bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence Motifs and Proteolytic Cleavage of the Collagen-Like Glycoprotein BclA Required for Its Attachment to the Exosporium of
Bacillus anthracis
Authors: Tan Li , Turnbough Charles L. 
Published: December 2009

ABSTRACT

Bacillus anthracis
spores are enclosed by an exosporium comprised of a basal layer and an external hair-like nap. The filaments of the nap are composed of trimers of the collagen-like glycoprotein BclA. The attachment of essentially all BclA trimers to the exosporium requires the basal layer protein BxpB, and both proteins are included in stable high-molecular-mass exosporium complexes. BclA contains a proteolytically processed 38-residue amino-terminal domain (NTD) that is essential for basal-layer attachment. In this report, we identify three NTD submotifs (SM1a, SM1b, and SM2, located within residues 21 to 33) that are important for BclA attachment and demonstrate that residue A20, the amino-terminal residue of processed BclA, is not required for attachment. We show that the shortest NTD of BclA—or of a recombinant protein—sufficient for high-level basal-layer attachment is a 10-residue motif consisting of an initiating methionine, an apparently arbitrary second residue, SM1a or SM1b, and SM2. We also demonstrate that cleavage of the BclA NTD is necessary for efficient attachment to the basal layer and that the site of cleavage is somewhat flexible, at least in certain mutant NTDs. Finally, we propose a mechanism for BclA attachment and discuss the possibility that analogous mechanisms are involved in the attachment of many different collagen-like proteins of
B. anthracis
and closely related
Bacillus
species.
Coordinated Regulation of 23S rRNA Maturation in
Escherichia coli
Authors: Gutgsell Nancy S. , Jain Chaitanya 
Published: December 2009

ABSTRACT

In
Escherichia coli
, rRNAs are transcribed as precursors and require processing at the 3′ and 5′ ends to generate mature RNA molecules. The largest of these RNAs, 23S rRNA, is matured at the 3′ end by a set of exonucleases and at the 5′ end by an unknown RNase. Whether the 3′ and 5′ maturation steps occur independently or are coupled has previously been unclear. By assessing the levels of precursors accumulating at the 3′ and 5′ ends, we provide evidence that these processes may be linked. Thus, each of several conditions that led to precursor accumulation at one end also did so at the other end. We also observed that each end undergoes maturation at similar rates, suggesting that the two processes could be coupled. Finally, we provide evidence that processing at the 3′ end facilitates 5′-end maturation. A model to explain the basis for the observed directionality of the reactions is proposed. This information will aid in the search for the enzyme responsible for final maturation of the 5′ end of 23S rRNA.
Coproporphyrin Excretion and Low Thiol Levels Caused by Point Mutation in the
Rhodobacter sphaeroides S
-Adenosylmethionine Synthetase Gene
Authors: Sabaty Monique , Adryanczyk Géraldine , Roustan Chloë , Cuiné Stephan , Lamouroux Christine , Pignol David 
Published: December 2009

ABSTRACT

A spontaneous mutant of
Rhodobacter sphaeroides
f. sp.
denitrificans
IL-106 was found to excrete a large amount of a red compound identified as coproporphyrin III, an intermediate in bacteriochlorophyll and heme synthesis. The mutant, named PORF, is able to grow under phototrophic conditions but has low levels of intracellular cysteine and glutathione and overexpresses the cysteine synthase CysK. The expression of molybdoenzymes such as dimethyl sulfoxide (DMSO) and nitrate reductases is also affected under certain growth conditions. Excretion of coproporphyrin and overexpression of CysK are not directly related but were both found to be consequences of a diminished synthesis of the key metabolite
S
-adenosylmethionine (SAM). The wild-type phenotype is restored when the gene
metK
encoding SAM synthetase is supplied in
trans
. The
metK
gene in the mutant strain has a mutation leading to a single amino acid change (H145Y) in the encoded protein. This point mutation is responsible for a 70% decrease in intracellular SAM content which probably affects the activities of numerous SAM-dependent enzymes such as coproporphyrinogen oxidase (HemN); uroporphyrinogen III methyltransferase (CobA), which is involved in siroheme synthesis; and molybdenum cofactor biosynthesis protein A (MoaA). We propose a model showing that the attenuation of the activities of SAM-dependent enzymes in the mutant could be responsible for the coproporphyrin excretion, the low cysteine and glutathione contents, and the decrease in DMSO and nitrate reductase activities.
ClpP of
Streptococcus mutans
Differentially Regulates Expression of Genomic Islands, Mutacin Production, and Antibiotic Tolerance
Authors: Chattoraj Partho , Banerjee Anirban , Biswas Saswati , Biswas Indranil 
Published: December 2009

