bluuebunny/crossref_metadata_2025 huggingface dataset:
Human skin cell stress response to GSM‐900 mobile phone signals
Authors: Sanchez Sandrine , Milochau Alexandra , Ruffie Gilles , Poulletier de Gannes Florence , Lagroye Isabelle , Haro Emmanuelle , Surleve‐Bazeille Jean‐Etienne , Billaudel Bernard , Lassegues Maguy , Veyret Bernard
Published: November 2006

In recent years, possible health hazards due to radiofrequency radiation (RFR) emitted by mobile phones have been investigated. Because several publications have suggested that RFR is stressful, we explored the potential biological effects of Global System for Mobile phone communication at 900 MHz (GSM‐900) exposure on cultures of isolated human skin cells and human reconstructed epidermis (hRE) using human keratinocytes. As cell stress markers, we studied Hsc70, Hsp27 and Hsp70 heat shock protein (HSP) expression and epidermis thickness, as well as cell proliferation and apoptosis. Cells were exposed to GSM‐900 under optimal culture conditions, for 48 h, using a specific absorption rate (SAR) of 2 W·kg−1. This SAR level represents the recommended limit for local exposure to a mobile phone. The various biological parameters were analysed immediately after exposure. Apoptosis was not induced in isolated cells and there was no alteration in hRE thickness or proliferation. No change in HSP expression was observed in isolated keratinocytes. By contrast, a slight but significant increase in Hsp70 expression was observed in hREs after 3 and 5 weeks of culture. Moreover, fibroblasts showed a significant decrease in Hsc70, depending on the culture conditions. These results suggest that adaptive cell behaviour in response to RFR exposure, depending on the cell type and culture conditions, is unlikely to have deleterious effects at the skin level.
Inactivation of tyrosine phenol‐lyase by Pictet–Spengler reaction and alleviation by T15A mutation on intertwined N‐terminal arm
Authors: Lee Seung‐Goo , Hong Seung‐Pyo , Kim Do Young , Song Jae Jun , Ro Hyeon‐Su , Sung Moon‐Hee
Published: November 2006

Citrobacter freundii
l‐tyrosine phenol‐lyase (TPL) was inactivated by a Pictet–Spengler reaction between the cofactor and a substrate, 3,4‐dihydroxyphenyl‐l‐alanine (l‐dopa), in proportion to an increase in the reaction temperature. Random mutagenesis of the tpl gene resulted in the generation of a Thr15 to Ala mutant (T15A), which exhibited a two‐fold improved activity towards l‐DOPA as the substrate. The Thr15 residue was located on the intertwined N‐terminal arm of the TPL structure, and comprised an H‐bond network in proximity to the hydrophobic core between the catalytic dimers. The maximum activity of the mutant and native enzymes with l‐DOPA was detected at 45 and 40 °C, respectively, which was 15 °C lower than when using l‐tyrosine as the substrate. The half‐lives at 45 °C were about 16.8 and 6.4 min for the mutant and native enzymes, respectively, in 10 mm l‐DOPA. On treatment with excess pyridoxal‐5′‐phosphate (PLP), the l‐DOPA‐inactivated enzymes recovered over 80% of their original activities, thereby attributing the inactivation to a loss of the cofactor through Pictet–Spengler condensation with l‐DOPA. Consistent with the extended half‐life, the apparent Michaelis constant of the T15A enzyme for PLP (Km,PLP) increased slowly when increasing the temperature, while that of the native enzyme showed a sharp increase at temperatures higher than 50 °C, implying that the loss of the cofactor with the Pictet–Spengler reaction was prevented by the tighter binding and smaller release of the cofactor in the mutant enzyme.
Absence of association between two insertion/deletion coding genetic polymorphisms of TIM‐1 gene and asthma in Chinese Han population
Authors: Li J. S. , Liu Q. J. , Wang P. , Li H. C. , Wei C. H. , Guo C. H. , Gong Y. Q.
Published: November 2006

TIM‐1, a member of T‐cell immunoglobulin domain and mucin domain (TIM) gene family, was implicated as an asthma susceptibility gene in previous studies. TIM‐1 was expressed on CD4+ T cells after activation and its expression was sustained preferentially in T‐helper type 2 (TH2) but not in TH1 cells, therefore TIM‐1 became a good candidate gene for atopic diseases. Recent studies indicated that two insertion/deletion (ins/del) coding genetic polymorphisms in exon 4 of TIM‐1 were associated with asthma susceptibility in some but not in all populations. In order to investigate the relationship between TIM‐1 genetic polymorphisms and asthma in Chinese Han population, we performed a case‐control study for two insertion/deletion polymorphisms in TIM‐1 exon 4 (5383_5397ins/del and 5509_5511delCAA) and a single nucleotide polymorphism (SNP) in intron 8 (IVS 8+9 G/A) between a healthy control group of 309 people and an asthma patient group of 352 people recruited from Chinese Han population. The polymorphisms were genotyped and the allele and genotype frequencies were analysed, but none of the three polymorphisms showed association with asthma susceptibility in single‐locus association analyses. Linkage disequilibrium (LD) analyses demonstrated that the two insertion/deletion polymorphisms were in strong LD but the haplotypes constructed from these two polymorphisms showed no significant association with asthma. In conclusion, our findings suggest that 5383_5397ins/del, 5509_5511delCAA and SNP IVS 8+9 G/A polymorphisms are not associated with asthma susceptibility in Chinese Han population.
A Multilevel System for High‐Resolution Monitoring in Rotasonic Boreholes
Authors: Parker Beth L. , Cherry John A. , Swanson Benjamin J.
Published: November 2006

