bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural-scaled entropy predicts the effects of nonlinear frequency compression on speech perception
Authors: Hariram Varsha , Alexander Joshua
Published: October 2014

Signal processing schemes used in hearing aids, such as nonlinear frequency compression (NFC) recode speech information by moving high-frequency information to lower frequency regions. Perceptual studies have shown that depending on the dominant speech sound, compression occurs and the amount of compression can have a significant effect on perception. Very little is understood about how frequency-lowered information is encoded by the auditory periphery. We have developed a measure that is sensitive to information in the altered speech signal in an attempt to predict optimal hearing aid settings for individual hearing losses. The Neural-Scaled Entropy (NSE) model examines the effects of frequency-lowered speech at the level of the inner hair cell synapse of an auditory nerve model [Zilany et al. 2013, Assoc. Res. Otolaryngol.]. NSE quantifies the information available in speech by the degree to which the pattern of neural firing across frequency changes relative to its past history (entropy). Nonsense syllables with different NFC parameters were processed in noise. Results are compared with perceptual data across the NFC parameters as well as across different vowel-defining parameters, consonant features, and talker gender. NSE successfully captured the overall effects of varying NFC parameters across the different sound classes.
Perceptual versus cognitive speed in a time-compressed speech task
Authors: Molis Michelle R. , Gallun Frederick J. , Srinivasan Nirmal
Published: October 2014

Time-compression retains the information-bearing spectral change present uncompressed speech, although at a rate that may outstrip cognitive processing speed. To compare the relative importance of perceptual and cognitive processing speed, we compared the understanding of (1) time-compressed stimuli expanded in time via gaps with (2) uncompressed stimuli where spectral change information was removed. We hypothesized that, despite the initial compression, the compressed and expanded stimuli would be more intelligible as it would retain relatively more information-bearing spectral change. Participants were somewhat older listeners (mid-1950s to mid-1960s) with normal hearing or mild hearing loss. Stimuli were spoken seven-digit strings time-compressed via pitch synchronous overlap and add (PSOLA) at three uniform compression ratios (2:1, 3:1, and 5:1). In gap insertion conditions, the total duration of the compressed stimuli was restored via introduction of periodic gaps. This produced signal-to-gap ratios of 1:1, 1:2, and 1:4. For comparison, segments of unaccelerated strings, equal to the duration of the inserted gaps, were zeroed out resulting in the same signal-to-gap ratios. Listeners identified the final four digits of the strings presented in quiet and in a steady-state, speech-shaped background noise (SNR + 5). Our hypothesis was supported for the fastest compression rates. [Work supported by VA RR&D.]
Information-bearing acoustic changes are important for understanding vocoded speech in a simulation of cochlear implant processing strategies
Authors: Stilp Christian
Published: October 2014

Information-bearing acoustic changes (IBACs) in the speech signal are important for understanding speech. This was demonstrated with cochlea-scaled entropy for cochlear implants (CSECI), which measures perceptually significant intervals of noise-vocoded speech (Stilp et al., 2013 JASA; Stilp, 2014 JASA; Stilp & Goupell, 2014 ASA). However, vocoding does not necessarily mimic CI processing. Some CI processing strategies present acoustic information in all channels at all times (e.g., CIS) while others present only the n-highest-amplitude channels out of m at any time (e.g., ACE). Here, IBACs were explored in a simulation of ACE processing. Sentences were divided into 22 channels spanning 188–7938 Hz and noise-vocoded. In each 1-ms interval (simulating 1000 pulses/second stimulation rate), only the eight highest-amplitude channels were retained. CSECI was calculated between 1-ms or 16-ms sentence segments, then summed into 80-ms intervals. High-CSECI or low-CSECI intervals were replaced by speech-shaped noise. Consistent with previous studies, replacing high-CSECI intervals impaired sentence intelligibility more than replacing an equal number of low-CSECI intervals. Importantly, performance was comparable when 1- or 16-ms IBACs were replaced by noise. Results reveal the perceptual importance of IBACs on rapid timescales after simulated ACE processing, indicating this information is likely available to CI users for understanding speech.
Talker intelligibility across clear and sinewave vocoded speech
Authors: Loebach Jeremy , Scharenbroch Gina , Berg Katelyn
Published: October 2014

