bluuebunny/crossref_metadata_2025 huggingface dataset:
Adequacy of Oral Health Information for Patients with Diabetes
Authors: Yuen Hon K. , Mountford William K. , Magruder Kathryn M. , Bandyopadhyay Dipankar , Hudson Pemra L. , Summerlin Lisa M. , Salinas Carlos F.
Published: January 2009

Objective: We investigated the perception of dental hygienists regarding their adequacy of providing diabetics with diabetes‐related oral health preventive education. Methods: A one‐page questionnaire printed on both sides was mailed to 2,237 licensed registered dental hygienists with a South Carolina (SC) mailing address. In addition to the dental hygienists' background and practice characteristics, their perception of adequacy for educating patients with diabetes on various diabetes‐related oral health topics and reasons for inadequate coverage of materials were queried in the survey. Results: After two follow‐up mailings, 995 completed and usable surveys were returned. An average of 93.6 percent of respondents indicated that they adequately covered topics of oral hygiene and general oral health issues. However, about 60 percent of respondents reported not covering all essential materials related to oral health when educating diabetic patients. The three most common reasons were: a) insufficient time (60.1 percent); b) patient disinterest (41.2 percent); and c) insufficient information on oral care and diabetes (39.7 percent). Respondents reporting insufficient information were less likely to adequately address the effect of periodontal disease on diabetes (P < 0.001), effect of uncontrolled diabetes on periodontal disease (P < 0.001), and dry mouth management (P = 0.03). Conclusion: This study indicates that SC dental hygienists do not routinely provide patient education on diabetes‐related oral health and healthy lifestyle topics. Lack of time, patient disinterest, and insufficient information were the three main reasons for respondents not covering these essentials. A practical method for improving dental hygienists' comprehensive service to patients with diabetes is to offer them more continuing education on diabetes and oral health to supplement their knowledge, skills, and confidence to educate this growing population.
Assessing Levels of Agreement between Two Commonly Used Oral Health‐Related Quality of Life Measures
Authors: Bernabé Eduardo , De Oliveira Cesar M. , Sheiham Aubrey , Tsakos Georgios
Published: January 2009

Objective:This study aimed to assess the level of agreement between two commonly used oral health‐related quality of life (OHRQoL) measures, the short form of the Oral Health Impact Profile (OHIP14) and the Oral Impacts on Daily Performances (OIDP).Methods:A sample of 1,675 15‐ to 16‐year‐old students attending all schools in Bauru (Sao Paulo, Brazil) was selected. The impact of oral conditions on quality of life in the last 6 months was reported using both OHIP14 and OIDP. To allow for comparison with the 100 percent OIDP score, OHIP14 scores were converted to percentages. Then, agreement between the two OHRQoL measures was analyzed using the Bland and Altman method.Results:The mean difference between OHIP14 and OIDP was 6.48 percent [confidence interval95%(6.08; 6.89)], with higher scores reported for OHIP14 than for OIDP. Besides, 95 percent of the differences between the two OHRQoL measures were between −10.59 and 23.56 percent. Finally, differences between OHIP14 and OIDP increased significantly as the magnitude of their average increased (P < 0.001).Conclusion:There was a moderate level of agreement between OHIP14 and OIDP, which may be partly due to the fact that both OHRQoL measures assess different levels of oral impacts on quality of life in addition to having different scoring systems.
Implementing a Tobacco Assisted Referral Program in Dental Practices
Authors: Little Sally J. , Hollis Jack F. , Fellows Jeffrey L. , Snyder John J. , Dickerson John F.
Published: January 2009

Objectives: The objectives of this study are to design and implement a system‐level tobacco‐control intervention in a large prepaid dental group practice and assess effects on staff performance measures and patient satisfaction. Methods: We matched 14 dental facilities on size, socioeconomic status, smoking rate, and periodontal status, and then randomly assigned them to intervention or usual‐care control. We trained intervention staff in an “Assisted Referral” team approach for assessing tobacco use, providing tailored advice and brief counseling, and encouraging smokers to talk by telephone with a specially trained tobacco counselor. Patients could call from the office or ask that the counselor call them later. Telephone counselors helped patients explore motivations and barriers for quitting; review available cessation‐support strategies, programs, and medications; and identify next steps. Results: During the 14‐month study period, 66,516 members had annual‐ or new‐patient examinations. Both intervention and control sites had high rates of tobacco assessment (97 percent) and advice (93 percent). Intervention patients were more likely than controls (69 percent versus 3 percent, P < 0.01) to receive additional chair‐side tobacco counseling and assistance, and 11 percent agreed to receive additional telephone counseling. Intervention patients were more satisfied than controls with the dental team's tobacco‐control efforts (P < 0.03). Referral rates varied substantially for different staff. Conclusions: The Assisted Referral approach was successfully integrated into routine dental care, was well received by patients, and resulted in increased patient satisfaction. Because free telephone‐based tobacco counseling is now available nationwide, the approach may be a practical strategy for most dental‐care settings.
Characteristics of African‐American Male Caregivers in a Study of Oral Health in Detroit – A Brief Communication1
Authors: Reisine Susan , Ajrouch Kristine J. , Sohn Woosung , Lim Sungwoo , Ismail Amid
Published: January 2009

