bluuebunny/crossref_metadata_2025 huggingface dataset:
A Functional Analysis of the Benthic Macrofauna of the São Sebastião Channel (Southeastern Brazil)
Authors: Arasaki Emilia , Muniz Pablo , Pires‐Vanin Ana Maria S.
Published: December 2004

Abstract.  The major problem in coastal areas of developing countries is disturbance caused by anthropogenic influence. This disturbance can be quantified by analysing the distribution and composition of marine communities using uni‐ and multivariate techniques and the biotic index. A study of benthic macrofauna was carried out along the São Sebastião Channel, northern coast of São Paulo State, Brazil, in an area with a submarine outfall, a petroleum terminal and a commercial harbour. Sampling was undertaken seasonally, by means of a van Veen grab (0.1 m2) at 15 oceanographic stations, from November 1993 to August 1994. A total of 392 species were identified (129 Polychaeta, 127 Mollusca, 98 Crustacea, 28 Echinodermata and 10 other phyla). The sedimentary pattern recorded for the São Sebastião Channel is very heterogeneous, influenced mainly by strong wind‐driven currents, and differs from nearby shelf areas. The study area could be divided into three regions based on sediment texture and fauna: one region dominated by medium and coarse sand with low values of organic carbon; a second area where pelitic fractions were dominant with high values of organic carbon and nitrogen; and a third region characterised by fine and very fine sand, presenting intermediate organic carbon values. No temporal significant variation in abundance and species composition was found, except in autumn. The use of the ‘marine Biotic Coefficient’ showed the same ecological trend as the faunal abundance and demonstrated that the central continental region of the channel is affected by human activities.
Facts, Fiction, and the Fourth Estate
Authors: Anderson William L.
Published: December 2004

Abstract.  This paper examines the reaction of the market to news that the Washington Post had won a Pulitzer Prize for a story that was demonstrably false. The reaction to the stock price of the Post as well as the stock prices of other newspapers is examined using dummy variables for two days, four days, and six days. The results show that while the decline in the Post's stock price was relatively small, the t‐statistics for all of the dummy variables are significant. The paper also examines the McChesney (1987) hypothesis that the nature of the newspaper business is such that it is difficult for the residual claimants of the paper to receive the financial gains of important news stories. These rents, he points out, are distributed to others. We look to see whether or not residual claimants of that newspaper can be harmed if that newspaper publishes a false story and receives large amounts of bad publicity for its error.
Does the Henry George Theorem Provide a Practical Guide to Optimal City Size?
Authors: Arnott Richard
Published: December 2004

Abstract.  The spatial distribution of economic activity is determined by a balancing of increasing and decreasing returns to scale activities. The Henry George Theorem states roughly that, if economic activity is efficiently organized over a “large” space, aggregate land rents equal the aggregate losses from the decreasing returns to scale activities. Kanemoto, Ohkawara, and Suzuki have tentatively applied the Henry George Theorem to investigate whether Tokyo has too large a population. This paper has two aims. The first is to explore the Theorem and its generality; the second is to examine whether it provides a promising conceptual foundation for estimating whether particular cities are over‐ or underpopulated.
George on Land Speculation and the Winner's Curse
Authors: Tideman Nicolaus
Published: December 2004

Abstract.  Henry George anticipated the winner's curse phenomenon and suggested an antidote to prevent wasteful land speculation. In these ways his economic ideas still resonate today as part of modern finance theory.
On Indirect Reciprocity
Authors: Tullberg Jan
Published: December 2004

Abstract.  Indirect reciprocity, defined as a beneficial act whose return comes from someone other than the act's recipient, is a common phenomenon in human societies. However, it is a poorly analyzed phenomenon with respect to payoffs. Are the expectations of return realistic, or not? Are these expectations pro‐social attitudes, or illusions induced through manipulation? I discuss four categories of putative indirect reciprocity, two of which pertain to interaction between individuals and two of which involve social systems. The conclusion is that two of these categories, reciprocal reputation and institutionalized reciprocity, are strongly linked to reciprocity, whereas the other two categories, generous reputation and metaphysical reward, are likely to involve only an element of illusionary reciprocity and a substantial degree of altruism.
Analysis of speech-based speech transmission index methods with implications for nonlinear operations
Authors: Goldsworthy Ray L. , Greenberg Julie E.
Published: December 2004

The Speech Transmission Index (STI) is a physical metric that is well correlated with the intelligibility of speech degraded by additive noise and reverberation. The traditional STI uses modulated noise as a probe signal and is valid for assessing degradations that result from linear operations on the speech signal. Researchers have attempted to extend the STI to predict the intelligibility of nonlinearly processed speech by proposing variations that use speech as a probe signal. This work considers four previously proposed speech-based STI methods and four novel methods, studied under conditions of additive noise, reverberation, and two nonlinear operations (envelope thresholding and spectral subtraction). Analyzing intermediate metrics in the STI calculation reveals why some methods fail for nonlinear operations. Results indicate that none of the previously proposed methods is adequate for all of the conditions considered, while four proposed methods produce qualitatively reasonable results and warrant further study. The discussion considers the relevance of this work to predicting the intelligibility of cochlear-implant processed speech.
Development of an accelerometer-based underwater acoustic intensity sensor
Authors: Kim Kang , Gabrielson Thomas B. , Lauchle Gerald C.
Published: December 2004

