bluuebunny/crossref_metadata_2025 huggingface dataset:
Motion in the Schwarzschild Metric
Authors: Markley F. Landis
Published: September 2005

We study the motion of a particle in the Schwarzschild metric, using a coordinate system in which the radial speed of light is unity. The similarity between the variational equation for geodesics and Hamilton's principle makes many of the results of Hamiltonian mechanics applicable. We conclude that the gravitational force in this case is attractive in general relativity, just as it is in Newtonian theory.
Propagation of a Localized Impulse on a One-Dimensional Lattice
Authors: Merchant Deborah L. , Brill Orville L.
Published: September 2005

A chain of N atoms, each of mass M, with an interatomic distance a and coupled by identical massless ideal springs is considered to be in an equilibrium state with the interconnecting springs at equilibrium length at time t=0. With the system in this state of equilibrium an impulse is given to one of the atoms in the chain. The atomic displacements and corresponding velocities for the disturbed chain are derived and expressed in terms of the dispersion relation for the chain by using Fourier expansions and by assuming periodic boundary conditions. It is shown that the k=0 mode of the Fourier expansion involved in the solutions for the displacement and velocity carries all of the momentum given to the chain during the impulse. The propagator which describes the atomic displacements in the chain resulting from the application of a space and time dependent force is presented. Graphical displays of the results of computations of the atomic displacements at various times illustrate the propagation through the chain of the initially localized pulse.
Magnetic Induction and the Linear Air Track
Authors: Fox John N. , Reiber Daniel G.
Published: September 2005

The present paper introduces the linear air track to the electricity and magnetism laboratory. A coil carried by an air cart passes through an external magnetic field. The mechanical energy loss of the system is compared to the resulting Joule heat generated in the coil. Design features and data are presented.
Concerning the Absolute Temperature Function
Authors: Buchdahl H. A.
Published: September 2005

The principal purpose of this work is didactic. The existence of the absolute temperature function is inferred without prior introduction of the concept of (empirical) temperature. To this end an ancillary law is postulated which replaces the Zeroth Law and which, like the Second Law itself, is a statement about adiabatic accessibility and so forms a natural complement to it. Granted this additional postulate the existence of the metrical entropy function, its additivity, and the one-sided conservation law to which it is subject can be discussed in entire isolation from the concepts of energy, heat, and temperature.
Low-Cost Cryostat for Laboratory Instruction in Physics
Authors: Martin Frank E. , Sidles Paul H.
Published: September 2005

An inexpensive cryostat built and used by college students to study charge carriers in semiconductors is described. Sufficient details of construction and operation are discussed for our results to be duplicated in other student laboratories. Procedures for measurement of electrical conductivity and Hall coefficient are discussed and results obtained by students on germanium and magnesium stannide are presented. From these results such fundamental properties as carrier concentrations, carrier mobilities, and energy gaps are derived. With different sample holders the cryostat may be used for other experiments.
Applying Science to Public Technology
Authors: Chapman Seville
Published: September 2005

We live in a technological era of accelerating change, increasing pressures, and diminishing resources. If science and technology are to be useful in the solution of social problems, then scientists and engineers must participate in public discussions and in the decision-making process. To do so they must match their scientific understanding with appreciation of the economic, political, and social aspects of problems. Then they must become involved with federal, state, and local officials who will be making decisions. They must do this in the context not of the scientist, hut of the officials. This communication process is neither easy nor familiar to the scientist. It involves mutual education. Degree of success and time of effect should not be judged on scientific grounds, but rather on those of social adaptation. Patience, persistence, and breadth of view are even more necessary than deep sophistication. A list is given of things that professionals and/or professional societies can do. Development of a base of public understanding, an important kind of general education, is a prerequisite for political action.
Non-Uniform Gravitational Fields and Clock Paradoxes
Authors: Durso John W. , Nicholson Howard W.
Published: September 2005

Two experiments which can be performed in arbitrarily small volumes of space and without reference to external fixed objects to determine the geometry of a satellite orbit in a spherically symmetric gravitational field are described. They are of interest in explaining the aging asymmetry which occurs in a recently published variation of the relativistic “twins” or clock paradox.
The influence of cortical end-plate on broadband ultrasound attenuation measurements at the human calcaneus using scanning confocal ultrasound
Authors: Xia Yi , Lin Wei , Qin Yi-Xian
Published: September 2005

Quantitative ultrasound (QUS) assessment, including broadband ultrasound attenuation (BUA), is an efficient technique for assessing bone quality in various statuses, e.g., osteoporosis. While assessing trabecular bone loss is essential to bone quality, the existence of cortical bone can substantially reduce the accuracy of BUA measurement. In this study, we developed an approach to quantify the influence of the cortical end-plate in the QUS on 18 cadaver calcanei using both analytical and experimental analyses. A simplified cortical-trabecular-cortical sandwich model has been developed for simulation of wave propagations. Results show that the cortical end-plate has a significant effect on BUA (yielding 8.5±3.6dB∕MHz in cortical bone alone), approximately 15% of the BUA value over the whole bone BUA measurement (54.1±20.1dB∕MHz). The phenomenon has been predicted by the developed analytical model with a high correlation (r2=0.63,p<0.0001). The data have suggested that the mechanism of the BUA attributed to the cortical end-plate is primarily due to the ultrasonic wave transmission and reflection within the cortical layers. Therefore, the influence of the cortical end-plate in BUA can be quantified and incorporated into the QUS assessment for bone quality, which may provide insight into BUA measurement for accurate diagnosis of bone diseases.
Impedance and Brewster angle measurement for thick porous layers
Authors: Hickey Craig J. , Leary Del , Allard Jean F. , Henry Michel
Published: September 2005

