bluuebunny/crossref_metadata_2025 huggingface dataset:
Epitaxial growth of ferromagnetic La2NiMnO6 with ordered double-perovskite structure
Authors: Hashisaka M. , Kan D. , Masuno A. , Takano M. , Shimakawa Y. , Terashima T. , Mibu K.
Published: July 2006

Epitaxial thin films of ordered double-perovskite La2NiMnO6 were deposited on SrTiO3, (LaAlO3)0.3–(Sr2AlTaO6)0.7, and LaAlO3 substrates by a pulsed-laser deposition method. A rock-salt-type ordering for Ni2+ and Mn4+ ions was confirmed through structural and magnetic measurements. Despite the difference in heteroepitaxial constraints on the crystal structure, the magnetic properties of the films were quite similar to each other and also to those of bulk La2NiMnO6.
Femtosecond pulses chirping compensation by using one-dimensional compact multiple-defect photonic crystals
Authors: Belardini A. , Bosco A. , Leahu G. , Centini M. , Fazio E. , Sibilia C. , Bertolotti M. , Zhukovsky S. , Gaponenko S. V.
Published: July 2006

Transmission properties of ultrashort pulses propagating through one-dimensional photonic crystals with multiple defects (cavities) were experimentally investigated. Coupling between multiple cavities is responsible for a wide resonance inside the photonic crystal gap suitable to distortion free propagation of 70fs pulses at 800nm. Geometry-induced anomalous dispersion across the resonance allows a compensation of 15% chirp preinduced on Fourier transform limited 70fs pulses.
Bidirectional thermal expansion measurement for evaluating Poisson’s ratio of thin films
Authors: Ye Jiping , Shimizu Satoshi , Sato Shigeo , Kojima Nobuo , Noro Junnji
Published: July 2006

An original and practical method is demonstrated for determining Poisson’s ratio of thin films by detecting thermal expansion in two directions perpendicular to each other. In the direction within the film, the temperature gradient of the biaxial thermal stress Δσf∕ΔT was obtained by substrate curvature measurements; in the direction perpendicular to the film, the temperature gradient of the whole thermal expansion strain Δd∕dΔT along the film thickness d was measured by x-ray reflectivity. It was found that Poisson’s ratio of thin films with a thickness of several hundred nanometers can be determined from Δσf∕ΔT, Δd∕dΔT, reduced modulus Er of the film, and from the thermal expansion coefficient αs of the substrate.
Rethinking the Port
Authors: Olivier Daniel , Slack Brian
Published: July 2006

Structural change in container port operation and ownership over the past decade has seen the emergence of port-operating transnational corporations (TNCs). The emergence of the port-operating TNC requires a fundamental epistemological shift in reconceptualising the port, from a single, fixed, spatial entity to a network of terminals operating under a corporate logic. This shift is twofold. First, because under port reforms corporate entry occurs overwhelmingly at the terminal level, the terminal rather than the port becomes the relevant spatial unit of analysis. Second, although spatial theories of the firm represent a longstanding stream in economic geography, such theories have yet to find general application in port studies. Consequently, in addressing the interface between transport and economic geographies, the authors suggest a geography of the port-operating TNC as a potential bridge. A decade of privatization in the port sector has rendered the industry an appropriate empirical ground for enquiry into spatial theories of the firm. Evidence from Asian port systems and business networks are put forward in sketching a new research agenda.
Local Embeddedness and Rural Entrepreneurship: Case-Study Evidence from Cumbria, England
Authors: Kalantaridis Christos , Bika Zografia
Published: July 2006

There is a growing realisation among scholars and policymakers of the role of local contextual factors and circumstances in influencing the behaviour of key economic agents, including the entrepreneur. This approach has stretched the boundaries of academic inquiry well beyond mainstream conceptualisations of economic agency as isolated from its setting. An assumption that underpinned research and policymaking in the new learning is that economic activity is typically socially embedded, which is generally taken to imply local embeddedness. In our paper, drawing upon the findings of extensive research in rural Cumbria, we question this assumption. We argue that in the context of rural Cumbria, the conceptualisation of locality may go beyond territorial notions. This argument does not support a return to the notion of the isolated economic agent, but advocates a move forward to the detailed exploration of the interface between agency and context.
Alteration of the brood pouch morphology during gestation of male seahorses, Hippocampus kuda
Authors: Laksanawimol Parichart , Damrongphol Praneet , Kruatrachue Maleeya
Published: July 2006

The brood pouch of seahorses can be divided into four sequential stages based on the characteristics of the altered tissue layers during gestation: the normal stage, the embryo-carrying stage, the embryo-release stage and the repair stage. The brood pouch is composed of a folded inner pseudostratified columnar epithelium and a smooth outer stratified cuboidal epithelium. Three tissue layers between the inner and the outer epithelia are an inner loose connective tissue layer, a middle smooth muscle layer and an outer dense irregular connective tissue layer. In the normal stage, the inner loose connective tissue layer is thick and vascularised with small blood vessels; the muscle layer consists of scattered unorganised muscle fibres. In the embryo-carrying stage, the inner epithelial and inner loose connective tissue layers become distended and highly vascularised with enlarged blood vessels. In the embryo-release stage, the inner loose connective tissue layer is extensively vascularised with very large blood vessels and the smooth muscle fibres invade the outer dense irregular connective tissue layer. Structures altered during gestation gradually resume their normal condition in the repair stage. Extensive vascularisation of the brood pouch during gestation suggests an intricate paternal–embryo relationship implying other significant roles besides protective function of the pouch.
Decomposition of leaves in coastal brackish water and their use by the macroinvertebrate Anisogammarus pugettensis (Gammaridea)
Authors: Kochi Kaori , Yanai Seiji
Published: July 2006