Objective:The role of fathers among African‐American men, particularly related to oral health, has received relatively little scholarly attention. This paper describes the characteristics of African‐American men who self‐identified as primary caregiver to an index child participating in the Detroit Dental Health Project.Methods:Of 1,021 caregiver–child pairs recruited to this oral health study, 52 were male. Data were collected at a central site in Detroit on: 1) demographics; 2) social support; 3) oral health beliefs, behaviors, and knowledge; 4) caregivers' and child's oral health.Results:Participants reported good availability of social support and high perceived self‐efficacy to take care of their child's teeth, yet, they possessed limited knowledge on preventing oral health problems. Moreover, male caregivers had high levels of caries, missing teeth, and poor hygiene.Conclusions:Findings may inform the development of effective interventions aimed at male caregivers to improve knowledge and understanding of the caries process, particularly concerning their children.
Prevalence of Early Childhood Caries Among Very Young Urban Boston Children Compared with US Children
Authors: Nunn Martha E. , Dietrich Thomas , Singh Harpreet K. , Henshaw Michelle M. , Kressin Nancy R.
Published: January 2009

Objectives:
The aims of this study were to compare prevalence of early childhood caries (ECC) in 1‐ to 3‐year‐old children seeing primary‐care pediatricians at two urban medical centers in Boston to the prevalence of ECC in similarly aged US children surveyed as part of the Third National Health and Nutrition Examination Survey (NHANES III) and to assess risk factors for ECC among this cohort of children compared with risk factors among similarly aged US children. Methods: Characteristics of 787 1‐ to 3‐year‐old children from two urban Boston medical centers were compared with those of 3,644 similarly aged US children surveyed as part of NHANES III. Demographic and social characteristics and ECC prevalence by putative risk factors were compared. A multiple logistic regression model was fit to assess putative risk factors and difference between groups simultaneously. Results: Race, age, previous dental visit, parents' education, and household income were significantly associated with ECC prevalence. Parents' place of birth was a significant effect modifier with lower ECC among Boston children of immigrants than among US children of immigrants. Conclusions: Lower ECC prevalence among urban Boston children of immigrant parents compared with US children of immigrant parents may reflect changing immigrant composition in the United States since NHANES III or a different immigrant composition in the Boston area compared with the United States. This finding reinforces the need for further research of immigrants in order to understand cultural practices that may affect oral health. Finally, low ECC prevalence among very young children reinforces the importance of early intervention in reducing ECC.
Characterization of novel microsatellites from Drosophila transversa
Authors: RÄISÄNEN L. , ROININEN E. , LIIMATAINEN J. O.
Published: January 2009

We investigated a partial genomic library of Drosophila transversa for microsatellites and developed 12 markers for genetic analyses. This is the first time that microsatellite primers from the quinaria species group have been described. Four loci were cross‐amplified in D. phalerata. Nine out of the 12 microsatellite markers developed are likely to be on the X chromosome.
Effects of a prior high‐intensity knee‐extension exercise on muscle recruitment and energy cost: a combined local and global investigation in humans
Authors: Layec Gwenael , Bringard Aurélien , Le Fur Yann , Vilmen Christophe , Micallef Jean‐Paul , Perrey Stéphane , Cozzone Patrick J. , Bendahan David
Published: January 2009

The effects of a priming exercise bout on both muscle energy production and the pattern of muscle fibre recruitment during a subsequent exercise bout are poorly understood. The purpose of the present study was to determine whether a prior exercise bout which is known to increase O2 supply and to induce a residual acidosis could alter energy cost and muscle fibre recruitment during a subsequent heavy‐intensity knee‐extension exercise. Fifteen healthy subjects performed two 6 min bouts of heavy exercise separated by a 6 min resting period. Rates of oxidative and anaerobic ATP production, determined with 31P‐magnetic resonance spectroscopy, and breath‐by‐breath measurements of pulmonary oxygen uptake were obtained simultaneously. Changes in muscle oxygenation and muscle fibre recruitment occurring within the quadriceps were measured using near‐infrared spectroscopy and surface electromyography. The priming heavy‐intensity exercise increased motor unit recruitment (P < 0.05) in the early part of the subsequent exercise bout but did not alter muscle energy cost. We also observed a reduced deoxygenation time delay, whereas the deoxygenation amplitude was increased (P < 0.01). These changes were associated with an increased oxidative ATP cost after ∼50 s (P < 0.05) and a slight reduction in the overall anaerobic rate of ATP production (0.11 ± 0.04 mm min−1 W−1 for bout 1 and 0.06 ± 0.11 mm min−1 W−1 for bout 2; P < 0.05). We showed that a priming bout of heavy exercise led to an increased recruitment of motor units in the early part of the second bout of heavy exercise. Considering the increased oxidative cost and the unaltered energy cost, one could suggest that our results illustrate a reduced metabolic strain per fibre.
Facilitating modularity and reuse: guidelines for structuring CellML 1.1 models by isolating common biophysical concepts
Authors: Wimalaratne S. M. , Halstead M. D. B. , Lloyd C. M. , Cooling M. T. , Crampin E. J. , Nielsen P. F.
Published: January 2009

