bluuebunny/crossref_metadata_2025 huggingface dataset:
A localization algorithm based on head-related transfer functions
Authors: MacDonald Justin A.
Published: June 2008

Two sound localization algorithms based on the head-related transfer function were developed. Each of them uses the interaural time delay, interaural level difference, and monaural spectral cues to estimate the location of a sound source. Given that most localization algorithms will be required to function in background noise, the localization performance of one of the algorithms was tested at signal-to-noise ratios (SNRs) from 40to−40dB. Stimuli included ten real-world, broadband sounds located at 5° intervals in azimuth and at 0° elevation. Both two- and four-microphone versions of the algorithm were implemented to localize sounds to 5° precision. The two-microphone version of the algorithm exhibited less than 2° mean localization error at SNRs of 20dB and greater, and the four-microphone version committed approximately 1° mean error at SNRs of 10dB or greater. Potential enhancements and applications of the algorithm are discussed.
Distortion product otoacoustic emission fine structure is responsible for variability of distortion product otoacoustic emission contralateral suppression
Authors: Sun Xiao-Ming
Published: June 2008

Alteration of the distortion product otoacoustic emission (DPOAE) level by a contralateral sound, which is known as DPOAE contralateral suppression, has been attributed to the feedback mechanism of the medial olivocochlear efferents. However, the limited dynamic range and large intra- and intersubject variabilities in the outcome of the measurement restrict its application in assessing the efferent function. In this study, the 2f1−f2 DPgram was measured with a high frequency resolution in six human ears, which exhibits a fine structure with the quasiperiodic appearance of peaks and dips. In the presence of contralateral noise, the DPOAE level increased, decreased, or remained unchanged depending on the frequency. At the peaks, DPOAEs were mostly suppressed with a larger change, while those at the dips had greater variance, with increased occurrence of enhancement or no change. The difference between the peak and dip frequencies in the DPOAE-level change was significant. A switch from suppression to enhancement of the DPOAE level or vice versa with a small change in frequency was noted. These results imply that the DPOAE fine structure is a main source of the variability in DPOAE contralateral suppression measurement. The study suggests that the DPOAE contralateral suppression test would be improved if it is conducted for frequencies at major peaks of the DPOAE fine structure.
The effect of visual and auditory cues on seat preference in an opera theater
Authors: Jeon Jin Yong , Kim Yong Hee , Cabrera Densil , Bassett John
Published: June 2008

Opera performance conveys both visual and auditory information to an audience, and so opera theaters should be evaluated in both domains. This study investigates the effect of static visual and auditory cues on seat preference in an opera theater. Acoustical parameters were measured and visibility was analyzed for nine seats. Subjective assessments for visual-only, auditory-only, and auditory-visual preferences for these seat positions were made through paired-comparison tests. In the cases of visual-only and auditory-only subjective evaluations, preference judgment tests on a rating scale were also employed. Visual stimuli were based on still photographs, and auditory stimuli were based on binaural impulse responses convolved with a solo tenor recording. For the visual-only experiment, preference is predicted well by measurements taken related to the angle of seats from the theater midline at the center of the stage, the size of the photographed stage view, the visual obstruction, and the distance from the stage. Sound pressure level was the dominant predictor of auditory preference in the auditory-only experiment. In the cross-modal experiments, both auditory and visual preferences were shown to contribute to overall impression, but auditory cues were more influential than the static visual cues. The results show that both a positive visual-only or a positive auditory-only evaluations positively contribute to the assessments of seat quality.
Doppler-shift compensation behavior by Wagner’s mustached bat, Pteronotus personatus
Authors: Smotherman Michael , Guillén-Servent Antonio
Published: June 2008

Doppler-shift compensation behavior (DSC) is a highly specialized vocal response displayed by bats that emit pulses with a prominent constant frequency (CF) component and adjust the frequency of their CF component to compensate for flight-speed induced Doppler shifts in the frequency of the returning echoes. DSC has only been observed in one member of the Neotropical Mormoopidae, a family of bats that use pulses with prominent CF components, leading researchers to suspect that DSC is a uniquely derived trait in the single species Pteronotus parnellii. Yet recent phylogenetic data indicate that the lineage of P. parnellii originates from the most basal node in the evolutionary history of the genus Pteronotus. DSC behavior was investigated in another member of this family, Pteronotus personatus, because molecular data indicated that this species stems from the second most basal node in Pteronotus. DSC was tested for by swinging the bats on a pendulum. P. personatus performed DSC as well as P. parnellii under identical conditions. Two other closely related mormoopids, Pteronotus davyi and Mormoops megalophylla, were also tested and neither shifted the peak frequency of their pulses. These results shed light on the evolutionary history of DSC among the mormoopids.
A finite difference analysis of the field present behind an acoustically impenetrable two-layer barrier
Authors: Hurrell Andrew M.
Published: June 2008

