bluuebunny/crossref_metadata_2025 huggingface dataset:
Perception of familiar contrasts in unfamiliar positions
Authors: Broersma Mirjam
Published: June 2005

This paper investigates the perception of non-native phoneme contrasts which exist in the native language, but not in the position tested. Like English, Dutch contrasts voiced and voiceless obstruents. Unlike English, Dutch allows only voiceless obstruents in word-final position. Dutch and English listeners’ accuracy on English final voicing contrasts and their use of preceding vowel duration as a voicing cue were tested. The phonetic structure of Dutch should provide the necessary experience for a native-like use of this cue. Experiment 1 showed that Dutch listeners categorized English final /z/–/s/, /v/–/f/, /b/–/p/, and /d/–/t/ contrasts in nonwords as accurately as initial contrasts, and as accurately as English listeners did, even when release bursts were removed. In experiment 2, English listeners used vowel duration as a cue for one final contrast, although it was uninformative and sometimes mismatched other voicing characteristics, whereas Dutch listeners did not. Although it should be relatively easy for them, Dutch listeners did not use vowel duration. Nevertheless, they attained native-like accuracy, and sometimes even outperformed the native listeners who were liable to be misled by uninformative vowel duration information. Thus, native-like use of cues for non-native but familiar contrasts in unfamiliar positions may hardly ever be attained.
Echolocation clicks of free-ranging Cuvier’s beaked whales (Ziphius cavirostris)
Authors: Zimmer Walter M. X. , Johnson Mark P. , Madsen Peter T. , Tyack Peter L.
Published: June 2005

Strandings of beaked whales of the genera Ziphius and Mesoplodon have been reported to occur in conjunction with naval sonar use. Detection of the sounds from these elusive whales could reduce the risk of exposure, but descriptions of their vocalizations are at best incomplete. This paper reports quantitative characteristics of clicks from deep-diving Cuvier’s beaked whales (Ziphius cavirostris) using a unique data set. Two whales in the Ligurian Sea were simultaneously tagged with sound and orientation recording tags, and the dive tracks were reconstructed allowing for derivation of the range and relative aspect between the clicking whales. At depth, the whales produced trains of regular echolocation clicks with mean interclick intervals of 0.43 s (±0.09) and 0.40 s (±0.07). The clicks are frequency modulated pulses with durations of ∼200 μs and center frequencies around 42 kHz, −10 dB bandwidths of 22 kHz, and Q3 dB of 4. The sound beam is narrow with an estimated directionality index of more than 25 dB, source levels up to 214 dBpp re: 1 μPa at 1 m, and energy flux density of 164 dB re: 1 μPa2 s. As the spectral and temporal properties are different from those of nonziphiid odontocetes the potential for passive detection is enhanced.
Prediction of underwater sound levels from rain and wind
Authors: Ma Barry B. , Nystuen Jeffrey A. , Lien Ren-Chieh
Published: June 2005

Wind and rain generated ambient sound from the ocean surface represents the background baseline of ocean noise. Understanding these ambient sounds under different conditions will facilitate other scientific studies. For example, measurement of the processes producing the sound, assessment of sonar performance, and helping to understand the influence of anthropogenic generated noise on marine mammals. About 90 buoy-months of ocean ambient sound data have been collected using Acoustic Rain Gauges in different open-ocean locations in the Tropical Pacific Ocean. Distinct ambient sound spectra for various rainfall rates and wind speeds are identified through a series of discrimination processes. Five divisions of the sound spectra associated with different sound generating mechanisms can be predicted using wind speed and rainfall rate as input variables. The ambient sound data collected from the Intertropical Convergence Zone are used to construct the prediction algorithms, and are tested on the data from the Western Pacific Warm Pool. This physically based semi-empirical model predicts the ambient sound spectra (0.5–50 kHz) at rainfall rates from 2–200 mm/h and wind speeds from 2 to 14 m/s.
Moving average fields, macro-scale response measures, and homogenizing micro-scale variation
Authors: McCoy John J.
Published: June 2005

There are two critical issues when deriving a macro-scale prediction model starting from a more complete, underlying model. The first is the precise relationship of the fields predicted by the more complete model and the fields predicted by the macro-scale model. The second is the manner of solving a closure problem that is invariably encountered in all such derivations. The understanding that moving averages of the fields predicted by the more complete model are the fields predicted by the macro-scale model is challenged on the grounds that accomplishing a moving average does not eliminate micro-scale variation, it only appears to do so in one representation of the moving average field. The solution of a closure problem by assumption is challenged on the grounds that the most common assumptions are demonstrably invalid, even while leading to prediction models that can provide reasonable estimates of the macro-scale response in some scenarios. In presenting the challenges, it is further shown how a multiresolution analysis by an orthogonal wavelet system provides a framework for both precisely defining macro-scale response fields, i.e., fields from which all micro-scale variation has been eliminated, and presenting a formally exact solution for a precisely described closure problem.
Adaptive instant record signals applied to detection with time reversal operator decomposition
Authors: Folegot Thomas , de Rosny Julien , Prada Claire , Fink Mathias
Published: June 2005

