bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil
Authors: Yuan Yanli , Conrad Ralf , Lu Yahai 
Published: January 2011

SummaryMethane production in paddy soil is substantially suppressed after even a brief exposure of soil to oxygen. We hypothesized that the strong response of methanogen activity is reflected in the transcription of functional genes rather than in the composition of the community of methanogens. Therefore, we determined the community composition and the transcriptional response of methanogens in a rice field soil by targeting the mcrA gene (encoding the α subunit of methyl‐coenzyme M reductase). Transcription of mcrA genes measured by quantitative PCR decreased by an order of magnitude after brief exposure to O2. Terminal restriction fragment length polymorphism of mcrA genes and gene transcripts showed that although the community structure of methanogens did not change, the composition of transcripts dramatically responded to O2 exposure. In the beginning, transcripts of Methanocellales were the relatively most abundant, indicating resistance of these hydrogenotrophic methanogens against O2 stress. Later on, mcrA transcripts of acetoclastic methanogens became relatively more abundant coinciding with the turnover of acetate. The transcription of Methanosarcinaceae was relatively greater when acetate accumulated while Methanosaetaceae became more active when acetate concentrations decreased. In the presence of methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, mcrA transcription by Methanosaetaceae was greatly suppressed while that of Methanosarcinaceae was less affected. Our study showed that in contrast to constant community structure as revealed by DNA‐based fingerprinting the transcription of functional mcrA genes strongly responded to O2 stress and the presence of inhibitor CH3F. The response patterns reflected the genomic and physiological traits of individual methanogens.
Staphylococcus aureus virulence and metabolism are dramatically affected by Lactococcus lactis in cheese matrix
Authors: Cretenet Marina , Nouaille Sébastien , Thouin Jennifer , Rault Lucie , Stenz Ludwig , François Patrice , Hennekinne Jacques‐Antoine , Piot Michel , Maillard Marie Bernadette , Fauquant Jacques , Loubière Pascal , Le Loir Yves , Even Sergine 
Published: January 2011

SummaryIn complex environments such as cheeses, the lack of relevant information on the physiology and virulence expression of pathogenic bacteria and the impact of endogenous microbiota has hindered progress in risk assessment and control. Here, we investigated the behaviour of Staphylococcus aureus, a major foodborne pathogen, in a cheese matrix, either alone or in the presence of Lactococcus lactis, as a dominant species of cheese ecosystems. The dynamics of S. aureus was explored in situ by coupling a microbiological and, for the first time, a transcriptomic approach. Lactococcus lactis affected the carbohydrate and nitrogen metabolisms and the stress response of S. aureus by acidifying, proteolysing and decreasing the redox potential of the cheese matrix. Enterotoxin expression was positively or negatively modulated by both L. lactis and the cheese matrix itself, depending on the enterotoxin type. Among the main enterotoxins involved in staphylococcal food poisoning, sea expression was slightly favoured in the presence of L. lactis, whereas a strong repression of sec4 was observed in cheese matrix, even in the absence of L. lactis, and correlated with a reduced saeRS expression. Remarkably, the agr system was downregulated by the presence of L. lactis, in part because of the decrease in pH. This study highlights the intimate link between environment, metabolism and virulence, as illustrated by the influence of the cheese matrix context, including the presence of L. lactis, on two major virulence regulators, the agr system and saeRS.
The influences of course effort, mastery and performance goals, grade expectancies, and earned course grades on student ratings of course satisfaction
Authors: Svanum Soren , Aigner Carrie 
Published: January 2011

Background.  The positive relation between course grades and student ratings of course satisfaction is well established but controversy continues concerning the magnitude, interpretation, and implications of this association.Aims.  This study examined the within course relations of a set of variables often implicated as potential contributors to the grade‐student rating relation.Sample.  Two‐hundred and twenty students enrolled in an internet‐based university course.Method.  Measures of course mastery and performance goals, expected grades, course effort, cumulative GPA, and final course grade were prospectively collected. The dependent variable was a global measure of course satisfaction obtained at the end of the semester.Results.  A path model fit the data very well and all study variables directly or indirectly predicted course satisfaction. Grades had a moderately strong effect, half of which was independent of other model variables. Adjusting for all model variables, students high on mastery course goals evaluated the course more positively whereas students high on performance goals provided less favourable evaluations.Conclusions.  Students can assess the same course and instructor in different ways depending upon such factors as their degree of success, their motivations for taking the course, and the amount of effort invested. Course satisfaction, then, can be substantially influenced by factors loosely or unrelated to course or teacher effectiveness.
The cognitive underpinnings of emerging mathematical skills: Executive functioning, patterns, numeracy, and arithmetic
Authors: Lee Kerry , Ng Swee Fong , Pe Madeline Lee , Ang Su Yin , Hasshim Muhammad Nabil Azhar Mohd , Bull Rebecca 
Published: January 2011

