bluuebunny/crossref_metadata_2025 huggingface dataset:
Discharge patterns and amplitude modulation encoding in the torus semicircularis of the frog
Authors: Bibikov Nikolay G.
Published: October 2005

Responses to pure and sinusoidally 20-Hz amplitude-modulated tone bursts (612,5-ms stimulus on time at the rate of once per 2.2 s) were recorded in 202 units of the torus semicircularis (midbrain auditory center) in the immobilized grass frogs (Ranatemporaria). Best frequency tones at 30 dB re: minimum threshold were used. The largest values of synchronization coefficients (SCs) to 80% amplitude-modulated stimuli were observed for same phasic units. The proportion of the responses with a good phase-locking ( SC ≳ 0.5) was, however, higher in the tonic unit’s population. Only in a few phasic units was the sustained response to 10% modulated stimuli observed. These particular units demonstrated, however, extremely high SCs. On the other hand, the phase-locking response to tones at 10% modulation depth was observed in 65% of the tonic units. In the majority of these neurons the partial SCs for successive modulation periods increased considerably from the initial to the terminal modulation periods. The psychophysical correlates of this physiological ‘‘overshoot’’ effect are discussed. [Work supported by ISF and RFFI.]
Direct observation of microbubble oscillations
Authors: Tian Yuren , Riegel Daniel , Ketterling Jeff , Apfel Robert E.
Published: October 2005

The study of microbubble oscillations is important for the understanding of sonoluminescence phenomena. Bubble dynamic behavior is conventionally detected with light scattering techniques. This method generally gives little information about the shapes of a bubble during its oscillation. In order to observe the bubble shapes, a direct imaging system was set up. The shape of a bubble levitated in a liquid is magnified and displayed on a TV screen. The bubble is illuminated with an LED lamp which is strobed at a frequency slightly different from the driving sound field. This technique can slow the moving image of the bubble, allowing one to observe the shape of a bubble oscillating between 5 to 100 μm in diameter. Experiments show that when a bubble oscillates with sonoluminescence, it keeps a closely spherical shape during the entire oscillation period. However, with the increase of gas concentration in the host liquid, sonoluminescence disappears and higher mode shapes are developed during the bubble’s shrinking period. Experiments also show that the asymmetric shape of the bubble may cause the levitated bubble to become unstable. [Work supported by NASA through JPL, contract 958722.]
Total scattering cross section of two acoustically coupling balls
Authors: Lebedev Andrey V. , Khilko Alexander I.
Published: October 2005

The problem of a plane acoustic wave scattering at two acoustically coupled balls is considered. The solution is obtained via the theorem of addition for spherical functions. Asymptotic cases of extremely low- and high frequency are analyzed. It is shown that in a general case in a low-frequency region total scattering cross section is two times more than for uncoupled balls. In the case of acoustically soft balls the coupling leads to decrease this value due to mutual damping of vibrations via near fields. It was found that in this case there is the optimal ratio of balls radii when the total scattering cross section reaches maximum. In the high-frequency region one can see clearly manifested spatial scales that are conditioned by geometrical sizes of the coupling system. It leads to character oscillations in the frequency dependence of scattering cross section. Maximal influence of the coupling effects in the high-frequency region is manifested when one of the balls is in the shadow of the other. In this case, dominant oscillations are defined by condition kd=πn (‘‘d’’ is the distance between the balls’ centers) and caused by perturbations of the scattering pattern by the shading ball. [Work sponsored by ISF.]
Two complex effective lengths for musical wind instruments
Authors: Ayers R. Dean
Published: October 2005

The definition of effective length has been generalized to all frequencies by Pyle, working in the context of lossless plane-wave horn theory [R. W. Pyle, Jr., J. Acoust. Soc. Am. 57, 1309–1317 (1975)]. In this paper, losses due to radiation and visco-thermal damping are included by letting the effective length become complex. With that additional generalization, effective length, pressure reflection coefficient, and relative input impedance carry exactly equivalent information. There are two choices of boundary condition at the downstream end of an idealized, uniform pipe: open or closed. The effective length to a closed end was used implicitly by Pyle, and a practical application for it is found in a doubly closed pipe model for the brass wind instruments.
Infant psychometric functions for detection: Mechanisms of immature sensitivity
Authors: Bargones Jill Y. , Werner Lynne A. , Marean G. Cameron
Published: October 2005

Psychometric functions are described for individual 6- to 9-month-old infants and for individual adults for auditory detection of repeated, long- and short-duration tone bursts in quiet and for single, long-duration tone bursts in quiet and in noise. In general, infant psychometric functions have reduced upper asymptotes, shallower slopes, and poorer thresholds than adult psychometric functions. Infant–adult differences in slope and threshold are greater for short-duration tones than for other stimuli. Infant upper asymptotes are around 0.85 correct for all stimuli. One explanation for these findings is that infants are inattentive a certain proportion of time during the detection task. This model cannot account for the very shallow short-duration stimulus slope, nor can it account for infant–adult threshold differences for any stimulus. Other models of immature attention, or listening strategies, may be able to account for the slope and upper asymptote as well as the threshold of infant psychometric functions. Some combination of inattentiveness and primary neural immaturity may also account for the data. Although immaturities exist, some aspects of the detection process appear to be quantitatively similar in infants and adults.
Standards and the Acoustical Society
Authors: Embleton Tony
Published: October 2005