A modular multilevel system was adapted for high‐resolution, depth‐discrete monitoring of hydraulic head and ground water quality in rotasonic boreholes or boreholes produced with similar dual‐casing drilling methods. The system accommodates up to 15 monitoring intervals within one hole and can be used to monitor overburden and/or bedrock to depths of 100 m (330 feet) or more. It is most effective where static water levels are shallower than 9 m (30 feet) below ground surface. Sand packs around each monitoring port define the monitoring interval, and bentonite seals placed above and below each sand pack isolate the intervals. Each sand and bentonite layer has a practical minimum length of 0.5 m (1.6 feet); therefore, a 15 port system can monitor, with maximum detail, a minimum vertical span of 15 m (50 feet). All system components, primarily flush joint polyvinyl chloride (PVC) casing segments, stainless steel ports, Teflon® tubing, and PVC centralizers, are commercially available and require little preconstruction. An open 6‐mm (¼‐inch) inner diameter tube is connected to each port for manual hydraulic head measurements and water sampling with a peristaltic pump. To assess installation and performance of the new system, nine rotasonic holes in overburden and bedrock between 20‐ and 30‐m (65‐ and 100‐feet) deep were monitored at two sites. This detailed vertical monitoring provided important information on hydraulic head and contaminant distributions that would have been missed with fewer monitoring intervals. The monitoring system offers unique advantages where detailed monitoring in heterogeneous settings is needed to understand ground water flow and contaminant migration or evaluate the performance of remediation efforts.
Taxonomic review of the Cleridae (Coleoptera) in Korea (Part 3): Korynetinae, Tarsosteninae and Tillinae
Authors: KIM Jin Ill , JUNG Boo Hee
Published: November 2006

A taxonomic review of three clerid subfamilies (Korynetinae, Tarsosteninae and Tillinae) in Korea is presented in this paper. Eight species, including Opetiopalpus sabulos (Motschulsky, 1840), a new Korean record, are reported. A key to the Korean species, genera and subfamilies, description, habitus photographs of adults, and illustrations of diagnostic characters are provided.
Animal welfare provision for land‐based livestock industries in Australia
Authors: Petherick JC
Published: November 2006

The land‐based livestock industries in Australia face particular challenges in assuring high animal welfare standards due to large land areas and stock numbers, climatic extremes and relatively low inputs in terms of manpower and infrastructure. These factors make a major contribution to welfare issues associated with nutrition, health, mustering and handling, and transportation. In addition, welfare is seriously compromised by the invasive procedures that are conducted on livestock, such as castration, dehorning, mulesing and tail‐docking. At least partial solutions to welfare issues associated with nutrition, health, mustering and handling are available now and should be universally adopted. There are potential solutions available for castration and dehorning, which require some further research and development. Genetic technologies can also provide a solution for dehorning, mulesing and tail‐docking. Inevitably, all livestock experience transportation, and research and development is required to determine optimal practices for Australian conditions in order to minimise the negative impacts on animal welfare.
An Investigation of an Impact Vibration Absorber With Hysteresis Damping
Authors: Aoki Shigeru , Watanabe Takeshi
Published: November 2006

The dynamic vibration absorber is a device for reducing the vibration of many structures and mechanical equipment. It consists of a small mass which is attached to the primary vibrating system or main mass. The impact damper is one of such dynamic vibration absorbers in which motion of auxiliary mass is limited by motion-limiting stop or placed inside a container. In this paper, in order to consider energy loss for an impact represented by the coefficient of restitution and duration of collision, an analytical model with hysteresis damping is introduced. Using this model, dynamic response of the system under harmonic and that under random excitations are analyzed. Some numerical results are shown.
Residual Stresses Evaluation in Welds and Implications for Design for Pressure Vessel Applications
Authors: Price John W. H. , Pardowska Anna M. , Ibrahim Raafat , Finlayson Trevor R.
Published: November 2006

Welding residual stresses have important consequences on the performance of engineering components. High residual stresses may lead to loss of performance in corrosion, fatigue, and fracture but as yet these consequences are poorly quantified. The major cause of this is that residual stress often remains the single largest unknown in industrial damage situations since it is difficult to measure or estimate theoretically. One of the key issues in the study of residual stress is that the detail of the stress distribution on a small scale (in the order of millimeters) can be important. In this paper, the neutron diffraction technique is used which while it is a very expensive technique, is capable of nondestructively measuring residual stresses at this scale up to a depth of 35mm. The investigation reported compares the residual stress characteristics due to various restraints for a single bead and in fully restrained samples with different numbers of beads. This paper considers the results of the neutron diffraction studies in relation to fitness for purpose guidance and implication for pressure vessel design.
An Experimental Investigation of Heat Transport Capability in a Nanofluid Oscillating Heat Pipe
Authors: Ma H. B. , Wilson C. , Yu Q. , Park K. , Choi U. S. , Tirumala Murli
Published: November 2006

An experimental investigation of a nanofluid oscillating heat pipe (OHP) was conducted to determine the nanofluid effect on the heat transport capability in an OHP. The nanofluid consisted of HPLC grade water and 1.0vol% diamond nanoparticles of 5-50nm. These diamond nanoparticles settle down in the motionless base fluid. However, the oscillating motion of the OHP suspends the diamond nanoparticles in the working fluid. Experimental results show that the heat transport capability of the OHP significantly increased when it was charged with the nanofluid at a filling ratio of 50%. It was found that the heat transport capability of the OHP depends on the operating temperature. The investigated OHP could reach a thermal resistance of 0.03°C∕W at a heat input of 336W. The nanofluid OHP investigated here provides a new approach in designing a highly efficient next generation of heat pipe cooling devices.
Influence of thermal annealing on the resistivity of titanium/platinum thin films
Authors: Schmid U. , Seidel H.
Published: November 2006

