bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex Expression of the Cellulolytic Transcriptome of Saccharophagus degradans
Authors: Zhang Haitao , Hutcheson Steven W. 
Published: June 2011

ABSTRACT

Saccharophagus degradans
is an aerobic marine bacterium that can degrade cellulose by the induced expression of an unusual cellulolytic system composed of multiple endoglucanases and glucosidases. To understand the regulation of the cellulolytic system, transcript levels for the genes predicted to contribute to the cellulolytic system were monitored by quantitative real-time PCR (qRT-PCR) during the transition to growth on cellulose. Four glucanases of the cellulolytic system exhibited basal expression during growth on glucose. All but one of the predicted cellulolytic system genes were induced strongly during growth on Avicel, with three patterns of expression observed. One group showed increased expression (up to 6-fold) within 4 h of the nutritional shift, with the relative expression remaining constant over the next 22 h. A second group of genes was strongly induced between 4 and 10 h after nutritional transfer, with relative expression declining thereafter. The third group of genes was slowly induced and was expressed maximally after 24 h. Cellodextrins and cellobiose, products of the predicted basally expressed endoglucanases, stimulated expression of representative cellulase genes. A model is proposed by which the activity of basally expressed endoglucanases releases cellodextrins from Avicel that are then perceived and transduced to initiate transcription of each of the regulated cellulolytic system genes forming an expression pattern.
Adherent-Invasive Escherichia coli Phenotype Displayed by Intestinal Pathogenic E. coli Strains from Cats, Dogs, and Swine
Authors: Martinez-Medina Margarita , Garcia-Gil Jesus , Barnich Nicolas , Wieler Lothar H. , Ewers Christa 
Published: June 2011

ABSTRACT

The adherent-invasive
Escherichia coli
(AIEC) pathotype, which has been associated with Crohn's disease, shows similar traits to human and animal extraintestinal pathogenic
E. coli
(ExPEC) with respect to their phylogenetic origin and virulence gene profiles. Here, we demonstrate that animal ExPEC strains generally do not share the AIEC phenotype. In contrast, this phenotype is very frequent among animal intestinal pathogenic
E. coli
(InPEC) strains, particularly of feline and canine origin, that genetically resemble ExPEC. These results strengthen the particular identity and disease specificity of the AIEC pathotype and the putative role animals might play in the transmission of AIEC-like strains to humans.
The Fsr Quorum-Sensing System of Enterococcus faecalisModulates Surface Display of the Collagen-Binding MSCRAMM Ace through Regulation of
gelE
Authors: Pinkston Kenneth L. , Gao Peng , Diaz-Garcia Daniel , Sillanpää Jouko , Nallapareddy Sreedhar R. , Murray Barbara E. , Harvey Barrett R. 
Published: June 2011

ABSTRACT

Ace, a known virulence factor and the first identified microbial surface component recognizing adhesive matrix molecule (MSCRAMM) of
Enterococcus faecalis
is associated with host cell adherence and endocarditis. The Fsr quorum-sensing system of
E. faecalis
, a two-component signal transduction system, has also been repeatedly linked to virulence in
E. faecalis
, due in part to the transcriptional induction of an extracellular metalloprotease, gelatinase (GelE). In this study, we discovered that disruption of the Fsr pathway significantly increased the levels of Ace on the cell surface in the latter phases of growth. Furthermore, we observed that, in addition to
fsrB
mutants, other strains identified as deficient in GelE activity also demonstrated a similar phenotype. Additional experiments demonstrated the GelE-dependent cleavage of Ace from the surface of
E. faecalis
, confirming that GelE specifically reduces Ace cell surface display. In addition, disruption of the Fsr system or GelE expression significantly improved the ability of
E. faecalis
to adhere to collagen, which is consistent with higher levels of Ace on the
E. faecalis
surface. These results demonstrate that the display of Ace is mediated by quorum sensing through the action of GelE, providing insight into the complicated world of Gram-positive pathogen adhesion and colonization.
Complete Genome Sequence of the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Alteromonas sp. Strain SN2
Authors: Jin Hyun Mi , Jeong Haeyoung , Moon Eun-Joung , Math Renukaradhya K. , Lee Kangseok , Kim Hae-Jin , Jeon Che Ok , Oh Tae Kwang , Kim Jihyun F. 
Published: June 2011