Background: Exposure to mathematical pattern tasks is often deemed important for developing children's algebraic thinking skills. Yet, there is a dearth of evidence on the cognitive underpinnings of pattern tasks and how early competencies on these tasks are related to later development.Aims: We examined the domain‐specific and domain‐general determinants of performances on pattern tasks by using (a) a standardized test of numerical and arithmetic proficiency and (b) measures of executive functioning, respectively.Sample: Participants were 163 6‐year‐olds enrolled in primary schools that typically serve families from low to middle socioeconomic backgrounds.Method: Children were administered a battery of executive functioning (inhibitory, switching, updating), numerical and arithmetic proficiency (the Numerical Operations task from the Wechsler Individual Achievement Test‐II), and three types of pattern tasks.Results: Contrary to findings from the adult literature, we found all the executive functioning measures coalesced into two factors: updating and an inhibition/switch factor. Only the updating factor predicted performances on the pattern tasks. Although performance on the pattern tasks were correlated with numerical and arithmetic proficiency, findings from structural equation modelling showed that there were no direct or independent relationships between them.Conclusions: The findings suggest that the bivariate relationships between pattern, numeracy, and arithmetic tasks are likely due to their shared demands on updating resources. Unlike older children, these findings suggest that for 6‐year‐olds, better numerical and arithmetic proficiency, without accompanying advantages in updating capacities, will no more likely lead to better performance on the pattern tasks.
Development and Validation of a Multiplex Microsphere-Based Assay for Detection of Domestic Cat (
Felis catus
) Cytokines
Authors: Wood Britta A. , O'Halloran Kevin P. , VandeWoude Sue 
Published: January 2011

ABSTRACT

Cytokines are essential signaling molecules that mediate the innate immune response, and therefore their presence can be of diagnostic, prognostic, and pathogenic significance. Microsphere-based immunoassays allow rapid and accurate evaluation of cytokine levels in several species, including humans, dogs, and mice; however, technology to evaluate domestic cat (
Felis catus
) cytokines has been limited to single-analyte enzyme-linked immunosorbent assays (ELISAs). Microsphere-based immunoassays provide an attractive alternative technology for detecting and quantifying multiple analytes in a single assay using as little as 50 μl of sample. We describe the development and validation of a microsphere-based assay for three commonly analyzed domestic cat cytokines (gamma interferon, interleukin-10, and interleukin-12/interleukin-23 p40) using reagents from commercially available ELISAs. The assay was optimized for capture and detection antibody concentrations, streptavidin-phycoerythrin concentration, and number of microspheres. The validated lower and upper quantitation limits were 31 and 1,000 pg/ml for gamma interferon, 63 and 2,000 pg/ml for interleukin-10, and 39 and 625 pg/ml for interleukin-12/interleukin-23 p40. Cytokine concentrations in peripheral blood mononuclear cell supernatants were measured, and results obtained by the microsphere assay were correlated with values obtained with commercially available ELISA kits. This technology is a convenient and reproducible assay to evaluate domestic cat cytokine responses elicited by a variety of diseases.
Prevalence of Antibodies against Seasonal Influenza A and B Viruses in Children in Netherlands
Authors: Bodewes R. , de Mutsert G. , van der Klis F. R. M. , Ventresca M. , Wilks S. , Smith D. J. , Koopmans M. , Fouchier R. A. M. , Osterhaus A. D. M. E. , Rimmelzwaan G. F. 
Published: January 2011

