bluuebunny/crossref_metadata_2025 huggingface dataset:
Acoustic radiation force on a rigid sphere in a resonance chamber
Authors: Leung E. , Jacobi N. , Wang T.
Published: October 2005

The acoustic radiation force on a rigid sphere has been measured in a resonance chamber for a range of pressures, positions, sizes, and for various gases. In the low to medium intensity region (<150 dB) the measured force is consistent with King’s theory [Proc. R. Soc. London, Ser. A 147, 212 (1934)] when analyzed in terms of the fundamental pressure. However, in the high intensity region (≳150 dB), the measured force starts to deviate systematically from King’s calculations.
Transient response of a submerged fluid-coupled double-walled shell structure to a pressure pulse
Authors: Neilson H. C. , Everstine G. C. , Wang Y. F.
Published: October 2005

A solution is presented for the interactive transient response of a submerged double-walled elastic sphere, flooded between the walls, to a plane step pressure pulse, using the general purpose finite element structural analysis computer program nastran with the doubly asymptotic approximation (DAA) for external surface interaction loading and explicitly modeled fluid finite elements for between-wall coupling. The methods used are described and problems encountered in implementation are discussed, along with approaches used in overcoming them. Results are compared with an available exact solution for the same configuration, and with exact and approximate solutions for the inner shell as a stand-alone submerged structure. The comparisons indicate generally satisfactory results, verifying the applicability of these methods for a submerged, double-walled structure. In addition, the double-single shell comparisons suggest a hitherto untried means of improving the later-time accuracy of a finite element/DAA computation for a single-walled submerged structure by including in the structural model a few layers of fluid finite elements adjacent to the outer surface, and applying the DAA loading at the outer surface of this fluid envelope.
Comments on ’’Diffraction of sound by an impedance paraboloid,’’ [J. Acoust. Soc. Am. 68, 1193–1198 (1980)]
Authors: Filippi Paul J. T. , Habault D.
Published: October 2005

The aim of this letter is to point out an error which appears in the use of the variables separation technique to determine the sound field [J. Acoust. Soc. Am. 68, 1193–1198 (1980), Sec. I]. The rigorous method is recalled on a simple example. A technique, leading to an exact solution,is proposed.
Radiation pattern of partially electroded piezoelectric transducers
Authors: Noorbehesht Behzad
Published: October 2005

The radiation pattern of piezoelectric plates, excited by strip electrodes or other similar electrodes, has been observed to consist essentially of a single beam. Here we give an alternative explanation of this phenomenon to that given previously by other authors.
Reply to ’’Radiation pattern of partially electroded piezoelectric transducers’’
Authors: Breazeale M. A. , Martin Franklin D. , Blackburn Bruce
Published: October 2005

The radiation pattern of transducers excited by a strip electrode and a ground plane closely approximates a Gaussian function, and hence is a single beam if the ratio of the electrode width to the transducer thickness is between 2 and 4. We calculate the electric fringing at the surface of the transducer and show the extent to which electric fringing accounts for the radiation pattern.
Piezoelectricity, its history and applications
Authors: Mason Warren P.
Published: October 2005

This is the 100th anniversary of the discovery of the piezoelectric effect by the brothers Curie. While this was a scientific curiosity for the next third of a century, with the work of Langevin it produced one of the principal electromechanical transducer effects. Quartz, first used as a transducer, also received wide use in controlling oscillators and in selective wave filters. Quartz was soon replaced by Rochelle salt for transducers. This is a rather unstable crystal, which, however, was the first ferroelectric having an intrinsic polarization between its two Curie temperatures. A theory of this effect was given by the writer. Most crystal transducers have been replaced by ferroelectric ceramics. A material somewhat similar to a ferroelectric is an electret. These have become very useful in transmitters and receivers. Finally, thin films of piezoelectric crystals are useful for producing high frequencies in such devices as the acoustic microscope.
Electroelastic interactions and the piezoelectric equations
Authors: Tiersten H. F.
Published: October 2005

The relation between the equations of linear piezoelectricity and the more general nonlinear electroelastic equations is discussed. The influence of nonlinear deformation theory and rotational invariance is noted. The linear equations for small dynamic fields superposed on a static bias are presented. An equation for the perturbation of the eigenvalue of the piezoelectric solution due to a bias is exhibited. Some applications of the perturbation equation are given.
Piezoelectric ceramics: Characteristics and applications
Authors: Berlincourt Don
Published: October 2005

Piezoelectric ceramics have been used for a little over 30 years. The first piezoelectric ceramic was barium titanate and it is still used. The lead titanate zirconate ceramics were introduced about 1955 and quickly became the most widely used piezoelectric material. Compositions were developed for many specific applications, as the strength of ferroelectricity in lead titanate zirconate allowed major chemical modification. The development and characteristics of these materials are described and applications are reviewed. Major emphasis is placed on consumer applications, as it is these that account for the major business in piezoelectric ceramic materials.
Piezoelectricity in polyvinylidenefluoride
Authors: Sessler G. M.
Published: October 2005

