ranges of defect motion involved in these two reactions are markedly different: When the H2 center is emptied of hole it disappears near room temperature by several defect jumps to the near neighbor sites, whereas when it is occupied with hole it annihilates at 370–380 K by long-range defect motion. The observed defect motions are well described by the simple charge state effect upon the defect which has two distinct reaction branches.
Distributed feedback laser line narrowing with external fiber resonators
Authors: Fuchs M. , Hoppe W.
Published: July 2002

A simple distributed feedback (DFB) laser line narrowing arrangement consisting of an adapted coupler and a cleaved fiber end resonator has been realized. Linewidths below 100 kHz have been obtained for different commercial 1300 nm and 1550 nm DFB lasers.
Molecular beam epitaxial GaAs optical detectors on silica fibers
Authors: Li Wei-Qi , Chin Albert , Bhattacharya Pallab , DiVita S.
Published: July 2002

By using molecular beam epitaxy and post-growth annealing techniques, we have successfully made GaAs interdigitated photoconductive detectors on D-shaped silica fibers. The detectors exhibit low leakage current and internal photoconductive gains of up to 15 are measured. To our knowledge this is the first realization of active III-V optoelectronic devices on fibers and opens up the possibility of realizing optoelectronic integration and circuits directly on fibers.
Specific lattice location of Zn in CdTe determined by ion-channeling methods
Authors: Haga T. , Suzuki H. , Rashid M. H. , Abe Y. , Tanaka A.
Published: July 2002

The specific lattice location of Zn in CdTe single crystals has been investigated by ion-channeling methods combined with particle-induced x-ray emission. Observing the asymmetry effects of channeling dips around the [110] axis and analyzing the asymmetry factors for host atoms and doped Zn atoms, it is revealed that almost all Zn atoms occupy the Cd sublattice sites, and Zn-doped CdTe crystals grown by vertical Bridgman methods appear to be almost completely free from the segregation of doped Zn atoms.
Interaction of an electron beam with CdCl2 thin films
Authors: Bloch J. , Shamir N. , Zeiri Y.
Published: July 2002

The effect of electron irradiation on CdCl2 thin films was studied using Auger and electron loss spectroscopies. It was found that coloration takes place together with a reduction of the Cl/Cd intensity ratio. The loss spectrum is also changed during irradiation. It was shown that the irradiation-induced changes can diffuse out of the irradiated area.
Release of As from SiO2 by a temperature gradient and formation of buried n+ conductive layers in Si-on-SiO2 structures
Authors: Celler G. K. , Trimble L. E.
Published: July 2002

We demonstrate the utility of a temperature gradient ∇T in transporting dopants, such as As, unidirectionally through SiO2 and into Si. The transport, based on thermomigration of dopant-rich precipitates toward the heat source, turns oxide into an efficient diffusion source. It also provides the only possible method of forming buried n+ conductive layers in recrystallized, thick Si-on-SiO2 structures. To build such structures, arsenic is implanted into the oxide, where it remains trapped during deposition of polycrystalline Si and its recrystallization from the melt, but is subsequently released into the Si film by a directional drift in the ∇T. In the future, controlling dopant transport with two independent parameters (temperature and ∇T), instead of the temperature alone, may allow processing of three-dimensional circuits at higher temperatures than would be otherwise possible.
Mode-locked and Q-switched operation of a diode laser pumped Nd:YAG laser operating at 1.064 μm
Authors: Maker G. T. , Keen S. J. , Ferguson A. I.
Published: July 2002

We describe the performance of a mode-locked and Q-switched Nd:YAG laser operating at 1.064 μm, optically pumped by a 500 mW diode laser. The cw mode-locked system provides bandwidth-limited pulses of 55 ps duration, with a corresponding peak power of 3.3 W. When Q-switched the energy within the 100 ns pulse envelope is 10 μJ giving a peak power in the largest pulse of 7 kW. Preliminary results for operation at 1.32 μm are also reported.
Significantly extended analytical potential of Rutherford backscattering spectrometry by i
n s
i
t
u combination with low-energy sputtering
Authors: Wittmaack K. , Menzel N.
Published: July 2002

