bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Genome Analysis of “CandidatusPhytoplasma australiense” (Subgrouptuf-Australia I;rp-A) and “Ca. Phytoplasma asteris” Strains OY-M and AY-WB
Authors: Tran-Nguyen L. T. T. , Kube M. , Schneider B. , Reinhardt R. , Gibb K. S. 
Published: March 2008

ABSTRACTThe chromosome sequence of “CandidatusPhytoplasma australiense” (subgrouptuf-Australia I;rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of “Ca.Phytoplasma australiense” with “Ca.Phytoplasma asteris” strains OY-M and AY-WB showed that the gene order was more conserved between the closely related “Ca.Phytoplasma asteris” strains than to “Ca. Phytoplasma australiense.” Differences observed between “Ca.Phytoplasma australiense” and “Ca.Phytoplasma asteris” strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function.
Cooperative Binding of Phosphorylated DevR to Upstream Sites Is Necessary and Sufficient for Activation of the Rv3134c-
devRS
Operon in
Mycobacterium tuberculosis
: Implication in the Induction of DevR Target Genes
Authors: Chauhan Santosh , Tyagi Jaya Sivaswami 
Published: March 2008

ABSTRACT

The DevR-DevS two-component system of
Mycobacterium tuberculosis
mediates bacterial adaptation to hypoxia, a condition believed to be associated with the initiation and maintenance of dormant bacilli during latent tuberculosis. The activity of the Rv3134c-
devRS
operon was studied in
M. tuberculosis
using several transcriptional fusions comprised of promoter regions and the
gfp
reporter gene under inducing and aerobic conditions. Aerobic transcription was DevR independent, while hypoxic induction was completely DevR dependent. The hypoxia transcriptional start point, T
H
, was mapped at −40 bp upstream of Rv3134c. In contrast, the divergently transcribed Rv3135 gene was not induced under hypoxic conditions. DNase I footprinting and mutational analyses demonstrated that induction required the interaction of DevR∼P with binding sites centered at bp −42.5 and −63.5 relative to T
H
. Binding to the distal site (D) was necessary to recruit another molecule of DevR∼P to the proximal site (P), and interaction with both sequences was essential for promoter activation. These sites did not bind to either unphosphorylated or phosphorylation-defective DevR protein, which was consistent with an essential role for DevR∼P in activation. Phosphorylated DevR also bound to three copies of the motif at the
hspX
promoter. The Rv3134c and
hspX
promoters have a similar architecture, wherein the proximal DevR∼P binding site overlaps with the promoter −35 element. A model for the likely mode of action of DevR at these promoters is discussed.
Multiple Genes Repress Motility in Uropathogenic
Escherichia coli
Constitutively Expressing Type 1 Fimbriae
Authors: Simms Amy N. , Mobley Harry L. T. 
Published: March 2008

ABSTRACT

Two surface organelles of uropathogenic
Escherichia coli
(UPEC), flagella and type 1 fimbriae, are critical for colonization of the urinary tract but mediate opposite actions. Flagella propel bacteria through urine and along mucus layers, while type 1 fimbriae allow bacteria to adhere to specific receptors present on uroepithelial cells. Constitutive expression of type 1 fimbriae leads to repression of motility and chemotaxis in UPEC strain CFT073, suggesting that UPEC may coordinately regulate motility and adherence. To identify genes involved in this regulation of motility by type 1 fimbriae, transposon mutagenesis was performed on a phase-locked type 1 fimbrial ON variant of strain CFT073 (CFT073
fim
L-ON), followed by a screen for restoration of motility in soft agar. Functions of the genes identified included attachment, metabolism, transport, DNA mismatch repair, and transcriptional regulation, and a number of genes had hypothetical function. Isogenic deletion mutants of these genes were also constructed in CFT073
fim
L-ON. Motility was partially restored in six of these mutants, including complementable mutations in four genes encoding known transcriptional regulators,
lrhA, lrp, slyA
, and
papX
; a mismatch repair gene,
mutS
; and one hypothetical gene,
ydiV
. Type 1 fimbrial expression in these mutants was unaltered, and the majority of these mutants expressed larger amounts of flagellin than the
fim
L-ON parental strain. Our results indicate that repression of motility in CFT073
fim
L-ON is not solely due to the constitutive expression of type 1 fimbriae on the surfaces of the bacteria and that multiple genes may contribute to this repression.
Roles of
pgaABCD
Genes in Synthesis, Modification, and Export of the
Escherichia coli
Biofilm Adhesin Poly-β-1,6-
N
-Acetyl-
d
-Glucosamine
Authors: Itoh Yoshikane , Rice John D. , Goller Carlos , Pannuri Archana , Taylor Jeannette , Meisner Jeffrey , Beveridge Terry J. , Preston James F. , Romeo Tony 
Published: March 2008