ABSTRACT

Alteromonas
sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2's adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility.
Complete Genome Sequence of Lactobacillus kefiranofaciens ZW3
Authors: Wang Yanping , Wang Jingrui , Ahmed Zaheer , Bai Xiaojia , Wang Jinju 
Published: June 2011

ABSTRACT

Lactobacillus kefiranofaciens
ZW3 was isolated in Tibet, China, from kefir grain, a traditional dairy product that is known to provide many health benefits to humans. Here, we present the genome features of
L. kefiranofaciens
ZW3 and the identification of a gene cluster related to the synthesis of exopolysaccharide, an important constituent of the Tibetan kefir.
High Levels of Recombination among Streptococcus pneumoniae Isolates from the Gambia
Authors: Donkor E. S. , Bishop C. J. , Antonio M. , Wren B. , Hanage W. P. 
Published: June 2011

ABSTRACT

We carried out multilocus sequence typing (MLST) on 148 pneumococcal carriage isolates collected from children <24 months old in the Upper River Division, the Gambia. MLST revealed a diverse population. Seventy-six different sequence types (STs) were found, the most common of which were 802 and 919, associated with 23F and 6A serotypes, respectively. Comparison with the MLST database showed that only 11 of the STs found in the present sample had been reported outside Africa. Six STs showed evidence of capsular switching (172, 802, 847, 1730, 1736, and 1737). Serotype switches were confirmed by microarrays that detected capsule genes. Of isolates analyzed by using microarrays, 40/69 (58%) harbored the
tetM
resistance determinant. A statistical genetic analysis to detect recombination found that 49/144 (34%) isolates showed significant (
P
< 0.05) evidence of admixture, which is greater than that observed in similar samples from the United Kingdom (5%) and Finland (2%). We hypothesize that large amounts of admixture could reflect the high prevalence of multiple carriage in this region, leading to more opportunities for homologous recombination between strains. This could have consequences for the population response to conjugate vaccination.

IMPORTANCE
The population structure of the pneumococcus in sub-Saharan Africa has barely been studied despite the high levels of morbidity and mortality due to pneumococcal disease in this region. We report the largest sample to date from carriage in sub-Saharan Africa to be typed by sequencing (multilocus sequence typing [MLST]) and microarray analysis. The results clearly show that the population is highly distinct and divergent from others studied in the United States and Europe. Moreover, in contrast with samples from developed countries, the population contains a high proportion of isolates showing a history of homologous recombination, which shuffles genetic information into new combinations and can generate drug-resistant and vaccine escape strains. This is likely to have important consequences for the evolutionary response of the pneumococcal population to conjugate vaccination targeting a subset of pneumococcal serotypes, which is under way in the Gambia and other countries.
Urinary biomarkers of exposure to glycol ethers and chlorinated solvents during pregnancy: determinants of exposure and comparison with indirect methods of exposure assessment
Authors: Garlantézec Ronan , Multigner Luc , Labat Laurence , Bonvallot Nathalie , Pulkkinen Juha , Dananché Brigitte , Monfort Christine , Rouget Florence , Cordier Sylvaine 
Published: June 2011