The American National Standards Institute (ANSI) develops standards by several different processes. One process is to accredit a Standards Committee, and its Secretariat, provided they operate under procedures that conform to strict ANSI requirements. Development of many standards in acoustics follows this process monitored by the Acoustical Society of America. ASA provides the Secretariat for four ANSI Accredited Standards Committees (S1 Acoustics, S2 Shock and Vibration, S3 Bioacoustics, and S12 Noise). The present system has evolved for about 60 years. Today these Committees are responsible for the maintenance of about 100 American acoustical standards, and they provide US Technical Advisory Groups for the corresponding committees of the International Organization for Standardization and the International Electrotechnical Commission. Assisting the four Accredited S Committees in the development of draft standards and formulating the US position on international documents are some 100 Working Groups, often meeting at the semi-annual ASA meetings. In addition to its organizational members, each S Committee has about 20 individual members with broad expertise in the subject. Altogether some 650 persons are involved. The membership of ASA is a valuable resource and its geographical diversity has led naturally to cooperation in standards activity between the US and Canada, and recently with Mexico.
Rayleigh’s influence on engineering vibration theory
Authors: Crandall Stephen H.
Published: October 2005

The first ten chapters of ‘‘The Theory of Sound’’ constitute an unprecedented exposition of vibration theory. This tour-de-force set the mold for the teaching of vibration for more than a century. The central core is linear modal analysis applied to lumped parameter systems and to strings, bars, beams, membranes, plates, and shells. In addition there are preliminary investigations of nonlinear vibrations, parametrically excited vibrations, and random vibrations. Most of the textbooks on vibrations for engineers that have appeared in the past 50 years may be viewed as attempts to explain Rayleigh’s ideas to university students. Rayleigh’s paradigm has served us well for a century but it appears that we are now on the threshold of major changes in the way vibration theory is taught. These changes are being driven by the tremendous advances in instrumentation and data processing facilities. Although Rayleigh introduced the concept of the transfer function in vibration he did not develop it to any extent. He chose instead the concept of modal decomposition as his primary analysis tool. It is suggested that future introductory vibration texts may well reverse the relative importance attached to these concepts.
Performance of ultrasonic speckle tracking in various tissues
Authors: Chen Eric J. , Jenkins W. Kenneth , O’Brien William D.
Published: October 2005

The purpose of this study was to investigate the accuracy of ultrasound speckle tracking in various tissues. Results from two-dimensional tissue speckle tracking in liver, muscle, fat, and sponge samples are presented, while keeping other speckle tracking parameters constant. Speckle tracking performance was characterized both in terms of the magnitude of tracking errors and in terms of the percentage of correctly tracked displacement vectors. Speckle tracking in muscle tissue, which contains myofibrils and significant tissue microstructure, produced the highest percentage of correctly tracked vectors and smallest tracking errors relative to other tissues.
Propagation from a point source over a rough finite impedance boundary
Authors: Attenborough Keith , Taherzadeh Shahram
Published: October 2005

Measurements of the excess attenuation of sound from a point source over artificially rough surfaces in an anechoic chamber are compared with predictions from modified forms of theories by Howe [J. Sound Vib. 98, 83–94 (1985)] and by Tolstoy [J. Acoust. Soc. Am. 72, 960–072 (1982)]. The modified theories agree with each other and are in tolerable agreement with data over hard or nearly hard boundaries. The modified Tolstoy formulation, which allows the roughnesses to have an impedance that differs from the impedance of the surrounding plane, is found to give better agreement with data for propagation over rough finite impedance surfaces.
Lord Rayleigh’s foundations of aeroacoustics
Authors: Powell Alan
Published: October 2005

The relevance of some of Lord Rayleigh’s work to the relatively new subject of aeroacoustics is illustrated by reference to: the adaptation of his use of the inhomogeneous wave equation to analyze sound generation by convected inhomogeneities in a space varying flow; the scattering of sound by turbulence and to the generation of aerodynamic noise; his suggestion of the mode of operation of the birdcall, common to many flow resonances in the absence of a resonator and in which a key role is played by jet flow instability; his pioneering analyses of flow instability stimulated by his observations of the influence of sound on ‘‘sensitive’’ jets; and his treatment of the spatially periodic structure of supersonic jets which is an important determinant in the feedback mechanism of the screech phenomenon. His keen interest in similitude is illustrated by reference to his work on æolian tones and on sensitive jets.
Information integration of pooled versus paired samples
Authors: Weber Daniel L.
Published: October 2005

The sample-discrimination procedure asks listeners to identify from which of two possible distributions a given set of samples has been drawn. Typically, discriminability (d′ for a single sample) and information integration (inferred from the increase in d′ after n samples) are not as good as predicted by the observation-integration model. This research examined whether information integration could be improved by presenting n pairs of samples from the two distributions rather than presenting all n samples from one distribution then all n samples from the other (pooling samples). Pooled and paired presentations (n=1, 2, 3, 4, 5, 6, 8, 12, and 16) were examined for ‘‘easy’’ and ‘‘hard’’ conditions (large and small separations between means of the two distributions) for both duration discrimination and frequency discrimination. For all four of these conditions, higher d′s were always obtained for the pooled presentations. Pairing the samples failed to improve performance and, for the ‘‘hard’’ conditions, instead made information integration worse.
Signal properties that reduce masking by simultaneous, random-frequency maskers
Authors: Neff Donna L.
Published: October 2005