Talker intelligibility was compared across clear and sinewave vocoded speech. Ten talkers (5 female) from the Midwest and Western dialect regions recorded samples of 210 meaningful IEEE sentences, 206 semantically anomalous sentences, and 300 MRT words. Ninety-three normal hearing participants provided open set transcriptions of the materials presented in the clear over headphones. Forty-one different normal hearing participants provided open set transcriptions of the materials processed with an eight-channel sinewave vocoder. Transcription accuracy was highest for clear speech compared to vocoded speech, and for meaningful sentences, followed by anomalous sentences and words for both conditions. Weak talker effects were observed for the meaningful sentences in the clear (ranging from 97.7% to 98.2%), but were more pronounced for vocoded versions (68.5% to 85.5%). Weak talker effects were observed for semantically anomalous sentences in the clear (89.4%-93.3%), but more variability was observed across talkers in the vocoded condition (54.4%–73.7%). Finally, stronger talker effects were observed for clear and vocoded MRT words (83.8%–95.6%, 46.3%–59.0%, respectively). Talker rankings differed across stimulus conditions, as well as across processing conditions, but significant positive correlations between conditions were observed for meaningful and anomalous sentences, but not MRT words. Acoustic and dialect influences on intelligibility will be discussed.
Vowels of four-year-old children with cerebral palsy in Mandarin-learning environment
Authors: Chen Li-mei , Lin Yu Ching , Hsu Wei Chen , Yeh Meng-Hsin
Published: October 2014

Characteristics of vowel productions of children with cerebral palsy (CP) were investigated with data from two 4-year-old children with CP and two typically-developing (TD) children in Mandarin-learning environment. Clear vowel productions from picture naming and natural conversation in three 50-minute audio recordings of each child were transcribed and analyzed. Seven parameters were examined: vowel duration of /a/, F2 slope in transition of CV sequence, cumulative change of F2 for vowel /a/, degree of nasalization in oral vowel (A1-P1), percent of jitter, percent of shimmer, and the signal to noise ratio (SNR). Major findings are: (1) The CP group showed shorter vowel duration of /a/; (2) TD group has larger F2 slope in CV transition; (3) No obvious differences were found between TD and CP groups in cumulative change of F2 for vowel /a/, degree of nasalization (A1-P1), and voice perturbation (percent of jitter, percent of shimmer, and SNR). Further study with more participants and with careful data selection can verify findings of this study in search for valid parameters to characterize vowel production of children with CP.
Pitch production of a Mandarin-learning infant with cerebral palsy
Authors: Yeh Meng-Hsin , Chen Li-mei , Lin Chyi-Her , Lin Yuh-Jyh , Lin Yung-Chieh
Published: October 2014

In this study, pitch production were investigated in two Mandarin-learning infants at 6 months of age, an infant with cerebral palsy (CP) and a typically developing (TD) infant. Words with distinct tones in Mandarin differ in meaning. In order to produce a correct tone, having good control of the respiratory and the laryngeal mechanisms are necessary. Thus, producing a correct tone and reaching intelligibility for children with CP is considered to be relatively difficult. In previous studies, Kent and Murray (1982) pointed out that falling contours predominated in infant vocalizations at 3, 6, and 9 months. A study by Chen et al (2013) with 4-year-old children indicated that the mean pitch duration of CP children is 1.3–1.8 times longer than TD counterparts. In adults, Jeng, Weismer, and Kent (2006) found that the pitch slopes of Mandarin in CP adults are smaller than in healthy adults. Three measures were employed in this current study and the major findings are: (1) Both TD and CP infants produced more falling than rising pitch; (2) The mean duration of pitch in CP is 2.3 times longer than that of TD; (3) The pitch slope in CP is smaller than that of TD.
Hearing and hearing-impaired children's acoustic–phonetic adaptations to an interlocutor with a hearing impairment
Authors: Granlund Sonia , Hazan Valerie , Mahon Merle
Published: October 2014

In England, the majority of children with a hearing impairment attend mainstream schools. However, little is known about the communication strategies used by children when interacting with a peer with hearing loss. This study examined how children with normal-hearing (NH) and those with a hearing impairment (HI) adapt to the needs of a HI interlocutor, focusing on the acoustic–phonetic properties of their speech. Eighteen NH and 18 HI children between the ages of 9 and 15 years performed two problem-solving communicative tasks in pairs: one session was completed with a friend with normal hearing (NH-directed speech) and one session was done with a friend with a hearing impairment (HI-directed speech). As expected, task difficulty increased in interactions involving a HI interlocutor. HI speakers had a slower speech rate, higher speech intensity, and greater F0 range than NH speakers. However, both HI and NH participants decreased their speech rate, and increased their F0 range, mean F0 and the intensity of their speech in HI-directed speech compared to NH-directed speech. This suggests that both NH and HI children are able to adapt to the needs of their interlocutor, even though speech production is more effortful for HI children than their NH peers.
Identification of dialect cues by dyslexic and non-dyslexic listeners
Authors: Fox Robert A. , Long Gayle , Jacewicz Ewa
Published: October 2014