Time reversal arrays are becoming common tools whether for detection or tomography. These applications require the measurement of the response from the array to one or several receivers. The most natural way to record the impulse responses for several sources is to generate pulses successively from each emitting point and record simultaneously the signals from the receivers. However, this method is very time consuming or inefficient in terms of signal-to-noise ratio. To overcome this limitation quasi-orthogonal pseudonoise signals like Kasami sequences can be used. For guided wave propagation, a very high degree of orthogonality between the signal is necessary to allow an accurate measure of the whole multipath structure of the transfer function. Hence, in this work, we propose a new family of pseudo-orthogonal signals that is adapted to the environment and more specifically, to highly dispersive media. These adaptive instant records signals are used experimentally to detect targets using the time reversal operator decomposition method. The accuracy of the 15×15 transfer functions acquired simultaneously, and therefore the detection capability, are demonstrated in an experimental ultrasonic waveguide as a small-scale model of shallow water propagation including bottom absorption and reverberation.
Comparison of multifrequency acoustic and in situ measurements of zooplankton abundances in Knight Inlet, British Columbia
Authors: Trevorrow Mark V. , Mackas David L. , Benfield Mark C.
Published: June 2005

An investigation of midwater zooplankton aggregations in a coastal fjord was conducted in November 2002. This study focused on quantitative comparisons between a calibrated, three-frequency (38, 120, and 200 kHz) vessel-based echo-sounder, a multinet towed zooplankton sampler (BIONESS), and a high-resolution underwater camera (ZOOVIS). Daytime layers of euphausiids and amphipods near 70–90-m depth were observed in lower parts of the inlet, especially concentrated by tidal flows around a sill. Quantitative backscatter measurements of euphausiids and amphipods, combined with in situ size and abundance estimates, and using an assumed tilt-angle distribution, were in agreement with averaged fluid-cylinder scattering models produced by Stanton and Chu [ICES J. Mar. Sci. 57, 793–807, (2000)]. Acoustic measurements of physonect siphonophores in the upper inlet were found to have a strong 38-kHz scattering strength, in agreement with a damped bubble scattering model using a diameter of 0.4 mm. In relatively dense euphausiid layers, ZOOVIS abundance estimates were found to be a factor of 2 to 4 higher than the acoustic estimates, potentially due to deviations from assumed euphausiid orientation. Nocturnal near-surface euphausiid scattering exhibited a strong (15 dB) and rapid (seconds) sensitivity to vessel lights, interpreted as due to changing animal orientation.
Longitudinal and lateral low frequency head wave analysis in soft media
Authors: Benech Nicolás , Negreira Carlos A.
Published: June 2005

This article studies the influence of the head wave in the lateral and longitudinal components of the displacements generated by the radiation of low-frequency elastic waves in an isotropic and homogeneous soft solid. Low-frequency shear waves are used to characterize elastic properties of soft tissues. In this context, it is useful to have a detailed study of the low-frequency wave field in this kind of material. A soft medium is characterized by the fact that the head wave is found in the source’s axis. Even though its amplitude is small compared with the shear wave, it is possible to be observed experimentally by recording consecutive ultrasonic A-lines while the low-frequency wave propagates inside the medium. A standard one-dimensional speckle tracking technique is employed to measure the displacements. Experimental results were interpreted through the exact Green’s function solution to the half-space problem. According to the theoretical and experimental analysis, the head wave and surface related terms in general contribute to the displacements in the low-frequency range. This article thoroughly analyzes and experimentally shows the contribution of the head wave for the lateral component, which is not fully addressed by the literature.
Dead regions and pitch perception
Authors: Huss Martina , Moore Brian C. J.
Published: June 2005

The perception of pitch for pure tones with frequencies falling inside low- or high-frequency dead regions (DRs) was examined. Subjects adjusted a variable-frequency tone to match the pitch of a fixed tone. Matches within one ear were often erratic for tones falling in a DR, indicating unclear pitch percepts. Matches across ears of subjects with asymmetric hearing loss, and octave matches within ears, indicated that tones falling within a DR were perceived with an unclear pitch and/or a pitch different from “normal” whenever the tones fell more than 0.5 octave within a low- or high-frequency DR. One unilaterally impaired subject, with only a small surviving region between 3 and 4 kHz, matched a fixed 0.5-kHz tone in his impaired ear with, on average, a 3.75-kHz tone in his better ear. When asked to match the 0.5-kHz tone with an amplitude-modulated tone, he adjusted the carrier and modulation frequencies to about 3.8 and 0.5 kHz, respectively, suggesting that some temporal information was still available. Overall, the results indicate that the pitch of low-frequency tones is not conveyed solely by a temporal code. Possibly, there needs to be a correspondence between place and temporal information for a normal pitch to be perceived.
Acoustic cluster control of noise radiated from a planar structure
Authors: Tanaka Nobuo , Fukuda Ryoji , Hansen Colin H.
Published: June 2005

Acoustic cluster control is proposed for the purpose of achieving global sound attenuation of a planar structure. First, acoustic cluster filtering using a point sensor array is presented, which enables the grouping of sound radiated from a target object into a set of clusters, such that each cluster possesses the same common characteristics. This allows the possibility of extracting the cluster of interest without causing observation spillover. Based on the principle of reciprocity, cluster actuation using a point source array is then presented. Driving the source array in accordance with a proposed control law, the excitation of the designated cluster is performed without causing control spillover. Moreover, by combining both acoustic cluster filtering and acoustic cluster actuation, acoustic cluster control may be performed. In implementing acoustic cluster control, the necessary and sufficient condition for the acoustic cluster control is illustrated. It is also shown that the sound radiated from a planar structure may be captured in appropriate acoustic cluster filtering so that acoustic cluster control may be implemented. Experiment was conducted demonstrating the capability as well as the validity of the acoustic cluster filtering, actuation, and control for suppressing the noise radiated from a rectangular panel.
Active control of energy density in a one-dimensional waveguide: A cautionary note (L)
Authors: Cazzolato Ben S. , Petersen Dick , Howard Carl Q. , Zander Anthony C.
Published: June 2005

