bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal Structure of an Iron-Dependent Group III Dehydrogenase That Interconvertsl-Lactaldehyde andl-1,2-Propanediol inEscherichia coli
Authors: Montella Cristina , Bellsolell Lluis , Pérez-Luque Rosa , Badía Josefa , Baldoma Laura , Coll Miquel , Aguilar Juan 
Published: July 2005

ABSTRACTThe FucO protein, a member of the group III “iron-activated” dehydrogenases, catalyzes the interconversion betweenl-lactaldehyde andl-1,2-propanediol inEscherichia coli. The three-dimensional structure of FucO in a complex with NAD+was solved, and the presence of iron in the crystals was confirmed by X-ray fluorescence. The FucO structure presented here is the first structure for a member of the group III bacterial dehydrogenases shown experimentally to contain iron. FucO forms a dimer, in which each monomer folds into an α/β dinucleotide-binding N-terminal domain and an all-α-helix C-terminal domain that are separated by a deep cleft. The dimer is formed by the swapping (between monomers) of the first chain of the β-sheet. The binding site for Fe2+is located at the face of the cleft formed by the C-terminal domain, where the metal ion is tetrahedrally coordinated by three histidine residues (His200, His263, and His277) and an aspartate residue (Asp196). The glycine-rich turn formed by residues 96 to 98 and the following α-helix is part of the NAD+recognition locus common in dehydrogenases. Site-directed mutagenesis and enzyme kinetic assays were performed to assess the role of different residues in metal, cofactor, and substrate binding. In contrast to previous assumptions, the essential His267 residue does not interact with the metal ion. Asp39 appears to be the key residue for discriminating against NADP+. Modelingl-1,2-propanediol in the active center resulted in a close approach of the C-1 hydroxyl of the substrate to C-4 of the nicotinamide ring, implying that there is a typical metal-dependent dehydrogenation catalytic mechanism.
PhoR1-PhoP1, a Third Two-Component System of the Family PhoRP from
Myxococcus xanthus
: Role in Development
Authors: Carrero-Lérida Juana , Moraleda-Muñoz Aurelio , García-Hernández Raquel , Pérez Juana , Muñoz-Dorado José 
Published: July 2005

ABSTRACT

The pair PhoR1-PhoP1 is the third two-component system of the family PhoRP reported in
M. xanthus
. PhoR1 is a histidine kinase anchored to the membrane through a transmembrane domain located in the amino-terminal portion of the protein. As a result, 93% of the protein is located in the cytoplasm. This topology is unusual in the PhoR-type histidine kinases. PhoP1 is a response regulator with a helix-loop-helix motif typical of the DNA-binding proteins. Although the operon
phoPR1
is expressed during vegetative growth, it peaks during development. The expression levels of this operon are higher in phosphate-containing media than in those in which the nutrient is absent. A deletion mutant in this system exhibits a delay in aggregation and the formation of fruiting bodies larger than those of the wild-type strain. The expression of the operon is autoregulated. This system is also partially responsible for the expression of Mg-independent acid and neutral phosphatases, but it is not required for the expression of alkaline phosphatases.
Extrachromosomal DNA of the SymbiontSodalis glossinidius
Authors: Darby A. C. , Lagnel J. , Matthew C. Z. , Bourtzis K. , Maudlin I. , Welburn S. C. 
Published: July 2005

ABSTRACTThe extrachromosomal DNA ofSodalis glossinidiusfrom two tsetse fly species was sequenced and contained four circular elements: three plasmids, pSG1 (82 kb), pSG2 (27 kb), and pSG4 (11 kb), and a bacteriophage-like pSG3 (19 kb) element. The information suggestsS. glossinidiusis evolving towards an obligate association with tsetse flies.
Functional and Topological Analysis of the
Burkholderia cenocepacia
Priming Glucosyltransferase BceB, Involved in the Biosynthesis of the Cepacian Exopolysaccharide
Authors: Videira Paula A. , Garcia Abbner P. , Sá-Correia Isabel 
Published: July 2005

