bluuebunny/crossref_metadata_2025 huggingface dataset:
The Plasmodium circumsporozoite protein is proteolytically processed during cell invasion
Authors: Coppi Alida , Pinzon-Ortiz Consuelo , Hutter Christina , Sinnis Photini
Published: January 2005

The circumsporozoite protein (CSP) is the major surface protein of Plasmodium sporozoites, the infective stage of malaria. Although CSP has been extensively studied as a malaria vaccine candidate, little is known about its structure. Here, we show that CSP is proteolytically cleaved by a papain family cysteine protease of parasite origin. Our data suggest that the highly conserved region I, found just before the repeat region, contains the cleavage site. Cleavage occurs on the sporozoite surface when parasites contact target cells. Inhibitors of CSP processing inhibit cell invasion in vitro, and treatment of mice with E-64, a highly specific cysteine protease inhibitor, completely inhibits sporozoite infectivity in vivo.
NKT cells promote antibody-induced joint inflammation by suppressing transforming growth factor β1 production
Authors: Kim Hye Young , Kim Hyun Jung , Min Hye Sook , Kim Sanghee , Park Weon Seo , Park Seong Hoe , Chung Doo Hyun
Published: January 2005

Although NKT cells has been known to exert protective roles in the development of autoimmune diseases, the functional roles of NKT cells in the downstream events of antibody-induced joint inflammation remain unknown. Thus, we explored the functional roles of NKT cells in antibody-induced arthritis using the K/BxN serum transfer model. NKT cell–deficient mice were resistant to the development of arthritis, and wild-type mice administrated with α-galactosyl ceramide, a potent NKT cell activator, aggravated arthritis. In CD1d−/− mice, transforming growth factor (TGF)-β1 was found to be elevated in joint tissues, and the blockade of TGF-β1 using neutralizing monoclonal antibodies restored arthritis. The administration of recombinant TGF-β1 into C57BL/6 mice reduced joint inflammation. Moreover, the adoptive transfer of NKT cells into CD1d−/− mice restored arthritis and reduced TGF-β1 production. In vitro assay demonstrated that interleukin (IL)-4 and interferon (IFN)-γ were involved in suppressing TGF-β1 production in joint cells. The adoptive transfer of NKT cells from IL-4−/− or IFN-γ−/− mice did not reverse arthritis and TGF-β1 production in CD1d−/− mice. In conclusion, NKT cells producing IL-4 and IFN-γ play a role in immune complex–induced joint inflammation by regulating TGF-β1.
Toll-like receptor 9 mediates innate immune activation by the malaria pigment hemozoin
Authors: Coban Cevayir , Ishii Ken J. , Kawai Taro , Hemmi Hiroaki , Sato Shintaro , Uematsu Satoshi , Yamamoto Masahiro , Takeuchi Osamu , Itagaki Sawako , Kumar Nirbhay , Horii Toshihiro , Akira Shizuo
Published: January 2005

Malaria parasites within red blood cells digest host hemoglobin into a hydrophobic heme polymer, known as hemozoin (HZ), which is subsequently released into the blood stream and then captured by and concentrated in the reticulo-endothelial system. Accumulating evidence suggests that HZ is immunologically active, but the molecular mechanism(s) through which HZ modulates the innate immune system has not been elucidated. This work demonstrates that HZ purified from Plasmodium falciparum is a novel non-DNA ligand for Toll-like receptor (TLR)9. HZ activated innate immune responses in vivo and in vitro, resulting in the production of cytokines, chemokines, and up-regulation of costimulatory molecules. Such responses were severely impaired in TLR9−/− and myeloid differentiation factor 88 (MyD88)−/−, but not in TLR2, TLR4, TLR7, or Toll/interleukin 1 receptor domain–containing adaptor-inducing interferon β−/− mice. Synthetic HZ, which is free of the other contaminants, also activated innate immune responses in vivo in a TLR9-dependent manner. Chloroquine (CQ), an antimalarial drug, abrogated HZ-induced cytokine production. These data suggest that TLR9-mediated, MyD88-dependent, and CQ-sensitive innate immune activation by HZ may play an important role in malaria parasite–host interactions.
Ro/SSA autoantibodies directly bind cardiomyocytes, disturb calcium homeostasis, and mediate congenital heart block
Authors: Salomonsson Stina , Sonesson Sven-Erik , Ottosson Lars , Muhallab Saad , Olsson Tomas , Sunnerhagen Maria , Kuchroo Vijay K. , Thorén Peter , Herlenius Eric , Wahren-Herlenius Marie
Published: January 2005