Acoustic energy density has been shown to be a highly effective cost function for active noise control systems. Many researchers have used the sound field in a one-dimensional waveguide to trial their control strategies before moving onto more realistic three-dimensional sound fields. This letter aims to shed some light on the observations made in the early papers on one-dimensional energy density control and also shows that some of the analysis was incorrect and the conclusions reached may be flawed.
Fast calculation of pulsed photoacoustic fields in fluids usingk-space methods
Authors: Cox B. T. , Beard P. C.
Published: June 2005

Two related numerical models that calculate the time-dependent pressure field radiated by an arbitrary photoacoustic source in a fluid, such as that generated by the absorption of a short laser pulse, are presented. Frequency-wavenumber (k-space) implementations have been used to produce fast and accurate predictions. Model I calculates the field everywhere at any instant of time, and is useful for visualizing the three-dimensional evolution of the wave field. Model II calculates pressure time series for points on a straight line or plane and is therefore useful for simulating array measurements. By mapping the vertical wavenumber spectrum directly to frequency, this model can calculate time series up to 50 times faster than current numerical models of photoacoustic propagation. As the propagating and evanescent parts of the field are calculated separately, model II can be used to calculate far- and near-field radiation patterns. Also, it can readily be adapted to calculate the velocity potential and thus particle velocity and acoustic intensity vectors. Both models exploit the efficiency of the fast Fourier transform, and can include the frequency-dependent directional response of an acoustic detector straightforwardly. The models were verified by comparison with a known analytic solution and a slower, but well-understood, numerical model.
The effects of ignored seabed variability in geoacoustic inversion
Authors: Lapinski Anna-Liesa S. , Chapman David M. F.
Published: June 2005

Geoacoustic inversion using a matched-field inversion algorithm is a well-established technique for estimating the geoacoustic parameters of the seabed. This paper demonstrates how parameter estimation can be affected by unknown or wishfully ignored random range dependence of the true environment when the inversion model is—for practicality—assumed to be range independent. Simulations with controlled statistics were carried out using a simple shallow water model: an isospeed water column over a homogeneous elastic halfspace. The inversion parameters included water depth, compressional speed in the seabed, seabed density, and compressional wave attenuation. On average the environment is range independent: some parameters are constant while other parameters are random with range-independent means and variances. A Parabolic Equation underwater acoustic propagation model is used to calculate the simulated data fields for the range-dependent environment as well as to calculate the model fields for the range-independent inversion model. The Adaptive Simplex Simulated Annealing inversion algorithm is used to estimate the best-fit solution. It is found that ignoring the variability of even a single geoacoustic parameter leads to significant and correlated uncertainty (bias and variance) in the estimation of all inverted parameters. Results are presented for range variation of compressional sound speed and water depth.
Marine mammals and noise: Problems with root mean square sound pressure levels for transients
Authors: Madsen P. T.
Published: June 2005

Current mitigation levels for noise transients impinging on marine mammals are specified by rms pressures. The rms measure critically relies upon choosing the size of averaging window for the squared pressures. Derivation of this window is not standardized, which can lead to 2–12 dB differences in rms sound pressure for the same wave forms. rms pressure does not represent the energy of the noise pulse and it does not prevent exposure to high peak pressures. Safety levels for transients should therefore be given by received peak–peak sound pressure and energy flux density instead of rms sound pressure levels.
Identification of laser generated acoustic waves in the two-dimensional transient response of cylinders
Authors: Pan Y. , Rossignol C. , Audoin B.
Published: June 2005

The published model [Appl. Phys. Lett. 82, 4379–4381 (2003)] for the two-dimensional transient wave propagation in a cylinder is modified to avoid the inherited integration of the numerical inverse scheme. The Fourier series expansion is introduced for one spatial coordinate to resolve the transient response problem: theoretical radial displacements in either the ablation or the thermoelastic regime are obtained with little numerical noise and short computation time. The normal mode expansion method fails to deliver results with the same accuracy. Acoustic waves are fully identified by the ray trajectory analysis. These identified waves are further verified on the experimental results observed with the laser ultrasonic technique.
On the externalization of virtual sound images in headphone reproduction: A Wiener filter approach
Authors: Kim Sang-Myeong , Choi Wonjae
Published: June 2005

In-head localization of sound images is a critical problem in headphone reproduction. The paper investigates the degree of externalization in terms of the distance of auditory images for various synthesis and reproduction cases. An effective binaural headphone system was constructed by way of binaural synthesis using head-related impulse responses and individual headphone equalization using Wiener filter theory. The headphone system designed had an average reproduction performance error of 2.4% for five subjects with a random noise input, and was used to perform some subjective tests with a set of virtual sources equally spaced and distanced from the center of each subject’s head in the horizontal plane. The effects of individual and nonindividual binaural syntheses and those of equalized and nonequalized reproductions were separately investigated. In the tests, each subject was instructed to indicate the distance of auditory images. The results obtained demonstrate that individual equalization is important for externalization, and individual synthesis is important for consistent distance perception. Thus, a combined use of both individual equalization and individual synthesis resulted in externalized sound images of a consistent distance.
Sound transmission across duct constrictions with and without tapered sections
Authors: Lau C. K. , Tang S. K.
Published: June 2005