An underwater acoustic intensity sensor is described. This sensor derives acoustic intensity from simultaneous, co-located measurement of the acoustic pressure and one component of the acoustic particle acceleration vector. The sensor consists of a pressure transducer in the form of a hollow piezoceramic cylinder and a pair of miniature accelerometers mounted inside the cylinder. Since this sensor derives acoustic intensity from measurement of acoustic pressure and acoustic particle acceleration, it is called a p-a intensity probe. The sensor is ballasted to be nearly neutrally buoyant. It is desirable for the accelerometers to measure only the rigid body motion of the assembled probe and for the effective centers of the pressure sensor and accelerometer to be coincident. This is achieved by symmetric disposition of a pair of accelerometers inside the ceramic cylinder. The response of the intensity probe is determined by comparison with a reference hydrophone in a predominantly reactive acoustic field.
Age effects in the human middle ear: Wideband acoustical measures
Authors: Feeney M. Patrick , Sanford Chris A.
Published: December 2004

Studies that have examined age effects in the human middle ear using either admittance measures at 220 or 660 Hz or multifrequency tympanometry from 200 to 2000 Hz have had conflicting results. Several studies have suggested an increase in admittance with age, while several others have suggested a decrease in admittance with age. A third group of studies found no significant age effect. This study examined 226 Hz tympanometry and wideband energy reflectance and impedance at ambient pressure in a group of 40 young adults and a group of 30 adults with age ⩾60 years. The groups did not differ in admittance measures of the middle ear at 226 Hz. However, significant age effects were found in wideband energy reflectance and impedance. In particular, in older adults there was a comparative decrease in reflectance from 800 to 2000 Hz but an increase near 4000 Hz. The results suggest a decrease in middle-ear stiffness with age. The findings of this study hold relevance for understanding the aging process in the auditory system, for the establishment of normative data for wideband energy reflectance, for the possibility of a conductive component to presbycusis, and for the interpretation of otoacoustic emission measurements.
Attenuation of ultrasonic waves in rolled metals
Authors: Yang Liyong , Turner Joseph A.
Published: December 2004

Scattering of ultrasonic waves in polycrystals with texture is studied in this article. The attenuations of the three wave modes are determined as a function of dimensionless frequency and propagation direction, respectively, for given orientation distribution coefficients (ODCs). The calculation is done in the case of a statistically orthorhombic sample made up of cubic crystallites. The wave propagation and scattering model is formulated by the Dyson equation using an anisotropic Green’s function approach. Within the limits of the first-order smoothing approximation, the Dyson equation is solved in the spatial Fourier transform domain. The results presented are shown to be directional dependent, frequency dependent, and especially dependent on the texture coefficients (ODCs) for the quasilongitudinal and two quasishear waves. The theoretical results presented may be used to improve the understanding of the microstructure during recrystallization processes.
Distortion product otoacoustic emission (2f1–f2) suppression in 3-month-old infants: Evidence for postnatal maturation of human cochlear function?
Authors: Abdala Carolina
Published: December 2004

The complete timeline for maturation of human cochlear function has not been defined. Distortion product otoacoustic emission (DPOAE)-based measures of cochlear function show non-adult-like responses from premature and term-born neonates at high f2 frequencies; however, older infants were not included in these studies. In the present experiment, previously collected DPOAE ipsilateral suppression data from premature neonates were combined with new data collected from adults, term-born neonates, and 3-month-old infants to further examine the time course for maturation of cochlear function. DPOAE suppression tuning curves (STC) and suppression growth patterns were measured in the three age groups at f2=6000 Hz, L1=65, L2=55 dB SPL, with an f2/f1 of 1.2. Results indicate that term-born neonates and 3-month-old infants have non-adult-like STC width, slope on the low-frequency flank, and tip features. However, the two infant groups are not significantly different from one another. Suppression growth patterns for low-frequency suppressor tones show a clear developmental progression. In general, the younger the infant, the more shallow and compressive the suppression growth for the lowest suppressor frequencies. These findings suggest a high-frequency postnatal immaturity in cochlear function as measured by DPOAE suppression. Results may have been influenced by noncochlear factors, such as middle-ear immaturity. These factors are reviewed and considered.
Experimental demonstration of remote, passive acousto-optic sensing
Authors: Antonelli Lynn , Blackmon Fletcher
Published: December 2004

Passively detecting underwater sound from the air can allow aircraft and surface vessels to monitor the underwater acoustic environment. Experimental research into an optical hydrophone is being conducted for remote, aerial detection of underwater sound. A laser beam is directed onto the water surface to measure the velocity of the vibrations occurring as the underwater acoustic signal reaches the water surface. The acoustically generated surface vibrations modulate the phase of the laser beam. Sound detection occurs when the laser is reflected back towards the sensor. Therefore, laser alignment on the specularly reflecting water surface is critical. As the water surface moves, the laser beam is reflected away from the photodetector and no signal is obtained. One option to mitigate this problem is to continually steer the laser onto a spot on the water surface that provides a direct back-reflection. Results are presented from a laboratory test that investigates the feasibility of the acousto-optic sensor detection on hydrostatic and hydrodynamic surfaces using a laser Doppler vibrometer in combination with a laser-based, surface normal glint tracker for remotely detecting underwater sound. This paper outlines the acousto-optic sensor and tracker concepts and presents experimental results comparing sensor operation under various sea surface conditions.
On the acoustic modes in a cylindrical duct with an arbitrary wall impedance distribution
Authors: Campos L. M. B. C. , Oliveira J. M. G. S.
Published: December 2004

