bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of uncertainty in the heading or placement of a sub-array on passive ranging accuracy
Authors: Hassab J. C.
Published: October 2005

Generalized results are derived for predicting the statistical performance of passive wave-front curvature ranging. The bias and variance for the range estimates are developed for noncollinear and unequally separated sub-arrays whose acoustic centers are subjected to heading fluctuations. The generalized bias and variance results are reduced, for certain specific cases, to previously found results in the literature. Using the generalized results, several figures are given to depict the size and variation in bias and variance as a function of the design elements that define those statistical measures.
Temporary threshold shifts after onset and offset of moderately loud low-frequency maskers
Authors: Zwicker Eberhard , Hesse Alexander
Published: October 2005

Moderately loud low-frequency maskers produce temporary threshold shifts which oscillate for a few minutes in reproducible patterns not only after their offset, but also after their onset. The temporal variations of threshold show ‘‘bounces’’ similar to those found by Hirsh and Ward [J. Acoust. Soc. Am. 24, 131–141 (1952)] after the offset of very loud maskers. In the present paper, threshold shifts of up to 30 dB are reported for pauses of 3-min duration in continuous maskers. These effects could originate in the internal cochlear metabolism, the steady-state condition of which seems to be influenced by the moderately loud low-frequency tones.
Use of a personal computer to model the electroacoustics of hearing aids
Authors: Bade Priscilla F. , Engebretson A. Maynard , Heidbreder Arnold F. , Niemoeller Arthur F.
Published: October 2005

The electro-acoustic behavior of a hearing aid receiver in an acoustic system similar to that found in many hearing aids was predicted by the method described by Egolf [D. P. Egolf and R. G. Leonard, ‘‘Experimental scheme for analyzing the dynamic behavior of electro-acoustic transducers,’’ J. Acoust. Soc. Am. 62, 1013–1023 (1977)] using an inexpensive desktop computer.
Time delay estimation via coherence: An adaptive approach
Authors: Youn D. H. , Ahmed N.
Published: October 2005

This paper concerns an adaptive method for estimating the time delay between two-sensor outputs. The time delay is obtained from the phase information of the squared coherence (SC) function which is estimated using a pair of transfer functions of adaptive filters. The filter coefficients are updated using the least-mean-square (LMS) algorithm. An analysis of the corresponding estimation error for constant delay parameter is included. Also, the performance of the method is demonstrated via computer simulations when the delay functions are time-varying as well as a constant.
A unified theory for elastic wave propagation in polycrystalline materials
Authors: Stanke Fred E. , Kino G. S.
Published: October 2005

We have developed a unified approach to solve for the attenuation and phase velocity variations of elastic waves in single-phase, polycrystalline media due to scattering. Our approach is a perturbation method applicable for any material whose single-crystal anisotropy is not large, regardless of texture, grain elongation, or multiple scattering. It accurately accounts for the anisotropy of the individual grains. It is valid for time-harmonic waves with all ratios of grain size to wavelength. It uses an autocorrelation function to characterize the geometry of the grains, and thereby avoids coherent artifacts that occur if the grains are assumed to have symmetrical shapes and suggests new methods for characterizing distributions of grains that are irregularly shaped. We have carried out numerical calculations for materials that are untextured and equiaxed, and have cubic-symmetry grains and an inverse exponential spatial autocorrelation function. These calculations agree with the previous calculations which are valid in the Rayleigh, stochastic, and geometric regions, and show the transitions between these regions. The complex transition between the Rayleigh and stochastic regions for longitudinal waves, and the severe limitations of the stochastic region for grains with fairly large anisotropy are of particular interest.
Explososcan: A parallel processing technique for high speed ultrasound imaging with linear phased arrays
Authors: Shattuck David P. , Weinshenker Marc D. , Smith Stephen W. , von Ramm Olaf T.
Published: October 2005

The data acquisition rate in medical ultrasonic imaging devices is limited by the acoustic propagation velocity in the tissues. Typically in such machines the image lines are produced sequentially one line per transmitted pulse. A parallel processing scheme has been implemented which enables the data acquisition rate to increase by a factor of four through the simultaneous acquisition of four B-mode image lines from each individual broadened transmit pulse. The higher data rate can be used to increase the image frame rate to produce independent images that can be averaged in the image frame to reduce noise, or to produce a conventional image at standard video frame rates while reducing patient exposure. Alternatively, the field of view can be increased over that of a normal scan without sacrificing frame rate. These advantages are achieved with little reduction in the measured resolution. The design and performance of this device are described. A sample in vivo image is included.
In-plane accelerations and forces on frequency changes in doubly rotated quartz plates
Authors: Lee P. C. Y. , Wu Kuang-Ming
Published: October 2005

