bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations
Authors: Blyton Michaela D. J. , Pi Hongfei , Vangchhia Belinda , Abraham Sam , Trott Darren J. , Johnson James R. , Gordon David M. 
Published: May 2015

ABSTRACT

The manner and extent to which birds associate with humans may influence the genetic attributes and antimicrobial resistance of their commensal
Escherichia
communities through strain transmission and altered selection pressures. In this study, we determined whether the distribution of the different
Escherichia coli
phylogenetic groups and cryptic clades, the occurrence of 49 virulence associated genes, and/or the prevalence of resistance to 12 antimicrobials differed between four groups of birds from Australia with contrasting types of human association. We found that birds sampled in suburban and wilderness areas had similar
Escherichia
communities. The
Escherichia
communities of backyard domestic poultry were phylogenetically distinct from the
Escherichia
communities sourced from all other birds, with a large proportion (46%) of poultry strains belonging to phylogenetic group A and a significant minority (17%) belonging to the cryptic clades. Wild birds sampled from veterinary and wildlife rehabilitation centers (in-care birds) carried
Escherichia
isolates that possessed particular virulence-associated genes more often than
Escherichia
isolates from birds sampled in suburban and wilderness areas. The
Escherichia
isolates from both the backyard poultry and in-care birds were more likely to be multidrug resistant than the
Escherichia
isolates from wild birds. We also detected a multidrug-resistant
E. coli
strain circulating in a wildlife rehabilitation center, reinforcing the importance of adequate hygiene practices when handling and caring for wildlife. We suggest that the relatively high frequency of antimicrobial resistance in the in-care birds and backyard poultry is due primarily to the use of antimicrobials in these animals, and we recommend that the treatment protocols used for these birds be reviewed.
Automated Sampling Procedures Supported by High Persistence of Bacterial Fecal Indicators and Bacteroidetes Genetic Microbial Source Tracking Markers in Municipal Wastewater during Short-Term Storage at 5°C
Authors: Mayer R. E. , Vierheilig J. , Egle L. , Reischer G. H. , Saracevic E. , Mach R. L. , Kirschner A. K. T. , Zessner M. , Sommer R. , Farnleitner A. H. 
Published: May 2015

ABSTRACT

Because of high diurnal water quality fluctuations in raw municipal wastewater, the use of proportional autosampling over a period of 24 h at municipal wastewater treatment plants (WWTPs) to evaluate carbon, nitrogen, and phosphorus removal has become a standard in many countries. Microbial removal or load estimation at municipal WWTPs, however, is still based on manually recovered grab samples. The goal of this study was to establish basic knowledge regarding the persistence of standard bacterial fecal indicators and
Bacteroidetes
genetic microbial source tracking markers in municipal wastewater in order to evaluate their suitability for automated sampling, as the potential lack of persistence is the main argument against such procedures. Raw and secondary treated wastewater of municipal origin from representative and well-characterized biological WWTPs without disinfection (organic carbon and nutrient removal) was investigated in microcosm experiments at 5 and 21°C with a total storage time of 32 h (including a 24-h autosampling component and an 8-h postsampling phase). Vegetative
Escherichia coli
and enterococci, as well as
Clostridium perfringens
spores, were selected as indicators for cultivation-based standard enumeration. Molecular analysis focused on total (AllBac) and human-associated genetic
Bacteroidetes
(BacHum-UCD, HF183 TaqMan) markers by using quantitative PCR, as well as 16S rRNA gene-based next-generation sequencing. The microbial parameters showed high persistence in both raw and treated wastewater at 5°C under the storage conditions used. Surprisingly, and in contrast to results obtained with treated wastewater, persistence of the microbial markers in raw wastewater was also high at 21°C. On the basis of our results, 24-h autosampling procedures with 5°C storage conditions can be recommended for the investigation of fecal indicators or
Bacteroidetes
genetic markers at municipal WWTPs. Such autosampling procedures will contribute to better understanding and monitoring of municipal WWTPs as sources of fecal pollution in water resources.
Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii Circulation in a Dairy Farm and Sources of Milk Contamination
Authors: Giacometti Federica , Lucchi Alex , Di Francesco Antonietta , Delogu Mauro , Grilli Ester , Guarniero Ilaria , Stancampiano Laura , Manfreda Gerardo , Merialdi Giuseppe , Serraino Andrea 
Published: May 2015

