bluuebunny/crossref_metadata_2025 huggingface dataset:
Pulse-number discrimination by Cope's gray treefrog (Hyla chrysoscelis) in modulated and unmodulated noise
Authors: Vélez Alejandro , Linehan-Skillings Betsy Jo , Gu Yuwen , Sun Yuting , Bee Mark A.
Published: October 2013

In Cope's gray treefrog (Hyla chrysoscelis), thresholds for recognizing conspecific calls are lower in temporally modulated noise backgrounds compared with unmodulated noise. The effect of modulated noise on discrimination among different conspecific calls is unknown. In quiet, females prefer calls with relatively more pulses. This study tested the hypotheses that noise impairs selectivity for longer calls and that processes akin to dip listening in modulated noise can ameliorate this impairment. In two-stimulus choice tests, female subjects were allowed to choose between an average-length call and a shorter or longer alternative. Tests were replicated at two signal levels in quiet and in the presence of chorus-shaped noise that was unmodulated, modulated by a sinusoid, or modulated by envelopes resembling natural choruses. When subjects showed a preference, it was always for the relatively longer call. Noise reduced preferences for longer calls, but the magnitude of this reduction was unrelated to whether the noise envelope was modulated or unmodulated. Together, the results are inconsistent with the hypothesis that dip listening improves a female gray treefrog's ability to select longer calls in modulated compared with unmodulated noise.
Ocean noise in the tropical and subtropical Pacific Ocean
Authors: Širović Ana , Wiggins Sean M. , Oleson Erin M.
Published: October 2013

Ocean ambient noise is well studied in the North Pacific and North Atlantic but is poorly described for most of the worlds' oceans. Calibrated passive acoustic recordings were collected during 2009–2010 at seven locations in the central and western tropical and subtropical Pacific. Monthly and hourly mean power spectra (15–1000 Hz) were calculated in addition to their skewness, kurtosis, and percentile distributions. Overall, ambient noise at these seven sites was 10–20 dB lower than reported recently for most other locations in the North Pacific. At frequencies <100 Hz, spectrum levels were equivalent to those predicted for remote or light shipping. Noise levels in the 40 Hz band were compared to the presence of nearby and distant ships as reported to the World Meteorological Organization Voluntary Observing Ship Scheme (VOS) project. There was a positive, but nonsignificant correlation between distant shipping and low frequency noise (at 40 Hz). There was a seasonal variation in ambient noise at frequencies >200 Hz with higher levels recorded in the winter than in the summer. Several species of baleen whales, humpback (Megaptera novaeangliae), blue (Balaenoptera musculus), and fin (B. physalus) whales, also contributed seasonally to ambient noise in characteristic frequency bands.
A steered response power iterative method for high-accuracy acoustic source localization
Authors: Marti Amparo , Cobos Maximo , Lopez Jose J. , Escolano Jose
Published: October 2013

Source localization using the steered response power (SRP) usually requires a costly grid-search procedure. To address this issue, a modified SRP algorithm was recently introduced, providing improved robustness when using coarser spatial grids. In this letter, an iterative method based on the modified SRP is presented. A coarse spatial grid is initially evaluated with the modified SRP, selecting the point with the highest accumulated value. Then, its corresponding volume is iteratively decomposed by using a finer spatial grid. Experiments have shown that this method provides almost the same accuracy as the fine-grid search with a substantial reduction of functional evaluations.
Just noticeable difference of tone pitch contour change for English- and Chinese-native listeners
Authors: Liu Chang
Published: October 2013

Just noticeable differences of tone pitch contour discrimination were examined for young English- and Mandarin Chinese-native listeners to examine categorical features of tone perception for the two groups of listeners. Three types of stimuli were used: A Mandarin Chinese vowel, an English vowel, and tonal glides. Level, rising, and falling tones within or across tone boundaries served as the standard stimuli to measure thresholds of tone pitch discrimination. Performance was equivalent between English- and Chinese-native listeners for level tones, but significantly differed for rising and falling tones, regardless of the type of stimuli. English listeners showed significantly lower thresholds at the offset of F0 shifts than Chinese listeners, while Chinese listeners discriminated tone pitch changes at the onset with significantly lower thresholds than their English peers. These psychophysical results, combined with tone perception reported in other studies, indicated that Mandarin-native listeners perceived lexical tones in a categorical manner, based on their lexical tone experience, whereas English-native listeners perceived tones on a psychophysical base.
Effect of mismatched place-of-stimulation on binaural fusion and lateralization in bilateral cochlear-implant users
Authors: Kan Alan , Stoelb Corey , Litovsky Ruth Y. , Goupell Matthew J.
Published: October 2013