ObjectivesTo describe urine levels of metabolites of glycol ethers and chlorinated solvents in a sample of pregnant women from the general population, to study their occupational and non-occupational determinants and to compare them with the results of indirect assessment methods of solvent exposure.MethodsA sample of 451 pregnant women was randomly selected from a general population cohort. At inclusion, the women in this sample completed a self-administered questionnaire about their social and medical characteristics, occupation and exposure to different products at work and in non-occupational activities. Occupational exposure to solvents was assessed from the woman's self-report and from a job-exposure matrix. Eight alkoxycarboxylic acids and trichloroacetic acid and trichloroethanol were measured with chromatography in urine samples collected at inclusion. Associations between metabolite levels and job titles, exposure to products used at work, and solvent exposure were studied.ResultsThe different glycol ether metabolites were detected in 5.3%–96.4% of the urine samples, trichloroacetic acid in 6.4% and trichloroethanol in 5.5%. Nurses had butoxyacetic acid and phenoxyacetic acid in their urine most often, whereas methoxyethoxyacetic acid was the most frequent among nursing aides. Among cleaners, ethoxyacetic acid and ethoxyethoxyacetic acid were the most frequent. The occupation of hairdresser was associated with urinary excretion of ethoxyacetic acid, ethoxyethoxyacetic acid, butoxyacetic acid and phenoxyacetic acid. Among the women classified as exposed to solvents, the agents identified most often were ethoxyacetic acid, ethoxy-ethoxyacetic acid, butoxyacetic acid, phenoxyacetic acid, trichloroacetic acid and trichloroethanol. Ethoxyethoxyacetic acid was the only metabolite associated with non-occupational exposure.ConclusionsMetabolites of glycol ethers and chlorinated solvents were present at low levels in the urine of pregnant women. Most metabolites were associated with occupational exposure.
Iron Deficiency in Community-Dwelling US Adults With Self-Reported Heart Failure in the National Health and Nutrition Examination Survey III
Authors: Parikh Ankit , Natarajan Sundar , Lipsitz Stuart R. , Katz Stuart D. 
Published: June 2011

Background—
Iron deficiency has been proposed as a potential therapeutic target in heart failure, but its prevalence and association with anemia and clinical outcomes in community-dwelling adults with heart failure have not been well characterized.

Methods and Results—

Using data from the Third National Health and Nutrition Examination Survey, we evaluated the associations between iron deficiency, hemoglobin, C-reactive protein (CRP), and all-cause and cardiovascular mortality in 574 adults with self-reported heart failure. Iron deficiency was defined in both absolute and functional terms as a ferritin level <100 μg/L or between 100 and 299 μg/L if the transferrin saturation was <20%. Iron deficiency was present in 61.3% of participants and was associated with reduced mean hemoglobin (13.6 versus 14.2 g/dL,
P
=0.007) and increased mean CRP (0.95 versus 0.63 mg/dL,
P
=0.04). Over a median of 6.7 years of follow-up, there were 300 all-cause deaths, 193 of which were from cardiovascular causes. In age- and sex-adjusted Cox proportional hazards models, hemoglobin, CRP, and transferrin saturation but not iron deficiency were significantly associated with all-cause and cardiovascular mortality. In multivariate models, hemoglobin remained an independent predictor of cardiovascular mortality, whereas CRP remained an independent predictor of both all-cause and cardiovascular mortality.

Conclusions—
Iron deficiency is common in heart failure and is associated with decreased hemoglobin and increased CRP. In multivariate analysis, hemoglobin was associated with cardiovascular mortality while CRP was associated with both all-cause and cardiovascular mortality. Iron deficiency was not associated with all-cause or cardiovascular mortality in this cohort.
Climate Hazard Assessment for Stakeholder Adaptation Planning in New York City
Authors: Horton Radley M. , Gornitz Vivien , Bader Daniel A. , Ruane Alex C. , Goldberg Richard , Rosenzweig Cynthia 
Published: June 2011

AbstractThis paper describes a time-sensitive approach to climate change projections that was developed as part of New York City’s climate change adaptation process and that has provided decision support to stakeholders from 40 agencies, regional planning associations, and private companies. The approach optimizes production of projections given constraints faced by decision makers as they incorporate climate change into long-term planning and policy. New York City stakeholders, who are well versed in risk management, helped to preselect the climate variables most likely to impact urban infrastructure and requested a projection range rather than a single “most likely” outcome. The climate projections approach is transferable to other regions and is consistent with broader efforts to provide climate services, including impact, vulnerability, and adaptation information. The approach uses 16 GCMs and three emissions scenarios to calculate monthly change factors based on 30-yr average future time slices relative to a 30-yr model baseline. Projecting these model mean changes onto observed station data for New York City yields dramatic changes in the frequency of extreme events such as coastal flooding and dangerous heat events. On the basis of these methods, the current 1-in-10-year coastal flood is projected to occur more than once every 3 years by the end of the century and heat events are projected to approximately triple in frequency. These frequency changes are of sufficient magnitude to merit consideration in long-term adaptation planning, even though the precise changes in extreme-event frequency are highly uncertain.
A New Single-Layer Urban Canopy Model for Use in Mesoscale Atmospheric Models
Authors: Ryu Young-Hee , Baik Jong-Jin , Lee Sang-Hyun 
Published: June 2011