In this study, the authors investigate the influence of thermal annealing up to temperatures of 700°C on the room-temperature resistivity of electron-beam-evaporated titanium/platinum thin films. Oxidized silicon wafers are used as the substrate. The titanium has a fixed thickness of 5nm and serves as an adhesion layer. The thickness of the platinum top is varied between 21 and 97nm. Up to annealing temperatures of 450°C, the film resistivity of the bilayer system is a linear correlation with the reciprocal platinum film thickness, as expected from the size effect. In this annealing regime, the change in intrinsic film stress dominates the electrical behavior. At annealing temperatures of 600°C and above, however, the diffusion of titanium into the top layer leads to an enhanced increase in film resistivity, especially at low platinum thicknesses. The onset of plastic deformation of the platinum layer causes an additional effect that decreases the electrical conductivity above average.
Modeling distortion product otoacoustic emission input/output functions using segmented regression
Authors: Goldman Bryan , Sheppard Lianne , Kujawa Sharon G. , Seixas Noah S.
Published: November 2006

Distortion product otoacoustic emissions (DPOAEs) are low-level acoustic signals, the detection of which involves extraction from a background of noise. Boege and Janssen [J. Acoust. Soc. Am. 111, 1810–1818 (2002)] described a method for modeling the presence and growth of these responses. While improving growth function parameter estimation, this technique excludes a significant fraction of the data (especially low-level responses), and relies on ad hoc model fit acceptance criteria. The statistical difficulties associated with these limitations are described, and a weighted segmented linear regression model that avoids them is proposed. A simple test is presented for the presence of DPOAE growth. This technique is compared to that of Boege and Janssen in a dataset of 9 556 input/output (I/O) functions collected over 4years on 866 ears from 379 construction apprentices and 63 age-matched controls. Comparisons are made on the entire dataset and within audiometric hearing loss categories. Segmented regression avoids the statistical pitfalls of the previous method, allows estimation of the threshold and slope of auditory response on a far greater number of I/O functions, and improves estimation of these parameters in this dataset. The potential for this method to yield more sensitive metrics of hearing function and compromise is discussed.
Measurements of temporal coherence of sound transmissions through shallow water
Authors: Yang T. C.
Published: November 2006

In this paper we report the measurements of temporal coherence of acoustic signals propagating through shallow water using data from three experiments in three different parts of the world, with sound speed standard deviation (STD) varying from 0.3 to 5m∕s near the layer depth. Temporal coherence is estimated from the autocorrelations of broadband channel impulse functions, the latter are deduced from broadband signals transmitted through the ocean during the experiments. The measurements covered three frequency bands: low frequencies below 1.2kHz, midfrequencies between 2 and 5kHz, and high frequencies between 18 and 22kHz. The source-receiver range covers 3, 5, 10, and 42km. The signal coherence-time is defined and deduced from the data. Motivated by previous theoretical work in deep water on the signal coherence-time as a function of the signal frequency, the source-receiver range, and sound speed STD, a similar but empirical analysis is applied to the measured data in shallow water. While the range dependence agrees with the theory, the data exhibit a different dependence on the signal frequency than the theoretical prediction for deep water.
Temporal and spectral cues in Mandarin tone recognition
Authors: Kong Ying-Yee , Zeng Fan-Gang
Published: November 2006

This study evaluates the relative contributions of envelope and fine structure cues in both temporal and spectral domains to Mandarin tone recognition in quiet and in noise. Four sets of stimuli were created. Noise-excited vocoder speech was used to evaluate the temporal envelope. Frequency modulation was then added to evaluate the temporal fine structure. Whispered speech was used to evaluate the spectral envelope. Finally, equal-amplitude harmonics were used to evaluate the spectral fine structure. Results showed that normal-hearing listeners achieved nearly perfect tone recognition with either spectral or temporal fine structure in quiet, but only 70%–80% correct with the envelope cues. With the temporal envelope, 32 spectral bands were needed to achieve performance similar to that obtained with the original stimuli, but only four bands were necessary with the additional temporal fine structure. Envelope cues were more susceptible to noise than fine structure cues, with the envelope cues producing significantly lower performance in noise. These findings suggest that tonal pattern recognition is a robust process that can make use of both spectral and temporal cues. Unlike speech recognition, the fine structure is more important than the envelope for tone recognition in both temporal and spectral domains, particularly in noise.
Is fundamental frequency a cue to aspiration in initial stops?
Authors: Francis Alexander L. , Ciocca Valter , Wong Virginia Ka Man , Chan Jess Ka Lam
Published: November 2006