The CellML language was developed in response to the need for a high‐level language to represent and exchange mathematical models of biological processes. The flexible structure of CellML allows modellers to construct mathematical models of the same biological system in many different ways. However, some modelling styles do not naturally lead to clear abstractions of the biophysical concepts and produce CellML models that are hard to understand and from which it is difficult to isolate parts that may be useful for constructing other models. In this article, we advocate building CellML models which isolate common biophysical concepts and, using these, to build mathematical models of biological processes that provide a close correspondence between the CellML model and the underlying biological process. Subsequently, models of higher complexity can be constructed by reusing these modularized CellML models in part or in whole. Development of CellML models that best describe the underlying biophysical concepts thus avoids the need to code models from scratch and enhances the extensibility, reusability, consistency and interpretation of the models.
Rabbit, a relevant model for the study of cardiac β3‐adrenoceptors
Authors: Audigane Leslie , Kerfant Benoît‐Gilles , El Harchi Aziza , Lorenzen‐Schmidt Ilka , Toumaniantz Gilles , Cantereau Anne , Potreau Daniel , Charpentier Flavien , Noireaud Jacques , Gauthier Chantal
Published: January 2009

The β3‐adrenoceptors (β3‐ARs) have been identified and characterized in the human heart. Specific β3‐AR stimulation, unlike β1‐AR or β2‐AR stimulation, decreases cardiac contractility, partly via the Gi–NO pathway. However, the precise role of cardiac β3‐ARs is not yet completely understood. Indeed, under normal conditions, the β3‐AR response is present only to a very low degree in rats and mice. Therefore, we evaluated whether β3‐ARs were present and functional in rabbit ventricular cardiomyocytes, and whether the rabbit could serve as a relevant model for the study of cardiac β3‐ARs. We used RT‐PCR and Western blot to measure the β3‐AR transcripts and protein levels in rabbit ventricular cardiomyocytes. We also analysed the effect of β3‐AR stimulation using isoproterenol in combination with nadolol or SR 58611A on cardiomyocyte shortening, Ca2+transient, L‐type Ca2+current (ICa,L), delayed rectifier potassium current (IKs) and action potential duration (APD). For the first time, we show that β3‐ARs are expressed in rabbit ventricular cardiomyocytes. The mRNA and protein sequences present a high homology to those of rat and human β3‐ARs. Furthermore, β3‐AR stimulation decreases cardiomyocyte shortening, Ca2+transient andICa,Lamplitudes, via a Gi–NO pathway. Importantly, β3‐AR stimulation enhancesIKsamplitude and shortens the APD. Taken together, our results indicate that the rabbit provides a relevant model, easily used in laboratories, to study the roles of cardiac β3‐ARs in physiological conditions.
Chamber‐specific effects of hypokalaemia on ventricular arrhythmogenicity in isolated, perfused guinea‐pig heart
Authors: Osadchii Oleg E. , Bentzen Bo Hjorth , Olesen Soren Peter
Published: January 2009

Diuretic‐induced hypokalaemia has been shown to promote cardiac arrhythmias in hypertensive patients. The present study was designed to determine whether hypokalaemia increases arrhythmic susceptibility of the left ventricle (LV) or the right ventricle (RV), or both. Proarrhythmic effects of hypokalaemic perfusion (2.5 mmK+for 30 min) were assessed in isolated guinea‐pig heart preparations using simultaneous recordings of volume‐conducted electrocardiogram and monophasic action potentials from six ventricular epicardial sites. Effective refractory periods, ventricular fibrillation thresholds and inducibility of tachyarrhythmias by programmed electrical stimulation and tachypacing were determined at the LV and the RV epicardial stimulation sites. Hypokalaemia promoted spontaneous ventricular ectopic activity, an effect attributed to non‐uniform prolongation of ventricular repolarization resulting in increased RV‐to‐LV transepicardial dispersion of refractoriness and action potential duration. Furthermore, hypokalaemic perfusion was associated with reduced ventricular fibrillation threshold and increased inducibility of tachyarrhythmias by programmed electrical stimulation and tachypacing as determined at the LV stimulation site. In contrast, the RV stimulation revealed no change in arrhythmic susceptibility of the RV chamber. Consistently, hypokalaemia reduced the LV effective refractory period but had no effect on the RV refractoriness. This change enabled generation of premature propagating responses by extrastimulus application at earlier time points during LV repolarization. Increased prematurity of extrastimulus‐evoked propagating responses was associated with exaggerated local inhomogeneities in intraventricular conduction and action potential duration in hypokalaemic LV, thus creating a favourable stage for re‐entrant tachyarrhythmias. Taken together, these findings suggest that proarrhythmic effects of hypokalaemia are mostly attributed to increased LV arrhythmogenicity in the guinea‐pig heart.
Generation of N‐ethyl‐N‐nitrosourea‐induced mouse mutants with deviations in plasma enzyme activities as novel organ‐specific disease models
Authors: Aigner Bernhard , Rathkolb Birgit , Klaften Matthias , Sedlmeier Reinhard , Klempt Martina , Wagner Sibylle , Michel Dian , Mayer Ulrike , Klopstock Thomas , Hrabé de Angelis Martin , Wolf Eckhard
Published: January 2009