A review of the physical properties of polyvinylidenefluoride (PVDF) with particular emphasis on its piezoelectric activity is given and the applications of this material are discussed. PVDF is a semicrystalline polymer whose crystalline domains appear in four different forms. These forms may be interconverted by the application of heat, electrical fields, and pressure. Thermal poling or corona poling will orient the molecular dipoles in the crystalline parts and thus yield a permanent polarization. This polarization causes, by means of differences in the dielectric and elastic properties of the amorphous and crystalline parts, the piezoelectricity of PVDF. The piezoelectric constant d31 reaches values of about 35 pC/N at room temperature. At decreasing temperatures a drop of d31 and d33 is observed. Compared to other piezoelectric materials, PVDF has such unique properties as flexibility, ruggedness, availability as thin films, and low acoustic impedance, but a somewhat smaller electromechanical coupling factor. Applications of PVDF are in transducers for audiofrequency, ultrasonic, underwater, and electromechanical use and in pyroelectric and optical devices.
Piezoelectricity in thin film materials
Authors: Foster Norman F.
Published: October 2005

The need for efficient ultrasonic transducers in the 100 MHz to several GHz frequency range has stimulated the development of a number of transducer structures using piezoelectric thin films. Starting in the early 1960’s with primarily longitudinal bulk mode transduction in CdS films, the piezoelectric thin film transducer technology has progressed over the years to the controlled generation and detection of both longitudinal and shear waves in films of CdS, ZnO, and other materials. While most of the early work was directed towards bulk waves, the more recent strong interest in SAW devices has encouraged the use of piezoelectric thin films, primarily ZnO, in this arena also. A combination of experimental work and theoretical studies has generated a rather comprehensive understanding of the structure and behavior of piezoelectric thin films for both bulk and surface wave applications.
Noise-induced shifts in the pitch of pure and complex tones
Authors: Houtsma Adrianus J. M.
Published: October 2005

The influence of masking noise on the pitch of dichotic two-tone complexes and on the pure-tone pitches of their spectral components is investigated by matching both to the pitch of a binaural periodic pulse comparison signal. It is found that noise-induced shifts in the pitch of pure tones are considerably larger than induced shifts in complex tone or ’’residue’’ pitch. A pitch matching experiment with pure tones and contralateral noise reveals a general, central effect of noise on pitch. If empirical pitch matching data are corrected for this central effect, complex-tone pitch is found to be independent of the influence of masking noise, whereas pure-tone pitch remains subject to significant induced shifts. This finding is inconsistent with some of the modern pitch theories. It is consistent with the notion that pure-tone pitch is mediated by spatial, and complex-tone pitch by temporal encoding in peripheral auditory units.
Paper noise in an impact line printer
Authors: Busch–Vishniac I. J. , Lyon R. H.
Published: October 2005

In many paper handling machines, the sound radiated from impacts on paper is a major noise source. It is shown that in typical impact line printers both nonresonant and resonant paper vibration are significant mechanisms of sound generation. Both can probably be controlled by increasing the backing bar stiffness of the printer while keeping the printing force constant. The paper–hammer impact on the backing bar dominates paper impact noise below 1250 Hz. Above 2500 Hz the hammer impact on the paper is the dominant source. From 1250–2500 Hz the two impacts contribute equally to the sound generation. Finally, consideration of the design of a ’’quiet’’ paper leads to the suggestion of a paper with high density and low bending rigidity. This might be accomplished through microcreping of the paper.
Direct comparison of community response to road traffic noise and to aircraft noise
Authors: Hall Fred L. , Birnie Susan E. , Taylor S. Martin , Palmer John E.
Published: October 2005

Previous efforts to synthesize information on community responses to various noise sources have been forced to rely on a variety of surveys conducted in different countries over a number of years. Comparability of both the noise measurements and the questions asked has been limited, and has of necessity relied on professional judgment. Data collected recently around Toronto International Airport provide a direct comparison of response to two sources, based on 673 interviews of persons exposed to a variety of levels of both aircraft and road traffic noise. The results of that analysis do not support the assumption that response to these two noise sources is the same. For the same value of Ldn, a greater percentage of the sample is highly annoyed by aircraft noise than by road traffic noise. Possible reasons for this contradiction of the results of a previous synthesis of noise surveys are discussed.
Effective density of air in open-cell polyurethane foam for ultrasonic frequencies
Authors: Matsuzawa Kiichiro , Hasegawa Takahi , Ochi Masayuki
Published: October 2005

This article deals with a theoretical analysis of the experimental results reported in a previous paper [K. Matsuzawa and M. Ochi, J. Acoust. Soc. Am. 68, 212–217 (1980)]. An approximate formula for the effective density of air in the foam is proposed as ρ = ρ0 [1+C(1+L)+M(1−j) δ1/(2R)], where ρ0 is the density of free air, C is the material concentration, j = (−1)1/2, δ1 is the viscous boundary layer thickness, R is the volume-to-area ratio of pores, and L and M are constants. Then, on the basis of the experimental data, it is found that L = 1.2 and M = 2.6 in common with the foam materials of various pore densities.
Ultrasonic attenuation in GaAs
Authors: Shukla S. S. , Yun S. S.
Published: October 2005

The temperature and frequency dependence of the attenuation coefficient, α, of both longitudinal and shear ultrasonic waves, propagating along [100], [110], and [111] directions of GaAs, has been measured by means of the pulse-echo technique. The temperature range investigated was 110° to 240 °K for shear waves and 110° to 300 °K for longitudinal waves. The frequencies used were in the range of 45 to 170 MHz. In the temperature range investigated, it was found that α∝ωn, with n = 2±0.2 for longitudinal waves and n = 1.7±0.1 for shear waves. By fitting our attenuation data to the theory given by Nava et al. [Phys. Rev. B 14, 800–807 (1976)], the temperature dependence of the effective ultrasonic Gruneissen parameter normalized to 300 °K for longitudinal waves and 240 °K for shear waves has been determined.
Inverse problem for a stratified ocean and bottom
Authors: Stickler D. C. , Deift P. A.
Published: October 2005