Two-dimensional equations of motion of doubly rotated quartz plates for the thickness-shear, flexure, and extensional vibrations under in-plane initial stresses are employed to predict changes in the fundamental thickness-shear frequencies due to initial stresses. Two types of initial stresses are considered: (1) stresses due to a pair of diametral forces, and (2) stresses due to steady accelerations for a three-point ‘‘T’’-shaped mount and a four point ‘‘+’’-shaped mount configurations. Force sensitivity and acceleration sensitivity coefficients are computed and compared with experimental data and existing computed results. For both ‘‘T’’- and ‘‘+’’-shaped mount configurations, mount orientations corresponding to the maximum and minimum of acceleration sensitivity are predicted.
Concurrent minimum audible angle: A re-examination of the concept of auditory spatial acuity
Authors: Perrott David R.
Published: October 2005

Minimum audible angle was measured for simultaneous acoustic events. Localization of concurrent events was found to be a direct function of the spectral differences between the events, the angle between the sources, and the location of the sources within the field defined by the subject. In the latter case, the m.a.a. was smallest with sources placed symmetrically about the listener’s median plane and maximal at the extreme lateral portions. Post-hoc tests were completed which indicate that the spectral limits for concurrent localization is dependent both upon the angular separation of the sources and the position within the field as defined by the locus of the subject. The functions obtained approach the values reported by Mills [J. Acoust. Soc. Am. 30, 237–246 (1958)] as the temporal overlap between the concurrent events decreased. The present results suggest that a single localization function may exist with the optimal performance observed with fully successive stimuli and poorest performance in the condition involving simultaneous events. The implications of these results are discussed.
Rayleigh wave transmission reciprocity past a step change in elevation
Authors: Chamuel Jacques R.
Published: October 2005

Contradicting experimental, approximate theoretical, and numerical results have been reported in the literature by several authors on Rayleigh wave transmission coefficient past a step change in elevation. In this paper, reciprocity for wave propagation in both directions across a step is demonstrated experimentally using a new ratio technique eliminating error sources introduced from elastic wave generation, coupling, and detection. Two-dimensional ultrasonic models were use to obtain the data. The experimental transmission coefficient measurements are compared with other published results. The ratio of step height to Rayleigh wavelength tested ranged from 0.159 to 1.33. The effect of step height on the interference of the transmitted wave components is examined. The conversion between Rayleigh and shear waves at the step plays an important role in the transmission coefficient.
Does silence simply separate speech components?
Authors: Pastore Richard E. , Szczesiul Rosemary , Rosenblum Lawrence
Published: October 2005

A study was conducted to test one possible acoustic explanation of one role played by silent intervals in the perception of stop consonants. We hypothesized that silence creates a separation between the different components of a speech stimulus, thus reducing the magnitude of the auditory interaction between the stimulus components. In order to test this auditory separation hypothesis, we attempted to trade silence against an auditory separation based upon the selective lateralization of the stimulus components created by an interaural phase shift. In finding no such trading relation, we failed to support the auditory separation hypothesis.
ESPI—The ultimate holographic tool for vibration analysis?
Authors: Lo/kberg Ole J.
Published: October 2005

Holographic interferometry opened new worlds of research by making possible accurate, global mapping of small dynamic surface displacements in a two-step process. A technique, called Electronic Speckle Pattern Interferometry or ESPI, has been developed in various forms to provide similar results instantly. ESPI’s principal capabilities, and some practical applications in industry, biomedicine, and acoustical research are described in an overview in the hope of encouraging its use by researchers who were deterred by the relatively cumbersome process of holography. In various forms, ESPI is shown to be capable of measuring phase and amplitude of dynamic displacements between 0.01 nm and 10 μm over an area of up to 1 m2.
Temporal averaging of subjective magnitude and proposed rating scale for fluctuating noise
Authors: Hiramatsu Kozo , Takagi Koichi , Yamamoto Takeo
Published: October 2005

A method for predicting the effective sound level (ESL) is proposed in this paper. The effective sound level is the sound level of a steady noise which produces the same subjective magnitude as a fluctuating noise and may be measured as the point of subjective equality by means of psychometric methods. The proposed method gives the predicted value of ESL which is denoted as Leff, based on an assumption of integration and averaging of subjective magnitude. It has been shown that Leff can be expressed by an equation which contains the probability density function of the level distribution and two empirical parameters, the values of exponents for sound pressure and duration in the psychophysical function. The practical significance of the descriptor Leff was discussed in terms of the definition of the number of events. High correlation between Leff and the subjects’ response was found.
An approximated closed form of the transient acoustic pressure distribution generated by a linear source
Authors: Denisenko N. , Pappalardo M. , D’Ottavi E. , Matteucci M.
Published: October 2005

In this letter, following a time domain approach, we describe an approximated closed form of the transient acoustic pressure distribution of a linear source.
Sequential Proton Transfer Through Water Bridges in Acid-Base Reactions
Authors: Mohammed Omar F. , Pines Dina , Dreyer Jens , Pines Ehud , Nibbering Erik T. J.
Published: October 2005