AbstractA new single-layer urban canopy model for use in mesoscale atmospheric models is developed and validated. The urban canopy model represents a built-up area as a street canyon, two facing buildings, and a road. In this model, the two facing walls are divided into sunlit and shaded walls on the basis of solar azimuth angle and canyon orientation, and individual surface temperature and energy budget are calculated for each wall. In addition, for better estimation of turbulent energy exchange within the canyon, a computational fluid dynamics model is employed to incorporate the effects of canyon aspect ratio (height-to-width ratio) and reference wind direction on canyon wind speed. The model contains the essential physical processes occurring in an urban canopy: absorption and reflection of shortwave and longwave radiation, exchanges of turbulent energy and water between surfaces (roof, two facing walls, and road) and adjacent air, and heat transfer by conduction through substrates. The developed urban canopy model is validated using datasets obtained at two urban sites: Marseille, France, and Basel, Switzerland. The model satisfactorily reproduces canyon air temperatures, surface temperatures, net radiation, sensible heat fluxes, latent heat fluxes, and storage heat fluxes for both sites. Extensive experiments are conducted to examine the sensitivities of the urban surface energy balance to meteorological factors and urban surface parameters. The reference wind speed is found to be a more crucial meteorological factor than the reference air temperature in altering urban surface energy balance, especially for weak winds. The urban surface energy balance is most sensitive to the roof albedo among urban surface parameters. The roof fraction, canyon aspect ratio, and ratio of roughness length for momentum to that for heat for the roof play important roles in altering urban surface energy balance.
Dependency of Feedbacks on Forcing and Climate State in Physics Parameter Ensembles
Authors: Yoshimori Masakazu , Hargreaves Julia C. , Annan James D. , Yokohata Tokuta , Abe-Ouchi Ayako 
Published: June 2011

Abstract
Climate sensitivity is one of the most important metrics for future climate projections. In previous studies the climate of the last glacial maximum has been used to constrain the range of climate sensitivity, and similarities and differences of temperature response to the forcing of the last glacial maximum and to idealized future forcing have been investigated. The feedback processes behind the response have not, however, been fully explored in a large model parameter space. In this study, the authors first examine the performance of various feedback analysis methods that identify important feedbacks for a physics parameter ensemble in experiments simulating both past and future climates. The selected methods are then used to reveal the relationship between the different ensemble experiments in terms of individual feedback processes. For the first time, all of the major feedback processes for an ensemble of paleoclimate simulations are evaluated. It is shown that the feedback and climate sensitivity parameters depend on the nature of the forcing and background climate state. The forcing dependency arises through the shortwave cloud feedback while the state dependency arises through the combined water vapor and lapse-rate feedback. The forcing dependency is, however, weakened when the feedback is estimated from the forcing that includes tropospheric adjustments. Despite these dependencies, past climate can still be used to provide a useful constraint on climate sensitivity as long as the limitation is properly taken into account because the strength of each feedback correlates reasonably well between the ensembles. It is, however, shown that the physics parameter ensemble does not cover the range of results simulated by structurally different models, which suggests the need for further study exploring both structural and parameter uncertainties.
Future Change in Extratropical Cyclones Associated with Change in the Upper Troposphere
Authors: Mizuta Ryo , Matsueda Mio , Endo Hirokazu , Yukimoto Seiji 
Published: June 2011