ABSTRACT
To gain insight into the age at which children become infected with influenza viruses for the first time, we analyzed the seroprevalence of antibodies against influenza viruses in children 0 to 7 years of age in the Netherlands. Serum samples were collected during a cross-sectional population-based study in 2006 and 2007 and were tested for the presence of antibodies against influenza A/H1N1, A/H3N2, and B viruses representative of viruses present in previous influenza seasons using the hemagglutination inhibition assay. The seroprevalence of antibodies to influenza virus was higher in children 1 to 6 months of age than in children 7 to 12 months of age, which likely reflects the presence of maternally derived antibodies. The proportion of study subjects >1 year of age with detectable antibodies against influenza viruses gradually increased with age until they reached the age of 6 years, when they all had antibodies to at least one influenza A virus. These findings may have implications for the development of vaccination strategies aiming at the protection of young children against seasonal and/or pandemic influenza virus infection.
Molecular Epidemiology of Mycobacterium avium subsp. paratuberculosis in a Longitudinal Study of Three Dairy Herds
Authors: Pradhan Abani K. , Mitchell Rebecca M. , Kramer Aagje J. , Zurakowski Michael J. , Fyock Terry L. , Whitlock Robert H. , Smith Julia M. , Hovingh Ernest , Van Kessel Jo Ann S. , Karns Jeffrey S. , Schukken Ynte H. 
Published: January 2011

ABSTRACTThe objective of this study was to evaluate whether cows that were low shedders ofMycobacterium aviumsubsp.paratuberculosiswere passively shedding or truly infected withM. aviumsubsp.paratuberculosis. We also investigated whether it is possible that theseM. aviumsubsp.paratuberculosis-infected animals could have been infected as adults by contemporary high-shedding animals (supershedders). TheM. aviumsubsp.paratuberculosisisolates were obtained from a longitudinal study of three dairy herds in the northeastern United States. Isolates were selected from fecal samples and tissues at slaughter from all animals that were culture positive at the same time that supershedders were present in the herds. Shedding levels (CFU ofM. aviumsubsp.paratuberculosis/g of feces) for the animals at each culture-positive occasion were determined. Using a multilocus short-sequence-repeat technique, we found 15 different strains ofM. aviumsubsp.paratuberculosisfrom a total of 142 isolates analyzed. Results indicated herd-specific infection patterns; there was a clonal infection in herd C, with 89% of isolates from animals sharing the same strain, whereas herds A and B showed several different strains infecting the animals at the same time. Tissues from 80% of cows with at least one positive fecal culture (other than supershedders) were culture positive, indicating a trueM. aviumsubsp.paratuberculosisinfection. The results ofM. aviumsubsp.paratuberculosisstrain typing and observed shedding levels showed that at least 50% of low shedders have the same strain as that of a contemporary supershedder. Results of this study suggest that in a dairy herd, more of the low-shedding cows are truly infected withM. aviumsubsp.paratuberculosisthan are passively sheddingM. aviumsubsp.paratuberculosis. The sharing of strains between low shedders and the contemporary supershedders suggests that low shedders may have been infected by environmental exposure ofM. aviumsubsp.paratuberculosis.
Ribosomal RNA Sequence Analysis of Brucella Infection Misidentified as Ochrobactrum anthropi Infection
Authors: Horvat Rebecca T. , El Atrouni Wissam , Hammoud Kassem , Hawkinson Dana , Cowden Scott 
Published: January 2011

ABSTRACT

A
Brucella
isolate was identified from purulent material collected during a hip surgery. Two previous blood cultures from the same patient yielded
Ochrobactrum anthropi
. After rRNA sequencing, all the isolates were identified as
Brucella
species and subsequently serotyped as
Brucella suis
. Misidentification of
Brucella
species remains a problem with bacterial identification systems.
Comparison of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometer to BD Phoenix Automated Microbiology System for Identification of Gram-Negative Bacilli
Authors: Saffert Ryan T. , Cunningham Scott A. , Ihde Sherry M. , Monson Jobe Kristine E. , Mandrekar Jayawant , Patel Robin 
Published: January 2011