The proton transfer mechanism between aqueous Brønsted acids and bases, forming an encounter pair, has been studied in real time with ultrafast infrared spectroscopy. The transient intermediacy of a hydrated proton, formed by ultrafast dissociation from an optically triggered photoacid proton donor ROH, is implicated by the appearance of an infrared absorption marker band before protonation of the base, B
–
. Thus, proton exchange between an acid and a base in aqueous solution is shown to proceed by a sequential, von Grotthuss–type, proton-hopping mechanism through water bridges. The spectra suggest a hydronium cation H
3
O
+
structure for the intermediate, stabilized in the Eigen configuration in the ionic complex RO
–
···H
3
O
+
···B
–
.
Salmonella enterica
Virulence Genes Are Required for Bacterial Attachment to Plant Tissue
Authors: Barak Jeri D. , Gorski Lisa , Naraghi-Arani Pejman , Charkowski Amy O.
Published: October 2005

Numerous
Salmonella enterica
food-borne illness outbreaks have been associated with contaminated vegetables, in particular sprouted seeds, and the incidence of reported contamination has steadily risen. In order to understand the physiology of
S. enterica
serovar Newport on plants, a screen was developed to identify transposon mutants that were defective in attachment to alfalfa sprouts. Twenty independent mutants from a pool of 6,000 were selected for reduced adherence to alfalfa sprouts. Sixty-five percentage of these mutants had insertions in uncharacterized genes. Among the characterized genes were strains with insertions in the intergenic region between
agfB
, the surface-exposed aggregative fimbria (curli) nucleator, and
agfD
, a transcriptional regulator of the LuxR superfamily, and
rpoS
, the stationary-phase sigma factor. Both AgfD and RpoS have been reported to regulate curli and cellulose production and RpoS regulates other adhesins such as pili. The intergenic and
rpoS
mutants were reduced in initial attachment to alfalfa sprouts by 1 log unit compared to the wild type. Mutations of
agfA
, curli subunit, and
agfB
in
S. enterica
serovar Enteritidis differentially affected attachment to plant tissue. The
agfA
mutation was not reduced in ability to attach to or colonize alfalfa sprouts, whereas the
agfB
mutation was reduced. Thus,
agfB
alone can play a role in attachment of
S. enterica
to plant tissue. These results reveal that
S. enterica
genes important for virulence in animal systems are also required for colonization of plants, a secondary host that can serve as a vector of
S. enterica
from animal to animal.
Quantifying Transmission of
Campylobacter
spp. among Broilers
Authors: Van Gerwe T. J. W. M. , Bouma A. , Jacobs-Reitsma W. F. , van den Broek J. , Klinkenberg D. , Stegeman J. A. , Heesterbeek J. A. P.
Published: October 2005

Campylobacter
species are frequently identified as a cause of human gastroenteritis, often from eating or mishandling contaminated poultry products. Quantitative knowledge of transmission of
Campylobacter
in broiler flocks is necessary, as this may help to determine the moment of introduction of
Campylobacter
in broiler flocks more precisely. The aim of this study was to determine the transmission rate parameter in broiler flocks. Four experiments were performed, each with four
Campylobacter-
inoculated chicks housed with 396 contact chicks per group. Colonization was monitored by regularly testing fecal samples for
Campylobacter
. A mathematical model was used to quantify the transmission rate, which was determined to be 1.04 new cases per colonized chick per day. This would imply that, for example, in a flock of 20,000 broilers, the prevalence of
Campylobacter
would increase from 5% to 95% within 6 days after
Campylobacter
introduction. The model and the estimated transmission rate parameter can be used to develop a suitable sampling scheme to determine transmission in commercial broiler flocks, to estimate whether control measures can reduce the transmission rate, or to estimate when
Campylobacter
was introduced into a colonized broiler flock on the basis of the time course of transmission in the flock.
Development of a Functional Genomics Platform for
Sinorhizobium meliloti
: Construction of an ORFeome
Authors: Schroeder Brenda K. , House Brent L. , Mortimer Michael W. , Yurgel Svetlana N. , Maloney Scott C. , Ward Kristel L. , Kahn Michael L.
Published: October 2005

The nitrogen-fixing, symbiotic bacterium
Sinorhizobium meliloti
reduces molecular dinitrogen to ammonia in a specific symbiotic context, supporting the nitrogen requirements of various forage legumes, including alfalfa. Determining the DNA sequence of the
S. meliloti
genome was an important step in plant-microbe interaction research, adding to the considerable information already available about this bacterium by suggesting possible functions for many of the >6,200 annotated open reading frames (ORFs). However, the predictive power of bioinformatic analysis is limited, and putting the role of these genes into a biological context will require more definitive functional approaches. We present here a strategy for genetic analysis of
S. meliloti
on a genomic scale and report the successful implementation of the first step of this strategy by constructing a set of plasmids representing 100% of the 6,317 annotated ORFs cloned into a mobilizable plasmid by using efficient PCR and recombination protocols. By using integrase recombination to insert these ORFs into other plasmids in vitro or in vivo (B. L. House et al., Appl. Environ. Microbiol. 70:2806-2815, 2004), this ORFeome can be used to generate various specialized genetic materials for functional analysis of
S. meliloti
, such as operon fusions, mutants, and protein expression plasmids. The strategy can be generalized to many other genome projects, and the
S. meliloti
clones should be useful for investigators wanting an accessible source of cloned genes encoding specific enzymes.
Inducible Gene Expression in
Lactobacillus reuteri
LTH5531 during Type II Sourdough Fermentation
Authors: Dal Bello Fabio , Walter Jens , Roos Stefan , Jonsson Hans , Hertel Christian
Published: October 2005