Bilateral cochlear implants (CIs) have provided some success in improving spatial hearing abilities to patients, but with large variability in performance. One reason for the variability is that there may be a mismatch in the place-of-stimulation arising from electrode arrays being inserted at different depths in each cochlea. Goupell et al. [(2013b). J. Acoust. Soc. Am. 133(4), 2272–2287] showed that increasing interaural mismatch led to non-fused auditory images and poor lateralization of interaural time differences in normal hearing subjects listening to a vocoder. However, a greater bandwidth of activation helped mitigate these effects. In the present study, the same experiments were conducted in post-lingually deafened bilateral CI users with deliberate and controlled interaural mismatch of single electrode pairs. Results show that lateralization was still possible with up to 3 mm of interaural mismatch, even when off-center, or multiple, auditory images were perceived. However, mismatched inputs are not ideal since it leads to a distorted auditory spatial map. Comparison of CI and normal hearing listeners showed that the CI data were best modeled by a vocoder using Gaussian-pulsed tones with 1.5 mm bandwidth. These results suggest that interaural matching of electrodes is important for binaural cues to be maximally effective.
Echo thresholds for reflections from acoustically diffusive architectural surfaces
Authors: Robinson Philip W. , Walther Andreas , Faller Christof , Braasch Jonas
Published: October 2013

When sound reflects from an irregular architectural surface, it spreads spatially and temporally. Extensive research has been devoted to prediction and measurement of diffusion, but less has focused on its perceptual effects. This paper examines the effect of temporal diffusion on echo threshold. There are several notable differences between the waveform of a reflection identical to the direct sound and one from an architectural surface. The onset and offset are damped and the energy is spread in time; hence, the reflection response has a lower peak amplitude, and is decorrelated from the direct sound. The perceptual consequences of these differences are previously undocumented. Echo threshold tests are conducted with speech and music signals, using direct sound and a simulated reflection that is either identical to the direct sound or has various degrees of diffusion. Results indicate that for a speech signal, diffuse reflections are less easily detectable as a separate auditory event than specular reflections of the same total energy. For a music signal, no differences are observed between the echo thresholds for reflections with and without temporal diffusion. Additionally, echo thresholds are found to be shorter for speech than for music, and shorter for spatialized than for diotic presentation of signals.
An algorithm to improve speech recognition in noise for hearing-impaired listeners
Authors: Healy Eric W. , Yoho Sarah E. , Wang Yuxuan , Wang DeLiang
Published: October 2013

Despite considerable effort, monaural (single-microphone) algorithms capable of increasing the intelligibility of speech in noise have remained elusive. Successful development of such an algorithm is especially important for hearing-impaired (HI) listeners, given their particular difficulty in noisy backgrounds. In the current study, an algorithm based on binary masking was developed to separate speech from noise. Unlike the ideal binary mask, which requires prior knowledge of the premixed signals, the masks used to segregate speech from noise in the current study were estimated by training the algorithm on speech not used during testing. Sentences were mixed with speech-shaped noise and with babble at various signal-to-noise ratios (SNRs). Testing using normal-hearing and HI listeners indicated that intelligibility increased following processing in all conditions. These increases were larger for HI listeners, for the modulated background, and for the least-favorable SNRs. They were also often substantial, allowing several HI listeners to improve intelligibility from scores near zero to values above 70%.
Vowel identification by cochlear implant users: Contributions of static and dynamic spectral cues
Authors: Donaldson Gail S. , Rogers Catherine L. , Cardenas Emily S. , Russell Benjamin A. , Hanna Nada H.
Published: October 2013

Previous research has shown that normal hearing listeners can identify vowels in syllables on the basis of either quasi-static or dynamic spectral cues; however, it is not known how well cochlear implant (CI) users with current-generation devices can make use of these cues. The present study assessed vowel identification in adult CI users and a comparison group of young normal hearing (YNH) listeners. Stimuli were naturally spoken /dVd/ syllables and modified syllables that retained only quasi-static spectral cues from an 80-ms segment of the vowel center (“C80” stimuli) or dynamic spectral cues from two 20-ms segments of the vowel edges (“E20” stimuli). YNH listeners exhibited near-perfect performance for the unmodified (99.8%) and C80 (92.9%) stimuli and maintained good performance for the E20 stimuli (70.2%). CI users exhibited poorer average performance than YNH listeners for the Full stimuli (72.3%) and proportionally larger reductions in performance for the C80 stimuli (41.8%) and E20 stimuli (29.0%). Findings suggest that CI users have difficulty identifying vowels on the basis of spectral cues in the absence of duration cues, and have limited access to brief dynamic spectral cues. Error analyses suggest that CI users may rely strongly on vowel duration cues when those cues are available.
Room geometry inference based on spherical microphone array eigenbeam processing
Authors: Mabande Edwin , Kowalczyk Konrad , Sun Haohai , Kellermann Walter
Published: October 2013