The brackish waters along the Hokkaido coast contain a mixture of plant material of both marine and terrestrial origin that provide food and habitat sources for many macroinvertebrates. Field and laboratory experiments were used to investigate the amount of breakdown of seaweed (kelp) and terrestrial oak leaves (green, senescent, and stream-water soaked (‘conditioned’)). In addition, the consumption and growth rates of Anisogammarus pugettensis were compared for the different leaf treatments. The breakdown of kelp was greater than that of terrestrial leaves. Among the three types of oak leaves, the amount of breakdown of green leaves was smallest and the breakdown of conditioned senescent oak leaves was 1.5 times greater than that of senescent leaves. Conditioning of leaves in fresh water enhances leaf decomposition in brackish water. The growth rates of A. pugettensis were similar and fastest when fed seaweed and a seaweed–leaf mixture (0.035 ± 0.009 and 0.043 ± 0.013 mg mg–1 day–1, respectively). The rapid colonisation of oak, despite its low nutritional value, suggests that leaves are important as a habitat, rather than as a food resource. Availability of both seaweed and terrestrial leaves as food resources and habitat would yield benefits for seawater-inhabiting macroinvertebrates.
Vital demographic statistics and management of the baldchin groper (Choerodon rubescens) from the Houtman Abrolhos Islands
Authors: Nardi Kim , Newman Stephen J. , Moran Michael J. , Jones Geoffrey P.
Published: July 2006

In order to evaluate appropriate management strategies, the life history and demography of the baldchin groper (Choerodon rubescens) was examined from speared samples and commercial catches at the Houtman Abrolhos Islands, Western Australia. Ages were estimated from sections of sagittal otoliths, validated by oxytetracycline labelling of fish recaptured after a minimum of 12 months at liberty. Male C. rubescens (n = 147; 373–639 mm) ranged from ages 5 to 20 years, and females (n = 354; 226–610 mm) ranged from 2 to 13 years. The population underwent a transition in dominance from females to males at age 11–12 years and 500–550 mm total length. Gonad development was seasonal and spawning was evident from spring to summer (September–January), with evidence of aggregation behaviour. Indirect estimates of the annual instantaneous rate of natural mortality (M) ranged from 0.05 to 0.58 and total mortality (Z), ranged from 0.21 to 0.56, rendering stock assessment highly uncertain. The limited geographic range, slow growth, long potential life span, protogynous sex change, aggregative spawning and high discard mortality rates render C. rubescens susceptible to overfishing. In order to manage this mobile species successfully, marine protected areas must continue to be supplemented by strict catch controls in fished areas.
Genes and pathways downstream of telomerase in melanoma metastasis
Authors: Bagheri Sepideh , Nosrati Mehdi , Li Shang , Fong Sylvia , Torabian Sima , Rangel Javier , Moore Dan H. , Federman Scot , LaPosa Rebecca R. , Baehner Frederick L. , Sagebiel Richard W. , Cleaver James E. , Haqq Christopher , Debs Robert J. , Blackburn Elizabeth H. , Kashani-Sabet Mohammed
Published: July 2006

Recent studies have demonstrated a role for telomerase in driving tumor progression, but its mechanism of action remains unclear. Here we show that stable, ribozyme-mediated suppression of mouse telomerase RNA reduced telomerase RNA expression, telomerase activity, and telomere length, which significantly reduced tumor invasion and metastatic potential. Our studies reveal that previously unidentified effects of telomerase may mediate its tumor-promoting effects. First, reducing telomerase activity induced a more dendritic morphology, accompanied by increased melanin content and increased expression of tyrosinase, a key enzyme in melanin biosynthesis. Second, gene expression profiling revealed that telomerase targeting down-regulated expression of several glycolytic pathway genes, with a corresponding decrease in glucose consumption and lactate production. Thus, telomerase activity controls the glycolytic pathway, potentially altering the energy state of tumor cells and thereby modulating tyrosinase activity and melanin production. These studies have important implications for understanding the mechanisms by which telomerase promotes tumor invasion and metastasis.
Shapes of embedded minimal surfaces
Authors: Colding Tobias H. , Minicozzi William P.
Published: July 2006

Surfaces that locally minimize area have been extensively used to model physical phenomena, including soap films, black holes, compound polymers, protein folding, etc. The mathematical field dates to the 1740s but has recently become an area of intense mathematical and scientific study, specifically in the areas of molecular engineering, materials science, and nanotechnology because of their many anticipated applications. In this work, we show that all minimal surfaces are built out of pieces of the surfaces in
Figs. 1
and
2
.
Analysis of a Picard modular group
Authors: Francsics Gábor , Lax Peter D.
Published: July 2006

Our main goal is to analyze the geometric and spectral properties of the Picard modular group with Gaussian integer entries acting on the two-dimensional complex hyperbolic space.
A global topology map of the
Saccharomyces cerevisiae
membrane proteome
Authors: Kim Hyun , Melén Karin , Österberg Marie , von Heijne Gunnar
Published: July 2006