Large amounts of simultaneous masking can be produced by changing the frequency content of multicomponent maskers with each presentation. Much of this masking appears to be informational, that is, produced by stimulus uncertainty. This study examined whether relatively simple changes in the properties or presentation mode of the signal could increase the saliency of the signal and reduce this masking. The number of masker components varied from 2 to 100 across conditions. The reference signal was a 200-ms, 1000-Hz sinusoid, presented monaurally with the masker. Across experiments, changes in masking relative to the reference condition were examined for different signal types (amplitude-modulated, quasifrequency-modulated, or narrow-band noise), durations (100 or 10 ms), and presentation modes (diotic, dichotic, or cross ear). The use of AM and NBN signals improved performance more consistently than the QFM signal, which degraded performance for some listeners. Lower masking in the reference condition for these listeners may have limited the effects of signal type. Dichotic (versus monaural) presentation produced larger reductions in masking for more listeners and conditions. Comparisons to results with broadband maskers and other patterns in the data, however, suggest the dichotic advantage may not clearly reflect a reduction of masking due to uncertainty. Separating masker and signal onset/offset times by shortening signal duration produced the largest and most consistent reductions in masking produced by masker-frequency uncertainty.
Evaluation of reverberation times using a nonlinear regression approach
Authors: Xiang Ning
Published: October 2005

Reverberation decay curves can be obtained by the backward integration of room impulse responses proposed by M. R. Schroeder. The evaluation of reverberation times is often achieved by a linear regression line fitting the reverberation decay curves. However, under noisy conditions, the successful application of this method requires either a careful choice of the integration limit or a precise estimate of the mean-square value of the background noise. In the present paper, an alternative method using a nonlinear iterative regression approach for evaluating reverberation times from Schroeder’s decay curves is proposed. A nonlinear model of the decay curves, established according to the nature of Schroeder’s decay curves, is used for the regression process rather than the linear model used in linear regression. The regression process is based on the generalized least-squares error principle in which a rapid convergence can be observed. Preliminary experiments show a slight dependence of the reverberation time T30 dB on both the integration limit and the background noise. Using this approach, a high precision of reverberation time evaluations can be achieved without either careful selection of the integration limit or precise estimation of the mean square value of the background noise.
Discrimination of wideband noises modulated by a temporally asymmetric function
Authors: Akeroyd Michael A. , Patterson Roy D.
Published: October 2005

‘‘Damped’’ wideband noises and ‘‘ramped’’ wideband noises were constructed; the former have a repeating, exponentially decaying amplitude-modulation function, the latter a repeating, exponentially rising amplitude-modulation function. They sound remarkably different; there is a continuous background hiss in the ramped percept that is absent in the damped percept. An experiment is reported showing that listeners could reliably discriminate the two over a wide range of modulation half-lives and periods. The short half-life at which discrimination failed was between 0.5 and 1 ms, similar to other measures of temporal resolution. The longest half-life at which discrimination failed increased with increasing modulation period, from 6 (12.5-ms period) to 160 ms (100-ms period). The leaky integrator model of temporal resolution, together with either the standard deviation or max/min decision statistics, failed to predict the psychometric functions. The auditory-image model, which preserves phase-locking information through the integration process, can predict the psychometric functions. The decision statistic is the hiss correlate, the activity present within the auditory image averaged across frequency, integration interval, and time. The current simulations are the first to use the auditory-image model to predict quantitatively psychophysical data.
Lord Rayleigh and nonlinear acoustics
Authors: Beyer Robert T.
Published: October 2005

Lord Rayleigh’s contributions to the foundations of nonlinear acoustics are reviewed. The subjects of radiation pressure, streaming, Aeolian tones, finite amplitude sound propagation, and cavitation are included.
Binaural interference effects measured with masking-level difference and with ITD- and IID-discrimination paradigms
Authors: Bernstein Leslie R. , Trahiotis Constantine
Published: October 2005

The results of several studies have demonstrated that the ability to process binaural information within discrete spectral regions may be degraded by the presence of information at other, even remote, spectral loci. This study focused on binaural interference produced by low-frequency noises (centered at 500 Hz) on the processing of interaural disparities within high-frequency bands of noise (centered on 4 kHz). The bandwidths of the interferers and ‘‘targets’’ were either the same (either 100 or 400 Hz) or different (interferer: 100 Hz; target: 400 Hz). Within a single group of listeners, interference was measured with a masking-level difference paradigm (NoSo vs NoSπ), and in ITD- and IID-discrimination tasks. An important feature of the experiments was the utilization, parametrically, in all three tasks, of pulsed and continuous interferers that were either diotic or were interaurally uncorrelated. As reported in previous experiments, the amounts of interference obtained with pulsed interferers were much greater than those obtained with continuous interferers. The present experiment extends that general finding to discrimination of IIDs. In addition, in all three tasks, pulsed, interaurally uncorrelated interferers produced greater amounts of interference than did pulsed, diotic interferers. The patterns of interference effects found across bandwidths and listeners for the four interference conditions (pulsed-diotic, continuous-diotic, pulsed-uncorrelated, and continuous-uncorrelated) in the MLD paradigm were different than those obtained in either the ITD- or IID-discrimination tasks. One factor that may account for the diverging patterns of interference is that the interaural cues produced by adding the Sπ signal to the diotic masker fluctuated in magnitude over time. In contrast, the ITDs and IIDs in the discrimination task were static. Finally, no interference was measured in MLD control conditions when both the masker and signal were presented diotically (NoSo). This outcome reinforces the notion that the interference effects observed were restricted to the processing of interaural disparities.
Multipartite Regulation ofrctB, the Replication Initiator Gene ofVibrio choleraeChromosome II
Authors: Pal Debasish , Venkova-Canova Tatiana , Srivastava Preeti , Chattoraj Dhruba K.
Published: October 2005

