bluuebunny/crossref_metadata_2025 huggingface dataset:
Matched-field geoacoustic inversion with a horizontal array and low-level source
Authors: Tollefsen Dag , Dosso Stan E. , Wilmut Michael J.
Published: September 2006

This paper applies geoacoustic inversion to acoustic-field data collected on a bottom-moored horizontal line array due to a continuous-wave towed source at a shallow water site in the Barents Sea. The source transmitted tones in the frequency band of 30–160Hz at levels comparable to those of a merchant ship, with resulting signal-to-noise ratios of 9–15dB. Bayesian inversion is applied to cross-spectral density matrices formed by averaging spectra from a sequence of time-series segments (snapshots). Quantifying data errors, including measurement and theory errors, is an important component of Bayesian inversion. To date, data error estimation for snapshot-averaged data has assumed either that averaging reduces errors as if they were fully independent between snapshots, or that averaging does not reduce errors at all. This paper quantifies data errors assuming that averaging reduces measurement error (dominated by ambient noise) but does not reduce theory (modeling) error, providing a physically reasonable intermediary between the two assumptions. Inversion results in the form of marginal posterior probability distributions are compared for the different approaches to data error estimation, and for data collected at several source ranges and bearings. Geoacoustic parameter estimates are compared with data from supporting geophysical measurements and historical data from the region.
Comparing tongue shapes from ultrasound imaging using smoothing spline analysis of variance
Authors: Davidson Lisa
Published: September 2006

Ultrasound imaging of the tongue is increasingly common in speech production research. However, there has been little standardization regarding the quantification and statistical analysis of ultrasound data. In linguistic studies, researchers may want to determine whether the tongue shape for an articulation under two different conditions (e.g., consonants in word-final versus word-medial position) is the same or different. This paper demonstrates how the smoothing spline ANOVA (SS ANOVA) can be applied to the comparison of tongue curves [Gu, Smoothing Spline ANOVA Models (Springer, New York, 2002)]. The SS ANOVA is a technique for determining whether or not there are significant differences between the smoothing splines that are the best fits for two data sets being compared. If the interaction term of the SS ANOVA model is statistically significant, then the groups have different shapes. Since the interaction may be significant even if only a small section of the curves are different (i.e., the tongue root is the same, but the tip of one group is raised), Bayesian confidence intervals are used to determine which sections of the curves are statistically different. SS ANOVAs are illustrated with some data comparing obstruents produced in word-final and word-medial coda position.
Spectral and threshold effects on recognition of speech at higher-than-normal levels
Authors: Dubno Judy R. , Horwitz Amy R. , Ahlstrom Jayne B.
Published: September 2006

To examine spectral and threshold effects for speech and noise at high levels, recognition of nonsense syllables was assessed for low-pass-filtered speech and speech-shaped maskers and high-pass-filtered speech and speech-shaped maskers at three speech levels, with signal-to-noise ratio held constant. Subjects were younger adults with normal hearing and older adults with normal hearing but significantly higher average quiet thresholds. A broadband masker was always present to minimize audibility differences between subject groups and across presentation levels. For subjects with lower thresholds, the declines in recognition of low-frequency syllables in low-frequency maskers were attributed to nonlinear growth of masking which reduced “effective” signal-to-noise ratio at high levels, whereas the decline for subjects with higher thresholds was not fully explained by nonlinear masking growth. For all subjects, masking growth did not entirely account for declines in recognition of high-frequency syllables in high-frequency maskers at high levels. Relative to younger subjects with normal hearing and lower quiet thresholds, older subjects with normal hearing and higher quiet thresholds had poorer consonant recognition in noise, especially for high-frequency speech in high-frequency maskers. Age-related effects on thresholds and task proficiency may be determining factors in the recognition of speech in noise at high levels.
Vector intensity field scattered by a rigid prolate spheroid
Authors: Rapids Brian R. , Lauchle Gerald C.
Published: September 2006

The short-wavelength, steady-state vector intensity field scattered by a rigid prolate spheroid (10:1 fineness ratio) is investigated analytically. The intensity field is the product of the scalar acoustic pressure and the acoustic particle velocity fields which are computed from the Helmholtz equation in prolate spheroidal coordinates. Particular emphasis is placed on results in the forward-scattered direction. It is found that the equivalent plane wave intensity varies by less than ±0.5dB (relative to the incident acoustic intensity) in the far-forward-scattered direction with the selected parameters. This illustrates that the forward-scattered pressure is masked by and interferes with the incident wave. The reactive intensity in the forward-scattered direction is found to be −25dB relative to the incident active intensity, and the computed phase difference between pressure and particle velocity is 4° at ranges approaching 10 spheroid lengths at a reduced frequency of h=41.7; in the absence of the spheroid, the phase difference due to the incident plane wave alone is exactly 0°. The study demonstrates that unique information, extending beyond direction-of-arrival estimation, can be derived from the total acoustic intensity field and may allow inferences to be made regarding the presence or absence of the spheroid.
The viability of reflection loss measurement inversion to predict broadband acoustic behavior
Authors: Isakson Marcia J. , Neilsen Tracianne B.
Published: September 2006

