bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of continuum radio emission associated with Geminga
Authors: Pellizzoni A. , Govoni F. , Esposito P. , Murgia M. , Possenti A. 
Published: July 2011

Abstract
A deep Very Large Array observation of the Geminga pulsar field led to the discovery, at a higher than 10σ significance level, of radio emission trailing the neutron star proper motion. This ∼10 arcsec long radio feature, detected with a flux of ∼0.4 mJy at 4.8 GHz, is marginally displaced (2.7 ± 1.8 arcsec) from the pulsar (which, at any rate, is unlikely to contribute with magnetospheric pulsed emission more than 15 per cent to the total observed radio luminosity, ∼1026 erg s−1) and positionally coincident with the X-ray axial tail recently discovered by Chandra and ascribed to the pulsar wind nebula (PWN). Overall, the Geminga radio tail is compatible with the scenario of a synchrotron-emitting PWN, but the present data do not allow us to discriminate between different (and not always necessarily mutually exclusive) possible processes for producing that. If this radio feature results not from intrinsic peculiarities of Geminga, but from its proximity and radio-quiet nature (both helping in not hindering the faint diffuse radio emission), other relatively near and energetic radio-quiet pulsars could show similar structures in dedicated interferometric observations.
Risk Factor Profiles of South Asians with Cerebrovascular Disease
Authors: Itrat Ahmad , Ahmed Bilal , Khan Maria , Muhammad Murtaza , Thaver Danyal , Khowaja Zubair , Ali Shehzad , Bawa Zeeshan , Rahat Muhammad , Kamal Ayeesha Kamran 
Published: July 2011

Background There is a paucity of population based data about the coexistent proportions of risk factors for stroke in South Asians. Methods In this cross sectional survey performed in an urban slum, individuals 35 years of age or older were invited for participation through a simple random sample drawn from baseline census data. For each participant a systematic history and examination was performed to confirm the following risk factors: diabetes, hypertension, obesity, tobacco use, coronary artery disease, family history of coronary artery disease and/or stroke. Cerebrovascular events (stroke and TIA) were verified by a vascular neurologist. We report the association of risk factor groups and the presence of contemporaneous cerebrovascular event. Results Five hundred and forty-five individuals (49.4% females) participated in the study. One hundred and nineteen (21.8%) individuals had a cerebrovascular event (stroke and / or TIA). Obesity was found to be the predominant risk factor, occurring in 310 individuals (56.9%), followed by total hypertension (284; 52.1 %) and tobacco use respectively (213; 39 %). Cerebrovascular event increased in percentage with quantitative increase in risk factors. Cerebrovascular event prevalence was 14.3% with one risk factor, 22% with two, 27% with three, 33% with four, and 86% with five risk factors respectively. The combination of 4 risk factors (hypertension, diabetes, obesity and cigarette smoking) conferred the highest odds of having cerebrovascular event at 4.9 ( P 0.03). Conclusion South Asians in an urban slum often have multiple modifiable risk factors for cerebrovascular event, increasing numbers of risk factors increase the risk of stroke and TIA.
Decrease in the Autotrophic-to-Heterotrophic Biomass Ratio of Picoplankton in Oligotrophic Marine Waters Due to Bottle Enclosure
Authors: Calvo-Díaz Alejandra , Díaz-Pérez Laura , Suárez Luis Ángel , Morán Xosé Anxelu G. , Teira Eva , Marañón Emilio 
Published: July 2011