ABSTRACT

Streptococcus mutans
is the primary etiological agent of human dental caries and, at times, of infective endocarditis. Within the oral cavity, the pathogen is subjected to conditions of stress. A well-conserved protein complex named ClpP (caseinolytic protease) plays a vital role in adaptation under stress conditions. To gain a better understanding of the global role of the ClpP protease in cellular homeostasis, a transcriptome analysis was performed using a Δ
clpP
mutant strain. The expression levels of more than 100 genes were up- or downregulated in the Δ
clpP
mutant compared to the wild type. Notably, the expression of genes in several genomic islands, such as TnSmu1 and TnSmu2, was differentially modulated in the Δ
clpP
mutant strain. ClpP deficiency also increased the expression of genes associated with a putative CRISPR locus. Furthermore, several stress-related genes and genes encoding bacteriocin-related peptides and many transcription factors were also found to be altered in the Δ
clpP
mutant strain. A comparative analysis of the two-dimensional protein profile of the wild type and the Δ
clpP
mutant strains showed altered protein profiles. Comparison of the transcriptome data with the proteomic data identified four common gene products, suggesting that the observed altered protein expression of these genes could be due to altered transcription. The results presented here indicate that ClpP-mediated proteolysis plays an important global role in the regulation of several important traits in this pathogen.
Validation of Satellite-Based High-Resolution Rainfall Products over the Korean Peninsula Using Data from a Dense Rain Gauge Network
Authors: Sohn B. J. , Han Hyo-Jin , Seo Eun-Kyoung 
Published: December 2009

Abstract
Four independently developed high-resolution precipitation products [HRPPs; the Tropical Rainfall Measuring Mission (TRMM) Multisatellite Precipitation Analysis (TMPA), the Climate Prediction Center Morphing Method (CMORPH), Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN), and the National Research Laboratory (NRL) blended precipitation dataset (NRL-blended)], with a spatial resolution of 0.25° and a temporal resolution of 3 h, were compared with surface rain measurements for the four summer seasons (June, July, and August) from 2003 to 2006. Surface measurements are 1-min rain gauge data from the Automated Weather Station (AWS) network operated by the Korean Meteorological Administration (KMA) over South Korea, which consists of about 520 sites. The summer mean rainfall and diurnal cycles of TMPA are comparable to those of the AWS, but with larger magnitudes. The closer agreement of TMPA with surface observations is due to the adjustment of the real-time version of TMPA products to monthly gauge measurements. However, the adjustment seems to result in significant overestimates for light or moderate rain events and thus increased RMS error. In the other three products (CMORPH, PERSIANN, and NRL-blended), significant underestimates are evident in the summer mean distribution and in scatterplots for the grid-by-grid comparison. The magnitudes of the diurnal cycles of the three products appear to be much smaller than those suggested by AWS, although CMORPH shows nearly the same diurnal phase as in AWS. Such underestimates by three methods are likely due to the deficiency of the passive microwave (PMW)-based rainfall retrievals over the South Korean region. More accurate PMW measurements (in particular by the improved land algorithm) seem to be a prerequisite for better estimates of the rain rate by HRPP algorithms. This paper further demonstrates the capability of the Korean AWS network data for validating satellite-based rain products.
Atmospheric Boundary Layer Response to Mesoscale SST Anomalies in the Kuroshio Extension
Authors: Koseki Shunya , Watanabe Masahiro 
Published: December 2009