The yeast
Saccharomyces cerevisiae
is, arguably, the best understood eukaryotic model organism, yet comparatively little is known about its membrane proteome. Here, we report the cloning and expression of 617
S. cerevisiae
membrane proteins as fusions to a C-terminal topology reporter and present experimentally constrained topology models for 546 proteins. By homology, the experimental topology information can be extended to ≈15,000 membrane proteins from 38 fully sequenced eukaryotic genomes.
A Trapped Intracellular Cation Modulates K+ Channel Recovery From Slow Inactivation
Authors: Ray Evan C. , Deutsch Carol
Published: July 2006

Upon depolarization, many voltage-gated potassium channels undergo a time-dependent decrease in conductance known as inactivation. Both entry of channels into an inactivated state and recovery from this state govern cellular excitability. In this study, we show that recovery from slow inactivation is regulated by intracellular permeant cations. When inactivated channels are hyperpolarized, closure of the activation gate traps a cation between the activation and inactivation gates. The identity of the trapped cation determines the rate of recovery, and the ability of cations to promote recovery follows the rank order K+ > NH4+ > Rb+ > Cs+ >> Na+, TMA. The striking similarity between this rank order and that for single channel conductance suggests that these two processes share a common feature. We propose that the rate of recovery from slow inactivation is determined by the ability of entrapped cations to move into a binding site in the channel's selectivity filter, and refilling of this site is required for recovery.
Publisher and author partnerships: a changing landscape
Authors: Regazzi John J. , Caliguiri Nicole A.
Published: July 2006

This article discusses the changing relationships of authors and publishers, the current trends and challenges they face, and the direction of these relationships in the future. As the STM publishing industry finds itself in the midst of significant technological and economic changes, this article provides background to these changes and looks at the key elements, including open access business development, institutional repository trends, and emerging public financing policies in the future.
Book Reviews
Authors: Wilmot Charlotte , Oppenheim Charles , Robinson Lesley
Published: July 2006

Zuckerman: Scientist Extraordinary by Bernard Donovan BioScientifica, Bristol, 2005, 555pp. ISBN 1‐901978249 £24.95

Negotiating licences for digital resources by Fiona Durrant Facet Publishing, 2006, ISBN 1 85604 586 2

Metadata for Information Management and Retrieval By David Haynes Facet Publishing, 2004, ISBN 1 85604 4890
Publishing and electronic piracy
Authors: Taylor Alasdair
Published: July 2006

Electronic piracy is perceived as a growing threat to the publishing industry. This article looks at the technology of copyright infringement and the channels for distribution of infringing electronic copies. It considers the English legal framework for dealing with electronic piracy, and the practical steps that publishers can take to reduce the risks of piracy.
Oxford Scholarship Online
Authors: Goldsworthy Sophie
Published: July 2006

An account is given of Oxford Scholarship Online (OSO), a website containing a growing collection of new and backlist titles from Oxford University Press. The technical set‐up, the design of the site, and its business model are described. It is proposed as an important step towards solving the so‐called ‘monograph crisis’ and improving the availability of scholarship world‐wide.
Bordetella holmesii DNA is not detected in nasopharyngeal swabs from Finnish and Dutch patients with suspected pertussis
Authors: Antila Mia , He Qiushui , de Jong Caroline , Aarts Ingrid , Verbakel Harold , Bruisten Sylvia , Keller Suzanne , Haanperä Marjo , Mäkinen Johanna , Eerola Erkki , Viljanen Matti K. , Mertsola Jussi , van der Zee Anneke
Published: July 2006

Bordetella holmesii is a Gram-negative bacterium first identified in 1995. It can cause pertussis-like symptoms in humans. B. holmesii contains insertion sequences IS481 and IS1001, two frequently used targets in the PCR diagnosis of Bordetella pertussis and Bordetella parapertussis infections. To investigate the prevalence of B. holmesii in Finnish and Dutch patients with pertussis-like symptoms and whether B. holmesii has caused any false-positive results in diagnostic PCRs, B. holmesii-specific real-time PCRs were developed. The Finnish methods were conventional IS481 PCR and B. holmesii-specific real-time PCR (LightCycler, Roche) targeting the B. holmesii recA gene. The Dutch methods were IS481 and IS1001 PCRs with conventional or real-time formats and B. holmesii-specific real-time PCR targeting the homologue of IS1001. Of 11 319 nasopharyngeal swabs, 2804 were collected from Finnish patients from 2000 to 2003, and 8515 from Dutch patients from 1992 to 2003. B. holmesii DNA was not found in the samples analysed. The results suggest that B. holmesii is not among the causative agents of pertussis-like symptoms in Finnish and Dutch patients and thus does not in practice confound IS481 and IS1001 PCRs.
Molecular typing of enteroviruses associated with viral meningitis in Cyprus, 2000–2002
Authors: Richter Jan , Koptides Dana , Tryfonos Christina , Christodoulou Christina
Published: July 2006

Human enteroviruses are responsible for a wide spectrum of clinical diseases affecting many different organ systems. Although infection is usually asymptomatic, infections of the central nervous system manifested as meningitis or encephalitis can pose a serious public health problem, especially during outbreaks. In this study, samples from 218 patients diagnosed with enteroviral meningitis between January 2000 and December 2002 were analysed in order to assess the epidemiology of human enteroviruses as a cause of viral meningitis in Cyprus. A new typing strategy, based on partial sequencing of the 5′ non-coding region (5′NCR), prediction of type, and selection of type-specific primers for sensitive VP1 PCR amplification, was developed. As clustering in the 5′NCR was concordant with clustering in the VP1 region, quick and reliable typing by VP1 sequencing was achieved without virus isolation in cell culture. The most frequent enterovirus serotypes identified were Human echovirus 30 (55.5 %), Human echovirus 13 (15.1 %), Human echovirus 6 (13.8 %) and Human echovirus 9 (8.3 %). Human coxsackieviruses B2, B1 and B5, Human echovirus 4, Human enterovirus 71 and Human coxsackievirus A6 represented rather rare serotypes. This is the first molecular epidemiological study of enterovirus meningitis in Cyprus. Serotype distribution corresponded basically with observations in other European countries, suggesting the spread of enteroviruses by tourism.
Gene-expression profiles in gastric epithelial cells stimulated with spiral and coccoid Helicobacter pylori
Authors: Liu Zhi-Fang , Chen Chun-Yan , Tang Wei , Zhang Jian-Ye , Gong Yao-Qin , Jia Ji-Hui
Published: July 2006