Congenital heart block develops in fetuses after placental transfer of Ro/SSA autoantibodies from rheumatic mothers. The condition is often fatal and the majority of live-born children require a pacemaker at an early age. The specific antibody that induces the heart block and the mechanism by which it mediates the pathogenic effect have not been elucidated. In this study, we define the cellular mechanism leading to the disease and show that maternal autoantibodies directed to a specific epitope within the leucine zipper amino acid sequence 200–239 (p200) of the Ro52 protein correlate with prolongation of fetal atrioventricular (AV) time and heart block. This finding was further confirmed experimentally in that pups born to rats immunized with p200 peptide developed AV block. p200-specific autoantibodies cloned from patients bound cultured cardiomyocytes and severely affected Ca2+ oscillations, leading to accumulating levels and overload of intracellular Ca2+ levels with subsequent loss of contractility and ultimately apoptosis. These findings suggest that passive transfer of maternal p200 autoantibodies causes congenital heart block by dysregulating Ca2+ homeostasis and inducing death in affected cells.
Can genetically modified Escherichia coli with neutral buoyancy induced by gas vesicles be used as an alternative method to clinorotation for microgravity studies?
Authors: Benoit Michael , Klaus David
Published: January 2005

Space flight has been shown to affect various bacterial growth parameters. It is proposed that weightlessness allows the cells to remain evenly distributed, consequently altering the chemical makeup of their surrounding fluid, and hence indirectly affecting their physiological behaviour. In support of this argument, ground-based studies using clinostats to partially simulate the quiescent environment attained in microgravity have generally been successful in producing bacterial growth characteristics that mimic responses reported under actual space conditions. A novel approach for evaluating the effects of reduced cell sedimentation is presented here through use ofEscherichia colicultures genetically modified to be neutrally buoyant. Since clinorotation would not (or would only minimally) affect cell distribution of this already near-colloidal cell system, it was hypothesized that the effects on final population density would be eliminated relative to a static control. Gas-vesicle-producingE. colicultures were grown under clinostat and static conditions and the culture densities at 60 h were compared. As a control,E. colithat do not produce gas vesicles, but were otherwise identical to the experimental strain, were also grown under clinostat and static conditions. As hypothesized, no significant difference was observed in cell populations at 60 h between the clinorotated and static gas-vesicle-producingE. colicultures, while the cells that did not produce gas vesicles showed a mean increase in population density of 10·5 % (P=0·001). These results further suggest that the lack of cumulative cell sedimentation is the dominant effect of space flight on non-stirred,in vitroE. colicultures.
Generation and functional in vivo characterization of a lipid kinase defective phosphatidylinositol 3-kinase Vps34p of Candida albicans
Authors: Günther Juliane , Nguyen Monika , Härtl Albert , Künkel Waldemar , Zipfel Peter F. , Eck Raimund
Published: January 2005