Measurement of plasma enzyme activities is part of routine medical examination protocols and provides valuable parameters for the diagnosis of various organ diseases. In the phenotype‐driven Munich N‐ethyl‐N‐nitrosourea (ENU) mouse mutagenesis project, clinical chemical blood analysis was carried out on more than 20 000 G1 and G3 offspring of chemically mutagenized inbred C3H mice to detect dominant and recessive mutations leading to deviations in the plasma enzyme activities of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, α‐amylase and creatine kinase. We identified a large number of animals that consistently exhibited altered plasma enzyme activities. Transmission of the phenotypic deviations to the subsequent generations led to the successful establishment of mutant lines for each parameter. Breeding experiments in selected lines detected the linkage of the causative mutations to defined chromosomal regions. Subsequently, identification of the mutated genes was successfully carried out in chosen lines, resulting in a novel alkaline phosphatase liver/bone/kidney (Alpl) alteration in one line and the strong indication for a dystrophin (Dmd) alteration in another line. The mouse mutants with abnormal plasma enzyme activities recovered in the Munich ENU project are novel tools for the systematic dissection of the pathogenesis of organ diseases.
Chromosome-Based Genetic Complementation System forXylella fastidiosa
Authors: Matsumoto Ayumi , Young Glenn M. , Igo Michele M.
Published: January 2009

Xylella fastidiosais a xylem-limited, gram-negative bacterium that causes Pierce's disease of grapevine. Here, we describe the construction of four vectors that facilitate the insertion of genes into a neutral site (NS1) in theX. fastidiosachromosome. These vectors carry acolE1-like (pMB1) replicon and DNA sequences from NS1 flanking a multiple-cloning site and a resistance marker for one of the following antibiotics: chloramphenicol, erythromycin, gentamicin, or kanamycin. InX. fastidiosa, vectors withcolE1-like (pMB1) replicons have been found to result primarily in the recovery of double recombinants rather than single recombinants. Thus, the ease of obtaining double recombinants and the stability of the resulting insertions at NS1 in the absence of selective pressure are the major advantages of this system. Based on in vitro and in planta characterizations, strains carrying insertions within NS1 are indistinguishable from wild-typeX. fastidiosain terms of growth rate, biofilm formation, and pathogenicity. To illustrate the usefulness of this system for complementation analysis, we constructed a strain carrying a mutation in theX. fastidiosa cpeBgene, which is predicted to encode a catalase/peroxidase, and showed that the sensitivity of this mutant to hydrogen peroxide could be overcome by the introduction of a wild-type copy ofcpeBat NS1. Thus, this chromosome-based complementation system provides a valuable genetic tool for investigating the role of specific genes inX. fastidiosacell physiology and virulence.
Isolation and Identification of Cellulose-Binding Proteins from Sheep Rumen Contents
Authors: Toyoda Atsushi , Iio Wataru , Mitsumori Makoto , Minato Hajime
Published: January 2009

To extend our understanding of the mechanisms of plant cell wall degradation in the rumen, cellulose-binding proteins (CBPs) from the contents of a sheep rumen were directly isolated and identified using a metaproteomics approach. The rumen CBPs were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and some CBPs revealed endoglucanase activities toward carboxymethyl cellulose. Using mass spectrometry analyses, four CBPs were identified and annotated as known proteins from the predominant rumen cellulolytic bacterium
Fibrobacter succinogenes
: tetratricopeptide repeat domain protein, OmpA family protein, fibro-slime domain protein, and cellulose-binding endoglucanase F (EGF). Another CBP was identified as the cellulosomal glycosyl hydrolase family 6 exoglucanase, Cel6A, of
Piromyces equi. F. succinogenes
cells expressing EGF were found to be major members of the bacterial community on the surface or at the inner surface of hay stems by immunohistochemical analyses using anti-EGF antibody. The finding that four of the five CBPs isolated and identified from sheep rumen contents were from
F. succinogenes
indicates that
F. succinogenes
is significantly involved in cellulose degradation in the rumen.
Enhancement of UV Light Sensitivity of a
Vibrio parahaemolyticus
O3:K6 Pandemic Strain Due to Natural Lysogenization by a Telomeric Phage
Authors: Zabala Beatriz , García Katherine , Espejo Romilio T.
Published: January 2009

The
Vibrio parahaemolyticus
O3:K6 pandemic clonal strain was first observed in southern Chile in 2004 and has since caused approximately 8,000 seafood-related diarrhea cases in this region. The massive proliferation of the original clonal population offers a unique opportunity to study the evolution of a bacterial pathogen in its natural environment by detection and characterization of emerging bacterial variants. Here, we describe a group of pandemic variants characterized by the presence of a 42-kb extrachromosomal DNA that can be recovered by alkaline extraction. Upon treatment with mitomycin C, these variants lyse with production of a myovirus containing DNA of equal size to the plasmid but which cannot be recovered by alkaline extraction. Plasmid and phage DNAs show similar restriction patterns corresponding to enzyme sites in a circular permutation. Sequenced regions showed 81 to 99% nucleotide similarity to bacteriophage VHML of
Vibrio harveyi
. Altogether these observations indicate that the 42-kb plasmid corresponds to a prophage, consisting of a linear DNA with terminal hairpins of a telomeric temperate phage with a linear genome. Bacteria containing the prophage were 7 to 15 times more sensitive to UV radiation, likely due to phage induction by UV irradiation as plasmid curing restored the original sensitivity. The enhanced UV sensitivity could have a significant role in reducing the survival and propagation capability of the
V. parahaemolyticus
pandemic strain in the ocean.
Role of Cold Shock Proteins in Growth of
Listeria monocytogenes
under Cold and Osmotic Stress Conditions
Authors: Schmid Barbara , Klumpp Jochen , Raimann Eveline , Loessner Martin J. , Stephan Roger , Tasara Taurai
Published: January 2009