Human gastric epithelial immortalized GES-1 cells were infected with spiral and coccoidHelicobacter pylori. Scanning electron microscopy was used to determine the ability of the two forms ofH. pylorito adhere to GES-1 cells. GES-1 cell apoptosis induced by coccoid and spiralH. pyloriwas analysed using flow cytometry. A cDNA microarray for 22 000 human genes was used to identify the gene-expression differences in GES-1 cells infected with the two forms ofH. pylori, and the gene expression identified by the cDNA microarray was confirmed by RT-PCR. Scanning electron microscope observation showed that both coccoid and spiral bacteria can adhere to GES-1 cells. After 4 h infection, apoptosis induction was 27.4 % for spiral-form infection and 10.2 % for coccoid-form infection. Of 268 differentially expressed genes identified by cDNA microarray, 166 showed higher expression with the spiralH. pyloriinfection than with the coccoidH. pyloriinfection. To the best of the authors' knowledge, this is the first report that GES-1 cells infected with spiralH. pylorihave higher expression of cxcl10, ccl11, ccl5, groα, TLR5, ATF3, fos, fosl2, gadd45a and myc. The cells infected with coccoidH. pylorihad higher expression of survivin. The global profile of gene expression in GES-1 cells infected with coccoid and spiralH. pyloriis described for the first time.
Superantigen gene profile, emm type and antibiotic resistance genes among group A streptococcal isolates from Barcelona, Spain
Authors: Rivera Alba , Rebollo Montserrat , Miró Elisenda , Mateo Míriam , Navarro Ferran , Gurguí Mercé , Mirelis Beatriz , Coll Pere
Published: July 2006

Group A streptococcus (GAS) has been described as an emerging cause of severe invasive infections. A retrospective hospital-based study was conducted, including GAS isolates causing invasive or non-invasive infections from January 1999 to June 2003 in Barcelona. Demographic and clinical information on the invasive cases was obtained from medical files. GAS isolates collected from 27 patients with invasive infections and 99 patients with non-invasive infections were characterized by emm type and subtype, superantigen (SAg) gene profile (speA–C, speF–J, speL, speM, ssa and smeZ), allelic variants of speA and smeZ genes, antibiotic susceptibility and genetic resistance determinants. The most prevalent emm type was emm1 (17.5 %), followed by emm3 (8.7 %), emm4 (8.7 %), emm12 (7.1 %) and emm28 (7.1 %). The smeZ allele and SAg gene profiles were closely associated with the emm type. The speA2, speA3 and speA4 alleles were found in emm1, emm3 and emm6 isolates, respectively. Overall, 27.8, 25.4 and 11.9 % of isolates were resistant to erythromycin, tetracycline or both agents, respectively. Reduced susceptibility to ciprofloxacin and levofloxacin (MIC 2–4 μg ml−1) was found in 3.2 % of isolates. mef(A)-positive emm types 4, 12 and 75, and erm(B)-positive emm types 11 and 25 were responsible for up to 80 % of the erythromycin-resistant isolates. No significant differences in emm-type distribution, SAg gene profile or resistance rates were found between invasive and non-invasive isolates. The SAg and antibiotic resistance genes appeared to be associated with the emm type and were independent of the disease type.
The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients
Authors: Bibiloni Rodrigo , Mangold Marco , Madsen Karen L. , Fedorak Richard N. , Tannock Gerald W.
Published: July 2006

The bacterial community (microbiota) that inhabits the gut of humans appears to be an important source of antigens that drive the chronic immunological processes characteristic of Crohn's disease (CD) and ulcerative colitis (UC). Most of the members of the microbiota have not yet been cultured, but nucleic-acid-based methods of detection and enumeration can provide information about the community. This investigation used these methods to obtain information about the bacteria associated with mucosal surfaces in the gut of 20 CD and 15 UC patients. Biopsies were collected from inflamed and non-inflamed sites in the intestines of newly diagnosed, untreated patients. Biopsies were also collected from several intestinal sites of 14 healthy subjects. The bacterial collections associated with the biopsies were analysed by generating PCR/denaturing gradient gel electrophoresis (DGGE) profiles, the preparation of 16S rRNA gene clone libraries, and qualitative PCR to detect specific groups of bacteria. The total numbers of bacteria associated with the biopsies were determined by real-time quantitative PCR. DGGE profiles generated from the terminal ileum and various colonic regions were characteristic of each individual but differed between subjects. DGGE profiles and 16S rRNA gene libraries showed that the bacteria associated with inflamed and non-inflamed tissues did not differ. UC patients had more bacteria associated with biopsies than did CD patients (P<0.01). Statistical analysis of the composition of 16S rRNA gene libraries showed that the bacterial collections in UC and CD patients differed (P<0.05). Unclassified members of the phylum Bacteroidetes were more prevalent in CD than in UC patients. Therefore, the types and numbers of bacteria associated with biopsy samples were distinctly different for UC and CD patients. The observations made in this study should permit targeting of specific bacteriological abnormalities in investigations of the pathogenesis of inflammatory bowel diseases and provide targets for medical interventions.
Increased prostanoid dependency of arterial relaxation in Chlamydia pneumoniae-infected mice
Authors: Törmäkangas Liisa , Ketonen Juha , Leinonen Maija , Saikku Pekka , Paakkari Ilari
Published: July 2006