Spoken language encodes two different forms of information: linguistic (related to the message) and indexical (e.g., speaker’s age, gender, and regional dialect). However, some speech-language impairments (such as dyslexia) can reduce a listener’s ability to process both linguistic and indexical speech cues. For example, Perrachione et al. (Science, 333, 2011) demonstrated that individuals with dyslexia were less able to identify new voices than were control listeners. This study examines the ability of listeners with and without dyslexia to identify speaker dialect. Eighty listeners—40 adults and 40 children (20 in each group were dyslexic, 20 were not; 40 were males and 40 were females)—listened to a set of 80 sentences produced by English speakers from Western North Carolina or central Ohio and were asked to identify which region the speaker came from. Results demonstrated that adult listeners were significantly better at dialect identification and that listeners with dyslexia were significantly poorer at dialect identification. More notably, there was a significant age by listener group interaction—the improvement in dialect identification between adults and children was significantly smaller in listeners with dyslexia. This indicates that an initial limitation in language learning can inhibit long-term development of speaker-specific phonetic representations.
Individual differences in the lexical processing of phonetically reduced speech
Authors: Turnbull Rory
Published: October 2014

There is widespread evidence that phonetically reduced speech is processed slower and more effortfully than unreduced speech. However, individual differences in degree and strategies of reduction, and their effects on lexical access, are largely unexplored. This study explored the role of autistic traits in the production and perception of reduced pronunciation variants. Stimuli were recordings of words produced in either high reduction (HR) or low reduction (LR) contexts, extracted from sentences produced by talkers ranging in autism-spectrum quotient (AQ) scores. The reductions in these stimuli were generally small temporal differences, rather than segmental-level alterations such as /t/-flapping. Listeners completed a lexical decision task with these stimuli and the autism-spectrum quotient (AQ) questionnaire. Confirming previous research, the results demonstrate that response times (RTs) to reduced words were slower than to unreduced words. No other effects on RT were observed. In terms of response accuracy, LR words were responded to more accurately than HR words, but this pattern was only observed for temporally reduced words. This LR word accuracy benefit was larger for listeners with more autistic personality traits. These results suggest that individuals differ in the extent to which unreduced speech provides a perceptual benefit.
Change of static characteristics of Japanese word utterances with aging
Authors: Mizumachi Mitsunori , Ogata Kazuto
Published: October 2014

Acoustical characteristics of elderly speech have been investigated in the various viewpoints. Elderly speech can be subjectively characterized by roughness, breathiness, asthenic, and hoarseness. Those characteristics have been individually explained in both medical science and speech science. In particular, the hoarseness, which is caused by a physiological problem with an aged vocal cord, is the most well-known static properties of elderly speech. Change of the hoarseness is quantitatively investigated with aging. Japanese phonetically-balanced 543 word utterances were collected with the cooperation of 153 speakers, whose ages ranged from 20 to 89 years old. Acoustical characteristics of the word utterances were examined in the viewpoints of age and auditory impression. In the static acoustical analysis of Japanese vowels /a/, /e/, /i/, /o/, and /u/, it is confirmed that energy in the high frequency region rises with aging. There is a remarkable energy lift over 4 kHz, and the amount of the energy lift is proportion to the degree of subjective hoarseness.
Sentence recognition in older adults
Authors: Faulkner Kathleen F. , Kidd Gary R. , Humes Larry E. , Pisoni David B.
Published: October 2014

Many older adults report difficulty when listening to speech in background noise. These difficulties may arise from some combination of factors, including age-related hearing loss, auditory sensory processing difficulties, and/or general cognitive decline. To perform well in everyday noisy environments, listeners must quickly adapt, switch attention, and adjust to multiple sources of variability in both the signal and listening environments. Sentence recognition tests in noise have been useful for assessing speech understanding abilities because they require a combination of basic sensory/perceptual abilities as well as cognitive resources and processing operations. This study was designed to explore several factors underlying individual differences in aided speech understanding in older adults. We examined the relations between measures of speech perception, cognition, and self-reported listening difficulties in a group of aging adults (N = 40, age range 60–86) and a group of young normal hearing listeners (N = 28, age range 18–30). All participants completed a comprehensive battery of tests, including cognitive, psychophysical, speech understanding, as well as the SSQ self-report scale. While controlling for audibility, speech understanding declined with age and was strongly correlated with psychophysical measures, cognition, and self-reported speech understanding difficulties. [Work supported by NIH: NIDCD grant T32-DC00012 and NIA grant R01-AG008293 to Indiana University.]
Individual differences in speech perception in noise: A neurocognitive genetic study
Authors: Xie Zilong , Maddox W. Todd , Knopik Valerie S. , McGeary John E. , Chandrasekaran Bharath
Published: October 2014

