bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater
Authors: Feld Louise , Nielsen Tue Kjærgaard , Hansen Lars Hestbjerg , Aamand Jens , Albers Christian Nyrop 
Published: November 2015

ABSTRACT

In this study, we investigated the establishment of natural bacterial degraders in a sand filter treating groundwater contaminated with the phenoxypropionate herbicides (
RS
)-2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP) and (
RS
)-2-(2,4-dichlorophenoxy)propanoic acid (DCPP) and the associated impurity/catabolite 4-chlorophenoxypropanoic acid (4-CPP). A pilot facility was set up in a contaminated landfill site. Anaerobic groundwater was pumped up and passed through an aeration basin and subsequently through a rapid sand filter, which is characterized by a short residence time of the water in the filter. For 3 months, the degradation of DCPP, MCPP, and 4-CPP in the sand filter increased to 15 to 30% of the inlet concentration. A significant selection for natural bacterial herbicide degraders also occurred in the sand filter. Using a most-probable-number (MPN) method, we found a steady increase in the number of culturable phenoxypropionate degraders, reaching approximately 5 × 10
5
degraders per g sand by the end of the study. Using a quantitative PCR targeting the two phenoxypropionate degradation genes,
rdpA
and
sdpA
, encoding stereospecific dioxygenases, a parallel increase was observed, but with the gene copy numbers being about 2 to 3 log units higher than the MPN. In general, the
sdpA
gene was more abundant than the
rdpA
gene, and the establishment of a significant population of bacteria harboring
sdpA
occurred faster than the establishment of an
rdpA
gene-carrying population. The identities of the specific herbicide degraders in the sand filter were assessed by Illumina MiSeq sequencing of 16S rRNA genes from sand filter samples and from selected MPN plate wells. We propose a list of potential degrader bacteria involved in herbicide degradation, including representatives belonging to the
Comamonadaceae
and
Sphingomonadales
.
Diversity and Ecology of Viruses in Hyperarid Desert Soils
Authors: Zablocki Olivier , Adriaenssens Evelien M. , Cowan Don 
Published: November 2015

ABSTRACT
In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.
A Livestock-Associated, Multidrug-Resistant, Methicillin-Resistant Staphylococcus aureus Clonal Complex 97 Lineage Spreading in Dairy Cattle and Pigs in Italy
Authors: Feltrin Fabiola , Alba Patricia , Kraushaar Britta , Ianzano Angela , Argudín María Angeles , Di Matteo Paola , Porrero María Concepción , Aarestrup Frank M. , Butaye Patrick , Franco Alessia , Battisti Antonio 
Published: November 2015

ABSTRACT

Pandemic methicillin-resistant
Staphylococcus aureus
(MRSA) clonal complex 97 (CC97) lineages originated from livestock-to-human host jumps. In recent years, CC97 has become one of the major MRSA lineages detected in Italian farmed animals. The aim of this study was to characterize and analyze differences in MRSA and methicillin-susceptible
S. aureus
(MSSA) mainly of swine and bovine origins. Forty-seven CC97 isolates, 35 MRSA isolates, and 6 MSSA isolates from different Italian pig and cattle holdings; 5 pig MRSA isolates from Germany; and 1 human MSSA isolate from Spain were characterized by macrorestriction pulsed-field gel electrophoresis (PFGE) analysis, multilocus sequence typing (MLST),
spa
typing, staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and antimicrobial resistance pattern analysis. Virulence and resistance genes were investigated by PCR and microarray analysis. Most of the isolates were of SCC
mec
type V (SCC
mec
V), except for two German MRSA isolates (SCC
mec
III). Five main clusters were identified by PFGE, with the German isolates (clusters I and II) showing 60.5% similarity with the Italian isolates, most of which (68.1%) grouped into cluster V. All CC97 isolates were Panton-Valentine leukocidin (PVL) negative, and a few (
n
= 7) tested positive for
sak
or
scn
. All MRSA isolates were multidrug resistant (MDR), and the main features were
erm
(B)- or
erm
(C)-mediated (
n
= 18) macrolide-lincosamide-streptogramin B resistance,
vga
(A)-mediated (
n
= 37) pleuromutilin resistance, fluoroquinolone resistance (
n
= 33),
tet
(K) in 32/37
tet
(M)-positive isolates, and
blaZ
in almost all MRSA isolates. Few host-associated differences were detected among CC97 MRSA isolates: their extensive MDR nature in both pigs and dairy cattle may be a consequence of a spillback from pigs of a MRSA lineage that originated in cattle as MSSA and needs further investigation. Measures should be implemented at the farm level to prevent spillover to humans in intensive farming areas.
MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently
Authors: Yun Choong-Soo , Takahashi Yurika , Shintani Masaki , Takeda Toshiharu , Suzuki-Minakuchi Chiho , Okada Kazunori , Yamane Hisakazu , Nojiri Hideaki 
Published: November 2015