The present paper considers the propagation of sound in a cylindrical duct, with a wall section of finite length covered by an acoustic liner whose impedance is an arbitrary function of position. The cases of (i) uniform wall impedance, and wall impedance varying along the (ii) circumference or (iii) axis of the duct, or (iv) both simultaneously, are explicitly considered. It is shown that a nonuniform wall impedance couples modes with distinct azimuthal l or axial m wave numbers, so that their radial wave numbers k can no longer be calculated separately for each pair (m,l). The radial wave numbers are the roots of an infinite determinant, in the case when the wall impedance varies either (i) circumferentially or (ii) radially. If the wall impedance varies (iv) both radially and circumferentially, then the radial wave numbers are the roots of a doubly infinite determinant, i.e., an infinite determinant in which each term is an infinite determinant. The infinite determinants specifying the radial wave numbers are written explicitly for sound in a cylindrical nozzle with a uniform axial flow, in which case the radial eigenfunctions are Bessel functions; the method of calculation of the radial wave numbers applies equally well to a cylindrical nozzle with shear flow and/or swirling flows, with the Bessel functions replaced by other eigenfunctions. The radial wave numbers are calculated by truncation of the infinite determinants, for several values of the aspect ratio, defined as the ratio of length to diameter. It is shown that a nonuniform wall impedance will give rise to additional modes compared with a uniform wall impedance. The radial wave numbers specify the eigenfrequencies for the acoustic modes in the duct; the imaginary parts of the eigenfrequencies specify the decay of the sound field with time, and thus the effectiveness of the acoustic liner.
Perception and annoyance due to wind turbine noise—a dose–response relationship
Authors: Pedersen Eja , Persson Waye Kerstin
Published: December 2004

Installed global wind power increased by 26% during 2003, with U.S and Europe accounting for 90% of the cumulative capacity. Little is known about wind turbines’ impact on people living in their vicinity. The aims of this study were to evaluate the prevalence of annoyance due to wind turbine noise and to study dose–response relationships. Interrelationships between noise annoyance and sound characteristics, as well as the influence of subjective variables such as attitude and noise sensitivity, were also assessed. A cross-sectional study was performed in Sweden in 2000. Responses were obtained through questionnaires (n=351; response rate 68.4%), and doses were calculated as A-weighted sound pressure levels for each respondent. A statistically significant dose–response relationship was found, showing higher proportion of people reporting perception and annoyance than expected from the present dose–response relationships for transportation noise. The unexpected high proportion of annoyance could be due to visual interference, influencing noise annoyance, as well as the presence of intrusive sound characteristics. The respondents’ attitude to the visual impact of wind turbines on the landscape scenery was found to influence noise annoyance.
The temporal representation of speech in a nonlinear model of the guinea pig cochlea
Authors: Holmes Stephen D. , Sumner Christian J. , O’Mard Lowel P. , Meddis Ray
Published: December 2004

The temporal representation of speechlike stimuli in the auditory-nerve output of a guinea pig cochlea model is described. The model consists of a bank of dual resonance nonlinear filters that simulate the vibratory response of the basilar membrane followed by a model of the inner hair cell/auditory nerve complex. The model is evaluated by comparing its output with published physiological auditory nerve data in response to single and double vowels. The evaluation includes analyses of individual fibers, as well as ensemble responses over a wide range of best frequencies. In all cases the model response closely follows the patterns in the physiological data, particularly the tendency for the temporal firing pattern of each fiber to represent the frequency of a nearby formant of the speech sound. In the model this behavior is largely a consequence of filter shapes; nonlinear filtering has only a small contribution at low frequencies. The guinea pig cochlear model produces a useful simulation of the measured physiological response to simple speech sounds and is therefore suitable for use in more advanced applications including attempts to generalize these principles to the response of human auditory system, both normal and impaired.
Rapid adaptation to foreign-accented English
Authors: Clarke Constance M. , Garrett Merrill F.
Published: December 2004

This study explored the perceptual benefits of brief exposure to non-native speech. Native English listeners were exposed to English sentences produced by non-native speakers. Perceptual processing speed was tracked by measuring reaction times to visual probe words following each sentence. Three experiments using Spanish- and Chinese-accented speech indicate that processing speed is initially slower for accented speech than for native speech but that this deficit diminishes within one minute of exposure. Control conditions rule out explanations for the adaptation effect based on practice with the task and general strategies for dealing with difficult speech. Further results suggest that adaptation can occur within as few as two to four sentence-length utterances. The findings emphasize the flexibility of human speech processing and require models of spoken word recognition that can rapidly accommodate significant acoustic-phonetic deviations from native language speech patterns.
Cochlear compression: Effects of low-frequency biasing on quadratic distortion product otoacoustic emission
Authors: Bian Lin
Published: December 2004