The interaction of an incident sound wave with an acoustically impenetrable two-layer barrier is considered. Of particular interest is the presence of several acoustic wave components in the shadow region of this barrier. A finite difference model capable of simulating this geometry is validated by comparison to the analytical solution for an idealized, hard-soft barrier. A panel comprising a high air-content closed cell foam backed with an elastic (metal) back plate is then examined. The insertion loss of this panel was found to exceed the dynamic range of the measurement system and was thus acoustically impenetrable. Experimental results from such a panel are shown to contain artifacts not present in the diffraction solution, when acoustic waves are incident upon the soft surface. A finite difference analysis of this experimental configuration replicates the presence of the additional field components. Furthermore, the simulated results allow the additional components to be identified as arising from the S0 and A0 Lamb modes traveling in the elastic plate. These Lamb mode artifacts are not found to be present in the shadow region when the acoustic waves are incident upon the elastic surface.
The effect of a precursor on growth of forward masking
Authors: Krull Vidya , Strickland Elizabeth A.
Published: June 2008

This study examined the effect of an on-frequency precursor on growth-of-masking (GOM) functions measured using an off-frequency masker. The signal was a 6-ms, 4-kHz tone. A GOM function was measured using a 40-ms, 2.8-kHz tone (the off-frequency masker). GOM functions were then measured with an on-frequency, fixed level precursor presented before the off-frequency masker. The precursor was 50 or 60dB SPL, and 160ms in duration. For the 60-dB SPL precursor, a 40-ms duration was also used. Two-line functions were fit to the GOM data to estimate the basilar membrane input-output function. The precursors reduced the gain of the input-output function, and this decrease was graded with precursor level. Both precursor durations had the same effect on gain. Changes in masking following a precursor were larger than would be predicted by additivity of masking. The observed decrease in gain may be consistent with activation of the medial olivocochlear reflex by the precursor.
Phrase boundary effects on the temporal kinematics of sequential tongue tip consonants
Authors: Byrd Dani , Lee Sungbok , Campos-Astorkiza Rebeka
Published: June 2008

This study evaluates the effects of phrase boundaries on the intra- and intergestural kinematic characteristics of blended gestures, i.e., overlapping gestures produced with a single articulator. The sequences examined are the juncture geminate [d(#)d], the sequence [d(#)z], and, for comparison, the singleton tongue tip gesture in [d(#)b]. This allows the investigation of the process of gestural aggregation [Munhall, K. G., and Löfqvist, A. (1992). “Gestural aggregation in speech: laryngeal gestures,” J. Phonetics 20, 93–110] and the manner in which it is affected by prosodic structure. Juncture geminates are predicted to be affected by prosodic boundaries in the same way as other gestures; that is, they should display prosodic lengthening and lesser overlap across a boundary. Articulatory prosodic lengthening is also investigated using a signal alignment method of the functional data analysis framework [Ramsay, J. O., and Silverman, B. W. (2005). Functional Data Analysis, 2nd ed. (Springer-Verlag, New York)]. This provides the ability to examine a time warping function that characterizes relative timing difference (i.e., lagging or advancing) of a test signal with respect to a given reference, thus offering a way of illuminating local nonlinear deformations at work in prosodic lengthening. These findings are discussed in light of the π-gesture framework of Byrd and Saltzman [(2003) “The elastic phrase: Modeling the dynamics of boundary-adjacent lengthening,” J. Phonetics 31, 149–180].
On the influence of spatial correlations on sound propagation in concentrated solutions of rigid particles
Authors: Baudoin Michael , Thomas Jean-Louis , Coulouvrat François
Published: June 2008

In a previous paper [J. Acoust. Soc. Am. 121, 3386–3387 (2007)], a self-consistent effective medium theory has been used to account for hydrodynamic interactions between neighboring rigid particles, which considerably affect the sound propagation in concentrated solutions. However, spatial correlations were completely left out in this model. They correspond to the fact that the presence of one particle at a given position locally affects the location of the other ones. In the present work, the importance of such correlations is demonstrated within a certain frequency range and particle concentration. For that purpose, spatial correlations are integrated in our two-phase formulation by using a closure scheme similar to the one introduced by Spelt et al. [‘‘Attenuation of sound in concentrated suspensions theory and experiments,” J. Fluid Mech. 430, 51–86 (2001)]. Then, the effect is shown through a careful comparison of the results obtained with this model, the ones obtained with different self-consistent approximations and the experiments performed by Hipp et al. [“Acoustical characterization of concentrated suspensions and emulsions. 2. Experimental validation,” Langmuir, 18, 391–404 (2002)]. With the present formulation, an excellent agreement is reached for all frequencies (within the limit of the long wavelength regime) and for concentrations up to 30% without any adjustable parameter.
Customization of the acoustic field produced by a piezoelectric array through interelement delays
Authors: Chitnis Parag V. , Barbone Paul E. , Cleveland Robin O.
Published: June 2008