The viability of using reflection loss measurements for the determination of sediment parameters and the predictions of broadband acoustic behavior is studied as a function of frequency for a dispersive ocean bottom. For this study, a deterministic set of reflection loss values from an idealized dispersive sediment is calculated as a function of grazing angle over a large frequency band 100Hz–1MHz. In each of the four decades of frequency a simulated annealing optimization process is used to invert for the sediment parameters. In addition, a set of rotated coordinates is calculated that reveals the the relative sensitivities of the reflection data to each of the sediment parameters and therefore the ability of the inversion process to converge. The accuracy and precision of each estimate is analyzed. The predicted broadband acoustic behavior from the inverted parameters from each decade band was compared to the original model. Only the estimates obtained from data that include frequencies in the transition region can successfully predict broadband behavior.
Vector sensors and vector sensor line arrays: Comments on optimal array gain and detection
Authors: D’Spain Gerald L. , Luby James C. , Wilson Gary R. , Gramann Richard A.
Published: September 2006

This paper examines array gain and detection performance of single vector sensors and vector sensor line arrays, with focus on the impact of nonacoustic self noise and finite spatial coherence of the noise between the vector sensor components. Analytical results based on maximizing the directivity index show that the particle motion channels should always be included in the processing for optimal detection, regardless of self noise level, as long as the self noise levels are taken into account. The vector properties of acoustic intensity can be used to estimate the levels of nonacoustic noise in ocean measurements. Application of conventional, minimum variance distortionless response, and white-noise-constrained adaptive beamforming methods with ocean acoustic data collected by a single vector sensor illustrate an increase in spatial resolution but a corresponding decrease in beamformer output with increasing beamformer adaptivity. Expressions for the spatial coherence of all pairs of vector sensor components in homogeneous, isotropic noise show that significant coherence exists at half-wavelength spacing between particle motion components. For angular intervals about broadside, an equal spacing of about one wavelength for all components provides maximum directivity index, whereas each of the component spacings should be different to optimize the directivity index for angular intervals about endfire.
The Wigner-Smith matrix in acoustic scattering: Application to fluid-loaded elastic plates
Authors: Franklin H. , Rembert P. , Lenoir O.
Published: September 2006

The Wigner-Smith matrix Q is built up by differentiation of the unitary condition of the scattering matrix S. The matrices Q and S both contain the same information but with different points of view. For structures with simple geometrical shapes such as plates or cavities, the acoustic scattering is a two channel scattering represented by a 2×2 S matrix. The elements of the Q matrix can be described: (i) by means of the phase derivatives of the elements of the matrix S, (ii) by means of the phase derivatives of the eigenvalues of the S matrix. The equivalence of these two descriptions allows one to express the phase derivatives of (i) in terms of the phase derivatives of (ii). The Wigner-Smith matrix concept enables one to unify and to improve both the phase gradient method and the eigenvalue method in the frame of the multichannel scattering. It obviously incorporates the resonance scattering theory. Approximate resonant formulas and numerical results are given for the case of fluid loaded elastic isotropic plates in order to check the validity of the method.
Nonreciprocal Green’s function retrieval by cross correlation
Authors: Wapenaar Kees
Published: September 2006

The cross correlation of two recordings of a diffuse acoustic wave field at different receivers yields the Green’s function between these receivers. In nearly all cases considered so far the wave equation obeys time-reversal invariance and the Green’s function obeys source-receiver reciprocity. Here the theory is extended for nonreciprocal Green’s function retrieval in a moving medium. It appears that the cross correlation result is asymmetric in time. The causal part represents the Green’s function from one receiver to the other whereas the acausal part represents the time-reversed version of the Green’s function along the reverse path.
Temporal properties in clear speech perception
Authors: Liu Sheng , Zeng Fan-Gang
Published: September 2006

Three experiments were conducted to study relative contributions of speaking rate, temporal envelope, and temporal fine structure to clear speech perception. Experiment I used uniform time scaling to match the speaking rate between clear and conversational speech. Experiment II decreased the speaking rate in conversational speech without processing artifacts by increasing silent gaps between phonetic segments. Experiment III created “auditory chimeras” by mixing the temporal envelope of clear speech with the fine structure of conversational speech, and vice versa. Speech intelligibility in normal-hearing listeners was measured over a wide range of signal-to-noise ratios to derive speech reception thresholds (SRT). The results showed that processing artifacts in uniform time scaling, particularly time compression, reduced speech intelligibility. Inserting gaps in conversational speech improved the SRT by 1.3dB, but this improvement might be a result of increased short-term signal-to-noise ratios during level normalization. Data from auditory chimeras indicated that the temporal envelope cue contributed more to the clear speech advantage at high signal-to-noise ratios, whereas the temporal fine structure cue contributed more at low signal-to-noise ratios. Taken together, these results suggest that acoustic cues for the clear speech advantage are multiple and distributed.
Perceptual recalibration in human sound localization: Learning to remediate front-back reversals
Authors: Zahorik Pavel , Bangayan Philbert , Sundareswaran V. , Wang Kenneth , Tam Clement
Published: September 2006