ABSTRACT

The BceB protein of the cystic fibrosis mucoid isolate
Burkholderia cenocepacia
IST432 is proposed to catalyze the first step of the exopolysaccharide repeat unit assembly. Extracts of
Escherichia coli
cells overexpressing BceB were shown to contain glycosyltransferase activity and mediate incorporation of glucose-1-phosphate into membrane lipids. The amino acid sequence of BceB exhibits two conserved regions, one comprising two invariant aspartic acid residues (Asp339 and Asp355) that are essential for catalysis, as substantiated by site-directed mutagenesis, and the other comprising a putative Rossmann fold motif. The results of protein topology analysis using PhoA and LacZ fusions supported in silico predictions that BceB has at least six transmembrane segments and two major cytoplasmic loops comprising the conserved regions described above.
The Gene Encoding the Glutamate Dehydrogenase in
Lactococcus lactis
Is Part of a Remnant Tn
3
Transposon Carried by a Large Plasmid
Authors: Tanous Catherine , Chambellon Emilie , Sepulchre Anne-Marie , Yvon Mireille 
Published: July 2005

ABSTRACT

The gene responsible for the uncommon glutamate dehydrogenase (GDH) activity of
Lactococcus lactis
was identified and characterized. It encodes a GDH of family I that is mainly active in glutamate biosynthesis, is carried by a large plasmid, and is included, with functional cadmium resistance genes, in a remnant Tn
3
-like transposon.
EspC Is Involved in Controlling the Timing of Development in
Myxococcus xanthus
Authors: Lee Bongsoo , Higgs Penelope I. , Zusman David R. , Cho Kyungyun 
Published: July 2005

ABSTRACT

The
espC
null mutation caused accelerated aggregation and formation of tiny fruiting bodies surrounded by spores, which were also observed in the
espA
mutant and in CsgA-overproducing cells in
Myxococcus xanthus
. In addition, the
espC
mutant appeared to produce larger amounts of the complementary C-signal than the wild-type strain. These findings suggest that EspC is involved in controlling the timing of fruiting body development in
M. xanthus.
Identification of
nlmTE
, the Locus Encoding the ABC Transport System Required for Export of Nonlantibiotic Mutacins in
Streptococcus mutans
Authors: Hale John D. F. , Heng Nicholas C. K. , Jack Ralph W. , Tagg John R. 
Published: July 2005

ABSTRACT

Streptococcus mutans
UA159, the genome sequence reference strain, exhibits nonlantibiotic bacteriocin (mutacin) activity. In this study, we have combined bioinformatic and mutational analyses to identify the ABC transporter designated NlmTE, which is required for mutacin biogenesis in strain UA159 as well as in another mutacin producer,
S. mutans
N.
Equine Infectious Anemia Virus Gag p9 Function in Early Steps of Virus Infection and Provirus Production
Authors: Jin Sha , Chen Chaoping , Montelaro Ronald C. 
Published: July 2005

ABSTRACT

We have previously reported that serial truncation of the Gag p9 protein of equine infectious anemia virus (EIAV) revealed a progressive loss in replication phenotypes in transfected cells, such that a proviral mutant (E32) expressing the N-terminal 31 amino acids of p9 produced infectious virus particles similarly to parental provirus, while a proviral mutant (K30) with two fewer amino acids produced replication-defective virus particles, despite containing apparently normal levels of processed Gag and Pol proteins (C. Chen, F. Li, and R. C. Montelaro, J. Virol.
75:
9762-9760, 2001). Based on these observations, we sought in the current study to identify the precise defect in K30 virion infection of permissive equine dermal (ED) cells. The results of these experiments clearly demonstrated that K30 virions entered target ED cells and produced early (minus-strand strong-stop) and late (Gag) viral DNA products as efficiently as did the replication-competent E32 mutant and parental EIAV
UK
viruses. However, in contrast to the replication-competent E32 mutant and parental viruses, infection with K30 mutant virus failed to produce detectable two-long-terminal-repeat DNA circles, stable integrated provirus, virus-specific Gag mRNA expression, or intracellular viral protein expression. Taken together, these data demonstrate that the K30 mutant is defective in the ability to produce sufficient nuclear viral DNA to establish a productive infection in ED cells. Thus, these observations indicate for the first time that the EIAV Gag p9 protein performs a critical role in viral DNA production and processing to provirus during EIAV infection, in addition to its previously defined role in viral budding mediated by the p9 L domain.
Plant Virus HC-Pro Is a Determinant of Eriophyid Mite Transmission
Authors: Stenger Drake C. , Hein Gary L. , Gildow Frederick E. , Horken Kempton M. , French Roy 
Published: July 2005

