bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Diversity of
Campylobacter coli
and
Campylobacter jejuni
Isolates Recovered from Free-Range Broiler Farms and Comparison with Isolates of Various Origins
Authors: Rivoal K. , Ragimbeau C. , Salvat G. , Colin P. , Ermel G. 
Published: October 2005

ABSTRACT

In many industrialized countries, the incidence of campylobacteriosis exceeds that of salmonellosis.
Campylobacter
bacteria are transmitted to humans mainly in food, especially poultry meat products. Total prevention of
Campylobacter
colonization in broiler flocks is the best way to reduce (or eliminate) the contamination of poultry products. The aim of this study was to establish the sources and routes of contamination of broilers at the farm level. Molecular typing methods (DNA macrorestriction pulsed-field gel electrophoresis and analysis of gene polymorphism by PCR-restriction fragment length polymorphism) were used to characterize isolates collected from seven broiler farms. The relative genomic diversity of
Campylobacter coli
and
Campylobacter jejuni
was determined. Analysis of the similarity among 116 defined genotypes was used to determine clusters within the two species. Furthermore, evidence of recombination suggested that there were genomic rearrangements within the
Campylobacter
populations. Recovery of related clusters from different broiler farms showed that some
Campylobacter
strains might be specifically adapted to poultry. Analysis of the
Campylobacter
cluster distribution on three broiler farms showed that soil in the area around the poultry house was a potential source of
Campylobacter
contamination. The broilers were infected by
Campylobacter
spp. between days 15 and 36 during rearing, and the type of contamination changed during the rearing period. A study of the effect of sanitary barriers showed that the chickens stayed
Campylobacter
spp. free until they had access to the open area. They were then rapidly colonized by the
Campylobacter
strains isolated from the soil.
Chaperone-Mediated Folding and Maturation of the Penicillin Acylase Precursor in the Cytoplasm of
Escherichia coli
Authors: Xu Yali , Weng Chiao-Ling , Narayanan Niju , Hsieh Ming-Yi , Anderson William A. , Scharer Jeno M. , Moo-Young Murray , Chou C. Perry 
Published: October 2005

ABSTRACT

Expression of the leaderless
pac
gene (LL
pac
), which lacks the coding region for the signal peptide of penicillin acylase (PAC), in
Escherichia coli
was conducted. It was demonstrated that the PAC precursor, proPAC, can be produced and even processed to form mature PAC in the cytoplasm, indicating that the posttranslational processing steps for PAC maturation can occur in both the periplasm and the cytoplasm of
E. coli
. The outcome of proPAC folding and PAC maturation could be affected by several factors, such as inducer type, proPAC formation rate, and chaperone availability. Misfolding of proPAC in the cytoplasm could be partially resolved through the coexpression of cytoplasmic chaperones, such as trigger factor, GroEL/ES, or DnaK/J-GrpE. The three chaperones tested showed different extents of the effect on proPAC solublization and PAC maturation, and trigger factor had the most prominent one. However, the chaperone-mediated solublization of proPAC did not guarantee its maturation, which is usually limited by the first autoproteolytic step. It was observed that arabinose could act as an effective inducer for the induction of LL
pac
expression regulated by the
lac
-derived promoter system of
trc
. In addition, PAC maturation could be highly facilitated by arabinose supplementation and coexpression of trigger factor, suggesting that the coordination of chaperone systems with proper culture conditions could dramatically impact recombinant protein production. This study suggests that folding/misfolding of proPAC could be a major step limiting the overproduction of PAC in
E. coli
and that the problem could be resolved through the search for appropriate chaperones for coexpression. It also demonstrates the analogy in the issues of proPAC misfolding as well as the expression bottleneck occurring in the cytoplasm (i.e., LL
pac
expression) and those occurring in the periplasm (i.e., wild-type
pac
expression).
Effect of Humic Substance Photodegradation on Bacterial Growth and Respiration in Lake Water
Authors: Anesio Alexandre M. , Granéli Wilhelm , Aiken George R. , Kieber David J. , Mopper Kenneth 
Published: October 2005