For thin nonlocally reacting porous layers, a method derived from the work of [Chien and Soroka, J. Sound Vib. 43, 9–20 (1975)] has been used to localize the pole of the reflection coefficient located at a complex angle close to π∕2 and to measure the surface impedance at this angle. Measurements are performed with a small source/receiver separation. The method is used in the present work to measure the surface impedance of acoustically thick porous layers of high flow resistivity. Simulations show that the measured impedance, which is related to a complex angle close to π∕2 like for thin porous layers, is close to the impedance at grazing incidence. It is also shown that for semi-infinite layers the method provides a measure of the Brewster angle of the medium. Measurements of the cosine of the complex angle and of the related impedance on two granular media of high flow resistivity, Ottawa sand and glass beads, are in a reasonable agreement with predictions for frequencies above 1kHz for a source/receiver separation of 30cm.
Aircraft noise annoyance in recreational areas after changes in noise exposure: Comments on Krog and Engdahl (2004)
Authors: Klæboe Ronny
Published: September 2005

When Gardermoen replaced Fornebu as the main airport for Oslo, aircraft noise levels increased in recreational areas near Gardermoen and decreased in areas near Fornebu. Krog and Engdahl [J. Acoust. Soc. Am. 116, 323–333 (2004)] estimate that recreationists’ annoyance from aircraft noise in these areas changed more than would be anticipated from the actual noise changes. However, the sizes of their estimated “situation” effects are not credible. One possible reason for the anomalous results is that standard regression assumptions become violated when motivational factors are inserted into the regression model. Standardized regression coefficients (beta values) should also not be utilized for comparisons across equations.
Voice gender identification by cochlear implant users: The role of spectral and temporal resolution
Authors: Fu Qian-Jie , Chinchilla Sherol , Nogaki Geraldine , Galvin John J.
Published: September 2005

The present study explored the relative contributions of spectral and temporal information to voice gender identification by cochlear implant users and normal-hearing subjects. Cochlear implant listeners were tested using their everyday speech processors, while normal-hearing subjects were tested under speech processing conditions that simulated various degrees of spectral resolution, temporal resolution, and spectral mismatch. Voice gender identification was tested for two talker sets. In Talker Set 1, the mean fundamental frequency values of the male and female talkers differed by 100 Hz while in Talker Set 2, the mean values differed by 10 Hz. Cochlear implant listeners achieved higher levels of performance with Talker Set 1, while performance was significantly reduced for Talker Set 2. For normal-hearing listeners, performance was significantly affected by the spectral resolution, for both Talker Sets. With matched speech, temporal cues contributed to voice gender identification only for Talker Set 1 while spectral mismatch significantly reduced performance for both Talker Sets. The performance of cochlear implant listeners was similar to that of normal-hearing subjects listening to 4–8 spectral channels. The results suggest that, because of the reduced spectral resolution, cochlear implant patients may attend strongly to periodicity cues to distinguish voice gender.
Simulations of string vibrations with boundary conditions of third kind using the functional transformation method
Authors: Trautmann L. , Petrausch S. , Bauer M.
Published: September 2005

The functional transformation method (FTM) is an established mathematical method for accurate simulation of multidimensional physical systems from various fields of science, including optics, heat and mass transfer, electrical engineering, and acoustics. It is a frequency-domain method based on the decomposition into eigenvectors and eigenfrequencies of the underlying physical problem. In this article, the FTM is applied to real-time simulations of vibrating strings which are ideally fixed at one end while the fixing at the other end is modeled by a frequency-dependent input impedance. Thus, boundary conditions of third kind are applied to the model at the end fixed with the input impedance. It is shown that accurate and stable simulations are achieved with nearly the same computational cost as with strings ideally fixed at both ends.
A time-variant impulse response method for acoustic scattering from moving two-dimensional surfaces
Authors: Keiffer Richard S. , Novarini Jorge C. , Scharstein Robert W.
Published: September 2005

A time-variant impulse response method is proposed, developed, tested, and shown to provide new insights into different scattering problems involving moving surfaces. The method proposed is general, conceptually straightforward, and can accommodate moving sources and receivers. While the time-variant impulse response method has been developed specifically in this study to extend the capability of the wedge assemblage (WA) model [e.g., R. S. Keiffer and J. C. Novarini, J. Acoust. Soc. Am. 107, 27–39 (2000)], the framework can be applied to other scattering models including those based in the frequency domain. Calculations involving moving periodic surfaces and moving receivers are presented and compared with good results to a generalized grating equation and small wave-height approximation perturbation theory. The time-variant impulse response model is also applied to time-evolving sea surfaces, and the previously published results of Pourkaviani and Willemsen [J. Acoust. Soc. Am. 90, 426–432 (1991)] are confirmed. It is also shown that windward-oriented backscatter geometries can lead to a Doppler spectrum that peaks at higher than expected Doppler shifts.
Control strategies for active noise barriers using near-field error sensing
Authors: Berkhoff Arthur P.
Published: September 2005