ABSTRACT

The linear homopolymer poly-β-1,6-
N
-acetyl-
d
-glucosamine (β-1,6-GlcNAc; PGA) serves as an adhesin for the maintenance of biofilm structural stability in diverse eubacteria. Its function in
Escherichia coli
K-12 requires the gene products of the
pgaABCD
operon, all of which are necessary for biofilm formation. PgaC is an apparent glycosyltransferase that is required for PGA synthesis. Using a monoclonal antibody directed against
E. coli
PGA, we now demonstrate that PgaD is also needed for PGA formation. The deletion of genes for the predicted outer membrane proteins PgaA and PgaB did not prevent PGA synthesis but did block its export, as shown by the results of immunoelectron microscopy (IEM) and antibody adsorption assays. IEM also revealed a conditional localization of PGA at the cell poles, the initial attachment site for biofilm formation. PgaA contains a predicted β-barrel porin and a superhelical domain containing tetratricopeptide repeats, which may mediate protein-protein interactions, implying that it forms the outer membrane secretin for PGA. PgaB contains predicted carbohydrate binding and polysaccharide
N
-deacetylase domains. The overexpression of
pgaB
increased the primary amine content (glucosamine) of PGA. Site-directed mutations targeting the
N
-deacetylase catalytic activity of PgaB blocked PGA export and biofilm formation, implying that
N
-deacetylation promotes PGA export through the PgaA porin. The results of previous studies indicated that
N
-deacetylation of β-1,6-GlcNAc in
Staphylococcus epidermidis
by the PgaB homolog, IcaB, anchors it to the cell surface. The deletion of
icaB
resulted in release of β-1,6-GlcNAc into the growth medium. Thus, covalent modification of β-1,6-GlcNAc by
N
-deacetylation serves distinct biological functions in gram-negative and gram-positive species, dictated by cell envelope differences.
Genome-Wide Transcriptional Responses ofEscherichia coliK-12 to Continuous Osmotic and Heat Stresses
Authors: Gunasekera Thusitha S. , Csonka Laszlo N. , Paliy Oleg 
Published: March 2008

ABSTRACTOsmotic stress is known to increase the thermotolerance and oxidative-stress resistance of bacteria by a mechanism that is not adequately understood. We probed the cross-regulation of continuous osmotic and heat stress responses by characterizing the effects of external osmolarity (0.3 M versus 0.0 M NaCl) and temperature (43°C versus 30°C) on the transcriptome ofEscherichia coliK-12. Our most important discovery was that a number of genes in the SoxRS and OxyR oxidative-stress regulons were up-regulated by high osmolarity, high temperature, or a combination of both stresses. This result can explain the previously noted cross-protection of osmotic stress against oxidative and heat stresses. Most of the genes shown in previous studies to be induced during the early phase of adaptation to hyperosmotic shock were found to be also overexpressed under continuous osmotic stress. However, there was a poorer overlap between the heat shock genes that are induced transiently after high temperature shifts and the genes that we found to be chronically up-regulated at 43°C. Supplementation of the high-osmolarity medium with the osmoprotectant glycine betaine, which reduces the cytoplasmic K+pool, did not lead to a universal reduction in the expression of osmotically induced genes. This finding does not support the hypothesis that K+is the central osmoregulatory signal inEnterobacteriaceae.
Expression and Porin Activity of P28 and OMP-1F during Intracellular
Ehrlichia chaffeensis
Development
Authors: Kumagai Yumi , Huang Haibin , Rikihisa Yasuko 
Published: March 2008