ABSTRACT

This study addresses how humic substance (HS) chemical composition and photoreactivity affect bacterial growth, respiration, and growth efficiency (BGE) in lake water. Aqueous solutions of HSs from diverse aquatic environments representing different dissolved organic matter sources (autochthonous and allochthonous) were exposed to artificial solar UV radiation. These solutions were added to lake water passed through a 0.7-μm-pore-size filter (containing grazer-free lake bacteria) followed by dark incubation for 5, 43, and 65 h. For the 5-h incubation, several irradiated HSs inhibited bacterial carbon production (BCP) and this inhibition was highly correlated with H
2
O
2
photoproduction. The H
2
O
2
decayed in the dark, and after 43 h, nearly all irradiated HSs enhanced BCP (average 39% increase relative to nonirradiated controls, standard error = 7.5%,
n
= 16). UV exposure of HSs also increased bacterial respiration (by ∼18%, standard error = 5%,
n
= 4), but less than BCP, resulting in an average increase in BGE of 32% (standard error = 10%,
n
= 4). Photoenhancement of BCP did not correlate to HS bulk properties (i.e., elemental and chemical composition). However, when the photoenhancement of BCP was normalized to absorbance, several trends with HS origin and extraction method emerged. Absorbance-normalized hydrophilic acid and humic acid samples showed greater enhancement of BCP than hydrophobic acid and fulvic acid samples. Furthermore, absorbance-normalized autochthonous samples showed ∼10-fold greater enhancement of BCP than allochthonous-dominated samples, indicating that the former are more efficient photoproducers of biological substrates.
Genome-Directed Isolation of the Key Nitrogen Fixer
Leptospirillum ferrodiazotrophum
sp. nov. from an Acidophilic Microbial Community
Authors: Tyson Gene W. , Lo Ian , Baker Brett J. , Allen Eric E. , Hugenholtz Philip , Banfield Jillian F. 
Published: October 2005

ABSTRACT

Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single
nif
operon. This was found on a genome fragment belonging to a member of
Leptospirillum
group III, a lineage in the
Nitrospirae
phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in
Leptospirillum
group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of ∼10
6
cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of
Leptospirillum
group III and that the culture is axenic. We propose the name
Leptospirillum ferrodiazotrophum
sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.
Characterization of Microbial Communities Removing Nitrogen Oxides from Flue Gas: the BioDeNOx Process
Authors: Kumaraswamy Rajkumari , van Dongen Udo , Kuenen J. Gijs , Abma Wiebe , van Loosdrecht Mark C. M. , Muyzer Gerard 
Published: October 2005

ABSTRACTBioDeNOx is an integrated physicochemical and biological process for the removal of nitrogen oxides (NOx) from flue gases. In this process, the flue gas is purged through a scrubber containing a solution of Fe(II)EDTA2−, which binds the NOx to form an Fe(II)EDTA·NO2−complex. Subsequently, this complex is reduced in the bioreactor to dinitrogen by microbial denitrification. Fe(II)EDTA2−, which is oxidized to Fe(III)EDTA−by oxygen in the flue gas, is regenerated by microbial iron reduction. In this study, the microbial communities of both lab- and pilot-scale reactors were studied using culture-dependent and -independent approaches. A pure bacterial strain, KT-1, closely affiliated by 16S rRNA analysis to the gram-positive denitrifying bacteriumBacillus azotoformans, was obtained. DNA-DNA homology of the isolate with the type strain was 89%, indicating that strain KT-1 belongs to the speciesB. azotoformans. Strain KT-1 reduces Fe(II)EDTA·NO2−complex to N2using ethanol, acetate, and Fe(II)EDTA2−as electron donors. It does not reduce Fe(III)EDTA−. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene fragments showed the presence of bacteria closely affiliated with members of the phylumDeferribacteres, an Fe(III)-reducing group of bacteria. Fluorescent in situ hybridization with oligonucleotide probes designed for strain KT-1 and members of the phylumDeferribacteresshowed that the latter were more dominant in both reactors.
Subsurface Microbial Methanotrophic Mats in the Black Sea
Authors: Treude Tina , Knittel Katrin , Blumenberg Martin , Seifert Richard , Boetius Antje 
Published: October 2005

ABSTRACT
A nodule-shaped microbial mat was found subsurface in sediments of a gas seep in the anoxic Black Sea. This mat was dominated by ANME-1 archaea and consumed methane and sulfate simultaneously. We propose that such subsurface mats represent the initial stage of previously investigated microbial reefs.
High Prevalence of VanA-Type Vancomycin-Resistant Enterococci in Austrian Poultry
Authors: Eisner Alexandra , Feierl Gebhard , Gorkiewicz Gregor , Dieber Franz , Kessler Harald H. , Marth Egon , Köfer Josef 
Published: October 2005