In this paper it is shown how to use the methods of one-dimensional inverse scattering theory, in particular the new approach of Deift and Trubowitz [Comm. Pure Appl. Math. XXXII, 121–251 (1979)], to recover the sound speed for the case of a stratified ocean with a pressure release surface driven by a harmonic point source at a finite depth from a measurement of the normal derivative at the pressure release surface. The method is not a perturbation technique. For comparison, this same problem is examined when the sound speed is slightly perturbed from unity using a technique of Cohen and Bleistein [SIAM J. Appl. Math. 32, 784–799 (1977) and Geophysics 44, 1077–1087 (1979)].
Real-Time PCR Detection of
Vibrio vulnificus
in Oysters: Comparison of Oligonucleotide Primers and Probes Targeting
vvhA
Authors: Panicker Gitika , Bej Asim K.
Published: October 2005

We compared three sets of oligonucleotide primers and two probes designed for
Vibrio vulnificus hemolysin A
gene (
vvhA
) for TaqMan-based real-time PCR method enabling specific detection of
Vibrio vulnificus
in oysters. Two of three sets of primers with a probe were specific for the detection of all 81
V. vulnificus
isolates by TaqMan PCR. The 25 nonvibrio and 12 other vibrio isolates tested were negative. However, the third set of primers, F-vvh1059 and R-vvh1159, with the P-vvh1109 probe, although positive for all
V. vulnificus
isolates, also exhibited positive cycle threshold (

C
T

) values for other
Vibrio
spp. Optimization of the TaqMan PCR assay using F-vvh785/R-vvh990 or F-vvh731/R-vvh1113 primers and the P-vvh874 probe detected 1 pg of purified DNA and 10
3
V. vulnificus
CFU/ml in pure cultures. The enriched oyster tissue homogenate did not exhibit detectable inhibition to the TaqMan PCR amplification of
vvhA
. Detection of 3 × 10
3
CFU
V. vulnificus
, resulting from a 5-h enrichment of an initial inoculum of 1 CFU/g of oyster tissue homogenate, was achieved with F-vvh785/R-vvh990 or F-vvh731/R-vvh1113 primers and P-vvh875 probe. The application of the TaqMan PCR using these primers and probe, exhibited detection of
V. vulnificus
on 5-h-enriched natural oysters harvested from the Gulf of Mexico. Selection of appropriate primers and a probe on
vvhA
for TaqMan-PCR-based detection of
V. vulnificus
in post-harvest-treated oysters would help avoid false-positive results, thus ensuring a steady supply of safe oysters to consumers and reducing
V. vulnificus
-related illnesses and deaths.
Unexpectedly High Bacterial Diversity in Arctic Tundra Relative to Boreal Forest Soils, Revealed by Serial Analysis of Ribosomal Sequence Tags
Authors: Neufeld Josh D. , Mohn William W.
Published: October 2005

Arctic tundra and boreal forest soils have globally relevant functions that affect atmospheric chemistry and climate, yet the bacterial composition and diversity of these soils have received little study. Serial analysis of ribosomal sequence tags (SARST) and denaturing gradient gel electrophoresis (DGGE) were used to compare composite soil samples taken from boreal and arctic biomes. This study comprises an extensive comparison of geographically distant soil bacterial communities, involving the analysis of 12,850 ribosomal sequence tags from six composite soil samples. Bacterial diversity estimates were greater for undisturbed arctic tundra soil samples than for boreal forest soil samples, with the highest diversity associated with a sample from an extreme northern location (82
o
N). The lowest diversity estimate was obtained from an arctic soil sample that was disturbed by compaction and sampled from a greater depth. Since samples from the two biomes did not form distinct clusters on the basis of SARST data and DGGE fingerprints, factors other than latitude likely influenced the phylogenetic compositions of these communities. The high number of ribosomal sequences analyzed enabled the identification of possible cosmopolitan and endemic bacterial distributions in particular soils.
Increasing Prevalence of
Campylobacter jejuni
in Feedlot Cattle through the Feeding Period
Authors: Besser Thomas E. , LeJeune Jeffrey T. , Rice Daniel H. , Berg Janice , Stilborn R. P. , Kaya Katherine , Bae Wonki , Hancock Dale D.
Published: October 2005

The prevalence of
Campylobacter jejuni
in commercial feedlot cattle was monitored throughout the feeding period by repeated bacteriologic culture of feces. Fecal pats (
n
= 10) in 20 feedlot pens were sampled at 2-weeks interval beginning at entry into the feedlot and continuing until slaughter. The least-squares mean
C. jejuni
prevalence increased from 1.6% at the first sampling to 61.3% at the final sampling just prior to slaughter. Diverse
C. jejuni
pulsed-field gel electrophoresis macrorestriction profiles (MRP) were identified among the cattle isolates, but five prevalent MRP and minor variants accounted for >80% of all typed isolates. Chlorination of the water supplied to the water troughs of half of the pens did not affect
C. jejuni
prevalence in the cattle. Overall, the least-squares mean
C. jejuni
prevalences were 45.6 and 43.6% in chlorinated and nonchlorinated feedlot pens, respectively. The results of this study demonstrate apparent transmission of
C. jejuni
among feedlot cattle during the feeding period, unaffected by water chlorination, resulting in a high prevalence of
C. jejuni
excretion by cattle approaching slaughter.
Quantification of
Campylobacter
spp. in Chicken Rinse Samples by Using Flotation prior to Real-Time PCR
Authors: Wolffs Petra , Norling Börje , Hoorfar Jeffrey , Griffiths Mansel , Rådström Peter
Published: October 2005