Replication initiator proteins in bacteria not only allow DNA replication but also often regulate the rate of replication initiation as well. The regulation is mediated by limiting the synthesis or availability of initiator proteins. The applicability of this principle is demonstrated here for RctB, the replication initiator for the smaller of the two chromosomes ofVibrio cholerae. A strong promoter for therctBgene namedrctBpwas identified and found to be autoregulated inEscherichia coli. Promoter activity was lower inV. choleraethan inE. coli, and a part of this reduction is likely to be due to autorepression. Sequences upstream ofrctBp, implicated earlier in replication control, enhanced the repression. The action of the upstream sequences required that they be present incis, implying long-range interactions in the control of the promoter activity. A second gene specific for chromosome II replication,rctA, reducedrctBtranslation, most likely by antisense RNA control. Finally, optimalrctBpactivity was found to be dependent on Dam. Increasing RctB intransincreased the copy number of a miniplasmid carryingoriCIIVC, implying that RctB can be rate limiting for chromosome II replication. The multiple modes of control on RctB are expected to reduce fluctuations in the initiator concentration and thereby help maintain chromosome copy number homeostasis.
A Hypervariable 130-Kilobase Genomic Region of
Magnetospirillum gryphiswaldense
Comprises a Magnetosome Island Which Undergoes Frequent Rearrangements during Stationary Growth
Authors: Ullrich Susanne , Kube Michael , Schübbe Sabrina , Reinhardt Richard , Schüler Dirk
Published: October 2005

Genes involved in magnetite biomineralization are clustered in the genome of the magnetotactic bacterium
Magnetospirillum gryphiswaldense
. We analyzed a 482-kb genomic fragment, in which we identified an approximately 130-kb region representing a putative genomic “magnetosome island” (MAI). In addition to all known magnetosome genes, the MAI contains genes putatively involved in magnetosome biomineralization and numerous genes with unknown functions, as well as pseudogenes, and it is particularly rich in insertion elements. Substantial sequence polymorphism of clones from different subcultures indicated that this region undergoes frequent rearrangements during serial subcultivation in the laboratory. Spontaneous mutants affected in magnetosome formation arise at a frequency of up to 10
−2
after prolonged storage of cells at 4°C or exposure to oxidative stress. All nonmagnetic mutants exhibited extended and multiple deletions in the MAI and had lost either parts of or the entire
mms
and
mam
gene clusters encoding magnetosome proteins. The mutations were polymorphic with respect to the sites and extents of deletions, but all mutations were found to be associated with the loss of various copies of insertion elements, as revealed by Southern hybridization and PCR analysis. Insertions and deletions in the MAI were also found in different magnetosome-producing clones, indicating that parts of this region are not essential for the magnetic phenotype. Our data suggest that the genomic MAI undergoes frequent transposition events, which lead to subsequent deletion by homologous recombination under physiological stress conditions. This can be interpreted in terms of adaptation to physiological stress and might contribute to the genetic plasticity and mobilization of the magnetosome island.
Function of the Conserved S1 and KH Domains in Polynucleotide Phosphorylase
Authors: Stickney Leigh M. , Hankins Janet S. , Miao Xin , Mackie George A.
Published: October 2005

We have examined the roles of the conserved S1 and KH RNA binding motifs in the widely dispersed prokaryotic exoribonuclease polynucleotide phosphorylase (PNPase). These domains can be released from the enzyme by mild proteolysis or by truncation of the gene. Using purified recombinant enzymes, we have assessed the effects of specific deletions on RNA binding, on activity against a synthetic substrate under multiple-turnover conditions, and on the ability of truncated forms of PNPase to form a minimal RNA degradosome with RNase E and RhlB. Deletion of the S1 domain reduces the apparent activity of the enzyme by almost 70-fold under low-ionic-strength conditions and limits the enzyme to digest a single substrate molecule. Activity and product release are substantially regained at higher ionic strengths. This deletion also reduces the affinity of the enzyme for RNA, without affecting the enzyme's ability to bind to RNase E. Deletion of the KH domain produces similar, but less severe, effects, while deletion of both the S1 and KH domains accentuates the loss of activity, product release, and RNA binding but has no effect on binding to RNase E. We propose that the S1 domain, possibly arrayed with the KH domain, forms an RNA binding surface that facilitates substrate recognition and thus indirectly potentiates product release. The present data as well as prior observations can be rationalized by a two-step model for substrate binding.
Structure and Increased Thermostability ofRhodococcussp. Naphthalene 1,2-Dioxygenase
Authors: Gakhar Lokesh , Malik Zulfiqar A. , Allen Christopher C. R. , Lipscomb David A. , Larkin Michael J. , Ramaswamy S.
Published: October 2005