In this paper active noise control strategies for noise barriers are presented which are based on the use of sensors near the noise barrier. Virtual error signals are derived from these near-field sensor signals such that reductions of the far-field sound pressure are obtained with the active system. The performance of the control algorithm is compared for far-field error signals, near-field error signals, and virtual far-field error signals, with and without additional reference sensors. The virtual error signals are obtained by using separate transfer functions for the primary sources and secondary sources. These separate transfer functions are determined in such a way that the necessity of the separation of the virtual sensors for the primary field and for the secondary field can be judged by direct comparison. The systems are evaluated for independent broadband and randomly positioned primary sources, changing source spectra, moving sources, and configurations involving a nonvanishing wind speed.
On waveguide modeling of stiff piano strings
Authors: Ducasse Éric
Published: September 2005

Bensa et al. [J. Acoust. Soc. Am. 114, 1095–1107 (2003), Sec. IV] recently proposed a waveguide model for the transverse displacement of a stiff piano string. The study described here is an attempt to cast a complementary light on this topic, based on a common wave approach instead of a modal approach. A pair of weakly attenuated traveling waves and a pair of fast-decaying waves both satisfy the one-dimensional wave equation developed by Bensa et al. These solutions have to be carefully considered, however, for portions of string interacting with the hammer felt, the bridge, or the capo d’astro bar.
Analysis of models for the synapse between the inner hair cell and the auditory nerve
Authors: Zhang Xuedong , Carney Laurel H.
Published: September 2005

A general mathematical approach was proposed to study phenomenological models of the inner-hair-cell and auditory-nerve (AN) synapse complex. Two models (Meddis, J. Acoust. Soc. Am. 79(3), 702–711 (1986); Westerman and Smith, J. Acoust. Soc. Am. 83(6), 2266–2276 (1988)) were studied using this unified approach. The responses of both models to a constant-intensity stimulus were described mathematically, and the relationship between model parameters and response characteristics was investigated. The mathematical descriptions of the two models were essentially equivalent despite their structural differences. This analytical approach was used to study the effects of adaptation characteristics on model parameters and of model parameters on adaptation characteristics. The results provided insights into these models and the underlying biophysical processing. This analytical method was also used to study offset adaptation, and it was found that the offset adaptation of both models was limited by the models’ structures. A modified version of the synapse model, which has the same onset adaptation but improved offset adaptation, is proposed here. This modified synapse model produces more physiologically realistic offset adaptation and also enhances the modulation gain of model AN fiber responses, consistent with AN physiology.
Signal processing strategies that improve performance and understanding of the quantitative ultrasound SPECTRAL FIT algorithm
Authors: Bigelow Timothy A. , O’Brien William D.
Published: September 2005

Quantifying the size of the tissue microstructure using the backscattered power spectrum has had limited success due to frequency-dependent attenuation along the propagation path, thus masking the frequency dependence of the scatterer size. Previously, the SPECTRAL FIT algorithm was developed to solve for total attenuation and scatterer size simultaneously [Bigelow et al., J. Acoust. Soc. Am. 117, 1431–1439 (2005)]. Herein, the outcomes from signal processing strategies on the SPECTRAL FIT algorithm are investigated. The signal processing methods can be grouped into two categories, viz., methods that improve the performance of the algorithm and methods that provide insight. The methods that improve the performance include compensating for the windowing function used to gate the time-domain signal, averaging the spectra in the normal frequency domain rather than the log domain to improve the precision of the scatterer size and attenuation estimates, improving the selection of the usable frequency range for the SPECTRAL FIT algorithm, and improving the compensation for electronic noise. The methods that provide insight demonstrate that the anomalous rapid fluctuations of the backscattered power spectrum do not affect the SPECTRAL FIT algorithm, and accurate attenuation estimates can be obtained even when the correct scatterer geometry (i.e., form factor) is not known.
Polydisperse particle size characterization by ultrasonic attenuation spectroscopy for systems of diverse acoustic contrast in the large particle limit
Authors: Richter Andreas , Babick Frank , Ripperger Siegfried
Published: September 2005