Lactobacillus reuteri
LTH5531 is a dominant member of the microbiota of type II sourdough fermentations. To investigate the genetic background of the ecological performance of LTH5531, in vivo expression technology was used to identify promoters that show elevated levels of expression during growth of this organism in a type II sourdough fermentation. Thirty-eight sourdough-induced fusions were detected, and 29 genes could be identified on the basis of the available sequence information. Four genes encoded stress-related functions (e.g., acid and general stress response), reflecting the harsh conditions prevailing during sourdough fermentation. Further, eight genes were involved in acquisition and synthesis of amino acids and nucleotides, indicating their limited availability in sourdough. The remaining genes were either part of functionally unrelated pathways or encoded hypothetical proteins. The identification of a putative proteinase and a component of the arginine deiminase pathway is of technological interest, as they are potentially involved in the formation of aroma precursors. Our study allowed insight into the transcriptional response of
Lactobacillus reuteri
to the dough environment, which establishes the molecular basis to investigate bacterial properties that are likely to contribute to the ecological performance of the organism and influence the final outcome of the fermentation.
Genetic Diversity of
Listeria monocytogenes
Strains from a High-Prevalence Dairy Farm
Authors: Borucki Monica K. , Gay Clive C. , Reynolds James , McElwain Katherine L. , Kim So Hyun , Call Douglas R. , Knowles Donald P.
Published: October 2005

Listeria monocytogenes
is a significant food-borne human and veterinary pathogen. Contaminated silage commonly leads to disease in livestock, but the pervasive nature of the bacterium can make it difficult to identify the source of infection. An investigation of bovine listeriosis that occurred on a Pacific Northwest dairy farm (“farm A”) revealed that the clinical strain was closely related to fecal strains from asymptomatic cows, and that farm environment was heavily contaminated with a diversity of
L. monocytogenes
strains. In addition, the farm A clinical strain was closely related to clinical and environmental strains obtained 1 year prior from a second Northwest dairy farm (“farm B”). To investigate the source(s) of contamination on farm A, environmental samples were collected from farm A at two time points. Pulsed-field gel electrophoresis characterization of 538 isolates obtained from that farm identified 57 different AscI pulsovars. Fecal isolates obtained from individual cows were the most genetically diverse, with up to 94% of fecal samples containing more than one pulsovar. The maximum numbers of pulsovars and serotypes isolated from a fecal sample of one cow were 6 and 4, respectively. Serotype 1/2a was isolated most frequently at both time points. Microarray genotyping of bovine listeriosis, fecal, and silage strains from both farms identified four probes that differentiated listeriosis strains from environmental strains; however, no probe was common to both bovine listeriosis strains.
Ecological Differentiation within a Cosmopolitan Group of Planktonic Freshwater Bacteria (SOL Cluster,
Saprospiraceae
,
Bacteroidetes
)
Authors: Schauer Michael , Kamenik Christian , Hahn Martin W.
Published: October 2005

Members of the monophyletic SOL cluster are large filamentous bacteria inhabiting the pelagic zone of many freshwater habitats. The abundances of SOL bacteria and compositions of SOL communities in samples from 115 freshwater ecosystems around the globe were determined by fluorescence in situ hybridization with cluster- and subcluster-specific oligonucleotide probes. The vast majority (73%) of sampled ecosystems harbored SOL bacteria, and all three previously described SOL subclusters (LD2, HAL, and GKS2-217) were detected. The morphometric and chemicophysical parameters and trophic statuses of ecosystems were related to the occurrence and subcluster-specific composition of SOL bacteria by multivariate statistical methods. SOL bacteria did not occur in acidic lakes (pH < 6), and their abundance was negatively related to high trophy and pH. The subcluster-specific variation in the compositions of SOL communities could be related to the pH, electrical conductivity, altitude, and trophic status of ecosystems. All three known SOL subclusters differed in respect to their tolerated ranges of pH and conductivity. Complete niche separation was observed between the vicarious subclusters GKS2-217 and LD2; the former occurred in soft-water lakes, whereas the latter was found in a broad range of hard-water habitats. The third subgroup (HAL) showed a wide environmental tolerance and was usually found sympatrically with the LD2 or GKS2-217 subcluster. Ecological differentiation of SOL bacteria at the subcluster level was most probably driven by differential adaptation to water chemistry. The distribution of the two vicarious taxa seems to be predominantly controlled by the geological backgrounds of the catchment areas of the habitats.
Characterization of a
Corynebacterium glutamicum
Lactate Utilization Operon Induced during Temperature-Triggered Glutamate Production
Authors: Stansen Corinna , Uy Davin , Delaunay Stephane , Eggeling Lothar , Goergen Jean-Louis , Wendisch Volker F.
Published: October 2005