One production and one perception experiment were conducted to investigate the interaction of consonant voicing and fundamental frequency at the onset of voicing (onset f0) in Cantonese, a tonal language. Consonantal voicing in English can affect onset f0 up to 100ms after voicing onset, but existing research provides inconclusive information regarding the effects of voicing on f0 in tonal languages where f0 variability is constrained by the demands of the lexical tone system. Previous research on consonantal effects on onset f0 provides two contrasting theories: These effects may be automatic, resulting from physiological constraints inherent to the speech production mechanism or they may be controlled, produced as part of a process of cue enhancement for the perception of laryngeal contrasts. Results of experiment 1 showed that consonant aspiration affects onset f0 in Cantonese only within the first 10ms following voicing onset, comparable to results for other tonal languages. Experiment 2 showed that Cantonese listeners can use differences in onset f0 to cue perception of the voicing contrast, but the minimum extent of f0 perturbation necessary for this is greater than is found in Cantonese production, and comparable to that observed in acoustic studies of nontonal languages. These results suggest that consonantal effects on onset f0 are at least partially controlled by talkers, but that their role in the perception of voicing/aspiration may be a consequence of language independent properties of audition rather than listeners’ experience with the phonological contrasts of a specific language.
Adaptive focusing for transcranial ultrasound imaging using dual arrays
Authors: Vignon F. , Aubry J. F. , Tanter M. , Margoum A. , Fink M.
Published: November 2006

Ultrasonic brain imaging remains difficult and limited because of the strong aberrating effects of the skull (absorption, diffusion and refraction of ultrasounds): high resolution transcranial imaging would require adaptive focusing techniques in order to correct the defocusing effect of the skull. In this paper, a noninvasive brain imaging device is presented. It is made of two identical linear arrays of 128 transducers located on each side of the skull. It is possible to separate the respective influence of the two bone windows on the path of an ultrasonic wave propagating from one array to the other, and thus estimate at each frequency the attenuation and phase shift locally induced by each bone window. The information obtained on attenuation and phase is used to correct the wave fronts that have to be sent through the skull in order to obtain a good focusing inside the skull. Compared to uncorrected wave fronts, the spatial shift of the focal spot is corrected, the width of the focal spot is reduced, and the sidelobes level is decreased up to 17dB. Transcranial images of a phantom are presented and exhibit the improvement in image quality provided by this new noninvasive adaptive focusing method.
On first rahmonic amplitude in the analysis of synthesized aperiodic voice signals
Authors: Murphy Peter J.
Published: November 2006

Rahmonics comprise the prominent peaks in the cepstrum of voiced speech; their locations correspond to the fundamental period and its multiples. The amplitude of the first rahmonic, R1, has previously been used to indicate voice quality. Although a correspondence between R1 and the richness of the harmonic spectrum for voiced speech is well recognized, a formal description has remained absent. A theoretical description of rahmonic analysis of voiced speech containing aspiration noise is provided, leading to a characterization of R1. The theory suggests that R1 is directly proportional to the geometric mean harmonics-to-noise ratio (gmHNR), where the gmHNR is defined as the mean of the individual spectral (i.e. at specific frequency locations) harmonics-to-noise ratios in dB. This hypothesis is validated using synthetically generated voice signals. R1 is shown to be directly proportional to gmHNR (measured directly from the dB spectrum). It is shown that R1 (estimated from speech) is directly proportional to R1 taken from the glottal signal. R1 and gmHNR (measured spectrally) underestimate the actual gmHNR when (averaged) noise levels exceed harmonic levels. Limiting the number of harmonics in the analysis window overcomes this problem and also alleviates the (temporal) window length/f0 dependence of R1 when estimated period synchronously.
Response to Comments on "Statistical Independence of Escalatory Ecological Trends in Phanerozoic Marine Invertebrates"
Authors: Madin Joshua S. , Alroy John , Aberhan Martin , Fürsich Franz T. , Kiessling Wolfgang , Kosnik Matthew A. , Wagner Peter J.
Published: November 2006

Roopnarine
et al
. and Dietl and Vermeij do not challenge our results but argue that escalation can be seen only at fine scales. This claim diminishes the theory and needs to be tested, not asserted. Roopnarine

et al

. incorrectly presume that our data are dominated by carnivores. Dietl and Vermeij overlook the fact that in addition to having no effect on global diversity, escalation has no effect on occurrence frequency.
The Transcriptome of the Sea Urchin Embryo
Authors: Samanta Manoj P. , Tongprasit Waraporn , Istrail Sorin , Cameron R. Andrew , Tu Qiang , Davidson Eric H. , Stolc Viktor
Published: November 2006

The sea urchin
Strongylocentrotus purpuratus
is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the
S. purpuratus
embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.
Are We Dancing Apes?
Authors: Devlin Joseph T.
Published: November 2006

Toward an Evolutionary Biology of Language
.
By Philip Lieberman
. Harvard University Press, Cambridge MA, 2006, 441 pp. $49.95, £32.95, €46.10. ISBN 0-674-02184-3.

Rejecting the influential theories of language development that posit a single dedicated language module, the author argues that language is the product of a succession of evolutionary developments that natural selection has shaped to work together.
Human Hair Growth Deficiency Is Linked to a Genetic Defect in the Phospholipase Gene
LIPH
Authors: Kazantseva Anastasiya , Goltsov Andrey , Zinchenko Rena , Grigorenko Anastasia P. , Abrukova Anna V. , Moliaka Yuri K. , Kirillov Alexander G. , Guo Zhiru , Lyle Stephen , Ginter Evgeny K. , Rogaev Evgeny I.
Published: November 2006

The molecular mechanisms controlling human hair growth and scalp hair loss are poorly understood. By screening about 350,000 individuals in two populations from the Volga-Ural region of Russia, we identified a gene mutation in families who show an inherited form of hair loss and a hair growth defect. Affected individuals were homozygous for a deletion in the
LIPH
gene on chromosome 3q27, caused by short interspersed nuclear element–retrotransposon–mediated recombination. The
LIPH
gene is expressed in hair follicles and encodes a phospholipase called lipase H (alternatively known as membrane-associated phosphatidic acid–selective phospholipase A1α), an enzyme that regulates the production of bioactive lipids. These results suggest that lipase H participates in hair growth and development.
Resilient Machines Through Continuous Self-Modeling
Authors: Bongard Josh , Zykov Victor , Lipson Hod
Published: November 2006