Endothelial dysfunction plays an important role in the development of atherosclerosis. Previous studies have shown that inoculation withChlamydia pneumoniaecontributes to atherosclerotic development in rabbits and hypercholesterolaemic mice and causes endothelial dysfunction in apolipoprotein E-deficient mice. The effect of acuteC. pneumoniaeinfection on endothelial function in normocholesterolaemic C57BL/6J mice was studied by measuring the force of contraction of the descending aorta after noradrenaline stimulation and in response to methacholine-induced relaxation. In addition, the effects of the nitric oxide synthase inhibitorNω-nitro-l-arginine methyl ester (l-NAME) and the cyclooxygenase inhibitor diclofenac on relaxation were assessed. Pre-treatment of the aortas withl-NAME decreased the relaxation response in both the infected and uninfected groups and no significant difference was detected between these groups, whereas diclofenac significantly attenuated the relaxation response only in the infected animals. In conclusion, infection shifted the balance of endothelium-derived relaxing factors from nitric oxide towards vasorelaxing prostanoids in C57BL/6J mice.
Surveillance of invasive Streptococcus pneumoniae in Taiwan, 2002–2003
Authors: Chen Ying-Yan , Yao Shu-Man , Chou Chen-Ying , Chang Yi-Ching , Shen Pei-Wun , Huang Chung-Ter , Su Hsun-Pi , Li Shu-Ying
Published: July 2006

A total of 522 Streptococcus pneumoniae invasive isolates from diverse sources were collected from January 2002 to December 2003 in Taiwan in order to understand the serotype distribution of invasive isolates in Taiwan. The most frequently isolated serotypes of S. pneumoniae were types 14 (18.4 %), 23F (15.1 %), 3 (13.8 %), 19F (13.4 %), 6B (8.2 %), 9V (3.6 %) and 4 (2.5 %). The majority of cases were either under 5 years of age (24.1 %) or older than 65 years (36.6 %). Serotype distribution in adults aged over 14 years and children aged under 2 years was similar, except for that of type 3, which was more prevalent in adults. Penicillin-non-susceptible strains accounted for 67.7 % of all strains and were the predominant strains of serotypes 23F, 19F, 6B and 14. Most strains were susceptible to cephem drug, 85.7 % of isolates were susceptible to cefotaxime and 92.9 % were susceptible to ceftriaxone. A total of 72.6 % (379/522) of the isolates were resistant to at least two antibiotics. The 23-valent vaccine in the current commercial market would cover 87.2 % of the serotypes and 100 % of the penicillin-non-susceptible serotypes of S. pneumoniae in Taiwan. The coverage of 7- and 11-valent protein conjugate vaccines of the serotypes in children under 2 years of age would be 78.8 and 86.5 %, respectively. These results will help to assess the adequacy of the vaccine formulations marketed in Taiwan.
Pneumococci causing invasive disease in children prior to the introduction of pneumococcal conjugate vaccine in Scotland
Authors: Clarke Stuart C. , Jefferies Johanna M. C. , Smith Andrew J. , McMenamin Jim , Mitchell Timothy J. , Edwards Giles F. S.
Published: July 2006

This study aimed to determine the serotypes and sequence types (STs) of pneumococci causing paediatric invasive disease in Scotland prior to the introduction of pneumococcal conjugate vaccines (PCVs). All invasive pneumococci isolated between 2000 and 2004 from children aged less than 5 years in Scotland were used. The isolates were characterized by serotyping and multi-locus sequence typing. Two hundred and seventeen pneumococci were characterized into 22 different serogroups/types, the most common, in rank order, being 14, 19F, 6B, 18C, 23F, 9V, 4, 1, 19A and 6A. They were further genotyped into 77 different STs, the three most common being 9, 162 and 176. Common serotypes possessed multiple STs, but pneumococci of a particular clone were mostly associated with a particular serotype. The seven most common serotypes are included in the 7-valent polysaccharide conjugate vaccine (PCV7). Serotype coverage for PCV7 was 76.5 % in those aged less than 5 years but increased to 88.9 % for those aged 1 year. The introduction of PCV7 into the childhood immunization schedule would reduce the burden of pneumococcal disease in children, although continued surveillance of invasive pneumococcal disease will be required before, during and after the introduction of PCVs.
Control of pneumococcal disease in the United Kingdom – the start of a new era
Authors: Clarke Stuart C.
Published: July 2006