The phosphatidylinositol (PI) 3-kinase Vps34p ofCandida albicanshas lipid kinase and autophosphorylation activity and is involved in virulence and vesicular protein transport. In order to characterize the roles of lipid kinase activity, a chimeric Vps34 protein was created which lacks lipid kinase but retains autophosphorylation activity. To this end, six amino acids within the putative lipid-binding site of Vps34p were replaced by the homologous region of the PI 3-kinase-likeC. albicansTor protein. The resulting chimeric Vps34T protein was recombinantly expressed inEscherichia coliand shown to lack lipid kinase activity. The corresponding chimericVPS34TORgene was inserted into the genome ofC. albicans, and this lipid-kinase-defective strain had a distinctive phenotype compared to those of the wild-type strain SC5314 and thevps34null mutant. The lipid-kinase-defective strain was non-virulent, and showed altered hyphal growth, reduced adherence, as well as defective vacuole morphology and endosomal vesicle transport. These results demonstrate an important role for the lipid kinase activity of Vps34p in virulence and vesicular protein transport. On the other hand, the lipid-kinase-defective strain and thevps34null mutant differ in their temperature- and osmotic-stress response. This indicates a possible role for activities different from the lipid kinase function of Vps34p.
Melanization of Penicillium marneffei in vitro and in vivo
Authors: Youngchim Sirida , Hay Roderick J. , Hamilton Andrew J.
Published: January 2005

Melanins are found universally in nature and are implicated in the pathogenesis of several important human fungal pathogens. This study investigated whether the conidia and the yeast cells of the thermally dimorphic fungal pathogenPenicillium marneffeiproduce melanin or melanin-like compoundsin vitroand during infection. Treatment of conidia with proteolytic enzymes, denaturant and concentrated hot acid yielded dark particles that were similar in size and shape to the conidia. A melanin-binding monoclonal antibody (mAb) labelled pigmented conidia, yeast cells and the isolated particles as determined by immunofluorescence microscopy. Electron spin resonance spectroscopy revealed that particles derived from pigmented conidia contained a stable free radical compound, consistent with their identification as melanins. Skin tissue from penicilliosis marneffei patients contained yeast cells that were labelled by melanin-binding mAb. Additionally, sera fromP. marneffei-infected mice developed a significant antibody response (both IgG and IgM) against melanin. Phenoloxidase activity capable of synthesizing melanin froml-DOPA was detected in cytoplasmic yeast cell extracts. These findings indicate thatP. marneffeiconidia and yeast cells can produce melanin or melanin-like compoundsin vitroand that the yeast cells can synthesize pigmentin vivo. Accordingly this pigment may play some role in the virulence ofP. marneffei.
The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei
Authors: Pakula Tiina M. , Salonen Katri , Uusitalo Jaana , Penttilä Merja
Published: January 2005

Trichoderma reeseiwas cultivated in chemostat cultures on lactose-containing medium. The cultures were characterized for growth, consumption of the carbon source and protein production. Secreted proteins were produced most efficiently at low specific growth rates, 0·022–0·033 h−1, the highest specific rate of total protein production being 4·1 mg g−1 h−1at the specific growth rate 0·031 h−1. At low specific growth rates, up to 29 % of the proteins produced were extracellular, in comparison to only 6–8 % at high specific growth rates, 0·045–0·066 h−1. To analyse protein synthesis and secretion in more detail, metabolic labelling of proteins was applied to analyse production of the major secreted protein, cellobiohydrolase I (CBHI, Cel7A). Intracellular and extracellular labelled CBHI was quantified and analysed for pI isoforms in two-dimensional gels, and the synthesis and secretion rates of the molecule were determined. Both the specific rates of CBHI synthesis and secretion were highest at low specific growth rates, the optimum being at 0·031 h−1. However, at low specific growth rates the secretion rate/synthesis rate ratio was significantly lower than that at high specific growth rates, indicating that at low growth rates the capacity of cells to transport the protein becomes limiting. In accordance with the high level of protein production and limitation in the secretory capacity, the transcript levels of the unfolded protein response (UPR) target genespdi1andbip1as well as the gene encoding the UPR transcription factorhac1were induced.
Type III secretion chaperones ShcS1 and ShcO1 from Pseudomonas syringae pv. tomato DC3000 bind more than one effector
Authors: Kabisch Ute , Landgraf Angelika , Krause Jana , Bonas Ulla , Boch Jens
Published: January 2005