Previous work has demonstrated that individual listeners vary substantially in their ability to recognize speech in noisy environments. However, little is known about the underlying sources of individual differences in speech perception in noise. Noise varies in the levels of energetic masking (EM) and informational masking (IM) imposed on target speech. Relative to EM, release from IM places greater demand on selective attention. A polymorphism in exon III of the DRD4 gene has been shown to influence selective attention. Here we investigated whether this polymorphism contributes to individual variation in speech recognition ability. We assessed sentence recognition performance across a range of maskers (1-, 2-, and 8-talker babble, and speech-spectrum noise) among 104 young, normal-hearing adults. We also measured their working memory capacity with Operation Span Task, which relies on selective attention to update and maintain items in memory while performing a secondary task. Results showed that the long variant of the DRD4 gene significantly associated with better recognition performance in 1-talker babble conditions only, and that this relation was mediated by enhanced working memory capacity. These findings suggest that the DRD4 polymorphism can explain some of the individual differences in speech recognition ability, but is specific to IM conditions.
Potential sports concussion identification using acoustic-phonetic analysis of vowel productions
Authors: Horner Terry G. , Stokes Michael A.
Published: October 2014

Concussions impair cognitive function and muscle motor control; however, little is known about how this impairment affects speech production. In the present study, concussed athletes speech is recorded at the initial office visit and subsequent visits. The last recording, when the brain is determined to have recovered using present criteria, becomes the baseline. The vocabulary consists of seven h-vowel-d (hVd) words (who’d, heed, hood, hid, had, hud, and heard) produced three times each for a total of 21 productions. The study is focused on vowel characteristics and the limited coarticulatory effects of the hVd vocabulary make it ideal for the study. Duration measurements are made by experimenter analysis and the formant measurements are made using the automatic speech recognition engine ELBOW. The preliminary comparisons from the subjects completing the protocol show formant drift for three or more of the seven vowels, and duration is affected for each talker and each vowel. These results were anticipated since the impairment would affect articulatory movement and timing. The results as well as a discussion of development of an automated real-time concussion identification application will be presented.
An overview of internal wave observations and theory associated with canyons and slopes
Authors: Colosi John A.
Published: October 2014

Topographic environments such as canyons and slopes are known to be regions of complex internal-wave behavior associated with wave generation, propagation, and dissipation. Much of this anomalous behavior stems from the kinematic constraint that internal waves must maintain their angle of propagation with respect to the horizontal even after interaction with a sloping boundary. In canyons or on slopes, waves propagating in from deep water or generated locally (mostly by tidal flows) either reflect back out to sea or intensify in energy density as they propagate up slope. In particular, wave intensification can lead to nonlinear phenomena including steepening, breaking, and dissipation. This talk will provide and overview of internal wave observations, modeling, and theory in canyons and on slopes with a particular emphasis on acoustically relevant aspects of the wave field.
Analytic prediction of acoustic coherence time scales in continental-shelf environments with random internal waves
Authors: Gong Zheng , Chen Tianrun , Ratilal Purnima , Makris Nicholas C.
Published: October 2014

An analytical model derived from normal mode theory for the accumulated effects of range-dependent multiple forward scattering is applied to estimate the temporal coherence of the acoustic field forward propagated through a continental-shelf waveguide containing random three-dimensional internal waves. The modeled coherence time scale of narrow band low-frequency acoustic field fluctuations after propagating through a continental-shelf waveguide is shown to decay with a power-law of range to the -1/2beyond roughly 1 km, decrease with increasing internal wave energy, to be consistent with measured acoustic coherence time scales. The model should provide a useful prediction of the acoustic coherence time scale as a function of internal wave energy in continental-shelf environments. The acoustic coherence time scale is an important parameter in remote sensing applications because it determines (i) the time window within which standard coherent processing such as matched filtering may be conducted, and (ii) the number of statistically independent fluctuations in a given measurement period that determines the variance reduction possible by stationary averaging.
Modeling three dimensional environment and broadband acoustic propagation in Arctic shelf-basin region
Authors: Badiey Mohsen , Muenchow Andreas , Wan Lin , Ballard Megan S. , Knobles David P. , Sagers Jason D.
Published: October 2014

Rapid climate change over the last decade has created a renewed interest in the nature of underwater sound propagation in the Arctic Ocean. Changes in the oceanography and surface boundary conditions are expected to cause measurable changes in the propagation and scattering of low frequency sound. Recent measurements of a high-resolution three-dimensional (3-D) sound speed structure in a 50 x 50 km2 region in an open-water shelf-basin region of the Beaufort Sea offer a unique and rare opportunity to study the effects of a complex oceanography on the acoustic field as it propagates from the deep basin onto the continental shelf. The raw oceanography data were analyzed and processed to create a 3-D sound speed field for the water column in the basin-slope-shelf area. Recent advances in both 2-D and 3-D acoustic modeling capability allow one to study the effects of the range- and azimuth-dependent water column layers on the frequency-dependent acoustic modal structure. Of particular interest is the nature of the 3-D and mode-coupling effects on the frequency response induced by the oceanography. The results will likely be useful in designing acoustic experiments with serious logistical constraints in the rapidly changing Arctic Ocean.
Underwater jet noise simulation based on a Large Eddy Simulation/Lighthill hybrid method
Authors: Liu GuoQing , Zhang Tao , Zhang YongOu , Ouyang Huajiang , Li Xu
Published: October 2014