Gene expression changes of glutamate-producing
Corynebacterium glutamicum
were identified in transcriptome comparisons by DNA microarray analysis. During glutamate production induced by a temperature shift,
C. glutamicum
strain 2262 showed significantly higher mRNA levels of the NCgl2816 and NCgl2817 genes than its non-glutamate-producing derivative 2262NP. Reverse transcription-PCR analysis showed that the two genes together constitute an operon. NCgl2816 putatively codes for a lactate permease, while NCgl2817 was demonstrated to encode quinone-dependent
l
-lactate dehydrogenase, which was named LldD.
C. glutamicum
LldD displayed Michaelis-Menten kinetics for the substrate
l
-lactate with a

K
m

of about 0.51 mM. The specific activity of LldD was about 10-fold higher during growth on
l
-lactate or on an
l
-lactate-glucose mixture than during growth on glucose,
d
-lactate, or pyruvate, while the specific activity of quinone-dependent
d
-lactate dehydrogenase differed little with the carbon source. RNA levels of NCgl2816 and
lldD
were about 18-fold higher during growth on
l
-lactate than on pyruvate. Disruption of the NCgl2816-
lldD
operon resulted in loss of the ability to utilize
l
-lactate as the sole carbon source. Expression of
lldD
restored
l
-lactate utilization, indicating that the function of the permease gene NCgl2816 is dispensable, while LldD is essential, for growth of
C. glutamicum
on
l
-lactate.
Metabolism of Carbaryl via 1,2-Dihydroxynaphthalene by Soil Isolates
Pseudomonas
sp. Strains C4, C5, and C6
Authors: Swetha Vandana P. , Phale Prashant S.
Published: October 2005

Pseudomonas
sp. strains C4, C5, and C6 utilize carbaryl as the sole source of carbon and energy. Identification of 1-naphthol, salicylate, and gentisate in the spent media; whole-cell O
2
uptake on 1-naphthol, 1,2-dihydroxynaphthalene, salicylaldehyde, salicylate, and gentisate; and detection of key enzymes, viz, carbaryl hydrolase, 1-naphthol hydroxylase, 1,2-dihydroxynaphthalene dioxygenase, and gentisate dioxygenase, in the cell extract suggest that carbaryl is metabolized via 1-naphthol, 1,2-dihydroxynaphthalene, and gentisate. Here, we demonstrate 1-naphthol hydroxylase and 1,2-dihydroxynaphthalene dioxygenase activities in the cell extracts of carbaryl-grown cells. 1-Naphthol hydroxylase is present in the membrane-free cytosolic fraction, requires NAD(P)H and flavin adenine dinucleotide, and has optimum activity in the pH range 7.5 to 8.0. Carbaryl-degrading enzymes are inducible, and maximum induction was observed with carbaryl. Based on these results, the proposed metabolic pathway is carbaryl → 1-naphthol → 1,2-dihydroxynaphthalene → salicylaldehyde → salicylate → gentisate → maleylpyruvate.
Role of the Regulatory GenerirAin the Transcriptional Response ofSinorhizobium melilotito Iron Limitation
Authors: Chao Tzu-Chiao , Buhrmester Jens , Hansmeier Nicole , Pühler Alfred , Weidner Stefan
Published: October 2005

A regulatory network ofSinorhizobium melilotigenes involved in adaptation to iron-limiting conditions and the involvement of the rhizobial iron regulator gene (rirA) were analyzed by mutation and microarray analyses. A constructedS. meliloti rirAmutant exhibited growth defects and enhanced H2O2sensitivity in the presence of iron, but symbiotic nitrogen fixation was not affected. To identify iron-responsive and RirA-regulatedS. melilotigenes, a transcriptome approach using whole-genome microarrays was used. Altogether, 45 genes were found to be jointly derepressed by mutation ofrirAand under different iron-limited conditions. As expected, a number of genes involved in iron transport (e.g.,hmuPSTU,shmR,rhbABCDEF,rhtX, andrhtA) and also genes with predicted functions in energy metabolism (e.g.,fixN3,fixP3, andqxtAB) and exopolysaccharide production (e.g.,exoYandexoN) were found in this group of genes. In addition, the iron deficiency response ofS. melilotialso involvedrirA-independent expression changes, including repression of theS. melilotiflagellar regulon. Finally, the RirA modulon also includes genes that are not iron responsive, including a gene cluster putatively involved in Fe-S cluster formation (sufA,sufS,sufD,sufC, andsufB).
Comparison of
Bacteroides-Prevotella
16S rRNA Genetic Markers for Fecal Samples from Different Animal Species
Authors: Fogarty Lisa R. , Voytek Mary A.
Published: October 2005

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group
Bacteroides-Prevotella
as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of
Bacteroides-Prevotella
community T-RFLP profiles indicates that
Bacteroides-Prevotella
populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying
Bacteroides-Prevotella
molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.
Restoration of Gibberellin Production in
Fusarium proliferatum
by Functional Complementation of Enzymatic Blocks
Authors: Malonek S. , Rojas M. C. , Hedden P. , Hopkins P. , Tudzynski B.
Published: October 2005