A method for producing a prescribed acoustic pressure field from a piezoelectric array was investigated. The array consisted of 170 elements placed on the inner surface of a 15cm radius spherical cap. Each element was independently driven by using individual pulsers each capable of generating 1.2kV. Acoustic field customization was achieved by independently controlling the time when each element was excited. The set of time delays necessary to produce a particular acoustic field was determined by using an optimization scheme. The acoustic field at the focal plane was simulated by using the angular spectrum method, and the optimization searched for the time delays that minimized the least squared difference between the magnitudes of the simulated and desired pressure fields. The acoustic field was shaped in two different ways: the −6dB focal width was increased to different desired widths and the ring-shaped pressure distributions of various prescribed diameters were produced. For both cases, the set of delays resulting from the respective optimization schemes were confirmed to yield the desired pressure distributions by using simulations and measurements. The simulations, however, predicted peak positive pressures roughly half those obtained from the measurements, which was attributed to the exclusion of nonlinearity in the simulations.
Evidence for spatial representation of object shape by echolocating bats (Eptesicus fuscus)
Authors: DeLong Caroline M. , Bragg Rebecca , Simmons James A.
Published: June 2008

Big brown bats were trained in a two-choice task to locate a two-cylinder dipole object with a constant 5cm spacing in the presence of either a one-cylinder monopole or another two-cylinder dipole with a shorter spacing. For the dipole versus monopole task, the objects were either stationary or in motion during each trial. The dipole and monopole objects varied from trial to trial in the left-right position while also roving in range (10–40cm), cross range separation (15–40cm), and dipole aspect angle (0°–90°). These manipulations prevented any single feature of the acoustic stimuli from being a stable indicator of which object was the correct choice. After accounting for effects of masking between echoes from pairs of cylinders at similar distances, the bats discriminated the 5cm dipole from both the monopole and dipole alternatives with performance independent of aspect angle, implying a distal, spatial object representation rather than a proximal, acoustic object representation.
Passive acoustic detection and localization of whales: Effects of shipping noise in Saguenay–St. Lawrence Marine Park
Authors: Simard Yvan , Roy Nathalie , Gervaise Cédric
Published: June 2008

The performance of large-aperture hydrophone arrays to detect and localize blue and fin whales’ 15–85Hz signature vocalizations under ocean noise conditions was assessed through simulations from a normal mode propagation model combined to noise statistics from 15960h of recordings in Saguenay–St. Lawrence Marine Park. The probability density functions of 2482 summer noise level estimates in the call bands were used to attach a probability of detection/masking to the simulated call levels as a function of whale depth and range for typical environmental conditions. Results indicate that call detection was modulated by the calling depth relative to the sound channel axis and by modal constructive and destructive interferences with range. Masking of loud infrasounds could reach 40% at 30km for a receiver at the optimal depth. The 30dB weaker blue whale D-call were subject to severe masking. Mapping the percentages of detection and localization allowed assessing the performance of a six-hydrophone array under mean- and low-noise conditions. This approach is helpful for optimizing hydrophone configuration in implementing passive acoustic monitoring arrays and building their detection function for whale density assessment, as an alternative to or in combination with the traditional undersampling visual methods.
Monaural level discrimination under dichotic conditions
Authors: Shub Daniel E. , Durlach Nathaniel I. , Colburn H. Steven
Published: June 2008

The ability to make judgments about the stimulus at one ear when a stimulus is simultaneously presented to the other ear was tested. Specifically, subjects discriminated the level of a 600Hz target tone presented at the left ear while an identical-frequency distractor was simultaneously presented at the other ear. When there was no distractor, threshold was 0.7dB. Threshold increased to 1.1dB when a distractor with a fixed phase and level was introduced contra-aurally to the target. Further increases in threshold were observed when an across-presentation variability was introduced into the distractor phase (threshold of 1.6dB) or level (threshold of 5.8dB). When both the distractor level and phase varied, the largest threshold of 7.3dB was obtained. These increases in threshold cannot be predicted by common binaural models, which assume that a target stimulus at one ear can be processed without interference from the stimulus at the nontarget ear. The measured thresholds are consistent with a model that utilizes two binaural dimensions that roughly correspond to the loudness and the position of a fused binaural image. The results show that, with binaurally fused tonal stimuli, subjects are unable to listen to one ear.
Predicting absorption and dispersion in acoustics by direct simulation Monte Carlo: Quantum and classical models for molecular relaxation
Authors: Hanford Amanda D. , O’Connor Patrick D. , Anderson James B. , Long Lyle N.
Published: June 2008

In the current study, real gas effects in the propagation of sound waves are simulated using the direct simulation Monte Carlo method for a wide range of frequencies. This particle method allows for treatment of acoustic phenomena at high Knudsen numbers, corresponding to low densities and a high ratio of the molecular mean free path to wavelength. Different methods to model the internal degrees of freedom of diatomic molecules and the exchange of translational, rotational and vibrational energies in collisions are employed in the current simulations of a diatomic gas. One of these methods is the fully classical rigid-rotor/harmonic-oscillator model for rotation and vibration. A second method takes into account the discrete quantum energy levels for vibration with the closely spaced rotational levels classically treated. This method gives a more realistic representation of the internal structure of diatomic and polyatomic molecules. Applications of these methods are investigated in diatomic nitrogen gas in order to study the propagation of sound and its attenuation and dispersion along with their dependence on temperature. With the direct simulation method, significant deviations from continuum predictions are also observed for high Knudsen number flows.
Identification and discrimination of bilingual talkers across languages
Authors: Winters Stephen J. , Levi Susannah V. , Pisoni David B.
Published: June 2008