Distortion product otoacoustic emissions (DPOAEs) are generated from the nonlinear transduction in cochlear outer hair cells. The transducer function demonstrating a compressive nonlinearity can be estimated from low-frequency modulation of DPOAEs. Experimental results from the gerbils showed that the magnitude of quadratic difference tone (QDT, f2–f1) was either enhanced or suppressed depending on the phase of the low-frequency bias tone. Within one period of the bias tone, QDT magnitudes exhibited two similar modulation patterns, each resembling the absolute value of the second derivative of the transducer function. In the time domain, the center notches of the modulation patterns occurred around the zero crossings of the bias pressure, whereas peaks corresponded to the increase or decrease in bias pressure. Evaluated with respect to the bias pressure, modulated QDT magnitude displayed a double-modulation pattern marked by a separation of the center notches. Loading/unloading of the cochlear transducer or rise/fall in bias pressure shifted the center notch to positive or negative sound pressures, indicating a mechanical hysteresis. These results suggest that QDT arises from the compression that coexists with the active hysteresis in cochlear transduction. Modulation of QDT magnitude reflects the dynamic regulation of cochlear transducer gain and compression.
The complex equivalent source method for sound propagation over an impedance plane
Authors: Ochmann Martin
Published: December 2004

The sound field caused by a monopole source above an impedance plane can be calculated by using a superposition of equivalent point sources located along a line in the mirror space below the plane. Originally, such an approach for representing the half-space Green’s function was described by Sommerfeld at the beginning of the last century, in order to treat half-space problems of heat conduction. However, the representation converges only for masslike impedances and cannot be used for the more important case of reflecting planes with springlike surface impedances. The singular part of the line integral can be transformed into a Hankel function, which shows that surface waves are contained in the whole solution. Unfortunately, this representation suffers from the lack of validity at certain receiver points and from restrictions on wave number and impedance range to ensure the necessary convergence. The main idea of the present method is to use also a superposition of equivalent point sources, but to allow that these sources can be located at complex source points. The corresponding form of the half-space Green’s function is suitable for both masslike and springlike surface impedances, and can be used as a cornerstone for a boundary element method.
Anaerobicity Prepares
Saccharomyces cerevisiae
Cells for Faster Adaptation to Osmotic Shock
Authors: Krantz Marcus , Nordlander Bodil , Valadi Hadi , Johansson Mikael , Gustafsson Lena , Hohmann Stefan
Published: December 2004

Yeast cells adapt to hyperosmotic shock by accumulating glycerol and altering expression of hundreds of genes. This transcriptional response of
Saccharomyces cerevisiae
to osmotic shock encompasses genes whose products are implicated in protection from oxidative damage. We addressed the question of whether osmotic shock caused oxidative stress. Osmotic shock did not result in the generation of detectable levels of reactive oxygen species (ROS). To preclude any generation of ROS, osmotic shock treatments were performed in anaerobic cultures. Global gene expression response profiles were compared by employing a novel two-dimensional cluster analysis. The transcriptional profiles following osmotic shock under anaerobic and aerobic conditions were qualitatively very similar. In particular, it appeared that expression of the oxidative stress genes was stimulated upon osmotic shock even if there was no apparent need for their function. Interestingly, cells adapted to osmotic shock much more rapidly under anaerobiosis, and the signaling as well as the transcriptional response was clearly attenuated under these conditions. This more rapid adaptation is due to an enhanced glycerol production capacity in anaerobic cells, which is caused by the need for glycerol production in redox balancing. Artificially enhanced glycerol production led to an attenuated response even under aerobic conditions. These observations demonstrate the crucial role of glycerol accumulation and turgor recovery in determining the period of osmotic shock-induced signaling and the profile of cellular adaptation to osmotic shock.
Potential Link between the NIMA Mitotic Kinase and Nuclear Membrane Fission during Mitotic Exit inAspergillus nidulans
Authors: Davies Jonathan R. , Osmani Aysha H. , De Souza Colin P. C. , Bachewich Catherine , Osmani Stephen A.
Published: December 2004

We have isolated TINC as a NIMA-interacting protein by using the yeast two-hybrid system and have confirmed that TINC interacts with NIMA inAspergillus nidulans. The TINC-NIMA interaction is stabilized in the absence of phosphatase inhibitors and in the presence of kinase-inactive NIMA, suggesting that the interaction is enhanced when NIMA is not fully activated. TINC is a cytoplasmic protein. TINC homologues and a TINC-like protein (A. nidulansHETC) are conserved in other filamentous fungi. Neither deletion oftinCnor deletion of bothtinCandA. nidulans hetCis lethal, but deletion oftinCdoes produce cold sensitivity as well as osmotic sensitivity. Expression of an amino-terminal-truncated form of TINC (ΔN-TINC) inhibits colony growth inAspergillusand localizes to membrane-like structures within the cell. Examination of cell cycle progression in these cells reveals that they progress through multiple defective mitoses. Many cells contain large polyploid single nuclei, while some appear to have separated masses of DNA. Examination of the nuclear envelopes of cells containing more than one DNA mass reveals that both DNA masses are contained within a single nuclear envelope, indicating that nuclear membrane fission is defective. The ability of these cells to separate DNA segregation from nuclear membrane fission suggests that this coordination is normally a regulated process inA. nidulans. Additional experiments demonstrate that expression of ΔN-TINC results in premature NIMA disappearance in mitotic samples. We propose that TINC's interaction with NIMA and the cell cycle defects produced by ΔN-TINC expression suggest possible roles for TINC and NIMA during nuclear membrane fission.
Selection and Characterization of RNA Interference-Deficient Trypanosomes Impaired in Target mRNA Degradation
Authors: Shi Huafang , Chamond Nathalie , Tschudi Christian , Ullu Elisabetta
Published: December 2004