Abstract
The atmospheric boundary layer (ABL) response to mesoscale eddies in sea surface temperature (SST) in the Kuroshio Extension was investigated using a high-resolution (T213L30) atmospheric general circulation model. A control run was performed first by integrating the model for 40 days, driven by the satellite-derived, eddy-resolving SST during January 2006. The spatial pattern of surface wind anomalies—that is, a deviation from large-scale winds—reveals a positive correlation with the spatial pattern of mesoscale SST anomalies. The momentum budget analysis of the anomalous zonal wind was performed to investigate the formation of the ABL response. The most dominant term was the pressure gradient force; the advection term was comparable but in the opposite sense. Vertical mixing acts to weaken the anomalous zonal wind near the surface; however, the downward (upward) vertical turbulent flux anomalies were dominant near the ABL top over the warm (cold) SST anomalies, suggesting that the vertical mixing mechanism is effective. The role of the vertical mixing was further examined by a sensitivity experiment in which the turbulent diffusion coefficient for momentum was spatially smoothed. While the pressure gradient force and the advection terms were almost unchanged in the momentum budgets, the deceleration due to turbulence was enhanced because of the absence of the momentum input from the free atmosphere. The result is a reduction in the amplitude of the surface zonal wind anomalies to approximately half in the sensitivity experiment.
Tropical South America–Atlantic Sector Convective Margins and Their Relationship to Low-Level Inflow
Authors: Lintner Benjamin R. , Neelin J. David 
Published: December 2009

Abstract
The edges or margins of tropical convective zones are hypothesized to be sensitive to low-level inflow conditions. The present study evaluates where and to what extent convective margin variability is sensitive to low-level inflow variability using observed precipitation and reanalysis wind and total precipitable water data over the tropical South America–Atlantic sector in austral summer. Composite analysis based on an inflow measure defined by projecting low-level monthly-mean atmospheric boundary layer (ABL) or lower free troposphere (LFT) winds onto either mean horizontal precipitation or precipitable water gradients shows widespread contraction of the edges of convection zones in the direction of stronger convection for anomalously strong low-level inflow; such behavior is consistent with enhanced import of relatively dry air along the edges of convection zones. However, the distinction between ABL and LFT winds may be significant regionally, for example, along the Atlantic ITCZ’s northern margin. Back trajectory analysis is employed to estimate source regions of low-level air masses arriving at margin points over time scales (2–4 days) during which low-level air masses are expected to retain some memory of initial moisture conditions while also undergoing diabatic modification. Probability distribution functions of mean precipitation values encountered along trajectories facilitate objective quantification of the frequency with which trajectories approach the margin from drier areas outside the convection zone. While margin points in the ABL are strongly dominated by inflow (i.e., trajectories originating outside of the convection zone), points in the LFT may show inflow, outflow, or mixed inflow–outflow conditions. LFT locations dominated by inflow trajectories generally correspond to regions with composites exhibiting the clearest signatures of LFT wind variability on precipitation.
Challenges in Combining Projections from Multiple Climate Models
Authors: Knutti Reto , Furrer Reinhard , Tebaldi Claudia , Cermak Jan , Meehl Gerald A. 
Published: December 2009