ABSTRACT

Ehrlichia chaffeensis
, an obligatory intracellular gram-negative bacterium, must take up various nutrients and metabolic compounds because it lacks many genes involved in metabolism. Nutrient uptake by a gram-negative bacterium occurs primarily through pores or channels in the bacterial outer membrane. Here we demonstrate that isolated
E. chaffeensis
outer membranes have porin activities, as determined by a proteoliposome swelling assay. The activity was partially blocked by an antibody that recognizes the two most abundant outer membrane proteins, P28/OMP-19 and OMP-1F/OMP-18. Both proteins were predicted to have structural features characteristic of porins, including 12 transmembrane segments comprised of amphipathic and antiparallel β-strands. The sodium dodecyl sulfate stability of the two proteins was consistent with a β-barrel structure. Isolated native P28 and OMP-1F exhibited porin activities, with pore sizes similar to and larger than, respectively, that of OprF, which is the porin with the largest pore size known to date.
E. chaffeensis
experiences temperature changes during transmission by ticks. During the intracellular development of
E. chaffeensis
, both P28 and OMP-1F were expressed mostly in the mid-exponential growth phase at 37°C and the late-exponential growth phase at 28°C. The porin activity of proteoliposomes reconstituted with proteins from the outer membrane fractions derived from bacteria in the mid- and late-exponential growth phases at 28°C and 37°C correlated with the expression levels of P28 and OMP-1F. These results imply that P28 and OMP-1F function as porins with large pore sizes, suggesting that the differential expression of these two proteins might regulate nutrient uptake during intracellular
E. chaffeensis
development at both temperatures.
Lagrangian Diagnostics of Tropical Deep Convection and Its Effect upon Upper-Tropospheric Humidity
Authors: Horváth Ákos , Soden Brian J. 
Published: March 2008

AbstractThis study combines geostationary water vapor imagery with optical cloud property retrievals and microwave sea surface observations in order to investigate, in a Lagrangian framework, (i) the importance of cirrus anvil sublimation on tropical upper-tropospheric humidity and (ii) the sea surface temperature dependence of deep convective development. Although an Eulerian analysis shows a strong spatial correlation of ∼0.8 between monthly mean cirrus ice water path and upper-tropospheric humidity, the Lagrangian analysis indicates no causal link between these quantities. The maximum upper-tropospheric humidity occurs ∼5 h after peak convection, closely synchronized with the maximum cirrus ice water path, and lagging behind it by no more than 1.0 h. Considering that the characteristic e-folding decay time of cirrus ice water is determined to be ∼4 h, this short time lag does not allow for significant sublimative moistening. Furthermore, a tendency analysis reveals that cirrus decay and growth, in terms of both cloud cover and integrated ice content, is accompanied by the drying and moistening of the upper troposphere, respectively, a result opposite that expected if cirrus ice were a primary water vapor source. In addition, it is found that an ∼2°C rise in sea surface temperature results in a measurable increase in the frequency, spatial extent, and water content of deep convective cores. The larger storms over warmer oceans are also associated with slightly larger anvils than their counterparts over colder oceans; however, anvil area per unit cumulus area, that is, cirrus detrainment efficiency, decreases as SST increases.
The Impacts of Convective Parameterization and Moisture Triggering on AGCM-Simulated Convectively Coupled Equatorial Waves
Authors: Lin Jia-Lin , Lee Myong-In , Kim Daehyun , Kang In-Sik , Frierson Dargan M. W. 
Published: March 2008

Abstract
This study examines the impacts of convective parameterization and moisture convective trigger on convectively coupled equatorial waves simulated by the Seoul National University (SNU) atmospheric general circulation model (AGCM). Three different convection schemes are used, including the simplified Arakawa–Schubert (SAS) scheme, the Kuo (1974) scheme, and the moist convective adjustment (MCA) scheme, and a moisture convective trigger with variable strength is added to each scheme. The authors also conduct a “no convection” experiment with deep convection schemes turned off. Space–time spectral analysis is used to obtain the variance and phase speed of dominant convectively coupled equatorial waves, including the Madden–Julian oscillation (MJO), Kelvin, equatorial Rossby (ER), mixed Rossby–gravity (MRG), and eastward inertio-gravity (EIG) and westward inertio-gravity (WIG) waves.
The results show that both convective parameterization and the moisture convective trigger have significant impacts on AGCM-simulated, convectively coupled equatorial waves. The MCA scheme generally produces larger variances of convectively coupled equatorial waves including the MJO, more coherent eastward propagation of the MJO, and a more prominent MJO spectral peak than the Kuo and SAS schemes. Increasing the strength of the moisture trigger significantly enhances the variances and slows down the phase speeds of all wave modes except the MJO, and usually improves the eastward propagation of the MJO for the Kuo and SAS schemes, but the effect for the MCA scheme is small. The no convection experiment always produces one of the best signals of convectively coupled equatorial waves and the MJO.
Observed Inconsistencies between Snow Extent and Snow Depth Variability at Regional/Continental Scales
Authors: Ge Yan , Gong Gavin 
Published: March 2008