The efficacy of a sound localization training procedure that provided listeners with auditory, visual, and proprioceptive/vestibular feedback as to the correct sound-source position was evaluated using a virtual auditory display that used nonindividualized head-related transfer functions (HRTFs). Under these degraded stimulus conditions, in which the monaural spectral cues to sound-source direction were inappropriate, localization accuracy was initially poor with frequent front-back reversals (source localized to the incorrect front-back hemifield) for five of six listeners. Short periods of training (two 30-min sessions) were found to significantly reduce the rate of front-back reversal responses for four of five listeners that showed high initial reversal rates. Reversal rates remained unchanged for all listeners in a control group that did not participate in the training procedure. Because analyses of the HRTFs used in the display demonstrated a simple and robust front-back cue related to energy in the 3–7-kHz bandwidth, it is suggested that the reductions observed in reversal rates following the training procedure resulted from improved processing of this front-back cue, which is perhaps a form of rapid perceptual recalibration. Reversal rate reductions were found to generalize to untrained source locations, and persisted at least 4months following the training procedure.
Impact of local attenuation approximations when estimating correlation length from backscattered ultrasound echoes
Authors: Bigelow Timothy A. , O’Brien William D.
Published: September 2006

Estimating the characteristic correlation length of tissue microstructure from the backscattered power spectrum could improve the diagnostic capability of medical ultrasound. Previously, size estimates were obtained after compensating for source focusing, the frequency-dependent attenuation along the propagation path (total attenuation), and the frequency-dependent attenuation in the scattering region (local attenuation). In this study, the impact of approximations of the local attenuation on the scatterer size estimate was determined using computer simulations and theoretical analysis. The simulations used Gaussian impedance distributions with an effective radius of 25μm randomly positioned in a homogeneous half-space sonified by a spherically focused source (f∕1 to f∕4). The approximations of the local attenuation that were assessed neglected local attenuation (i.e., assume 0dB∕cm-MHz) neglected frequency dependence of the local attenuation, and assumed a finite frequency dependence (i.e., 0.5dB∕cm-MHz) independent of the true attenuation of the medium. Errors in the scatterer size estimate due to the local attenuation approximations increased with increasing window length, increasing true local attenuation and increasing f number. The most robust estimates were obtained when the local attenuation was approximated by a tissue-independent attenuation value that was greater than 70% of the largest attenuation expected in the tissue region of interest.
Some difference limens for the perception of breathiness
Authors: Shrivastav Rahul , Sapienza Christine M.
Published: September 2006

Perception of breathy voice quality appears to be cued by changes in the vowel spectrum. These changes are related to alterations in the intensity of aspiration noise and spectral slope of the harmonic energy [Shrivastav and Sapienza, J. Acoust. Soc. Am., 114 (4), 2217–2224 (2003)]. Ten young-adult listeners with normal hearing were tested using an adaptive listening task to determine the smallest change in signal-to-noise ratio that resulted in a change in breathiness. Six vowel continua, three female and three male, were generated using a Klatt synthesizer and served as stimuli. Results showed that listeners needed as much as 20-dB increase in aspiration noise to perceive a change in breathiness against a relatively normal voice. In contrast, listeners needed approximately an 11-dB increase in aspiration noise to discriminate breathiness against a severely breathy voice. The difference limens for breathiness were observed to vary across the six talkers. Voices having aspiration noise that was predominantly in the high frequencies had smaller difference limens. No significant differences for male and female voice were observed.
Relationship between time reversal and linear equalization in digital communications
Authors: Higley W. J. , Roux Philippe , Kuperman W. A.
Published: September 2006

Iterative time reversal has been suggested as both an efficient method of creating a spatio-temporal focus and for use in telecommunications as a form of equalization. In this paper, the equivalence of a passive, i.e., via computation, iterative time reversal to the Moore-Penrose pseudo-inverse of the propagation matrix is shown. In the context of communications, however, any received signal is corrupted by noise. Therefore, a regularization term is introduced to the iterative equations, causing convergence to the canonical minimum mean-squared error linear equalizer. Hence, a relationship between time reversal and equalization is demonstrated.
Herpes Simplex Virus Encephalitis in Human UNC-93B Deficiency
Authors: Casrouge Armanda , Zhang Shen-Ying , Eidenschenk Céline , Jouanguy Emmanuelle , Puel Anne , Yang Kun , Alcais Alexandre , Picard Capucine , Mahfoufi Nora , Nicolas Nathalie , Lorenzo Lazaro , Plancoulaine Sabine , Sénéchal Brigitte , Geissmann Frédéric , Tabeta Koichi , Hoebe Kasper , Du Xin , Miller Richard L. , Héron Bénédicte , Mignot Cyril , de Villemeur Thierry Billette , Lebon Pierre , Dulac Olivier , Rozenberg Flore , Beutler Bruce , Tardieu Marc , Abel Laurent , Casanova Jean-Laurent
Published: September 2006

Herpes simplex virus-1 (HSV-1) encephalitis (HSE) is the most common form of sporadic viral encephalitis in western countries. Its pathogenesis remains unclear, as it affects otherwise healthy patients and only a small minority of HSV-1–infected individuals. Here, we elucidate a genetic etiology for HSE in two children with autosomal recessive deficiency in the intracellular protein UNC-93B, resulting in impaired cellular interferon-α/β and -λ antiviral responses. HSE can result from a single-gene immunodeficiency that does not compromise immunity to most pathogens, unlike most known primary immunodeficiencies. Other severe infectious diseases may also reflect monogenic disorders of immunity.
Coherent Dynamics of Coupled Electron and Nuclear Spin Qubits in Diamond
Authors: Childress L. , Gurudev Dutt M. V. , Taylor J. M. , Zibrov A. S. , Jelezko F. , Wrachtrup J. , Hemmer P. R. , Lukin M. D.
Published: September 2006