ABSTRACT

Even though dairy cows are known carriers of
Arcobacter
species and raw or minimally processed foods are recognized as the main sources of human
Arcobacter
infections in industrialized countries, data on
Arcobacter
excretion patterns in cows and in milk are scant. This study aimed to identify potentially pathogenic
Arcobacter
species in a dairy herd and to investigate the routes of
Arcobacter
transmission among animals and the potential sources of cattle infection and milk contamination. A strategy of sampling the same 50 dairy animals, feed, water, and milk every month for a 10-month period, as well as the sampling of quarter milk, animal teats, the milking environment, and animals living on the farm (pigeons and cats), was used to evaluate, by pulsed-field gel electrophoresis (PFGE), the characteristic patterns in animals, their living environment, and the raw milk they produced. Of the 463 samples collected, 105 (22.6%) were positive for
Arcobacter
spp. by culture examination. All the matrices except quarter milk and pigeon gut samples were positive, with prevalences ranging from 15 to 83% depending on the sample. Only three
Arcobacter
species,
Arcobacter
cryaerophilus
(54.2%),
A. butzleri
(34.2%), and
A. skirrowii
(32.3%), were detected. PFGE analysis of 370 isolates from positive samples provided strong evidence of
Arcobacter
circulation in the herd: cattle likely acquire the microorganisms by orofecal transmission, either by direct contact or from the environment, or both. Water appears to be a major source of animal infection. Raw milk produced by the farm and collected from a bulk tank was frequently contaminated (80%) by
A. butzleri
; our PFGE findings excluded primary contamination of milk, whereas teats and milking machine surfaces could be sources of
Arcobacter
milk contamination.
Changes in Sodium, Calcium, and Magnesium Ion Concentrations That Inhibit Geobacillus Biofilms Have No Effect on Anoxybacillus flavithermus Biofilms
Authors: Somerton B. , Lindsay D. , Palmer J. , Brooks J. , Flint S. 
Published: May 2015

ABSTRACT

This study investigated the effects of varied sodium, calcium, and magnesium concentrations in specialty milk formulations on biofilm formation by
Geobacillus
spp. and
Anoxybacillus flavithermus
. The numbers of attached viable cells (log CFU per square centimeter) after 6 to 18 h of biofilm formation by three dairy-derived strains of
Geobacillus
and three dairy-derived strains of
A. flavithermus
were compared in two commercial milk formulations. Milk formulation B had relatively high sodium and low calcium and magnesium concentrations compared with those of milk formulation A, but the two formulations had comparable fat, protein, and lactose concentrations. Biofilm formation by the three
Geobacillus
isolates was up to 4 log CFU cm
−2
lower in milk formulation B than in milk formulation A after 6 to 18 h, and the difference was often significant (
P
≤ 0.05). However, no significant differences (
P
≤ 0.05) were found when biofilm formations by the three
A. flavithermus
isolates were compared in milk formulations A and B. Supplementation of milk formulation A with 100 mM NaCl significantly decreased (
P
≤ 0.05)
Geobacillus
biofilm formation after 6 to 10 h. Furthermore, supplementation of milk formulation B with 2 mM CaCl
2
or 2 mM MgCl
2
significantly increased (
P
≤ 0.05)
Geobacillus
biofilm formation after 10 to 18 h. It was concluded that relatively high free Na
+
and low free Ca
2+
and Mg
2+
concentrations in milk formulations are collectively required to inhibit biofilm formation by
Geobacillus
spp., whereas biofilm formation by
A. flavithermus
is not impacted by typical cation concentration differences of milk formulations.
Coupling the CRISPR/Cas9 System with Lambda Red Recombineering Enables Simplified Chromosomal Gene Replacement in Escherichia coli
Authors: Pyne Michael E. , Moo-Young Murray , Chung Duane A. , Chou C. Perry 
Published: May 2015