ABSTRACT

We investigated the effects of bottle enclosure on autotrophic and heterotrophic picoplankton in North and South subtropical Atlantic oligotrophic waters, where the biomass and metabolism of the microbial community are dominated by the picoplankton size class. We measured changes in both autotrophic (
Prochlorococcus
,
Synechococcus
, and picoeukaryotes) and heterotrophic picoplankton biomass during three time series experiments and in 16 endpoint experiments over 24 h in light and dark treatments. Our results showed a divergent effect of bottle incubation on the autotrophic and heterotrophic components of the picoplankton community. The biomass of picophytoplankton showed, on average, a >50% decrease, mostly affecting the picoeukaryotes and, to a lesser extent,
Prochlorococcus
. In contrast, the biomass of heterotrophic bacteria remained constant or increased during the incubations. We also sampled 10 stations during a Lagrangian study in the North Atlantic subtropical gyre, which enabled us to compare the observed changes in the auto- to heterotrophic picoplankton biomass ratio (AB:HB ratio) inside the incubation bottles with those taking place
in situ
. While the AB:HB ratio
in situ
remained fairly constant during the Lagrangian study, it decreased significantly during the 24 h of incubation experiments. Thus, the rapid biomass changes observed in the incubations are artifacts resulting from bottle confinement and do not take place in natural conditions. Our results suggest that short (<1 day) bottle incubations in oligotrophic waters may lead to biased estimates of the microbial metabolic balance by underestimating primary production and/or overestimating bacterial respiration.
Formation of Alkenes via Degradation of
tert
-Alkyl Ethers and Alcohols by Aquincola tertiaricarbonis L108 and Methylibium spp
Authors: Schäfer Franziska , Muzica Liudmila , Schuster Judith , Treuter Naemi , Rosell Mònica , Harms Hauke , Müller Roland H. , Rohwerder Thore 
Published: July 2011

ABSTRACT

Bacterial degradation pathways of fuel oxygenates such as methyl
tert
-butyl and
tert
-amyl methyl ether (MTBE and TAME, respectively) have already been studied in some detail. However, many of the involved enzymes are still unknown, and possible side reactions have not yet been considered. In
Aquincola tertiaricarbonis
L108,
Methylibium petroleiphilum
PM1, and
Methylibium
sp. strain R8, we have now detected volatile hydrocarbons as by-products of the degradation of the
tert
-alkyl ether metabolites
tert
-butyl and
tert
-amyl alcohol (TBA and TAA, respectively). The alkene isobutene was formed only during TBA catabolism, while the beta and gamma isomers of isoamylene were produced only during TAA conversion. Both
tert
-alkyl alcohol degradation and alkene production were strictly oxygen dependent. However, the relative contribution of the dehydration reaction to total alcohol conversion increased with decreasing oxygen concentrations. In resting-cell experiments where the headspace oxygen content was adjusted to less than 2%, more than 50% of the TAA was converted to isoamylene. Isobutene formation from TBA was about 20-fold lower, reaching up to 4% alcohol turnover at low oxygen concentrations. It is likely that the putative
tert
-alkyl alcohol monooxygenase MdpJ, belonging to the Rieske nonheme mononuclear iron enzymes and found in all three strains tested, or an associated enzymatic step catalyzed the unusual elimination reaction. This was also supported by the detection of
mdpJK
genes in MTBE-degrading and isobutene-emitting enrichment cultures obtained from two treatment ponds operating at Leuna, Germany. The possible use of alkene formation as an easy-to-measure indicator of aerobic fuel oxygenate biodegradation in contaminated aquifers is discussed.
Identification and Characterization of Potential Performance-Related Gut Microbiotas in Broiler Chickens across Various Feeding Trials
Authors: Torok Valeria A. , Hughes Robert J. , Mikkelsen Lene L. , Perez-Maldonado Rider , Balding Katherine , MacAlpine Ron , Percy Nigel J. , Ophel-Keller Kathy 
Published: July 2011

ABSTRACT

Three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. Trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. Gut microbial communities were investigated using microbial profiling. Eight common performance-linked operational taxonomic units (OTUs) were identified within both the ilea (180, 492, and 564–566) and ceca (140–142, 218–220, 284–286, 312, and 482) across trials. OTU 564–566 was associated with lower performance, while OTUs 140–142, 482, and 492 were associated with improved performance. Targeted cloning and sequencing of these eight OTUs revealed that they represented 26 bacterial species or phylotypes which clustered phylogenetically into seven groups related to
Lactobacillus
spp.,
Ruminococcaceae
,
Clostridiales
,
Gammaproteobacteria
,
Bacteroidales
,
Clostridiales
/
Lachnospiraceae
, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to the
Firmicutes
, with
Bacteroidetes
and
Proteobacteria
also identified. Some of the potential performance-related phylotypes showed high sequence identity with classified bacteria (
Lactobacillus salivarius
,
Lactobacillus aviarius
,
Lactobacillus crispatus
,
Faecalibacterium prausnitzii
,
Escherichia coli
,
Gallibacterium anatis
,
Clostridium lactatifermentans
,
Ruminococcus torques
,
Bacteroides vulgatus
, and
Alistipes finegoldii
). The 16S rRNA gene sequence information generated will allow quantitative assays to be developed which will enable elucidations of which of these phylotypes are truly performance related. This information could be used to monitor strategies to improve feed efficiency and feed formulation for optimal gut health.
Staphylococcus aureus Host Range and Human-Bovine Host Shift
Authors: Sakwinska Olga , Giddey Marlyse , Moreillon Martine , Morisset Delphine , Waldvogel Andreas , Moreillon Philippe 
Published: July 2011