Genetic analysis of the RNA interference (RNAi) pathway in
Trypanosoma brucei
has so far revealed one essential component, namely,
TbAGO1
, encoding a member of the Argonaute protein family. To gain further insight into the RNAi mechanism and its biological significance, we selected RNAi-deficient trypanosomes by using repeated cycles of electroporation with α-tubulin double-stranded RNA, a treatment that blocks cytokinesis in wild-type cells. Two independent clones, termed RiD-1 (for RNAi-deficient clone 1) and RiD-2, were characterized. At the cellular level, only RiD-1 trypanosomes showed a significant increase in doubling time with the concomitant accumulation of cells defective in the completion of cytokinesis. At the RNA level, both clones accumulated wild-type amounts of small interfering RNAs and displayed elevated levels of retroposon transcripts, the hallmark of RNAi deficiency in
T. brucei
. Importantly, both RiD-1 and RiD-2 clones were defective in the degradation of target mRNA, suggesting an impairment of the activity of AGO1, the putative RNAi endonuclease. Since in RiD cells the
AGO1
gene was not mutated and was expressed at wild-type levels, we propose that in trypanosomes the cleavage of mRNA by AGO1 is regulated by the interaction with another factor(s).
Morphogenetic Pathway of Spore Wall Assembly in
Saccharomyces cerevisiae
Authors: Coluccio Alison , Bogengruber Edith , Conrad Michael N. , Dresser Michael E. , Briza Peter , Neiman Aaron M.
Published: December 2004

The
Saccharomyces cerevisiae
spore is protected from environmental damage by a multilaminar extracellular matrix, the spore wall, which is assembled de novo during spore formation. A set of mutants defective in spore wall assembly were identified in a screen for mutations causing sensitivity of spores to ether vapor. The spore wall defects in 10 of these mutants have been characterized in a variety of cytological and biochemical assays. Many of the individual mutants are defective in the assembly of specific layers within the spore wall, leading to arrests at discrete stages of assembly. The localization of several of these gene products has been determined and distinguishes between proteins that likely are involved directly in spore wall assembly and probable regulatory proteins. The results demonstrate that spore wall construction involves a series of dependent steps and provide the outline of a morphogenetic pathway for assembly of a complex extracellular structure.
Saccharomyces cerevisiae
Aqr1 Is an Internal-Membrane Transporter Involved in Excretion of Amino Acids
Authors: Velasco Isabel , Tenreiro Sandra , Calderon Isabel L. , André Bruno
Published: December 2004

Excretion of amino acids by yeast cells was reported long ago but has not been characterized in molecular terms. It is typically favored by overproduction of the amino acid and/or impairment of its uptake. Here we describe the construction of a yeast strain excreting threonine and homoserine. Using this excretor strain, we then applied a reverse-genetics approach and found that the transporter encoded by the
YNL065w/AQR1
gene, a protein thought to mediate H
+
antiport, is involved in homoserine and threonine excretion. Furthermore, overexpression of
AQR1
led to increased excretion of several amino acids (alanine, aspartate, and glutamate) known to be relatively abundant in the cytosol. Transcription of the
AQR1
gene is induced severalfold by a number of amino acids and appears to be under the negative control of Gcn4. An Aqr1-green fluorescent protein fusion protein is located in multiple internal membrane structures and appears to cycle continuously between these compartments and the plasma membrane. The Aqr1 sequence is significantly similar to the vesicular amine transporters of secretory vesicles of neuronal cells. We propose that Aqr1 catalyzes transport of excess amino acids into vesicles, which then release them in the extracellular space by exocytosis.
Cas3p Belongs to a Seven-Member Family of Capsule Structure Designer Proteins
Authors: Moyrand Frédérique , Chang Yun C. , Himmelreich Uwe , Kwon-Chung Kyung J. , Janbon Guilhem
Published: December 2004

