bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of high-frequency energy changes in sustained vowels produced by singers
Authors: Monson Brian B. , Lotto Andrew J. , Ternström Sten
Published: April 2011

The human voice spectrum above 5 kHz receives little attention. However, there are reasons to believe that this high-frequency energy (HFE) may play a role in perceived quality of voice in singing and speech. To fulfill this role, differences in HFE must first be detectable. To determine human ability to detect differences in HFE, the levels of the 8- and 16-kHz center-frequency octave bands were individually attenuated in sustained vowel sounds produced by singers and presented to listeners. Relatively small changes in HFE were in fact detectable, suggesting that this frequency range potentially contributes to the perception of especially the singing voice. Detection ability was greater in the 8-kHz octave than in the 16-kHz octave and varied with band energy level.
Learned vocalizations in budgerigars (Melopsittacus undulatus): The relationship between contact calls and warble song
Authors: Tu Hsiao-Wei , Osmanski Michael S. , Dooling Robert J.
Published: April 2011

The budgerigar (Melopsittacus undulatus) has an extraordinarily complex, learned, vocal repertoire consisting of both the long rambling warble song of males and a number of short calls produced by both sexes. In warble, the most common elements (>30%) bear a strong resemblance to the highly frequency-modulated, learned contact calls that the birds produce as single utterances. However, aside from this apparent similarity, little else is known about the relationship between contact calls and warble call elements. Here, both types of calls were recorded from four male budgerigars. Signal analysis and psychophysical testing procedures showed that the acoustic features of these two vocalizations were acoustically different and perceived as distinctive vocalizations by birds. This suggests that warble call elements are not simple insertions of contact calls but are most likely different acoustic elements, created de novo, and used solely in warble. Results show that, like contact calls, warble call elements contain information about signaler identity. The fact that contact calls and warble call elements are acoustically and perceptually distinct suggests that they probably represent two phonological systems in the budgerigar vocal repertoire, both of which arise by production learning.
A waveguide invariant adaptive matched filter for active sonar target depth classification
Authors: Goldhahn Ryan , Hickman Granger , Krolik Jeffrey
Published: April 2011

This paper addresses depth discrimination of a water column target from bottom clutter discretes in wideband active sonar. To facilitate classification, the waveguide invariant property is used to derive multiple snapshots by uniformly sub-sampling the short-time Fourier transform (STFT) coefficients of a single ping of wideband active sonar data. The sub-sampled target snapshots are used to define a waveguide invariant spectral density matrix (WI-SDM), which allows the application of adaptive matched-filtering based approaches for target depth classification. Depth classification is achieved using a waveguide invariant minimum variance filter (WI-MVF) which matches the observed WI-SDM to depth-dependent signal replica vectors generated from a normal mode model. Robustness to environmental mismatch is achieved by adding environmental perturbation constraints (EPC) derived from signal covariance matrices averaged over the uncertain channel parameters. Simulation and real data results from the SCARAB98 and CLUTTER09 experiments in the Mediterranean Sea are presented to illustrate the approach. Receiver operating characteristics (ROC) for robust waveguide invariant depth classification approaches are presented which illustrate performance under uncertain environmental conditions.
Relative effects of increment and pedestal duration on the detection of intensity increments
Authors: Valente Daniel L. , Patra Harisadhan , Jesteadt Walt
Published: April 2011

The detection of a brief increment in the intensity of a longer duration pedestal is commonly used as a measure of intensity-resolution. Increment detection is known to improve with increasing duration of the increment and also with increasing duration of the pedestal, but the relative effects of these two parameters have not been explored in the same study. In several past studies of the effects of increment duration, pedestal duration was increased as increment duration increased. In the present study, increment and pedestal duration were independently manipulated. Increment-detection thresholds were determined for four subjects with normal-hearing using a 500- or 4000-Hz pedestal presented at 60 dB sound pressure level (SPL). Increment durations were 10, 20, 40, 80, 160, and 320 ms. Pedestal durations were 20, 40, 80, 160, and 320 ms. Each increment duration was combined with all pedestals of equal or greater duration. Multiple-regression analyses indicate that increment detection under these conditions is determined primarily by pedestal duration. Follow-up experiments ruled out effects of off-frequency listening or overshoot. The results suggest that effects of increment duration have been confounded by effects of pedestal duration in studies that co-varied increment and pedestal duration. Implications for models of temporal integration are discussed.
Variations in recorded acoustic gunshot waveforms generated by small firearms
Authors: Beck Steven D. , Nakasone Hirotaka , Marr Kenneth W.
Published: April 2011

Analysis of recorded acoustic gunshot signals to determine firearm waveform characteristics requires an understanding of the impulsive signal events, how the waveforms vary among different sources, and how the waveforms are affected by the environment and the recording system. This paper presents empirical results from waveforms produced by different small firearms and an analysis of their variations under different and controlled conditions. Acoustic signals were generated using multiple firearm makes and models firing different ammunition types. Simultaneous recordings from the microphones located at different distances from the source and at different azimuth angles (from the line-of-fire) were used to study source characteristics and sound propagation effects. The results indicate that recorded gunshot waveforms generally consist of multiple acoustic events, and these are observable depending on the received distance and azimuth angle. The source blast size, microphone distance, and microphone azimuth angle are the primary factors affecting the recorded muzzle blast characteristics. Ground or object reflections and ballistic shockwaves and their reflections can interfere with the muzzle blast waveform and its measurements. This experiment confirmed and quantified the wide range of correlation results between waveforms recorded from different source, microphone distance, and microphone angle configurations.
Sequential trans-dimensional Monte Carlo for range-dependent geoacoustic inversion
Authors: Dettmer Jan , Dosso Stan E. , Holland Charles W.
Published: April 2011