The knowledge of parameters characterizing an acoustic environment, such as the geometric information about a room, can be used to enhance the performance of several audio applications. In this paper, a novel method for three-dimensional room geometry inference based on robust and high-resolution beamforming techniques for spherical microphone arrays is presented. Unlike other approaches that are based on the measurement and processing of multiple room impulse responses, here, microphone array signal processing techniques for uncontrolled broadband acoustic signals are applied. First, the directions of arrival (DOAs) and time differences of arrival (TDOAs) of the direct signal and room reflections are estimated using high-resolution robust broadband beamforming techniques and cross-correlation analysis. In this context, the main challenges include the low reflected-signal to background-noise power ratio, the low energy of reflected signals relative to the direct signal, and their strong correlation with the direct signal and among each other. Second, the DOA and TDOA information is combined to infer the room geometry using geometric relations. The high accuracy of the proposed room geometry inference technique is confirmed by experimental evaluations based on both simulated and measured data for moderately reverberant rooms.
Partial differential equation-based localization of a monopole source from a circular array
Authors: Ando Shigeru , Nara Takaaki , Levy Tsukassa
Published: October 2013

Wave source localization from a sensor array has long been the most active research topics in both theory and application. In this paper, an explicit and time-domain inversion method for the direction and distance of a monopole source from a circular array is proposed. The approach is based on a mathematical technique, the weighted integral method, for signal/source parameter estimation. It begins with an exact form of the source-constraint partial differential equation that describes the unilateral propagation of wide-band waves from a single source, and leads to exact algebraic equations that include circular Fourier coefficients (phase mode measurements) as their coefficients. From them, nearly closed-form, single-shot and multishot algorithms are obtained that is suitable for use with band-pass/differential filter banks. Numerical evaluation and several experimental results obtained using a 16-element circular microphone array are presented to verify the validity of the proposed method.
The salience of enhanced components within inharmonic complexes
Authors: Byrne Andrew J. , Stellmack Mark A. , Viemeister Neal F.
Published: October 2013

A subjective listening task was used to measure the salience of enhanced components using typical intensity-enhancement stimuli, time-reversed versions of those stimuli, and stimuli which contained a frequency shift of the target component. Twenty-five listeners judged whether or not a pitch “stood out” within an inharmonic complex. For comparison, judgments also were made for stimuli with a single segment that consisted of a simultaneously masked target. The results indicate that the perceived salience of enhanced components is greater than might be predicted by the effective magnitude of those components, and that informational masking is likely involved.
Phase effects on the masking of speech by harmonic complexes: Variations with level
Authors: Green Tim , Rosen Stuart
Published: October 2013

Speech reception thresholds were obtained in normally hearing listeners for sentence targets masked by harmonic complexes constructed with different phase relationships. Maskers had either a constant fundamental frequency (F0), or had F0 changing over time, following a pitch contour extracted from natural speech. The median F0 of the target speech was very similar to that of the maskers. In experiment 1 differences in the masking produced by Schroeder positive and Schroeder negative phase complexes were small (around 1.5 dB) for moderate levels [60 dB sound pressure level (SPL)], but increased to around 6 dB for maskers at 80 dB SPL. Phase effects were typically around 1.5 dB larger for maskers that had naturally varying F0 contours than for maskers with constant F0. Experiment 2 showed that shaping the long-term spectrum of the maskers to match the target speech had no effect. Experiment 3 included additional phase relationships at moderate levels and found no effect of phase. Therefore, the phase relationship within harmonic complexes appears to have only minor effects on masking effectiveness, at least at moderate levels, and when targets and maskers are in the same F0 range.
Sound exposure of professional orchestral musicians during solitary practice
Authors: O'Brien Ian , Driscoll Tim , Ackermann Bronwen
Published: October 2013

It is broadly acknowledged that professional orchestral musicians risk noise-induced hearing pathologies due to sound exposure in rehearsal and performance. While much has been published regarding orchestral sound levels, little is known of the sound exposure these musicians experience during solitary practice, despite the many hours they spend engaged in this activity. This study aimed to determine sound exposure during solitary practice of 35 professional orchestral musicians, representing players of most orchestral instruments. To allow cross-comparison, participants were assessed playing similar repertoire in a controlled environment, recording simultaneously at each ear to determine sound exposure levels. Sound levels were recorded between 60 and 107 dB LAeq, with peak levels between 101 and 130 dB LC,peak. For average reported practice durations (2.1 h per day, five days a week) 53% would exceed accepted permissible daily noise exposure in solitary practice, in addition to sound exposure during orchestral rehearsals and performances. Significant inter-aural differences were noted in violin, viola, flute/piccolo, horn, trombone, and tuba. Only 40% used hearing protection at any time while practicing. These findings indicate orchestral musicians at risk of noise-induced hearing loss in ensemble face significant additional risks during solitary practice. Data presented will enable more effective and targeted management strategies for this population.
Two Histone Deacetylases, FfHda1 and FfHda2, Are Important for Fusarium fujikuroi Secondary Metabolism and Virulence
Authors: Studt L. , Schmidt F. J. , Jahn L. , Sieber C. M. K. , Connolly L. R. , Niehaus E.-M. , Freitag M. , Humpf H.-U. , Tudzynski B.
Published: October 2013