We have assembled a dual-beam system which allows solid samples to be analyzed by Rutherford backscattering spectrometry (RBS) at deliberately chosen stages of in situ sputter etching by low-energy ion bombardment. Using the novel setup we demonstrate that, for a large variety of samples, the analytical potential of conventional RBS can be extended remarkably. Apart from the obvious possibility of increasing the accessible depth of analysis, three specific advantages are illustrated: (i) removal of the interference between the signals due to buried dopants and a (low-mass) substrate, (ii) decoupling of the mass and the energy scale, and (iii) high-resolution depth analysis of deep-lying structures (glancing angle RBS) with the ability to circumvent the problems usually associated with sputter-related mixing effects.
Adhesion and deformation study of metal/polymer structures by a stretch deformation method
Authors: Ho P. S. , Faupel F.
Published: July 2002

A stretch deformation method has been developed for quantitative study of adhesion and deformation of metal/polymer structures. The adhesion energy is directly measured from the difference in the load versus elongation curves between film/substrate and substrate structures. This method has been applied to study structures formed with Cu, Cr, and Cu/Cr deposited on pyromellitic dianhydride-oxydianiline polyimide. The importance of crack formation in the metal layer for initiating interfacial delamination is demonstrated.
Detection of dilute iron impurities in CdTe
Authors: Bowman R. C. , Cooper Donald E.
Published: July 2002

CdTe single crystals from several sources have been examined to detect the presence of impurities which may be detrimental to applications in the fabrication of IR detectors. Distinctive electron paramagnetic resonance (EPR) signals from several donor impurities, including substitutional paramagnetic Fe, were found in several samples. A photoluminescence (PL) transition at 1.1 eV was also seen in these crystals and the amplitudes of the PL signals and the Fe EPR signals are strongly correlated. Elemental analysis of the samples indicates that EPR and PL are able to detect Fe concentrations of less than 0.1 ppm.
Diffraction-limited-beam, high-power operation from X-junction coupled phase-locked arrays of AlGaAs/GaAs diode lasers
Authors: Botez D. , Hayashida P. , Mawst L. J. , Roth T. J.
Published: July 2002

A novel type of phase-locked array is demonstrated. The device is a ten-element AlGaAs/GaAs array with both evanescent wave coupling as well as coupling via X-type junctions. The array selects and maintains operation in the highest order array mode of a ten-element device: mode L=10. Threshold currents are ∼300 mA. Diffraction-limited-beam operation is achieved to 2.8×threshold and ∼200 mW (front facet of devices with optimized facet coatings). The beam lobewidths remain under 1.5×diffraction limit to 6.3×threshold and 300 mW (both facets of uncoated devices). Near-field intensity patterns confirm the intrinsic stability of high-order array modes against gain spatial hole burning.
Experimental test of the transition layer model of atomic layer epitaxy
Authors: Juza P. , Sitter H. , Herman M. A.
Published: July 2002

Thermal desorption experiments concerning Te deposits on GaAs (100) surfaces have been performed using quadrupole mass spectrometry. The results give evidence that near the GaAs surface two regions of different Te adsorption can be distinguished. The first region nearest to the substrate surface consists of Te adparticles, which are chemisorbed to the substrate reevaporating at temperatures above 510–520 °C. The adparticles of the second physisorbed region begin to desorb at 350–360 °C, which is still considerably higher than the desorption temperature of the bulk Te deposits. The approximate thicknesses of these two regions are 1–2 monolayers and 3–10 monolayers of Te, respectively.
Importance of epidermal growth factor receptor signaling in establishment of adenomas and maintenance of carcinomas during intestinal tumorigenesis
Authors: Roberts Reade B. , Min Lu , Washington M. Kay , Olsen Sandra J. , Settle Stephen H. , Coffey Robert J. , Threadgill David W.
Published: July 2002

We used the hypomorphic
Egfr

wa2

allele to genetically examine the impact of impaired epidermal growth factor receptor (Egfr) signaling on the
Apc