ABSTRACT

To date, most genetic engineering approaches coupling the type II
Streptococcus pyogenes
clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system to lambda Red recombineering have involved minor single nucleotide mutations. Here we show that procedures for carrying out more complex chromosomal gene replacements in
Escherichia coli
can be substantially enhanced through implementation of CRISPR/Cas9 genome editing. We developed a three-plasmid approach that allows not only highly efficient recombination of short single-stranded oligonucleotides but also replacement of multigene chromosomal stretches of DNA with large PCR products. By systematically challenging the proposed system with respect to the magnitude of chromosomal deletion and size of DNA insertion, we demonstrated DNA deletions of up to 19.4 kb, encompassing 19 nonessential chromosomal genes, and insertion of up to 3 kb of heterologous DNA with recombination efficiencies permitting mutant detection by colony PCR screening. Since CRISPR/Cas9-coupled recombineering does not rely on the use of chromosome-encoded antibiotic resistance, or flippase recombination for antibiotic marker recycling, our approach is simpler, less labor-intensive, and allows efficient production of gene replacement mutants that are both markerless and “scar”-less.
Microbiota Dynamics Associated with Environmental Conditions and Potential Roles of Cellulolytic Communities in Traditional Chinese Cereal Starter Solid-State Fermentation
Authors: Li Pan , Liang Hebin , Lin Wei-Tie , Feng Feng , Luo Lixin 
Published: May 2015

ABSTRACT

Traditional Chinese solid-state fermented cereal starters contain highly complex microbial communities and enzymes. Very little is known, however, about the microbial dynamics related to environmental conditions, and cellulolytic communities have never been proposed to exist during cereal starter fermentation. In this study, we performed Illumina MiSeq sequencing combined with PCR-denaturing gradient gel electrophoresis to investigate microbiota, coupled with clone library construction to trace cellulolytic communities in both fermentation stages. A succession of microbial assemblages was observed during the fermentation of starters.
Lactobacillales
and
Saccharomycetales
dominated the initial stages, with a continuous decline in relative abundance. However, thermotolerant and drought-resistant
Bacillales
,
Eurotiales
, and
Mucorales
were considerably accelerated during the heating stages, and these organisms dominated until the end of fermentation.
Enterobacteriales
were consistently ubiquitous throughout the process. For the cellulolytic communities, only the genera
Sanguibacter
,
Beutenbergia
,
Agrobacterium
, and
Erwinia
dominated the initial fermentation stages. In contrast, stages at high incubation temperature induced the appearance and dominance of
Bacillus
,
Aspergillus
, and
Mucor
. The enzymatic dynamics of amylase and glucoamylase also showed a similar trend, with the activities clearly increased in the first 7 days and subsequently decreased until the end of fermentation. Furthermore, β-glucosidase activity continuously and significantly increased during the fermentation process. Evidently, cellulolytic potential can adapt to environmental conditions by changes in the community structure during the fermentation of starters.
Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation
Authors: Vivant Anne-Laure , Garmyn Dominique , Gal Laurent , Hartmann Alain , Piveteau Pascal 
Published: May 2015

ABSTRACT

In a recent paper, we demonstrated that inactivation of the Agr system affects the patterns of survival of
Listeria monocytogenes
(A.-L. Vivant, D. Garmyn, L. Gal, and P. Piveteau, Front Cell Infect Microbiol 4:160,
http://dx.doi.org/10.3389/fcimb.2014.00160
). In this study, we investigated whether the Agr-mediated response is triggered during adaptation in soil, and we compared survival patterns in a set of 10 soils. The fate of the parental strain
L. monocytogenes
L9 (a rifampin-resistant mutant of
L. monocytogenes
EGD-e) and that of a Δ
agrA
deletion mutant were compared in a collection of 10 soil microcosms. The Δ
agrA
mutant displayed significantly reduced survival in these biotic soil microcosms, and differential transcriptome analyses showed large alterations of the transcriptome when AgrA was not functional, while the variations in the transcriptomes between the wild type and the Δ
agrA
deletion mutant were modest under abiotic conditions. Indeed, in biotic soil environments, 578 protein-coding genes and an extensive repertoire of noncoding RNAs (ncRNAs) were differentially transcribed. The transcription of genes coding for proteins involved in cell envelope and cellular processes, including the phosphotransferase system and ABC transporters, and proteins involved in resistance to antimicrobial peptides was affected. Under sterilized soil conditions, the differences were limited to 86 genes and 29 ncRNAs. These results suggest that the response regulator AgrA of the Agr communication system plays important roles during the saprophytic life of
L. monocytogenes
in soil.
The NDR Kinase Cbk1 Downregulates the Transcriptional Repressor Nrg1 through the mRNA-Binding Protein Ssd1 in Candida albicans
Authors: Lee Hye-Jeong , Kim Jong-Myeong , Kang Woo Kyu , Yang Heebum , Kim Jeong-Yoon 
Published: May 2015