Ultrasonic attenuation spectroscopy offers advantages over other spectrometric methods for the determination of suspension and emulsion size distributions. One advantage is the possibility of conducting measurements in highly concentrated or optically opaque dispersions. Models useable for the inversion of measured attenuation spectra to calculate particle size distributions are available and widely used, but their applied forms only allow for the characterization of particles smaller than 10μm. In this paper, a methodology using the Faran model for elastic scatterers is examined in the region of micrometer-sized particles with respect to its suitability for the prediction of measured attenuation spectra and size distributions of various material combinations. All selected particle fractions and fluid materials were characterized independently from ultrasonic attenuation spectroscopy with respect to their material properties, size distributions, and shape. A comparison of measured and calculated attenuation spectra shows an acceptable agreement. The chosen methodology for particle sizing applications is further confirmed if a fit of the model to the measurement data is performed. In this approach, the solids volume fraction is treated as the only fit parameter. The findings indicate that the methodology is suitable for polydisperse particle size characterization for a wide range of acoustic contrast.
A Wigner approximation method for wave propagation
Authors: Loughlin Patrick J. , Cohen Leon
Published: September 2005

An approximation method for pulse propagation based on the Wigner position-wavenumber representation is presented. The method is very easy to apply and moreover is physically illuminating. One obtains the evolved approximate Wigner distribution from the initial Wigner distribution by a simple linear translation in phase space. Each phase space point propagates at constant velocity given by the group velocity at the phase space point. Dissipative propagation (damping) is also taken into account. From the approximate Wigner distribution, one can obtain the approximate magnitude of the evolved pulse and the approximate local wavenumber, that is, the spatial derivative of the phase of the pulse. Examples are given to illustrate the method.
A Human-Specific Gene in Microglia
Authors: Hayakawa Toshiyuki , Angata Takashi , Lewis Amanda L. , Mikkelsen Tarjei S. , Varki Nissi M. , Varki Ajit
Published: September 2005

Recent studies have shown multiple differences between humans and apes in sialic acid (Sia) biology, including Siglecs (Sia-recognizing-Ig-superfamily lectins). Comparisons with the chimpanzee genome indicate that human
SIGLEC11
emerged through human-specific gene conversion by an adjacent pseudogene. Conversion involved 5� untranslated sequences and the Sia-recognition domain. This human protein shows reduced binding relative to the ancestral form but recognizes oligosialic acids, which are enriched in the brain.
SIGLEC11
is expressed in human but not in chimpanzee brain microglia. Further studies will determine if this event was related to the evolution of
Homo
.
Spin Disorder on a Triangular Lattice
Authors: Nakatsuji Satoru , Nambu Yusuke , Tonomura Hiroshi , Sakai Osamu , Jonas Seth , Broholm Collin , Tsunetsugu Hirokazu , Qiu Yiming , Maeno Yoshiteru
Published: September 2005

As liquids crystallize into solids on cooling, spins in magnets generally form periodic order. However, three decades ago, it was theoretically proposed that spins on a triangular lattice form a liquidlike disordered state at low temperatures. Whether or not a spin liquid is stabilized by geometrical frustration has remained an active point of inquiry ever since. Our thermodynamic and neutron measurements on NiGa
2
S
4
, a rare example of a two-dimensional triangular lattice antiferromagnet, demonstrate that geometrical frustration stabilizes a low-temperature spin-disordered state with coherence beyond the two-spin correlation length. Spin liquid formation may be an origin of such behavior.
Factoring Risks to the Heart
Authors: Issa Amalia M.
Published: September 2005

A Change of Heart
. How the Framingham Heart Study Helped Unravel the Mysteries of Cardiovascular Disease.
By Daniel Levy and Susan Brink
. Knopf, New York, 2005. 268 pp. $26.95, C$37.95. ISBN 0-375-41275-1.

The authors blend together history, anecdotes, and lessons for reducing the risks of cardiovascular disease drawn from the almost 60 years of a landmark epidemiological study.
Earning from Risks
Authors: MacKenzie Donald
Published: September 2005

Fischer Black and the Revolutionary Idea of Finance
.
By Perry Mehrling
. Wiley, Hoboken, NJ, 2005. 392 pp. $29.95, C$38.99, £19.99. ISBN 0-471-45732-9.

This biography weaves together an informative portrait of an eccentric theorist and his work on the pricing of risk that played a crucial role in the development of derivatives markets.
Dissimilatory Iron Reduction and Odor Indicator Abatement by Biofilm Communities in Swine Manure Microcosms
Authors: Castillo-Gonzalez Hugo A. , Bruns Mary Ann
Published: September 2005

Animal waste odors arising from products of anaerobic microbial metabolism create community relations problems for livestock producers. We investigated a novel approach to swine waste odor reduction: the addition of FeCl3, a commonly used coagulant in municipal wastewater treatment, to stimulate degradation of odorous compounds by dissimilatory iron-reducing bacteria (DIRB). Two hypotheses were tested: (i) FeCl3is an effective source of redox-active ferric iron (Fe3+) for dissimilatory reduction by bacteria indigenous to swine manure, and (ii) dissimilatory iron reduction results in significant degradation of odorous compounds within 7 days. Our results demonstrated that Fe3+from FeCl3was reduced biologically as well as chemically in laboratory microcosms prepared with prefiltered swine manure slurry and limestone gravel, which provided pH buffering and a substrate for microbial biofilm development. Addition of a 1-g liter−1equivalent concentration of Fe3+from FeCl3, but not from presynthesized ferrihydrite, caused initial, rapid solids flocculation, chemical Fe3+reduction, and Ehincrease, followed by a 2-day lag period. Between 2 and 6 days of incubation, increases in Fe2+concentrations were accompanied by significant reductions in concentrations of volatile fatty acids used as odor indicators. Increases in Fe2+concentrations between 2 and 6 days did not occur in FeCl3-treated microcosms that were sterilized by gamma irradiation or amended with NaN3, a respiratory inhibitor. DNA sequences obtained from rRNA gene amplicons of bacterial communities in FeCl3-treated microcosms were closely related toDesulfitobacteriumspp., which are known representatives of DIRB. Use of iron respiration to abate wastewater odors warrants further investigation.
Changes in Antimicrobial Susceptibility of Native
Enterococcus faecium
in Chickens Fed Virginiamycin
Authors: McDermott Patrick F. , Cullen Patti , Hubert Susannah K. , McDermott Shawn D. , Bartholomew Mary , Simjee Shabbir , Wagner David D.
Published: September 2005