This study investigated the extent to which language familiarity affects the perception of the indexical properties of speech by testing listeners’ identification and discrimination of bilingual talkers across two different languages. In one experiment, listeners were trained to identify bilingual talkers speaking in only one language and were then tested on their ability to identify the same talkers speaking in another language. In the second experiment, listeners discriminated between bilingual talkers across languages in an AX discrimination paradigm. The results of these experiments indicate that there is sufficient language-independent indexical information in speech for listeners to generalize knowledge of talkers’ voices across languages and to successfully discriminate between bilingual talkers regardless of the language they are speaking. However, the results of these studies also revealed that listeners do not solely rely on language-independent information when performing these tasks. Listeners use language-dependent indexical cues to identify talkers who are speaking a familiar language. Moreover, the tendency to perceive two talkers as the “same” or “different” depends on whether the talkers are speaking in the same language. The combined results of these experiments thus suggest that indexical processing relies on both language-dependent and language-independent information in the speech signal.
Cross ΨB-energy operator-based signal detection
Authors: Boudraa Abdel-Ouahab , Cexus Jean-Christophe , Abed-Meraim Karim
Published: June 2008

In this paper, two methods for signal detection and time-delay estimation based on the cross ΨB-energy operator are proposed. These methods are well suited for mono-component AM-FM signals. The ΨB energy operator measures how much one signal is present in another one. The peak of the ΨB operator corresponds to the maximum of interaction between the two signals. Compared to the cross-correlation function, the ΨB operator includes temporal information and relative changes of the signal which are reflected in its first and second derivatives. The discrete version of the continuous-time form of the ΨB operator, which is used in its implementation, is presented. The methods are illustrated on synthetic and real signals and the results compared to those of the matched filter and the cross correlation. The real signals correspond to impulse responses of buried objects obtained by active sonar in iso-speed single path environments.
The acoustical cues to sound location in the rat: Measurements of directional transfer functions
Authors: Koka Kanthaiah , Read Heather L. , Tollin Daniel J.
Published: June 2008

The acoustical cues for sound location are generated by spatial- and frequency-dependent filtering of propagating sound waves by the head and external ears. Although rats have been a common model system for anatomy, physiology, and psychophysics of localization, there have been few studies of the acoustical cues available to rats. Here, directional transfer functions (DTFs), the directional components of the head-related transfer functions, were measured in six adult rats. The cues to location were computed from the DTFs. In the frontal hemisphere, spectral notches were present for frequencies from ∼16to30kHz; in general, the frequency corresponding to the notch increased with increases in source elevation and in azimuth toward the ipsilateral ear. The maximum high-frequency envelope-based interaural time differences (ITDs) were 130μs, whereas low-frequency (<3.5kHz) fine-structure ITDs were 160μs; both types of ITDs were larger than predicted from spherical head models. Interaural level differences (ILDs) strongly depended on location and frequency. Maximum ILDs were <10dB for frequencies <8kHz and were as large as 20–40dB for frequencies >20kHz. Removal of the pinna eliminated the spectral notches, reduced the acoustic gain and ILDs, altered the acoustical axis, and reduced the ITDs.
Testing a theory of aircraft noise annoyance: A structural equation analysis
Authors: Kroesen Maarten , Molin Eric J. E. , van Wee Bert
Published: June 2008

Previous research has stressed the relevance of nonacoustical factors in the perception of aircraft noise. However, it is largely empirically driven and lacks a sound theoretical basis. In this paper, a theoretical model which explains noise annoyance based on the psychological stress theory is empirically tested. The model is estimated by applying structural equation modeling based on data from residents living in the vicinity of Amsterdam Airport Schiphol in The Netherlands. The model provides a good model fit and indicates that concern about the negative health effects of noise and pollution, perceived disturbance, and perceived control and coping capacity are the most important variables that explain noise annoyance. Furthermore, the model provides evidence for the existence of two reciprocal relationships between (1) perceived disturbance and noise annoyance and (2) perceived control and coping capacity and noise annoyance. Lastly, the model yielded two unexpected results. Firstly, the variables noise sensitivity and fear related to the noise source were unable to explain additional variance in the endogenous variables of the model and were therefore excluded from the model. And secondly, the size of the total effect of noise exposure on noise annoyance was relatively small. The paper concludes with some recommended directions for further research.
A spectral/temporal method for robust fundamental frequency tracking
Authors: Zahorian Stephen A. , Hu Hongbing
Published: June 2008