Understanding and controlling the complex environment of solid-state quantum bits is a central challenge in spintronics and quantum information science. Coherent manipulation of an individual electron spin associated with a nitrogen-vacancy center in diamond was used to gain insight into its local environment. We show that this environment is effectively separated into a set of individual proximal
13
C nuclear spins, which are coupled coherently to the electron spin, and the remainder of the
13
C nuclear spins, which cause the loss of coherence. The proximal nuclear spins can be addressed and coupled individually because of quantum back-action from the electron, which modifies their energy levels and magnetic moments, effectively distinguishing them from the rest of the nuclei. These results open the door to coherent manipulation of individual isolated nuclear spins in a solid-state environment even at room temperature.
Tests of General Relativity from Timing the Double Pulsar
Authors: Kramer M. , Stairs I. H. , Manchester R. N. , McLaughlin M. A. , Lyne A. G. , Ferdman R. D. , Burgay M. , Lorimer D. R. , Possenti A. , D'Amico N. , Sarkissian J. M. , Hobbs G. B. , Reynolds J. E. , Freire P. C. C. , Camilo F.
Published: September 2006

The double pulsar system PSR J0737-3039A/B is unique in that both neutron stars are detectable as radio pulsars. They are also known to have much higher mean orbital velocities and accelerations than those of other binary pulsars. The system is therefore a good candidate for testing Einstein's theory of general relativity and alternative theories of gravity in the strong-field regime. We report on precision timing observations taken over the 2.5 years since its discovery and present four independent strong-field tests of general relativity. These tests use the theory-independent mass ratio of the two stars. By measuring relativistic corrections to the Keplerian description of the orbital motion, we find that the “post-Keplerian” parameter
s
agrees with the value predicted by general relativity within an uncertainty of 0.05%, the most precise test yet obtained. We also show that the transverse velocity of the system's center of mass is extremely small. Combined with the system's location near the Sun, this result suggests that future tests of gravitational theories with the double pulsar will supersede the best current solar system tests. It also implies that the second-born pulsar may not have formed through the core collapse of a helium star, as is usually assumed.
Comparative Genomic Hybridization Analysis of
Enterococcus faecalis
: Identification of Genes Absent from Food Strains
Authors: Lepage E. , Brinster S. , Caron C. , Ducroix-Crepy Céline , Rigottier-Gois L. , Dunny G. , Hennequet-Antier C. , Serror P.
Published: September 2006

Enterococcus faecalis
, a member of the natural microbiota of animal and human intestinal tracts, is also present as a natural contaminant in a variety of fermented foods. Over the last decade,
E. faecalis
has emerged as a major cause of nosocomial infections. We investigated the genetic diversity in 30 clinical and food isolates, including strains V583 and MMH594, in order to determine whether clinical and food isolates could be distinguished. Data were obtained using comparative genomic hybridization and specific PCR with a total of 202 probes of
E. faecalis
, selected using the available V583 genome sequence and part of the MMH594 pathogenicity island. The cognate genes encoded mainly exported proteins. Hybridization data were analyzed by a two-component mixture model that estimates the probability of any given gene to be either present or absent in the strains. A total of 78 genes were found to be variable, as they were absent in at least one isolate. Most of the variable genes were clustered in regions that, in the published V583 sequence, related to prophages or mobile genetic elements. The variable genes were distributed in three main groups: (i) genes equally distributed between clinical and dairy food isolates, (ii) genes absent from dairy food-related isolates, and (iii) genes present in MMH594 and V583 strains only. Further analysis of the distribution of the last gene group in 70 other isolates confirmed that six of the probed genes were always absent in dairy food-related isolates, whereas they were detected in clinical and/or commensal isolates. Two of them corresponded to prophages that were not detected in the cognate isolates, thus possibly extending the number of genes absent from dairy food isolates. Genes specifically detected in clinical isolates may prove valuable for the development of new risk assessment markers for food safety studies and for identification of new factors that may contribute to host colonization or infection.
TheEscherichia coliGTPase CgtAEIs Involved in Late Steps of Large Ribosome Assembly
Authors: Jiang Mengxi , Datta Kaustuv , Walker Angela , Strahler John , Bagamasbad Pia , Andrews Philip C. , Maddock Janine R.
Published: September 2006

The bacterial ribosome is an extremely complicated macromolecular complex the in vivo biogenesis of which is poorly understood. Although several bona fide assembly factors have been identified, their precise functions and temporal relationships are not clearly defined. Here we describe the involvement of anEscherichia coliGTPase, CgtAE, in late steps of large ribosomal subunit biogenesis. CgtAEbelongs to the Obg/CgtA GTPase subfamily, whose highly conserved members are predominantly involved in ribosome function. Mutations in CgtAEcause both polysome and rRNA processing defects; small- and large-subunit precursor rRNAs accumulate in acgtAEmutant. In this study we apply a new semiquantitative proteomic approach to show that CgtAEis required for optimal incorporation of certain late-assembly ribosomal proteins into the large ribosomal subunit. Moreover, we demonstrate the interaction with the 50S ribosomal subunits of specific nonribosomal proteins (including heretofore uncharacterized proteins) and define possible temporal relationships between these proteins and CgtAE. We also show that purified CgtAEassociates with purified ribosomal particles in the GTP-bound form. Finally, CgtAEcofractionates with the mature 50S but not with intermediate particles accumulated in other large ribosome assembly mutants.
Alterations of Cellular Physiology inEscherichia coliin Response to Oxidative Phosphorylation Impaired by Defective F1-ATPase
Authors: Noda Sakiko , Takezawa Yuji , Mizutani Tomohiko , Asakura Tomoaki , Nishiumi Eiichiro , Onoe Kazunori , Wada Masaru , Tomita Fusao , Matsushita Kazunobu , Yokota Atsushi
Published: September 2006