Abstract
Future changes in Northern Hemisphere wintertime storm activity as a consequence of global warming are investigated using the AGCM of Meteorological Research Institute (MRI-AGCM) with horizontal grid sizes of 60 and 20 km. A future (2075–99) climate experiment, in which the change in sea surface temperature (SST) derived from the Coupled Model Intercomparison Project phase 3 (CMIP3) multimodel ensemble mean is added to observed SST, is compared with a present-day (1979–2003) climate experiment. Results of three-member simulations using the 60-km model are presented. A single simulation using the 20-km model is also presented, showing that similar results are obtained.
In the future climate experiment, the number of intense cyclones (sea level pressure below 980 hPa) shows a significant increase whereas the number of total cyclones shows a significant decrease, similar to the results obtained from the CMIP3 models themselves. The increase in intense cyclones is seen on the polar side and downstream side of Atlantic and Pacific storm tracks. At the same time, the growth rate of the cyclones increases in areas upstream of these regions.
For the regions with the increasing growth rate, a high correlation is seen between the growth rate of the surface cyclones and upper-tropospheric zonal wind at a monthly-mean time scale. Months of high cyclone growth rate with strong zonal wind in these regions become more frequent, and months of low cyclone growth rate with weak zonal wind become less frequent. One of the possibilities that can explain this relationship is changes in the wave-breaking pattern, that is, a decrease in wave breakings in areas of cyclonic shear and an increase in wave breakings in areas of anticyclonic shear. Associated with these changes, rapid cyclone developments are more commonly seen, and weak, long-lived cyclones become less frequent.
Interannual Variability of High-Wind Occurrence over the North Atlantic*
Authors: Cheng Xuhua , Xie Shang-Ping , Tokinaga Hiroki , Du Yan 
Published: June 2011

Abstract
Interannual variability of high-wind occurrence over the North Atlantic is investigated based on observations from the satellite-borne Special Sensor Microwave Imager (SSM/I). Despite no wind direction being included, SSM/I data capture major features of high-wind frequency (HWF) quite well. Climatology maps show that HWF is highest in winter and is close to zero in summer. Remarkable interannual variability of HWF is found in the vicinity of the Gulf Stream, over open sea south of Iceland, and off Cape Farewell, Greenland. On interannual scales, HWF south of Iceland has a significant positive correlation with the North Atlantic Oscillation (NAO). An increase in the mean westerlies and storm-track intensity during a positive NAO event cause HWF to increase in this region. In the vicinity of the Gulf Stream, HWF is significantly correlated with the difference between sea surface temperature and surface air temperature (SST − SAT), indicative of the importance of atmospheric instability. Cross-frontal wind and an SST gradient are important for the instability of the marine atmospheric boundary layer on the warm flank of the SST front. Off Cape Farewell, high wind occurs in both westerly and easterly tip jets. Quick Scatterometer (QuikSCAT) data show that variability in westerly (easterly) HWF off Cape Farewell is positively (negatively) correlated with the NAO.
Forcing of the Arctic Oscillation by Eurasian Snow Cover
Authors: Allen Robert J. , Zender Charles S. 
Published: June 2011

AbstractThroughout much of the latter half of the twentieth century, the dominant mode of Northern Hemisphere (NH) extratropical wintertime circulation variability—the Arctic Oscillation (AO)—exhibited a positive trend, with decreasing high-latitude sea level pressure (SLP) and increasing midlatitude SLP. General circulation models (GCMs) show that this trend is related to several factors, including North Atlantic SSTs, greenhouse gas/ozone-induced stratospheric cooling, and warming of the Indo-Pacific warm pool. Over the last approximately two decades, however, the AO has been decreasing, with 2009/10 featuring the most negative AO since 1900. Observational and idealized modeling studies suggest that snow cover, particularly over Eurasia, may be important. An observed snow–AO mechanism also exists, involving the vertical propagation of a Rossby wave train into the stratosphere, which induces a negative AO response that couples to the troposphere. Similar to other GCMs, the authors show that transient simulations with the Community Atmosphere Model, version 3 (CAM3) yield a snow–AO relationship inconsistent with observations and dissimilar AO trends. However, Eurasian snow cover and its interannual variability are significantly underestimated. When the albedo effects of snow cover are prescribed in CAM3 (CAM PS) using satellite-based snow cover fraction data, a snow–AO relationship similar to observations develops. Furthermore, the late-twentieth-century increase in the AO, and particularly the recent decrease, is reproduced by CAM PS. The authors therefore conclude that snow cover has helped force the observed AO trends and that it may play an important role in future AO trends.