Real-time PCR is fast, sensitive, specific, and can deliver quantitative data; however, two disadvantages are that this technology is sensitive to inhibition by food and that it does not distinguish between DNA originating from viable, viable nonculturable (VNC), and dead cells. For this reason, real-time PCR has been combined with a novel discontinuous buoyant density gradient method, called flotation, in order to allow detection of only viable and VNC cells of thermotolerant campylobacters in chicken rinse samples. Studying the buoyant densities of different
Campylobacter
spp. showed that densities changed at different time points during growth; however, all varied between 1.065 and 1.109 g/ml. These data were then used to develop a flotation assay. Results showed that after flotation and real-time PCR, cell concentrations as low as 8.6 × 10
2
CFU/ml could be detected without culture enrichment and amounts as low as 2.6 × 10
3
CFU/ml could be quantified. Furthermore, subjecting viable cells and dead cells to flotation showed that viable cells were recovered after flotation treatment but that dead cells and/or their DNA was not detected. Also, when samples containing VNC cells mixed with dead cells were treated with flotation after storage at 4 or 20°C for 21 days, a similar percentage resembling the VNC cell fraction was detected using real-time PCR and 5-cyano-2,3-ditolyl tetrazolium chloride-4′,6′-diamidino-2-phenylindole staining (20% ± 9% and 23% ± 4%, respectively, at 4°C; 11% ± 4% and 10% ± 2%, respectively, at 20°C). This indicated that viable and VNC
Campylobacter
cells could be positively selected and quantified using the flotation method.
Cloning, Sequencing, and Expression of a
Eubacterium cellulosolvens
5 Gene Encoding an Endoglucanase (Cel5A) with Novel Carbohydrate-Binding Modules, and Properties of Cel5A
Authors: Yoda Kazutoyo , Toyoda Atsushi , Mukoyama Yoshihiro , Nakamura Yutaka , Minato Hajime
Published: October 2005

A novel
Eubacterium cellulosolvens
5 gene encoding an endoglucanase (Cel5A) was cloned and expressed in
Escherichia coli
, and its enzymatic properties were characterized. The
cel5A
gene consists of a 3,444-bp open reading frame and encodes a 1,148-amino-acid protein with a molecular mass of 127,047 Da. Cel5A is a modular enzyme consisting of an N-terminal signal peptide, two glycosyl hydrolase family 5 catalytic modules, two novel carbohydrate-binding modules (CBMs), two linker sequences, and a C-terminal sequence with an unknown function. The amino acid sequences of the two catalytic modules and the two CBMs are 94% and 73% identical to each other, respectively. Two regions that consisted of one CBM and one catalytic module were tandemly connected via a linker sequence. The CBMs did not exhibit significant sequence similarity with any other CBMs. Analyses of the hydrolytic activity of the recombinant Cel5A (rCel5A) comprising the CBMs and the catalytic modules showed that the enzyme is an endoglucanase with activities with carboxymethyl cellulose, lichenan, acid-swollen cellulose, and oat spelt xylan. To investigate the functions of the CBMs and the catalytic modules, truncated derivatives of rCel5A were constructed and characterized. There were no differences in the hydrolytic activities with various polysaccharides or in the hydrolytic products obtained from cellooligosaccharides between the two catalytic modules. Both CBMs had the same substrate affinity with intact rCel5A. Removal of the CBMs from rCel5A reduced the catalytic activities with various polysaccharides remarkably. These observations show that CBMs play an important role in the catalytic function of the enzyme.
Microarray Analysis of a Two-Component Regulatory System Involved in Acid Resistance and Proteolytic Activity inLactobacillus acidophilus
Authors: Azcarate-Peril M. Andrea , McAuliffe Olivia , Altermann Eric , Lick Sonja , Russell W. Michael , Klaenhammer Todd R.
Published: October 2005

Two-component regulatory systems are one primary mechanism for environmental sensing and signal transduction. Annotation of the complete genome sequence of the probiotic bacteriumLactobacillus acidophilusNCFM revealed nine two-component regulatory systems. In this study, the histidine protein kinase of a two-component regulatory system (LBA1524HPK-LBA1525RR), similar to the acid-related systemlisRK fromListeria monocytogenes(P. D. Cotter et al., J. Bacteriol. 181:6840-6843, 1999), was insertionally inactivated. A whole-genome microarray containing 97.4% of the annotated genes ofL. acidophiluswas used to compare genome-wide patterns of transcription at various pHs between the control and the histidine protein kinase mutant. The expression pattern of approximately 80 genes was affected by the LBA1524HPK mutation. Putative LBA1525RR target loci included two oligopeptide-transport systems present in theL. acidophilusgenome, other components of the proteolytic system, and a LuxS homolog, suspected of participating in synthesis of the AI-2 signaling compound. The mutant exhibited lower tolerance to acid and ethanol in logarithmic-phase cells and poor acidification rates in milk. Supplementation of milk with Casamino Acids essentially restored the acid-producing ability of the mutant, providing additional evidence for a role of this two component system in regulating proteolytic activity inL. acidophilus.
Legionella
Contamination in Hot Water of Italian Hotels
Authors: Borella Paola , Montagna Maria Teresa , Stampi Serena , Stancanelli Giovanna , Romano-Spica Vincenzo , Triassi Maria , Marchesi Isabella , Bargellini Annalisa , Tatò Daniela , Napoli Christian , Zanetti Franca , Leoni Erica , Moro Matteo , Scaltriti Stefania , Ribera D'Alcalà Gabriella , Santarpia Rosalba , Boccia Stefania
Published: October 2005