Rieske nonheme iron oxygenases form a large class of aromatic ring-hydroxylating dioxygenases found in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth, making them good candidates for use in synthesis of chiral intermediates and bioremediation. Studies of the chemical stability and thermostability of these enzymes thus become important. We report here the structure of free and substrate (indole)-bound forms of naphthalene dioxygenase fromRhodococcussp. strain NCIMB12038. The structure of theRhodococcusenzyme reveals that, despite a ∼30% sequence identity between these naphthalene dioxygenases, their overall structures superpose very well with a root mean square deviation of less than 1.6 Å. The differences in the active site of the two enzymes are pronounced near the entrance; however, indole binds to theRhodococcusenzyme in the same orientation as in thePseudomonasenzyme. Circular dichroism spectroscopy experiments show that theRhodococcusenzyme has higher thermostability than the naphthalene dioxygenase fromPseudomonasspecies. ThePseudomonasenzyme has an apparent melting temperature of 55°C while theRhodococcusenzyme does not completely unfold even at 95°C. Both enzymes, however, show similar unfolding behavior in urea, and theRhodococcusenzyme is only slightly more tolerant to unfolding by guanidine hydrochloride. Structure analysis suggests that the higher thermostability of theRhodococcusenzyme may be attributed to a larger buried surface area and extra salt bridge networks between the α and β subunits in theRhodococcusenzyme.
Transcriptome and Physiological Responses to Hydrogen Peroxide of the Facultatively Phototrophic Bacterium
Rhodobacter sphaeroides
Authors: Zeller Tanja , Moskvin Oleg V. , Li Kuanyu , Klug Gabriele , Gomelsky Mark
Published: October 2005

The transcriptome responses to hydrogen peroxide, H
2
O
2
, of the facultatively phototrophic bacterium
Rhodobacter sphaeroides
grown under semiaerobic conditions were investigated. At 7 min after the addition of 1 mM H
2
O
2
, the expression of approximately 9% of all genes (total, 394) was changed reliably by at least twofold. At 30 min, the number of genes (total, 88) and the magnitude of expression changes were much lower, indicating rapid recovery from stress. Two types of responses were observed: (i) an H
2
O
2
stress response per se and (ii) a shift to high-oxygen metabolism. The former response involved the upregulation of genes for H
2
O
2
detoxification, protein folding and proteolysis, DNA damage repair, iron transport and storage, iron-sulfur cluster repair, and the downregulation of genes for protein translation, motility, and cell wall and lipopolysaccharide synthesis. The shift to high-oxygen metabolism was evident from the differential regulation of genes for aerobic electron transport chain components and the downregulation of tetrapyrrole biosynthesis and photosystem genes. The abundance of photosynthetic complexes was decreased upon prolonged exposure of
R. sphaeroides
to H
2
O
2
, thus confirming the physiological significance of the transcriptome data. The regulatory pathways mediating the shift to high-oxygen metabolism were investigated. They involved the anaerobic activator FnrL and the antirepressor-repressor AppA-PpsR system. The transcription of FnrL-dependent genes was down at 7 min, apparently due to the transient inactivation by H
2
O
2
of the iron-sulfur cluster of FnrL. The transcription of the AppA-PpsR-dependent genes was down at 30 min, apparently due to the significant decrease in
appA
mRNA.
Functional Consequences of Genome Evolution inListeria monocytogenes: the lmo0423 and lmo0422 Genes Encode σCand LstR, a Lineage II-Specific Heat Shock System
Authors: Zhang Chaomei , Nietfeldt Joe , Zhang Min , Benson Andrew K.
Published: October 2005

Listeria monocytogenesstrains belonging to phylogenetic lineage II (serotypes 1/2a, 1/2c, and 3a) carry a lineage-specific genome segment encoding a putative sigma subunit of RNA polymerase (lmo0423, herein referred to assigC), a gene of unknown function (lmo0422) similar to thepadRfamily of regulators, and a gene that is similar to therodA-ftsWfamily of cell wall morphology genes (lmo0421). To understand the function of this set of genes, their expression patterns and the effects of null mutations in the lineage IIL. monocytogenesstrain 10403S were examined. The data are consistent with the three genes comprising an operon (thesigCoperon) that is highly induced by temperature upshift. The operon is transcribed from three different promoters, the proximal of which (P1) depends uponsigCitself. Null mutations insigCor lmo0422 increase the death rate at lethal temperatures and cause loss of thermal adaptive response, whereas the lmo0421 mutation causes only a loss of the adaptive response component. Only thesigCmutation affects transcription from the P1 promoter, whereas ectopic expression of lmo0422 from the PSPACpromoter complements the individual lmo0422 andsigCnull mutations, showing that lmo0422 is the actual thermal resistance regulator or effector whilesigCprovides a mechanism for temperature-dependent transcription of lmo0422 from P1. Our genetic and phylogenetic analyses are consistent with lmo0422—renamedlstR(for lineage-specific thermal regulator)—andsigCcomprising a system of thermal resistance that was ancestral to the genusListeriaand was subsequently lost during divergence of the lineage IL. monocytogenespopulation.
A Glycosyltransferase Involved in Biosynthesis of Triglycosylated Glycopeptidolipids inMycobacterium smegmatis: Impact on Surface Properties
Authors: Deshayes Caroline , Laval Françoise , Montrozier Henri , Daffé Mamadou , Etienne Gilles , Reyrat Jean-Marc
Published: October 2005