The gram-positive bacterium
Listeria monocytogenes
is a food-borne pathogen of both public health and food safety significance. It possesses three small, highly homologous protein members of the cold shock protein (Csp) family. We used gene expression analysis and a set of mutants with single, double, and triple deletions of the
csp
genes to evaluate the roles of CspA, CspB, and CspD in the cold and osmotic (NaCl) stress adaptation responses of
L. monocytogenes
. All three Csps are dispensable for growth at optimal temperature (37°C). These proteins are, however, required for efficient cold and osmotic stress tolerance of this bacterium. The hierarchies of their functional importance differ, depending on the environmental stress conditions: CspA>CspD>CspB in response to cold stress versus CspD>CspA/CspB in response to NaCl salt osmotic stress. The fact that Csps are promoting
L. monocytogenes
adaptation against both cold and NaCl stress has significant implications in view of practical food microbial control measures. The combined or sequential exposure of
L. monocytogenes
cells to these two stresses in food environments might inadvertently induce cross-protection responses.
Multimeric Hemicellulases Facilitate Biomass Conversion
Authors: Fan Zhanmin , Wagschal Kurt , Chen Wei , Montross Michael D. , Lee Charles C. , Yuan Ling
Published: January 2009

Two highly active trifunctional hemicellulases were constructed by linking the catalytic portion of a xylanase with an arabinofuranosidase and a xylosidase, using either flexible peptide linkers or linkers containing a cellulose-binding domain. The multifunctional enzymes retain the parental enzyme properties and exhibit synergistic effects in hydrolysis of natural xylans and corn stover.
Diversity of Beta-Propeller Phytase Genes in the Intestinal Contents of Grass Carp Provides Insight into the Release of Major Phosphorus from Phytate in Nature
Authors: Huang Huoqing , Shi Pengjun , Wang Yaru , Luo Huiying , Shao Na , Wang Guozeng , Yang Peilong , Yao Bin
Published: January 2009

Phytate is the most abundant organic phosphorus compound in nature, and microbial mineralization of phytate by phytase is a key process for phosphorus recycling in the biosphere. In the present study, beta-propeller phytase (BPP) gene fragments were readily amplified from the intestinal contents of grass carp (
Ctenopharyngodon idellus
) directly or from phytate-degrading isolates from the same source, confirming the widespread occurrence of BPP in aquatic communities. The amounts of sequences collected using these two methods differed (88 distinct genes versus 10 isolates), but the sequences showed the same general topology based on phylogenetic analysis. All of the sequences fell in five clusters and were distinct from those of
Anabaena
,
Gloeobacter
,
Streptomyces
,
Flavobacterium
,
Prosthecochloris
, and
Desulfuromonas
, which have never been found in the grass carp intestine. Analysis of the microbial diversity by denaturing gradient gel electrophoresis demonstrated that unculturable bacteria were dominant bacteria in the grass carp intestine and thus the predominant phytate-degrading organisms. The predominant cultured species corresponding to the phytate-degrading isolates,
Pseudomonas
,
Bacillus
and
Shewanella
species, might be the main source of known BPPs. A phytase from
Brevundimonas
was first obtained from cultured species. Combining our results with Lim et al.'s inference that phytate-mineralizing bacteria are widely distributed and highly diverse in nature (B. L. Lim, P. Yeung, C. Cheng, and J. E. Hill, ISME J.
1:
321-330, 2007), we concluded that BPP is the major phytate-degrading enzyme in nature, that most of this enzyme might originate from unculturable bacteria, and that the distribution of BPP may be related to the type of niche. To our knowledge, this is the first study to experimentally estimate BPP diversity in situ.
Bacteroidales
Diversity in Ring-Billed Gulls (
Laurus delawarensis
) Residing at Lake Michigan Beaches
Authors: Jeter Sonja N. , McDermott Colleen M. , Bower Patricia A. , Kinzelman Julie L. , Bootsma Melinda J. , Goetz Giles W. , McLellan Sandra L.
Published: January 2009