In 2000, a multi-valent pneumococcal conjugate vaccine, known as Prevnar, was licensed for use in infants and young children in the USA. The subsequent introduction of the vaccine into the childhood immunization schedule in that country led to a significant decrease in pneumococcal disease. The vaccine is effective against invasive and non-invasive pneumococcal infection, can be used in young children as well as adults and, like all conjugate vaccines, provides long-lasting immunity. Moreover, it reduces the incidence of antibiotic resistance because a number of resistant serotypes are targeted by the vaccine. Prevnar, also known as Prevenar, has since been licensed in numerous countries, including the UK. On 8 February 2006, the Departments of Health in England, Scotland and Wales announced the inclusion of Prevenar in the childhood immunization schedule. This announcement has important implications for pneumococcal infection, disease surveillance and immunization policy in the UK.
Endocarditis caused by Propionibacterium species: a report of three cases and a review of clinical features and diagnostic difficulties
Authors: Clayton James J. , Baig Wazir , Reynolds Gregory W. , Sandoe Jonathan A. T.
Published: July 2006

Propionibacteriumspecies are members of the normal flora of skin and the mouth but their pathogenic potential is often overlooked. Three fatal cases of endocarditis caused byPropionibacteriumspecies over an 8-year period are reported, and a review is presented of a further 33 cases from the world literature. In most cases, infection was protracted, with minimal signs in the early stages. Fourteen cases (42.4 %) involved native valves, 16 (48.5 %) involved prosthetic valves and three (9.1 %) were associated with other intracardiac prosthetic material. Intracardiac abscesses were commonly encountered, withPropionibacteriumendocarditis occurring in 28.6 % of native valve infections and 52.9 % of prosthetic valve infections. A very high proportion of all of the cases (70.6 %) required surgical intervention. Several factors appeared to delay institution of appropriate therapy and may have contributed to abscess formation, including an indolent clinical course, negative or delayed culture results, and the tendency to consider this organism as a blood-culture contaminant. The authors recommend careful clinical evaluation before disregarding a blood-culture isolate ofPropionibacteriumspp. as a skin contaminant, and consideration of this bacterium as a potential cause of apparently culture-negative endocarditis.
Central line-related bacteraemia due to Roseomonas mucosa in a neutropenic patient with acute myeloid leukaemia in Piraeus, Greece
Authors: Christakis G. B. , Perlorentzou S. , Alexaki P. , Megalakaki A. , Zarkadis I. K.
Published: July 2006

A case of central venous catheter-related bacteraemia due to Roseomonas mucosa in a neutropenic patient with acute myelogenous leukaemia is reported. The patient was successfully treated with amikacin and piperacillin-tazobactam. The clinical isolate was identified as R. mucosa by 16S rRNA gene sequencing.
Indole-3-acetic acid regulates the central metabolic pathways in Escherichia coli
Authors: Bianco C. , Imperlini E. , Calogero R. , Senatore B. , Pucci P. , Defez R.
Published: July 2006

The physiological changes induced by indoleacetic acid (IAA) treatment were investigated in the totally sequencedEscherichia coliK-12 MG1655. DNA macroarrays were used to measure the mRNA levels for all the 4290E. coliprotein-coding genes; 50 genes (1.1 %) exhibited significantly different expression profiles. In particular, genes involved in the tricarboxylic acid cycle, the glyoxylate shunt and amino acid biosynthesis (leucine, isoleucine, valine and proline) were up-regulated, whereas the fermentativeadhEgene was down-regulated. To confirm the indications obtained from the macroarray analysis the activity of 34 enzymes involved in central metabolism was measured; this showed an activation of the tricarboxylic acid cycle and the glyoxylate shunt. The malic enzyme, involved in the production of pyruvate, and pyruvate dehydrogenase, required for the channelling of pyruvate into acetyl-CoA, were also induced in IAA-treated cells. Moreover, it was shown that the enhanced production of acetyl-CoA and the decrease of NADH/NAD+ratio are connected with the molecular process of the IAA response. The results demonstrate that IAA treatment is a stimulus capable of inducing changes in gene expression, enzyme activity and metabolite level involved in central metabolic pathways inE. coli.
Global analysis of candidate genes important for fitness in a competitive biofilm using DNA-array-based transposon mapping
Authors: Junker Lauren M. , Peters Joseph E. , Hay Anthony G.
Published: July 2006

Escherichia coli strain PHL628 was subjected to saturating Tn5 transposon mutagenesis and then grown under competitive planktonic or biofilm conditions. The locations of transposon insertions from the remaining cells were then mapped on a gene array. The results from the array mapping indicated that 4.5 % of the E. coli genome was important under these conditions. Specifically, 114 genes were identified as important for the biofilm lifestyle, whereas 80 genes were important for the planktonic lifestyle. Four broad functional categories were identified as biofilm-important. These included genes encoding cell structures, small-molecule transport, energy metabolism and regulatory functions. For one of these genes, arcA, an insertion mutant was generated and its biofilm-related phenotype was examined. Results from both the transposon array and insertion mutagenesis indicated that arcA, which is known to be a negative response regulator of genes in aerobic pathways, was important for competitiveness in E. coli PHL628 biofilms. This work also demonstrated that ligation-mediated PCR, coupled with array-based transposon mapping, was an effective tool for identifying a large variety of candidate genes that are important for biofilm fitness.
Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from Sphingomonas sp. strain A4
Authors: Kouzuma Atsushi , Pinyakong Onruthai , Nojiri Hideaki , Omori Toshio , Yamane Hisakazu , Habe Hiroshi
Published: July 2006