This paper develops a sequential trans-dimensional Monte Carlo algorithm for geoacoustic inversion in a strongly range-dependent environment. The algorithm applies advanced Markov chain Monte Carlo methods in combination with sequential techniques (particle filters) to carry out geoacoustic inversions for consecutive data sets acquired along a track. Changes in model parametrization along the track (e.g., number of sediment layers) are accounted for with trans-dimensional partition modeling, which intrinsically determines the amount of structure supported by the data information content. Challenging issues of rapid environmental change between consecutive data sets and high information content (peaked likelihood) are addressed by bridging distributions implemented using annealed importance sampling. This provides an efficient method to locate high-likelihood regions for new data which are distant and/or disjoint from previous high-likelihood regions. The algorithm is applied to simulated reflection-coefficient data along a track, such as can be collected using a towed array close to the seabed. The simulated environment varies rapidly along the track, with changes in the number of layers, layer thicknesses, and geoacoustic parameters within layers. In addition, the seabed contains a geologic fault, where all layers are offset abruptly, and an erosional channel. Changes in noise level are also considered.
A radial propagator for axisymmetric pressure fields
Authors: Pees Edward H.
Published: April 2011

The concept of a propagator is central to the angular spectrum formulation of diffraction theory, which expresses the pressure field diffracted by a two-dimensional aperture as a superposition of a continuum of plane waves. In the conventional form, an exponential term, known as a propagator, is multiplied by the wavenumber spectrum obtained from a two-dimensional spatial Fourier transform of the aperture boundary condition, to obtain the wavenumber spectrum in a plane parallel to the boundary, offset by some distance specified in the propagator. By repeated use of this propagator and Fourier inversion, it is possible to completely construct the homogeneous part of the pressure field in the positive half-space beyond the planar boundary containing the aperture. Drawing upon preceding work relating the boundary condition to the axial pressure [Pees, J. Acoust. Soc. Am. 127(3), 1381–1390 (2010)], it is shown in this article that when the aperture is axially symmetric, an alternative type of propagator can be derived that propagates an axial wavenumber spectrum away from the axis of the aperture. Use of this radial propagator can be computationally advantageous since it allows for field construction using one-dimensional Fourier transforms instead of Hankel transforms or two-dimensional Fourier transforms.
Beamforming for directional sources: Additional estimator and evaluation of performance under different acoustic scenarios
Authors: Bouchard Christian , Havelock David I. , Bouchard Martin
Published: April 2011

Beamforming is done with an array of sensors to achieve a directional or spatially-specific response by using a model of the arriving wavefront. Conventionally, a plane wave or point source model is used and this can cause decreased array gain or even total breakdown of beamforming when the source is directional. To avoid this, the authors proposed in recent work an alternative beamforming method which defines a set of “sub-beamformers,” each designed to respond to a different spatial mode of the source. The outputs of the individual sub-beamformers are combined in a weighted sum to give an overall output of better quality than that of a monopole beamformer. This paper extends the previous work by introducing an additional estimator for the weighted sum and by presenting simulation results to demonstrate the relative performance of the proposed method and the different estimators for a directional source in the presence of diffuse noise, reverberation, and an interfering source. Gain optimization subject to a constraint on the white-noise gain with the proposed beamforming method is also introduced. Generally, when beamforming on directional sources, the proposed method outperforms beamforming with a point source model when the input signal-to-noise ratio (SNR) is 0 dB or higher.
A theoretical comparison of attenuation measurement techniques from backscattered ultrasound echoes
Authors: Labyed Yassin , Bigelow Timothy A.
Published: April 2011

Accurate characterization of tissue pathologies using ultrasonic attenuation is strongly dependent on the accuracy of the algorithm that is used to obtain the attenuation coefficient estimates. In this paper, computer simulations were used to compare the accuracy and the precision of the three methods that are commonly used to estimate the local ultrasonic attenuation within a region of interest (ROI) in tissue; namely, the spectral log difference method, the spectral difference method, and the hybrid method. The effects of the inhomgeneities within the ROI on the accuracy of the three algorithms were studied, and the optimal ROI size (the number of independent echoes laterally and the number of pulse lengths axially) was quantified for each method. The three algorithms were tested for when the ROI was homogeneous, the ROI had variations in scatterer number density, and the ROI had variations in effective scatterer size. The results showed that when the ROI was homogeneous, the spectral difference method had the highest accuracy and precision followed by the spectral log difference method and the hybrid method, respectively. Also, when the scatterer number density varied, the spectral difference method completely failed, while the log difference method and hybrid method still gave good results. Lastly, when the scatterer size varied, all of the methods failed.
Acoustic correlates of individuality in the vocal repertoire of a nocturnal primate (Microcebus murinus)
Authors: Leliveld Lisette M. C. , Scheumann Marina , Zimmermann Elke
Published: April 2011