This study investigated the occurrence and diversity of
Bacteroidales
fecal bacteria in gulls residing in the Great Lakes region. Members of this bacterial order have been widely employed as human and bovine host-specific markers of fecal pollution; however, few studies have focused on gulls, which can be a major source of fecal indicator bacteria and pathogens at beaches. We found a low but consistent occurrence of
Bacteroidales
in gulls at five beaches in three different counties spanning the Wisconsin shoreline of Lake Michigan. The percentages of gulls positive for
Bacteroidales
were 4 to 8% at beaches in the southern part of the state and 8 to 50% at beaches in the north. Sequencing of 931 clones from seven gull
Bacteroidales
16S rRNA gene libraries revealed a large amount of diversity in both individual and pooled gull fecal samples. Two libraries constructed from pooled gull fecal samples (
n
= 5 and
n
= 6) did not have a greater richness of sequences than individual samples, suggesting that even within a single gull diversity is high and an extensive sequencing effort is needed to characterize the populations. Estimates of the numbers of operational taxonomic units (OTUs) for the libraries obtained using different similarity levels revealed a large amount of microdiveristy with a limited number of OTUs at the 95% similarity level. Gull sequences were clustered by the beach from which they were collected, suggesting that there were geographic effects on the distribution of
Bacteriodales
. More than 53% of the 16S rRNA gene sequences from gulls at the southern beaches were associated with the family
Porphyromonadaceae
, primarily the genus
Parabacteroides
, whereas sequences from gulls at the northern beaches were comprised of
Bacteroidaceae
and
Prevotellaceae
sequences. Comparison of gull sequences with sequences from goose, canine, raccoon, and sewage sources revealed distinct clusters of closely related gull sequences; however, these sequences were widely dispersed across a dendrogram that included all other sources, including previously characterized gull
Bacteroidales
from other studies, suggesting that geographic influence or simply sample representation plays a greater role in the observed population structure than strictly the host gut environment.
Silver-Palladium Surfaces Inhibit Biofilm Formation
Authors: Chiang Wen-Chi , Schroll Casper , Hilbert Lisbeth Rischel , Møller Per , Tolker-Nielsen Tim
Published: January 2009

Undesired biofilm formation is a major concern in many areas. In the present study, we investigated biofilm-inhibiting properties of a silver-palladium surface that kills bacteria by generating microelectric fields and electrochemical redox processes. For evaluation of the biofilm inhibition efficacy and study of the biofilm inhibition mechanism, the silver-sensitive
Escherichia coli
J53 and the silver-resistant
E. coli
J53[pMG101] strains were used as model organisms, and batch and flow chamber setups were used as model systems. In the case of the silver-sensitive strain, the silver-palladium surfaces killed the bacteria and prevented biofilm formation under conditions of low or high bacterial load. In the case of the silver-resistant strain, the silver-palladium surfaces killed surface-associated bacteria and prevented biofilm formation under conditions of low bacterial load, whereas under conditions of high bacterial load, biofilm formation occurred upon a layer of surface-associated dead bacteria.
Growth of Enterococci in Unaltered, Unseeded Beach Sands Subjected to Tidal Wetting
Authors: Yamahara Kevan M. , Walters Sarah P. , Boehm Alexandria B.
Published: January 2009

Enterococci are indicator bacteria used to assess the risk of acquiring enteric disease from swimming in marine waters. Previous work identified beach sands as reservoirs of enterococci which can be transported from the sand to the sea, where they may instigate beach advisories. The present study establishes that naturally occurring enterococci can replicate in beach sands under environmentally relevant conditions. In unseeded, nonsterile microcosm experiments, it was shown that intermittent wetting of sands by seawater, like that which would occur at the high tide line, stimulates the transient replication of enterococci at rates of 0.20 to 0.63 per day (equivalent to doubling times of 1.1 to 3.5 days). Replication was not observed in control microcosms that were not subjected to wetting. Enterococci were enumerated using both culture-dependent (membrane filtration and mEI media) and culture-independent (quantitative PCR [QPCR], 23S rRNA gene based) techniques, which allowed tracking of both culturable and total enterococcus populations. Inhibition of QPCR and DNA extraction efficiencies were accounted for in the interpretation of the QPCR results. The results provide evidence that enterococci may not be an appropriate indicator of enteric disease risk at recreational beaches subject to nonpoint sources of pollution.
Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing
Authors: Sagaram Uma Shankar , DeAngelis Kristen M. , Trivedi Pankaj , Andersen Gary L. , Lu Shi-En , Wang Nian
Published: January 2009

The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. “
Candidatus
Liberibacter asiaticus” was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of “
Candidatus
Liberibacter asiaticus” in symptomatic leaves. These data implicate “
Candidatus
Liberibacter asiaticus” as the pathogen responsible for HLB disease.
Rapid Oligonucleotide-Based Recombineering of the Chromosome of
Salmonella enterica
Authors: Gerlach Roman G. , Jäckel Daniela , Hölzer Stefanie U. , Hensel Michael
Published: January 2009

Recombinant engineering using Red recombinase-based approaches offers efficient and rapid approaches to deletion and modification of genes. Here we describe a novel application of Red recombinant engineering that enables direct manipulation of chromosomal loci by electroporation with short synthetic DNA molecules. We demonstrate the use of this approach for the generation of scarless in-frame deletions in chromosomal genes of
Salmonella enterica
. Furthermore, we describe rapid site-directed mutagenesis within bacterial chromosomes without any requirement for cloning and mutating genes in vitro or for reintroducing mutant alleles into the chromosome. This approach can be expected to facilitate mutational analysis in
S. enterica
and in other bacterial species able to support Red-mediated recombination.
Prevalence ofRickettsiaSpecies in Canadian Populations ofDermacentor andersoniandD. variabilis
Authors: Dergousoff Shaun J. , Gajadhar Andrew J. A. , Chilton Neil B.
Published: January 2009