Histone modifications are crucial for the regulation of secondary metabolism in various filamentous fungi. Here we studied the involvement of histone deacetylases (HDACs) in secondary metabolism in the phytopathogenic fungusFusarium fujikuroi, a known producer of several secondary metabolites, including phytohormones, pigments, and mycotoxins. Deletion of three Zn2+-dependent HDAC-encoding genes,ffhda1,ffhda2, andffhda4, indicated that FfHda1 and FfHda2 regulate secondary metabolism, whereas FfHda4 is involved in developmental processes but is dispensable for secondary-metabolite production inF. fujikuroi. Single deletions offfhda1andffhda2resulted not only in an increase or decrease but also in derepression of metabolite biosynthesis under normally repressing conditions. Moreover, double deletion of both theffhda1andffhda2genes showed additive but also distinct phenotypes with regard to secondary-metabolite biosynthesis, and both genes are required for gibberellic acid (GA)-induced bakanae disease on the preferred host plant rice, as Δffhda1Δffhda2mutants resemble the uninfected control plant. Microarray analysis with a Δffhda1mutant that has lost the major HDAC revealed differential expression of secondary-metabolite gene clusters, which was subsequently verified by a combination of chemical and biological approaches. These results indicate that HDACs are involved not only in gene silencing but also in the activation of some genes. Chromatin immunoprecipitation with the Δffhda1mutant revealed significant alterations in the acetylation state of secondary-metabolite gene clusters compared to the wild type, thereby providing insights into the regulatory mechanism at the chromatin level. Altogether, manipulation of HDAC-encoding genes constitutes a powerful tool to control secondary metabolism in filamentous fungi.
Prevalence of Nonpolio Enteroviruses in the Sewage of Guangzhou City, China, from 2009 to 2012
Authors: Zheng Huanying , Lu Jing , Zhang Yong , Yoshida Hiromu , Guo Xue , Liu Leng , Li Hui , Zeng Hanri , Fang Ling , Mo Yanling , Yi Lina , Chosa Toru , Xu Wenbo , Ke Changwen
Published: October 2013

The human-pathogenic viruses in urban sewage have been extensively monitored to obtain information on circulating viruses in human communities. Enteroviruses (EVs) excreted by patients who present with diverse clinical syndromes can remain infectious in the environment for several weeks, and limited data on circulating environmental EVs are available. A 4-year (2009 to 2012) surveillance study was conducted to detect nonpolio enteroviruses (NPEVs) in the urban sewage of Guangzhou city, China. After the viruses in the sewage samples were concentrated and isolated, molecular identification was used to detect and type the NPEVs. During the 4-year study, 17 different NPEV serotypes were identified in the sewage of Guangzhou city. The most common serotypes were echovirus 11 (ECHO11), ECHO6, ECHO7, and ECHO12 and coxsackie group B viruses 5 (CVB5) and CVB3. The predominant serotypes were influenced by spatial and temporal factors and differed each year. CVB5 was commonly detected in 2009 and 2010 but was rarely isolated in 2011 and 2012. In contrast, CVB3 was not observed in 2009 and 2010 but was increasingly detected in 2011 and 2012. Our study provides an overview of the serotype distribution and circulation patterns of NPEVs in the sewage of Guangzhou, China. In the absence of a systematic EV disease surveillance system, the detection and characterization of sewage-borne NPEVs will help us better understand the changes in EV disease trends and the epidemic background of circulating EVs, which could help interpret the EV trends and warn of future outbreaks in this area.
Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor
Authors: Lloyd Karen G. , May Megan K. , Kevorkian Richard T. , Steen Andrew D.
Published: October 2013

There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent
in situ
hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.
Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes
Authors: Brown Celeste J. , Sen Diya , Yano Hirokazu , Bauer Matthew L. , Rogers Linda M. , Van der Auwera Geraldine A. , Top Eva M.
Published: October 2013

Broad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.
Isolation and Characterization of Burkholderia rinojensis sp. nov., a Non-Burkholderia cepacia Complex Soil Bacterium with Insecticidal and Miticidal Activities
Authors: Cordova-Kreylos Ana Lucia , Fernandez Lorena E. , Koivunen Marja , Yang April , Flor-Weiler Lina , Marrone Pamela G.
Published: October 2013