In mammals individual distinctiveness in vocalizations provides the basis for individual recognition and thus plays an important role in social behavior. In this study, first evidence is provided for a nocturnal primate that variation in individual distinctiveness across the vocal repertoire is to some extent determined by the context and the acoustic structure of the call types. Individual distinctiveness was investigated across call types in the gray mouse lemur, a nocturnal primate, living in a dispersed multi-male multi-female social system. To explore to what degree context and acoustic structure predict variations in individual distinctiveness, four major call types were examined (grunts, tsaks, short whistles, and trills). Call types differed in context and acoustic structure and were recorded under controlled experimental conditions. A discriminant function analysis revealed that all call types are individually distinct, but not to the same degree. The findings suggest that variations in individual distinctiveness can to some extent be explained by the context and the acoustic structure of the call types.
Mode propagation in curved waveguides and scattering by inhomogeneities: Application to the elastodynamics of helical structures
Authors: Treyssède Fabien
Published: April 2011

This paper reports on an investigation into the propagation of guided modes in curved waveguides and their scattering by inhomogeneities. In a general framework, the existence of propagation modes traveling in curved waveguides is discussed. The concept of translational invariance, intuitively used for the analysis of straight waveguides, is highlighted for curvilinear coordinate systems. Provided that the cross-section shape and medium properties do not vary along the waveguide axis, it is shown that a sufficient condition for invariance is the independence on the axial coordinate of the metric tensor. Such a condition is indeed checked by helical coordinate systems. This study then focuses on the elastodynamics of helical waveguides. Given the difficulty in achieving analytical solutions, a purely numerical approach is chosen based on the so-called semi-analytical finite element method. This method allows the computation of eigenmodes propagating in infinite waveguides. For the investigation of modal scattering by inhomogeneities, a hybrid finite element method is developed for curved waveguides. The technique consists in applying modal expansions at cross-section boundaries of the finite element model, yielding transparent boundary conditions. The final part of this paper deals with scattering results obtained in free-end helical waveguides. Two validation tests are also performed.
Maxima and minima of the displacement components for the Lamb modes
Authors: Chati Farid , Léon Fernand , Décultot Dominique , Maze Gérard
Published: April 2011

This paper revisits the vanishing of the transverse component of the particle displacement vector in free surfaces of an isotropic homogeneous plate, for both symmetric and antisymmetric Lamb waves. Drawing on well-known analytical expressions from Viktorov’s book [(1967) Rayleigh and Lamb Waves: Physical Theory Applications, Chap. II, pp. 67–121], two distinct frequency-thickness product expressions, in cases where this vanishing occurs, are derived: one for the symmetric modes and another for the antisymmetric modes. At these frequency-thickness products, phase and group velocities have appreciable values which are discussed herein. It appears that these velocities depend on the transverse bulk wave velocity only. This is the specific condition of the Lamé modes. Moreover, theoretical and experimental investigations of displacements in the surface of a plate in air have been carried out. The theoretical part shows that the normal and transverse displacements have, respectively, a local maximum and a local minimum in the vicinity of these frequency-thickness products. The experimental part corroborates the presence of the local maximum of the S0 Lamb mode for various materials.
Quasi-Gaussian Bessel-beam superposition: Application to the scattering of focused waves by spheres
Authors: Marston Philip L.
Published: April 2011

A superposition of zero-order Bessel beams is examined that closely resembles an idealized paraxial Gaussian beam, provided the superposition is not tightly focused. Plots compare wavefield properties in the focal region and in the far field for different values of kw0, the product of the wavenumber k, and the focal-spot-radius w0. The superposition (which is an exact solution of the Helmholtz equation) has the important property that the scattering by an isotropic sphere can be calculated without any approximations for the commonly considered case of linear waves propagating in an inviscid fluid. The nth partial wave amplitude is similar to the case of plane-wave illumination except for a weighting factor that depends on incomplete gamma functions. An approximation for the weighting factor is also discussed based on a generalization of the Van de Hulst localization principle for a sphere of radius a at the focus of a Gaussian beam. Examples display differences between the directionality of the scattering with the plane wave case even though for the cases displayed, ka does not exceed 2 and w0/a is not less than 2. Properties of tightly focused wavefields and the partial wave weighting factors are discussed.
Improvement of intelligibility of ideal binary-masked noisy speech by adding background noise
Authors: Cao Shuyang , Li Liang , Wu Xihong
Published: April 2011

When a target-speech/masker mixture is processed with the signal-separation technique, ideal binary mask (IBM), intelligibility of target speech is remarkably improved in both normal-hearing listeners and hearing-impaired listeners. Intelligibility of speech can also be improved by filling in speech gaps with un-modulated broadband noise. This study investigated whether intelligibility of target speech in the IBM-treated target-speech/masker mixture can be further improved by adding a broadband-noise background. The results of this study show that following the IBM manipulation, which remarkably released target speech from speech-spectrum noise, foreign-speech, or native-speech masking (experiment 1), adding a broadband-noise background with the signal-to-noise ratio no less than 4 dB significantly improved intelligibility of target speech when the masker was either noise (experiment 2) or speech (experiment 3). The results suggest that since adding the noise background shallows the areas of silence in the time-frequency domain of the IBM-treated target-speech/masker mixture, the abruption of transient changes in the mixture is smoothed and the perceived continuity of target-speech components becomes enhanced, leading to improved target-speech intelligibility. The findings are useful for advancing computational auditory scene analysis, hearing-aid/cochlear-implant designs, and understanding of speech perception under “cocktail-party” conditions.
Atmospheric effects on voice command intelligibility from acoustic hail and warning devices
Authors: Bostron Jason H. , Brungart Timothy A. , Barnard Andrew R. , McDevitt Timothy E.
Published: April 2011