The hrp-type III secretion (TTS) system is a key pathogenicity factor of the plant pathogen Pseudomonas syringae pv. tomato DC3000 that translocates effector proteins into the cytosol of the eukaryotic host cell. The translocation of a subset of effectors is dependent on specific chaperones. In this study an operon encoding a TTS chaperone (ShcS1) and the truncated effector HopS1′ was characterized. Yeast two-hybrid analysis and pull-down assays demonstrated that these proteins interact. Using protein fusions to AvrRpt2 it was shown that ShcS1 facilitates the translocation of HopS1′, suggesting that ShcS1 is a TTS chaperone for HopS1′ and that amino acids 1 to 118 of HopS1′ are required for translocation. P. syringae pv. tomato DC3000 carries two shcS1 homologues, shcO1 and shcS2, which are located in different operons, and both operons include additional putative effector genes. Transcomplementation experiments showed that ShcS1 and ShcO1, but not ShcS2, can facilitate the translocation of HopS1′ : : AvrRpt2. To characterize the specificities of the putative chaperones, yeast two-hybrid interaction studies were performed between the three chaperones and putative target effectors. These experiments showed that both ShcS1 and ShcO1 bind to two different effectors, HopS1′ and HopO1-1, that share only 16 % amino acid sequence identity. Using gel filtration it was shown that ShcS1 forms homodimers, and this was confirmed by yeast two-hybrid experiments. In addition, ShcS1 is also able to form heterodimers with ShcO1. These data demonstrate that ShcS1 and ShcO1 are exceptional class IA TTS chaperones because they can bind more than one target effector.
Gene expression diversity among Mycobacterium tuberculosis clinical isolates
Authors: Gao Qian , Kripke Katharine E. , Saldanha Alok J. , Yan Weihong , Holmes Susan , Small Peter M.
Published: January 2005

Intraspecies genetic diversity has been demonstrated to be important in the pathogenesis and epidemiology of several pathogens, such as HIV, influenza,HelicobacterandSalmonella. It is also important to consider strain-to-strain variation when identifying drug targets and vaccine antigens and developing tools for molecular diagnostics. Here, the authors present a description of the variability in gene expression patterns among ten clinical isolates ofMycobacterium tuberculosis, plus the laboratory strains H37Rv and H37Ra, growing in liquid culture. They identified 527 genes (15 % of those tested) that are variably expressed among the isolates studied. The remaining genes were divided into three categories based on their expression levels: unexpressed (38 %), low to undetectable expression (31 %) and consistently expressed (16 %). The expression categories were compared with functional categories and three biologically interesting gene lists: genes that are deleted among clinical isolates, T-cell antigens and essential genes. There were significant associations between expression variability and the classification of genes as T-cell antigens, involved in lipid metabolism, PE/PPE, insertion sequences and phages, and deleted among clinical isolates. This survey of mRNA expression among clinical isolates ofM. tuberculosisdemonstrates that genes with important functions can vary in their expression levels between strains grown under identical conditions.
A sulphite respiration system in the chemoheterotrophic human pathogen Campylobacter jejuni
Authors: Myers Jonathan D. , Kelly David J.
Published: January 2005