We determined the prevalence of rickettsiae inDermacentoradults at 15 localities in Canada.Rickettsia rickettsiiwas not detected in any tick, whereasRickettsia peacockiiwas present in 76% ofDermacentor andersoniadults andRickettsia montanensisin 8% ofDermacentor variabilisadults. This host specificity was maintained in localities where both tick species occurred in sympatry.
Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization
Authors: Rousk Johannes , Brookes Philip C. , Bååth Erland
Published: January 2009

The influence of pH on the relative importance of the two principal decomposer groups in soil, fungi and bacteria, was investigated along a continuous soil pH gradient at Hoosfield acid strip at Rothamsted Research in the United Kingdom. This experimental location provides a uniform pH gradient, ranging from pH 8.3 to 4.0, within 180 m in a silty loam soil on which barley has been continuously grown for more than 100 years. We estimated the importance of fungi and bacteria directly by measuring acetate incorporation into ergosterol to measure fungal growth and leucine and thymidine incorporation to measure bacterial growth. The growth-based measurements revealed a fivefold decrease in bacterial growth and a fivefold increase in fungal growth with lower pH. This resulted in an approximately 30-fold increase in fungal importance, as indicated by the fungal growth/bacterial growth ratio, from pH 8.3 to pH 4.5. In contrast, corresponding effects on biomass markers for fungi (ergosterol and phospholipid fatty acid [PLFA] 18:2ω6,9) and bacteria (bacterial PLFAs) showed only a two- to threefold difference in fungal importance in the same pH interval. The shift in fungal and bacterial importance along the pH gradient decreased the total carbon mineralization, measured as basal respiration, by only about one-third, possibly suggesting functional redundancy. Below pH 4.5 there was universal inhibition of all microbial variables, probably derived from increased inhibitory effects due to release of free aluminum or decreasing plant productivity. To investigate decomposer group importance, growth measurements provided significantly increased sensitivity compared with biomass-based measurements.
Uneven Distribution of Mating Types among Genotypes of
Candida glabrata
Isolates from Clinical Samples
Authors: Brisse Sylvain , Pannier Christine , Angoulvant Adela , de Meeus Thierry , Diancourt Laure , Faure Odile , Muller Héloïse , Peman Javier , Viviani Maria Anna , Grillot Renée , Dujon Bernard , Fairhead Cécile , Hennequin Christophe
Published: January 2009

In order to shed light on its basic biology, we initiated a population genetic analysis of
Candida glabrata
, an emerging pathogenic yeast with no sexual stage yet recognized. A worldwide collection of clinical strains was subjected to analysis using variable number of tandem repeats (VNTR) at nine loci. The clustering of strains obtained with this method was congruent with that obtained using sequence polymorphism of the
NMT1
gene, a locus previously proposed for lineage assignment. Linkage disequilibrium supported the hypothesis of a mainly clonal reproduction. No heterozygous diploid genotype was found. Minimum-spanning tree analysis of VNTR data revealed clonal expansions and associated genotypic diversification. Mating type analysis revealed that 80% of the strains examined are
MAT
a
and 20%
MAT
α and that the two alleles are not evenly distributed. The
MAT
a
genotype dominated within large clonal groups that contained only one or a few
MAT
α types. In contrast, two groups were dominated by
MAT
α strains. Our data are consistent with rare independent mating type switching events occurring preferentially from type
a
to α, although the alternative possibility of selection favoring type
a
isolates cannot be excluded.
Transcriptional Regulation of an Iron-Inducible Gene by Differential and Alternate Promoter Entries of Multiple Myb Proteins in the Protozoan Parasite
Trichomonas vaginalis
Authors: Hsu Hong-Ming , Ong Shiou-Jeng , Lee Ming-Chun , Tai Jung-Hsiang
Published: January 2009

Iron-inducible transcription of a malic enzyme gene (also reputed to be
ap65-1
) in
Trichomonas vaginalis
was previously shown to involve a Myb1 repressor and a Myb2 activator, each of which may preferentially select two closely spaced promoter sites, MRE-1/MRE-2r, which comprises overlapping promoter elements, and MRE-2f. In the present study, an iron-inducible ∼32-kDa Myb3 nuclear protein was demonstrated to bind only the MRE-1 element. Changes in the iron supply, which produced antagonistic effects on the levels of Myb2 and Myb3 expression, also resulted in temporal and alternate entries of Myb2 and Myb3 into the
ap65-1
promoter. Repression or activation of basal and iron-inducible
ap65-1
transcription was detected in transfected cells when Myb3 was, respectively, substantially knocked down or overexpressed. In the latter case, increased Myb3 promoter entry was detected with concomitant decrease in Myb2 promoter entry under specific conditions, while Myb3 promoter entry was inhibited under all test conditions in cells overexpressing Myb2. In contrast, concomitant promoter entries by Myb2 and Myb3 diminished in cells overexpressing Myb1, except that Myb3 promoter entry was slightly affected under prolonged iron depletion. Together, these results suggest that Myb2 and Myb3 may coactivate basal and iron-inducible
ap65-1
transcription against Myb1 through conditional and competitive promoter entries.
Patterns of Gene-Specific and Total Transcriptional Activity during thePlasmodium falciparumIntraerythrocytic Developmental Cycle
Authors: Sims Jennifer S. , Militello Kevin T. , Sims Peter A. , Patel Vishal P. , Kasper Jacob M. , Wirth Dyann F.
Published: January 2009