Min

mouse model of familial adenomatous polyposis. Transfer of the
Apc

Min

allele onto a homozygous
Egfr

wa2

background results in a 90% reduction in intestinal polyp number relative to
Apc

Min

mice carrying a wild-type
Egfr
allele. This
Egfr
effect is potentially synergistic with the actions of the modifier-of-min (
Mom1
) locus. Surprisingly, the size, expansion, and pathological progression of the polyps appear Egfr-independent. Histological examination of the ilea of younger animals revealed no differences in the number of microadenomas, the presumptive precursor lesions to gross intestinal polyps. Pharmacological inhibition with EKI-785, an Egfr tyrosine kinase inhibitor, produced similar results in the
Apc

Min

model. These data suggest that normal Egfr activity is required for establishment of intestinal tumors in the
Apc

Min

model between initiation and subsequent expansion of initiated tumors. The role of Egfr signaling during later stages of tumorigenesis was examined by using nude mice xenografts of two human colorectal cancer cell lines. Treatment with EKI-785 produced a dose-dependent reduction in tumor growth, suggesting that Egfr inhibitors may be useful for advanced colorectal cancer treatment.
Uncoating ATPase Hsc70 is recruited by invariant chain and controls the size of endocytic compartments
Authors: Lagaudrière-Gesbert Cécile , Newmyer Sherri L. , Gregers Tone F. , Bakke Oddmund , Ploegh Hidde L.
Published: July 2002

Targeting of class II major histocompatibility complex molecules to endocytic compartments is mediated by their association with the invariant chain (Ii). Although the identity of certain sorting signals located in Ii's cytoplasmic tail is known, proteins that interact with Ii's cytoplasmic tail in living cells remain to be identified. Synthesis of a biotinylated trimeric Ii cytoplasmic tail allowed the retrieval of two proteins that interact with this domain. We identify one of them as the 70-kDa heat-shock cognate protein (hsc70), the uncoating ATPase of clathrin-coated vesicles, and the other as its mitochondrial homologue, the glucose-regulated protein grp75. Expression of Ii in COS cells results in the formation of large endocytic compartments. We observe extensive colocalization of hsc70 with Ii in these macrosomes. Expression of a dominant-negative (K71M) green fluorescent protein-tagged version of hsc70 counteracted the ability of Ii to modify the endocytic pathway, demonstrating an interactionin vivoof Ii with hsc70 as part of the machinery responsible for macrosome formation.
Fit genotypes and escape variants of subgroup III
Neisseria meningitidis
during three pandemics of epidemic meningitis
Authors: Zhu Peixuan , van der Ende Arie , Falush Daniel , Brieske Norbert , Morelli Giovanna , Linz Bodo , Popovic Tanja , Schuurman Ilse G. A. , Adegbola Richard A. , Zurth Kerstin , Gagneux Sébastien , Platonov Alexander E. , Riou Jean-Yves , Caugant Dominique A. , Nicolas Pierre , Achtman Mark
Published: July 2002

The genetic variability at six polymorphic loci was examined within
a global collection of 502 isolates of subgroup III, serogroup A
Neisseria meningitidis.
Nine “genoclouds” were
identified, consisting of genotypes that were isolated repeatedly plus
48 descendent genotypes that were isolated rarely. These genoclouds
have caused three pandemic waves of disease since the mid-1960s, the
most recent of which was imported from East Asia to Europe and Africa
in the mid-1990s. Many of the genotypes are escape variants, resulting
from positive selection that we attribute to herd immunity. Despite
positive selection, most escape variants are less fit than their
parents and are lost because of competition and bottlenecks during
spread from country to country. Competition between fit genotypes
results in dramatic changes in population composition over short time
periods.
Galactosides in the rhizosphere: Utilization by
Sinorhizobium meliloti
and development of a biosensor
Authors: Bringhurst Ryan M. , Cardon Zoe G. , Gage Daniel J.
Published: July 2002