Isolate A396, a bacterium isolated from a Japanese soil sample demonstrated strong insecticidal and miticidal activities in laboratory bioassays. The isolate was characterized through biochemical methods, fatty acid methyl ester (FAME) analysis, sequencing of 16S rRNA, multilocus sequence typing and analysis, and DNA-DNA hybridization. FAME analysis matched A396 to
Burkholderia cenocepacia
, but this result was not confirmed by 16S rRNA or DNA-DNA hybridization. 16S rRNA sequencing indicated closest matches with
B. glumae
and
B. plantarii
. DNA-DNA hybridization experiments with
B. plantarii
,
B. glumae
,
B. multivorans
, and
B. cenocepacia
confirmed the low genetic similarity (11.5 to 37.4%) with known members of the genus. PCR-based screening showed that A396 lacks markers associated with members of the
B. cepacia
complex. Bioassay results indicated two mechanisms of action: through ingestion and contact. The isolate effectively controlled beet armyworms (
Spodoptera exigua
; BAW) and two-spotted spider mites (
Tetranychus urticae
; TSSM). In diet overlay bioassays with BAW, 1% to 4% (vol/vol) dilution of the whole-cell broth caused 97% to 100% mortality 4 days postexposure, and leaf disc treatment bioassays attained 75% ± 22% mortality 3 days postexposure. Contact bioassays led to 50% larval mortality, as well as discoloration, stunting, and failure to molt. TSSM mortality reached 93% in treated leaf discs. Activity was maintained in cell-free supernatants and after heat treatment (60°C for 2 h), indicating that a secondary metabolite or excreted thermostable enzyme might be responsible for the activity. Based on these results, we describe the novel species
Burkholderia rinojensis
, a good candidate for the development of a biocontrol product against insect and mite pests.
A Chrysodeixis chalcites Single-Nucleocapsid Nucleopolyhedrovirus Population from the Canary Islands Is Genotypically Structured To Maximize Survival
Authors: Bernal Alexandra , Simón Oihane , Williams Trevor , Muñoz Delia , Caballero Primitivo
Published: October 2013

A
Chrysodeixis chalcites
single-nucleocapsid nucleopolyhedrovirus wild-type isolate from the Canary Islands, Spain, named ChchSNPV-TF1 (ChchTF1-wt), appears to have great potential as the basis for a biological insecticide for control of the pest. An improved understanding of the genotypic structure of this wild-type strain population should facilitate the selection of genotypes for inclusion in a bioinsecticidal product. Eight genetically distinct genotypes were cloned
in vitro
: ChchTF1-A to ChchTF1-H. Quantitative real-time PCR (qPCR) analysis confirmed that ChchTF1-A accounted for 36% of the genotypes in the wild-type population. In bioassays, ChchTF1-wt occlusion bodies (OBs) were significantly more pathogenic than any of the component single-genotype OBs, indicating that genotype interactions were likely responsible for the pathogenicity phenotype of wild-type OBs. However, the wild-type population was slower killing and produced higher OB yields than any of the single genotypes alone. These results strongly suggested that the ChchTF1-wt population is structured to maximize its transmission efficiency. Experimental OB mixtures and cooccluded genotype mixtures containing the most abundant and the rarest genotypes, at frequencies similar to those at which they were isolated, revealed a mutualistic interaction that restored the pathogenicity of OBs. In OB and cooccluded mixtures containing only the most abundant genotypes, ChchTF1-ABC, OB pathogenicity was even greater than that of wild-type OBs. The ChchTF1-ABC cooccluded mixture killed larvae 33 h faster than the wild-type population and remained genotypically and biologically stable throughout five successive passages
in vivo
. In conclusion, the ChchTF1-ABC mixture shows great potential as the active ingredient of a bioinsecticide to control
C. chalcites
in the Canary Islands.
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
Authors: Contreras-Moreira Bruno , Vinuesa Pablo
Published: October 2013

GET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles, or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain composition of proteins using the HMMER3 package, by imposing desired pairwise alignment coverage cutoffs, or by selecting only syntenic genes. The resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation, and graphical display of core genome and pangenome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core genome and pangenome sizes, and high-quality graphics can be generated. Furthermore, pangenome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50
Streptococcus
genomes annotated in the Orthologous Matrix (OMA) browser as a benchmark case. The package can be downloaded at
http://www.eead.csic.es/compbio/soft/gethoms.php
and
http://maya.ccg.unam.mx/soft/gethoms.php
.
Oxidation of the Cyclic Ethers 1,4-Dioxane and Tetrahydrofuran by a Monooxygenase in Two Pseudonocardia Species
Authors: Sales Christopher M. , Grostern Ariel , Parales Juanito V. , Parales Rebecca E. , Alvarez-Cohen Lisa
Published: October 2013