The cell envelope of mycobacteria is a complex structure that plays an important role in the interactions of the cell with its environment and in the protection against the antimicrobial activity of the immune system. Glycopeptidolipids (GPLs) are species- or type species-specific glycolipids that are present at the surface of a number of mycobacteria and that are characterized by a high variability in glycosylation patterns. These GPLs possess various biological activities that depend mostly on the sugars capping the core molecule. InMycobacterium smegmatis, the GPL core can be substituted by either two or three deoxyhexoses. In this study, we show that Gtf3 is a glycosyltransferase responsible for the synthesis of the triglycosylated GPLs. Biochemical analysis of these molecules, with a combination of mass spectrometry and chemical degradation methods, has shown that they contain three deoxyhexose moieties. The presence of the triglycosylated GPLs is associated with cell surface modifications that lead to a decrease in sliding motility as well as a modification in cellular aggregation and colony appearance on Congo red. Phylogenetic analysis indicated that Gtf3 is a member of a yet-uncharacterized glycosyltransferase family conserved among the mycobacteria.
Whole-Genome Sequencing of
Staphylococcus haemolyticus
Uncovers the Extreme Plasticity of Its Genome and the Evolution of Human-Colonizing Staphylococcal Species
Authors: Takeuchi Fumihiko , Watanabe Shinya , Baba Tadashi , Yuzawa Harumi , Ito Teruyo , Morimoto Yuh , Kuroda Makoto , Cui Longzhu , Takahashi Mikio , Ankai Akiho , Baba Shin-ichi , Fukui Shigehiro , Lee Jean C. , Hiramatsu Keiichi
Published: October 2005

Staphylococcus haemolyticus
is an opportunistic bacterial pathogen that colonizes human skin and is remarkable for its highly antibiotic-resistant phenotype. We determined the complete genome sequence of
S.haemolyticus
to better understand its pathogenicity and evolutionary relatedness to the other staphylococcal species. A large proportion of the open reading frames in the genomes of
S.haemolyticus
,
Staphylococcus aureus
, and
Staphylococcus epidermidis
were conserved in their sequence and order on the chromosome. We identified a region of the bacterial chromosome just downstream of the origin of replication that showed little homology among the species but was conserved among strains within a species. This novel region, designated the “
oriC
environ,” likely contributes to the evolution and differentiation of the staphylococcal species, since it was enriched for species-specific nonessential genes that contribute to the biological features of each staphylococcal species. A comparative analysis of the genomes of
S.haemolyticus
,
S.aureus
, and
S.epidermidis
elucidated differences in their biological and genetic characteristics and pathogenic potentials. We identified as many as 82 insertion sequences in the
S.haemolyticus
chromosome that probably mediated frequent genomic rearrangements, resulting in phenotypic diversification of the strain. Such rearrangements could have brought genomic plasticity to this species and contributed to its acquisition of antibiotic resistance.
Defining Genes in the Genome of the Hyperthermophilic Archaeon
Pyrococcus furiosus
: Implications for All Microbial Genomes
Authors: Poole Farris L. , Gerwe Brian A. , Hopkins Robert C. , Schut Gerrit J. , Weinberg Michael V. , Jenney Francis E. , Adams Michael W. W.
Published: October 2005

The original genome annotation of the hyperthermophilic archaeon
Pyrococcus furiosus
contained 2,065 open reading frames (ORFs). The genome was subsequently automatically annotated in two public databases by the Institute for Genomic Research (TIGR) and the National Center for Biotechnology Information (NCBI). Remarkably, more than 500 of the originally annotated ORFs differ in size in the two databases, many very significantly. For example, more than 170 of the predicted proteins differ at their N termini by more than 25 amino acids. Similar discrepancies were observed in the TIGR and NCBI databases with the other archaeal and bacterial genomes examined. In addition, the two databases contain 60 (NCBI) and 221 (TIGR) ORFs not present in the original annotation of
P. furiosus
. In the present study we have experimentally assessed the validity of 88 previously unannotated ORFs. Transcriptional analyses showed that 11 of 61 ORFs examined were expressed in
P. furiosus
when grown at either 95 or 72°C. In addition, 7 of 54 ORFs examined yielded heat-stable recombinant proteins when they were expressed in
Escherichia coli
, although only one of the seven ORFs was expressed in
P. furiosus
under the growth conditions tested. It is concluded that the
P. furiosus
genome contains at least 17 ORFs not previously recognized in the original annotation. This study serves to highlight the discrepancies in the public databases and the problems of accurately defining the number and sizes of ORFs within any microbial genome.
Identification of the
rctA
Gene, Which Is Required for Repression of Conjugative Transfer of Rhizobial Symbiotic Megaplasmids
Authors: Pérez-Mendoza Daniel , Sepúlveda Edgardo , Pando Victoria , Muñoz Socorro , Nogales Joaquina , Olivares José , Soto Maria J. , Herrera-Cervera José A. , Romero David , Brom Susana , Sanjuán Juan
Published: October 2005