The sound power transmission loss across duct constrictions with linearly tapered sections is studied with the finite element method. Results show that the acoustic energy distributions of transmitted waves at high frequency depend critically on the exit configuration of the constriction. The corresponding strengths of these waves are very much affected by the entrance setup of the constriction. The difference between inlet and outlet impedance of a constriction leads to weaker resonant sound transmission.
Interferometric studies of a piano soundboard
Authors: Moore Thomas R.
Published: June 2005

Ongoing efforts to understand and model the dynamics of the modern piano are hampered by a lack of understanding of the deflection shapes of the soundboard, which are extremely complicated due to the complex construction. Often deflection shapes of harmonically vibrating objects can be determined using holographic or speckle pattern interferometry, but in practice the stability necessary to implement these methods is difficult to achieve for a large wooden structure such as a piano. We show theoretically and experimentally that the deflection shapes of large objects that are typically too unstable for interferometry can be determined by modifying the common form of the electronic speckle pattern interferometer. Furthermore, using this modified interferometer the decorrelation of the speckle due to ambient vibrations actually enhances the precision of the interferogram. We discuss some interesting observations of the deflection shapes of the soundboard of a fully assembled piano, compare the deflection shapes of the lowest resonances with simple models, and demonstrate how the interferograms can be used to determine the driving point impedance.
Disappearing Arctic Lakes
Authors: Smith L. C. , Sheng Y. , MacDonald G. M. , Hinzman L. D.
Published: June 2005

Historical archived satellite images were compared with contemporary satellite data to track ongoing changes in more than 10,000 large lakes in rapidly warming Siberia. A widespread decline in lake abundance and area has occurred since 1973, despite slight precipitation increases to the region. The spatial pattern of lake disappearance suggests (i) that thaw and "breaching" of permafrost is driving the observed losses, by enabling rapid lake draining into the subsurface; and (ii) a conceptual model in which high-latitude warming of permafrost triggers an initial but transitory phase of lake and wetland expansion, followed by their widespread disappearance.
The Structure of Interleukin-2 Complexed with Its Alpha Receptor
Authors: Rickert Mathias , Wang Xinquan , Boulanger Martin J. , Goriatcheva Natalia , Garcia K. Christopher
Published: June 2005

Interleukin-2 (IL-2) is an immunoregulatory cytokine that binds sequentially to the alpha (IL-2Rα), beta (IL-2Rβ), and common gamma chain (γ
c
) receptor subunits. Here we present the 2.8 angstrom crystal structure of a complex between human IL-2 and IL-2Rα, which interact in a docking mode distinct from that of other cytokine receptor complexes. IL-2Rα is composed of strand-swapped “sushi-like” domains, unlike the classical cytokine receptor fold. As a result of this domain swap, IL-2Rα uses a composite surface to dock into a groove on IL-2 that also serves as a binding site for antagonist drugs. With this complex, we now have representative structures for each class of hematopoietic cytokine receptor–docking modules.
A Fluoroquinolone Resistance Protein from
Mycobacterium tuberculosis
That Mimics DNA
Authors: Hegde Subray S. , Vetting Matthew W. , Roderick Steven L. , Mitchenall Lesley A. , Maxwell Anthony , Takiff Howard E. , Blanchard John S.
Published: June 2005

Fluoroquinolones are gaining increasing importance in the treatment of tuberculosis. The expression of MfpA, a member of the pentapeptide repeat family of proteins from
Mycobacterium tuberculosis
, causes resistance to ciprofloxacin and sparfloxacin. This protein binds to DNA gyrase and inhibits its activity. Its three-dimensional structure reveals a fold, which we have named the right-handed quadrilateral β helix, that exhibits size, shape, and electrostatic similarity to B-form DNA. This represents a form of DNA mimicry and explains both its inhibitory effect on DNA gyrase and fluoroquinolone resistance resulting from the protein's expression in vivo.
Anchorless Prion Protein Results in Infectious Amyloid Disease Without Clinical Scrapie
Authors: Chesebro Bruce , Trifilo Matthew , Race Richard , Meade-White Kimberly , Teng Chao , LaCasse Rachel , Raymond Lynne , Favara Cynthia , Baron Gerald , Priola Suzette , Caughey Byron , Masliah Eliezer , Oldstone Michael
Published: June 2005

In prion and Alzheimer's diseases, the roles played by amyloid versus nonamyloid deposits in brain damage remain unresolved. In scrapie-infected transgenic mice expressing prion protein (PrP) lacking the glycosylphosphatidylinositol (GPI) membrane anchor, abnormal protease-resistant PrPres was deposited as amyloid plaques, rather than the usual nonamyloid form of PrPres. Although PrPres amyloid plaques induced brain damage reminiscent of Alzheimer's disease, clinical manifestations were minimal. In contrast, combined expression of anchorless and wild-type PrP produced accelerated clinical scrapie. Thus, the PrP GPI anchor may play a role in the pathogenesis of prion diseases.
Production of Liquid Alkanes by Aqueous-Phase Processing of Biomass-Derived Carbohydrates
Authors: Huber George W. , Chheda Juben N. , Barrett Christopher J. , Dumesic James A.
Published: June 2005