Animals sustain the ability to operate after injury by creating qualitatively different compensatory behaviors. Although such robustness would be desirable in engineered systems, most machines fail in the face of unexpected damage. We describe a robot that can recover from such change autonomously, through continuous self-modeling. A four-legged machine uses actuation-sensation relationships to indirectly infer its own structure, and it then uses this self-model to generate forward locomotion. When a leg part is removed, it adapts the self-models, leading to the generation of alternative gaits. This concept may help develop more robust machines and shed light on self-modeling in animals.
Selective Etching of Metallic Carbon Nanotubes by Gas-Phase Reaction
Authors: Zhang Guangyu , Qi Pengfei , Wang Xinran , Lu Yuerui , Li Xiaolin , Tu Ryan , Bangsaruntip Sarunya , Mann David , Zhang Li , Dai Hongjie
Published: November 2006

Metallic and semiconducting carbon nanotubes generally coexist in as-grown materials. We present a gas-phase plasma hydrocarbonation reaction to selectively etch and gasify metallic nanotubes, retaining the semiconducting nanotubes in near-pristine form. With this process, 100% of purely semiconducting nanotubes were obtained and connected in parallel for high-current transistors. The diameter- and metallicity-dependent “dry” chemical etching approach is scalable and compatible with existing semiconductor processing for future integrated circuits.
Binding of Glucuronoxylomannan to the CD14 Receptor in Human A549 Alveolar Cells Induces Interleukin-8 Production
Authors: Barbosa Fabiane M. , Fonseca Fernanda L. , Figueiredo Rodrigo T. , Bozza Marcelo T. , Casadevall Arturo , Nimrichter Leonardo , Rodrigues Marcio L.
Published: November 2006

Glucuronoxylomannan (GXM) is the major capsular polysaccharide of
Cryptococcus neoformans
. GXM receptors have been characterized in phagocytes and endothelial cells, but epithelial molecules recognizing the polysaccharide remain unknown. In the current study, we demonstrate that GXM binds to the CD14 receptor in human type II alveolar epithelial cells, resulting in the production of the proinflammatory chemokine interleukin-8.
BOX Elements Modulate Gene Expression inStreptococcus pneumoniae: Impact on the Fine-Tuning of Competence Development
Authors: Knutsen Eivind , Johnsborg Ola , Quentin Yves , Claverys Jean-Pierre , Håvarstein Leiv Sigve
Published: November 2006

More than 100 BOX elements are randomly distributed in intergenic regions of the pneumococcal genome. Here we demonstrate that these elements can affect expression of neighboring genes and present evidence that they are mobile. Together, our findings show that BOX elements enhance genetic diversity and genomic plasticity inStreptococcus pneumoniae.
Revised Model for
Enterococcus faecalis fsr
Quorum-Sensing System: the Small Open Reading Frame
fsrD
Encodes the Gelatinase Biosynthesis-Activating Pheromone Propeptide Corresponding to Staphylococcal AgrD
Authors: Nakayama Jiro , Chen Shengmin , Oyama Nozomi , Nishiguchi Kenzo , Azab Essam A. , Tanaka Emi , Kariyama Reiko , Sonomoto Kenji
Published: November 2006

Gelatinase biosynthesis-activating pheromone (GBAP) is an autoinducing peptide involved in
Enterococcus faecalis fsr
quorum sensing, and its 11-amino-acid sequence has been identified in the C-terminal region of the 242-residue deduced
fsrB
product (J. Nakayama et al., Mol. Microbiol. 41:145-154, 2001). In this study, however, we demonstrated the existence of
fsrD
, encoding the GBAP propeptide, which is in frame with
fsrB
but is translated independently of
fsrB
. It was also demonstrated that FsrB′, an FsrD segment-truncated FsrB, functions as a cysteine protease-like processing enzyme to generate GBAP from FsrD. This revised model is consistent with the staphylococcal
agr
system.
Role of Bacteriocin Immunity Proteins in the Antimicrobial Sensitivity of
Streptococcus mutans
Authors: Matsumoto-Nakano Michiyo , Kuramitsu Howard K.
Published: November 2006

Bacteria utilize quorum-sensing systems to modulate environmental stress responses. The quorum-sensing system of
Streptococcus mutans
is mediated by the competence-stimulating peptide (CSP), whose precursor is encoded by the
comC
gene. A
comC
mutant of strain GS5 exhibited enhanced antimicrobial sensitivity to a wide variety of different agents. Since the addition of exogenous CSP did not complement this phenotype, it was determined that the increased tetracycline, penicillin, and triclosan sensitivities resulted from repression of the putative bacteriocin immunity protein gene,
bip
, which is located immediately upstream from
comC
. We further demonstrated that the inactivation of
bip
or
smbG
, another bacteriocin immunity protein gene present within the
smb
operon in
S. mutans
GS5, affected sensitivity to a variety of antimicrobial agents. Furthermore, both the
bip
and
smbG
genes were upregulated in the presence of low concentrations of antibiotics and were induced during biofilm formation relative to in planktonic cells. These results suggest, for the first time, that the antimicrobial sensitivity of a bacterium can be modulated by some of the putative bacteriocin immunity proteins expressed by the organism. The implications of these observations for the evolution of bacteriocin immunity protein genes as well as for potential new chemotherapeutic strategies are discussed.
Analysis ofPseudomonas aeruginosaConditional Psl Variants Reveals Roles for the Psl Polysaccharide in Adhesion and Maintaining Biofilm Structure Postattachment
Authors: Ma Luyan , Jackson Kara D. , Landry Rebecca M. , Parsek Matthew R. , Wozniak Daniel J.
Published: November 2006