In recent years, extensive researches about the numerical method for aeroacoustics noise simulation have been made. However, the research of hydrodynamic noise develops slowly. In this paper, a hybrid method of combining Large Eddy Simulation (LES) and Lighthill’s acoustic analogy theory is established to compute the hydrodynamic noise, which is based on the preliminary study of the method for aerodynamic noise prediction under low Mach number. First, the model of three-dimensional underwater jet is determined by an experimental model. Meanwhile, the CFD mesh and the acoustic mesh are both prepared. Then, the flow field of underwater jet is simulated with LES. The characteristics of turbulent flow are analyzed by the pressure difference and the uniformity coefficient of velocity. After that, the noise of underwater jet is simulated using the theory of Lighthill’s acoustic analogy. Finally, the solutions obtained by the hybrid method are compared with the experimental data available in open literature. In conclusion, the sound pressure level at the observation point agrees well with the experimental data. The LES/Lighthill hybrid method is able to compute the underwater jet noise and the hydrodynamic noise.
Ultra low frequency electromagnetic underwater sound source
Authors: Lu Wei , Lan Yu
Published: October 2014

A detail analysis is presented of one ultra low frequency sound source which is smaller and lighter than conventional piezoelectric ultra low frequency sound source. This sound source is single piston vibration using the electromagnetic principle. The radiation characteristic of sound source is researched by single piston radiation model in low frequency. The dynamic characteristic such as resonant frequency, vibrant displacement of sound source is researched by analytic method and finite element method. In analytic method, the electricity-magnetism, magnetism-force, and force-vibration conversion models of sound source are established by differential equations in different coupling physical fields, and the dynamic characteristics based on the conversion models are simulated by combining and solving differential equations using the Matlab/Simulink. In finite element method, using transient solver of electromagnetic analysis finite element software Ansoft, the dynamic characteristics of sound source are solved. Optimizing the dynamic characteristic of sound source by adjusting magnetic circuit, drive coil, and elastic component parameters, the resonant frequency and radiated sound power of sound source are determined. One prototype sound source design, in which the source level is 184 dB in frequency 73 Hz by calibration, is fabricated that demonstrated proof-of-concept.
The effects of geometrical confinement and viscosity ratio on the coalescence of droplet pairs in shear flow
Authors: De Bruyn Pieter , Chen Dongju , Moldenaers Paula , Cardinaels Ruth
Published: October 2014

The effects of geometrical confinement and viscosity ratio on droplet coalescence in shear flow are experimentally investigated by means of a counter rotating parallel plate device, equipped with a microscope. The ratio of droplet diameter to gap spacing is varied between 0.03 and 0.33 to study both bulk and confined conditions. Three grades of a Newtonian droplet material are combined with a Newtonian matrix, resulting in three different viscosity ratios, namely, 0.1, 1.1, and 2.6. The effects of confinement are qualitatively similar for all three viscosity ratios. For each system, confinement decreases the coalescence angle and renders coalescence possible up to higher capillary numbers and initial offsets. Moreover, for all three viscosity ratios, confinement induces a lower initial offset boundary below which the approaching droplets reverse flow direction without coalescence. However, there are quantitative differences between the systems. With increasing viscosity ratio, the critical capillary number and critical upper and lower offset boundaries decrease. Since the decrease of the upper offset boundary is more predominant, the coalescence efficiency decreases with viscosity ratio. The droplet trajectories of interacting droplets are affected by both the viscosity ratio and geometrical confinement, which clearly has implications on the coalescence behavior.
Comparisons of Ectomycorrhizal Colonization of Transgenic American Chestnut with Those of the Wild Type, a Conventionally Bred Hybrid, and Related Fagaceae Species
Authors: D'Amico Katherine M. , Horton Thomas R. , Maynard Charles A. , Stehman Stephen V. , Oakes Allison D. , Powell William A.
Published: October 2014

American chestnut (Castanea dentata[Marsh.] Borkh.) dominated the eastern forests of North America, serving as a keystone species both ecologically and economically until the introduction of the chestnut blight,Cryphonectria parasitica, functionally eradicated the species. Restoration efforts include genetic transformation utilizing genes such as oxalate oxidase to produce potentially blight-resistant chestnut trees that could be released back into the native range. However, before such a release can be undertaken, it is necessary to assess nontarget impacts. Since oxalate oxidase is meant to combat a fungal pathogen, we are particularly interested in potential impacts of this transgene on beneficial fungi. This study compares ectomycorrhizal fungal colonization on a transgenic American chestnut clone expressing enhanced blight resistance to a wild-type American chestnut, a conventionally bred American-Chinese hybrid chestnut, and other Fagaceae species. A greenhouse bioassay used soil from two field sites with different soil types and land use histories. The number of colonized root tips was counted, and fungal species were identified using morphology, restriction fragment length polymorphism (RFLP), and DNA sequencing. Results showed that total ectomycorrhizal colonization varied more by soil type than by tree species. Individual fungal species varied in their colonization rates, but there were no significant differences between colonization on transgenic and wild-type chestnuts. This study shows that the oxalate oxidase gene can increase resistance againstCryphonectria parasiticawithout changing the colonization rate for ectomycorrhizal species. These findings will be crucial for a potential deregulation of blight-resistant American chestnuts containing the oxalate oxidase gene.
Embedded Biofilm, a New Biofilm Model Based on the Embedded Growth of Bacteria
Authors: Jung Yong-Gyun , Choi Jungil , Kim Soo-Kyoung , Lee Joon-Hee , Kwon Sunghoon
Published: October 2014