Liquid alkanes with the number of carbon atoms ranging from C
7
to C
15
were selectively produced from biomass-derived carbohydrates by acid-catalyzed dehydration, which was followed by aldol condensation over solid base catalysts to form large organic compounds. These molecules were then converted into alkanes by dehydration/hydrogenation over bifunctional catalysts that contained acid and metal sites in a four-phase reactor, in which the aqueous organic reactant becomes more hydrophobic and a hexadecane alkane stream removes hydrophobic species from the catalyst before they go on further to form coke. These liquid alkanes are of the appropriate molecular weight to be used as transportation fuel components, and they contain 90% of the energy of the carbohydrate and H
2
feeds.
Gender-Specific Reproductive Tissue in Ratites and
Tyrannosaurus rex
Authors: Schweitzer Mary H. , Wittmeyer Jennifer L. , Horner John R.
Published: June 2005

Unambiguous indicators of gender in dinosaurs are usually lost during fossilization, along with other aspects of soft tissue anatomy. We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of
Tyrannosaurus rex
(Museum of the Rockies specimen number 1125) hindlimb elements, and we hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone. Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs.
Effect of Preslaughter Events on Prevalence of
Campylobacter jejuni
and
Campylobacter coli
in Market-Weight Turkeys
Authors: Wesley Irene V. , Muraoka Wayne T. , Trampel Darrell W. , Hurd H. Scott
Published: June 2005

The effects of events which occur prior to slaughter, such as loading, transport, and holding at an abattoir, on the prevalence of
Campylobacter
species, including
Campylobacter jejuni
and
Campylobacter coli
, were examined. Cloacal swabs from market-weight turkeys in each of five flocks were obtained on a farm prior to loading (time 1; 120 swabs per flock) and after transport and holding at the abattoir (time 2; 120 swabs per flock). A statistically significant increase in the overall prevalence of
Campylobacter
spp. was observed for cloacal swabs obtained from farm 3 following transport (
P
< 0.01). At time 2, an increase in the prevalence of
C. coli
was also noted for cloacal swabs from farms 3, 4, and 5 (
P
< 0.01). Neither the minimum time off of feed nor the distance transported from the farm to the abattoir was correlated with the increase in
C. coli
prevalence. Similarly, responses to an on-farm management questionnaire failed to detect any factors contributing to the observed changes in
Campylobacter
sp. prevalence. A SmaI macrorestriction analysis of
Campylobacter
sp. isolates recovered from flock 5 indicated that
C. coli
was more diverse than
C. jejuni
at both time 1 and time 2 (
P
< 0.01), based on a comparison of the Shannon indices of diversity and evenness.
Presence of GadD1 Glutamate Decarboxylase in Selected
Listeria monocytogenes
Strains Is Associated with an Ability To Grow at Low pH
Authors: Cotter Paul D. , Ryan Sheila , Gahan Cormac G. M. , Hill Colin
Published: June 2005

The glutamate decarboxylase (GAD) system is critical to the survival of
Listeria monocytogenes
LO28 at low-pH stress (<pH 4.0). The GAD system classically involves two proteins, a glutamate decarboxylase enzyme coupled to a glutamate/γ-aminobutyrate antiporter, which results in the consumption of an intracellular proton for each glutamate entering the system. Uniquely among prokaryotes, some strains of
L. monocytogenes
, including strain LO28, possess genes encoding three decarboxylases (
gadD1
,
gadD2
, and
gadD3
) and two antiporters (
gadT1
and
gadT2
). These are organized in two pairs (
gadD1T1
and
gadD2T2
) and a distinct
gadD3
. While the creation of a
gadD3
mutant has not been possible, analysis of 15 isogenic mutants has confirmed previous observations that GadD2/T2 are primarily responsible for surviving severe acid challenge (pH 2.8). However, we have now established that GadD1 plays a major role in growth at mildly acidic pHs (pH 5.1). When strain variation studies revealed that a large number of
L. monocytogenes
strains (including all serotype 4 strains) lack the
gadD1
gadT1
pair, low-pH growth assays were carried out. It was found that the majority of strains that grew poorly at pH 5.1 lacked these genes. The strain-variable ability to grow in mildly acidic conditions may explain why non-serotype 4 strains of
L. monocytogenes
predominate in foods.
Cultivation System Using Glass Beads Immersed in Liquid Medium Facilitates Studies of
Streptomyces
Differentiation
Authors: Nguyen Liem D. , Kalachová Ladislava , Novotná Jana , Holub Martin , Kofroňová Olga , Benada Oldřich , Thompson Charles J. , Weiser Jaroslav
Published: June 2005

A two-phase cultivation system was developed which will enable studies of streptomycete differentiation by molecular biological and global techniques such as transcriptomics and proteomics. The system is based on a solid phase formed by glass beads corresponding to particles in soil, clay, or sand natural habitats of streptomycetes. The beads are immersed in a liquid medium that allows easy modification or replacement of nutrients and growth factors as well as radioactive labeling of proteins. Scanning electron microscopy was used to analyze morphological differentiation of streptomycetes on glass beads and two-dimensional protein electrophoresis to demonstrate the potential of the system for analyses of protein synthesis profiles during the developmental program. This system facilitates studies of differentiation including expression and posttranslation modifications of streptomycetes proteins, secondary metabolite biosynthesis, and morphological development.
Efficacy of Various Pasteurization Time-Temperature Conditions in Combination with Homogenization on Inactivation ofMycobacterium aviumsubsp.paratuberculosisin Milk
Authors: Grant Irene R. , Williams Alan G. , Rowe Michael T. , Muir D. Donald
Published: June 2005