Voice command sound pressure levels (SPLs) were recorded at distances up to 1500 m. Received SPLs were related to the meteorological condition during sound propagation and compared with the outdoor sound propagation standard ISO 9613-2. Intelligibility of received signals was calculated using ANSI S3.5. Intelligibility results for the present voice command indicate that meteorological condition imposes little to no effect on intelligibility when the signal-to-noise ratio (SNR) is low (<−9 dB) or high (>0 dB). In these two cases the signal is firmly unintelligible or intelligible, respectively. However, at moderate SNRs, variations in received SPL can cause a fully intelligible voice command to become unintelligible, depending on the meteorological condition along the sound propagation path. These changes in voice command intelligibility often occur on time scales as short as minutes during upward refracting conditions, typically found above ground during the day or upwind of a sound source. Reliably predicting the intelligibility of a voice command in a moderate SNR environment can be challenging due to the inherent variability imposed by sound propagation through the atmosphere.
Assessment of accuracy of the structure-factor-size-estimator method in determining red blood cell aggregate size from ultrasound spectral backscatter coefficient
Authors: Saha Ratan K. , Franceschini Emilie , Cloutier Guy
Published: April 2011

A computer simulation study to produce ultrasonic backscatter coefficients (BSCs) from red blood cell (RBC) clusters is discussed. The simulation algorithm is suitable for generating non-overlapping, isotropic, and fairly identical RBC clusters. RBCs were stacked following the hexagonal close packing (HCP) structure to form a compact spherical aggregate. Such an aggregate was repeated and placed randomly under non-overlapping condition in the three-dimensional space to mimic an aggregated blood sample. BSCs were computed between 750 KHz and 200 MHz for samples of various cluster sizes at different hematocrits. Magnitudes of BSCs increased with mean aggregate sizes at low frequencies (<20 MHz). The accuracy of the structure-factor-size-estimator (SFSE) method in determining mean aggregate size and packing factor was also examined. A good correlation (R2 ≥ 0.94) between the mean size of aggregates predicted by the SFSE and true size was found for each hematocrit. This study shows that for spherical aggregates there exists a region for each hematocrit where SFSE works most accurately. Typically, error of SFSE in estimating mean cluster size was <20% for dimensions between 14 and 17 μm at 40% hematocrit. This study suggests that the theoretical framework of SFSE is valid under the assumption of isotropic aggregates.
Illusory transformation from speech to song
Authors: Deutsch Diana , Henthorn Trevor , Lapidis Rachael
Published: April 2011

An illusion is explored in which a spoken phrase is perceptually transformed to sound like song rather than speech, simply by repeating it several times over. In experiment I, subjects listened to ten presentations of the phrase and judged how it sounded on a five-point scale with endpoints marked “exactly like speech” and “exactly like singing.” The initial and final presentations of the phrase were identical. When the intervening presentations were also identical, judgments moved solidly from speech to song. However, this did not occur when the intervening phrases were transposed slightly or when the syllables were presented in jumbled orderings. In experiment II, the phrase was presented either once or ten times, and subjects repeated it back as they finally heard it. Following one presentation, the subjects repeated the phrase back as speech; however, following ten presentations they repeated it back as song. The pitch values of the subjects’ renditions following ten presentations were closer to those of the original spoken phrase than were the pitch values following a single presentation. Furthermore, the renditions following ten presentations were even closer to a hypothesized representation in terms of a simple tonal melody than they were to the original spoken phrase.
On the use of hollow tube geometries for resonant ultrasound spectroscopy
Authors: Jaglinski Tim , Wang Yun-Che
Published: April 2011

Resonant ultrasound spectroscopy (RUS) can nondestructively obtain the elastic constants of compact specimens, however many materials have hollow cross-sections and frequency analysis of such geometries is required before inclusion in the RUS methodology. Resonant mode shapes of tubes with length equal to diameter and varying ratios of tube inner to outer diameter (Λ) as well as Poisson’s ratio (ν) were identified by eigenvalue analysis using a commercial finite element code. Longitudinal and shear RUS experiments were conducted on tubes with Λ varying between 0 and 0.95 and compared to the numerical results. Simulations predict that the fundamental mode transitions from pure torsion to symmetric or antisymmetric ring bending at Λ = 0.3. The frequency of the first torsion mode is invariant to Λ and unequivocal identification of this mode is obscured by overlap of bending harmonics as Λ approaches 0.95. In the context of rapid calculation of isotropic elastic constants, shear moduli were calculated from the first torsional mode and Poisson’s ratio was inferred from the Demarest maps of the mode structure’s dependence upon Poisson’s ratio. An average shear modulus of 27.5 + 1.5/−0.6 GPa, about 5% larger than literature values for 6061 aluminum, and ν of 0.33 were inferred. Errors are attributed to tube aspect ratios slightly greater than 1 and weak material anisotropy. Existing analytical solutions for ring bending modes derived from shell approximations and for infinitely long tubes under plane strain assumptions do not adequately describe the fundamental modes for short tubes. The shear modulus can be calculated for all Λ using the existing analytical solution.
On the aeroacoustic tonal noise generation mechanism of a sharp-edged plate
Authors: Moreau Danielle J. , Brooks Laura A. , Doolan Con J.
Published: April 2011