The polysaccharide capsule is the main virulence factor of the basidiomycetous yeast
Cryptococcus neoformans
. Four genes (
CAP10
,
CAP59
,
CAP60
, and
CAP64
) essential for capsule formation have been previously identified, although their roles in the biosynthetic pathway remain unclear. A genetic and bioinformatics approach allowed the identification of six
CAP64
-homologous genes, named
CAS3
,
CAS31
,
CAS32
,
CAS33
,
CAS34
, and
CAS35
, in the
C. neoformans
genome. This gene family is apparently specific in a subclass of the basidiomycete fungi. Single as well as double deletions of these genes in all possible combinations demonstrated that none of the
CAP64
-homologous genes were essential for capsule formation, although the
cas35Δ
strains displayed a hypocapsular phenotype. The chemical structure of the glucuronomannan (GXM) produced by the
CAS
family deletants revealed that these genes determined the position and the linkage of the xylose and/or
O
-acetyl residues on the mannose backbone. Hence, these genes are all involved in assembly of the GXM structure in
C. neoformans
.
Cellular Localization and Role of Kinase Activity of
PMK1
in
Magnaporthe grisea
Authors: Bruno Kenneth S. , Tenjo Fernando , Li Lei , Hamer John E. , Xu Jin-Rong
Published: December 2004

A mitogen-activated protein (MAP) kinase gene,
PMK1
, is known to regulate appressorium formation and infectious hyphal growth in the rice blast fungus
Magnaporthe grisea
. In this study, we constructed a green fluorescent protein gene-
PMK1
fusion (GFP-
PMK1
) to examine the expression and localization of
PMK1
in
M. grisea
during infection-related morphogenesis. The GFP
-PMK1
fusion encoded a functional protein that complemented the defect of the
pmk1
deletion mutant in appressorium formation and plant infection. Although a weak GFP signal was detectable in vegetative hyphae, conidia, and germ tubes, the expression of GFP-Pmk1 was increased in appressoria and developing conidia. Nuclear localization of GFP-Pmk1 proteins was observed in a certain percentage of appressoria. A kinase-inactive allele and a nonphosphorylatable allele of
PMK1
were constructed by site-directed mutagenesis. Expression of these mutant
PMK1
alleles did not complement the
pmk1
deletion mutant. These data confirm that kinase activity and activation of
PMK1
by the upstream MAP kinase kinase are required for appressorium formation and plant infection in
M. grisea
. When overexpressed with the RP27 promoter in the wild-type strain, both the kinase-inactive and nonphosphorylatable
PMK1
fusion proteins caused abnormal germ tube branching. Overexpression of these
PMK1
mutant alleles may interfere with the function of native
PMK1
during appressorium formation.
The Histone Fold Domain of Cse4 Is Sufficient for
CEN
Targeting and Propagation of Active Centromeres in Budding Yeast
Authors: Morey Lisa , Barnes Kelly , Chen Yinhuai , Fitzgerald-Hayes Molly , Baker Richard E.
Published: December 2004

Centromere-specific H3-like proteins (CenH3s) are conserved across the eukaryotic kingdom and are required for packaging centromere DNA into a specialized chromatin structure required for kinetochore assembly. Cse4 is the CenH3 protein of the budding yeast
Saccharomyces cerevisiae
. Like all CenH3 proteins, Cse4 consists of a conserved histone fold domain (HFD) and a divergent N terminus (NT). The Cse4 NT contains an essential domain designated END (for essential N-terminal domain); deletion of END is lethal. To investigate the role of the Cse4 NT in centromere targeting, a series of deletion alleles (
cse4
Δ
NT
) were analyzed. No part of the Cse4 NT was required to target mutant proteins to centromere DNA in the presence of functional Cse4. A Cse4 degron strain was used to examine targeting of a Cse4ΔNT protein in the absence of wild-type Cse4. The END was not required for centromere targeting under these conditions, confirming that the HFD confers specificity of Cse4 centromere targeting. Surprisingly, overexpression of the HFD bypassed the requirement for the END altogether, and viable
S. cerevisiae
strains in which the cells express only the Cse4 HFD and six adjacent N-terminal amino acids (Cse4Δ129) were constructed. Despite the complete absence of the NT, mitotic chromosome loss in the
cse4
Δ
129
strain increased only 6-fold compared to a 15-fold increase in strains overexpressing wild-type Cse4. Thus, when overexpressed, the Cse4 HFD is sufficient for centromere function in
S. cerevisiae
, and no posttranslational modification or interaction of the NT with other kinetochore component(s) is essential for accurate chromosome segregation in budding yeast.
G-Protein β Subunit of
Cochliobolus heterostrophus
Involved in Virulence, Asexual and Sexual Reproductive Ability, and Morphogenesis
Authors: Ganem Sherif , Lu Shun-Wen , Lee Bee-Na , Chou David Yu-Te , Hadar Ruthi , Turgeon B. Gillian , Horwitz Benjamin A.
Published: December 2004