ABSTRACT

We compared the BD Phoenix automated microbiology system to the Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) system for identification of Gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. The BD Phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. The Bruker Biotyper correctly identified 408 (93%) and 360 (82%) isolates to the genus and species level, respectively. The 440 isolates were grouped into common (308) and infrequent (132) isolates in the clinical laboratory. For the 308 common isolates, the BD Phoenix and Bruker Biotyper correctly identified 294 (95%) and 296 (96%) of the isolates to the genus level, respectively. For species identification, the BD Phoenix and Bruker Biotyper correctly identified 93% of the common isolates (285 and 286, respectively). In contrast, for the 132 infrequent isolates, the Bruker Biotyper correctly identified 112 (85%) and 74 (56%) isolates to the genus and species level, respectively, compared to the BD Phoenix, which identified only 69 (52%) and 45 (34%) isolates to the genus and species level, respectively. Statistically, the Bruker Biotyper overall outperformed the BD Phoenix for identification of Gram-negative bacilli to the genus (
P
< 0.0001) and species (
P
= 0.0005) level in this sample set. When isolates were categorized as common or infrequent isolates, there was statistically no difference between the instruments for identification of common Gram-negative bacilli (
P
> 0.05). However, the Bruker Biotyper outperformed the BD Phoenix for identification of infrequently isolated Gram-negative bacilli (
P
< 0.0001).
High Rate of Exophiala dermatitidis Recovery in the Airways of Patients with Cystic Fibrosis Is Associated with Pancreatic Insufficiency
Authors: Kondori Nahid , Gilljam Marita , Lindblad Anders , Jönsson Bodil , Moore Edward R. B. , Wennerås Christine 
Published: January 2011

ABSTRACTThe black-pigmented fungusExophiala dermatitidisis considered to be a harmless colonizer of the airways of cystic fibrosis (CF) patients. The aim of this study was to establish the recovery rate ofE. dermatitidisin respiratory specimens from CF patients, transplant recipients, and subjects with other respiratory disorders in Sweden. Second, we wished to determine if particular clinical traits were associated withE. dermatitidiscolonization of the airways and the antifungal susceptibility profiles ofExophialastrains. Sputum and bronchoalveolar lavage samples (n= 492) derived from 275 patients were investigated.E. dermatitidiswas isolated in respiratory specimens from 19% (18/97) of the CF patients but in none of the other patient categories. All isolates were recovered after 6 to 25 days of incubation on erythritol-chloramphenicol agar (ECA) medium. Morphological and genetic analyses confirmed species identity. Pancreatic insufficiency was positively associated with the presence ofE. dermatitidisin sputum samples (P= 0.0198). Antifungal susceptibility tests demonstrated that voriconazole and posaconazole had the lowest MICs againstE. dermatitidis. In conclusion,E. dermatitidisis a frequent colonizer of the respiratory tract in CF patients in Sweden and appears to be associated with more advanced disease. WhetherE. dermatitidisis pathogenic remains to be elucidated.
Aminoglycoside-Resistant Aeromonas hydrophila as Part of a Polymicrobial Infection following a Traumatic Fall into Freshwater
Authors: Shak Joshua R. , Whitaker Jennifer A. , Ribner Bruce S. , Burd Eileen M. 
Published: January 2011

ABSTRACT

Amikacin is a first-line treatment for
Aeromonas
infection due to high efficacy. There are few reports of aminoglycoside-resistant
Aeromonas
spp. We report a soft tissue infection containing multiple pathogens, including a strain of
Aeromonas hydrophila
resistant to amikacin, tobramycin, and multiple cephalosporins.
Rapid Stool-Based Diagnosis of Clostridium difficile Infection by Real-Time PCR in a Children's Hospital
Authors: Luna Ruth Ann , Boyanton Bobby L. , Mehta Seema , Courtney Ebony M. , Webb C. Renee , Revell Paula A. , Versalovic James 
Published: January 2011