ABSTRACT

NDR (nuclear Dbf2-related) kinases are essential components for polarized morphogenesis, cytokinesis, cell proliferation, and apoptosis. The NDR kinase Cbk1 is required for the hyphal growth of
Candida albicans
; however, the molecular functions of Cbk1 in hyphal morphogenesis are largely unknown. Here, we report that Cbk1 downregulates the transcriptional repressor Nrg1 through the mRNA-binding protein Ssd1, which has nine Cbk1 phosphorylation consensus motifs. We found that deletion of
SSD1
partially suppressed the defective hyphal growth of the
C. albicans
cbk1
Δ/Δ mutant and that Ssd1 physically interacts with Cbk1. Cbk1 was required for Ssd1 localization to polarized growth sites. The phosphomimetic
SSD1
allele (
ssd1-9E
) allowed the
cbk1
Δ/Δ mutant to form short hyphae, and the phosphodeficient
SSD1
allele (
ssd1-9A
) resulted in shorter hyphae than did the wild-type
SSD1
allele, indicating that Ssd1 phosphorylation by Cbk1 is important for hyphal morphogenesis. Furthermore, we show that the transcriptional repressor Nrg1 does not disappear during hyphal initiation in the
cbk1
Δ/Δ mutant but is completely absent in the
cbk1
Δ/Δ
ssd1
Δ/Δ double mutant. Deletion of
SSD1
also increased Als3 expression and internalization of the
cbk1
Δ/Δ mutant in the human embryonic kidney cell line HEK293T. Collectively, our results suggest that one of the functions of Cbk1 in the hyphal morphogenesis of
C. albicans
is to downregulate Nrg1 through Ssd1.
The Candida albicans Exocyst Subunit Sec6 Contributes to Cell Wall Integrity and Is a Determinant of Hyphal Branching
Authors: Chavez-Dozal Alba A. , Bernardo Stella M. , Rane Hallie S. , Herrera Gloria , Kulkarny Vibhati , Wagener Jeanette , Cunningham Iain , Brand Alexandra C. , Gow Neil A. R. , Lee Samuel A. 
Published: May 2015

ABSTRACT

The yeast exocyst is a multiprotein complex comprised of eight subunits (Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70, and Exo84) which orchestrates trafficking of exocytic vesicles to specific docking sites on the plasma membrane during polarized secretion. To study
SEC6
function in
Candida albicans
, we generated a conditional mutant strain in which
SEC6
was placed under the control of a tetracycline-regulated promoter. In the repressed state, the tetR-
SEC6
mutant strain (denoted tSEC6) was viable for up to 27 h; thus, all phenotypic analyses were performed at 24 h or earlier. Strain tSEC6 under repressing conditions had readily apparent defects in cytokinesis and endocytosis and accumulated both post-Golgi apparatus secretory vesicles and structures suggestive of late endosomes. Strain tSEC6 was markedly defective in secretion of aspartyl proteases and lipases as well as filamentation under repressing conditions. Lack of
SEC6
expression resulted in markedly reduced lateral hyphal branching, which requires the establishment of a new axis of polarized secretion. Aberrant localization of chitin at the septum and increased resistance to zymolyase activity were observed, suggesting that
C. albicans
Sec6 plays an important role in mediating trafficking and delivery of cell wall components. The tSEC6 mutant was also markedly defective in macrophage killing, indicating a role of
SEC6
in
C. albicans
virulence. Taken together, these studies indicate that the late secretory protein Sec6 is required for polarized secretion, hyphal morphogenesis, and the pathogenesis of
C. albicans
.
Csr1/Zap1 Maintains Zinc Homeostasis and Influences Virulence in Candida dubliniensis but Is Not Coupled to Morphogenesis
Authors: Böttcher Bettina , Palige Katja , Jacobsen Ilse D. , Hube Bernhard , Brunke Sascha 
Published: May 2015