ABSTRACT

Staphylococcus aureus
is a major agent of bovine mastitis. The concomitant emergence of pig-associated methicillin-resistant
S. aureus
(MRSA) in human carriage and infection requires a reexamination of the host range and specificity of human- and cow-associated
S. aureus
strains, something which has not been systematically studied previously. The genetic relatedness of 500
S. aureus
isolates from bovine mastitis cases, 57 isolates from nasal carriage of farmers, and 133 isolates from nonfarmers was determined by amplified fragment length polymorphism (AFLP) analysis and
spa
typing. Multilocus sequence typing (MLST) was conducted on a subset of isolates to match AFLP clusters with MLST clonal complexes (CCs). This data set allowed us to study host range and host specificity and to estimate the extent of bovine-to-human transmission. The genotype compositions of
S. aureus
isolates from farmers and nonfarmers were very similar, while the mastitis isolates were quite distinct. Overall, transmission was low, but specific genotypes did show increased cow-to-human transmission. Unexpectedly, more than one-third of mastitis isolates belonged to CC8, a lineage which has not been considered to be bovine mastitis associated, but it is well known from human carriage and infection (i.e., USA300). Despite the fact that we did detect some transmission of other genotypes from cows to farmers, no transmission of CC8 isolates to farmers was detected, except for one tentative case. This was despite the close genetic relatedness of mastitis CC8 strains to nonfarmer carriage strains. These results suggest that the emergence of the new bovine-adapted genotype was due to a recent host shift from humans to cows concurrent with a loss of the ability to colonize humans. More broadly, our results indicate that host specificity is a lineage-specific trait that can rapidly evolve.
Repeated Anaerobic Microbial Redox Cycling of Iron
Authors: Coby Aaron J. , Picardal Flynn , Shelobolina Evgenya , Xu Huifang , Roden Eric E. 
Published: July 2011

ABSTRACTSome nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate-depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate-reducing and Fe(III)-reducing cultures were dominated by denitrifyingBetaproteobacteria(e.g.,Dechloromonas) and Fe(III)-reducingDeltaproteobacteria(Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures. The combined chemical and microbiological data suggest that bothGeobacterand variousBetaproteobacteriaparticipated in nitrate-dependent Fe(II) oxidation in the cycling cultures. Microbially driven Fe-N redox cycling may have important consequences for both the fate of N and the abundance and reactivity of Fe(III) oxides in sediments.
Pulsed-Field Gel Electrophoresis and PCR Characterization of Environmental Vibrio parahaemolyticus Strains of Different Origins
Authors: Suffredini E. , Lopez-Joven C. , Maddalena L. , Croci L. , Roque A. 
Published: July 2011

ABSTRACT

The present study used pulsed-field gel electrophoresis (PFGE) characterization to examine the intraspecies variability and genetic relationships among environmental isolates of
Vibrio parahaemolyticus
from different European countries. This is first study performed on environmental
V. parahaemolyticus
that included more than one European country.
Genetic and Biochemical Map for the Biosynthesis of Occidiofungin, an Antifungal Produced by Burkholderia contaminans Strain MS14
Authors: Gu Ganyu , Smith Leif , Liu Aixin , Lu Shi-En 
Published: July 2011