Nine biological species, or mating populations (MPs), denoted by letters A to I, and at least 29 anamorphic
Fusarium
species have been identified within the
Gibberella fujikuroi
species complex. Members of this species complex are the only species of the genus
Fusarium
that contain the gibberellin (GA) biosynthetic gene cluster or at least parts of it. However, the ability of fusaria to produce GAs is so far restricted to
Fusarium fujikuroi
, although at least six other MPs contain all the genes of the GA biosynthetic gene cluster. Members of
Fusarium proliferatum
, the closest related species, have lost the ability to produce GAs as a result of the accumulation of several mutations in the coding and 5′ noncoding regions of genes
P450
-
4
and
P450
-
1
, both encoding cytochrome P450 monooxygenases, resulting in metabolic blocks at the early stages of GA biosynthesis. In this study, we have determined additional enzymatic blocks at the first specific steps in the GA biosynthesis pathway of
F. proliferatum
: the synthesis of geranylgeranyl diphosphate and the synthesis of
ent
-kaurene. Complementation of these enzymatic blocks by transferring the corresponding genes from GA-producing
F. fujikuroi
to
F. proliferatum
resulted in the restoration of GA production. We discuss the reasons for
Fusarium
species outside the
G. fujikuroi
species complex having no GA biosynthetic genes, whereas species distantly related to
Fusarium
, e.g.,
Sphaceloma
spp. and
Phaeosphaeria
spp., produce GAs.
Investigation of Specific Substitutions in Virulence Genes Characterizing Phenotypic Groups of Low-Virulence Field Strains of
Listeria monocytogenes
Authors: Roche S. M. , Gracieux P. , Milohanic E. , Albert I. , Virlogeux-Payant I. , Témoin S. , Grépinet O. , Kerouanton A. , Jacquet C. , Cossart P. , Velge P.
Published: October 2005

Several models have shown that virulence varies from one strain of
Listeria monocytogenes
to another, but little is known about the cause of low virulence. Twenty-six field
L. monocytogenes
strains were shown to be of low virulence in a plaque-forming assay and in a subcutaneous inoculation test in mice. Using the results of cell infection assays and phospholipase activities, the low-virulence strains were assigned to one of four groups by cluster analysis and then virulence-related genes were sequenced. Group I included 11 strains that did not enter cells and had no phospholipase activity. These strains exhibited a mutated PrfA; eight strains had a single amino acid substitution, PrfAK220T, and the other three had a truncated PrfA, PrfAΔ174-237. These genetic modifications could explain the low virulence of group I strains, since mutated PrfA proteins were inactive. Group II and III strains entered cells but did not form plaques. Group II strains had low phosphatidylcholine phospholipase C activity, whereas group III strains had low phosphatidylinositol phospholipase C activity. Several substitutions were observed for five out of six group III strains in the
plcA
gene and for one out of three group II strains in the
plcB
gene. Group IV strains poorly colonized spleens of mice and were practically indistinguishable from fully virulent strains on the basis of the above-mentioned in vitro criteria. These results demonstrate a relationship between the phenotypic classification and the genotypic modifications for at least group I and III strains and suggest a common evolution of these strains within a group.
Intestinal Bacterial Communities That Produce Active Estrogen-Like Compounds Enterodiol and Enterolactone in Humans
Authors: Clavel Thomas , Henderson Gemma , Alpert Carl-Alfred , Philippe Catherine , Rigottier-Gois Lionel , Doré Joël , Blaut Michael
Published: October 2005

Lignans are dietary diphenolic compounds which require activation by intestinal bacteria to exert possible beneficial health effects. The intestinal ecosystem plays a crucial role in lignan metabolism, but the organisms involved are poorly described. To characterize the bacterial communities responsible for secoisolariciresinol (SECO) activation, i.e., the communities that produce the enterolignans enterodiol (ED) and enterolactone (EL), a study with 24 human subjects was undertaken. SECO activation was detected in all tested fecal samples. The intestinal bacteria involved in ED production were part of the dominant microbiota (6 × 10
8
CFU g
−1
), as revealed by most-probable-number enumerations. Conversely, organisms that catalyzed the formation of EL occurred at a mean concentration of approximately 3 × 10
5
CFU g
−1
. Women tended to have higher concentrations of both ED- and EL-producing organisms than men. Significantly larger amounts of EL were produced by fecal dilutions from individuals with moderate to high concentrations of EL-producing bacteria. Two organisms able to demethylate and dehydroxylate SECO were isolated from human feces. Based on 16S rRNA gene sequence analyses, they were named
Peptostreptococcus productus
SECO-Mt75m3 and
Eggerthella lenta
SECO-Mt75m2. A new 16S rRNA-targeted oligonucleotide probe specific for
P. productus
and related species was designed and further used in fluorescent in situ hybridization experiments, along with five additional group-specific probes. Significantly higher proportions of
P. productus
and related species (
P
= 0.012), as well as bacteria belonging to the
Atopobium
group (
P
= 0.035), were typical of individuals with moderate to high concentrations of EL-producing communities.
A
Lactobacillus acidophilus
Strain of Human Gastrointestinal Microbiota Origin Elicits Killing of Enterovirulent
Salmonella enterica
Serovar Typhimurium by Triggering Lethal Bacterial Membrane Damage
Authors: Coconnier-Polter Marie-Hélène , Liévin-Le Moal Vanessa , Servin Alain L.
Published: October 2005