ABSTRACT

MvaT proteins are members of the H-NS family of proteins in pseudomonads. The IncP-7 conjugative plasmid pCAR1 carries an
mvaT
-homologous gene,
pmr
. In
Pseudomonas putida
KT2440 bearing pCAR1,
pmr
and the chromosomally carried homologous genes,
turA
and
turB
, are transcribed at high levels, and Pmr interacts with TurA and TurB
in vitro
. In the present study, we clarified how the three MvaT proteins regulate the transcriptome of
P. putida
KT2440(pCAR1). Analyses performed by a modified chromatin immunoprecipitation assay with microarray technology (ChIP-chip) suggested that the binding regions of Pmr, TurA, and TurB in the
P. putida
KT2440(pCAR1) genome are almost identical; nevertheless, transcriptomic analyses using mutants with deletions of the genes encoding the MvaT proteins during the log and early stationary growth phases clearly suggested that their regulons were different. Indeed, significant regulon dissimilarity was found between Pmr and the other two proteins. Transcription of a larger number of genes was affected by Pmr deletion during early stationary phase than during log phase, suggesting that Pmr ameliorates the effects of pCAR1 on host fitness more effectively during the early stationary phase. Alternatively, the similarity of the TurA and TurB regulons implied that they might play complementary roles as global transcriptional regulators in response to plasmid carriage.
Validation of a Previously Developed Geospatial Model That Predicts the Prevalence of Listeria monocytogenes in New York State Produce Fields
Authors: Weller Daniel , Shiwakoti Suvash , Bergholz Peter , Grohn Yrjo , Wiedmann Martin , Strawn Laura K. 
Published: November 2015

ABSTRACT

Technological advancements, particularly in the field of geographic information systems (GIS), have made it possible to predict the likelihood of foodborne pathogen contamination in produce production environments using geospatial models. Yet, few studies have examined the validity and robustness of such models. This study was performed to test and refine the rules associated with a previously developed geospatial model that predicts the prevalence of
Listeria monocytogenes
in produce farms in New York State (NYS). Produce fields for each of four enrolled produce farms were categorized into areas of high or low predicted
L. monocytogenes
prevalence using rules based on a field's available water storage (AWS) and its proximity to water, impervious cover, and pastures. Drag swabs (
n
= 1,056) were collected from plots assigned to each risk category. Logistic regression, which tested the ability of each rule to accurately predict the prevalence of
L. monocytogenes
, validated the rules based on water and pasture. Samples collected near water (odds ratio [OR], 3.0) and pasture (OR, 2.9) showed a significantly increased likelihood of
L. monocytogenes
isolation compared to that for samples collected far from water and pasture. Generalized linear mixed models identified additional land cover factors associated with an increased likelihood of
L. monocytogenes
isolation, such as proximity to wetlands. These findings validated a subset of previously developed rules that predict
L. monocytogenes
prevalence in produce production environments. This suggests that GIS and geospatial models can be used to accurately predict
L. monocytogenes
prevalence on farms and can be used prospectively to minimize the risk of preharvest contamination of produce.
Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis
Authors: Morganti Marina , Scaltriti Erika , Cozzolino Paolo , Bolzoni Luca , Casadei Gabriele , Pierantoni Marco , Foni Emanuela , Pongolini Stefano 
Published: November 2015

ABSTRACT

The quantitative and qualitative patterns of environmental contamination by
Listeria monocytogenes
were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for
L. monocytogenes
, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of
L. monocytogenes
within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of
L. monocytogenes
within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments.
Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae
Authors: Ji Shi-Qi , Wang Bing , Lu Ming , Li Fu-Li 
Published: November 2015