The effect of various pasteurization time-temperature conditions with and without homogenization on the viability ofMycobacterium aviumsubsp.paratuberculosiswas investigated using a pilot-scale commercial high-temperature, short-time (HTST) pasteurizer and raw milk spiked with 101to 105M. aviumsubsp.paratuberculosiscells/ml. ViableM. aviumsubsp.paratuberculosiswas cultured from 27 (3.3%) of 816 pasteurized milk samples overall, 5 on Herrold's egg yolk medium and 22 by BACTEC culture. Therefore, in 96.7% of samples,M. aviumsubsp.paratuberculosishad been completely inactivated by HTST pasteurization, alone or in combination with homogenization. Heat treatments incorporating homogenization at 2,500 lb/in2, applied upstream (as a separate process) or in hold (at the start of a holding section), resulted in significantly fewer culture-positive samples than pasteurization treatments without homogenization (P< 0.001 for those in hold andP< 0.05 for those upstream). Where colony counts were obtained, the number of survivingM. aviumsubsp.paratuberculosiscells was estimated to be 10 to 20 CFU/150 ml, and the reduction in numbers achieved by HTST pasteurization with or without homogenization was estimated to be 4.0 to 5.2 log10. The impact of homogenization on clump size distribution inM. aviumsubsp.paratuberculosisbroth suspensions was subsequently assessed using a Mastersizer X spectrometer. These experiments demonstrated that large clumps ofM. aviumsubsp.paratuberculosiscells were reduced to single-cell or “miniclump” status by homogenization at 2,500 lb/in2. Consequently, when HTST pasteurization was being applied to homogenized milk, theM. aviumsubsp.paratuberculosiscells would have been present as predominantly declumped cells, which may possibly explain the greater inactivation achieved by the combination of pasteurization and homogenization.
Characterization of a Nucleus-Encoded Chitinase from the Yeast
Kluyveromyces lactis
Authors: Colussi Paul A. , Specht Charles A. , Taron Christopher H.
Published: June 2005

Endogenous proteins secreted from
Kluyveromyces lactis
were screened for their ability to bind to or to hydrolyze chitin. This analysis resulted in identification of a nucleus-encoded extracellular chitinase (KlCts1p) with a chitinolytic activity distinct from that of the plasmid-encoded killer toxin α-subunit. Sequence analysis of cloned
KlCTS1
indicated that it encodes a 551-amino-acid chitinase having a secretion signal peptide, an amino-terminal family 18 chitinase catalytic domain, a serine-threonine-rich domain, and a carboxy-terminal type 2 chitin-binding domain. The association of purified KlCts1p with chitin is stable in the presence of high salt concentrations and pH 3 to 10 buffers; however, complete dissociation and release of fully active KlCts1p occur in 20 mM NaOH. Similarly, secreted human serum albumin harboring a carboxy-terminal fusion with the chitin-binding domain derived from KlCts1p also dissociates from chitin in 20 mM NaOH, demonstrating the domain's potential utility as an affinity tag for reversible chitin immobilization or purification of alkaliphilic or alkali-tolerant recombinant fusion proteins. Finally, haploid
K. lactis
cells harboring a
cts1
null mutation are viable but exhibit a cell separation defect, suggesting that KlCts1p is required for normal cytokinesis, probably by facilitating the degradation of septum-localized chitin.
Energy Generation from the CO Oxidation-Hydrogen Production Pathway in
Rubrivivax gelatinosus
Authors: Maness Pin-Ching , Huang Jie , Smolinski Sharon , Tek Vekalet , Vanzin Gary
Published: June 2005

When incubated in the presence of CO gas,
Rubrivivax gelatinosus
CBS induces a CO oxidation-H
2
production pathway according to the stoichiometry CO + H
2
O → CO
2
+ H
2
. Once induced, this pathway proceeds equally well in both light and darkness. When light is not present, CO can serve as the sole carbon source, supporting cell growth anaerobically with a cell doubling time of nearly 2 days. This observation suggests that the CO oxidation reaction yields energy. Indeed, new ATP synthesis was detected in darkness following CO additions to the gas phase of the culture, in contrast to the case for a control that received an inert gas such as argon. When the CO-to-H
2
activity was determined in the presence of the electron transport uncoupler carbonyl-cyanide
m
-chlorophenylhydrazone (CCCP), the rate of H
2
production from CO oxidation was enhanced nearly 40% compared to that of the control. Upon the addition of the ATP synthase inhibitor
N
,
N
′-dicyclohexylcarbodiimide (DCCD), we observed an inhibition of H
2
production from CO oxidation which could be reversed upon the addition of CCCP. Collectively, these data strongly suggest that the CO-to-H
2
reaction yields ATP driven by a transmembrane proton gradient, but the detailed mechanism of this reaction is not yet known. These findings encourage additional research aimed at long-term H
2
production from gas streams containing CO.
Lactobacillus caseiDN-114 001 Inhibits the Ability of Adherent-InvasiveEscherichia coliIsolated from Crohn's Disease Patients To Adhere to and To Invade Intestinal Epithelial Cells
Authors: Ingrassia Isabelle , Leplingard Antony , Darfeuille-Michaud Arlette
Published: June 2005