Identifying the types and distributions of organic substrates that
support microbial activities around plant roots is essential for a full
understanding of plant–microbe interactions and rhizosphere ecology.
We have constructed a strain of the soil bacterium
Sinorhizobium
meliloti
containing a
gfp
gene fused to the
melA
promoter which is induced on exposure to galactose
and galactosides. We used the fusion strain as a biosensor to determine
that galactosides are released from the seeds of several different
legume species during germination and are also released from roots of
alfalfa seedlings growing on artificial medium. Galactoside presence in
seed wash and sterile root washes was confirmed by HPLC. Experiments
examining microbial growth on α-galactosides in seed wash suggested
that α-galactoside utilization could play an important role in
supporting growth of
S. meliloti
near germinating seeds
of alfalfa. When inoculated into microcosms containing legumes or
grasses, the biosensor allowed us to visualize the localized presence
of galactosides on and around roots in unsterilized soil, as well as
the grazing of fluorescent bacteria by protozoa. Galactosides were
present in patches around zones of lateral root initiation and around
roots hairs, but not around root tips. Such biosensors can reveal
intriguing aspects of the environment and the physiology of the
free-living soil
S. meliloti
before and during the
establishment of nodulation, and they provide a nondestructive,
spatially explicit method for examining rhizosphere soil chemical
composition.
Activation of mislocalized opsin kills rod cells: A novel mechanism for rod cell death in retinal disease
Authors: Alfinito Peter D. , Townes-Anderson Ellen
Published: July 2002

Rod photoreceptors are highly compartmentalized sensory neurons that maintain strict ultrastructural and molecular polarity. Structural subdivisions include the outer segment, inner segment, cell body, and synaptic terminal. The visual pigment rhodopsin is found predominantly in membranes of the rod cell outer segment but becomes mislocalized, appearing throughout the plasma membrane of the cell in many retinal diseases and injuries. Currently, there is no known link between rhodopsin redistribution and rod cell death. We propose that activation of mislocalized rhodopsin kills rod cells by stimulating normally inaccessible signaling pathways. This hypothesis was tested in primary retinal cell cultures, which contain photoreceptors. In rod photoreceptors, opsin immunofluorescence occurred throughout the rod cell plasma membrane. Activation of this mislocalized opsin by photostimulation after formation of isorhodopsin or by incubation with β-ionone (opsin agonist) killed 19–30% of rod cells. Rod cell death was apoptotic, as indicated by marked chromatin condensation and the requirement for caspase-3 activation. Rod cell death could be induced by forskolin (adenylate cyclase agonist), and conversely, β-ionone-induced cell death could be blocked by cotreatment with SQ22536 (an adenylate cyclase inhibitor). Pertussis toxin (a G protein inhibitor) also blocked β-ionone-induced cell death. The data support a mechanism by which activation of mislocalized opsin initiates apoptotic rod cell death through G protein stimulation of adenylate cyclase.
Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates
Authors: Zhang Jianzhi , Rosenberg Helene F.
Published: July 2002

An improved understanding of the evolution of gene function at the molecular level may provide significant insights into the origin of biological novelty and adaptation. With the approach of ancestral protein reconstruction, we here address the question of how a dramatically enhanced ribonucleolytic activity and the related antiviral activity evolved in a recently duplicated ribonuclease (eosinophil-derived neurotoxin) gene of higher primates. We show that the mother gene of the duplicated genes had already possessed a weak antiviral activity before duplication. After duplication, substitutions at two interacting sites (Arg-64→Ser and Thr-132→Arg) resulted in a 13-fold enhancement of the ribonucleolytic activity of eosinophil-derived neurotoxin. These substitutions are also necessary for the potent antiviral activity, with contributions from additional amino acid changes at interacting sites. Our observation that a change in eosinophil-derived neurotoxin function occurs only when both interacting sites are altered indicates the importance of complementary substitutions in protein evolution. Thus, neutral substitutions are not simply “noises” in protein evolution, as many have thought. They may play constructive roles by setting the intramolecular microenvironment for further complementary advantageous substitutions, which can lead to improved or altered function. Overall, our study illustrates the power of the “paleomolecular biochemistry” approach in delineating the complex interplays of amino acid substitutions in evolution and in identifying the molecular basis of biological innovation.
Characterization of a
Plasmodium falciparum
erythrocyte-binding protein paralogous to EBA-175
Authors: Mayer D. C. Ghislaine , Kaneko Osamu , Hudson-Taylor Diana E. , Reid Marion E. , Miller Louis H.
Published: July 2002