The ability to form biofilms in the airways of people suffering from cystic fibrosis is a critical element ofPseudomonas aeruginosapathogenesis. The 15-genepsloperon encodes a putative polysaccharide that plays an important role in biofilm initiation in nonmucoidP. aeruginosastrains. Biofilm initiation by aP. aeruginosaPAO1 strain with disruption ofpslAandpslB(ΔpslAB) was severely compromised, indicating thatpslhas a role in cell-surface interactions. In this study, we investigated the adherence properties of this ΔpslABmutant using biotic surfaces (epithelial cells and mucin-coated surfaces) and abiotic surfaces. Our results showed thatpslis required for attachment to a variety of surfaces, independent of the carbon source. To study the potential roles of Psl apart from attachment, we generated apsl-inducibleP. aeruginosastrain (Δpsl/pBAD-psl) by replacing thepslpromoter region witharaC-pBAD, so that expression ofpslcould be controlled by addition of arabinose. Analysis of biofilms formed by the Δpsl/pBAD-pslstrain indicated that expression of thepsloperon is required to maintain the biofilm structure at steps postattachment. Overproduction of the Psl polysaccharide led to enhanced cell-surface and intercellular adhesion ofP. aeruginosa. This translated into significant changes in the architecture of the biofilm. We propose that Psl has an important role inP. aeruginosaadhesion, which is critical for initiation and maintenance of the biofilm structure.
IS1301Fingerprint Analysis ofNeisseria meningitidisStrains Belonging to the ET-15 Clone
Authors: Elias Johannes , Vogel Ulrich
Published: November 2006

Meningococci of the ET-15 clone frequently cause clusters of invasive meningococcal disease (IMD) and are associated with a high case-fatality ratio. Timely typing of strains from outbreaks of IMD caused by this clone is hampered by the low variability of its surface antigens. We present a new Southern blot-based typing method for ET-15 meningococci based on the insertion element IS1301, which was present in all 70 ET-15 strains tested. Fingerprints were stable in vitro over a period of 100 days of cultivation on agar plates. The discriminatory power of IS1301fingerprinting exceeded that of typing by serogrouping and antigen sequencing of the outer membrane proteins PorA and FetA, as determined by the analysis of 52 epidemiologically unrelated strains. In addition, the method provided conclusive results with regard to the comparison of strains from clusters of IMD. The investigation of insertion sites of IS1301revealed several new intragenic insertions, among others, into open reading frames homologous tomafBandtspB. A previously described insertion innadAwas present in more than two-thirds of the strains analyzed, suggesting that NadA is probably an unreliable vaccine candidate for the prevention of ET-15 disease.
Rapid Detection and Identification of Metallo-β-Lactamase-Encoding Genes by Multiplex Real-Time PCR Assay and Melt Curve Analysis
Authors: Mendes Rodrigo E. , Kiyota Katia A. , Monteiro Jussimara , Castanheira Mariana , Andrade Soraya S. , Gales Ana C. , Pignatari Antonio C. C. , Tufik Sergio
Published: November 2006

Metallo-β-lactamase enzymes (MβL) are encoded by transferable genes, which appear to spread rapidly among gram-negative bacteria. The objective of this study was to develop a multiplex real-time PCR assay followed by a melt curve step for rapid detection and identification of genes encoding MβL-type enzymes based on the amplicon melting peak. The reference sequences of all genes encoding IMP and VIM types, SPM-1, GIM-1, and SIM-1 were downloaded from GenBank, and primers were designed to obtain amplicons showing different sizes and melting peak temperatures (

T
m

). The real-time PCR assay was able to detect all MβL-harboring clinical isolates, and the

T
m

-assigned genotypes were 100% coincident with previous sequencing results. This assay could be suitable for identification of MβL-producing gram-negative bacteria by molecular diagnostic laboratories.
Quality Control Limits for Posaconazole Disk Susceptibility Tests on Mueller-Hinton Agar with Glucose and Methylene Blue
Authors: Brown S. , Traczewski M.
Published: November 2006

A multilaboratory collaborative study was performed in order to propose quality control limits for posaconazole disk diffusion susceptibility tests on Mueller-Hinton agar supplemented with 2% glucose and 0.5 μg of methylene blue per ml. Replicate tests were performed on three lots of prepared media using 5-μg posaconazole disks in each of eight laboratories to generate data to propose quality control zone diameter ranges for tests of
Candida albicans
ATCC 90028 (24 to 34 mm),
C. parapsilosis
ATCC 22019 (25 to 36 mm),
C. tropicalis
ATCC 750 (23 to 33 mm), and
C. krusei
ATCC 6258 (23 to 31 mm).
A Hypervariable Region within the 3′
cis
-Acting Element of the Murine Coronavirus Genome Is Nonessential for RNA Synthesis but Affects Pathogenesis
Authors: Goebel Scott J. , Miller Timothy B. , Bennett Corey J. , Bernard Kristen A. , Masters Paul S.
Published: November 2006