ABSTRACT

A striking feature of
Burkholderia contaminans
strain MS14 is the production of a glycolipopeptide named occidiofungin. Occidiofungin has a broad range of antifungal activities against plant and animal pathogens. In this study, a complete covalent structure characterization and identification of the whole genomic DNA region for the occidiofungin gene (
ocf
) cluster are described. Discovery of the presence of 2,4-diaminobutyric acid and 3-chloro-β-hydroxytyrosine and elucidation of the structure of a novel C
18
fatty amino acid residue have been achieved. In addition, seven additional putative open reading frames (the genes from
ocfI
to
ocfN
[
ocfI-N
] and ORF16) were identified. Transcription of all the putative genes
ocfI-N
identified in the region except ORF16 was regulated by both
ambR1
and
ambR2
. Elucidation of the structure and the
ocf
gene cluster provides insight into the biosynthesis of occidiofungin and promotes future aims at understanding the biosynthetic machinery. This work provides new avenues for optimizing the production and synthesis of structural analogs of occidiofungin.
Quantitative Analysis of the Relative Transcript Levels of Four Chlorophenol Reductive Dehalogenase Genes in Desulfitobacterium hafniense PCP-1 Exposed to Chlorophenols
Authors: Bisaillon Ariane , Beaudet Réjean , Lépine François , Villemur Richard 
Published: July 2011

ABSTRACT

Relative to those of unexposed cultures, the transcript levels of the four CprA-type reductive dehalogenase genes (
cprA2
,
cprA3
,
cprA4
, and
cprA5
) in
Desulfitobacterium hafniense
PCP-1 were measured in cultures exposed to chlorophenols. In 2,4,6-trichlorophenol-amended cultures,
cprA2
and
cprA3
were upregulated, as was
cprA5
, but concomitantly with the appearance of 2,4-dichlorophenol (DCP). In 3,5-DCP-amended cultures, only
cprA5
was upregulated. In pentachlorophenol-amended cultures grown for 12 h,
cprA2
and
cprA3
were upregulated but not
cprA5. cprA4
was not upregulated significantly in cultures containing any tested chlorophenols.
Total and Viable Legionella pneumophila Cells in Hot and Natural Waters as Measured by Immunofluorescence-Based Assays and Solid-Phase Cytometry
Authors: Parthuisot N. , Binet M. , Touron-Bodilis A. , Pougnard C. , Lebaron P. , Baudart J. 
Published: July 2011

ABSTRACT

A new method was developed for the rapid and sensitive detection of viable
Legionella pneumophila
. The method combines specific immunofluorescence (IF) staining using monoclonal antibodies with a bacterial viability marker (ChemChrome V6 cellular esterase activity marker) by means of solid-phase cytometry (SPC). IF methods were applied to the detection and enumeration of both the total and viable
L. pneumophila
cells in water samples. The sensitivity of the IF methods coupled to SPC was 34 cells liter
−1
, and the reproducibility was good, with the coefficient of variation generally falling below 30%. IF methods were applied to the enumeration of total and viable
L. pneumophila
cells in 46 domestic hot water samples as well as in cooling tower water and natural water samples, such as thermal spring water and freshwater samples. Comparison with standard plate counts showed that (i) the total direct counts were always higher than the plate counts and (ii) the viable counts were higher than or close to the plate counts. With domestic hot waters, when the IF assay was combined with the viability test, SPC detected up to 3.4 × 10
3
viable but nonculturable
L. pneumophila
cells per liter. These direct IF methods could be a powerful tool for high-frequency monitoring of domestic hot waters or for investigating the occurrence of viable
L. pneumophila
in both man-made water systems and environmental water samples.
Novel Multiplex Single Nucleotide Polymorphism-Based Method for Identifying Epidemic Clones of Listeria monocytogenes
Authors: Lomonaco Sara , Knabel Stephen J. , Dalmasso Alessandra , Civera Tiziana , Bottero Maria Teresa 
Published: July 2011

ABSTRACT

A novel primer extension-based, multiplex minisequencing assay targeting six highly informative single nucleotide polymorphisms (SNPs) in four virulence genes correctly identified and differentiated all four epidemic clones (ECs) of
Listeria monocytogenes
and 9 other strains initially misclassified as non-ECs. This assay allows rapid, accurate, and high-throughput screening for all known ECs of
L. monocytogenes
.
Persistent Phytoplankton Bloom in Lake St. Lucia (iSimangaliso Wetland Park, South Africa) Caused by a Cyanobacterium Closely Associated with the Genus Cyanothece (Synechococcaceae, Chroococcales)
Authors: Muir David G. , Perissinotto Renzo 
Published: July 2011