The physiological changes in an F1-ATPase-defective mutant ofEscherichia coliW1485 growing in a glucose-limited chemostat included a decreased growth yield (60%) and increased specific rates of both glucose consumption (168%) and respiration (171%). Flux analysis revealed that the mutant showed approximately twice as much flow in glycolysis but only an 18% increase in the tricarboxylic acid (TCA) cycle, owing to the excretion of acetate, where most of the increased glycolytic flux was directed. Genetic and biochemical analyses of the mutant revealed the downregulation of many TCA cycle enzymes, including citrate synthase, and the upregulation of the pyruvate dehydrogenase complex in both transcription and enzyme activities. These changes seemed to contribute to acetate excretion in the mutant. No transcriptional changes were observed in the glycolytic enzymes, despite the enhanced glycolysis. The most significant alterations were found in the respiratory-chain components. The total activity of NADH dehydrogenases (NDHs) and terminal oxidases increased about twofold in the mutant, which accounted for its higher respiration rate. These changes arose primarily from the increased (3.7-fold) enzyme activity of NDH-2 and an increased amount of cytochromebdin the mutant. Transcriptional upregulation appeared to be involved in these phenomena. As NDH-2 cannot generate an electrochemical gradient of protons and as cytochromebdis inferior to cytochromebo3in this ability, the mutant was able to recycle NADH at a higher rate than the parent and avoid generating an excess proton-motive force. We discuss the physiological benefits of the alterations in the mutant.
Colocation of Genes Encoding a tRNA-mRNA Hybrid and a Putative Signaling Peptide on Complementary Strands in the Genome of the Hyperthermophilic BacteriumThermotoga maritima
Authors: Montero Clemente I. , Lewis Derrick L. , Johnson Matthew R. , Conners Shannon B. , Nance Elizabeth A. , Nichols Jason D. , Kelly Robert M.
Published: September 2006

In the genome of the hyperthermophilic bacteriumThermotoga maritima, TM0504 encodes a putative signaling peptide implicated in population density-dependent exopolysaccharide formation. Although not noted in the original genome annotation, TM0504 was found to colocate, on the opposite strand, with the gene encodingssrA, a hybrid of tRNA and mRNA (tmRNA), which is involved in atrans-translation process related to ribosome rescue and is ubiquitous in bacteria. Specific DNA probes were designed and used in real-time PCR assays to follow the separate transcriptional responses of the colocated open reading frames (ORFs) during transition from exponential to stationary phase, chloramphenicol challenge, and syntrophic coculture withMethanococcus jannaschii. TM0504 transcription did not vary under normal growth conditions. Transcription of the tmRNA gene, however, was significantly up-regulated during chloramphenicol challenge and inT. maritimabound in exopolysaccharide aggregates during methanogenic coculture. The significance of the colocation of ORFs encoding a putative signaling peptide and tmRNA inT. maritimais intriguing, since this overlapping arrangement (tmRNA associated with putative small ORFs) was found to be conserved in at least 181 bacterial genomes sequenced to date. Whether peptides related to TM0504 in other bacteria play a role in quorum sensing is not yet known, but their ubiquitous colocalization with respect to tmRNA merits further examination.
Loss of Expression of
cspC
, a Cold Shock Family Gene, Confers a Gain of Fitness in
Escherichia coli
K-12 Strains
Authors: Rath Devashish , Jawali Narendra
Published: September 2006

The CspA family of cold shock genes in
Escherichia coli
K-12 includes nine paralogs,
cspA
to
cspI
. Some of them have been implicated in cold stress adaptation. Screening for mutations among common laboratory
E. coli
strains showed a high degree of genetic diversity in
cspC
but not in
cspA
and
cspE
. This diversity in
cspC
was due to a wide spectrum of variations including insertions of IS elements, deletion, and point mutation. Northern analysis of these mutants showed loss of
cspC
expression in all but one case. Further analysis of the loss-of-function
cspC
mutants showed that they have a fitness advantage in broth culture after 24 h over their isogenic wild-type derivatives. Conversely, introduction of mutated
cspC
alleles conferred a competitive fitness advantage to AB1157, a commonly used laboratory strain. This provides the evidence that loss of
cspC
expression is both necessary and sufficient to confer a gain of fitness as seen in broth culture over 24 h. Together, these results ascribe a novel role in cellular growth at 37°C for CspC, a member of the cold shock domain-containing protein family.
Chromosome Rearrangement and Diversification of
Francisella tularensis
Revealed by the Type B (OSU18) Genome Sequence
Authors: Petrosino Joseph F. , Xiang Qin , Karpathy Sandor E. , Jiang Huaiyang , Yerrapragada Shailaja , Liu Yamei , Gioia Jason , Hemphill Lisa , Gonzalez Arely , Raghavan T. M. , Uzman Akif , Fox George E. , Highlander Sarah , Reichard Mason , Morton Rebecca J. , Clinkenbeard Kenneth D. , Weinstock George M.
Published: September 2006