A cross-sectional multicenter survey of Italian hotels was conducted to investigate
Legionella
spp. contamination of hot water. Chemical parameters (hardness, free chlorine concentration, and trace element concentrations), water systems, and building characteristics were evaluated to study risk factors for colonization. The hot water systems of Italian hotels were strongly colonized by
Legionella
; 75% of the buildings examined and 60% of the water samples were contaminated, mainly at levels of ≥10
3
CFU liter
−1
, and
Legionella pneumophila
was the most frequently isolated species (87%).
L. pneumophila
serogroup 1 was isolated from 45.8% of the contaminated sites and from 32.5% of the hotels examined. When a multivariate logistic model was used, only hotel age was associated with contamination, but the risk factors differed depending on the contaminating species and serogroup. Soft water with higher chlorine levels and higher temperatures were associated with
L. pneumophila
serogroup 1 colonization, whereas the opposite was observed for serogroups 2 to 14. In conclusion, Italian hotels, particularly those located in old buildings, represent a major source of risk for Legionnaires' disease due to the high frequency of
Legionella
contamination, high germ concentration, and major
L. pneumophila
serogroup 1 colonization. The possible role of chlorine in favoring the survival of
Legionella
species is discussed.
Use of 16S rRNA Gene Terminal Restriction Fragment Analysis To Assess the Impact of Solids Retention Time on the Bacterial Diversity of Activated Sludge
Authors: Saikaly Pascal E. , Stroot Peter G. , Oerther Daniel B.
Published: October 2005

Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes was used to investigate the reproducibility and stability in the bacterial community structure of laboratory-scale sequencing batch bioreactors (SBR) and to assess the impact of solids retention time (SRT) on bacterial diversity. Two experiments were performed. In each experiment two sets of replicate SBRs were operated for a periods of three times the SRT. One set was operated at an SRT of 2 days and another set was operated at an SRT of 8 days. Samples for T-RFLP analysis were collected from the two sets of replicate reactors. HhaI, MspI, and RsaI T-RFLP profiles were analyzed using cluster analysis and diversity statistics. Cluster analysis with Ward's method using Jaccard distance and Hellinger distance showed that the bacterial community structure in both sets of reactors from both experimental runs was dynamic and that replicate reactors were clustered together and evolved similarly from startup. Richness (
S
), evenness (
E
), the Shannon-Weaver index (
H
), and the reciprocal of Simpson's index (1/
D
) were calculated, and the values were compared between the two sets of reactors. Evenness values were higher for reactors operated at an SRT of 2 days. Statistically significant differences in diversity (
H
and
D
) between the two sets of reactors were tested using a randomization procedure, and the results showed that reactors from both experimental runs that were operated at an SRT of 2 days had higher diversity (
H
and
D
) at the 5% level. T-RFLP analysis with diversity indices proved to be a powerful tool to analyze changes in the bacterial community diversity in response to changes in the operational parameters of activated-sludge systems.
Photoheterotrophic Metabolism of Acrylamide by a Newly Isolated Strain of
Rhodopseudomonas palustris
Authors: Wampler David A. , Ensign Scott A.
Published: October 2005

Acrylamide, a neurotoxin and suspected carcinogen, is produced by industrial processes and during the heating of foods. In this study, the microbial diversity of acrylamide metabolism has been expanded through the isolation and characterization of a new strain of
Rhodopseudomonas palustris
capable of growth with acrylamide under photoheterotrophic conditions. The newly isolated strain grew rapidly with acrylamide under photoheterotrophic conditions (doubling time of 10 to 12 h) but poorly under anaerobic dark or aerobic conditions. Acrylamide was rapidly deamidated to acrylate by strain Ac1, and the subsequent degradation of acrylate was the rate-limiting reaction in cell growth. Acrylamide metabolism by succinate-grown cultures occurred only after a lag period, and the induction of acrylamide-degrading activity was prevented by the presence of protein or RNA synthesis inhibitors.
13
C nuclear magnetic resonance studies of [1,2,3-
13
C]acrylamide metabolism by actively growing cultures confirmed the rapid conversion of acrylamide to acrylate but failed to detect any subsequent intermediates of acrylate degradation. Using concentrated cell suspensions containing natural abundance succinate as an additional carbon source, [
13
C]acrylate consumption occurred with the production and then degradation of [
13
C]propionate. Although
R. palustris
strain Ac1 grew well and with comparable doubling times for each of acrylamide, acrylate, and propionate,
R. palustris
strain CGA009 was incapable of significant acrylamide- or acrylate-dependent growth over the same time course, but grew comparably with propionate. These results provide the first demonstration of anaerobic photoheterotrophic bacterial acrylamide catabolism and provide evidence for a new pathway for acrylate catabolism involving propionate as an intermediate.
Effects of Orally Administered Tetracycline on the Intestinal Community Structure of Chickens and on
tet
Determinant Carriage by Commensal Bacteria and
Campylobacter jejuni
Authors: Fairchild A. S. , Smith J. L. , Idris U. , Lu J. , Sanchez S. , Purvis L. B. , Hofacre C. , Lee M. D.
Published: October 2005