This letter presents an experimental study on the tonal noise generated by a sharp-edged flat plate at low-to-moderate Reynolds number. Flow and far-field noise data reveal that, in this particular case, the tonal noise appears to be governed by vortex shedding processes. Also related to the existence of the tonal noise is a region of separated flow slightly upstream of the trailing edge. Hydrodynamic fluctuations at selected vortex shedding frequencies are strongly amplified by the inflectional mean velocity profile in the separated shear layer. The amplified hydrodynamic fluctuations are diffracted by the trailing edge, producing strong tonal noise.
Effects of natural sounds on the perception of road traffic noise
Authors: Coensel Bert De , Vanwetswinkel Sofie , Botteldooren Dick
Published: April 2011

Recent studies show that introducing sound from water features in urban open spaces may reduce the loudness of road traffic noise, but it is not clear in which situations this measure also improves overall soundscape quality. This work describes a listening experiment on loudness, pleasantness, and eventfulness of stimuli that combine road traffic noise with fountain or bird sound at different sound levels. Adding fountain sound reduced the loudness of road traffic noise only if the latter had low temporal variability. Conversely, adding bird sound significantly enhanced soundscape pleasantness and eventfulness, more than what was achieved by adding fountain sound.
Bacterioneuston Community Structure in the Southern Baltic Sea and Its Dependence on Meteorological Conditions
Authors: Stolle Christian , Labrenz Matthias , Meeske Christian , Jürgens Klaus
Published: April 2011

The bacterial community in the sea surface microlayer (SML) (bacterioneuston) is exposed to unique physicochemical properties and stronger meteorological influences than the bacterial community in the underlying water (ULW) (bacterioplankton). Despite extensive research, however, the structuring factors of the bacterioneuston remain enigmatic. The aim of this study was to examine the effect of meteorological conditions on bacterioneuston and bacterioplankton community structures and to identify distinct, abundant, active bacterioneuston members. Nineteen bacterial assemblages from the SML and ULW of the southern Baltic Sea, sampled from 2006 to 2008, were compared. Single-strand conformation polymorphism (SSCP) fingerprints were analyzed to distinguish total (based on the 16S rRNA gene) and active (based on 16S rRNA) as well as nonattached and particle-attached bacterial assemblages. The nonattached communities of the SML and ULW were very similar overall (similarity: 47 to 99%; mean: 88%). As an exception, during low wind speeds and high radiation levels, the active bacterioneuston community increasingly differed from the active bacterioplankton community. In contrast, the particle-attached assemblages in the two compartments were generally less similar (similarity: 8 to 98%; mean: 62%), with a strong variability in the active communities that was solely related to wind speed. Both nonattached and particle-attached active members of the bacterioneuston, which were found exclusively in the SML, were related to environmental clones belonging to the
Cyanobacteria
,
Bacteroidetes
, and
Alpha
-,
Beta
-, and
Gammaproteobacteria
originally found in diverse habitats, but especially in water columns. These results suggest that bacterioneuston communities are strongly influenced by the ULW but that specific meteorological conditions favor the development of distinctive populations in the air-water interface.
Effects of Homologous Phosphoenolpyruvate-Carbohydrate Phosphotransferase System Proteins on Carbohydrate Uptake and Poly(3-Hydroxybutyrate) Accumulation in Ralstonia eutropha H16
Authors: Kaddor Chlud , Steinbüchel Alexander
Published: April 2011

Seven gene loci encoding putative proteins of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PEP-PTS) were identified in the genome of
Ralstonia eutropha
H16 by
in silico
analysis. Except the
N
-acetylglucosamine-specific PEP-PTS, an additional complete PEP-PTS is lacking in strain H16. Based on these findings, we generated single and multiple deletion mutants defective mainly in the PEP-PTS genes to investigate their influence on carbon source utilization, growth behavior, and poly(3-hydroxybutyrate) (PHB) accumulation. As supposed, the H16 Δ
frcACB
and H16 Δ
nagFEC
mutants exhibited no growth when cultivated on fructose and
N
-acetylglucosamine, respectively. Furthermore, a transposon mutant with a
ptsM-ptsH
insertion site did not grow on both carbon sources. The observed phenotype was not complemented, suggesting that it results from an interaction of genes or a polar effect caused by the Tn
5
::
mob
insertion.
ptsM
,
ptsH
, and
ptsI
single, double, and triple mutants stored much less PHB than the wild type (about 10 to 39% [wt/wt] of cell dry weight) and caused reduced PHB production in mutants lacking the H16_A2203, H16_A0384,
frcACB
, or
nagFEC
genes. In contrast, mutant H16 ΔH16_A0384 accumulated 11.5% (wt/wt) more PHB than the wild type when grown on gluconate and suppressed partially the negative effect of the
ptsMHI
deletion on PHB synthesis. Based on our experimental data, we discussed whether the PEP-PTS homologous proteins in
R. eutropha
H16 are exclusively involved in the complex sugar transport system or whether they are also involved in cellular regulatory functions of carbon and PHB metabolism.
Isolation and Bioaugmentation of an Estradiol-Degrading Bacterium and Its Integration into a Mature Biofilm
Authors: Iasur-Kruh Lilach , Hadar Yitzhak , Minz Dror
Published: April 2011