A member of a
Plasmodium
receptor family for
erythrocyte invasion was identified on chromosome 13 from the
Plasmodium falciparum
genome sequence of the Sanger
Centre (Cambridge, U.K.). The protein (named BAEBL) has homology to
EBA-175, a
P. falciparum
receptor that binds
specifically to sialic acid and the peptide backbone of glycophorin A
on erythrocytes. Both EBA-175 and BAEBL localize to the micronemes,
organelles at the invasive ends of the parasites that contain other
members of the family. Like EBA-175, the erythrocyte receptor for BAEBL
is destroyed by neuraminidase and trypsin, indicating that the
erythrocyte receptor is a sialoglycoprotein. Its specificity, however,
differs from that of EBA-175 in that BAEBL can bind to erythrocytes
that lack glycophorin A, the receptor for EBA-175. It has reduced
binding to erythrocytes with the Gerbich mutation found in another
erythrocyte, sialoglycoprotein (glycophorin C/D). The interest in
BAEBL's reduced binding to Gerbich erythrocytes derives from the high
frequency of the Gerbich phenotype in some regions of Papua New Guinea
where
P. falciparum
is hyperendemic.
Mutator clones of
Neisseria meningitidis
in epidemic serogroup A disease
Authors: Richardson Anthony R. , Yu Zhong , Popovic Tanja , Stojiljkovic Igor
Published: July 2002

Serogroup A
Neisseria meningitidis
has repeatedly caused widespread epidemics of meningitis and septicemia throughout the 20th century. Recently, in a limited collection of strains, epidemic serogroup A isolates were found to have elevated mutation rates that was caused by defects in mismatch repair pathways. To ascertain the role of these mutators in the epidemic spread of this serogroup, the prevalence of hypermutability in a collection of 95 serogroup A
N. meningitidis
invasive isolates was determined. Overall mutability in Neisseriae can be described by measuring both missense mutation rates as well as phase variation frequencies of “contingency loci.” Fifty-seven percent of serogroup A isolates possessed elevated mutability, which could be divided into two classes: intermediate and high level. Eleven of 20 high-level mutators, with phase variation rates >100-fold higher than wild-type isolates, were defective in mismatch repair. Ten of the 34 intermediate mutators possessing >10-fold increases in phase variation rates could be partially complemented by a wild-type
mutL
allele. A high prevalence of mutators in epidemic isolates indicates that hypermutability may play a major role in the transmission of this pathogen. The added diversity derived from increased phase variation rates may allow fixation of mutator alleles more frequently during epidemic spread.
Rapid plant diversification: Planning for an evolutionary future
Authors: Cowling R. M. , Pressey R. L.
Published: July 2002

Systematic conservation planning is a branch of conservation
biology that seeks to identify spatially explicit options for the
preservation of biodiversity. Alternative systems of conservation areas
are predictions about effective ways of promoting the persistence of
biodiversity; therefore, they should consider not only biodiversity
pattern but also the ecological and evolutionary processes that
maintain and generate species. Most research and application, however,
has focused on pattern representation only. This paper outlines the
development of a conservation system designed to preserve biodiversity
pattern and process in the context of a rapidly changing environment.
The study area is the Cape Floristic Region (CFR), a biodiversity
hotspot of global significance, located in southwestern Africa. This
region has experienced rapid (post-Pliocene) ecological diversification
of many plant lineages; there are numerous genera with large clusters
of closely related species (flocks) that have subdivided habitats at a
very fine scale. The challenge is to design conservation systems that
will preserve both the pattern of large numbers of species and various
natural processes, including the potential for lineage turnover. We
outline an approach for designing a system of conservation areas to
incorporate the spatial components of the evolutionary processes that
maintain and generate biodiversity in the CFR. We discuss the
difficulty of assessing the requirements for pattern versus process
representation in the face of ongoing threats to biodiversity, the
difficulty of testing the predictions of alternative conservation
systems, and the widespread need in conservation planning to
incorporate and set targets for the spatial components (or surrogates)
of processes.
The
Cia5
gene controls formation of the carbon concentrating mechanism in
Chlamydomonas reinhardtii
Authors: Xiang Youbin , Zhang Jun , Weeks Donald P.
Published: July 2002