A variety of systems have been developed to study biofilm formation. However, most systems are based on the surface-attached growth of microbes under shear stress. In this study, we designed a microfluidic channel device, called a microfluidic agarose channel (MAC), and found that microbial cells in the MAC system formed an embedded cell aggregative structure (ECAS). ECASs were generated from the embedded growth of bacterial cells in an agarose matrix and better mimicked the clinical environment of biofilms formed within mucus or host tissue under shear-free conditions. ECASs were developed with the production of extracellular polymeric substances (EPS), the most important feature of biofilms, and eventually burst to release planktonic cells, which resembles the full developmental cycle of biofilms. Chemical and genetic effects have also confirmed that ECASs are a type of biofilm. Unlike the conventional biofilms formed in the flow cell model system, this embedded-type biofilm completes the developmental cycle in only 9 to 12 h and can easily be observed with ordinary microscopes. We suggest that ECASs are a type of biofilm and that the MAC is a system for observing biofilm formation.
Evidence for Extraintestinal Growth of Bacteroidales Originating from Poultry Litter
Authors: Weidhaas Jennifer , Mantha Sirisha , Hair Elliott , Nayak Bina , Harwood Valerie J.
Published: October 2014

Water quality monitoring techniques that target microorganisms in the order
Bacteroidales
are potential alternatives to conventional methods for detection of fecal indicator bacteria.
Bacteroidales
and members of the genus
Bacteroides
have been the focus of microbial source tracking (MST) investigations for discriminating sources of fecal pollution (e.g., human or cattle feces) in environmental waters. For accurate source apportionment to occur, one needs to understand both the abundance of
Bacteroides
in host feces and the survival of these host-associated microbial markers after deposition in the environment. Studies were undertaken to evaluate the abundance, persistence, and potential for growth of
Bacteroidales
originating from poultry litter under oxic and anoxic environmental conditions.
Bacteroidales
abundance, as determined by quantitative PCR (qPCR) with GenBac primers and probe, increased 2 to 5 log gene copies ml
−1
and 2 log gene copies g litter
−1
under most conditions during incubation of poultry litter in a variety of laboratory microcosm and field mesocosm studies. DNA sequencing of the
Bacteroidales
organisms in the litter identified taxa with sequences corresponding exactly to the GenBac primer and probe sequences and that were closely related to
Bacteroides uniformis
,
B. ovatus
, and
B. vulgatus
. These results suggest that MST studies using qPCR methods targeting
Bacteroidales
in watersheds that are affected by poultry litter should be interpreted cautiously. Growth of
Bacteroidales
originating from poultry litter in environmental waters may occur while
Bacteroidales
growth from other fecal sources declines, thus confounding the interpretation of MST results.
Distribution of Human-Specific Bacteroidales and Fecal Indicator Bacteria in an Urban Watershed Impacted by Sewage Pollution, Determined Using RNA- and DNA-Based Quantitative PCR Assays
Authors: Kapoor Vikram , Pitkänen Tarja , Ryu Hodon , Elk Michael , Wendell David , Santo Domingo Jorge W.
Published: October 2014

The identification of fecal pollution sources is commonly carried out using DNA-based methods. However, there is evidence that DNA can be associated with dead cells or present as “naked DNA” in the environment. Furthermore, it has been shown that rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) assays can be more sensitive than rRNA gene-based qPCR assays since metabolically active cells usually contain higher numbers of ribosomes than quiescent cells. To this end, we compared the detection frequency of host-specific markers and fecal bacteria using RNA-based RT-qPCR and DNA-based qPCR methods for water samples collected in sites impacted by combined sewer overflows. As a group, fecal bacteria were more frequently detected in most sites using RNA-based methods. Specifically, 8, 87, and 85% of the samples positive for general enterococci,
Enterococcus faecalis
, and
Enterococcus faecium
markers, respectively, were detected using RT-qPCR, but not with the qPCR assay counterpart. On average, two human-specific
Bacteroidales
markers were not detected when using DNA in 12% of the samples, while they were positive for all samples when using RNA (cDNA) as the template. Moreover, signal intensity was up to three orders of magnitude higher in RT-qPCR assays than in qPCR assays. The human-specific
Bacteroidales
markers exhibited moderate correlation with conventional fecal indicators using RT-qPCR results, suggesting the persistence of nonhuman sources of fecal pollution or the presence of false-positive signals. In general, the results from this study suggest that RNA-based assays can increase the detection sensitivity of fecal bacteria in urban watersheds impacted with human fecal sources.
Identification of
ypqP
as a New Bacillus subtilis Biofilm Determinant That Mediates the Protection of Staphylococcus aureus against Antimicrobial Agents in Mixed-Species Communities
Authors: Sanchez-Vizuete Pilar , Le Coq Dominique , Bridier Arnaud , Herry Jean-Marie , Aymerich Stéphane , Briandet Romain
Published: October 2014