Bioaugmentation can alter the potential activity as well as the composition of the naturally occurring microbial biota during bioremediation of a contaminated site. The focus of the current study is the pollutant 17β-estradiol (E2), which can cause endocrine effects and is potentially harmful to aquatic biota and to public health. The community composition and function of biofilms, originating from a wetland system, as affected by augmentation of an estradiol-degrading bacterium (EDB-LI1) under different conditions, were investigated. EDB-LI1 inoculation into biofilm from two wetland ponds representing early and advanced water treatment stages, respectively, yielded three significant observations, as follows: (i) EDB-LI1, enriched from a biofilm of a constructed wetland wastewater treatment system, was detected (by quantitative PCR [qPCR] analysis) in this environment in the augmented biofilm only; (ii) the augmented biofilm acquired the ability to remove estradiol; and (iii) the bacterial community composition (analyzed by PCR-denaturing gradient gel electrophoresis [DGGE]) of the augmented biofilm differed from that of the control biofilm. Furthermore, EDB-LI1 bioaugmentation showed a higher level of removal of estradiol with biofilms that originated from the advanced-treatment-stage wetland pond than those from the early-treatment-stage pond. Hence, the bioaugmentation efficiency of EDB-LI1 depends on both the quality of the feed water and the microbial community composition in the pond.
Stochasticity of Bacterial Attachment and Its Predictability by the Extended Derjaguin-Landau-Verwey-Overbeek Theory
Authors: Chia Teck Wah R. , Nguyen Vu Tuan , McMeekin Thomas , Fegan Narelle , Dykes Gary A.
Published: April 2011

Bacterial attachment onto materials has been suggested to be stochastic by some authors but nonstochastic and based on surface properties by others. We investigated this by attaching pairwise combinations of two
Salmonella enterica
serovar Sofia (
S
. Sofia) strains (with different physicochemical and attachment properties) with one strain each of
S. enterica
serovar Typhimurium,
S. enterica
serovar Infantis, or
S. enterica
serovar Virchow (all with similar physicochemical and attachment abilities) in ratios of 0.428, 1, and 2.333 onto glass, stainless steel, Teflon, and polysulfone. Attached bacterial cells were recovered and counted. If the ratio of attached cells of each
Salmonella
serovar pair recovered was the same as the initial inoculum ratio, the attachment process was deemed stochastic. Experimental outcomes from the study were compared to those predicted by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory. Significant differences (
P
< 0.05) between the initial and the attached ratios for serovar pairs containing
S
. Sofia S1296a for all different ratios were apparent for all materials. For
S
. Sofia S1635-containing pairs, 7 out of 12 combinations of serovar pairs and materials had attachment ratios not significantly different (
P
> 0.05) from the initial ratio of 0.428. Five out of 12 and 10 out of 12 samples had attachment ratios not significantly different (
P
> 0.05) from the initial ratios of 1 and 2.333, respectively. These results demonstrate that bacterial attachment to different materials is likely to be nonstochastic only when the key physicochemical properties of the bacteria were significantly different (
P
< 0.05) from each other. XDLVO theory could successfully predict the attachment of some individual isolates to particular materials but could not be used to predict the likelihood of stochasticity in pairwise attachment experiments.
Distinct Acid Resistance and Survival Fitness Displayed by Curli Variants of Enterohemorrhagic Escherichia coli O157:H7
Authors: Carter Michelle Q. , Brandl Maria T. , Louie Jacqueline W. , Kyle Jennifer L. , Carychao Diana K. , Cooley Michael B. , Parker Craig T. , Bates Anne H. , Mandrell Robert E.
Published: April 2011

Curli are adhesive fimbriae of
Enterobacteriaceae
and are involved in surface attachment, cell aggregation, and biofilm formation. Here, we report that both inter- and intrastrain variations in curli production are widespread in enterohemorrhagic
Escherichia coli
O157:H7. The relative proportions of curli-producing variants (C
+
) and curli-deficient variants (C
−
) in an
E. coli
O157:H7 cell population varied depending on the growth conditions. In variants derived from the 2006 U.S. spinach outbreak strains, the shift between the C
+
and C
−
subpopulations occurred mostly in response to starvation and was unidirectional from C
−
to C
+
; in variants derived from the 1993 hamburger outbreak strains, the shift occurred primarily in response to oxygen depletion and was bidirectional. Furthermore, curli variants derived from the same strain displayed marked differences in survival fitness: C
+
variants grew to higher concentrations in nutrient-limited conditions than C
−
variants, whereas C
−
variants were significantly more acid resistant than C
+
variants. This difference in acid resistance does not appear to be linked to the curli fimbriae
per se
, since a
csgA
deletion mutant in either a C
+
or a C
−
variant exhibited an acid resistance similar to that of its parental strain. Our data suggest that natural curli variants of
E. coli
O157:H7 carry several distinct physiological properties that are important for their environmental survival. Maintenance of curli variants in an
E. coli
O157:H7 population may provide a survival strategy in which C
+
variants are selected in a nutrient-limited environment, whereas C
−
variants are selected in an acidic environment, such as the stomach of an animal host, including that of a human.
Physiological Adaptation of Desulfitobacterium hafniense Strain TCE1 to Tetrachloroethene Respiration
Authors: Prat Laure , Maillard Julien , Grimaud Régis , Holliger Christof
Published: April 2011