Wild-type
Chlamydomonas reinhardtii
cells shifted
from high concentrations (5%) of CO
2
to low, ambient
levels (0.03%) rapidly increase transcription of mRNAs from several
CO
2
-responsive genes. Simultaneously, they develop a
functional carbon concentrating mechanism that allows the cells to
greatly increase internal levels of CO
2
and
HCO

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. The
cia5
mutant is defective in
all of these phenotypes. A newly isolated gene, designated
Cia5
, restores transformed
cia5
cells to
the phenotype of wild-type cells. The 6,481-bp gene produces a 5.1-kb
mRNA that is present constitutively in light in high and low
CO
2
both in wild-type cells and the
cia5
mutant. It encodes a protein that has features of a putative
transcription factor and that, likewise, is present constitutively in
low and high CO
2
conditions. Complementation of
cia5
can be achieved with a truncated
Cia5
gene that is missing the coding information for 54
C-terminal amino acids. Unlike wild-type cells or
cia5
mutants transformed with an intact
Cia5
gene,
cia5
mutants complemented with the truncated gene
exhibit constitutive synthesis of mRNAs from CO
2
-responsive
genes in light under both high and low CO
2
conditions.
These discoveries suggest that posttranslational changes to the
C-terminal domain control the ability of CIA5 to act as an inducer and
directly or indirectly control transcription of
CO
2
-responsive genes. Thus, CIA5 appears to be a master
regulator of the carbon concentrating mechanism and is intimately
involved in the signal transduction mechanism that senses and allows
immediate responses to fluctuations in environmental CO
2
and HCO

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concentrations.
Decoupled evolution of coding region and mRNA expression patterns after gene duplication: Implications for the neutralist-selectionist debate
Authors: Wagner Andreas
Published: July 2002

The neutralist perspective on molecular evolution maintains that the vast majority of mutations affecting gene function are neutral or deleterious. After a gene duplication where both genes are retained, it predicts that original and duplicate genes diverge at clock-like rates. This prediction is usually tested for coding sequences, but can also be applied to another important aspect of gene function, the genes' expression pattern. Moreover, if both sequence and expression pattern diverge at clock-like rates, a correlation between divergence in sequence and divergence in expression patterns is expected. Duplicate gene pairs with more highly diverged sequences should also show more highly diverged expression patterns. This prediction is tested for a large sample of duplicated genes in the yeast
Saccharomyces cerevisiae
, using both genome sequence and microarray expression data. Only a weak correlation is observed, suggesting that coding sequence and mRNA expression patterns of duplicate gene pairs evolve independently and at vastly different rates. Implications of this finding for the neutralist–selectionist debate are discussed.
Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation
Authors: McGlynn Peter , Lloyd Robert G.
Published: July 2002

Modification of damaged replication forks is emerging as a crucial factor for efficient chromosomal duplication and the avoidance of genetic instability. The RecG helicase of
Escherichia coli
, which is involved in recombination and DNA repair, has been postulated to act on stalled replication forks to promote replication restart via the formation of a four-stranded (Holliday) junction. Here we show that RecG can actively unwind the leading and lagging strand arms of model replication fork structures
in vitro
. Unwinding is achieved in each case by simultaneous interaction with and translocation along both the leading and lagging strand templates at a fork. Disruption of either of these interactions dramatically inhibits unwinding of the opposing duplex arm. Thus, RecG translocates simultaneously along two DNA strands, one with 5′-3′ and the other with 3′-5′ polarity. The unwinding of both nascent strands at a damaged fork, and their subsequent annealing to form a Holliday junction, may explain the ability of RecG to promote replication restart. Moreover, the preferential binding of partial forks lacking a leading strand suggests that RecG may have the ability to target stalled replication intermediates
in vivo
in which lagging strand synthesis has continued beyond the leading strand.
An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images
Authors: Miao Jianwei , Hodgson Keith O. , Sayre David
Published: July 2002