The relationships among gene regulatory mechanisms in the malaria parasitePlasmodium falciparumthroughout its asexual intraerythrocytic developmental cycle (IDC) remain poorly understood. To investigate the level and nature of transcriptional activity and its role in controlling gene expression during the IDC, we performed nuclear run-on on whole-transcriptome samples from time points throughout the IDC and found a peak in RNA polymerase II-dependent transcriptional activity related to both the number of nuclei per parasite and variable transcriptional activity per nucleus over time. These differential total transcriptional activity levels allowed the calculation of the absolute transcriptional activities of individual genes from gene-specific nuclear run-on hybridization data. For half of the genes analyzed, sense-strand transcriptional activity peaked at the same time point as total activity. The antisense strands of several genes were substantially transcribed. Comparison of the transcriptional activity of the sense strand of each gene to its steady-state RNA abundance across the time points assayed revealed both correlations and discrepancies, implying transcriptional and posttranscriptional regulation, respectively. Our results demonstrate that such comparisons can effectively indicate gene regulatory mechanisms inP. falciparumand suggest that genes with diverse transcriptional activity levels and patterns combine to produce total transcriptional activity levels tied to parasite development during the IDC.
Correlation between Biofilm Formation and the Hypoxic Response in
Candida parapsilosis
Authors: Rossignol Tristan , Ding Chen , Guida Alessandro , d'Enfert Christophe , Higgins Desmond G. , Butler Geraldine
Published: January 2009

The ability of
Candida parapsilosis
to form biofilms on indwelling medical devices is correlated with virulence. To identify genes that are important for biofilm formation, we used arrays representing approximately 4,000 open reading frames (ORFs) to compare the transcriptional profile of biofilm cells growing in a microfermentor under continuous flow conditions with that of cells in planktonic culture. The expression of genes involved in fatty acid and ergosterol metabolism and in glycolysis, is upregulated in biofilms. The transcriptional profile of
C. parapsilosis
biofilm cells resembles that of
Candida albicans
cells grown under hypoxic conditions. We therefore subsequently used whole-genome arrays (representing 5,900 ORFs) to determine the hypoxic response of
C. parapsilosis
and showed that the levels of expression of genes involved in the ergosterol and glycolytic pathways, together with several cell wall genes, are increased. Our results indicate that there is substantial overlap between the hypoxic responses of
C. parapsilosis
and
C. albicans
and that this may be important for biofilm development. Knocking out an ortholog of the cell wall gene
RBT1
, whose expression is induced both in biofilms and under conditions of hypoxia in
C. parapsilosis
, reduces biofilm development.
Phylogeny and Phenotypic Characterization of PathogenicCryptococcusSpecies and Closely Related Saprobic Taxa in the Tremellales
Authors: Findley Keisha , Rodriguez-Carres Marianela , Metin Banu , Kroiss Johannes , Fonseca Álvaro , Vilgalys Rytas , Heitman Joseph
Published: January 2009

The basidiomycetous yeastsCryptococcus neoformansandCryptococcus gattiiare closely related sibling species that cause respiratory and neurological disease in humans and animals. Within these two recognized species, phylogenetic analysis reveals at least six cryptic species defined as molecular types (VNI/II/B, VNIV, VGI, VGII, VGIII, and VGIV) that comprise the pathogenicCryptococcusspecies complex. These pathogenic species are clustered in theFilobasidiellaclade within the order Tremellales. Previous studies have shown that theFilobasidiellaclade also includes several saprobic fungi isolated from insect frass, but information evaluating the relatedness of the saprobes and pathogens within this cluster is limited. Here, the phylogeny encompassing a subset of species in the Tremellales lineage that clusters closely with the pathogenicCryptococcusspecies complex was resolved by employing a multilocus sequencing approach for phylogenetic analysis. Six highly conserved genomic loci from 15 related basidiomycete species were sequenced, and the alignments from the concatenated gene sequences were evaluated with different tree-building criteria. Furthermore, these 15 species were subjected to virulence and phenotype assays to evaluate their pathogenic potential. These studies revealed thatCryptococcus amylolentusandTsuchiyaea wingfieldii, two nonpathogenic sibling species, are the taxa most closely related to the pathogensC. neoformansandC. gattiiand together withFilobasidiella depauperataform aCryptococcussensu stricto group. Five other saprobic yeast species form theKwoniellaclade, which appears to be a part of a more distantly related sensu lato group. This study establishes a foundation for future comparative genomic approaches that will provide insight into the structure, function, and evolution of the mating type locus, the transitions in modes of sexual reproduction, and the emergence of human pathogenic species from related or ancestral saprobic species.
Contribution of Peroxisomes to Penicillin Biosynthesis in
Aspergillus nidulans
Authors: Spröte Petra , Brakhage Axel A. , Hynes Michael J.
Published: January 2009

Peroxisomal localization of the third enzyme of the penicillin biosynthesis pathway of
Aspergillus nidulans
, acyl-coenzyme A:IPN acyltransferase (IAT), is mediated by its atypical peroxisomal targeting signal 1 (PTS1). However, mislocalization of IAT by deletion of either its PTS1 or of genes encoding proteins involved in peroxisome formation or transport does not completely abolish penicillin biosynthesis. This is in contrast to the effects of IAT mislocalization in
Penicillium chrysogenum
.