Abstract
Snow extent and snow depth are two related characteristics of a snowpack, but they do not need to be mutually consistent. Differences between these two variables at local scales are readily apparent. However, at larger scales, which interact with atmospheric circulation and climate, snow extent is the primary variable considered, owing largely to the scarcity of snow depth data. In this study, three regional-/continental-scale gridded snow depth/snow water equivalent (SWE) datasets, derived from station observations or passive microwave satellite sensors, are utilized to quantitatively evaluate the relationship between snow extent and snow depth/SWE over North America. Various statistical methods are used to ensure the robustness of the results, including correlations, composites, and singular value decomposition analyses.
Results indicate that continental-scale snow depth variations are substantial in their own right and that depth and extent anomalies are largely unrelated over broad high-latitude regions north of the snow line. Snow extent and snow depth vary more consistently in the vicinity of the snow line, especially in autumn and spring, during which precipitation and ablation can affect both variables. It is also found that deeper (shallower) winter snow translates into larger (smaller) snow-covered areas in the following spring/summer season, and also a longer (shorter) snow season, but only in specific regions. These results suggest a possible influence of snow depth on spring and summer climate. Overall, the observed lack of mutual consistency between these two snowpack variables at continental/regional scales suggests that snow depth variations may be of sufficiently large magnitude, spatial scope, and temporal duration to interact with regional–hemispheric climate, in a manner unrelated to the more extensively studied snow extent variations.
Sensitivity of Thermal Infrared Radiation at the Top of the Atmosphere and the Surface to Ice Cloud Microphysics
Authors: Dubuisson Philippe , Giraud Vincent , Pelon Jacques , Cadet Bertrand , Yang Ping 
Published: March 2008

Abstract
This paper reports on the sensitivity of the brightness temperatures associated with radiances at the surface and the top of the atmosphere, simulated for the Imaging Infrared Radiometer (IIR) 8.7-, 10.6-, and 12-μm channels under ice cloudy conditions, to the optical and microphysical properties of ice clouds. The 10.6- and 12-μm channels allow simultaneous retrieval of ice cloud optical thickness and effective particle size (Deff) less than 100 μm. It is illustrated that the particle shape and size distributions of ice crystals have noticeable effects on the brightness temperatures. Using the split window technique based on the 10.6- and 12-μm channels in conjunction with cloud properties assumed a priori, the authors show that the influence of the cloud microphysical properties can lead to differences on the order of ±10% and ±25% in retrieved effective particle sizes for small (Deff &lt; 20 μm) and large particles (Deff &gt; 40 μm), respectively. The impact of cloud model on retrieved optical thickness is on the order of ±10%. Different particle habits may lead to ±25% differences in ice water path (IWP). Theoretically, the use of an additional channel (i.e., 8.7 μm) can give a stronger constraint on cloud model and improve the retrieval of Deff and IWP. The present simulations have confirmed that cloud microphysics has a significant impact on the 8.7-μm brightness temperatures mainly because of particle shape. This impact is larger than the errors of the IIR measurements for cloud optical thicknesses (at 12 μm) ranging from 0.3 to 8. Furthermore, it is shown that the characterization of optical and microphysical properties of ice clouds from ground-based measurements is quite challenging. Especially, water vapor in the atmosphere has an important impact on ground-based cloud retrievals. Observation stations at higher altitudes or airborne measurements would minimize the atmospheric effect.
Modeling the View Angle Dependence of Gap Fractions in Forest Canopies: Implications for Mapping Fractional Snow Cover Using Optical Remote Sensing
Authors: Liu Jicheng , Woodcock Curtis E. , Melloh Rae A. , Davis Robert E. , McKenzie Ceretha , Painter Thomas H. 
Published: March 2008