ABSTRACT

Fecal samples from humans and food-producing animals were analyzed for the presence of vancomycin-resistant enterococci (VRE). The VRE carriage rate in humans was 6%, and there was a predominance of VanC-type resistance.
Enterococcus faecium
with
vanA
-mediated resistance was frequent in broiler chickens (42%) but rare in cattle and pig samples.
Equine and Canine
Anaplasma phagocytophilum
Strains Isolated on the Island of Sardinia (Italy) Are Phylogenetically Related to Pathogenic Strains from the United States
Authors: Alberti Alberto , Zobba Rosanna , Chessa Bernardo , Addis Maria Filippa , Sparagano Olivier , Pinna Parpaglia Maria Luisa , Cubeddu Tiziana , Pintori Gianpaolo , Pittau Marco 
Published: October 2005

ABSTRACT

The presence of
Anaplasma phagocytophilum
, a tick-transmitted zoonotic pathogen, was investigated in Sardinia using a molecular approach. Phylogenetic analysis revealed that Sardinian strains are genetically distinct from the two lineages previously described in Europe and are closely related to strains isolated in different areas of the United States.
Community Structure and Diversity of Biofilms from a Beer Bottling Plant as Revealed Using 16S rRNA Gene Clone Libraries
Authors: Timke Markus , Wang-Lieu Ngoc Quynh , Altendorf Karlheinz , Lipski André 
Published: October 2005

ABSTRACT

The microbial composition of biofilms from a beer bottling plant was analyzed by a cultivation independent analysis of the 16S rRNA genes. Clone libraries were differentiated by amplified 16S rRNA gene restriction analysis and representative clones from each group were sequenced. The diversity of the clone libraries was comparable with the diversity found for environmental samples. No evidences for the presence of strictly anaerobic taxa or important beer spoilers were found, indicating that biofilms developed for more than 6 months at the plant formed no appropriate habitat for those microorganisms. The genus
Methylobacterium
was one of the dominating groups of the clone libraries. The size of this population was assessed by fluorescence in situ hybridization and fatty acid analysis. In addition, considerable numbers of clones were assigned to uncultivated organisms.
Emission Characteristics of Fluorescent Labels with Respect to Temperature Changes and Subsequent Effects on DNA Microchip Studies
Authors: Liu Wen-Tso , Wu Jer-Horng , Li Emily Sze-Ying , Selamat Ezrein Shah 
Published: October 2005

ABSTRACT
The effects of temperature, salt concentration, and formamide concentration on the emission characteristics of commonly used fluorescent labels were evaluated on DNA microchips. The emission intensities of different fluorophores without hybridization were observed to vary, each to a different extent, to mainly temperature changes. Rhodamine red, TAMRA (tetramethylrhodamine), and dyes from the carbocyanide group exhibited the largest variations, and Texas Red and Oregon Green exhibited the smallest variations. This temperature dependency was shown to affect results obtained during melting curve analysis in DNA microarray studies. To minimize the bias associated with the temperature-dependent emission of different fluorescent labels, a normalization step was proposed.
Baroclinic Instability and Loss of Balance
Authors: Molemaker M. Jeroen , McWilliams James C. , Yavneh Irad 
Published: October 2005

Abstract
Under the influences of stable density stratification and the earth’s rotation, large-scale flows in the ocean and atmosphere have a mainly balanced dynamics—sometimes called the slow manifold—in the sense that there are diagnostic hydrostatic and gradient-wind momentum balances that constrain the fluid acceleration. The nonlinear balance equations are a widely successful, approximate model for this regime, and mathematically explicit limits of their time integrability have been identified. It is hypothesized that these limits are indicative, at least approximately, of the transition from the larger-scale regime of inverse energy cascades by anisotropic flows to the smaller-scale regime of forward energy cascade to dissipation by more nearly isotropic flows and intermittently breaking inertia–gravity waves. This paper analyzes the particular example of an unbalanced instability of a balanced, horizontally uniform, vertically sheared current, as it occurs within the Boussinesq equations. This ageostrophic, anticyclonic, baroclinic instability is investigated with an emphasis on how it relates to the breakdown of balance in the neighborhood of loss of balanced integrability and on how its properties compare with other examples of ageostrophic anticyclonic instability of rotating, stratified, horizontally sheared currents. It is also compared with the more familiar types of instability for a vertically sheared current: balanced (geostrophic) baroclinic instability, centrifugal instability, and Kelvin–Helmholtz instability.
Nonnormal Amplification of the Thermohaline Circulation
Authors: Zanna Laure , Tziperman Eli 
Published: October 2005