ABSTRACT

The supply and intracellular homeostasis of trace metals are essential for every living organism. Therefore, the struggle for micronutrients between a pathogen and its host is an important determinant in the infection process. In this work, we focus on the acquisition of zinc by
Candida dubliniensis
, an emerging pathogen closely related to
Candida albicans
. We show that the transcription factor Csr1 is essential for
C. dubliniensis
to regulate zinc uptake mechanisms under zinc limitation: it governs the expression of the zinc transporter genes
ZRT1
,
ZRT2
, and
ZRT3
and of the zincophore gene
PRA1
. Exclusively, artificial overexpression of
ZRT2
partially rescued the growth defect of a
csr1
Δ/Δ mutant in a zinc-restricted environment. Importantly, we found that, in contrast to what is seen in
C. albicans
,
Csr1
(also called
Zap1
) is not a major regulator of dimorphism in
C. dubliniensis
. However, although a
csr1
Δ/Δ strain showed normal germ tube formation, we detected a clear attenuation in virulence using an embryonated chicken egg infection model. We conclude that, unlike in
C. albicans
, Csr1 seems to be a virulence factor of
C. dubliniensis
that is not coupled to filamentation but is strongly linked to zinc acquisition during pathogenesis.
Effects of Acupressure on Anxiety: A Systematic Review and Meta-Analysis
Authors: Au Doreen W H , Tsang Hector W H , Ling Paul P M , Leung Christie H T , Ip P K , Cheung W M 
Published: May 2015

Objective To evaluate the evidence from randomised controlled trials (RCTs) and quantify the effects of acupressure on anxiety among adults. Methodology RCTs published between January 1997 and February 2014, comparing acupressure with sham control, were identified from the databases Science Citation Index/Social Sciences Citation Index, Scopus, PubMed and PsycINFO. Meta-analysis of eligible studies was performed and the magnitude of the overall effect size was calculated for the anxiety outcome. Revised STRICTA (the Standards for Reporting Interventions in Clinical Trials of Acupuncture) criteria were used to appraise the acupressure procedures, and the Cochrane risk of bias tool was used to assess the methodological quality of the studies. Results Of 39 potentially relevant studies, seven RCTs met the inclusion criteria for review while five studies met the criteria for meta-analysis. All studies reported the positive effect of acupressure on relieving anxiety from the anticipation of surgery or treatment. EX-HN3 ( Yintang), HT7 ( Shenmen) were the commonest points selected and two studies used bilateral points. The acupressure procedure was generally well reported and studies had a low risk of bias. The combined results of the five trials showed a greater overall reduction in anxiety in the acupressure group than in the sham controls (standardised mean differences (SMD)=−1.11; 95% CI −1.61 to −0.61; p<0.0001 heterogeneity: I2=75%; χ2=16.17; p=0.003; r=0.485). Conclusions Acupressure seems to be effective in providing immediate relief of pretreatment anxiety among adults, and has a medium effect size. However, conflicting results were found for the improvements on physiological indicators. More rigorous reporting, including allocation concealment procedure, is needed to strengthen the results.
The Athlete Sleep Screening Questionnaire: a new tool for assessing and managing sleep in elite athletes
Authors: Samuels Charles , James Lois , Lawson Doug , Meeuwisse Willem 
Published: May 2015

Background/aimThe purpose of this study was to develop a subjective, self-report, sleep-screening questionnaire for elite athletes. This paper describes the development of the Athlete Sleep Screening Questionnaire (ASSQ).MethodsA convenience sample of 60 elite athletes was randomly distributed into two groups; 30 athletes completed a survey composed of current psychometric tools, and 30 athletes completed a revised survey and a sleep specialist structured clinical interview. An item analysis was performed on the revised survey with comparison to clinical decisions regarding appropriate intervention based on a sleep specialist assessment.ResultsA comparison of existing sleep-screening tools with determination of clinical need from a sleep specialist showed low consistency, indicating that current sleep-screening tools are unsuitable for assessing athlete sleep. A new 15-item tool was developed (ASSQ) by selecting items from existing tools that more closely associated with the sleep specialist's reviews. Based on test-retest percentage agreement and the κ-statistic, we found good internal consistency and reliability of the ASSQ. To date, 349 athletes have been screened, and 46 (13.2%) identified as requiring follow-up consultation with a sleep specialist. Results from the follow-up consultations demonstrated that those athletes identified by the ASSQ as abnormal sleepershaverequired intervention.ConclusionsThe research developed a new athlete-specific sleep-screening questionnaire. Our findings suggest that existing sleep-screening tools are unsuitable for assessing sleep in elite athletes. The ASSQ appears to be more accurate in assessing athlete sleep (based on comparison with expert clinical assessment). The ASSQ can be deployed online and provides clinical cut-off scores associated with specific clinical interventions to guide management of athletes’ sleep disturbance. The next phase of the research is to conduct a series of studies comparing results from the ASSQ to blinded clinical reviews and to data from objective sleep monitoring to further establish the validity of the ASSQ as a reliable sleep screening tool for elite athletes.