ABSTRACTThe eriophyid mite transmittedWheat streak mosaic virus(WSMV; genusTritimovirus, familyPotyviridae) shares a common genome organization with aphid transmitted species of the genusPotyvirus. Although both tritimoviruses and potyviruses encode helper component-proteinase (HC-Pro) homologues (required for nonpersistent aphid transmission of potyviruses), sequence conservation is low (amino acid identity, ∼16%), and a role for HC-Pro in semipersistent transmission of WSMV by the wheat curl mite (Aceria tosichella[Keifer]) has not been investigated. Wheat curl mite transmissibility was abolished by replacement of WSMV HC-Pro with homologues of an aphid transmitted potyvirus (Turnip mosaic virus), a rymovirus (Agropyron mosaic virus) vectored by a different eriophyid mite, or a closely related tritimovirus (Oat necrotic mottle virus; ONMV) with no known vector. In contrast, both WSMV-Sidney 81 and a chimeric WSMV genome bearing HC-Pro of a divergent strain (WSMV-El Batán 3; 86% amino acid sequence identity) were efficiently transmitted byA. tosichella. Replacing portions of WSMV-Sidney 81 HC-Pro with the corresponding regions from ONMV showed that determinants of wheat curl mite transmission map to the 5′-proximal half of HC-Pro. WSMV genomes bearing HC-Pro of heterologous species retained the ability to form virions, indicating that loss of vector transmissibility was not a result of failure to encapsidate. Although titer in systemically infected leaves was reduced for all chimeric genomes relative to WSMV-Sidney 81, titer was not correlated with loss of vector transmissibility. Collectively, these results demonstrate for the first time that HC-Pro is required for virus transmission by a vector other than aphids.
Essential and Nonessential Elements in the 3′ Nontranslated Region of Bovine Viral Diarrhea Virus
Authors: Pankraz Alexander , Thiel Heinz-Jürgen , Becher Paul 
Published: July 2005

ABSTRACT

The 3′ nontranslated region (NTR) of the pestivirus
Bovine viral diarrhea virus
(BVDV), a close relative of human
Hepatitis C virus
, consists of three stem-loops which are separated by two single-stranded regions. As in other positive-stranded RNA viruses, the 3′ NTR of pestiviruses is involved in crucial processes of the viral life cycle. While several studies characterized
cis
-acting elements within the 3′ NTR of a BVDV replicon, there are no studies addressing the significance of these elements in the context of a replicating virus. To examine the functional importance of 3′ NTR elements, a set of 4-base deletions and deletions of each of the three stem-loops were introduced into an infectious BVDV cDNA clone. Emerging mutant viruses were characterized with regard to plaque phenotype, growth kinetics, and synthesis of viral RNA. The results indicated that presence of stem-loop (SL) I and the 3′-terminal part of the single-stranded region between stem-loops I and II are indispensable for pestiviral replication. In contrast, deletions within SL II and SL III as well as absence of either SL II or SL III still allowed efficient viral replication; however, a mutant RNA lacking both SL II and SL III was not infectious. The results of this study provide a detailed map of the essential and nonessential elements within the 3′ NTR of BVDV and contribute to our understanding of sequence and structural elements important for efficient viral replication of pestiviruses in natural host cells.
Basic Study to Develop Biosensors Using Surface Acoustic Waves
Authors: Kim Gi-Beum , Chong Woo-Suk , Kwon Tae-Kyu , Hohkawa Kohji , Hong Chul-Un , Kim Nam-Gyun 
Published: July 2005