Abstract
Forest canopies influence the proportion of the land surface that is visible from above, or the viewable gap fraction (VGF). The VGF limits the amount of information available in satellite data about the land surface, such as snow cover in forests. Efforts to recover fractional snow cover from the spectral mixture analysis model Moderate Resolution Imaging Spectroradiometer (MODIS) snow-covered area and grain size (MODSCAG) indicate the importance of view angle effects in forested landscapes. The VGF can be estimated using both hemispherical photos and forest canopy models. For a set of stands in the Cold Land Field Processes Experiment (CLPX) sites in the Fraser Experimental Forest in Colorado, the convergence of both measurements and models of the VGF as a function of view angle supports the idea that VGF can be characterized as a function of forest properties. A simple geometric optical (GO) model that includes only between-crown gaps can capture the basic shape of the VGF as a function of view zenith angle. However, the GO model tends to underestimate the VGF compared with estimates derived from hemispherical photos, particularly at high view angles. The use of a more complicated geometric optical–radiative transfer (GORT) model generally improves estimates of the VGF by taking into account within-crown gaps. Small footprint airborne lidar data are useful for mapping forest cover and height, which makes the parameterization of the GORT model possible over a landscape. Better knowledge of the angular distribution of gaps in forest canopies holds promise for improving remote sensing of snow cover fraction.
NASA Cold Land Processes Experiment (CLPX 2002/03): Atmospheric Analyses Datasets
Authors: Liston Glen E. , Birkenheuer Daniel L. , Hiemstra Christopher A. , Cline Donald W. , Elder Kelly 
Published: March 2008

Abstract
This paper describes the Local Analysis and Prediction System (LAPS) and the 20-km horizontal grid version of the Rapid Update Cycle (RUC20) atmospheric analyses datasets, which are available as part of the Cold Land Processes Field Experiment (CLPX) data archive. The LAPS dataset contains spatially and temporally continuous atmospheric and surface variables over Colorado, Wyoming, and parts of the surrounding states. The analysis used a 10-km horizontal grid with 21 vertical levels and an hourly temporal resolution. The LAPS archive includes forty-six 1D surface fields and nine 3D upper-air fields, spanning the period 1 September 2001 through 31 August 2003. The RUC20 dataset includes hourly 3D atmospheric analyses over the contiguous United States and parts of southern Canada and northern Mexico, with 50 vertical levels. The RUC20 archive contains forty-six 1D surface fields and fourteen 3D upper-air fields, spanning the period 1 October 2002 through 31 September 2003. The datasets are archived at the National Snow and Ice Data Center (NSIDC) in Boulder, Colorado.
Intercomparison of Evapotranspiration Estimates at the Different Ecological Zones in Jordan
Authors: Suleiman Ayman , Al-Bakri Jawad , Duqqah Mohammad , Crago Rich 
Published: March 2008

Abstract
An estimate of evapotranspiration (ET) is needed for many applications in diverse disciplines such as agriculture, hydrology, and meteorology. The objective of this study was to compare two methods for estimating daily actual ET (ETa) from six sites located in four different ecological zones within Jordan. The first method used the analytical land–atmosphere radiometer model (ALARM) and the dimensionless temperature procedure, whereas the second method used ETa calculated from the FAO-56 reference evapotranspiration. ALARM converts general remotely sensed surface temperatures to aerodynamic temperature. Standard meteorological data from weather stations were used with both methods, and the Moderate Resolution Imaging Spectroradiometer (MODIS)–based leaf area index, surface temperature, and albedo were obtained to estimate ETa, using the former method. A validation study was conducted on an alfalfa field in Jordan Valley using ALARM and the American Society of Civil Engineers’ (ASCE) method, which is very similar to FAO-56 except it uses alfalfa as a reference crop. Because this alfalfa field was irrigated and because of warm air advection, ET rates based on measurements of soil moisture change ranged from about 6 to 10 mm day−1. For this range, the root-mean-square error (RMSE) for ALARM was 0.87 mm day−1 and the coefficient of determination r 2 was 0.36, whereas the RMSE for ASCE was 1.25 mm day−1 and r 2 = 0.06. There was good agreement between minimum, maximum, and average ETa for the two methods at all sites except for Irbid, for which the minimum and, consequently, the average were different. Much of the site-to-site and temporal variability was found to be statistically significant. Reasons for this variability include soil types, vegetation cover, irrigation, and warm advection.