ABSTRACT

Brown algae are one of the largest groups of oceanic primary producers for CO
2
removal and carbon sinks for coastal regions. However, the mechanism for brown alga assimilation remains largely unknown in thermophilic microorganisms. In this work, a thermophilic alginolytic community was enriched from coastal sediment, from which an obligate anaerobic and thermophilic bacterial strain, designated Alg1, was isolated. Alg1 shared a 16S rRNA gene identity of 94.6% with
Defluviitalea saccharophila
LIND6LT2
T
. Phenotypic, chemotaxonomic, and phylogenetic studies suggested strain Alg1 represented a novel species of the genus
Defluviitalea
, for which the name
Defluviitalea phaphyphila
sp. nov. is proposed. Alg1 exhibited an intriguing ability to convert carbohydrates of brown algae, including alginate, laminarin, and mannitol, to ethanol and acetic acid. Three gene clusters participating in this process were predicted to be in the genome, and candidate enzymes were successfully expressed, purified, and characterized. Six alginate lyases were demonstrated to synergistically deconstruct alginate into unsaturated monosaccharide, followed by one uronic acid reductase and two 2-keto-3-deoxy-
d
-gluconate (KDG) kinases to produce pyruvate. A nonclassical mannitol 1-phosphate dehydrogenase, catalyzing
d
-mannitol 1-phosphate to fructose 1-phosphate in the presence of NAD
+
, and one laminarase also were disclosed. This work revealed that a thermophilic brown alga-decomposing system containing numerous novel thermophilic alginate lyases and a unique mannitol 1-phosphate dehydrogenase was adopted by the natural ethanologenic strain Alg1 during the process of evolution in hostile habitats.
Tolerance of Listeria monocytogenes to Quaternary Ammonium Sanitizers Is Mediated by a Novel Efflux Pump Encoded by emrE
Authors: Kovacevic Jovana , Ziegler Jennifer , Wałecka-Zacharska Ewa , Reimer Aleisha , Kitts David D. , Gilmour Matthew W. 
Published: November 2015

ABSTRACT

A novel genomic island (LGI1) was discovered in
Listeria monocytogenes
isolates responsible for the deadliest listeriosis outbreak in Canada, in 2008. To investigate the functional role of LGI1, the outbreak strain 08-5578 was exposed to food chain-relevant stresses, and the expression of 16 LGI1 genes was measured. LGI1 genes with putative efflux (
L. monocytogenes
emrE
[

emrE
Lm

]), regulatory (
lmo1851
), and adhesion (
sel1
) functions were deleted, and the mutants were exposed to acid (HCl), cold (4°C), salt (10 to 20% NaCl), and quaternary ammonium-based sanitizers (QACs). Deletion of
lmo1851
had no effect on the
L. monocytogenes
stress response, and deletion of
sel1
did not influence Caco-2 and HeLa cell adherence/invasion, whereas deletion of
emrE
resulted in increased susceptibility to QACs (
P
< 0.05) but had no effect on the MICs of gentamicin, chloramphenicol, ciprofloxacin, erythromycin, tetracycline, acriflavine, and triclosan. In the presence of the QAC benzalkonium chloride (BAC; 5 μg/ml), 14/16 LGI1 genes were induced, and
lmo1861
(putative repressor gene) was constitutively expressed at 4°C, 37°C, and 52°C and in the presence of UV exposure (0 to 30 min). Following 1 h of exposure to BAC (10 μg/ml), upregulation of
emrE
(49.6-fold),
lmo1851
(2.3-fold),
lmo1861
(82.4-fold), and
sigB
(4.1-fold) occurred. Reserpine visibly suppressed the growth of the Δ

emrE
Lm

strain, indicating that QAC tolerance is due at least partially to efflux activity. These data suggest that a minimal function of LGI1 is to increase the tolerance of
L. monocytogenes
to QACs via

emrE
Lm

. Since QACs are commonly used in the food industry, there is a concern that
L. monocytogenes
strains possessing
emrE
will have an increased ability to survive this stress and thus to persist in food processing environments.
Memory for gist and detail information in patients with Parkinson's disease
Authors: Yu Rwei-Ling , Tan Chun-Hsiang , Wu Yih-Ru , Wu Ruey-Meei , Chiu Ming-Jang , Hua Mau-Sun 
Published: November 2015

ObjectiveMemory formation is proposed to be a dual process that involves the simultaneous memorisation of both detailed information (item-specific memory) and gist information (gist memory). Memory deficits have been reported in patients with Parkinson's disease (PD); however, few studies have explicitly addressed the nature of these deficits. To obtain a detailed understanding of memory dysfunction in patients with PD, it is of crucial importance to establish whether item-specific memory and gist memory performance are impaired. The aim of this study is to explore whether gist memory and item-specific memory performance are still intact in patients with PD, as well as to determine which psychological mechanisms are responsible for memory formation.SettingTwo hospitals in northern Taiwan.ParticipantsThirty-nine patients with PD and 28 normal controls were recruited. Each participant received a gist-based recognition test following the Deese-Roediger-McDermott paradigm, as well as neuropsychological tests and measures of clinical characteristics.ResultsGist memory was impaired in patients with advanced-stage disease (Hoehn and Yahr (H&Y) stage: III) (F2,64=3.58, p=0.033), whereas item-specific memory was preserved throughout all disease stages. Correlation analysis showed that item-specific memory was related to executive functions in normal controls and early-stage patients with PD (H&Y stage: I–II); however, item-specific memory was related to episodic memory, rather than to executive functions, in advanced-stage patients with PD. Moreover, gist memory was related to episodic memory, but only in early-stage patients with PD.ConclusionsWe discovered that impaired gist memory is found in advanced-stage, but not in early-stage, patients with PD. Our findings suggest that the techniques used to take advantage of the relatively preserved gist memory in early-stage patients with PD, as well as the preserved item-specific memory in patients with PD of all stages, could be useful for memory rehabilitation programmes.
What methods are used to apply positive deviance within healthcare organisations? A systematic review
Authors: Baxter Ruth , Taylor Natalie , Kellar Ian , Lawton Rebecca 
Published: November 2015