In this paper, we present a study of the bonding between piezoelectric substrates and semiconductor materials. We have studied [O. S. Wolfbesis: Fiber Optic Chemical Sensors and Biosensors, 1st ed. (CRC Press, Boca Raton, 1991) p. 21.] the surface state (hydrophilic) of GaAs, LiNbO3 and quartz substrates after different treatments methods [R. Hughes, A. Ricco, M. Butler and S. Martin: Science 254 (1991) 74.], the effects of migration of water molecules out of bonding surfaces induced by microwave and laser radiation. When Pb(Mg1/3Nb2/3)O3-PbTiO3 (PMN-PT) is used as a piezoelectric material, we have evaluated if PMN-PT can be made practically available for a new surface acoustic wave (SAW) biosensor detecting protein. The experimental results clarified that improvements in the bonding process are effective in obtaining a stronger bonding interface between the piezoelectric substrate and semiconductor materials. The frequency filtering of the central frequency of the PMN-PT substrate is also superior to that of the LiTaO3 substrate, but the result was not completely satisfactory. However, the electromechanical coupling coefficient of the PMN-PT substrate is excellent, therefore it will be used as a SAW sensor, in the near future, provided that new interdigital transducer (IDT) design will also be available to increase the frequency of filtering.
Optical Disk Recorder (ODR) for Satellite Use
Authors: Tanaka Kunimaro , Itoh Osamu , Iwai Hitoshi , Kasuya Masahiro 
Published: July 2005

An earth-observing satellite flies at an altitude of 800 km. The data acquired while the satellite flies at the opposite side of the earth from a telemetry station has to be stored in the satellite because it is difficult to establish a communication channel between the telemetry station and the satellite. The use of the first optical disk recorder (ODR) in space has been planned [H. Anegawa, T. Fukuda, S. Yamamoto, D. Maeusli and M. Kasuya: Proc. Int. Symp. Optical Memory '91, (1991) p. 115; H. Anegawa, K. Tanaka and N. Tsuya: Proc. Optical Data Storage '92 p. 1 MD4 (1992)]. To make the optical disk drive work in space, the following measure was taken. The large acceleration during launching was solved using the launch lock mechanism. The temperature control mechanism was used to cope with a wide temperature change. Optical components were carefully selected for cosmic ray. ADEOS-II at which the ODR was installed was launched on December 14, 2002. The ODR had worked correctly for about ten months until the solar cell of the satellite stopped functioning. It was proved that the optical disk drive can work in space when an appropriate measure is taken.
The Anti-Terrorist Legislation in the US: Inter Arma Silent Leges?
Authors: Vervaele John 
Published: July 2005

AbstractThe greatest danger posed by terrorism to our democracy and to our constitutional republic may be our executive branch’s overreaction to terrorism and its use of terrorism to erode the constitutionally mandated checks and balances and sharing of powers in foreign affairs, war powers and combating international crime. (Blakesley, 1992)
Advanced Methods for Characterizing the Immersion Factor of Irradiance Sensors
Authors: Hooker Stanford B. , Zibordi Giuseppe 
Published: July 2005

Abstract
Two new immersion factor methods are evaluated by comparing them with the so-called traditional (or incremental) method. For the first method, the optical measurements taken at discrete water depths are substituted by continuous profiles created by removing the water from the tank used in the experimental procedure at a constant flow rate with a pump. In the second method, the commonly used large tank is replaced by a small water vessel with sidewall baffles, which permits the use of a quality-assured volume of water. The summary of the validation results produced for the different methods shows a significant convergence of the two new methods with the traditional method with differences generally well below 1%. The average repeatabilities for single-sensor characterizations (across seven wavelengths) of the three methods are very similar and approximately 0.5%. The evaluation of the continuous method demonstrates its full applicability in the determination of immersion factors with a significant time savings. The results obtained with the small water vessel demonstrate the possibility of significantly reducing the size of the tank (along with decreasing the execution time) and permitting a completely reproducible methodology (based on the use of pure water). The small tank approach readily permits the isolation and quantification of individual sources of uncertainty, the results of which confirm the following aspects of the general experimental methodology: (a) pure water is preferred over tap water, (b) the water should not be recycled (so it does not age), (c) bubbles should be removed from all wetted surfaces, (d) the water surface should be kept as clean as possible, (e) sidewall reflections can be properly minimized with internal baffles, and (f) a pure water characterization can be easily corrected to produce an appropriate seawater characterization. Within the context of experimental efficiency and reproducibility, this study suggests that the combination of a properly baffled small tank with a constant-flow pump would be an optimal system.
Impact of Radar Tilt and Ground Clutter on Wind Measurements in Clear Air
Authors: Martin William J. , Shapiro Alan 
Published: July 2005