The γ-proteobacterium
Francisella tularensis
is one of the most infectious human pathogens, and the highly virulent organism
F. tularensis
subsp.
tularensis
(type A) and less virulent organism
F. tularensis
subsp.
holarctica
(type B) are most commonly associated with significant disease in humans and animals. Here we report the complete genome sequence and annotation for a low-passage type B strain (OSU18) isolated from a dead beaver found near Red Rock, Okla., in 1978. A comparison of the
F. tularensis
subsp.
holarctica
sequence with that of
F. tularensis
subsp.
tularensis
strain Schu4 (P. Larsson et al., Nat. Genet.
37:
153-159, 2005) highlighted genetic differences that may underlie different pathogenicity phenotypes and the evolutionary relationship between type A and type B strains. Despite extensive DNA sequence identity, the most significant difference between type A and type B isolates is the striking amount of genomic rearrangement that exists between the strains. All but two rearrangements can be attributed to homologous recombination occurring between two prominent insertion elements, IS
Ftu1
and IS
Ftu2
. Numerous pseudogenes have been found in the genomes and are likely contributors to the difference in virulence between the strains. In contrast, no rearrangements have been observed between the OSU18 genome and the genome of the type B live vaccine strain (LVS), and only 448 polymorphisms have been found within non-transposase-coding sequences whose homologs are intact in OSU18. Nonconservative differences between the two strains likely include the LVS attenuating mutation(s).
The
atlA
Operon of
Streptococcus mutans
: Role in Autolysin Maturation and Cell Surface Biogenesis
Authors: Ahn Sang-Joon , Burne Robert A.
Published: September 2006

The Smu0630 protein (AtlA) was recently shown to be involved in cell separation, biofilm formation, and autolysis. Here, transcriptional studies revealed that
atlA
is part of a multigene operon under the control of at least three promoters. The morphology and biofilm-forming capacity of a nonpolar
altA
mutant could be restored to that of the wild-type strain by adding purified AtlA protein to the medium. A series of truncated derivatives of AtlA revealed that full activity required the C terminus and repeat regions. AtlA was cell associated and readily extractable from with sodium dodecyl sulfate. Of particular interest, the surface protein profile of AtlA-deficient strains was dramatically altered compared to the wild-type strain, as was the nature of the association of the multifunctional adhesin P1 with the cell wall. In addition, AtlA-deficient strains failed to develop competence as effectively as the parental strain. Mutation of
thmA
, which can be cotranscribed with
atlA
and encodes a putative pore-forming protein, resulted in a phenotype very similar to that of the AtlA-deficient strain. ThmA was also shown to be required for efficient processing of AtlA to its mature form, and treatment of the
thmA
mutant strain with full-length AtlA protein did not restore normal cell separation and biofilm formation. The effects of mutating other genes in the operon on cell division, biofilm formation, or AtlA biogenesis were not as profound. This study reveals that AtlA is a surface-associated protein that plays a critical role in the network connecting cell surface biogenesis, biofilm formation, genetic competence, and autolysis.
Role of an RNase III Binding Site in Transcription Termination at λ
nutL
by HK022 Nun Protein
Authors: Washburn Robert S. , Court Donald L. , Gottesman Max E.
Published: September 2006

The phage HK022 Nun protein excludes phage λ by binding nascent λ
p
L
and
p
R
transcripts at
nutL
and
nutR
, respectively, and inducing transcription termination just downstream of these sites. Termination is more efficient at
nutL
than at
nutR
. One difference between
nutL
and
nutR
is the presence of RNase III processing sites (rIII) located immediately promoter distal to λ
nutL
. We found that deletion of rIII dramatically reduced Nun transcription arrest in vitro but had little effect on termination in vivo. However, consistent with the in vitro results, overexpression of a transcript carrying
nutL
and rIII efficiently titrated Nun, allowing λ to grow on a strain that expressed Nun, whereas a transcript carrying only
nutL
or
nutL-
rIII with nucleotides 97 to 141 deleted was ineffective. Rnc70, an RNase III mutant that binds but does not cleave rIII, also prevented Nun-mediated λ exclusion. We propose that rIII enhances the on-rate of Nun at
nutL
, stimulating Nun-mediated arrest in vitro. We have shown that a specific element in rIII, i.e., box C (G
89
GUGUGUG), strongly enhances arrest on rIII

+

templates. Nun-rIII interactions do not stimulate Nun termination in vivo, presumably because formation of the Nun-
nutL
complex is normally not rate-limiting in the cell. In contrast to Nun, N is not occluded by Rnc70 and is not efficiently titrated by a
nutL
-rIII transcript.
Differential Dependence of StpA on H-NS in Autoregulation of
stpA
and in Regulation of
bgl
Authors: Wolf Tinka , Janzen Wiebke , Blum Corinna , Schnetz Karin
Published: September 2006