BackgroundThe positive deviance approach focuses on those who demonstrate exceptional performance, despite facing the same constraints as others. ‘Positive deviants’ are identified and hypotheses about how they succeed are generated. These hypotheses are tested and then disseminated within the wider community. The positive deviance approach is being increasingly applied within healthcare organisations, although limited guidance exists and different methods, of varying quality, are used. This paper systematically reviews healthcare applications of the positive deviance approach to explore how positive deviance is defined, the quality of existing applications and the methods used within them, including the extent to which staff and patients are involved.MethodsPeer-reviewed articles, published prior to September 2014, reporting empirical research on the use of the positive deviance approach within healthcare, were identified from seven electronic databases. A previously defined four-stage process for positive deviance in healthcare was used as the basis for data extraction. Quality assessments were conducted using a validated tool, and a narrative synthesis approach was followed.Results37 of 818 articles met the inclusion criteria. The positive deviance approach was most frequently applied within North America, in secondary care, and to address healthcare-associated infections. Research predominantly identified positive deviants and generated hypotheses about how they succeeded. The approach and processes followed were poorly defined. Research quality was low, articles lacked detail and comparison groups were rarely included. Applications of positive deviance typically lacked staff and/or patient involvement, and the methods used often required extensive resources.ConclusionFurther research is required to develop high quality yet practical methods which involve staff and patients in all stages of the positive deviance approach. The efficacy and efficiency of positive deviance must be assessed and compared with other quality improvement approaches.PROSPERO registration numberCRD42014009365.
A behaviourally anchored rating scale for evaluating the use of the WHO surgical safety checklist: development and initial evaluation of the WHOBARS
Authors: Devcich Daniel A , Weller Jennifer , Mitchell Simon J , McLaughlin Scott , Barker Lauren , Rudolph Jenny W , Raemer Daniel B , Zammert Martin , Singer Sara J , Torrie Jane , Frampton Chris MA , Merry Alan F 
Published: November 2015

BackgroundRealising the full potential of the WHO Surgical Safety Checklist (SSC) to reduce perioperative harm requires the constructive engagement of all operating room (OR) team members during its administration. To facilitate research on SSC implementation, a valid and reliable instrument is needed for measuring OR team behaviours during its administration. We developed a behaviourally anchored rating scale (BARS) for this purpose.MethodsWe used a modified Delphi process, involving 16 subject matter experts, to compile a BARS with behavioural domains applicable to all three phases of the SSC. We evaluated the instrument in 80 adult OR cases and 30 simulated cases using two medical student raters and seven expert raters, respectively. Intraclass correlation coefficients were calculated to assess inter-rater reliability. Internal consistency and instrument discrimination were explored. Sample size estimates for potential study designs using the instrument were calculated.ResultsThe Delphi process resulted in a BARS instrument (the WHOBARS) with five behavioural domains. Intraclass correlation coefficients calculated from the OR cases exceeded 0.80 for 80% of the instrument's domains across the SSC phases. The WHOBARS showed high internal consistency across the three phases of the SSC and ability to discriminate among surgical cases in both clinical and simulated settings. Fewer than 20 cases per group would be required to show a difference of 1 point between groups in studies of the SSC, where α=0.05 and β=0.8.ConclusionWe have developed a generic instrument for comprehensively rating the administration of the SSC and informing initiatives to realise its full potential. We have provided data supporting its capacity for discrimination, internal consistency and inter-rater reliability. Further psychometric evaluation is warranted.
A rare and unusual hyperkeratotic disorder
Authors: Ahmad Amna , Chaudhry Iskander H , Robson Alistair 
Published: November 2015

Clinical questionA 78-year-old female presented with a pruritic rash on her legs for many years. A biopsy was taken from the right leg. Review the high-quality, interactive digital Aperio slide athttp://virtualacp.com/JCP_Case/index.phpand consider your diagnosis.What is your diagnosis?Atrophic lichen planusHyperkeratosis lenticularis perstansLichenoid drug reactionLichenoid keratosisPorokeratosis