Abstract
From geometrical considerations, the optimum tilt angle for a meteorological radar at which the best possible vertical resolution results is derived. This optimum angle is a compromise between the effects of beam divergence and range gate spacing. For typical S-band radar parameters, this optimum tilt angle is found to be about 7°. However, wind analyses at this tilt angle were found not to be accurate in practice because of ground clutter contamination, and suboptimal angles need to be used. Most of the ground clutter was found to be sensed in the radar beam sidelobes. The data presented here imply that ground clutter is a serious contaminant at tilt angles as high as 45°. For clear-air wind profiling in the boundary layer, the impact of ground clutter contamination increased as the tilt angle was increased.
Data presented from four radars [the Goodland, Kansas, Weather Surveillance Radar-1988 Doppler (WSR-88D); the University of Oklahoma’s Doppler on Wheels; NCAR’s S-band dual-polarization Doppler radar (S-Pol); and NSSL’s Cimarron] suggest that a fairly narrow range of tilt angles from 1° to 2° is generally acceptable for wind profiling of the boundary layer in clear-air conditions. Tilt angles outside this range lead to significant systematic errors, primarily from ground clutter contamination.
Comparisons of Scatterometer and TAO Winds Reveal Time-Varying Surface Currents for the Tropical Pacific Ocean*
Authors: Kelly Kathryn A. , Dickinson Suzanne , Johnson Gregory C. 
Published: July 2005

Abstract
The differences between Tropical Atmosphere Ocean (TAO) anemometer and QuikSCAT scatterometer winds are analyzed over a period of 3 yr. Systematic differences are expected owing to ocean currents because the anemometer measures absolute air motion, whereas a radar measures the motion of the air relative to the ocean. Monthly averaged collocated wind differences (CWDs) are compared with available near-surface current data at 15-m depth from drifters, at 25-m depth from acoustic Doppler current profilers (ADCPs), and at 10-m depth from current meters and with geostrophic currents at the surface from the TOPEX/Poseidon radar altimeter. Because direct current observations are so sparse, comparisons are also made with climatological currents from these same sources. Zonal CWDs are in good agreement with the zonal current observations, particularly from 2°S to 2°N where there are strong currents and a robust seasonal cycle, with the altimeter-derived anomalous currents giving the best match. At higher latitudes there is qualitative agreement at buoys with relatively large currents. The overall variance of the zonal component of the CWDs is reduced by approximately 25% by subtracting an estimate of the zonal currents. The meridional CWDs are nearly as large as the zonal CWDs but are unpredictable. The mean CWDs show a robust divergence pattern about the equator, which is suggestive of Ekman currents, but with unexpectedly large magnitudes.
Coefficients for estimating climatological zonal surface currents from the altimeter at the TAO buoys are tabulated: the amplitudes and phases for the annual and semiannual harmonics, and a linear regression against the Southern Oscillation index, are combined with the mean from the drifter currents. Examples are shown of the application of these estimators to data from SeaWinds on the Midori satellite. These estimators are also useful for deriving air–sea fluxes from TAO winds.
Wide-Angle Imaging Lidar Deployment at the ARM Southern Great Plains Site: Intercomparison of Cloud Property Retrievals
Authors: Polonsky Igor N. , Love Steven P. , Davis Anthony B. 
Published: July 2005

Abstract
The Wide-Angle Imaging Lidar (WAIL), a new instrument that measures cloud optical and geometrical properties by means of off-beam lidar returns, was deployed as part of a multi-instrument campaign to probe a cloud field at the Atmospheric Radiation Measurement (ARM) Southern Great Plain (SGP) site on 25 March 2002. WAIL is designed to determine physical and geometrical characteristics using the off-beam component of the lidar return that can be adequately modeled within the diffusion approximation. Using WAIL data, the extinction coefficient and geometrical thickness of a dense cloud layer is estimated, from which optical thickness is inferred. Results from the new methodology agree well with counterparts obtained from other instruments located permanently at the SGP ARM site and from the WAIL-like airborne instrument that flew over the site during our observation period.