Previous work established that mutations in mitogen-activated protein (MAP) kinase (
CHK1
) and heterotrimeric G-protein α (Gα) subunit (
CGA1
) genes affect the development of several stages of the life cycle of the maize pathogen
Cochliobolus heterostrophus
. The effects of mutating a third signal transduction pathway gene,
CGB1
, encoding the Gβ subunit, are reported here.
CGB1
is the sole Gβ subunit-encoding gene in the genome of this organism.
cgb1
mutants are nearly wild type in vegetative growth rate; however, Cgb1 is required for appressorium formation, female fertility, conidiation, regulation of hyphal pigmentation, and wild-type virulence on maize. Young hyphae of
cgb1
mutants grow in a straight path, in contrast to those of the wild type, which grow in a wavy pattern. Some of the phenotypes conferred by mutations in
CGA1
are found in
cgb1
mutants, suggesting that Cgb1 functions in a heterotrimeric G protein; however, there are also differences. In contrast to the deletion of
CGA1
, the loss of
CGB1
is not lethal for ascospores, evidence that there is a Gβ subunit-independent signaling role for Cga1 in mating. Furthermore, not all of the phenotypes conferred by mutations in the MAP kinase
CHK1
gene are found in
cgb1
mutants, implying that the Gβ heterodimer is not the only conduit for signals to the MAP kinase
CHK1
module. The additional phenotypes of
cgb1
mutants, including severe loss of virulence on maize and of the ability to produce conidia, are consistent with
CGB1
being unique in the genome. Fluorescent DNA staining showed that there is often nuclear degradation in mature hyphae of
cgb1
mutants, while comparable wild-type cells have intact nuclei. These data may be genetic evidence for a novel cell death-related function of the Gβ subunit in filamentous fungi.
Prm1 Prevents Contact-Dependent Lysis of Yeast Mating Pairs
Authors: Jin Hui , Carlile Candice , Nolan Scott , Grote Eric
Published: December 2004

Membrane fusion requires localized destabilization of two phospholipid bilayers, but unrestrained membrane destabilization could result in lysis.
prm1
mutant yeast cells have a defect at the plasma membrane fusion stage of mating that typically results in the accumulation of prezygotes that have fingers of membrane-bound cytoplasm projecting from one cell of each pair into its mating partner in the direction of the osmotic gradient between the cells. However, some
prm1
mating pairs fuse successfully whereas the two cells in other
prm1
mating pairs simultaneously lyse. Lysis only occurs if both mating partners are
prm1
mutants. Osmotic stabilization does not protect
prm1
mating pairs from lysis, indicating that lysis is not caused by a cell wall defect.
prm1
mating pairs without functional mitochondria still lyse, ruling out programmed cell death. No excess lysis was found after pheromone treatment of haploid
prm1
cells, and lysis did not occur in mating pairs when
prm1
was combined with the
fus1
and
fus2
mutations to block cell wall remodeling. Furthermore, short (<1 μm) cytoplasmic microfingers indicating the completion of cell wall remodeling appeared immediately before lysis. In combination, these results demonstrate that plasma membrane contact is a prerequisite for lysis. Cytoplasmic microfingers are unlikely to cause lysis since most
prm1
mating pairs with microfingers do not lyse, and microfingers were also detected before fusion in some wild-type mating pairs. The lysis of
prm1
mutant mating pairs suggests that the Prm1 protein stabilizes the membrane fusion event of yeast mating.
New Insights into Type II NAD(P)H:Quinone Oxidoreductases
Authors: Melo Ana M. P. , Bandeiras Tiago M. , Teixeira Miguel
Published: December 2004

Type II NAD(P)H:quinone oxidoreductases (NDH-2) catalyze the
two-electron transfer from NAD(P)H to quinones, without any
energy-transducing site. NDH-2 accomplish the turnover of NAD(P)H,
regenerating the NAD(P)
+
pool, and may contribute to
the generation of a membrane potential through complexes III and IV.
These enzymes are usually constituted by a nontransmembrane polypeptide
chain of ∼50 kDa, containing a flavin moiety. There are a few
compounds that can prevent their activity, but so far no general
specific inhibitor has been assigned to these enzymes. However, they
have the common feature of being resistant to the complex I classical
inhibitors rotenone, capsaicin, and piericidin A. NDH-2 have particular
relevance in yeasts like
Saccharomyces cerevisiae
and in
several prokaryotes, whose respiratory chains are devoid of complex I,
in which NDH-2 keep the
[NADH]/[NAD
+
] balance and are
the main entry point of electrons into the respiratory chains. Our
knowledge of these proteins has expanded in the past decade, as a
result of contributions at the biochemical level and the sequencing of
the genomes from several organisms. The latter showed that most
organisms contain genes that potentially encode NDH-2. An overview of
this development is presented, with special emphasis on microbial
enzymes and on the identification of three subfamilies of
NDH-2.
Streamlined Regulation and Gene Loss as Adaptive Mechanisms in
Prochlorococcus
for Optimized Nitrogen Utilization in Oligotrophic Environments
Authors: García-Fernández Jose Manuel , de Marsac Nicole Tandeau , Diez Jesús
Published: December 2004

Prochlorococcus
is one of the dominant cyanobacteria and a key primary producer in oligotrophic intertropical oceans. Here we present an overview of the pathways of nitrogen assimilation in
Prochlorococcus
, which have been significantly modified in these microorganisms for adaptation to the natural limitations of their habitats, leading to the appearance of different ecotypes lacking key enzymes, such as nitrate reductase, nitrite reductase, or urease, and to the simplification of the metabolic regulation systems. The only nitrogen source utilizable by all studied isolates is ammonia, which is incorporated into glutamate by glutamine synthetase. However, this enzyme shows unusual regulatory features, although its structural and kinetic features are unchanged. Similarly, urease activities remain fairly constant under different conditions. The signal transduction protein P
II
is apparently not phosphorylated in
Prochlorococcus
, despite its conserved amino acid sequence. The genes
amt1
and
ntcA
(coding for an ammonium transporter and a global nitrogen regulator, respectively) show noncorrelated expression in
Prochlorococcus
under nitrogen stress; furthermore, high rates of organic nitrogen uptake have been observed. All of these unusual features could provide a physiological basis for the predominance of
Prochlorococcus
over
Synechococcus
in oligotrophic oceans.
Type V Protein Secretion Pathway: the Autotransporter Story
Authors: Henderson Ian R. , Navarro-Garcia Fernando , Desvaux Mickaël , Fernandez Rachel C. , Ala'Aldeen Dlawer
Published: December 2004

Gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. To overcome this barrier, bacteria have developed several systems for protein secretion. The type V secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type Vc or AT-2 family of proteins. Since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the advent of the genomic age, to become the largest group of secreted proteins in gram-negative bacteria. Several of these proteins play essential roles in the pathogenesis of bacterial infections and have been characterized in detail, demonstrating a diverse array of function including the ability to condense host cell actin and to modulate apoptosis. However, most of the autotransporter proteins remain to be characterized. In light of new discoveries and controversies in this research field, this review considers the autotransporter secretion process in the context of the more general field of bacterial protein translocation and exoprotein function.
INCUMBENCY AND THE DISRUPTIVE REGULATOR: THE CASE OF ELECTRIC VEHICLES IN CALIFORNIA
Authors: PILKINGTON ALAN , DYERSON ROMANO
Published: December 2004

For much of the past century, the automobile sector has been dominated by a handful of oligopolistic firms, protected through path dependencies and the build up of complementary assets. But that very dominance built upon years of experience and translated into the periodic release of incrementally innovative new car designs, may now be threatened by the actions of regulators in California and elsewhere, in mandating emission friendly cars.

The biggest challenge in this area has been the demand for zero emission vehicles resulting from Californian regulations. Zero emission legislation mandates the use of technologies radically different from those used in the development of internal combustion engines. Such technology acts in a disruptive manner on the existing skills base of the automobile firms, negating some of the benefits of incumbency. With little or no experience of the systems needed to develop a viable electric vehicle — batteries, electric motors and controllers — the established automobile manufacturers have struggled with a strategic question: how to incorporate disruptive elements into a mature organisation. This paper explores the nature of the regulatory threat and the strategic responses generated by the automobile firms.
ENTERPRISE RESOURCE PLANNING (ERP) AND ITS IMPACT ON THE INNOVATIVE CAPABILITY OF THE FIRM
Authors: TROTT P. , HOECHT A.
Published: December 2004

Enterprise Resource Planning (ERP) business software has become one of the most successful products in the world. Microsoft, ICI, UBS and Procter & Gamble are a few of the firms that have claimed it has changed the way they work (Gartner, 2002). Indeed, substantial claims are made about the software's capabilities. A complete system could take several years and several hundred million dollars to deploy. SAP, Oracle, Baan and PeopleSoft are the market leaders and SAP has over 20,000 R/3 products installed worldwide; Oracle has installed databases in nearly every one of the world's top 500 companies. This paper surveys the literature and identifies that there is increasing evidence that firms fail to obtain the benefits of these investments within the anticipated timeframes (Pollock et al., 2003). Moreover, and more worrying for senior managers is the extent to which these fully integrated systems using on-line transactional processing are affecting the firm's innovative ability. We argue in this paper that there is a fundamental clash of underlying principles between ERP systems requirements and the success factors of innovative organisations that lie at the heart of the innovation dilemma caused by the introduction of ERP systems into organisations.
TECHNICAL KNOWLEDGE-SEEKING IN A YOUNG AND GROWING TECHNOLOGY-BASED FIRM: INCENTIVES AND DIRECTION
Authors: SAEMUNDSSON RÖGNVALDUR J.
Published: December 2004

The purpose of the paper is to investigate technical knowledge-seeking activities in young and growing technology-based firms. Changes in technical knowledge-seeking activities were traced using a single illustrative case study of a young and growing technology-based firm. The results of the study show how strong commitment to the business concept of the emerging firm affected the direction of technical knowledge-seeking in a way that increases the vulnerability of the firm. New employees who were not as familiar with or committed to the original business concept brought with them different incentives for knowledge-seeking, which lead to search in new directions. These knowledge-seeking activities were important for the renewal of the firm's knowledge base. It is therefore suggested that differences in individual incentives may affect the direction of technical knowledge-seeking activities, and correspondingly, that multiple incentives are an important source of diversity in technical knowledge creation.
CITIZENSHIP AND CIVIC ENGAGEMENT
Authors: Theiss-Morse Elizabeth , Hibbing John R.
Published: December 2004

▪ Abstract  Is it possible for people to join their way to good citizenship? Contemporary thinking, both academic and popular, often leaves the impression that it is, but a careful investigation of the evidence raises serious doubts. In actuality, belonging to voluntary associations is a woefully inadequate foundation for good citizenship for three primary reasons: People join groups that are homogeneous, not heterogeneous; civic participation does not lead to, and may turn people away from, political participation; and not all groups promote democratic values. Good citizens need to learn that democracy is messy, inefficient, and conflict-ridden. Voluntary associations do not teach these lessons.