Abstract
A simple zonally averaged coupled ocean–atmosphere model, with a relatively high resolution in the meridional direction, is used to examine physical mechanisms leading to transient amplification of thermohaline circulation (THC) anomalies. It is found that in a stable regime, in which small perturbations eventually decay, there are optimal initial conditions leading to a dramatic amplification of initial temperature and salinity anomalies in addition to the THC amplification. The maximum amplification occurs after about 40 years, and the eventual decay is on a centennial time scale. The initial temperature and salinity anomalies are considerably amplified by factors of a few hundreds and 20, respectively. The initial conditions leading to this amplification are characterized by mutually canceling initial temperature and salinity anomalies contributions to the THC anomaly, such that the initial THC anomaly vanishes. The mechanism of amplification is analyzed and found to be the result of an interaction between a few damped (oscillatory and nonoscillatory) modes with decay time scales lying in a range of 20–800 years. The amplification mechanism is also found to be distinct from the advective feedback leading to THC instabilities for large freshwater forcing.
Mixing, 3D Mapping, and Lagrangian Evolution of a Thermohaline Intrusion
Authors: Alford Matthew H. , Gregg Michael C. , D’Asaro Eric A. 
Published: October 2005

Abstract
Observations of the three-dimensional structure and evolution of a thermohaline intrusion in a wide, deep fjord are presented. In an intensive two-ship study centered on an acoustically tracked neutrally buoyant float, a cold, fresh, low-oxygen tongue of water moving southward at about 0.03 m s−1 out of Possession Sound, Washington, was observed. The feature lay across isopycnal surfaces in a 50–80-m depth range. The large-scale structures of temperature, salinity, velocity, dissolved oxygen, and chlorophyll were mapped with a towed, depth-cycling instrument from one ship while the other ship measured turbulence close to the float with loosely tethered microstructure profilers. Observations from both ships were expressed in a float-relative (Lagrangian) reference frame, minimizing advection effects. A float deployed at the tongue’s leading edge warmed 0.2°C in 24 h, which the authors argue resulted from mixing. Diapycnal heat fluxes inferred from microstructure were 1–2 orders of magnitude too small to account for the observed warming. Instead, lateral stirring along isopycnals appears responsible, implying isopycnal diffusivities O(1 m2 s−1). These are consistent with estimates, using measured temperature microstructure, from an extension of the Osborn–Cox model that allows for lateral gradients. Horizontal structures with scales O(100 m) are seen in time series and spatial maps, supporting this interpretation.
Long-term clearance from small airways decreases with age
Authors: Svartengren M. , Falk R. , Philipson K. 
Published: October 2005

The prevalence of respiratory symptoms increases with age. Age has been found to be negatively associated with large airway clearance. The small airways region is considered important for development of airway disease.Clearance after the first 24 h was studied in 46 healthy subjects with a wide age distribution, (mean 42, range 19–81 yrs). All subjects inhaled monodisperse 6 μm Teflon particles labelled with111In, with an extremely slow inhalation flow (0.05 L·s−1). The particles were mainly deposited in the small conducting airways. Lung retention was measured at 0 and 24 h, and at 7, 14 and 21 days after inhalation.Significant relationships were found for the individual 24 h “large” airway clearance in per cent of initial lung deposition with age, forced expiratory volume in one second and forced vital capacity. Age was negatively associated with “small” airway clearance after 24 h as estimated at 2, 7, 14 and 21 days. Using stepwise linear regression only age remained significantly associated to clearance.In conclusion, small airway clearance over 21 days was found to decrease with age. This might be one factor associated with the high prevalence of respiratory symptoms associated among the elderly.
Results of a case-detection programme for α1-antitrypsin deficiency in COPD patients
Authors: de la Roza C. , Rodríguez-Frías F. , Lara B. , Vidal R. , Jardí R. , Miravitlles M. 
Published: October 2005