The extent of transfer of antimicrobial resistance from agricultural environments to humans is controversial. To assess the potential hazard posed by streptogramin use in food animals, this study evaluated the effect of virginiamycin exposure on antimicrobial resistance in
Enterococcus faecium
recovered from treated broilers. Four consecutive broiler feeding trials were conducted using animals raised on common litter. In the first three trials, one group of birds was fed virginiamycin continuously in feed at 20 g/ton, and a second group served as the nontreated control. In the fourth trial, antimicrobial-free feed was given to both groups. Fecal samples were cultured 1 day after chickens hatched and then at 1, 3, 5, and 7 weeks of age. Isolates from each time point were tested for susceptibility to a panel of different antimicrobials. Quinupristin/dalfopristin-resistant
E. faecium
appeared after 5 weeks of treatment in trial 1 and within 7 days of trials 2 to 4. Following removal of virginiamycin in trial 4, no resistant isolates were detected after 5 weeks. PCR failed to detect
vat
,
vgb
, or
erm
(B) in any of the streptogramin-resistant
E. faecium
isolates, whereas the
msr
(C) gene was detected in 97% of resistant isolates. In an experimental setting using broiler chickens, continuous virginiamycin exposure was required to maintain a stable streptogramin-resistant population of
E. faecium
in the animals. The bases of resistance could not be explained by known genetic determinants.
Heterogeneity of Times Required for Germination and Outgrowth from Single Spores of Nonproteolytic
Clostridium botulinum
Authors: Stringer Sandra C. , Webb Martin D. , George Susan M. , Pin Carmen , Peck Michael W.
Published: September 2005

Knowledge of the distribution of growth times from individual spores and quantification of this biovariability are important if predictions of growth in food are to be improved, particularly when, as for
Clostridium botulinum
, growth is likely to initiate from low numbers of spores. In this study we made a novel attempt to determine the distributions of times associated with the various stages of germination and subsequent growth from spores and the relationships between these stages. The time to germination (
t
germ
), time to emergence (
t
emerg
), and times to reach the lengths of one (
t
C1
) and two (
t
C2
) mature cells were quantified for individual spores of nonproteolytic
C. botulinum
Eklund 17B using phase-contrast microscopy and image analysis. The times to detection for wells inoculated with individual spores were recorded using a Bioscreen C automated turbidity reader and were compatible with the data obtained microscopically. The distributions of times to events during germination and subsequent growth showed considerable variability, and all stages contributed to the overall variability in the lag time. The times for germination (
t
germ
), emergence (
t
emerg
−
t
germ
), cell maturation (
t
C1
−
t
emerg
), and doubling (
t
C2
−
t
C1
) were not found to be correlated. Consequently, it was not possible to predict the total duration of the lag phase from information for just one of the stages, such as germination. As the variability in postgermination stages is relatively large, the first spore to germinate will not necessarily be the first spore to produce actively dividing cells and start neurotoxin production. This information can make a substantial contribution to improved predictive modeling and better quantitative microbiological risk assessment.
Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity
Authors: De Wever Aaike , Muylaert Koenraad , Van der Gucht Katleen , Pirlot Samuel , Cocquyt Christine , Descy Jean-Pierre , Plisnier Pierre-Denis , Vyverman Wim
Published: September 2005

Vertical and latitudinal differences in bacterial community composition (BCC) in Lake Tanganyika were studied during the dry season of 2002 by means of denaturing gradient gel electrophoresis analysis of PCR-amplified 16S RNA fragments. Dominant bands were sequenced and identified as members of theCyanobacteria,Actinobacteria,Nitrospirae, green nonsulfur bacteria, andFirmicutesdivisions and theGamma- andDeltaproteobacteriasubdivisions. The BCC in the lake displayed both vertical and latitudinal variation. Vertical changes in BCC were related to the thermal water column stratification, which influences oxygen and nutrient concentrations. Latitudinal variation was related to upwelling of deep water and increased primary production in the south of the lake. The number of bands per sample increased with bacterial production in the epilimnion of the lake, suggesting a positive diversity-productivity relationship.
Maltotriose Utilization by Industrial
Saccharomyces
Strains: Characterization of a New Member of the α-Glucoside Transporter Family
Authors: Salema-Oom Madalena , Valadão Pinto Vera , Gonçalves Paula , Spencer-Martins Isabel
Published: September 2005