In this paper, a fundamental frequency (F0) tracking algorithm is presented that is extremely robust for both high quality and telephone speech, at signal to noise ratios ranging from clean speech to very noisy speech. The algorithm is named “YAAPT,” for “yet another algorithm for pitch tracking.” The algorithm is based on a combination of time domain processing, using the normalized cross correlation, and frequency domain processing. Major steps include processing of the original acoustic signal and a nonlinearly processed version of the signal, the use of a new method for computing a modified autocorrelation function that incorporates information from multiple spectral harmonic peaks, peak picking to select multiple F0 candidates and associated figures of merit, and extensive use of dynamic programming to find the “best” track among the multiple F0 candidates. The algorithm was evaluated by using three databases and compared to three other published F0 tracking algorithms by using both high quality and telephone speech for various noise conditions. For clean speech, the error rates obtained are comparable to those obtained with the best results reported for any other algorithm; for noisy telephone speech, the error rates obtained are lower than those obtained with other methods.
Identification of some perceptual dimensions underlying loudspeaker dissimilarities
Authors: Lavandier Mathieu , Meunier Sabine , Herzog Philippe
Published: June 2008

This study investigated the dimensions underlying perceived differences between loudspeakers. Listeners compared the sound reproduction of 12 loudspeakers in a room, using three musical excerpts. For the loudspeakers to be compared one just after the other in exactly the same conditions, the sounds radiated by the loudspeakers were recorded in a listening room, and the recorded sounds were submitted to paired comparisons using headphones. The resulting perceptual dissimilarities were analyzed by using a multidimensional scaling technique, revealing two main perceptual dimensions used by listeners to discriminate the loudspeakers. These dimensions were identical for the three musical excerpts. As the signals heard by listeners were directly accessible, they were used to define acoustical attributes describing the perceptual dimensions. Instead of arbitrarily choosing one acoustical analysis to define these attributes, several analyses were compared. The temporal, spectral, and time-frequency domains were investigated, and different auditory models were tested. These auditory models allowed the best description of the differences perceived by listeners, and were used to define two acoustical attributes describing our perceptual dimensions: the bass/treble balance and the medium emergence.
Selective acoustic cues for French voiceless stop consonants
Authors: Bonneau Anne , Laprie Yves
Published: June 2008

The objective of this study is to define selective cues that identify only certain realizations of a feature, more precisely the place of articulation of French unvoiced stops, but have every realization identified with a very high level of confidence. The method is based on the delimitation of “distinctive regions” for well chosen acoustic criteria, which contains some exemplars of a feature and (almost) no other exemplar of any other feature in competition. Selective cues, which correspond to distinctive regions, must not be combined with less reliable acoustic cues and their evaluation should be done on reliable elementary acoustic detector outputs. A set of selective cues has been defined for the identification of the place of /p,t,k/, and then tested on a corpus of sentences. The cues were estimated from formant transitions and the transient segment (an automatic segmentation of the transient part of the burst has been designed). About 38% of the feature realizations have been identified by selective cues on the basis of their very distinctive patterns. The error rate, which constitutes the crucial test of our approach, was 0.7%. This opens the way to interesting applications for the improvement of oral comprehension, lexical access, or automatic speech recognition.
Duration differences in the articulation and acoustics of Swiss German word-initial geminate and singleton stops
Authors: Kraehenmann Astrid , Lahiri Aditi
Published: June 2008

Stops in Swiss German contrast only in quantity in all word positions; aspiration and voicing play no role. As in most languages with consonant quantity contrast, geminate stops are produced with significantly longer closure duration (CD) than singletons in an intersonorant context. This holds word medially as well as phrase medially, e.g., [oni tto:sə] “without roar” versus [oni to:sə] “without can.” Since the stops are voiceless, no CD cue distinguishes geminates from singletons phrase initially. Nevertheless, do speakers utilize articulatory means to maintain the contrast? By using electropalatography, the articulatory and acoustic properties of word-initial alveolar stops were investigated in phrase-initial and phrase-medial contexts. The results are threefold. First, as expected, CD and contact duration of the articulators mirror each other within a phrase: Geminates are longer than singletons. Second, phrase initially, the contact data unequivocally establish a quantity distinction. This means that—even without acoustic CD cues for perception—geminates are articulated with substantially longer oral closure than singletons. Third, stops are longer in phrase-initial than phrase-medial position, indicating articulatory strengthening. Nevertheless, the difference between geminates and singletons phrase initially is proportionately less than in phrase-medial position.
A method of measuring the Green’s function in an enclosure
Authors: Luan Yu , Jacobsen Finn
Published: June 2008

The acoustic Green’s function can be measured using a device with two matched microphones mounted in a tube driven by a loudspeaker combined with another microphone that represents the observation point. Good agreement is obtained between the measured and theoretical Green’s function in a rectangular room below 320Hz. At higher frequencies the agreement is less good because of the imperfect geometry of the room.
Genome Sequence and Characteristics of Lrm1, a Prophage from Industrial
Lactobacillus rhamnosus
Strain M1
Authors: Durmaz Evelyn , Miller Michael J. , Azcarate-Peril M. Andrea , Toon Stephen P. , Klaenhammer Todd R.
Published: June 2008