StpA has functional similarity to its homologue, the nucleoid structuring protein H-NS. It binds to AT-rich, planar, bent DNA and constrains DNA supercoils. In addition, StpA acts as an RNA chaperone. StpA and H-NS also form heterodimers. However, cellular levels of StpA are low due to repression of
stpA
by H-NS and negative autoregulation. Here we show that effective (30-fold) repression of
stpA
transcription requires a downstream regulator element located within the
stpA
coding region. In addition, we show that StpA represses
stpA
threefold in an
hns
null mutant. In contrast, repression of the
bgl
operon, another H-NS-repressed system, is not achieved by StpA alone. It becomes StpA dependent in the presence of a fusion protein encompassing the N-terminal 37 amino acids of H-NS, which comprise the core of the dimerization domain. StpA also effectively complements H-NS-I119T, a mutant defective in specific DNA binding, in repression of the
bgl
operon. Thus, StpA complements H-NS proteins defective in DNA binding to repress
bgl
, while in autoregulation of
stpA
it acts autonomously, indicating a difference in the mechanisms of repression.
Characterization of Adhesion Threads of
Deinococcus geothermalis
as Type IV Pili
Authors: Saarimaa C. , Peltola M. , Raulio M. , Neu T. R. , Salkinoja-Salonen M. S. , Neubauer P.
Published: September 2006

Deinococcus geothermalis
E50051 forms tenuous biofilms on paper machine surfaces. Field emission electron microscopy analysis revealed peritrichous appendages which mediated cell-to-surface and cell-to-cell interactions but were absent in planktonically grown cells. The major protein component of the extracellular extract of
D. geothermalis
had an N-terminal sequence similar to the fimbrial protein pilin annotated in the
D. geothermalis
DSM 11300 draft sequence. It also showed similarity to the type IV pilin sequence of
D. radiodurans
and several gram-negative pathogenic bacteria. Other proteins in the extract had N-terminal sequences identical to
D. geothermalis
proteins with conservative motifs for serine proteases, metallophosphoesterases, and proteins whose function is unknown. Periodic acid-Schiff staining for carbohydrates indicated that these extracellular proteins may be glycosylated. A further confirmation for the presence of glycoconjugates on the cell surface was obtained by confocal laser scanning imaging of living
D. geothermalis
cells stained with
Amaranthus caudatus
lectin, which specifically binds to galactose residues. The results indicate that the thread-like appendages of
D. geothermalis
E50051 are glycosylated type IV pili, bacterial attachment organelles which have thus far not been described for the genus
Deinococcus
.
Characterization of the
Staphylococcus aureus
Heat Shock, Cold Shock, Stringent, and SOS Responses and Their Effects on Log-Phase mRNA Turnover
Authors: Anderson Kelsi L. , Roberts Corbette , Disz Terrence , Vonstein Veronika , Hwang Kaitlyn , Overbeek Ross , Olson Patrick D. , Projan Steven J. , Dunman Paul M.
Published: September 2006

Despite its being a leading cause of nosocomal and community-acquired infections, surprisingly little is known about
Staphylococcus aureus
stress responses. In the current study, Affymetrix
S. aureus
GeneChips were used to define transcriptome changes in response to cold shock, heat shock, stringent, and SOS response-inducing conditions. Additionally, the RNA turnover properties of each response were measured. Each stress response induced distinct biological processes, subsets of virulence factors, and antibiotic determinants. The results were validated by real-time PCR and stress-mediated changes in antimicrobial agent susceptibility. Collectively, many
S. aureus
stress-responsive functions are conserved across bacteria, whereas others are unique to the organism. Sets of small stable RNA molecules with no open reading frames were also components of each response. Induction of the stringent, cold shock, and heat shock responses dramatically stabilized most mRNA species. Correlations between mRNA turnover properties and transcript titers suggest that
S. aureus
stress response-dependent alterations in transcript abundances can, in part, be attributed to alterations in RNA stability. This phenomenon was not observed within SOS-responsive cells.
Identification and Characterization of a Major Zn(II) Resistance Determinant of
Mycobacterium smegmatis
Authors: Grover Amit , Sharma Rakesh
Published: September 2006

A zinc ion-sensitive mutant of
Mycobacterium smegmatis
was isolated. The transposon insertion was located in
zitA
(MSMEG0750), a gene coding for a cation diffusion facilitator family protein. Zinc ions specifically induced expression of
zitA
. In silico analysis revealed that environmental and opportunistic pathogenic species contain higher numbers of cation diffusion facilitator genes than do obligate pathogens.
PurF-Independent Phosphoribosyl Amine Formation inyjgFMutants ofSalmonella entericaUtilizes the Tryptophan Biosynthetic Enzyme Complex Anthranilate Synthase-Phosphoribosyltransferase
Authors: Browne Beth Ann , Ramos A. Itzel , Downs Diana M.
Published: September 2006

InSalmonella enterica, the biosynthetic pathways for the generation of purines and the essential cofactor thiamine pyrophosphate branch after sharing five enzymatic steps. Phosphoribosyl amine (PRA) is the first intermediate in the common portion of the pathway and is generated from phosphoribosylpyrophosphate and glutamine by the PurF enzyme (phosphoribosylpyrophosphate amidotransferase). A null mutation inyjgFallows PurF-independent PRA formation by an unknown mechanism. The tryptophan biosynthetic enzyme complex anthranilate synthase-phosphoribosyltransferase, composed of the TrpD and TrpE proteins, was shown to be essential for PRA formation in strains lacking bothyjgFandpurF. The activity generating PRA in ayjgFmutant background has features that distinguish it from the TrpDE-mediated PRA formation shown previously for this enzyme in strains with an active copy ofyjgF. The data presented here are consistent with a model in which the absence of YjgF uncovers a new catalytic activity of TrpDE.
Biochemical and Molecular Characterization of the Biosynthesis of Glutamine and Glutamate, Two Major Compatible Solutes in the Moderately Halophilic Bacterium
Halobacillus halophilus
Authors: Saum Stephan H. , Sydow Jasmin F. , Palm Peter , Pfeiffer Friedhelm , Oesterhelt Dieter , Müller Volker
Published: September 2006