In most habitats, microbial life is organized in biofilms, three-dimensional edifices sustained by extracellular polymeric substances that enable bacteria to resist harsh and changing environments. Under multispecies conditions, bacteria can benefit from the polymers produced by other species (“public goods”), thus improving their survival under toxic conditions. A recent study showed that a
Bacillus subtilis
hospital isolate (NDmed) was able to protect
Staphylococcus aureus
from biocide action in multispecies biofilms. In this work, we identified
ypqP
, a gene whose product is required in NDmed for thick-biofilm formation on submerged surfaces and for resistance to two biocides widely used in hospitals. NDmed and
S. aureus
formed mixed biofilms, and both their spatial arrangement and pathogen protection were mediated by YpqP. Functional
ypqP
is present in other natural
B. subtilis
biofilm-forming isolates. However, the gene is disrupted by the SPβ prophage in the weak submerged-biofilm-forming strains NCIB3610 and 168, which are both less resistant than NDmed to the biocides tested. Furthermore, in a 168 laboratory strain cured of the SPβ prophage, the reestablishment of a functional
ypqP
gene led to increased thickness and resistance to biocides of the associated biofilms. We therefore propose that YpqP is a new and important determinant of
B. subtilis
surface biofilm architecture, protection against exposure to toxic compounds, and social behavior in bacterial communities.
Response of Bacterioplankton Communities to Cadmium Exposure in Coastal Water Microcosms with High Temporal Variability
Authors: Wang Kai , Zhang Demin , Xiong Jinbo , Chen Xinxin , Zheng Jialai , Hu Changju , Yang Yina , Zhu Jianlin
Published: October 2014

Multiple anthropogenic disturbances to bacterial diversity have been investigated in coastal ecosystems, in which temporal variability in the bacterioplankton community has been considered a ubiquitous process. However, far less is known about the temporal dynamics of a bacterioplankton community responding to pollution disturbances such as toxic metals. We used coastal water microcosms perturbed with 0, 10, 100, and 1,000 μg liter
−1
of cadmium (Cd) for 2 weeks to investigate temporal variability, Cd-induced patterns, and their interaction in the coastal bacterioplankton community and to reveal whether the bacterial community structure would reflect the Cd gradient in a temporally varying system. Our results showed that the bacterioplankton community structure shifted along the Cd gradient consistently after a 4-day incubation, although it exhibited some resistance to Cd at low concentration (10 μg liter
−1
). A process akin to an arms race between temporal variability and Cd exposure was observed, and the temporal variability overwhelmed Cd-induced patterns in the bacterial community. The temporal succession of the bacterial community was correlated with pH, dissolved oxygen, NO
3
−
-N, NO
2
−
-N, PO
4
3−
-P, dissolved organic carbon, and chlorophyll
a
, and each of these parameters contributed more to community variance than Cd did. However, elevated Cd levels did decrease the temporal turnover rate of community. Furthermore, key taxa, affiliated to the families
Flavobacteriaceae
,
Rhodobacteraceae
,
Erythrobacteraceae
,
Piscirickettsiaceae
, and
Alteromonadaceae
, showed a high frequency of being associated with Cd levels during 2 weeks. This study provides direct evidence that specific Cd-induced patterns in bacterioplankton communities exist in highly varying manipulated coastal systems. Future investigations on an ecosystem scale across longer temporal scales are needed to validate the observed pattern.
Thermoadaptation-Directed Enzyme Evolution in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426
Authors: Suzuki Hirokazu , Kobayashi Jyumpei , Wada Keisuke , Furukawa Megumi , Doi Katsumi
Published: October 2014

Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile
Geobacillus kaustophilus
HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that
G. kaustophilus
had substantially higher mutability than
Escherichia coli
and
Bacillus subtilis
. The predominant mutations in
G. kaustophilus
were A · T→G · C and C · G→T · A transitions, implying that the high mutability of
G. kaustophilus
was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in
G. kaustophilus
, deletions of the
mutSL
,
mutY
,
ung
, and
mfd
genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic
pyrF
gene. Although the strain harboring
Bacillus subtilis
pyrF
was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating
B. subtilis
PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes.
amoA
Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom
Authors: Li Jialin , Nedwell David B. , Beddow Jessica , Dumbrell Alex J. , McKew Boyd A. , Thorpe Emma L. , Whitby Corinne
Published: October 2014

Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (
amoA
) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw]
−1
day
−1
in June, increasing to 37.4 μmol N gdw
−1
day
−1
in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw
−1
day
−1
in June, increasing to 11.7 μmol N gdw
−1
day
−1
in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB
amoA
gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally.
Nitrosomonas
spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA
amoA
gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly
Nitrosomonas
spp.) were of major significance in nitrification.
Transcriptional Activation of Multiple Operons Involved in
para
-Nitrophenol Degradation by Pseudomonas sp. Strain WBC-3
Authors: Zhang Wen-Mao , Zhang Jun-Jie , Jiang Xuan , Chao Hongjun , Zhou Ning-Yi
Published: October 2014

Pseudomonas
sp. strain WBC-3 utilizes
para
-nitrophenol (PNP) as a sole carbon and energy source. The genes involved in PNP degradation are organized in the following three operons:
pnpA
,
pnpB
, and
pnpCDEFG
. How the expression of the genes is regulated is unknown. In this study, an LysR-type transcriptional regulator (LTTR) is identified to activate the expression of the genes in response to the specific inducer PNP. While the LTTR coding gene
pnpR
was found to be not physically linked to any of the three catabolic operons, it was shown to be essential for the growth of strain WBC-3 on PNP. Furthermore, PnpR positively regulated its own expression, which is different from the function of classical LTTRs. A regulatory binding site (RBS) with a 17-bp imperfect palindromic sequence (GTT-N
11
-AAC) was identified in all
pnpA
,
pnpB
,
pnpC
, and
pnpR
promoters. Through electrophoretic mobility shift assays and mutagenic analyses, this motif was proven to be necessary for PnpR binding. This consensus motif is centered at positions approximately −55 bp relative to the four transcriptional start sites (TSSs). RBS integrity was required for both high-affinity PnpR binding and transcriptional activation of
pnpA
,
pnpB
, and
pnpR
. However, this integrity was essential only for high-affinity PnpR binding to the promoter of
pnpCDEFG
and not for its activation. Intriguingly, unlike other LTTRs studied, no changes in lengths of the PnpR binding regions of the
pnpA
and
pnpB
promoters were observed after the addition of the inducer PNP in DNase I footprinting.
Discovery of a Conjugative Megaplasmid in Bifidobacterium breve
Authors: Bottacini Francesca , O'Connell Motherway Mary , Casey Eoghan , McDonnell Brian , Mahony Jennifer , Ventura Marco , van Sinderen Douwe
Published: October 2014

Bifidobacterium breve
is a common and sometimes very abundant inhabitant of the human gut. Genome sequencing of
B. breve
JCM 7017 revealed the presence of an extrachromosomal element, designated pMP7017 consisting of >190 kb, thus representing the first reported bifidobacterial megaplasmid.
In silico
characterization of this element revealed several genomic features supporting a stable establishment of the megaplasmid in its host, illustrated by predicted CRISPR-Cas functions that are known to protect the host against intrusion of foreign DNA. Interestingly, pMP7017 is also predicted to encode a conjugative DNA transfer apparatus and, consistent with this notion, we demonstrate here the conjugal transfer of pMP7017 to representative strains of
B. breve
and
B. longum
subsp.
longum
. We also demonstrate the presence of a megaplasmid with homology to pMP7017 in three
B. longum
subsp.
longum
strains.
Nationwide Surveillance Study of Clostridium difficile in Australian Neonatal Pigs Shows High Prevalence and Heterogeneity of PCR Ribotypes
Authors: Knight Daniel R. , Squire Michele M. , Riley Thomas V.
Published: October 2014

Clostridium difficile
is an important enteric pathogen of humans and the cause of diarrhea and enteritis in neonatal pigs. Outside Australia, prevalence in piglets can be up to 73%, with a single PCR ribotype (RT), 078, predominating. We investigated the prevalence and genotype of
C. difficile
in Australian pig herds. Rectal swabs (
n
= 229) were collected from piglets aged <7 days from 21 farms across Australia. Selective culture for
C. difficile
was performed and isolates characterized by PCR for toxin genes and PCR ribotyping.
C. difficile
was isolated from 52% of samples by direct culture on chromogenic agar and 67% by enrichment culture (
P
= 0.001). No association between
C. difficile
recovery or genotype and diarrheic status of either farm or piglets was found. The majority (87%; 130/154) of isolates were toxigenic. Typing revealed 23 different RTs, several of which are known to cause disease in humans, including RT014, which was isolated most commonly (23%; 36/154). RT078 was not detected. This study shows that colonization of Australian neonatal piglets with
C. difficile
is widespread in the herds sampled.