Sphingomonas sp. strain A4 is capable of utilizing acenaphthene as its sole carbon and energy source. To isolate the genes responsible for acenaphthene degradation, transposon mutagenesis was performed on strain A4 and four mini-Tn5-inserted mutants lacking the ability to utilize acenaphthene were isolated. In three of the four mini-Tn5 inserted mutants, the mini-Tn5s were inserted into the same locus (within about 16 kb) as the arhA1A2 genes, which had previously been identified as the genes encoding the terminal oxygenase components for the initial oxygenation of acenaphthene. The nucleotide sequence analysis of the corresponding 16.4 kb DNA fragment revealed the existence of 16 ORFs and a partial ORF. From these ORFs, the genes encoding the ferredoxin (ArhA3) and ferredoxin reductase (ArhA4) complementary to ArhA1A2 were identified. RT-PCR analysis suggested that a 13.5 kb gene cluster, consisting of 13 ORFs and including all the arhA genes, forms an operon, although it includes several ORFs that are apparently unnecessary for acenaphthene degradation. Furthermore, using gene disruption and quantitative RT-PCR analyses, the LysR-type activator, ArhR, required for expression of the 13.5 kb gene cluster was also identified. Transcription of the gene cluster by ArhR was induced in the presence of acenaphthene (or its metabolite), and a putative binding site (T-N11-A motif) for ArhR was found upstream from the transcription start point of arhA3.
Effects of the type III secreted pseudomonal toxin ExoS in the yeast Saccharomyces cerevisiae
Authors: Stirling Fiona R. , Evans Tom J.
Published: July 2006

Pseudomonas aeruginosasecretes a number of toxins by a type III system, and these are important in virulence. One of them, ExoS, is a bifunctional toxin, with a GTPase-activating protein domain, as well as ADP ribosyltransferase (ADPRT) activity. These two domains have numerous potential cellular targets, but the overall mechanism of ExoS action remains unclear. The effects of ExoS in a simple eukaryotic system, the yeastSaccharomyces cerevisiae, using a tetracycline-regulated expression system were studied. This system allowed controlled expression of ExoS in yeast, which was not possible using a galactose-induced system. ExoS was found to be an extremely potent inhibitor of yeast growth, and to be largely dependent on the activity of its ADPRT domain. ExoS produced a dramatic alteration in actin distribution, with the appearance of large aggregates of cortical actin, and thickened disorganized cables, entirely dependent on the ADPRT domain. This phenotype is suggestive of actin stabilization, which was verified by showing that the cortical aggregates of actin induced by ExoS were resistant to treatment with latrunculin A, an agent that prevents actin polymerization. ExoS increased the numbers of mating projections produced following growth arrest with mating pheromone, and prevented subsequent DNA replication, an effect that is again dependent on the ADPRT domain. Following pheromone removal, ExoS produced altered development of the mating projections, which became elongated with a swollen bud-like tip. These results suggest alternative pathways for ExoS action in eukaryotic cells that may result from activation of small GTPases, and this yeast expression system is well suited to explore these pathways.
Reduction of 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt (XTT) is dependent on CaFRE10 ferric reductase for Candida albicans grown in unbuffered media
Authors: Knight Simon A. B. , Dancis Andrew
Published: July 2006

The reduction of 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt (XTT) and other tetrazolium salts is widely used as an assay for bacterial, fungal and mammalian cell viability, but the genes encoding the reductase activities have not been defined. Here, it was shown that XTT and plasma membrane ferric reductase activities were 10–40-fold greater inCandida albicansthan inSaccharomyces cerevisiae. XTT reductase activity was induced fivefold inC. albicansgrown in low-iron conditions compared with iron-replete conditions, and for cells grown in unbuffered (pH 4.0–4.4) medium, XTT reductase activity was largely dependent onCaFRE10. XTT reductase activity ofC. albicansgrown in medium buffered to pH 6.8 was independent ofCaFRE10but, nonetheless, was upregulated in cells deprived of iron. Reduction of 2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide (MTT), a membrane-permeable tetrazolium salt, occurred at an intracellular location and was independent ofCaFRE10. However, MTT activity was induced by iron deprivation inC. albicansbut not inS. cerevisiae.C. albicanspossessed multiple iron- and pH-regulated reductase activities capable of reducing tetrazolium salts, but, when grown in unbuffered medium,CaFRE10was required for XTT reductase activity.
Functional characterization of cell-wall-associated protein WapA in Streptococcus mutans
Authors: Zhu Lin , Kreth Jens , Cross Sarah E. , Gimzewski James K. , Shi Wenyuan , Qi Fengxia
Published: July 2006

Streptococcus mutansis known as a primary pathogen responsible for dental caries. One of the virulence factors ofS. mutansin cariogenicity is its ability to attach to the tooth surface and form a biofilm. Several surface proteins have been shown to be involved in this process. A 29 kDa surface protein named wall-associated protein A (WapA, antigen A or antigen III), was previously used as a vaccine in animal studies for immunization against dental caries. However, the function of WapA inS. mutansis still not clear. This study characterized the function of WapA in cell surface structure and biofilm formation. Compared to the wild-type, thewapAmutant had much-reduced cell chain length, diminished cell–cell aggregation, altered cell surface ultrastructure, and unstructured biofilm architecture. Furthermore,in vivoforce spectroscopy revealed that the cell surface of thewapAmutant was less sticky than that of the wild-type cells. More interestingly, these phenotypic differences diminished as sucrose concentration in the medium was increased to 0.5 %. Real-time RT-PCR analysis demonstrated that sucrose strongly repressedwapAgene expression in both planktonic and biofilm cells. These results suggest that the WapA protein plays an important structural role on the cell surface, which ultimately affects sucrose-independent cell–cell aggregation and biofilm architecture.
A connection between iron–sulfur cluster metabolism and the biosynthesis of 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate in Salmonella enterica
Authors: Dougherty Michael J. , Downs Diana M.
Published: July 2006