The bacteriumPseudonocardia dioxanivoransCB1190 grows on the cyclic ethers 1,4-dioxane (dioxane) and tetrahydrofuran (THF) as sole carbon and energy sources. Prior transcriptional studies indicated that an annotated THF monooxygenase (THF MO) gene cluster,thmADBC, located on a plasmid in CB1190 is upregulated during growth on dioxane. In this work, transcriptional analysis demonstrates that upregulation ofthmADBCoccurs during growth on the dioxane metabolite β-hydroxyethoxyacetic acid (HEAA) and on THF. Comparison of the transcriptomes of CB1190 grown on THF and succinate (an intermediate of THF degradation) permitted the identification of other genes involved in THF metabolism. Dioxane and THF oxidation activity of the THF MO was verified inRhodococcus jostiiRHA1 cells heterologously expressing the CB1190thmADBCgene cluster. Interestingly, thesethmADBCexpression clones accumulated HEAA as a dead-end product of dioxane transformation, indicating that despite its genes being transcriptionally upregulated during growth on HEAA, the THF MO enzyme is not responsible for degradation of HEAA in CB1190. Similar activities were also observed in RHA1 cells heterologously expressing thethmADBCgene cluster fromPseudonocardia tetrahydrofuranoxydansK1.
Lysozyme and Penicillin Inhibit the Growth of Anaerobic Ammonium-Oxidizing Planctomycetes
Authors: Hu Ziye , van Alen Theo , Jetten Mike S. M. , Kartal Boran
Published: October 2013

Anaerobic ammonium-oxidizing (anammox) planctomycetes oxidize ammonium in the absence of molecular oxygen with nitrite as the electron acceptor. Although planctomycetes are generally assumed to lack peptidoglycan in their cell walls, recent genome data imply that the anammox bacteria have the genes necessary to synthesize peptidoglycan-like cell wall structures. In this study, we investigated the effects of two antibacterial agents that target the integrity and synthesis of peptidoglycan (lysozyme and penicillin G) on the anammox bacterium
Kuenenia stuttgartiensis
. The effects of these compounds were determined in both short-term batch incubations and long-term (continuous-cultivation) growth experiments in membrane bioreactors. Lysozyme at 1 g/liter (20 mM EDTA) lysed anammox cells in less than 60 min, whereas penicillin G did not have any observable short-term effects on anammox activity. Penicillin G (0.5, 1, and 5 g/liter) reversibly inhibited the growth of anammox bacteria in continuous-culture experiments. Furthermore, transcriptome analyses of the penicillin G-treated reactor and the control reactor revealed that penicillin G treatment resulted in a 10-fold decrease in the ribosome levels of the cells. One of the cell division proteins (Kustd1438) was downregulated 25-fold. Our results suggested that anammox bacteria contain peptidoglycan-like components in their cell wall that can be targeted by lysozyme and penicillin G-sensitive proteins were involved in their synthesis. Finally, we showed that a continuous membrane reactor system with free-living planktonic cells was a very powerful tool to study the physiology of slow-growing microorganisms under physiological conditions.
Differential Induction of Antimicrobial REGIII by the Intestinal Microbiota and Bifidobacterium breve NCC2950
Authors: Natividad Jane M. M. , Hayes Christina L. , Motta Jean-Paul , Jury Jennifer , Galipeau Heather J. , Philip Vivek , Garcia-Rodenas Clara L. , Kiyama Hiroshi , Bercik Premysl , Verdu Elena F.
Published: October 2013

The intestinal microbiota is a key determinant of gut homeostasis, which is achieved, in part, through regulation of antimicrobial peptide secretion. The aim of this study was to determine the efficiency by which members of the intestinal microbiota induce the antimicrobial peptide REGIII and to elucidate the underlying pathways. We showed that germfree mice have low levels of REGIII-γ in their ileum and colon compared to mice with different intestinal microbiota backgrounds. Colonization with a microbiota of low diversity (altered Schaedler flora) did not induce the expression of REGIII-γ as effectively as a complex community (specific pathogen free). Monocolonization with the probiotic
Bifidobacterium breve
, but not with the nonprobiotic commensal
Escherichia coli
JM83, upregulated REGIII-γ expression. Induction of REGIII-γ by
B. breve
was abrogated in mice lacking MyD88 and Ticam1 signaling. Both live and heat-inactivated
B. breve
but not spent culture medium from
B. breve
induced the expression of REGIII-α, the human ortholog and homolog of REGIII-γ, in human colonic epithelial cells (Caco-2). Taken together, the results suggest that REGIII-γ expression in the intestine correlates with the richness of microbiota composition. Also, specific bacteria such as
Bifidobacterium breve
NCC2950 effectively induce REGIII production in the intestine via the
MyD88-Ticam1
pathway. Treatment with this probiotic may enhance the mucosal barrier and protect the host from infection and inflammation.
Induction of the Cpx Envelope Stress Pathway Contributes to Escherichia coli Tolerance to Antimicrobial Peptides
Authors: Audrain Bianca , Ferrières Lionel , Zairi Amira , Soubigou Guillaume , Dobson Curtis , Coppée Jean-Yves , Beloin Christophe , Ghigo Jean-Marc
Published: October 2013