Ileal lesions in 36.4% of patients with Crohn's disease are colonized by pathogenic adherent-invasiveEscherichia coli. The aim of this study was to determine the in vitro inhibitory effects of the probiotic strain,Lactobacillus caseiDN-114 001, on adhesion to and invasion of human intestinal epithelial cells by adherent-invasiveE. coliisolated from Crohn's disease patients. The experiments were performed with undifferentiated Intestine-407 cells and with undifferentiated or differentiated Caco-2 intestinal epithelial cells. Bacterial adhesion to and invasion of intestinal epithelial cells were assessed by counting CFU. The inhibitory effects ofL. caseiwere determined after coincubation with adherent-invasiveE. colior after preincubation of intestinal cells withL. caseiprior to infection with adherent-invasiveE. coli. Inhibitory effects ofL. caseion adherent-invasiveE. coliadhesion to differentiated and undifferentiated intestinal epithelial cells reached 75% to 84% in coincubation and 43% to 62% in preincubation experiments, according to the cell lines used. Addition ofL. caseiculture supernatant to the incubation medium increasedL. caseiadhesion to intestinal epithelial cells and enhanced the inhibitory effects ofL. casei. The inhibitory effects onE. coliinvasion paralleled those on adhesion. This effect was not due to a bactericidal effect on adherent-invasiveE. colior to a cytotoxic effect on epithelial intestinal cells. AsLactobacillus caseiDN-114 001 strongly inhibits interaction of adherent-invasiveE. coliwith intestinal epithelial cells, this finding suggests that the probiotic strain could be of therapeutic value in Crohn's disease.
Versatile Use oforiCPlasmids for Functional Genomics ofMycoplasma capricolumsubsp.capricolum
Authors: Janis Carole , Lartigue Carole , Frey Joachim , Wróblewski Henri , Thiaucourt François , Blanchard Alain , Sirand-Pugnet Pascal
Published: June 2005

ReplicativeoriCplasmids were recently developed for several mollicutes, including threeMycoplasmaspecies belonging to the mycoides cluster that are responsible for bovine and caprine diseases:Mycoplasma mycoidessubsp.mycoidessmall-colony type,Mycoplasma mycoidessubsp.mycoideslarge-colony type, andMycoplasma capricolumsubsp.capricolum. In this study,oriCplasmids were evaluated inM. capricolumsubsp.capricolumas genetic tools for (i) expression of heterologous proteins and (ii) gene inactivation by homologous recombination. The reporter genelacZ, encoding β-galactosidase, and the gene encoding spiralin, an abundant surface lipoprotein of the related mollicuteSpiroplasma citri, were successfully expressed. FunctionalEscherichia coliβ-galactosidase was detected in transformedMycoplasma capricolumsubsp.capricolumcells despite noticeable codon usage differences. The expression of spiralin inM. capricolumsubsp.capricolumwas assessed by colony and Western blotting. Accessibility of this protein at the cell surface and its partition into the Triton X-114 detergent phase suggest a correct maturation of the spiralin precursor. The expression of a heterologous lipoprotein in a mycoplasma raises potentially interesting applications, e.g., the use of these bacteria as live vaccines. Targeted inactivation of genelppAencoding lipoprotein A was achieved inM. capricolumsubsp.capricolumwith plasmids harboring a replication origin derived fromS. citri. Our results suggest that the selection of the infrequent events of homologous recombination could be enhanced by the use oforiCplasmids derived from related mollicute species. Mycoplasma gene inactivation opens the way to functional genomics in a group of bacteria for which a large wealth of genome data are already available and steadily growing.
Mapping of Neutralizing Epitopes on
Renibacterium salmoninarum
p57 by Use of Transposon Mutagenesis and Synthetic Peptides
Authors: Wiens Gregory D. , Owen Jennifer
Published: June 2005

Renibacterium salmoninarum
is a gram-positive bacterium that causes bacterial kidney disease in salmonid fish. The virulence mechanisms of
R. salmoninarum
are not well understood. Production of a 57-kDa protein (p57) has been associated with isolate virulence and is a diagnostic marker for
R. salmoninarum
infection. Biological activities of p57 include binding to eukaryotic cells and immunosuppression. We previously isolated three monoclonal antibodies (4D3, 4C11, and 4H8) that neutralize p57 activity. These monoclonal antibodies (MAbs) bind to the amino-terminal region of p57 between amino acids 32 though 243; however, the precise locations of the neutralizing epitopes were not determined. Here, we use transposon mutagenesis to map the 4D3, 4C11, and 4H8 epitopes. Forty-five transposon mutants were generated and overexpressed in
Escherichia coli
BL21(DE3). The ability of MAbs 4D3, 4H8, and 4C11 to bind each mutant protein was assessed by immunoblotting. Transposons inserting between amino acids 51 and 112 disrupted the 4H8 epitope. Insertions between residues 78 and 210 disrupted the 4C11 epitope, while insertions between amino acids 158 and 234 disrupted the 4D3 epitope. The three MAbs failed to bind overlapping, 15-mer peptides spanning these regions, suggesting that the epitopes are discontinuous in conformation. We conclude that recognition of secondary structure on the amino terminus of p57 is important for neutralization. The epitope mapping studies suggest directions for improvement of MAb-based immunoassays for detection of
R. salmoninarum
-infected fish.
Cloning and Characterization of the Glucosidase II Alpha Subunit Gene of
Trichoderma reesei
: a Frameshift Mutation Results in the Aberrant Glycosylation Profile of the Hypercellulolytic Strain Rut-C30
Authors: Geysens Steven , Pakula Tiina , Uusitalo Jaana , Dewerte Isabelle , Penttilä Merja , Contreras Roland
Published: June 2005