Desulfitobacterium
spp. are ubiquitous organisms with a broad metabolic versatility, and some isolates have the ability to use tetrachloroethene (PCE) as terminal electron acceptor. In order to identify proteins involved in this organohalide respiration process, a comparative proteomic analysis was performed. Soluble and membrane-associated proteins obtained from cells of
Desulfitobacterium hafniense
strain TCE1 that were growing on different combinations of the electron donors lactate and hydrogen and the electron acceptors PCE and fumarate were analyzed. Among proteins increasingly expressed in the presence of PCE compared to fumarate as electron acceptor, a total of 57 proteins were identified by mass spectrometry analysis, revealing proteins involved in stress response and associated regulation pathways, such as PspA, GroEL, and CodY, and also proteins potentially participating in carbon and energy metabolism, such as proteins of the Wood-Ljungdahl pathway and electron transfer flavoproteins. These proteomic results suggest that
D. hafniense
strain TCE1 adapts its physiology to face the relative unfavorable growth conditions during an apparent opportunistic organohalide respiration.
Increase of Eicosapentaenoic Acid in Thraustochytrids through Thraustochytrid Ubiquitin Promoter-Driven Expression of a Fatty Acid Δ5 Desaturase Gene
Authors: Kobayashi Takumi , Sakaguchi Keishi , Matsuda Takanori , Abe Eriko , Hama Yoichiro , Hayashi Masahiro , Honda Daiske , Okita Yuji , Sugimoto Shinichi , Okino Nozomu , Ito Makoto
Published: April 2011

Thraustochytrids, marine protists known to accumulate polyunsaturated fatty acids (PUFAs) in lipid droplets, are considered an alternative to fish oils as a source of PUFAs. The major fatty acids produced in thraustochytrids are palmitic acid (C
16:0
),
n
− 6 docosapentaenoic acid (DPA) (C
22:5

n

− 6
), and docosahexaenoic acid (DHA) (C
22:6

n

− 3
), with eicosapentaenoic acid (EPA) (C
20:5

n

− 3
) and arachidonic acid (AA) (C
20:4

n

− 6
) as minor constituents. We attempted here to alter the fatty acid composition of thraustochytrids through the expression of a fatty acid Δ5 desaturase gene driven by the thraustochytrid ubiquitin promoter. The gene was functionally expressed in
Aurantiochytrium limacinum
mh0186, increasing the amount of EPA converted from eicosatetraenoic acid (ETA) (C
20:4

n

− 3
) by the Δ5 desaturase. The levels of EPA and AA were also increased by 4.6- and 13.2-fold in the transgenic thraustochytrids compared to levels in the mock transfectants when ETA and dihomo-γ-linolenic acid (DGLA) (C
20:3

n

− 6
) were added to the culture at 0.1 mM. Interestingly, the amount of EPA in the transgenic thraustochytrids increased in proportion to the amount of ETA added to the culture up to 0.4 mM. The rates of conversion and accumulation of EPA were much higher in the thraustochytrids than in baker's yeasts when the desaturase gene was expressed with the respective promoters. This report describes for the first time the finding that an increase of EPA could be accomplished by introducing the Δ5 desaturase gene into thraustochytrids and indicates that molecular breeding of thraustochytrids is a promising strategy for generating beneficial PUFAs.
Bottom-Up versus Top-Down Control of Hypo- and Epilimnion Free-Living Bacterial Community Structures in Two Neighboring Freshwater Lakes
Authors: Berdjeb Lyria , Ghiglione Jean-François , Jacquet Stéphan
Published: April 2011

Bacterioplankton plays a central role in the microbial functioning of lacustrine ecosystems; however, factors that constrain its structural variation are still poorly understood. Here we evaluated the driving forces exerted by a large set of environmental and biological parameters on the temporal and spatial dynamics of free-living bacterial community structures (BCS) in two neighboring perialpine lakes, Lake Bourget and Lake Annecy, which differ in trophic status. We analyzed monthly data from a 1-year sampling period at two depths situated in the epi- and hypolimnia for each lake. Overall, denaturing gradient gel electrophoresis (DGGE) revealed significant differences in the BCS in the two lakes, characterized by a higher number of bands in the oligotrophic ecosystem (i.e., Lake Annecy). The temporal dynamics of BCS differed greatly between depths and lakes, with temporal scale patterns being much longer in the mesotrophic Lake Bourget. Direct-gradient multivariate ordination analyses showed that a complex array of biogeochemical parameters was the driving force behind BCS shifts in both lakes. Our results indicated that 60 to 80% of the variance was explained only by the bottom-up factors in both lakes, indicating the importance of nutrients and organic matter from autotrophic origin in controlling the BCS. Top-down regulation by flagellates together with ciliates or viruses was found only in the hypolimnion and not in the epilimnion for both lakes and explained less than 18% of the bacterial community changes during the year. Our study suggests that the temporal dynamics of the free-living bacterial community structure in deep perialpine lakes are dependent mainly on bottom-up factors and to a lesser extent on top-down factors, whatever the specific environmental conditions of these lakes.
Fecal Carriage and Shedding Density of CTX-M Extended-Spectrum β-Lactamase-Producing Escherichia coli in Cattle, Chickens, and Pigs: Implications for Environmental Contamination and Food Production
Authors: Horton R. A. , Randall L. P. , Snary E. L. , Cockrem H. , Lotz S. , Wearing H. , Duncan D. , Rabie A. , McLaren I. , Watson E. , La Ragione R. M. , Coldham N. G.
Published: April 2011