Maltotriose utilization by
Saccharomyces cerevisiae
and closely related yeasts is important to industrial processes based on starch hydrolysates, where the trisaccharide is present in significant concentrations and often is not completely consumed. We undertook an integrated study to better understand maltotriose metabolism in a mixture with glucose and maltose. Physiological data obtained for a particularly fast-growing distiller's strain (PYCC 5297) showed that, in contrast to what has been previously reported for other strains, maltotriose is essentially fermented. The respiratory quotient was, however, considerably higher for maltotriose (0.36) than for maltose (0.16) or glucose (0.11). To assess the role of transport in the sequential utilization of maltose and maltotriose, we investigated the presence of genes involved in maltotriose uptake in the type strain of
Saccharomyces carlsbergensis
(PYCC 4457). To this end, a previously constructed genomic library was used to identify maltotriose transporter genes by functional complementation of a strain devoid of known maltose transporters. One gene, clearly belonging to the
MAL
transporter family, was repeatedly isolated from the library. Sequence comparison showed that the novel gene (designated
MTY1
) shares 90% and 54% identity with
MAL31
and
AGT1
, respectively. However, expression of Mty1p restores growth of the
S. cerevisiae
receptor strain on both maltose and maltotriose, whereas the closely related Mal31p supports growth on maltose only and Agt1p supports growth on a wider range of substrates, including maltose and maltotriose. Interestingly, Mty1p displays higher affinity for maltotriose than for maltose, a new feature among all the α-glucoside transporters described so far.
Amylomaltase ofPyrobaculum aerophilumIM2 Produces Thermoreversible Starch Gels
Authors: Kaper Thijs , Talik Boguslawa , Ettema Thijs J. , Bos Herman , van der Maarel Marc J. E. C. , Dijkhuizen Lubbert
Published: September 2005

Amylomaltases are 4-α-glucanotransferases (EC 2.4.1.25) of glycoside hydrolase family 77 that transfer α-1,4-linked glucans to another acceptor, which can be the 4-OH group of an α-1,4-linked glucan or glucose. The amylomaltase-encoding gene (PAE1209) from the hyperthermophilic archaeonPyrobaculum aerophilumIM2 was cloned and expressed inEscherichia coli, and the gene product (PyAMase) was characterized. PyAMase displays optimal activity at pH 6.7 and 95°C and is the most thermostable amylomaltase described to date. The thermostability of PyAMase was reduced in the presence of 2 mM dithiothreitol, which agreed with the identification of two possible cysteine disulfide bridges in a three-dimensional model of PyAMase. The kinetics for the disproportionation of malto-oligosaccharides, inhibition by acarbose, and binding mode of the substrates in the active site were determined. Acting on gelatinized food-grade potato starch, PyAMase produced a thermoreversible starch product with gelatin-like properties. This thermoreversible gel has potential applications in the food industry. This is the first report on an archaeal amylomaltase.
Phylogeny and Molecular Identification of Vibrios on the Basis of Multilocus Sequence Analysis
Authors: Thompson F. L. , Gevers D. , Thompson C. C. , Dawyndt P. , Naser S. , Hoste B. , Munn C. B. , Swings J.
Published: September 2005

We analyzed the usefulness ofrpoA,recA, andpyrHgene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documentedVibrionaceaestrains and 16 presumptiveVibrioisolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The familiesVibrionaceae,Photobacteriaceae,Enterovibrionaceae, andSalinivibrionaceaewere all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94%rpoA,recA, andpyrHgene sequence similarity, respectively. The genusVibriowas heterogeneous and polyphyletic, withVibrio fischeri,V. logei, andV. wodanisgrouping closer to thePhotobacteriumgenus.V. halioticoli-,V. harveyi-,V. splendidus-, andV. tubiashii-related species formed groups within the genusVibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within theV. splendidusandV. tubiashiigroup,rpoAgene sequences were slightly less discriminatory thanrecAandpyrHsequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94%rpoA,recA, andpyrHgene sequence similarity, respectively.
Longitudinal Study of Microbial Diversity and Seasonality in the Mexico City Metropolitan Area Water Supply System
Authors: Mazari-Hiriart Marisa , López-Vidal Yolanda , Ponce-de-León Sergio , Calva Juan José , Rojo-Callejas Francisco , Castillo-Rojas Gonzalo
Published: September 2005