ABSTRACT

Clostridium difficile
is a major cause of nosocomial antibiotic-associated infectious diarrhea and pseudomembranous colitis. Detection of
C. difficile
by anaerobic bacterial culture and/or cytotoxicity assays has been largely replaced by rapid enzyme immunoassays (EIA). However, due to the lack of sensitivity of stool EIA, we developed a multiplex real-time PCR assay targeting the
C. difficile
toxin genes
tcdA
and
tcdB
. Stool samples from hospitalized pediatric patients suspected of having
C. difficile
-associated disease were prospectively cultured on cycloserine-cefoxitin-fructose agar following alcohol shock. Six testing modalities were evaluated, including stool EIA, culture EIA, and real-time PCR (
tcdA
and
tcdB
) of cultured isolates and stool samples. Real-time PCR detection was performed with
tcdA
and
tcdB
gene-specific primers and hydrolysis probes using the LightCycler platforms (Roche Diagnostics, Indianapolis, IN). A total of 157 samples from 96 pediatric patients were analyzed. The sensitivities of stool real-time PCR and stool EIA were 95% and 35%, respectively, with a specificity of 100% for both methods. The lower limit of detection of the stool real-time PCR was 30 CFU/ml of stool sample per reaction for
tcdA
and
tcdB
. This study highlights the poor performance of stool toxin EIAs in pediatric settings. Direct detection of
C. difficile
toxin genes in stool samples by real-time PCR showed sensitivity superior to that of stool and culture EIAs and performance comparable to that of real-time PCR assay of cultured isolates. Real-time PCR of DNA from stool samples is a rapid and cost-effective diagnostic modality for children that should facilitate appropriate patient management and halt the practice of serial testing by EIA.
Distribution of Putative Virulence Genes in Streptococcus mutans Strains Does Not Correlate with Caries Experience
Authors: Argimón Silvia , Caufield Page W. 
Published: January 2011

ABSTRACT

Streptococcus mutans
, a member of the human oral flora, is a widely recognized etiological agent of dental caries. The cariogenic potential of
S. mutans
is related to its ability to metabolize a wide variety of sugars, form a robust biofilm, produce copious amounts of lactic acid, and thrive in the acid environment that it generates. The remarkable genetic variability present within the species is reflected at the phenotypic level, notably in the differences in the cariogenic potential between strains. However, the genetic basis of these differences is yet to be elucidated. In this study, we surveyed by PCR and DNA hybridization the distribution of putative virulence genes, genomic islands, and insertion sequences across a collection of 33 strains isolated from either children with severe early childhood caries (S-ECC) or those who were caries free (CF). We found this genetically diverse group of isolates to be remarkably homogeneous with regard to the distribution of the putative virulence genes and genetic elements analyzed. Our findings point to the role of other factors in the pathogenesis of S-ECC, such as uncharacterized virulence genes, differences in gene expression and/or enzymatic activity, cooperation between
S. mutans
strains or with other members of the oral biota, and host factors.
Comparison of Two Mycoplasma genitalium Real-Time PCR Detection Methodologies
Authors: Twin Jimmy , Taylor Nicole , Garland Suzanne M. , Hocking Jane S. , Walker Jennifer , Bradshaw Catriona S. , Fairley Christopher K. , Tabrizi Sepehr N. 
Published: January 2011

ABSTRACT

Established in-house quantitative PCR (qPCR) assays to detect the
Mycoplasma genitalium
adhesion protein (MgPa) and the 16S rRNA gene were found to be comparable for screening purposes, with a kappa value of 0.97 (95% confidence interval [CI], 0.94 to 1.01) and no difference in bacterial load quantified (
P
= 0.4399).
Comparison of the Broth Microdilution Methods of the European Committee on Antimicrobial Susceptibility Testing and the Clinical and Laboratory Standards Institute for Testing Itraconazole, Posaconazole, and Voriconazole against Aspergillus Isolates
Authors: Pfaller M. , Boyken L. , Hollis R. , Kroeger J. , Messer S. , Tendolkar S. , Diekema D. 
Published: January 2011

ABSTRACT

We compared EUCAST and CLSI antifungal susceptibility testing methods for itraconazole, posaconazole, and voriconazole by testing 245
Aspergillus
clinical isolates. The essential agreement (EA) between methods was excellent: 100% (itraconazole), 98.4% (posaconazole), and 99.6% (voriconazole) assessing EA at ±2 dilutions and 99.6% (itraconazole), 87.7% (posaconazole), and 96.3% (voriconazole) at ±1 dilution.
Methicillin-Resistant Staphylococcus aureus Colonization at Different Body Sites: a Prospective, Quantitative Analysis
Authors: Mermel Leonard A. , Cartony Jennifer M. , Covington Pauline , Maxey Gail , Morse Dan 
Published: January 2011

ABSTRACTWe quantified methicillin-resistantStaphylococcus aureus(MRSA) carriage. The greater the log10count in samples from the nares, the greater the likelihood that other body sites had been colonized. Log10counts among body sites were correlated. The greatest sensitivity value (98%) was determined for the combined results from 2 sites: the nares and the groin.