α1-Antitrypsin (α1-AT) deficiency is an underdiagnosed condition in patients with chronic obstructive pulmonary disease (COPD). The present authors have conducted a nationwide case detection programme of α1-AT deficiency in unselected patients with COPD using dried blood spots.The first phase analysed samples from 971 patients by determining α1-AT concentrations and identifying the deficient Z allele by genotyping using rapid real-time PCR. The second phase analysed 1,166 samples with α1-AT concentrations and identified both the S and the Z allele, but only in samples with low α1-AT concentrations.A total of eight (0.37%) individuals with the severe deficiency PiZZ were detected. In addition, three patients were identified with the PiSZ genotype in the second phase (0.3%). The global cost of the programme was \#8364;41,512, which represents \#8364;19.42 per sample and \#8364;5,189 per PiZZ detected. A sensitivity analysis demonstrated that performing Z genotype to all samples would have resulted in increased costs of \#8364;28 per sample and \#8364;7,479.5 per PiZZ case identified.In conclusion, a case detection programme of α1-antitrypsin deficiency in patients with chronic obstructive pulmonary disease using dried blood spots is feasible and at a reasonable cost per case detected. Diagnostic yield and costs depend largely on inclusion criteria and the protocol for processing of samples.
Normal values for respiratory resistance using forced oscillation in subjects >65 years old
Authors: Guo Y. F. , Herrmann F. , Michel J-P. , Janssens J-P. 
Published: October 2005

The aim of the present study was to determine reference values and predictive variables for respiratory impedance (Zrs) by the forced oscillation technique (FOT) in subjects aged >65 yrs.The investigation involved a prospective study of nonsmoking subjects, with normal forced expiratory volumes. TheZrsparameters, which included average resistance between 4–16 Hz (R4–16), average resistance between 4–30 Hz (RM), resonant frequency (FN), capacitance (C) and inertance (I), were measured along with forced expiratory manoeuvres. Every subject had each parameter measured in the same sequence using FOT and spirometry.A total of 223 subjects aged 83±8 yrs were included in the study. The mean values for forced expiratory volume in one second (FEV1) % predicted were 110±23. The forced vital capacity (FVC) % pred was 114±21 and the FEV1/FVC % pred was 112±11. The mean values for theZrsparameters were:R4–16: 0.25±0.07 kPa·s−1·L−1;RM: 0.25±0.06 kPa·s−1·L−1; FN: 11.0±2.8 Hz; I: 1.17±0.26 Pa·L−1·s−2; and C: 20.5±9.0 mL·hPa−1. In multiple regression models adjusted for age, sex, height and weight, height was the most influential predictor forZrsparameters based on the magnitude of the regression coefficient.In conclusion, it was found that height was the best predictor for respiratory impedance parameters. Contribution of age and weight was negligible. However, the level of predictability for respiratory impedance parameters by regression equations was low.
Aerosol delivery of chemotherapy in an orthotopic model of lung cancer
Authors: Gagnadoux F. , Pape A. L. , Lemarié E. , Lerondel S. , Valo I. , Leblond V. , Racineux J-L. , Urban T. 
Published: October 2005

The aim of this study was to evaluate the effect on tumour growth of gemcitabine delivered by aerosol in an orthotopic model of lung carcinoma.Large cell carcinoma (NCI-H460) cells were implanted intrabronchially in 24 male BALB/c nude mice on day (d) 0. Aerosols were delivered once a week from d1 to d29 using an endotracheal sprayer. Altogether, 16 animals received gemcitabine at 8 (n = 8) and 12 mg·kg−1(n = 8), and eight received a vehicle aerosol. Animals were sacrificed on d36 for histological examination.All animals in the vehicle group developed a large infiltrating carcinoma. Comparatively, four of 13 (31%) animals treated with gemcitabine had no visible tumour and nine of 13 (69%) had a smaller carcinoma with a mean±semlargest tumour diameter of 2.05±0.7versus5±0.3 mm in the vehicle group. Gemcitabine was well tolerated at 8 mg·kg−1. At 12 mg·kg−1, three cases of fatal pulmonary oedema were observed, prompting a dose reduction to 8 mg·kg−1in the remaining animals. A dose effect was observed, with more marked tumour growth inhibition in the animals treated at 12 mg·kg−1on d1 and d8.In conclusion, in this study, an animal model of aerosolised chemotherapy in lung cancer was developed and demonstrated inhibition of orthotopic tumour growth by aerosol delivery of gemcitabine.