We describe an approach to the high-resolution
three-dimensional structural determination of macromolecules that
utilizes ultrashort, intense x-ray pulses to record diffraction data in
combination with direct phase retrieval by the oversampling technique.
It is shown that a simulated molecular diffraction pattern at 2.5-Å
resolution accumulated from multiple copies of single rubisco
biomolecules, each generated by a femtosecond-level x-ray free electron
laser pulse, can be successfully phased and transformed into an
accurate electron density map comparable to that obtained by more
conventional methods. The phase problem is solved by using an iterative
algorithm with a random phase set as an initial input. The convergence
speed of the algorithm is reasonably fast, typically around a few
hundred iterations. This approach and phasing method do not require any
ab initio
information about the molecule, do not require an
extended ordered lattice array, and can tolerate high noise and some
missing intensity data at the center of the diffraction pattern. With
the prospects of the x-ray free electron lasers, this approach could
provide a major new opportunity for the high-resolution
three-dimensional structure determination of single biomolecules.
Ullrich scleroatonic muscular dystrophy is caused by recessive mutations in collagen type VI
Authors: Camacho Vanegas Olga , Bertini Enrico , Zhang Rui-Zhu , Petrini Stefania , Minosse Claudia , Sabatelli Patrizia , Giusti Betti , Chu Mon-Li , Pepe Guglielmina
Published: July 2002

Ullrich syndrome is a recessive congenital muscular dystrophy affecting connective tissue and muscle. The molecular basis is unknown. Reverse transcription–PCR amplification performed on RNA extracted from fibroblasts or muscle of three Ullrich patients followed by heteroduplex analysis displayed heteroduplexes in one of the three genes coding for collagen type VI (COL6). In patient A, we detected a homozygous insertion of a C leading to a premature termination codon in the triple-helical domain of COL6A2 mRNA. Both healthy consanguineous parents were carriers. In patient B, we found a deletion of 28 nucleotides because of an A → G substitution at nucleotide −2 of intron 17 causing the activation of a cryptic acceptor site inside exon 18. The second mutation was an exon skipping because of a G → A substitution at nucleotide −1 of intron 23. Both mutations are present in an affected brother. The first mutation is also present in the healthy mother, whereas the second mutation is carried by their healthy father. In patient C, we found only one mutation so far—the same deletion of 28 nucleotides found in patient B. In this case, it was a
de novo
mutation, as it is absent in her parents. mRNA and protein analysis of patient B showed very low amounts of COL6A2 mRNA and of COL6. A near total absence of COL6 was demonstrated by immunofluorescence in fibroblasts and muscle. Our results demonstrate that Ullrich syndrome is caused by recessive mutations leading to a severe reduction of COL6.
Distinct functions and cooperative interaction of the subunits of the transporter associated with antigen processing (TAP)
Authors: Karttunen Jaana T. , Lehner Paul J. , Gupta Soma Sen , Hewitt Eric W. , Cresswell Peter
Published: July 2002

The ATP-binding cassette (ABC) transporter TAP translocates peptides from the cytosol to awaiting MHC class I molecules in the endoplasmic reticulum. TAP is made up of the TAP1 and TAP2 polypeptides, which each possess a nucleotide binding domain (NBD). However, the role of ATP in peptide binding and translocation is poorly understood. We present biochemical and functional evidence that the NBDs of TAP1 and TAP2 are non-equivalent. Photolabeling experiments with 8-azido-ATP demonstrate a cooperative interaction between the two NBDs that can be stimulated by peptide. The substitution of key lysine residues in the Walker A motifs of TAP1 and TAP2 suggests that TAP1-mediated ATP hydrolysis is not essential for peptide translocation but that TAP2-mediated ATP hydrolysis is critical, not only for translocation, but for peptide binding.