ABSTRACT

Lake St. Lucia, iSimangaliso Wetland Park, South Africa, is the largest estuarine lake in Africa. Extensive use and manipulation of the rivers flowing into it have reduced freshwater inflow, and the lake has also been subject to a drought of 10 years. For much of this time, the estuary has been closed to the Indian Ocean, and salinities have progressively risen throughout the system, impacting the biotic components of the ecosystem, reducing zooplankton and macrobenthic biomass and diversity in particular. In June 2009, a bloom of a red/orange planktonic microorganism was noted throughout the upper reaches of Lake St. Lucia. The bloom persisted for at least 18 months, making it the longest such bloom on record. The causative organism was characterized by light and electron microscopy and by 16S rRNA sequencing and was shown to be a large, unicellular cyanobacterium most strongly associated with the genus
Cyanothece
. The extent and persistence of the bloom appears to be unique to Lake St. Lucia, and it is suggested that the organism's resistance to high temperatures, to intense insolation, and to hypersalinity as well as the absence of grazing pressure by salinity-sensitive zooplankton all contributed to its persistence as a bloom organism until a freshwater influx, due to exceptionally heavy summer rains in 2011, reduced the salinity for a sufficient length of time to produce a crash in the cyanobacterium population as a complex, low-salinity biota redeveloped.
Transcription Analysis of a Lantibiotic Gene Cluster from Bifidobacterium longum DJO10A
Authors: Lee Ju-Hoon , Li Xiulan , O'Sullivan Daniel J. 
Published: July 2011

ABSTRACTBifidobacterium longumDJO10A was previously demonstrated to produce a lantibiotic, but only during growth on agar media. To evaluate the feasibility of production of this lantibiotic in broth media, a transcription analysis of thelanAgene was undertaken. Comparative microarray analysis of broth and agar cultures ofB. longumDJO10A revealed that the lantibiotic production, modification, transport/peptidase, and immunity genes were significantly upregulated in agar cultures, while the two-component regulatory genes were expressed equally under both conditions. This suggested that the signal transduction regulatory system should function in broth cultures. Real-time PCR and Northern hybridization confirmed thatlanAgene expression was significantly repressed in broth cultures. A crude lantibiotic preparation from an agar-grown culture was obtained, and its antimicrobial spectrum analysis revealed a broad inhibition range. Addition of this extract to broth cultures ofB. longumDJO10A inducedlanAgene expression in a dose-dependent fashion. Subinoculation using >10% of an induced broth culture maintainedlanAexpression. The expression oflanAwas log-phase specific, being significantly downregulated in stationary phase. Transcription start analysis oflanArevealed a 284-bp 5′ untranslated region, which was proposed to be involved in repression of transcription, while an inverted repeat structure located at bp −75 relative to the transcription start was strategically located to likely function as a binding site for the two-component response regulator. Understanding the transcription regulation of thislanAgene is the first step toward enabling production of this novel and potentially interesting lantibiotic in broth cultures.
Mechanism of Copper Surface Toxicity in Vancomycin-Resistant Enterococci following Wet or Dry Surface Contact
Authors: Warnes S. L. , Keevil C. W. 
Published: July 2011

ABSTRACT

Contaminated touch surfaces have been implicated in the spread of hospital-acquired infections, and the use of biocidal surfaces could help to reduce this cross-contamination. In a previous study we reported the death of aqueous inocula of pathogenic
Enterococcus faecalis
or
Enterococcus faecium
isolates, simulating fomite surface contamination, in 1 h on copper alloys, compared to survival for months on stainless steel. In our current study we observed an even faster kill of over a 6-log reduction of viable enterococci in less than 10 min on copper alloys with a “dry” inoculum equivalent to touch contamination. We investigated the effect of copper(I) and copper(II) chelation and the quenching of reactive oxygen species on cell viability assessed by culture and their effects on genomic DNA, membrane potential, and respiration
in situ
on metal surfaces. We propose that copper surface toxicity for enterococci involves the direct or indirect action of released copper ionic species and the generation of superoxide, resulting in arrested respiration and DNA breakdown as the first stages of cell death. The generation of hydroxyl radicals by the Fenton reaction does not appear to be the dominant instrument of DNA damage. The bacterial membrane potential is unaffected in the early stages of wet and dry surface contact, suggesting that the membrane is not compromised until after cell death. These results also highlight the importance of correct surface cleaning protocols to perpetuate copper ion release and prevent the chelation of ions by contaminants, which could reduce the efficacy of the surface.