The ability to use sulphite as a respiratory electron donor is usually associated with free-living chemolithotrophic sulphur-oxidizing bacteria. However, this paper shows that the chemoheterotrophic human pathogen Campylobacter jejuni has the ability to respire sulphite, with oxygen uptake rates of 23±8 and 28±15 nmol O2 min−1 (mg cell protein)−1 after the addition of 0·5 mM sodium sulphite or metabisulphite, respectively, to intact cells. The C. jejuni NCTC 11168 Cj0004c and Cj0005c genes encode a monohaem cytochrome c and molybdopterin oxidoreductase, respectively, homologous to the sulphite : cytochrome c oxidoreductase (SOR) of Starkeya novella. Western blots of C. jejuni periplasm probed with a SorA antibody demonstrated cross-reaction of a 45 kDa band, consistent with the size of Cj0005. The Cj0004c gene was inactivated by insertion of a kanamycin-resistance cassette. The resulting mutant showed wild-type rates of formate-dependent respiration but was unable to respire with sulphite or metabisulphite as electron donors. 2-Heptyl-4-hydroxyquinoline-N-oxide (HQNO), a cytochrome bc
1 complex inhibitor, did not affect sulphite respiration at concentrations up to 25 μM, whereas formate respiration (which occurs partly via a bc
1 dependent route) was inhibited 50 %, thus suggesting that electrons from sulphite enter the respiratory chain after the bc
1 complex at the level of cytochrome c. Periplasmic extracts of wild-type C. jejuni 11168 showed a symmetrical absorption peak at 552 nm after the addition of sulphite, demonstrating the reduction of cytochrome c. No cytochrome c reduction was observed after addition of sulphite to periplasmic extracts of the Cj0004c mutant. A fractionation study confirmed that the majority of the SOR activity is located in the periplasm in C. jejuni, and this activity was partially purified by ion-exchange chromatography. The presence of a sulphite respiration system in C. jejuni is another example of the surprising diversity of the electron-transport chain in this small-genome pathogen. Sulphite respiration may be of importance for survival in environmental microaerobic niches and some foods, and may also provide a detoxification mechanism for this normally growth-inhibitory compound.
Evolution of the Beckwith-Wiedemann syndrome region in vertebrates
Authors: Paulsen Martina , Khare Tarang , Burgard Christopher , Tierling Sascha , Walter Jörn
Published: January 2005

In the animal kingdom, genomic imprinting appears to be restricted to mammals. It remains an open question how structural features for imprinting evolved in mammalian genomes. The clustering of genes around imprinting control centers (ICs) is regarded as a hallmark for the coordinated imprinted regulation. Hence imprinted clusters might be structurally distinct between mammals and nonimprinted vertebrates. To address this question we compared the organization of the Beckwith Wiedemann syndrome (BWS) gene cluster in mammals, chicken, Fugu (pufferfish), and zebrafish. Our analysis shows that gene synteny is apparently well conserved between mammals and birds, and is detectable but less pronounced in fish. Hence, clustering apparently evolved during vertebrate radiation and involved two major duplication events that took place before the separation of the fish and mammalian lineages. A cross-species analysis of imprinting center regions showed that some structural features can already be recognized in nonimprinted amniotes in one of the imprinting centers (IC2). In contrast, the imprinting center IC1 is absent in chicken. This suggests a progressive and stepwise evolution of imprinting control elements. In line with that, imprinting centers in mammals apparently exhibit a high degree of structural and sequence variation despite conserved epigenetic marking.
Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional “strand-switch” domain as a major feature
Authors: Obado Samson O. , Taylor Martin C. , Wilkinson Shane R. , Bromley Elizabeth V. , Kelly John M.
Published: January 2005

Trypanosomatids are an ancient family that diverged from the main eukaryotic lineage early in evolution, which display several unique features of gene organization and expression. Although genome sequencing is now complete, the nature of centromeres in these and other parasitic protozoa has not been resolved. Here, we report the functional mapping of a centromere in the American trypanosome, Trypanosoma cruzi, a parasite with an unusual mechanism of genetic exchange that involves the generation of aneuploidy by nuclear hybridization. Using a telomere-associated chromosome fragmentation approach, we show that the region required for the mitotic stability of chromosome 3 encompasses a transcriptional “strand-switch” domain constituted by a 16-kb GC-rich island. The domain contains several degenerate retrotransposon-like insertions, but atypically, lacks the arrays of satellite repeats normally associated with centromeric regions. This unusual type of organization may represent a paradigm for centromeres in T. cruzi and other primitive eukaryotes.
High-throughput functional screen of mouse gastrula cDNA libraries reveals new components of endoderm and mesoderm specification
Authors: Chiao Eric , Leonard Jeff , Dickinson Kari , Baker Julie C.
Published: January 2005