Prophage Lrm1 was induced with mitomycin C from an industrial
Lactobacillus rhamnosus
starter culture, M1. Electron microscopy of the lysate revealed relatively few intact bacteriophage particles among empty heads and disassociated tails. The defective
Siphoviridae
phage had an isometric head of approximately 55 nm and noncontractile tail of about 275 nm with a small baseplate. In repeated attempts, the prophage could not be cured from
L. rhamnosus
M1, nor could a sensitive host be identified. Sequencing of the phage Lrm1 DNA revealed a genome of 39,989 bp and a G+C content of 45.5%. A similar genomic organization and mosaic pattern of identities align Lrm1 among the closely related
Lactobacillus casei
temperate phages A2, ΦAT3, and LcaI and with
L. rhamnosus
virulent phage Lu-Nu. Of the 54 open reading frames (ORFs) identified, all but 8 shared homology with other phages of this group. Five unknown ORFs were identified that had no homologies in the databases nor predicted functions. Notably, Lrm1 encodes a putative endonuclease and a putative DNA methylase with homology to a methylase in
Lactococcus lactis
phage Tuc2009. Possibly, the DNA methylase, endonuclease, or other Lrm1 genes provide a function crucial to
L. rhamnosus
M1 survival, resulting in the stability of the defective prophage in its lysogenic state. The presence of a defective prophage in an industrial strain could provide superinfection immunity to the host but could also contribute DNA in recombination events to produce new phages potentially infective for the host strain in a large-scale fermentation environment.
Babesia
Species Occurring in Austrian
Ixodes ricinus
Ticks
Authors: Blaschitz Marion , Narodoslavsky-Gföller Melanie , Kanzler Michaela , Stanek Gerold , Walochnik Julia
Published: June 2008

Babesiosis is a tick-transmitted disease of veterinary and medical importance. The first Austrian case of human babesiosis was recently recorded. In the current study, ticks at all life cycle stages (instars), including 853
Ixodes ricinus
and 11
Haemaphysalis concinna
ticks, from sampling sites throughout Austria were examined for the presence of
Babesia
spp. by using 18S rRNA gene PCR and sequencing, and the overall mean infection rate was 51.04%. The infection rates for sampling sites were highly variable, ranging from 0% to almost 100%. Different instars and different sexes were infected almost equally.
Babesia
isolates occurring in Austrian ticks were identified as
Babesia divergens
,
Babesia divergens
-like, and
Babesia
sp. strain DD by sequencing a fragment of the heat shock protein 70 gene and internal transcribed spacer regions 1 and 2. To our knowledge, this is the first investigation of
Babesia
spp. in Austrian ticks.
Analysis of the Genome Sequence ofLactobacillus gasseriATCC 33323 Reveals the Molecular Basis of an Autochthonous Intestinal Organism
Authors: Azcarate-Peril M. Andrea , Altermann Eric , Goh Yong Jun , Tallon Richard , Sanozky-Dawes Rosemary B. , Pfeiler Erika A. , O'Flaherty Sarah , Buck B. Logan , Dobson Alleson , Duong Tri , Miller Michael J. , Barrangou Rodolphe , Klaenhammer Todd R.
Published: June 2008

This study presents the complete genome sequence ofLactobacillus gasseriATCC 33323, a neotype strain of human origin and a native species found commonly in the gastrointestinal tracts of neonates and adults. The plasmid-free genome was 1,894,360 bp in size and predicted to encode 1,810 genes. The GC content was 35.3%, similar to the GC content of its closest relatives,L. johnsoniiNCC 533 (34%) andL. acidophilusNCFM (34%). Two identical copies of the prophage LgaI (40,086 bp), of the Sfi11-likeSiphoviridaephage family, were integrated tandomly in the chromosome. A number of unique features were identified in the genome ofL. gasserithat were likely acquired by horizontal gene transfer and may contribute to the survival of this bacterium in its ecological niche.L. gasseriencodes two restriction and modification systems, which may limit bacteriophage infection.L. gasserialso encodes an operon for production of heteropolysaccharides of high complexity. A unique alternative sigma factor was present similar to that ofB. caccaeATCC 43185, a bacterial species isolated from human feces. In addition,L. gasseriencoded the highest number of putative mucus-binding proteins (14) among lactobacilli sequenced to date. Selected phenotypic characteristics that were compared between ATCC 33323 and other humanL. gasseristrains included carbohydrate fermentation patterns, growth and survival in bile, oxalate degradation, and adhesion to intestinal epithelial cells, in vitro. The results from this study indicated high intraspecies variability from a genome encoding traits important for survival and retention in the gastrointestinal tract.
Improved Cloning Vectors for Bifidobacteria, Based on the
Bifidobacterium catenulatum
pBC1 Replicon
Authors: Álvarez-Martín Pablo , Belén Flórez Ana , Margolles Abelardo , del Solar Gloria , Mayo Baltasar
Published: June 2008