There is a growing concern that antibiotic usage in animal production has selected for resistant food-borne bacteria. Since tetracyclines are common therapeutic antibiotics used in poultry production, we sought to evaluate the effects of oral administration on the resistance of poultry commensal bacteria and the intestinal bacterial community structure. The diversity indices calculated from terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA amplicons did not indicate significant changes in the cecal bacterial community in response to oxytetracycline. To evaluate its effects on cultivable commensals,
Enterococcus
spp.,
Escherichia coli
, and
Campylobacter
spp. were isolated from the cecal droppings of broiler chickens.
Enterococcus
spp. and
E. coli
expressed tetracycline MICs of >8 μg/ml and harbored a variety of
tet
resistance determinants regardless of the tetracycline exposure history of the birds. The enterococcal isolates possessed
tetM
(61%),
tetL
(25.4%), and
tetK
(1.3%), as well as
tetO
(52.5%), the determinant known to confer a tetracycline resistance phenotype in
Campylobacter jejuni. E. coli
isolates harbored
tetA
(32.2%) or
tetB
(30.5%). Tetracycline MICs remained at <2 μg/ml for
Campylobacter
isolates before and after tetracycline treatment of the chickens, even though isolates expressing MICs of >16 μg/ml were commonly cultured from flocks that did not receive oxytetracycline. The results imply that complex ecological and genetic factors contribute to the prevalence of antibiotic resistance arising from resistance gene transfer in the production environment.
Factors Influencing Germination of
Bacillus subtilis
Spores via Activation of Nutrient Receptors by High Pressure
Authors: Black Elaine P. , Koziol-Dube Kasia , Guan Dongsheng , Wei Jie , Setlow Barbara , Cortezzo Donnamaria E. , Hoover Dallas G. , Setlow Peter
Published: October 2005

Different nutrient receptors varied in triggering germination of
Bacillus subtilis
spores with a pressure of 150 MPa, the GerA receptor being more responsive than the GerB receptor and even more responsive than the GerK receptor. This hierarchy in receptor responsiveness to pressure was the same as receptor responsiveness to a mixture of nutrients. The levels of nutrient receptors influenced rates of pressure germination, since the GerA receptor is more abundant than the GerB receptor and elevated levels of individual receptors increased spore germination by 150 MPa of pressure. However, GerB receptor variants with relaxed specificity for nutrient germinants responded as well as the GerA receptor to this pressure. Spores lacking dipicolinic acid did not germinate with this pressure, and pressure activation of the GerA receptor required covalent addition of diacylglycerol. However, pressure activation of the GerB and GerK receptors displayed only a partial (GerB) or no (GerK) diacylglycerylation requirement. These effects of receptor diacylglycerylation on pressure germination are similar to those on nutrient germination. Wild-type spores prepared at higher temperatures germinated more rapidly with a pressure of 150 MPa than spores prepared at lower temperatures; this was also true for spores with only one receptor, but receptor levels did not increase in spores made at higher temperatures. Changes in inner membrane unsaturated fatty acid levels, lethal treatment with oxidizing agents, or exposure to chemicals that inhibit nutrient germination had no major effect on spore germination by 150 MPa of pressure, except for strong inhibition by HgCl
2
.
Improvement of NaNO
2
-Oxidizing Activity in
Nitrobacter vulgaris
by Coentrapment in Polyacrylamide Containing Polydimethylsiloxane Copolymer and DEAE-Sephadex
Authors: Zhang Songping , Norrlöw Olof , Dey Estera Szwajcer
Published: October 2005

Removal of nitrite and nitrate from drinking water has attracted great attention in recent years because of the human health risk induced by the exposure to contaminated groundwater and surface water. We have therefore tested a model nitrite oxidation system by coentrapping the NaNO
2
oxidizer
Nitrobacter vulgaris
with polydimethylsiloxane (PDMS) copolymer and DEAE-Sephadex in a polyacrylamide gel. The copolymer and the anion exchanger facilitate the diffusion of oxygen and NaNO
2
, respectively, into the gel matrix. To test the nitrite-oxidizing activity, the entrapped cells were coupled to a thermal sensor. Coentrapment of 5% (wt/vol) DEAE-Sephadex with
Nitrobacter vulgaris
increased the nitrite-oxidizing activity by a factor of 3.7 compared to entrapped cells alone, and by the addition of 0.86% (wt/vol) artificial oxygen carrier PDMS copolymer increased the activity further to 4.3 times higher. Operational and storage stability of the coentrapped
N
.
vulgaris
also improved. This suggests that this enhanced immobilized cell system can also be used for nitrite oxidation to nitrate in drinking water as an on-line thermally monitored bioreactor.
Specific Detection, Isolation, and Characterization of Selected, Previously Uncultured Members of the Freshwater Bacterioplankton Community
Authors: Gich Frederic , Schubert Karin , Bruns Alke , Hoffelner Herbert , Overmann Jörg
Published: October 2005