The human gastrointestinal microbiota produces antagonistic activities against gastrointestinal bacterial pathogens. We undertook a study to investigate the mechanism(s) by which a
Lactobacillus acidophilus
strain of human microbiota origin antagonizes the gram-negative enteroinvasive pathogen
Salmonella enterica
serovar Typhimurium. We showed that the cell-free culture supernatant of
L. acidophilus
strain LB (LB-CFCS) induced the following effects in
S. enterica
SL1344: (i) a decrease in intracellular ATP that paralleled bacterial death, (ii) the release of lipopolysaccharide, (iii) permeabilization of the bacterial membrane, and (iv) an increase in the sensitivity of
Salmonella
to the lytic action of sodium dodecyl sulfate. Finally, we showed using two mutant strains of
Salmonella
, PhoP MS7953s and PmrA JKS1170, that the two-component regulatory systems PhoP-PhoQ and PmrA-PmrB that regulate the mechanisms of resistance to antibacterial agents in
Salmonella
did not influence the anti-
Salmonella
effect of LB-CFCS.
Formation of Catechols via Removal of Acid Side Chains from Ibuprofen and Related Aromatic Acids
Authors: Murdoch Robert W. , Hay Anthony G.
Published: October 2005

Although ibuprofen [2-(4-isobutylphenyl)-propionic acid] is one of the most widely consumed drugs in the world, little is known regarding its degradation by environmental bacteria.
Sphingomonas
sp. strain Ibu-2 was isolated from a wastewater treatment plant based on its ability to use ibuprofen as a sole carbon and energy source. A slight preference toward the
R
enantiomer was observed, though both ibuprofen enantiomers were metabolized. A yellow color, indicative of
meta
-cleavage, accumulated transiently in the culture supernatant when Ibu-2 was grown on ibuprofen. When and only when 3-flurocatechol was used to poison the
meta
-cleavage system, isobutylcatechol was identified in the culture supernatant via gas chromatography-mass spectrometry analysis. Ibuprofen-induced washed-cell suspensions also metabolized phenylacetic acid and 2-phenylpropionic acid to catechol, while 3- and 4-tolylacetic acids and 2-(4-tolyl)-propionic acid were metabolized to the corresponding methyl catechols before ring cleavage. These data suggest that, in contrast to the widely distributed coenzyme A ligase, homogentisate, or homoprotocatechuate pathway for metabolism of phenylacetic acid and similar compounds, Ibu-2 removes the acidic side chain of ibuprofen and related compounds prior to ring cleavage.
Fermentation of Fructooligosaccharides and Inulin by Bifidobacteria: a Comparative Study of Pure and Fecal Cultures
Authors: Rossi Maddalena , Corradini Claudio , Amaretti Alberto , Nicolini Marcello , Pompei Anna , Zanoni Simona , Matteuzzi Diego
Published: October 2005

The utilization of fructooligosaccharides (FOS) and inulin by 55
Bifidobacterium
strains was investigated. Whereas FOS were fermented by most strains, only eight grew when inulin was used as the carbon source. Residual carbohydrates were analyzed by high-performance anion-exchange chromatography with pulsed amperometric detection after batch fermentation. A strain-dependent capability to degrade fructans of different lengths was observed. During batch fermentation on inulin, the short fructans disappeared first, and then the longer ones were gradually consumed. However, growth occurred through a single uninterrupted exponential phase without exhibiting polyauxic behavior in relation to the chain length. Cellular β-fructofuranosidases were found in all of the 21
Bifidobacterium
strains tested. Four strains were tested for extracellular hydrolytic activity against fructans, and only the two strains which ferment inulin showed this activity. Batch cultures inoculated with human fecal slurries confirmed the bifidogenic effect of both FOS and inulin and indicated that other intestinal microbial groups also grow on these carbon sources. We observed that bifidobacteria grew by cross-feeding on mono- and oligosaccharides produced by primary inulin intestinal degraders, as evidenced by the high hydrolytic activity of fecal supernatants. FOS and inulin greatly affected the production of short-chain fatty acids in fecal cultures; butyrate was the major fermentation product on inulin, whereas mostly acetate and lactate were produced on FOS.
Diversity of the Microeukaryotic Community in Sulfide-Rich Zodletone Spring (Oklahoma)
Authors: Luo Qingwei , Krumholz Lee R. , Najar Fares Z. , Peacock Aaron D. , Roe Bruce A. , White David C. , Elshahed Mostafa S.
Published: October 2005