This study reports the development of several cloning vectors for bifidobacteria based on the replicon of pBC1, a cryptic plasmid from
Bifidobacterium catenulatum
L48 thought to replicate via the theta mode. These vectors, in which antibiotic resistance genes encoding either erythromycin or tetracycline resistance acted as selection markers, were able to replicate in a series of eight
Bifidobacterium
species at frequencies ranging from 4.0 × 10
1
to 1.0 × 10
5
transformants μg
−1
but not in
Lactococcus lactis
or
Lactobacillus casei
. They showed a relative copy number of around 30 molecules per chromosome equivalent and a good segregational stability, with more than 95% of the cells retaining the vectors after 80 to 100 generations in the absence of selection. Vectors contain multiple cloning sites of different lengths, and the
lacZ
α peptide gene was introduced into one of the molecules, thus allowing the easy selection of colonies harboring recombinant plasmids in
Escherichia coli
. The functionality of the vectors for engineering
Bifidobacterium
strains was assessed by cloning and examining the expression of an α-
l
-arabinofuranosidase gene belonging to
Bifidobacterium longum. E. coli
and
Bifidobacterium pseudocatenulatum
recombinant clones were stable and showed an increase in α-arabinofuranosidase activity of over 100-fold compared to that of the untransformed hosts.
Variations in the Degree of
d
-Alanylation of Teichoic Acids in
Lactococcus lactis
Alter Resistance to Cationic Antimicrobials but Have No Effect on Bacterial Surface Hydrophobicity and Charge
Authors: Giaouris Efstathios , Briandet Romain , Meyrand Mickael , Courtin Pascal , Chapot-Chartier Marie-Pierre
Published: June 2008

An increase of the degree of
d
-alanylation of teichoic acids in
Lactococcus lactis
resulted in a significant increase of bacterial resistance toward the cationic antimicrobials nisin and lysozyme, whereas the absence of
d
-alanylation led to a decreased resistance toward the same compounds. In contrast, the same variations of the
d
-alanylation degree did not modify bacterial cell surface charge and hydrophobicity. Bacterial adhesion to polystyrene and glass surfaces was not modified either.
Specific Interaction of the Unmodified Bacteriocin Lactococcin 972 with the Cell Wall Precursor Lipid II
Authors: Martínez Beatriz , Böttiger Tim , Schneider Tanja , Rodríguez Ana , Sahl Hans-Georg , Wiedemann Imke
Published: June 2008

Lactococcin 972 (Lcn972) is a nonlantibiotic bacteriocin that inhibits septum biosynthesis in
Lactococcus lactis
rather than forming pores in the cytoplasmic membrane. In this study, a deeper analysis of the molecular basis of the mode of action of Lcn972 was performed. Of several lipid cell wall precursors, only lipid II antagonized Lcn972 inhibitory activity in vivo. Likewise, Lcn972 only coprecipitated with lipid II micelles. This bacteriocin inhibited the in vitro polymerization of lipid II by the recombinant
S. aureus
PBP2 and the addition to lipid II of the first glycine catalyzed by FemX. These experiments demonstrate that Lcn972 specifically interacts with lipid II, the substrate of both enzymes. In the presence of Lcn972, nisin pore formation was partially hindered in whole cells. However, binding of Lcn972 to lipid II could not compete with nisin in lipid II-doped 1,2-dioleoyl-
sn
-glycero-3-phosphocholine (DOPC) liposomes, possibly indicating a distinct binding site. The existence of a putative cotarget for Lcn972 activity is discussed in the context of its narrow inhibitory spectrum and the localized action at the division septum. To our knowledge, this is the first unmodified bacteriocin that binds to the cell wall precursor lipid II.
Reduced Lysis upon Growth of
Lactococcus lactis
on Galactose Is a Consequence of Decreased Binding of the Autolysin AcmA
Authors: Steen Anton , Buist Girbe , Kramer Naomi E. , Jalving Ruud , Benus Germaine F. J. D. , Venema Gerard , Kuipers Oscar P. , Kok Jan
Published: June 2008

When
Lactococcus lactis
subsp.
lactis
IL1403 or
L. lactis
subsp.
cremoris
MG1363 is grown in a medium with galactose as the carbon source, the culture lyses to a lesser extent in stationary phase than when the bacteria are grown in a medium containing glucose. Expression of AcmA, the major autolysin of
L. lactis
, is not influenced by the carbon source. Binding studies with a fusion protein consisting of the MSA2 protein of
Plasmodium falciparum
and the C-terminal peptidoglycan-binding domain of AcmA revealed that cell walls of cells from both subspecies grown on galactose bind less AcmA than cell walls of cells grown on glucose. Cells grown on glucose or galactose and treated with trichloroacetic acid prior to AcmA binding bind similar amounts of AcmA. Analysis of the composition of the lipoteichoic acids (LTAs) of
L. lactis
IL1403 cells grown on glucose or galactose showed that the LTA composition is influenced by the carbon source: cells grown on galactose contain LTA with less galactose than cells grown on glucose. In conclusion, growth of
L. lactis
on galactose changes the LTA composition in the cell wall in such a way that less AcmA is able to bind to the peptidoglycan, resulting in a decrease in autolysis.
Engineering of a Human Vaginal
Lactobacillus
Strain for Surface Expression of Two-Domain CD4 Molecules
Authors: Liu Xiaowen , Lagenaur Laurel A. , Lee Peter P. , Xu Qiang
Published: June 2008