An analysis of the conjugative transfer of pRetCFN42d, the symbiotic plasmid (pSym) of
Rhizobium etli
, has revealed a novel gene,
rctA
, as an essential element of a regulatory system for silencing the conjugative transfer of
R. etli
pSym by repressing the transcription of conjugal transfer genes in standard laboratory media. The
rctA
gene product lacks sequence conservation with other proteins of known function but may belong to the winged-helix DNA-binding subfamily of transcriptional regulators. Similar to that of many transcriptional repressors,
rctA
transcription seems to be positively autoregulated.
rctA
expression is greatly reduced upon overexpression of another gene,
rctB
, previously identified as a putative activator of
R. etli
pSym conjugal transfer. Thus,
rctB
seems to counteract the repressive action of
rctA. rctA
homologs are present in at least three other bacterial genomes within the order
Rhizobiales
, where they are invariably located adjacent to and divergently transcribed from putative
virB
-like operons. We show that similar to that of
R. etli
pSym, conjugative transfer of the 1.35-Mb symbiotic megaplasmid A of
Sinorhizobium meliloti
is also subjected to the inhibitory action of
rctA
. Our data provide strong evidence that the
R. etli
and
S. meliloti
pSym plasmids are indeed self-conjugative plasmids and that this property would only be expressed under optimal, as yet unknown conditions that entail inactivation of the
rctA
function. The
rctA
gene seems to represent novel but probably widespread regulatory systems controlling the transfer of conjugative elements within the order
Rhizobiales
.
Type III Restriction Is Alleviated by Bacteriophage (RecE) Homologous Recombination Function but Enhanced by Bacterial (RecBCD) Function
Authors: Handa Naofumi , Kobayashi Ichizo
Published: October 2005

Previous works have demonstrated that DNA breaks generated by restriction enzymes stimulate, and are repaired by, homologous recombination with an intact, homologous DNA region through the function of lambdoid bacteriophages lambda and Rac. In the present work, we examined the effect of bacteriophage functions, expressed in bacterial cells, on restriction of an infecting tester phage in a simple plaque formation assay. The efficiency of plaque formation on an
Escherichia coli
host carrying EcoRI, a type II restriction system, is not increased by the presence of Rac prophage—presumably because, under the single-infection conditions of the plaque assay, a broken phage DNA cannot find a homologue with which to recombine. To our surprise, however, we found that the efficiency of plaque formation in the presence of a type III restriction system, EcoP1 or EcoP15, is increased by the bacteriophage-mediated homologous recombination functions
recE
and
recT
of Rac prophage. This type III restriction alleviation does not depend on
lar
on Rac, unlike type I restriction alleviation. On the other hand, bacterial RecBCD-homologous recombination function enhances type III restriction. These results led us to hypothesize that the action of type III restriction enzymes takes place on replicated or replicating DNA in vivo and leaves daughter DNAs with breaks at nonallelic sites, that bacteriophage-mediated homologous recombination reconstitutes an intact DNA from them, and that RecBCD exonuclease blocks this repair by degradation from the restriction breaks.
Ribose-5-Phosphate Biosynthesis in
Methanocaldococcus jannaschii
Occurs in the Absence of a Pentose-Phosphate Pathway
Authors: Grochowski Laura L. , Xu Huimin , White Robert H.
Published: October 2005

Recent work has raised a question as to the involvement of erythrose-4-phosphate, a product of the pentose phosphate pathway, in the metabolism of the methanogenic archaea (R. H. White, Biochemistry
43:
7618-7627, 2004). To address the possible absence of erythrose-4-phosphate in
Methanocaldococcus jannaschii
, we have assayed cell extracts of this methanogen for the presence of this and other intermediates in the pentose phosphate pathway and have determined and compared the labeling patterns of sugar phosphates derived metabolically from [6,6-
2
H
2
]- and [U-
13
C]-labeled glucose-6-phosphate incubated with cell extracts. The results of this work have established the absence of pentose phosphate pathway intermediates erythrose-4-phosphate, xylose-5-phosphate, and sedoheptulose-7-phosphate in these cells and the presence of
d
-
arabino
-3-hexulose-6-phosphate, an intermediate in the ribulose monophosphate pathway. The labeling of the
d
-
ara-bino
-3-hexulose-6-phosphate, as well as the other sugar-Ps, indicates that this hexose-6-phosphate was the precursor to ribulose-5-phosphate that in turn was converted into ribose-5-phosphate by ribose-5-phosphate isomerase. Additional work has demonstrated that ribulose-5-phosphate is derived by the loss of formaldehyde from
d
-
arabino
-3-hexulose-6-phosphate, catalyzed by the protein product of the MJ1447 gene.
σ
B
Activity in a
Staphylococcus aureus hemB
Mutant
Authors: Senn Maria M. , Bischoff Markus , von Eiff Christof , Berger-Bächi Brigitte
Published: October 2005

Inactivation of
hemB
in
Staphylococcus aureus
strain Newman resulted in a small-colony phenotype and was accompanied by an altered expression pattern of global regulators and control of virulence factor production. Transcription profiles followed over 15 h by Northern blot analyses revealed that transcripts of the global regulators
arl
,
rot
,
sae
,
sarR
,
sarS
,
srr
,
svrA
, and
sigB
disappeared after the exponential phase and that both
agr
transcripts were completely absent in the
hemB
mutant. Apart from a general concentration of transcriptional activity to the exponential phase, premature gene expression was observed for
rot
,
hla
, and
spa
. Nevertheless, reported σ
B
-dependent transcripts, such as
sarC
and
clfA
, were produced throughout the 15-h growth period monitored. The absence of these transcripts in a
hemB sigB
double mutant demonstrated their dependence on σ
B
and indicated an unexpected, permanent σ
B
activity in the
hemB
mutant. Variations in the extents of the directly σ
B
-controlled
asp23
,
rsbVW-sigB
, and
sarC
transcripts argue for additional factors modulating σ
B
activity. This study provides the first extended synopsis of the transcriptional patterns of different regulators over the entire growth cycle in the widely used Newman strain.
Resolvase-In Vivo Expression Technology Analysis of theSalmonella entericaSerovar Typhimurium PhoP and PmrA Regulons in BALB/c Mice
Authors: Merighi Massimo , Ellermeier Craig D. , Slauch James M. , Gunn John S.
Published: October 2005