The 3′
cis
-acting element for mouse hepatitis virus (MHV) RNA synthesis resides entirely within the 301-nucleotide 3′ untranslated region (3′ UTR) of the viral genome and consists of three regions. Encompassing the upstream end of the 3′ UTR are a bulged stem-loop and an overlapping RNA pseudoknot, both of which are essential to MHV and common to all group 2 coronaviruses. At the downstream end of the genome is the minimal signal for initiation of negative-strand RNA synthesis. Between these two ends is a hypervariable region (HVR) that is only poorly conserved between MHV and other group 2 coronaviruses. Paradoxically, buried within the HVR is an octanucleotide motif (oct), 5′-GGAAGAGC-3′, which is almost universally conserved in coronaviruses and is therefore assumed to have a critical biological function. We conducted an extensive mutational analysis of the HVR. Surprisingly, this region tolerated numerous deletions, rearrangements, and point mutations. Most striking, a mutant deleted of the entire HVR was only minimally impaired in tissue culture relative to the wild type. By contrast, the HVR deletion mutant was highly attenuated in mice, causing no signs of clinical disease and minimal weight loss compared to wild-type virus. Correspondingly, replication of the HVR deletion mutant in the brains of mice was greatly reduced compared to that of the wild type. Our results show that neither the HVR nor oct is essential for the basic mechanism of MHV RNA synthesis in tissue culture. However, the HVR appears to play a significant role in viral pathogenesis.
GLUT1 Is Not the Primary Binding Receptor but Is Associated with Cell-to-Cell Transmission of Human T-Cell Leukemia Virus Type 1
Authors: Takenouchi Norihiro , Jones Kathryn S. , Lisinski Ivonne , Fugo Kazunori , Yao Karen , Cushman Samuel W. , Ruscetti Francis W. , Jacobson Steven
Published: November 2006

GLUT1 has recently been suggested to be a binding receptor for human T-cell leukemia virus type 1 (HTLV-1). We used a novel, short-term assay to define the role of GLUT1 in cell-to-cell transmission. Although increasing cell surface levels of GLUT1 enhanced HTLV-I transfer, efficient virus spread correlated largely with heparan sulfate proteoglycan (HSPG) expression on target cells. Moreover, since activated CD4
+
T cells and cord blood lymphocytes that are susceptible to HTLV-1 infection expressed undetectable levels of surface GLUT1, these results indicate that GLUT1 and HSPGs are important for efficient cell-to-cell transmission of HTLV-1 but raise concerns on the role of GLUT1 as the HTLV-1 primary binding receptor.
Genetic Studies of the β-Hairpin Loop of Rous Sarcoma Virus Capsid Protein
Authors: Spidel Jared L. , Wilson Carol B. , Craven Rebecca C. , Wills John W.
Published: November 2006

The first few residues of the Rous sarcoma virus (RSV) CA protein comprise a structurally dynamic region that forms part of a Gag-Gag interface in immature virus particles. Dissociation of this interaction during maturation allows refolding and formation of a β-hairpin structure important for assembly of CA monomers into the mature capsid shell. A consensus binding site for the cellular Ubc9 protein was previously identified within this region, suggesting that binding of Ubc9 and subsequent small ubiquitin-like modifier protein 1 (SUMO-1) modification of CA may play a role either in regulating the assembly activity of CA in immature particles or mature cores or in controlling postentry function(s) during the establishment of infection. In the present study, mutations designed to eliminate the consensus binding site were used to dissect the potentially overlapping functions of these residues. The resulting replication defects could not be traced to a failure to form particles of normal composition but, rather, to a deficit in genome replication. Genetic suppressors of two detrimental β-hairpin mutations improved infectivity without restoring the consensus site or creating a novel one elsewhere. Optimal restoration of infectivity to a Lys-to-Arg mutant required a combination of secondary changes, one on the surface of each domain of CA. Rather than arguing for a critical role of Ubc9 and SUMO in RSV replication, these findings provide strong support for a structural role of the N-terminal residues and a particularly striking example of long-range interactions between regions of CA in achieving a functional core competent for genome replication.
Severe Acute Respiratory Syndrome Coronavirus Open Reading Frame (ORF) 3b, ORF 6, and Nucleocapsid Proteins Function as Interferon Antagonists
Authors: Kopecky-Bromberg Sarah A. , Martínez-Sobrido Luis , Frieman Matthew , Baric Ralph A. , Palese Peter
Published: November 2006

The severe acute respiratory syndrome coronavirus (SARS-CoV) is highly pathogenic in humans, with a death rate near 10%. This high pathogenicity suggests that SARS-CoV has developed mechanisms to overcome the host innate immune response. It has now been determined that SARS-CoV open reading frame (ORF) 3b, ORF 6, and N proteins antagonize interferon, a key component of the innate immune response. All three proteins inhibit the expression of beta interferon (IFN-β), and further examination revealed that these SARS-CoV proteins inhibit a key protein necessary for the expression of IFN-β, IRF-3. N protein dramatically inhibited expression from an NF-κB-responsive promoter. All three proteins were able to inhibit expression from an interferon-stimulated response element (ISRE) promoter after infection with Sendai virus, while only ORF 3b and ORF 6 proteins were able to inhibit expression from the ISRE promoter after treatment with interferon. This indicates that N protein inhibits only the synthesis of interferon, while ORF 3b and ORF 6 proteins inhibit both interferon synthesis and signaling. ORF 6 protein, but not ORF 3b or N protein, inhibited nuclear translocation but not phosphorylation of STAT1. Thus, it appears that these three interferon antagonists of SARS-CoV inhibit the interferon response by different mechanisms.
Synthesis and Structure Assignment of 2-(4-Methoxybenzyl)cyclohexyl β-D-Glucopyranoside Enantiomers
Authors: Šaman David , Kratina Pavel , Moravcová Jitka , Wimmerová Martina , Wimmer Zdeněk
Published: November 2006