Abstract
Recent coordinated efforts, in which numerous general circulation climate models have been run for a common set of experiments, have produced large datasets of projections of future climate for various scenarios. Those multimodel ensembles sample initial conditions, parameters, and structural uncertainties in the model design, and they have prompted a variety of approaches to quantifying uncertainty in future climate change. International climate change assessments also rely heavily on these models. These assessments often provide equal-weighted averages as best-guess results, assuming that individual model biases will at least partly cancel and that a model average prediction is more likely to be correct than a prediction from a single model based on the result that a multimodel average of present-day climate generally outperforms any individual model. This study outlines the motivation for using multimodel ensembles and discusses various challenges in interpreting them. Among these challenges are that the number of models in these ensembles is usually small, their distribution in the model or parameter space is unclear, and that extreme behavior is often not sampled. Model skill in simulating present-day climate conditions is shown to relate only weakly to the magnitude of predicted change. It is thus unclear by how much the confidence in future projections should increase based on improvements in simulating present-day conditions, a reduction of intermodel spread, or a larger number of models. Averaging model output may further lead to a loss of signal—for example, for precipitation change where the predicted changes are spatially heterogeneous, such that the true expected change is very likely to be larger than suggested by a model average. Last, there is little agreement on metrics to separate “good” and “bad” models, and there is concern that model development, evaluation, and posterior weighting or ranking are all using the same datasets. While the multimodel average appears to still be useful in some situations, these results show that more quantitative methods to evaluate model performance are critical to maximize the value of climate change projections from global models.
The Mean Along-Isobath Heat and Salt Balances over the Middle Atlantic Bight Continental Shelf
Authors: Lentz Steven J. 
Published: December 2009

Abstract
The mean heat and salt balances over the Middle Atlantic Bight continental shelf are investigated by testing the hypothesis that surface fluxes of heat or freshwater are balanced by along-isobath fluxes resulting from the mean, depth-averaged, along-isobath flow acting on the mean, depth-averaged, along-isobath temperature or salinity gradient. This hypothesized balance is equivalent in a Lagrangian frame to a column of water, for example, warming because of surface heating as it is advected southward along isobath by the mean flow.
Mean depth-averaged temperatures increase from north to south along isobath at a rate of 2°C (1000 km)−1 at midshelf, which is consistent with the hypothesized balance and mean surface heat flux estimates from the 50-yr NCEP Reanalysis. However, mean surface heat flux estimates from the higher-resolution 20-yr Objectively Analyzed Air–Sea Fluxes (OAFlux) reanalysis are too small to balance the along-isobath heat flux divergence implying a cross-shelf heat flux convergence. It is unclear which surface heat flux estimate, NCEP or OAFlux, is more accurate. The cross-shelf heat flux convergence resulting from the mean cross-shelf circulation is too small to balance the along-isobath heat flux divergence.
Mean depth-averaged salinities increase from north to south along isobath at a rate of 1 (psu) (1000 km)−1 at midshelf. Mean precipitation and evaporation rates nearly balance so that the net freshwater flux is too small by more than an order of magnitude to account for the observed along-isobath increase in salinity. The cross-shelf salt flux divergence resulting from the mean cross-shelf circulation has the wrong sign to balance the divergence in the along-isobath salt flux. These results imply there must be an onshore “eddy” salt flux resulting from the time-dependent current and salinity variability.
The along-isobath temperature and salinity gradients compensate for each other so that the mean, depth-averaged, along-isobath density gradient is approximately zero. This suggests that there may be a feedback between the along-isobath density gradient and the onshore salt and heat fluxes that maintains the density gradient near zero.
An Inexpensive Method for Measurements of Static Pressure Fluctuations
Authors: Liberzon Dan , Shemer Lev 
Published: December 2009

Abstract
An application of a commercially available and inexpensive pressure probe and transducer, originally designed for pressure drop measurements in air conditioning conduits, is suggested for accurate and reliable measurements of static pressure fluctuations in airflow, with a particular application to wind interaction with water waves. It is demonstrated that this static pressure probe is a robust instrument that offers efficient dynamic pressure elimination while having low directional sensitivity and sufficiently high dynamic response. A series of measurements in a wind-wave flume was carried out to validate the characteristics of the sensor and of the pressure transducer.
A Novel Lightweight Low-Power Dual-Beam Ozone Photometer Utilizing Solid-State Optoelectronics
Authors: Kalnajs Lars E. , Avallone Linnea M. 
Published: December 2009