High-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. A total of 570 bacterial cultures were obtained by employing the most probable number and MicroDrop techniques. The majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the α
-Proteobacteria
, β
-Proteobacteria
,
Actinobacteria
,
Firmicutes
, or
Flavobacteria-Cytophaga
lineage. Correspondingly, the natural bacterioplankton community was analyzed by high-resolution phylogenetic fingerprinting of these five bacterial lineages. 16S rRNA gene fragments were generated for each lineage and subsequently separated by denaturing gradient gel electrophoresis. By the combination of five group-specific PCR protocols, the total number of 16S rRNA gene fingerprints generated from the natural communities was increased sixfold compared to conventional (eubacterial) fingerprinting. Four of the environmental α-
Proteobacteria
16S rRNA gene sequences obtained from the natural community were found to be identical to those of bacterial isolates. One of these phylotypes was detected in 14 different cultures and hence represented the most frequently cultured bacterium. Three of these 14 strains were characterized in detail. Their complete 16S rRNA gene sequences showed only 93% similarity to that of
Sandaracinobacter sibiricus
, the closest relative described so far. The novel phylotype of bacterium is a strict aerobe capable of using numerous organic carbon substrates and contains bacteriochlorophyll
a
bound to two different photosynthetic light-harvesting complexes. Dot blot hybridization revealed that the strains occur in lakes of different trophic status and constitute up to 2% of the microbial community.
Diversity and Functional Analysis of Bacterial Communities Associated with Natural Hydrocarbon Seeps in Acidic Soils at Rainbow Springs, Yellowstone National Park
Authors: Hamamura Natsuko , Olson Sarah H. , Ward David M. , Inskeep William P.
Published: October 2005

In this paper we describe the bacterial communities associated with natural hydrocarbon seeps in nonthermal soils at Rainbow Springs, Yellowstone National Park. Soil chemical analysis revealed high sulfate concentrations and low pH values (pH 2.8 to 3.8), which are characteristic of acid-sulfate geothermal activity. The hydrocarbon composition of the seep soils consisted almost entirely of saturated, acyclic alkanes (e.g.,
n-
alkanes with chain lengths of C
15
to C
30
, as well as branched alkanes, predominately pristane and phytane). Bacterial populations present in the seep soils were phylogenetically characterized by 16S rRNA gene clone library analysis. The majority of the sequences recovered (>75%) were related to sequences of heterotrophic acidophilic bacteria, including
Acidisphaera
spp. and
Acidiphilium
spp. of the α-
Proteobacteria
. Clones related to the iron- and sulfur-oxidizing chemolithotroph
Acidithiobacillus
spp. were also recovered from one of the seep soils. Hydrocarbon-amended soil-sand mixtures were established to examine [
14
C]hexadecane mineralization and corresponding changes in the bacterial populations using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Approximately 50% of the [
14
C]hexadecane added was recovered as
14
CO
2
during an 80-day incubation, and this was accompanied by detection of heterotrophic acidophile-related sequences as dominant DGGE bands. An alkane-degrading isolate was cultivated, whose 16S rRNA gene sequence was identical to the sequence of a dominant DGGE band in the soil-sand mixture, as well as the clone sequence recovered most frequently from the original soil. This and the presence of an
alkB
gene homolog in this isolate confirmed the alkane degradation capability of one population indigenous to acidic hydrocarbon seep soils.
Development of an F57 Sequence-Based Real-Time PCR Assay for Detection ofMycobacterium aviumsubsp.paratuberculosisin Milk
Authors: Tasara T. , Stephan R.
Published: October 2005

A light cycler-based real-time PCR (LC-PCR) assay that amplifies the F57 sequence ofMycobacterium aviumsubsp.paratuberculosiswas developed. This assay also includes an internal amplification control template to monitor the amplification conditions in each reaction. The targeted F57 sequence element is unique forM.aviumsubsp.paratuberculosisand is not known to exist in any other bacterial species. The assay specificity was demonstrated by evaluation of 10 knownM. aviumsubsp.paratuberculosisisolates and 33 other bacterial strains. The LC-PCR assay has a broad linear range (2 × 101to 2 ×106copies) for quantitative estimation of the number ofM. aviumsubsp.paratuberculosisF57 target copies in positive samples. To maximize the assay's detection sensitivity, an efficient strategy for isolation ofM. aviumsubsp.paratuberculosisDNA from spiked milk samples was also developed. The integrated procedure combining optimalM. aviumsubsp.paratuberculosisDNA isolation and real-time PCR detection had a reproducible detection limit of about 10M. aviumsubsp.paratuberculosiscells per ml when a starting sample volume of 10 ml ofM. aviumsubsp.paratuberculosis-spiked milk was analyzed. The entire process can be completed within a single working day and is suitable for routine monitoring of milk samples forM. aviumsubsp.paratuberculosiscontamination. The applicability of this protocol for naturally contaminated milk was also demonstrated using milk samples from symptomaticM. aviumsubsp.paratuberculosis-infected cows, as well as pooled samples from a dairy herd with a confirmed history of paratuberculosis.
Geobacteraceae
Community Composition Is Related to Hydrochemistry and Biodegradation in an Iron-Reducing Aquifer Polluted by a Neighboring Landfill
Authors: Lin Bin , Braster Martin , van Breukelen Boris M. , van Verseveld Henk W. , Westerhoff Hans V. , Röling Wilfred F. M.
Published: October 2005