Glucosylation of the cis- and trans-isomers of 2-(4-methoxybenzyl)cyclohexan-1-ol (1a/1b, 2a/2b, 1a or 2a) was performed to prepare the corresponding alkyl β-D-glucopyranosides, mainly to get analytical data of pure enantiomers of the glucosides (3a-6b), required for subsequent investigations of related compounds with biological activity. One of the employed modifications of the Koenigs-Knorr synthesis resulted in achieving 85-95% yields of pure β-anomers 3a/3b, 4a/4b, 3a or 4a of protected intermediates, with several promoters and toluene as solvent, yielding finally the deprotected products 5a/5b, 6a/6b, 5a or 6a as pure β-anomers. To obtain enantiomerically pure β-anomers of the target structure (3a, 4a, 5a and 6a) for unambiguous structure assignment, an enzymic reduction of 2-(4-methoxybenzyl)cyclohexan-1-one by Saccharomyces cerevisiae whole cells was performed to get (1S,2S)- and (1S,2R)-enantiomers (1a and 2a) of 2-(4-methoxybenzyl)cyclohexan-1-ol. The opposite enantiomers of alkyl β-D-glucopyranosides (5b and 6b) were obtained by separation of the diastereoisomeric mixtures 5a/5b and 6a/6b by chiral HPLC. All stereoisomers of the products (3a-6b) were subjected to a detailed 1H NMR and 13C NMR analysis.
Epoxide Migration and Pseudo-Epoxide Migration of 1,6:2,3- and 1,6:3,4-Dianhydro-β-D-hexopyranoses. Synthesis of Some Deoxy Halo Derivatives of 1,6-Anhydro-β-D-hexopyranoses
Authors: Džoganová Martina , Černý Miloslav , Buděšínský Miloš , Dračínský Martin , Trnka Tomáš
Published: November 2006

Epoxide or pseudo-epoxide migration of 1,6:2,3-dianhydro- and 1,6:3,4-dianhydro-β-D-hexopyranoses was effected by treatment with aqueous sodium hydroxide or sodium iodide in acetone to give equilibrium mixtures. Various iodo derivatives of 1,6-anhydro-β-D-hexopyranoses were prepared as potential intermediates for pseudo-epoxide migration. NMR was used for following the reaction mechanism of epoxide and pseudo-epoxide migrations and analysis of reaction mixtures. Experimental data were compared with DFT calculations. Chair-boat equilibration of 1,6-anhydro-3-deoxy-3-halo-β-D-glucopyranoses was discussed.
Molecular diversity and relationships amongElymus trachycaulus,E. subsecundus,E. virescens,E. violaceus, andE. hyperarcticus(Poaceae: Triticeae) as determined by amplified fragment length polymorphism
Authors: Sun Genlou , Shee Jennifer , Salomon Bjorn
Published: November 2006

Morphological similarity among E. trachycaulus, E. virescens, E. violaceus, and E. hyperarcticus has often been noted. Taxonomists have tried to discriminate among these taxa using morphological characters and a number of different relationships among them have been suggested. However, the genetic relationships among these taxa are still unknown. AFLP analysis was used to characterize the molecular diversity of these taxa and to examine genetic relationships among them. A high degree of genetic identity was apparent among 7 accessions of E. virescens. The similarity values ranged from 0.90 to 0.99 with an average of 0.94. The mean similarity values among 3 E. hyperarcticus and among 5 E. violaceus accessions were 0.84 (0.81–0.87) and 0.77 (0.66–0.90), respectively. The similarity values among 17 E. trachycaulus accessions ranged from 0.49 to 0.92 with an average of 0.75. The 5 accessions of E. subsecundus displayed high variation, with similarity values between 0.52 and 0.68 and a mean value of 0.59. Both maximum-parsimony (MP) and neighbor-joining (NJ) analyses showed that all 7 accessions of E. virescens formed a clade, indicating a monophyletic origin. On the other hand, Elymus trachycaulus, E. subsecundus, and E. violaceus were each paraphyletic and separated into different genetically distinct groups. Among these 5 taxa, E. virescens was genetically similar to E. trachycaulus, and E. violaceus was genetically similar to E. hyperarcticus.
The Sbm1 locus conferring resistance to Soil-borne cereal mosaic virus maps to a gene-rich region on 5DL in wheat
Authors: Bass C. , Hendley R. , Adams M.J. , Hammond-Kosack K.E. , Kanyuka K.
Published: November 2006

A mosaic disease caused by Soil-borne cereal mosaic virus (SBCMV) is becoming increasingly important, particularly in winter wheat in Europe. As there are currently no effective cultural practices or practical environmentally friendly chemicals for disease control, host plant resistance is an important objective in breeding programs. However, development of resistant cultivars is slow owing to difficulties in germplasm screening for resistance. Therefore, there is a need to identify molecular markers linked to SBCMV-resistance gene(s), so that quick and accurate laboratory-based marker-assisted selection rather than prolonged field-based screens for resistance can be used in developing resistant cultivars. We previously demonstrated that resistance to SBCMV in Triticum aestivum ‘Cadenza’ is controlled by a single locus. In this work, we used AFLP and microsatellite technology to map this resistance locus, with the proposed name Sbm1, to the distal end of chromosome 5DL. Interestingly, several expressed disease-resistance gene analogues also map to this gene-rich region on 5DL. Closely linked (~17 cM interval) markers, BARC110 and WMC765, RRES01 and BARC144, that flank Sbm1 will be very useful in breeding for selection of germplasm carrying Sbm1.