Abstract
Recent advances in semiconductor materials and fabrication techniques have allowed the development of light-emitting diodes (LEDs) with wavelengths extending down into the UV-C region (λ &lt; 280 nm). A new ozone photometer has been developed utilizing these novel light sources. The application of solid-state technology to the proven dual-beam UV absorption technique has improved instrument performance while reducing power consumption and weight compared to existing instrumentation. The newly developed instrument is expected to have an accuracy of 1% at surface level pressure, a resolution better than 1 ppb, and measurement rates up to 1 Hz over the range of ozone mixing ratios encountered from the earth’s surface to the middle stratosphere. Size, weight, and power consumption have also been significantly reduced, with a mass of 3 kg and a power consumption of less than 5 W. Initial development is focused on an instrument suitable for measurements from autonomous platforms and in harsh environments; however, the technology is highly adaptable to other applications.
Estimation and Assessment of Errors Related to Antenna Pattern Distortion in CODAR SeaSonde High-Frequency Radar Ocean Current Measurements
Authors: Laws Kenneth , Paduan Jeffrey D. , Vesecky John 
Published: December 2009

Abstract
A simulation-based investigation of errors in HF radar–derived, near-surface ocean current measurements is presented. The simulation model is specific to Coastal Ocean Dynamics Application Radar (CODAR) SeaSonde radar systems that employ a compact, collocated antenna geometry. In this study, radial current retrievals are obtained by processing simulated data using unmodified CODAR data processing software. To avoid limiting the results to specific ocean current and wind wave scenarios, the analyses employ large ensembles of randomly varying simulated environmental conditions. The effect of antenna pattern distortion on the accuracy of retrievals is investigated using 40 different antenna sensitivity patterns of varying levels of distortion. A single parameter is derived to describe the level of the antenna pattern distortion. This parameter is found to be highly correlated with the rms error of the simulated radial currents (r = 0.94) and therefore can be used as a basis for evaluating the severity of site-specific antenna pattern distortions. Ensemble averages of the subperiod simulated current retrieval standard deviations are found to be highly correlated with the antenna pattern distortion parameter (r = 0.92). Simulations without distortions of the antenna pattern indicate that an rms radial current error of 2.9 cm s−1 is a minimum bound on the error of a SeaSonde ocean radar system, given a typical set of operating parameters and a generalized ensemble of ocean conditions.
Enhancements of Satellite Data Assimilation over Antarctica
Authors: Bouchard Aurélie , Rabier Florence , Guidard Vincent , Karbou Fatima 
Published: December 2009

Abstract
The Concordiasi field experiment, which is taking place in Antarctica, involves the launching of radiosoundings and stratospheric balloons. One of the main goals of this campaign is the validation of the Infrared Atmospheric Sounding Interferometer (IASI) radiance assimilation. Prior to the campaign, it was necessary to improve satellite data assimilation at high latitudes. Two types of sensors, microwave and infrared, have been considered to help with this issue. A major problem associated with microwave satellite data is the calculation of the surface emissivity. An innovative approach, based on satellite observations, improves the surface emissivity modeling over land and sea ice within the constraints of the four-dimensional variational data assimilation (4D-VAR) system. With this new calculation of emissivity, it has been possible to include many more microwave observations during the assimilation. In this study, this method has been applied to high latitudes, after some adjustments have been made to assimilate additional Advanced Microwave Sounding Unit-A/B (AMSU-A/B) data over sea ice and snow. The use of additional data from IASI and the Atmospheric Infrared Sounder (AIRS) sensors over land and sea ice has also been tested. The use of the microwave and infrared data over this polar area has modified the dynamical and thermodynamical model fields such as the snow precipitation quantity. Additional data have been found to have a positive impact on the skill of a model specially tuned for Antarctica.