The number and proportion of CTX-M positive
Escherichia coli
organisms were determined in feces from cattle, chickens, and pigs in the United Kingdom to provide a better understanding of the risk of the dissemination of extended-spectrum β-lactamase (ESBL) bacteria to humans from food animal sources. Samples of bovine (
n
= 35) and swine (
n
= 20) feces were collected from farms, and chicken cecal contents (
n
= 32) were collected from abattoirs. There was wide variation in the number of CTX-M-positive
E. coli
organisms detected; the median (range) CFU/g were 100 (100 × 10
6
to 1 × 10
6
), 5,350 (100 × 10
6
to 3.1 × 10
6
), and 2,800 (100 × 10
5
to 4.7 × 10
5
) for cattle, chickens, and pigs, respectively. The percentages of
E. coli
isolates that were CTX-M positive also varied widely; median (range) values were 0.013% (0.001 to 1%) for cattle, 0.0197% (0.00001 to 28.18%) for chickens, and 0.121% (0.0002 to 5.88%) for pigs. The proportion of animals designated high-density shedders (≥1 × 10
4
CFU/g) of CTX-M
E. coli
was 3/35, 15/32, and 8/20 for cattle, chickens, and pigs, respectively. We postulate that high levels of CTX-M
E. coli
in feces facilitate the dissemination of
bla
CTX-M
genes during the rearing of animals for food, and that the absolute numbers of CTX-M bacteria should be given greater consideration in epidemiological studies when assessing the risks of food-borne transmission.
Infaunal Burrows Are Enrichment Zones for Vibrio parahaemolyticus
Authors: Gamble Megan D. , Lovell Charles R.
Published: April 2011

Vibrio parahaemolyticus
, a species that includes strains known to be pathogenic in humans, and other
Vibrionaceae
are common, naturally occurring bacteria in coastal environments. Understanding the ecology and transport of these organisms within estuarine systems is fundamental to predicting outbreaks of pathogenic strains. Infaunal burrows serve as conduits for increased transport of tidal waters and
V. parahaemolyticus
cells by providing large open channels from the sediment to salt marsh tidal creeks. An extensive seasonal study was conducted at the North Inlet Estuary in Georgetown, SC, to quantify
Vibrionaceae
and specifically
V. parahaemolyticus
bacteria in tidal water, fiddler crab (
Uca pugilator
,
Uca pugnax
) burrow water, and interstitial pore water. Numbers of
V. parahaemolyticus
bacteria were significantly higher within burrow waters (4,875 CFU ml
−1
) than in creek water (193 CFU ml
−1
) and interstitial pore water (128 CFU ml
−1
), demonstrating that infaunal burrows are sites of
V. parahaemolyticus
enrichment. A strong seasonal trend of increased abundances of
Vibrionaceae
and
V. parahaemolyticus
organisms during the warmer months of May through September was observed. Multilocus sequence typing (MLST) analysis of isolates presumed to be
V. parahaemolyticus
from creek water, pore water, and burrow water identified substantial strain-level genetic variability among
V. parahaemolyticus
bacteria. Analysis of carbon substrate utilization capabilities of organisms presumed to be
V. parahaemolyticus
also indicated physiological diversity within this clade, which helps to explain the broad distribution of these strains within the estuary. These burrows are “hot spots” of
Vibrionaceae
and
V. parahaemolyticus
cell numbers and strain diversity and represent an important microhabitat.
Engineering Saccharomyces cerevisiae To Release 3-Mercaptohexan-1-ol during Fermentation through Overexpression of an S. cerevisiae Gene,
STR3
, for Improvement of Wine Aroma
Authors: Holt Sylvester , Cordente Antonio G. , Williams Simon J. , Capone Dimitra L. , Jitjaroen Wanphen , Menz Ian R. , Curtin Chris , Anderson Peter A.
Published: April 2011

Sulfur-containing aroma compounds are key contributors to the flavor of a diverse range of foods and beverages. The tropical fruit characters of
Vitis vinifera
L. cv. Sauvignon blanc wines are attributed to the presence of the aromatic thiols 3-mercaptohexan-1-ol (3MH), 3-mercaptohexan-1-ol-acetate, and 4-mercapto-4-methylpentan-2-one (4MMP). These volatile thiols are found in small amounts in grape juice and are formed from nonvolatile cysteinylated precursors during fermentation. In this study, we overexpressed a
Saccharomyces cerevisiae
gene,
STR3
, which led to an increase in 3MH release during fermentation of a
V. vinifera
L. cv. Sauvignon blanc juice. Characterization of the enzymatic properties of Str3p confirmed it to be a pyridoxal-5′-phosphate-dependent cystathionine β-lyase, and we demonstrated that this enzyme was able to cleave the cysteinylated precursors of 3MH and 4MMP to release the free thiols. These data provide direct evidence for a yeast enzyme able to release aromatic thiols
in vitro
that can be applied in the development of self-cloned yeast to enhance wine flavor.