Salmonella entericamodulates resistance to antimicrobial peptides in part via covalent modifications of the lipopolysaccharide (LPS). The two-component systems PhoP/PhoQ and PmrA/PmrB are activated during infection and regulate several genes involved in LPS modifications by responding to signals such as pH, iron, magnesium, and antimicrobial peptides. A recombination-based in vivo expression technology approach was adopted to analyze the spatial-temporal patterns of in vivo expression of genes of the PhoP and PmrA regulons and to identify the in vivo signals modulating their transcription. In vitro, we showed PhoP- and/or PmrA-dependent induction ofpmrH(LPS aminoarabinose modification operon) by acidic pH, low levels of magnesium, or high levels of Fe(III). Upregulation in cultured J774A.1 macrophages was shown forpmrH,pagP(LPS palmitate addition), andssaB(pathogenicity island II secretion) but not forprgH(pathogenicity island I secretion). Increased levels ofpmrH,phoP, andprgHtranscription but notssaBwere observed in bacteria isolated from the lumen of the distal ileum. Bacteria isolated from spleens of orally inoculated mice showed no further induction ofprgHbut had the highest expression ofpmrH,pagP, andssaB. In vivo induction ofpmrHwas fully dependent onpmrAandphoP, and buffering stomach acidity, iron chelation, or low-iron diets did not affect the expression ofpmrHin the intestinal lumen. The observation ofpmrHandpagPexpression in the intestine refutes the paradigm of PhoP/PhoQ and PmrA/PmrB in vivo expression as solely intracellularly induced and supports previous data demonstrating peroral virulence attenuation ofpmrHmutants.
NspS, a Predicted Polyamine Sensor, Mediates Activation of
Vibrio cholerae
Biofilm Formation by Norspermidine
Authors: Karatan Ece , Duncan Tammi R. , Watnick Paula I.
Published: October 2005

Vibrio cholerae
is both an environmental bacterium and a human intestinal pathogen. The attachment of bacteria to surfaces in biofilms is thought to be an important feature of the survival of this bacterium both in the environment and within the human host. Biofilm formation occurs when cell-surface and cell-cell contacts are formed to make a three-dimensional structure characterized by pillars of bacteria interspersed with water channels. In monosaccharide-rich conditions, the formation of the
V. cholerae
biofilm requires synthesis of the VPS exopolysaccharide. MbaA (locus VC0703), an integral membrane protein containing a periplasmic domain as well as cytoplasmic GGDEF and EAL domains, has been previously identified as a repressor of
V. cholerae
biofilm formation. In this work, we have studied the role of the protein NspS (locus VC0704) in
V. cholerae
biofilm development. This protein is homologous to PotD, a periplasmic spermidine-binding protein of
Escherichia coli
. We show that the deletion of
nspS
decreases biofilm development and transcription of exopolysaccharide synthesis genes. Furthermore, we demonstrate that the polyamine norspermidine activates
V. cholerae
biofilm formation in an MbaA- and NspS-dependent manner. Based on these results, we propose that the interaction of the norspermidine-NspS complex with the periplasmic portion of MbaA diminishes the ability of MbaA to inhibit
V. cholerae
biofilm formation. Norspermidine has been detected in bacteria, archaea, plants, and bivalves. We suggest that norspermidine serves as an intercellular signaling molecule that mediates the attachment of
V. cholerae
to the biotic surfaces presented by one or more of these organisms.
Biochemical and Mutational Analysis of Glutamine Synthetase Type III from the Rumen Anaerobe
Ruminococcus albus
8
Authors: Amaya Kensey R. , Kocherginskaya Svetlana A. , Mackie Roderick I. , Cann Isaac K. O.
Published: October 2005

Two different genes encoding glutamine synthetase type I (GSI) and GSIII were identified in the genome sequence of
R. albus
8. The identity of the GSIII protein was confirmed by the presence of its associated conserved motifs. The
glnN
gene, encoding the GSIII, was cloned and expressed in
Escherichia coli
BL21 cells. The recombinant protein was purified and subjected to biochemical and physical analyses. Subunit organization suggested a protein present in solution as both monomers and oligomers. Kinetic studies using the forward and the γ-glutamyl transferase (γ-GT) assays were carried out. Mutations that changed conserved glutamic acid residues to alanine in the four GSIII motifs resulted in drastic decreases in GS activity using both assays, except for an E380A mutation, which rather resulted in an increase in activity in the forward assay compared to the wild-type protein. Reduced GSIII activity was also exhibited by mutating, individually, two lysines (K308 and K318) located in the putative nucleotide-binding site to alanine. Most importantly, the presence of mRNA transcripts of the
glnN
gene in
R. albus
8 cells grown under ammonia limiting conditions, whereas little or no transcript was detected in cells grown under ammonia sufficient conditions, suggested an important role for the GSIII in the nitrogen metabolism of
R. albus
8. Furthermore, the mutational studies on the conserved GSIII motifs demonstrated, for the first time, their importance in the structure and/or function of a GSIII protein.