Antimicrobial peptides produced by multicellular organisms as part of their innate system of defense against microorganisms are currently considered potential alternatives to conventional antibiotics in case of infection by multiresistant bacteria. However, while the mode of action of antimicrobial peptides is relatively well described, resistance mechanisms potentially induced or selected by these peptides are still poorly understood. In this work, we studied the mechanisms of action and resistance potentially induced by ApoEdpL-W, a new antimicrobial peptide derived from human apolipoprotein E. Investigation of the genetic response of
Escherichia coli
upon exposure to sublethal concentrations of ApoEdpL-W revealed that this antimicrobial peptide triggers activation of RcsCDB, CpxAR, and σ
E
envelope stress pathways. This genetic response is not restricted to ApoEdpL-W, since several other antimicrobial peptides, including polymyxin B, melittin, LL-37, and modified S
4
dermaseptin, also activate several
E. coli
envelope stress pathways. Finally, we demonstrate that induction of the CpxAR two-component system directly contributes to
E. coli
tolerance toward ApoEdpL-W, polymyxin B, and melittin. These results therefore show that
E. coli
senses and responds to different antimicrobial peptides by activation of the CpxAR pathway. While this study further extends the understanding of the array of peptide-induced stress signaling systems, it also provides insight into the contribution of Cpx envelope stress pathway to
E. coli
tolerance to antimicrobial peptides.
Exploring the Mechanism of Biocatalyst Inhibition in Microbial Desulfurization
Authors: Abin-Fuentes Andres , Mohamed Magdy El-Said , Wang Daniel I. C. , Prather Kristala L. J.
Published: October 2013

Microbial desulfurization, or biodesulfurization (BDS), of fuels is a promising technology because it can desulfurize compounds that are recalcitrant to the current standard technology in the oil industry. One of the obstacles to the commercialization of BDS is the reduction in biocatalyst activity concomitant with the accumulation of the end product, 2-hydroxybiphenyl (HBP), during the process. BDS experiments were performed by incubating
Rhodococcus erythropolis
IGTS8 resting-cell suspensions with hexadecane at 0.50 (vol/vol) containing 10 mM dibenzothiophene. The resin Dowex Optipore SD-2 was added to the BDS experiments at resin concentrations of 0, 10, or 50 g resin/liter total volume. The HBP concentration within the cytoplasm was estimated to decrease from 1,100 to 260 μM with increasing resin concentration. Despite this finding, productivity did not increase with the resin concentration. This led us to focus on the susceptibility of the desulfurization enzymes toward HBP. Dose-response experiments were performed to identify major inhibitory interactions in the most common BDS pathway, the 4S pathway. HBP was responsible for three of the four major inhibitory interactions identified. The concentrations of HBP that led to a 50% reduction in the enzymes' activities (IC
50
s) for DszA, DszB, and DszC were measured to be 60 ± 5 μM, 110 ± 10 μM, and 50 ± 5 μM, respectively. The fact that the IC
50
s for HBP are all significantly lower than the cytoplasmic HBP concentration suggests that the inhibition of the desulfurization enzymes by HBP is responsible for the observed reduction in biocatalyst activity concomitant with HBP generation.
Release of Free DNA by Membrane-Impaired Bacterial Aerosols Due to Aerosolization and Air Sampling
Authors: Zhen Huajun , Han Taewon , Fennell Donna E. , Mainelis Gediminas
Published: October 2013

We report here that stress experienced by bacteria due to aerosolization and air sampling can result in severe membrane impairment, leading to the release of DNA as free molecules.
Escherichia coli
and
Bacillus atrophaeus
bacteria were aerosolized and then either collected directly into liquid or collected using other collection media and then transferred into liquid. The amount of DNA released was quantified as the cell membrane damage index (

I
D

), i.e., the number of 16S rRNA gene copies in the supernatant liquid relative to the total number in the bioaerosol sample. During aerosolization by a Collison nebulizer, the

I
D

of
E. coli
and
B. atrophaeus
in the nebulizer suspension gradually increased during 60 min of continuous aerosolization. We found that the

I
D

of bacteria during aerosolization was statistically significantly affected by the material of the Collison jar (glass > polycarbonate;
P
< 0.001) and by the bacterial species (
E. coli
>
B. atrophaeus
;
P
< 0.001). When
E. coli
was collected for 5 min by filtration, impaction, and impingement, its

I
D

values were within the following ranges: 0.051 to 0.085, 0.16 to 0.37, and 0.068 to 0.23, respectively; when it was collected by electrostatic precipitation, the