Several cellular pathways have been identified which affect the efficiency of thiamine biosynthesis inSalmonella enterica. Mutants defective in iron–sulfur (Fe–S) cluster metabolism are less efficient at synthesis of the pyrimidine moiety of thiamine. These mutants are compromised for the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P), not the synthesis of AIR. The gene product ThiC contains potential ligands for an Fe–S cluster that are required for functionin vivo. The conversion of AIR to HMP-P is sensitive to oxidative stress, and variants of ThiC have been identified that have increased sensitivity to oxidative growth conditions. The data are consistent with ThiC or an as-yet-unidentified protein involved in HMP-P synthesis containing an Fe–S cluster required for its physiological function.
Mutational analysis of Salmonella translocated effector members SifA and SopD2 reveals domains implicated in translocation, subcellular localization and function
Authors: Brown Nat F. , Szeto Jason , Jiang Xiuju , Coombes Brian K. , Finlay B. Brett , Brumell John H.
Published: July 2006

Salmonella enterica serovar Typhimurium is a facultative intracellular pathogen causing disease in several hosts. These bacteria use two distinct type III secretion systems that inject effector proteins into the host cell for invasion and to alter maturation of the Salmonella-containing vacuole. Members of the Salmonella translocated effector (STE) family contain a conserved N-terminal translocation signal of approximately 140 aa. In this study, the STE family member SifA was examined using deletion strategies. Small deletions (approx. 20 residues long) throughout SifA were sufficient to block its secretion and/or translocation into host cells. Transfection of HeLa cells with a GFP-SifA fusion was previously shown to be sufficient to induce formation of Sif-like tubules resembling structures present in Salmonella-infected cells. The present study showed that both N- and C-terminal domains of SifA are required for this phenotype. Furthermore, both domains could induce aggregation of Lamp1-positive compartments, provided they were coupled to the minimal C-terminal membrane-anchoring motif of SifA. Mutation or deletion of the conserved STE N-terminal WEK(I/M)xxFF translocation motif of SopD2 disrupted its association with Lamp1-positive compartments, implicating these residues in both effector translocation and subcellular localization. Interestingly, one GFP-SifA deletion mutant lacking residues 42–101, but retaining the WEK(I/M)xxFF motif, targeted the Golgi apparatus. In addition, short peptides containing the signature WEK(I/M)xxFF motif derived from the N-termini of Salmonella effectors SopD2, SseJ and SspH2 were sufficient to localize GFP to the Golgi. These studies suggest that Salmonella effectors contain multifunctional motifs or domains that regulate several effector traits, including protein secretion/translocation, localization and subversion of host cell systems. Conditions that perturb the tertiary structure of effectors can influence their localization in host cells by liberating cryptic intracellular targeting motifs.
Deinococcus radiodurans engineered for complete toluene degradation facilitates Cr(VI) reduction
Authors: Brim Hassan , Osborne Jeffrey P. , Kostandarithes Heather M. , Fredrickson James K. , Wackett Lawrence P. , Daly Michael J.
Published: July 2006

Toluene and other fuel hydrocarbons are commonly found in association with radionuclides at numerous US Department of Energy sites, frequently occurring together with Cr(VI) and other heavy metals. In this study, the extremely radiation-resistant bacteriumDeinococcus radiodurans, which naturally reduces Cr(VI) to the less mobile and less toxic Cr(III), was engineered for complete toluene degradation by cloned expression oftodandxylgenes ofPseudomonas putida. The recombinant Tod/Xyl strain showed incorporation of carbon from14C-labelled toluene into cellular macromolecules and carbon dioxide, in the absence or presence of chronic ionizing radiation. The engineered bacteria were able to oxidize toluene under both minimal and complex nutrient conditions, and recombinant cells reduced Cr(VI) in sediment microcosms. As such, the Tod/Xyl strain could provide a model for examining the reduction of metals coupled to organic contaminant oxidation in aerobic radionuclide-contaminated sediments.
Function of the MAPK scaffold protein, Ste5, requires a cryptic PH domain
Authors: Garrenton Lindsay S. , Young Susan L. , Thorner Jeremy
Published: July 2006

Ste5, the prototypic mitogen-activated protein kinase (MAPK) scaffold protein, associates with plasma membrane-tethered Gβγ freed upon pheromone receptor occupancy, thereby initiating downstream signaling. We demonstrate that this interaction and membrane binding of an N-terminal amphipathic α-helix (PM motif) are not sufficient for Ste5 action. Rather, Ste5 contains a pleckstrin-homology (PH) domain (residues 388–518) that is essential for its membrane recruitment and function. Altering residues (R407S K411S) equivalent to those that mediate phosphoinositide binding in other PH domains abolishes Ste5 function. The isolated PH domain, but not a R407S K411S derivative, binds phosphoinositides in vitro. Ste5(R407S K411S) is expressed normally, retains Gβγ and Ste11 binding, and oligomerizes, yet is not recruited to the membrane in response to pheromone. Artificial membrane tethering of Ste5(R407S K411S) restores signaling. R407S K411S loss-of-function mutations abrogate the constitutive activity of gain-of-function Ste5 alleles, including one (P44L) that increases membrane affinity of the PM motif. Thus, the PH domain is essential for stable membrane recruitment of Ste5, and this association is critical for initiation of downstream signaling because it allows Ste5-bound Ste11 (MAPKKK) to be activated by membrane-bound Ste20 (MAPKKKK).