The microeukaryotic community in Zodletone Spring, a predominantly anaerobic sulfide and sulfur-rich spring, was examined using an 18S rRNA gene cloning and sequencing approach. The majority of the 288 clones sequenced from three different locations at Zodletone Spring belonged to theStramenopiles,Alveolata, andFungi, with members of the phylumCercozoa, orderDiplomonadida, and familyJakobidaerepresenting a minor fraction of the clone library. No sequences suggesting the presence of novel kingdom level diversity were detected in any of the three libraries. A large fraction of stramenopile clones encountered were monophyletic with either members of the genusCafeteria(orderBicosoecida) or members of the orderLabyrinthulida(slime nets), both of which have so far been encountered mainly in marine habitats. The majority of the observed fungal clone sequences belonged to the ascomycetous yeasts (orderSaccharomycetales), were closely related to yeast genera within theHymenobasidiomycetes(phylumBasidiomycetes), or formed a novel fungal lineage with several previously published or database-deposited clones. To determine whether the unexpected abundance of fungal sequences in Zodletone Spring clone libraries represents a general pattern in anaerobic habitats, we generated three clone libraries from three different anaerobic settings (anaerobic sewage digester, pond sediment, and hydrocarbon-exposed aquifer sediments) and partially sequenced 210 of these clones. Phylogenetic analysis indicated that clone sequences belonging to the kingdomFungirepresent a significant fraction of all three clone libraries, an observation confirmed by phospholipid fatty acid and ergosterol analysis. Overall, this work reveals an unexpected abundance ofFungiin anaerobic habitats, describes a novel, yet-uncultured group ofFungithat appears to be widespread in anaerobic habitats, and indicates that several of the previously considered marine protists could also occur in nonmarine habitats.
Genetic and Transcriptional Organization of the
clpC
Locus in
Bifidobacterium breve
UCC 2003
Authors: Ventura Marco , Fitzgerald Gerald F. , van Sinderen Douwe
Published: October 2005

A homolog of the
clpC
ATPase gene was identified in the genome of
Bifidobacterium breve
UCC 2003. Since this gene is very well conserved among eubacteria, we employed a PCR-based approach using primers based on highly conserved regions of ClpC proteins in order to identify homologous genes in other bifidobacterial species. Analysis by slot blot, Northern blot, and primer extension experiments showed that transcription of
clpC
is induced in response to moderate heat shock regimes. Moreover, we identified in the genome sequence of
B. breve
UCC 2003 a gene, designated
clgR
, which is predicted to encode a transcriptional regulator involved in regulation of the bifidobacterial
clpC
gene. The role of this protein in the regulation of
B. breve
UCC 2003
clpC
gene expression was investigated by performing gel retardation experiments. We show that a biologically active ClgR molecule requires one or more proteinaceous coactivators to assist in the specific binding of ClgR to the
clpC
promoter region.
Speciation of
Campylobacter coli
,
C. jejuni
,
C. helveticus
,
C. lari
,
C. sputorum
, and
C. upsaliensis
by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Mandrell Robert E. , Harden Leslie A. , Bates Anna , Miller William G. , Haddon William F. , Fagerquist Clifton K.
Published: October 2005

Multiple strains of
Campylobacter coli
,
C. jejuni
,
C. helveticus
,
C. lari
,
C. sputorum
, and
C. upsaliensis
isolated from animal, clinical, or food samples have been analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Whole bacterial cells were harvested from colonies or confluent growth on agar and transferred directly into solvent and then to a spot of dried 3-methoxy-4-hydroxycinnamic acid (matrix). Multiple ions in the 5,000- to 15,000-Da mass range were evident in spectra for each strain; one or two ions in the 9,500- to 11,000-Da range were consistently high intensity. “Species-identifying” biomarker ions (SIBIs) were evident from analyses of multiple reference strains for each of the six species, including the genome strains
C. jejuni
NCTC 11168 and
C. jejuni
RM1221. Strains grown on nine different combinations of media and atmospheres yielded SIBI masses within ±5 Da with external instrument calibration. The highest-intensity
C. jejuni
SIBIs were cytosolic proteins, including GroES, HU/HCj, and RplL. Multiple intraspecies SIBIs, corresponding probably to nonsynonymous nucleotide polymorphisms, also provided some intraspecies strain differentiation. MALDI-TOF MS analysis of 75 additional
Campylobacter
strains isolated from humans, poultry, swine, dogs, and cats revealed (i) associations of SIBI type with source, (ii) strains previously speciated incorrectly, and (iii) “strains” composed of more than one species. MALDI-TOF MS provides an accurate, sensitive, and rapid method for identification of multiple
Campylobacter
species relevant to public health and food safety.
Microbiological and Geochemical Heterogeneity in an In Situ Uranium Bioremediation Field Site
Authors: Vrionis Helen A. , Anderson Robert T. , Ortiz-Bernad Irene , O'Neill Kathleen R. , Resch Charles T. , Peacock Aaron D. , Dayvault Richard , White David C. , Long Philip E. , Lovley Derek R.
Published: October 2005

The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order
Desulfobacterales
in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family
Geobacteraceae
. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of
Geobacteraceae
16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.