I
D

values (0.011 to 0.034) were significantly lower (
P
< 0.05) than those with other sampling methods. Air samples collected inside an equine facility for 2 h by filtration and impingement exhibited

I
D

values in the range of 0.30 to 0.54. The data indicate that the amount of cell damage during bioaerosol sampling and the resulting release of DNA can be substantial and that this should be taken into account when analyzing bioaerosol samples.
Anaerobic Benzene Oxidation via Phenol in Geobacter metallireducens
Authors: Zhang Tian , Tremblay Pier-Luc , Chaurasia Akhilesh Kumar , Smith Jessica A. , Bain Timothy S. , Lovley Derek R.
Published: October 2013

Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated inGeobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (<0.5 μM) of phenol accumulated in cultures ofGeobacter metallireducensanaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures ofGeobacter sulfurreducens, aGeobacterspecies that cannot metabolize benzene. The phenol produced inG. metallireducenscultures was labeled with18O during growth in H218O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in whichGeobacterspecies are considered to play an important role in anaerobic benzene degradation.
Involvement of Botrytis cinerea Small GTPases BcRAS1 and BcRAC in Differentiation, Virulence, and the Cell Cycle
Authors: Minz Dub Anna , Kokkelink Leonie , Tudzynski Bettina , Tudzynski Paul , Sharon Amir
Published: October 2013

Small GTPases of the Ras superfamily are highly conserved proteins that are involved in various cellular processes, in particular morphogenesis, differentiation, and polar growth. Here we report on the analysis of RAS1 and RAC homologues from the gray mold fungusBotrytis cinerea. We show that these small GTPases are individually necessary for polar growth, reproduction, and pathogenicity, required for cell cycle progression through mitosis (BcRAC), and may lie upstream of the stress-related mitogen-activated protein kinase (MAPK) signaling pathway.bcras1andbcracdeletion strains had reduced growth rates, and their hyphae were hyperbranched and deformed. In addition, both strains were vegetatively sterile and nonpathogenic. A strain expressing a constitutively active (CA) allele of the BcRAC protein had partially similar but milder phenotypes. Similar to the deletion strains, the CA-BcRAC strain did not produce any conidia and had swollen hyphae. In contrast to the two deletion strains, however, the growth rate of the CA-BcRAC strain was normal, and it caused delayed but well-developed disease symptoms. Microscopic examination revealed an increased number of nuclei and disturbance of actin localization in the CA-BcRAC strain. Further work with cell cycle- and RAC-specific inhibitory compounds associated the BcRAC protein with progression of the cell cycle through mitosis, possibly via an effect on microtubules. Together, these results show that the multinucleate phenotype of the CA-BcRAC strain could result from at least two defects: disruption of polar growth through disturbed actin localization and uncontrolled nuclear division due to constitutive activity of BcRAC.
Strategies To Discover the Structural Components of Cyst and Oocyst Walls
Authors: Samuelson John , Bushkin G. Guy , Chatterjee Aparajita , Robbins Phillips W.
Published: October 2013

Cysts of
Giardia lamblia
and
Entamoeba histolytica
and oocysts of
Toxoplasma gondii
and
Cryptosporidium parvum
are the infectious and sometimes diagnostic forms of these parasites. To discover the structural components of cyst and oocyst walls, we have developed strategies based upon a few simple assumptions. Briefly, the most abundant wall proteins are identified by monoclonal antibodies or mass spectrometry. Structural components include a sugar polysaccharide (chitin for
Entamoeba
, β-1,3-linked glucose for
Toxoplasma
, and β-1,3-linked GalNAc for
Giardia
) and/or acid-fast lipids (
Toxoplasma
and
Cryptosporidium
). Because
Entamoeba
cysts and
Toxoplasma
oocysts are difficult to obtain, studies of walls of nonhuman pathogens (
E. invadens
and
Eimeria
, respectively) accelerate discovery. Biochemical methods to dissect fungal walls work well for cyst and oocyst walls, although the results are often unexpected. For example, echinocandins, which inhibit glucan synthases and kill fungi, arrest the development of oocyst walls and block their release into the intestinal lumen.
Candida
walls are coated with mannans, while
Entamoeba
cysts are coated in a dextran-like glucose polymer. Models for cyst and oocyst walls derive from their structural components and organization within the wall. Cyst walls are composed of chitin fibrils and lectins that bind chitin (
Entamoeba
) or fibrils of the β-1,3-GalNAc polymer and lectins that bind the polymer (
Giardia
). Oocyst walls of
Toxoplasma
have two distinct layers that resemble those of fungi (β-1,3-glucan in the inner layer) or mycobacteria (acid-fast lipids in the outer layer). Oocyst walls of
Cryptosporidium
have a rigid bilayer of acid-fast lipids and inner layer of oocyst wall proteins.