In the Mexico City metropolitan area (MCMA), 70% of the water for 18 million inhabitants is derived from the Basin of Mexico regional aquifer. To provide an overview of the quality of the groundwater, a longitudinal study was conducted, in which 30 sites were randomly selected from 1,575 registered extraction wells. Samples were taken before and after chlorine disinfection during both the rainy and dry seasons (2000-2001). Microbiological parameters (total coliforms, fecal coliforms, streptococci, and
Vibrio
spp.), the presence of
Helicobacter pylori
, and physicochemical parameters, including the amount of trihalomethanes (THMs), were determined. Although microorganisms and inorganic and organic compounds were evident, they did not exceed current permissible limits. Chlorine levels were low, and the bacterial counts were not affected by chlorine disinfection. Eighty-four bacterial species from nine genera normally associated with fecal contamination were identified in water samples.
H. pylori
was detected in at least 10% of the studied samples. About 40% of the samples surpassed the THM concentration allowed by Mexican and U.S. regulations, with levels of chloroform being high. The quality of the water distributed to the MCMA varied between the rainy and dry seasons, with higher levels of pH, nitrates, chloroform, bromodichloromethane, total organic carbon, and fecal streptococci during the dry season. This study showed that the groundwater distribution system is susceptible to contamination and that there is a need for a strict, year-round disinfection strategy to ensure adequate drinking-water quality. This situation in one of the world's megacities may reflect what is happening in large urban centers in developing countries which rely on a groundwater supply.
Fate of
Escherichia coli
during Ensiling of Wheat and Corn
Authors: Chen Y. , Sela S. , Gamburg M. , Pinto R. , Weinberg Z. G.
Published: September 2005

A recombinant
Escherichia coli
strain carrying a plasmid with an antibiotic resistance marker and expressing the green fluorescent protein was inoculated at a concentration of 3.8 × 10
8
CFU/g into direct-cut wheat (348 g of dry matter kg
−1
), wilted wheat (450 g of dry matter kg
−1
), and corn (375 g of dry matter kg
−1
). The forages were ensiled in mini-silos. The treatments included control (no
E. coli
added), application of tagged
E. coli
, and delayed sealing of the inoculated wheat. Three silos per treatment were sampled on predetermined dates, and the numbers of
E. coli
were determined on Chromocult TBX medium with or without kanamycin. Colonies presumptively identified as
E. coli
were also tested for fluorescence activity. Addition of
E. coli
at the time of ensiling resulted in a more rapid decrease in the pH but had almost no effect on the chemical composition of the final silages or their aerobic stability.
E. coli
disappeared from the silages when the pH decreased below 5.0. It persisted longer in silages of wilted wheat, in which the pH declined more slowly. Control silages of all crops also contained bacteria, presumptively identified as
E. coli
, that were resistant to the antibiotic, which suggests that some epiphytic strains are naturally resistant to antibiotics.
Novel Lectin-Like Bacteriocins of Biocontrol Strain
Pseudomonas fluorescens
Pf-5
Authors: Parret Annabel H. A. , Temmerman Koen , De Mot René
Published: September 2005

Bacteriocin LlpA, produced by
Pseudomonas
sp. strain BW11M1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (A. H. A. Parret, G. Schoofs, P. Proost, and R. De Mot, J. Bacteriol.
185:
897-908, 2003). Biocontrol strain
Pseudomonas fluorescens
Pf-5 contains two
llpA
-like genes, named
llpA1
Pf-5
and
llpA2
Pf-5
. Recombinant
Escherichia coli
cells expressing
llpA1
Pf-5
or
llpA2
Pf-5
acquired bacteriocin activity and secreted a 31-kDa protein cross-reacting with LlpA
BW11M1
antibodies. Antibacterial activity of the recombinant proteins was evidenced by gel overlay assays. Analysis of the antimicrobial spectrum indicated that LlpA1
Pf-5
and LlpA2
Pf-5
are able to inhibit
P. fluorescens
strains, as well as the related mushroom pathogen
Pseudomonas tolaasii
. LlpA-type bacteriocins are characterized by a domain structure consisting of tandem monocot mannose-binding lectin (MMBL) domains. Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired from different ancestral sources. Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.
Artificial Neural Network Prediction of Viruses in Shellfish
Authors: Brion Gail , Viswanathan Chandramouli , Neelakantan T. R. , Lingireddy Srinivasa , Girones Rosina , Lees David , Allard Annika , Vantarakis Apostolos
Published: September 2005

A database was probed with artificial neural network (ANN) and multivariate logistic regression (MLR) models to investigate the efficacy of predicting PCR-identified human adenovirus (ADV), Norwalk-like virus (NLV), and enterovirus (EV) presence or absence in shellfish harvested from diverse countries in Europe (Spain, Sweden, Greece, and the United Kingdom). The relative importance of numerical and heuristic input variables to the ANN model for each country and for the combined data was analyzed with a newly defined relative strength effect, which illuminated the importance of bacteriophages as potential viral indicators. The results of this analysis showed that ANN models predicted all types of viral presence and absence in shellfish with better precision than MLR models for a multicountry database. For overall presence/absence classification accuracy, ANN modeling had a performance rate of 95.9%, 98.9%, and 95.7% versus 60.5%, 75.0%, and 64.6% for the MLR for ADV, NLV, and EV, respectively. The selectivity (prediction of viral negatives) was greater than the sensitivity (prediction of viral positives) for both models and with all virus types, with the ANN model performing with greater sensitivity than the MLR. ANN models were able to illuminate site-specific relationships between microbial indicators chosen as model inputs and human virus presence. A validation study on ADV demonstrated that the MLR and ANN models differed in sensitivity and selectivity, with the ANN model correctly identifying ADV presence with greater precision.
Adhesion of the Entomopathogenic Fungus
Beauveria
(
Cordyceps
)
bassiana
to Substrata
Authors: Holder Diane J. , Keyhani Nemat O.
Published: September 2005