The moderately halophilic, chloride-dependent bacterium
Halobacillus halophilus
produces glutamate and glutamine as main compatible solutes at external salinities of 1.0 to 1.5 M NaCl. The routes for the biosynthesis of these solutes and their regulation were examined. The genome contains two genes potentially encoding glutamate dehydrogenases and two genes for the small subunit of a glutamate synthase, but only one gene for the large subunit. However, the expression of these genes was not salt dependent, nor were the corresponding enzymatic activities detectable in cell extracts of cells grown at different salinities. In contrast, glutamine synthetase activity was readily detectable in
H. halophilus
. Induction of glutamine synthetase activity was strictly salt dependent and reached a maximum at 3.0 M NaCl; chloride stimulated the production of active enzyme by about 300%. Two potential genes encoding a glutamine synthetase,
glnA1
and
glnA2
, were identified. The expression of
glnA2
but not of
glnA1
was increased up to fourfold in cells adapted to high salt, indicating that GlnA2 is the glutamine synthetase involved in the synthesis of the solutes glutamate and glutamine. Furthermore, expression of
glnA2
was stimulated twofold by the presence of chloride ions. Chloride exerted an even more pronounced effect on the enzymatic activity of preformed enzyme: in the absence of chloride in the assay buffer, glutamine synthetase activity was decreased by as much as 90%. These data demonstrate for the first time a regulatory role of a component of common salt, chloride, in the biosynthesis of compatible solutes.
PhoP-Induced Genes withinSalmonellaPathogenicity Island 1
Authors: Aguirre Andrés , Cabeza María Laura , Spinelli Silvana V. , McClelland Michael , García Véscovi Eleonora , Soncini Fernando C.
Published: September 2006

The invasive pathogenSalmonella entericahas evolved a sophisticated device that allows it to enter nonphagocytic host cells. This process requires the expression ofSalmonellapathogenicity island 1 (SPI-1), which encodes a specialized type III protein secretion system (TTSS). This TTSS delivers a set of effectors that produce a marked rearrangement of the host cytoskeleton, generating a profuse membrane ruffling at the site of interaction, driving bacterial entry. It has been shown that the PhoP/PhoQ two-component system represses the expression of the SPI-1 machinery by down-regulating the transcription of its master regulator, HilA. In this work, we reveal the presence of a PhoP-activated operon within SPI-1. This operon is composed of theorgBandorgCgenes, which encode a protein that interacts with the InvC ATPase and a putative effector protein of the TTSS, respectively. Under PhoP-inducing conditions, expression of this operon is directly activated by the phosphorylated form of the response regulator, which recognizes a PhoP box located at the −35 region relative to the transcription start site. Additionally, under invasion-inducing conditions,orgBCexpression is driven both by theprgHpromoter, induced by the SPI-1 master regulator HilA, and by the directly controlled PhoP/PhoQ promoter. Together, these results indicate that in contrast to the rest of the genes encompassed in the SPI-1 locus,orgBCis expressed during and afterSalmonellaentry into its host cell, and they suggest a role for the products of this operon after host cell internalization.
Molecular and Population Analyses of a Recombination Event in the Catabolic Plasmid pJP4
Authors: Larraín-Linton Juanita , De la Iglesia Rodrigo , Melo Francisco , González Bernardo
Published: September 2006

Cupriavidus necator
JMP134(pJP4) harbors a catabolic plasmid, pJP4, which confers the ability to grow on chloroaromatic compounds. Repeated growth on 3-chlorobenzoate (3-CB) results in selection of a recombinant strain, which degrades 3-CB better but no longer grows on 2,4-dichlorophenoxyacetate (2,4-D). We have previously proposed that this phenotype is due to a double homologous recombination event between inverted repeats of the multicopies of this plasmid within the cell. One recombinant form of this plasmid (pJP4-F3) explains this phenotype, since it harbors two copies of the chlorocatechol degradation
tfd
gene clusters, which are essential to grow on 3-CB, but has lost the
tfdA
gene, encoding the first step in degradation of 2,4-D. The other recombinant plasmid (pJP4-FM) should harbor two copies of the
tfdA
gene but no copies of the
tfd
gene clusters. A molecular analysis using a multiplex PCR approach to distinguish the wild-type plasmid pJP4 from its two recombinant forms, was carried out. Expected PCR products confirming this recombination model were found and sequenced. Few recombinant plasmid forms in cultures grown in several carbon sources were detected. Kinetic studies indicated that cells containing the recombinant plasmid pJP4-FM were not selectable by sole carbon source growth pressure, whereas those cells harboring recombinant plasmid pJP4-F3 were selected upon growth on 3-CB. After 12 days of repeated growth on 3-CB, the complete plasmid population in
C. necator
JMP134 apparently corresponds to this form. However, wild-type plasmid forms could be recovered after growing this culture on 2,4-D, indicating that different plasmid forms can be found in
C. necator
JMP134 at the population level.