We describe isolation and characterization of the gene encoding the glucosidase II alpha subunit (GIIα) of the industrially important fungus
Trichoderma reesei
. This subunit is the catalytic part of the glucosidase II heterodimeric enzyme involved in the structural modification within the endoplasmic reticulum (ER) of N-linked oligosaccharides present on glycoproteins. The gene encoding GIIα (
gls2
α) in the hypercellulolytic strain Rut-C30 contains a frameshift mutation resulting in a truncated gene product. Based on the peculiar monoglucosylated N-glycan pattern on proteins produced by the strain, we concluded that the truncated protein can still hydrolyze the first α-1,3-linked glucose residue but not the innermost α-1,3-linked glucose residue from the Glc
2
Man
9
GlcNAc
2
N-glycan ER structure. Transformation of the Rut-C30 strain with a repaired
T. reesei gls2
α gene changed the glycosylation profile significantly, decreasing the amount of monoglucosylated structures and increasing the amount of high-mannose N-glycans. Full conversion to high-mannose carbohydrates was not obtained, and this was probably due to competition between the endogenous mutant subunit and the introduced wild-type GIIα protein. Since glucosidase II is also involved in the ER quality control of nascent polypeptide chains, its transcriptional regulation was studied in a strain producing recombinant tissue plasminogen activator (tPA) and in cultures treated with the stress agents dithiothreitol (DTT) and brefeldin A (BFA), which are known to block protein transport and to induce the unfolded protein response. While the mRNA levels were clearly upregulated upon tPA production or BFA treatment, no such enhancement was observed after DTT addition.
Accelerated Sulfur Cycle in Coastal Marine Sediment beneath Areas of Intensive Shellfish Aquaculture
Authors: Asami Hiroki , Aida Masato , Watanabe Kazuya
Published: June 2005

Prokaryotes in marine sediments taken from two neighboring semienclosed bays (the Yamada and Kamaishi bays) at the Sanriku coast in Japan were investigated by the culture-independent molecular phylogenetic approach coupled with chemical and activity analyses. These two bays were chosen in terms of their similar hydrogeological and chemical characteristics but different usage modes; the Yamada bay has been used for intensive shellfish aquaculture, while the Kamaishi bay has a commercial port and is not used for aquaculture. Substantial differences were found in the phylogenetic composition of 16S rRNA gene clone libraries constructed for the Yamada and Kamaishi sediments. In the Yamada library, phylotypes affiliated with δ
-Proteobacteria
were the most abundant, and those affiliated with γ
-Proteobacteria
were the second-most abundant. In contrast, the Kamaishi library was occupied by phylotypes affiliated with
Planctomycetes
, γ
-Proteobacteria
, δ
-Proteobacteria
, and
Crenarchaeota
. In the γ
-Proteobacteria
, many Yamada phylotypes were related to free-living and symbiotic sulfur oxidizers, whereas the Kamaishi phylotype was related to the genus
Pseudomonas
. These results allowed us to hypothesize that sulfate-reducing and sulfur-oxidizing bacteria have become abundant in the Yamada sediment. This hypothesis was supported by quantitative competitive PCR (qcPCR) with group-specific primers. The qcPCR also suggested that organisms closely related to
Desulfotalea
in the
Desulfobulbaceae
were the major sulfate-reducing bacteria in these sediments. In addition, potential sulfate reduction and sulfur oxidation rates in the sediment samples were determined, indicating that the sulfur cycle has become active in the Yamada sediment beneath the areas of intensive shellfish aquaculture.
FLO11-Based Model for Air-Liquid Interfacial Biofilm Formation bySaccharomyces cerevisiae
Authors: Zara Severino , Bakalinsky Alan T. , Zara Giacomo , Pirino Giorgia , Demontis Maria Antonietta , Budroni Marilena
Published: June 2005

Sardinian wine strains ofSaccharomyces cerevisiaeused to make sherry-like wines form a biofilm at the air-liquid interface at the end of ethanolic fermentation, when grape sugar is depleted and further growth becomes dependent on access to oxygen. Here, we show thatFLO11, which encodes a hydrophobic cell wall glycoprotein, is required for the air-liquid interfacial biofilm and that biofilm cells have a buoyant density greater than the suspending medium. We propose a model for biofilm formation based on an increase in cell surface hydrophobicity occurring at the diauxic shift. This increase leads to formation of multicellular aggregates that effectively entrap carbon dioxide, providing buoyancy. A visible biofilm appears when a sufficient number of hydrophobic cell aggregates are carried to and grow on the liquid surface.
Influence of Stress on Individual Lag Time Distributions of
Listeria monocytogenes
Authors: Guillier L. , Pardon P. , Augustin J.-C.
Published: June 2005

The effects of nine common food industry stresses on the times to the turbidity (
T
d
) distribution of
Listeria monocytogenes
were determined. It was established that the main source of the variability of
T
d
for stressed cells was the variability of individual lag times. The distributions of
T
d
revealed that there was a noticeable difference in response to the stresses encountered by the
L. monocytogenes
cells. The applied stresses led to significant changes of the shape, the mean, and the variance of the distributions. The variance of
T
d
of wells inoculated with single cells issued from a culture in the exponential growth phase was multiplied by at least 6 and up to 355 for wells inoculated with stressed cells. These results suggest stress-induced variability may be important in determining the reliability of predictive microbiological models.