This study describes a cross-species functional screen of mouse gastrula cDNA libraries for components of endoderm and mesoderm specification. Pools of 96 cDNAs from arrayed mouse gastrula cDNA libraries were transcribed into mRNA and injected into either the presumptive mesoderm or the ectoderm of one-cell Xenopus laevis embryos. Injected embryos were examined at gastrula stage by in situ hybridization with endoderm or mesoderm markers. Using this approach, we screened over 700 pools or ∼60,000 cDNAs. We identified 17 unique cDNAs that function during mesoderm and/or endoderm specification and 16 that cause general morphology changes. Identified molecules fall into eight general functional groups as follows: cell cycle components (seven), transcription factors (four), extracellular secreted molecules (seven), transmembrane receptors (one), intracellular signaling components (five), microtubule components (two), metabolism molecules (three), and unknown (four). Several of the genes we identified would not have been predicted to be involved in endoderm or mesoderm specification, highlighting the usefulness of nonbiased screening approaches. This includes Otx2, which we show is a downstream target of Xsox17β. The speed, low cost, and high efficiency of this cross-species screen makes it an ideal method for examining cDNAs from difficult-to-obtain sources. Therefore, this approach complements the current mouse molecular genetics systems and provides a powerful means for the genome-wide examination of mammalian gene function.
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
Authors: Bourque Guillaume , Zdobnov Evgeny M. , Bork Peer , Pevzner Pavel A. , Tesler Glenn
Published: January 2005

Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome sequencing provides an unprecedented level of detailed sequence data to infer genome rearrangements through comparative approaches. The comparative analysis of recently sequenced rodent genomes with the human genome revealed evidence for a larger number of rearrangements than previously thought and led to the reconstruction of the putative genomic architecture of the murid rodent ancestor, while the architecture of the ancestral mammalian genome and the rate of rearrangements in the human lineage remained unknown. Sequencing the chicken genome provides an opportunity to reconstruct the architecture of the ancestral mammalian genome by using chicken as an outgroup. Our analysis reveals a very low rate of rearrangements and, in particular, interchromosomal rearrangements in chicken, in the early mammalian ancestor, or in both. The suggested number of interchromosomal rearrangements between the mammalian ancestor and chicken, during an estimated 500 million years of evolution, only slightly exceeds the number of interchromosomal rearrangements that happened in the mouse lineage, over the course of about 87 million years.
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Authors: Ovcharenko Ivan , Loots Gabriela G. , Giardine Belinda M. , Hou Minmei , Ma Jian , Hardison Ross C. , Stubbs Lisa , Miller Webb
Published: January 2005

Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short- and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multispecies comparisons of the GATA3 gene locus and the identification of elements that are conserved in a different way in avians than in other genomes, allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://www.bx.psu.edu/miller_lab/.
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
Authors: Hubbard Simon J. , Grafham Darren V. , Beattie Kevin J. , Overton Ian M. , McLaren Stuart R. , Croning Michael D.R. , Boardman Paul E. , Bonfield James K. , Burnside Joan , Davies Robert M. , Farrell Elizabeth R. , Francis Matthew D. , Griffiths-Jones Sam , Humphray Sean J. , Hyland Christopher , Scott Carol E. , Tang Haizhou , Taylor Ruth G. , Tickle Cheryll , Brown William R.A. , Birney Ewan , Rogers Jane , Wilson Stuart A.
Published: January 2005