Relationships between community composition of the iron-reducing
Geobacteraceae
, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent
Geobacteraceae
16S rRNA gene-targeting techniques. Numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles and sequencing revealed a high
Geobacteraceae
diversity and showed that community composition within the leachate plume differed considerably from that of the unpolluted aquifer. This suggests that pollution has selected for specific species out of a large pool of
Geobacteraceae
. DGGE profiles of polluted groundwater taken near the landfill (6- to 39-m distance) clustered together. DGGE profiles from less-polluted groundwater taken further downstream did not fall in the same cluster. Several individual DGGE bands were indicative of either the redox process or the level of pollution. This included a pollution-indicative band that dominated the DGGE profiles from groundwater samples taken close to the landfill (6 to 39 m distance). The clustering of these profiles and the dominance by a single DGGE band corresponded to the part of the aquifer where organic micropollutants and reactive dissolved organic matter were attenuated at relatively high rates.
Identifying Host Sources of Fecal Pollution: Diversity of
Escherichia coli
in Confined Dairy and Swine Production Systems
Authors: Lu Zexun , Lapen David , Scott Andrew , Dang Angela , Topp Edward
Published: October 2005

Repetitive extragenic palindromic PCR fingerprinting of
Escherichia coli
is one microbial source tracking approach for identifying the host source origin of fecal pollution in aquatic systems. The construction of robust known-source libraries is expensive and requires an informed sampling strategy. In many types of farming systems, waste is stored for several months before being released into the environment. In this study we analyzed, by means of repetitive extragenic palindromic PCR using the enterobacterial repetitive intergenic consensus primers and comparative analysis using the Bionumerics software, collections of
E. coli
obtained from a dairy farm and from a swine farm, both of which stored their waste as a slurry in holding tanks. In all fecal samples, obtained from either barns or holding tanks, the diversity of the
E. coli
populations was underrepresented by collections of 500 isolates. In both the dairy and the swine farms, the diversity of the
E. coli
community was greater in the manure holding tank than in the barn, when they were sampled on the same date. In both farms, a comparison of stored manure samples collected several months apart suggested that the community composition changed substantially in terms of the detected number, absolute identity, and relative abundance of genotypes. Comparison of
E. coli
populations obtained from 10 different locations in either holding tank suggested that spatial variability in the
E. coli
community should be accounted for when sampling. Overall, the diversity in
E. coli
populations in manure slurry storage facilities is significant and likely is problematic with respect to library construction for microbial source tracking applications.
pH-, Lactic Acid-, and Non-Lactic Acid-Dependent Activities of Probiotic Lactobacilli against
Salmonella enterica
Serovar Typhimurium
Authors: Fayol-Messaoudi Domitille , Berger Cédric N. , Coconnier-Polter Marie-Hélène , Liévin-Le Moal Vanessa , Servin Alain L.
Published: October 2005

The mechanism(s) underlying the antibacterial activity of probiotic
Lactobacillus
strains appears to be multifactorial and includes lowering of the pH and the production of lactic acid and of antibacterial compounds, including bacteriocins and nonbacteriocin, non-lactic acid molecules. Addition of Dulbecco's modified Eagle's minimum essential medium to the incubating medium delays the killing activity of lactic acid. We found that the probiotic strains
Lactobacillus johnsonii
La1,
Lactobacillus rhamnosus
GG,
Lactobacillus casei
Shirota YIT9029,
L. casei
DN-114 001, and
L. rhamnosus
GR1 induced a dramatic decrease in the viability of
Salmonella enterica
serovar Typhimurium SL1344 mainly attributable to non-lactic acid molecule(s) present in the cell-free culture supernatant (CFCS). These molecules were more active against serovar Typhimurium SL1344 in the exponential growth phase than in the stationary growth phase. We also showed that the production of the non-lactic acid substance(s) responsible for the killing activity was dependent on growth temperature and that both unstable and stable substances with killing activity were present in the CFCSs. We found that the complete inhibition of serovar Typhimurium SL1344 growth results from a pH-lowering effect.
Clustering of
Mycobacterium avium
subsp.
paratuberculosis
in Rabbits and the Environment: How Hot Is a Hot Spot?
Authors: Judge Johanna , Kyriazakis Ilias , Greig Alastair , Allcroft David J. , Hutchings Michael R.
Published: October 2005

Clustering of pathogens in the environment leads to hot spots of diseases at local, regional, national, and international levels. Scotland contains regional hot spots of Johne's disease (caused by
Mycobacterium avium
subsp.
paratuberculosis
) in rabbits, and there is increasing evidence of a link between paratuberculosis infections in rabbits and cattle. The spatial and temporal dynamics of paratuberculosis in rabbits within a hot spot region were studied with the overall aim of determining environmental patterns of infection and thus the risk of interspecies transmission to livestock. The specific aims were to determine if prevalence of paratuberculosis in rabbits varies temporally between seasons and whether the heterogeneous spatial environmental distribution of
M. avium
subsp.
paratuberculosis
on a large scale (i.e., regional hot spots) is replicated at finer resolutions within a hot spot. The overall prevalence of
M. avium
subsp.
paratuberculosis
in rabbits was 39.7%; the temporal distribution of infection in rabbits followed a cyclical pattern, with a peak in spring of 55.4% and a low in summer of 19.4%. Spatially,
M. avium
subsp.
paratuberculosis
-infected rabbits and, thus, the risk of interspecies transmission were highly clustered in the environment. However, this is mostly due to the clustered distribution of rabbits. The patterns of
M. avium
subsp.
paratuberculosis
infection in rabbits are discussed in relation to the host's socioecology and risk to livestock.