Women are at significant risk of heterosexually transmitted human immunodeficiency virus (HIV) infection, with the mucosal epithelium of the cervix and vagina serving as a major portal of entry. The cervicovaginal mucosa naturally harbors dynamic microflora composed predominantly of lactobacilli, which may be genetically modified to serve as a more efficient protective barrier against the heterosexual transmission of HIV. We selected a vaginal strain of
Lactobacillus
,
L. jensenii
1153, for genetic modification to display surface-anchored anti-HIV proteins. Genomic sequencing analyses revealed that
L. jensenii
1153 encodes several unique high-molecular-weight cell wall-anchored proteins with a C-terminal cell wall sorting LPQTG motif. In this report, we employed these proteins to express a surface-anchored two-domain CD4 (2D CD4) molecule in
L. jensenii
1153. Our studies indicated that the C-terminal cell wall sorting signal LPQTG motif alone is insufficient to drive the surface expression of heterologous proteins, and the display of surface-anchored 2D CD4 molecules required native sequences of a defined length upstream of the unique C-terminal LPQTG cell wall sorting signal and the positively charged C terminus in a
Lactobacillus
-based expression system. The modified
L. jensenii
strain displayed 2D CD4 molecules that were uniformly distributed on bacterial surfaces. The surface-anchored 2D CD4 molecule was recognized by a conformation-dependent anti-CD4 antibody, suggesting that the expressed proteins adopted a native conformation. The establishment of this
Lactobacillus
-based surface expression system, with potential broad applicability, represents a major step toward developing an inexpensive yet durable approach to topical microbicides for the mitigation of heterosexual transmission of HIV and other mucosally transmitted viral pathogens.
Influence of Shifting Positions of Ser, Thr, and Cys Residues in Prenisin on the Efficiency of Modification Reactions and on the Antimicrobial Activities of the Modified Prepeptides
Authors: Lubelski Jacek , Overkamp Wout , Kluskens Leon D. , Moll Gert N. , Kuipers Oscar P.
Published: June 2008

Since the recent discovery that the nisin modification and transport machinery can be used to produce and modify peptides unrelated to nisin, specific questions arose concerning the specificity of the modification enzymes involved and the limits of their promiscuity with respect to the dehydration and cyclization processes. The nisin leader peptide has been postulated to fulfill a recognition and binding function required for these modifications. Here, we investigated whether the relative positions of the modifiable residues in the nisin prepeptide, with respect to the leader peptide, could influence the efficiency of their modification. We conducted a systematic study on the insertion of one to four alanines in front of either ring A or ring D to change the “reading frame” of modifiable residues, resulting in altered distance and topology of the modifiable residues relative to the leader. The insertion of N-terminal and hinge-located Ala residues had only a modest influence on the modification efficiency, demonstrating that the “phasing” of these residues relative to the leader peptide is not a critical factor in determining modification. However, in all cases, but especially with the N-terminal insertions, the antimicrobial activities of the fully modified nisin species were decreased.
Transcriptome Analysis of the
Lactococcus lactis
ArgR and AhrC Regulons
Authors: Larsen Rasmus , van Hijum Sacha A. F. T. , Martinussen Jan , Kuipers Oscar P. , Kok Jan
Published: June 2008

In previous studies, we have shown that direct protein-protein interaction between the two regulators ArgR and AhrC in
Lactococcus lactis
is required for arginine-dependent repression of the biosynthetic
argC
promoter and the activation of the catabolic
arcA
promoter. Here, we establish the global ArgR and AhrC regulons by transcriptome analyses and show that both regulators are dedicated to the control of arginine metabolism in
L. lactis
.
Morphology, Genome Sequence, and Structural Proteome of Type Phage P335 from
Lactococcus lactis
Authors: Labrie Simon J. , Josephsen Jytte , Neve Horst , Vogensen Finn K. , Moineau Sylvain
Published: June 2008

Lactococcus lactis
phage P335 is a virulent type phage for the species that bears its name and belongs to the
Siphoviridae
family. Morphologically, P335 resembled the
L. lactis
phages TP901-1 and Tuc2009, except for a shorter tail and a different collar/whisker structure. Its 33,613-bp double-stranded DNA genome had 50 open reading frames. Putative functions were assigned to 29 of them. Unlike other sequenced genomes from lactococcal phages belonging to this species, P335 did not have a lysogeny module. However, it did carry a dUTPase gene, the most conserved gene among this phage species. Comparative genomic analyses revealed a high level of identity between the morphogenesis modules of the phages P335, ul36, TP901-1, and Tuc2009 and two putative prophages of
L. lactis
SK11. Differences were noted in genes coding for receptor-binding proteins, in agreement with their distinct host ranges. Sixteen structural proteins of phage P335 were identified by liquid chromatography-tandem mass spectrometry. A 2.8-kb insertion was recognized between the putative genes coding for the activator of late transcription (Alt) and the small terminase subunit (TerS). Four genes within this region were autonomously late transcribed and possibly under the control of Alt. Three of the four deduced proteins had similarities with proteins from
Streptococcus pyogenes
prophages, suggesting that P335 acquired this module from another phage genome. The genetic diversity of the P335 species indicates that they are exceptional models for studying the modular theory of phage evolution.