The entomopathogenic fungus
Beauveria bassiana
produces at least three distinct single-cell propagules, aerial conidia, vegetative cells termed blastospores, and submerged conidia, which can be isolated from agar plates, from rich broth liquid cultures, and under nutrient limitation conditions in submerged cultures, respectively. Fluorescently labeled fungal cells were used to quantify the kinetics of adhesion of these cell types to surfaces having various hydrophobic or hydrophilic properties. Aerial conidia adhered poorly to weakly polar surfaces and rapidly to both hydrophobic and hydrophilic surfaces but could be readily washed off the latter surfaces. In contrast, blastospores bound poorly to hydrophobic surfaces, forming small aggregates, bound rapidly to hydrophilic surfaces, and required a longer incubation time to bind to weakly polar surfaces than to hydrophilic surfaces. Submerged conidia displayed the broadest binding specificity, adhering to hydrophobic, weakly polar, and hydrophilic surfaces. The adhesion of the
B. bassiana
cell types also differed in sensitivity to glycosidase and protease treatments, pH, and addition of various carbohydrate competitors and detergents. The outer cell wall layer of aerial conidia contained sodium dodecyl sulfate-insoluble, trifluoroacetic acid-soluble proteins (presumably hydrophobins) that were not present on either blastospores or submerged conidia. The variations in the cell surface properties leading to the different adhesion qualities of
B. bassiana
aerial conidia, blastospores, and submerged conidia could lead to rational design decisions for improving the efficacy and possibly the specificity of entomopathogenic fungi for host targets.
Improving the Activity and Stability of GL-7-ACA Acylase CA130 by Site-Directed Mutagenesis
Authors: Zhang Wei , Liu Yuan , Zheng Huabao , Yang Sheng , Jiang Weihong
Published: September 2005

In the present study, glutaryl-7-amino cephalosporanic acid acylase fromPseudomonassp. strain 130 (CA130) was mutated to improve its enzymatic activity and stability. Based on the crystal structure of CA130, two series of amino acid residues, one from those directly involved in catalytic function and another from those putatively involved in surface charge, were selected as targets for site-directed mutagenesis. In the first series of experiments, several key residues in the substrate-binding pocket were substituted, and the genes were expressed inEscherichia colifor activity screening. Two of the mutants constructed, Y151αF and Q50βN, showed two- to threefold-increased catalytic efficiency (kcat/Km) compared to wild-type CA130. TheirKmvalues were decreased by ca. 50%, and thekcatvalues increased to 14.4 and 16.9 s−1, respectively. The ability of these mutants to hydrolyze adipoyl 6-amino penicillinic acid was also improved. In the second series of mutagenesis, several mutants with enhanced stabilities were identified. Among them, R121βA and K198βA had a 30 to 58% longer half-life than wild-type CA130, and K198βA and D286βA showed an alkaline shift of optimal pH by about 1.0 to 2.0 pH units. To construct an engineered enzyme with the properties of both increased activity and stability, the double mutant Q50βN/K198βA was expressed. This enzyme was purified and immobilized for catalytic analysis. The immobilized mutant enzyme showed a 34.2% increase in specific activity compared to the immobilized wild-type CA130.
Differential Expression of the Two
kdp
Operons in the Nitrogen-Fixing Cyanobacterium
Anabaena
sp. Strain L-31
Authors: Ballal Anand , Apte Shree K.
Published: September 2005

In several types of bacteria, the Kdp ATPase (comprising of the KdpABC complex) is an inducible, high-affinity potassium transporter that scavenges K
+
from the environment. The cyanobacterium
Anabaena
sp. strain L-31 showed the presence of not one but two distinct
kdp
operons in its genome. The
kdp1
consisted of
kdpA1B1G1C1D
genes, whereas the
kdp2
contained the
kdpA2B2G2C2
genes. Among the regulatory genes, the
kdpD
open reading frame of
Anabaena
sp. strain L-31 was truncated compared to the
kdpD
of other bacteria, whereas a
kdpE
-like gene was absent in the vicinity of the two
kdp
operons. In response to K
+
limitation (<0.05 mM external K
+
), only
kdp2
(and not
kdp1
) expression could be detected as a 5.3-kb transcript on Northern blots, indicating that
kdpA2B2G2C2
genes constitute a polycystronic operon. Unlike
E. coli
, addition of osmolytes like NaCl, or a change in pH of the medium did not enhance the
kdp
expression in
Anabaena
sp. strain L-31. Interestingly, the
Anabaena
sp. strain L-31
kdp2
operon was strongly induced in response to desiccation stress. The addition of K
+
to K
+
-starved cultures resulted in repression and degradation of
kdp2
transcripts. Our results clearly show that
kdp2
is the major
kdp
operon expressed in
Anabaena
sp. strain L-31 and may play an important role in adaptation to K
+
limitation and desiccation stress.