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.
Expression of late myogenic differentiation markers in sarcoplasmic masses of patients with myotonic dystrophy
Authors: Vattemi G. , Tomelleri G. , Filosto M. , Savio C. , Rizzuto N. , Tonin P.
Published: January 2005

Sarcoplasmic masses contain disorganized myofibrillar material and are a striking feature of myotonic dystrophy. However their significance is still unclear. Using immunocytochemistry we studied the expression of cytoskeletal proteins (desmin and vimentin), dystrophin, markers of myogenic differentiation (foetal myosin, neural cell adhesion molecule, bcl‐2, insulin‐like growth factor‐I, fibroblast growth factor, retinoblastoma protein and myoD1), cell cycle regulators (Cdk2, p16, p27 and p57) and muscle proteases (ubiquitin, µ and m calpain and cathepsin D) in muscle biopsies from four patients with myotonic dystrophy. Sarcoplasmic masses were strongly positive for desmin, neural cell adhesion molecule, bcl‐2, insulin‐like growth factor I, retinoblastoma protein and p57, weakly positive for dystrophin and p16 and negative for vimentin, fibroblast growth factor, myoD1, Cdk2 and p27. Immunoreactivity for foetal myosin was detected only in a few fibres (< 1%). Our data suggest that the late myogenic differentiation programme is activated in sarcoplasmic masses although these areas do not reach complete maturation.
Value creation and the UK economy: a review of strategic options
Authors: Edwards Tim , Battisti Giuliana , Neely Andy
Published: January 2005

In this review paper, we ask how UK business might realize improved productivity through value creation. Our aim is to evaluate the ability of UK firms to reduce the productivity gap by assessing the challenges associated with the following strategic options: (a) increasing efficiency and effectiveness through the adoption of better practices; (b) innovating to produce products or services that generate more revenue (through either higher prices or larger volumes) while remaining at the same position in the value chain; and (c) fundamentally changing position in the value or supply chain and moving to a position where the products and services that are delivered inherently generate more value. To this end, we contend that the core issues that affect such endeavours relate to the conceptualization and management of change and innovation. By considering the interconnections between firm‐level activities and wider institutional processes and structures, we assess the links between knowledge production, skills provision and productivity, including the role of the state and other institutions in the context of the micro‐processes of innovation. We conclude with a discussion of the research and policy implications of the attempt to make more sense of innovation and reduce the UK's productivity gap.
Social Comparison, Perceived Control, and Occupational Burnout
Authors: Michinov Nicolas
Published: January 2005

Deux études transversales ont porté sur 72 officiers des douanes (recherche no. 1) et sur cent officiers de police (recherche no. 2) dans le but d’approfondir la relation entre la direction de la comparaison sociale et des variables comme le burnout, des plaintes relatives à la santé ou la satisfaction liée au travail. La comparaison sociale a été mesurée par la fréquence avec laquelle les sujets disaient se comparer avec des salariés mieux et moins bien lotis sur plusieurs dimensions professionnelles. On a mené des analyses de corrélation plusieurs et de médiation pour mettre à l’épreuve deux hypothèses complémentaires. Premièrement, la comparaison ascendante était supposée être positivement liée au contrôle perçu et à la satisfaction professionnelle, et négativement aux ennuis de santé et au burnout. Deuxièmement, le contrôle perçu devait avoir un impact sur la relation entre la direction de la comparaison et des variables comme le burnout, les plaintes relatives à la santé ou la satisfaction liée au travail. Les résultats des deux études ont partiellement validé ces attentes et montré que seule la composante émotionnelle du burnout, l’épuisement émotionnel, était affectée par la direction de la comparaison sociale et médiatisée par le contrôle perçu.

Two cross‐sectional studies were conducted among 72 customs officers (Study 1) and 100 police officers (Study 2) to examine the relationship between the direction of social comparison and outcomes such as occupational burnout, health complaints, and job satisfaction. Social comparison was measured by the frequency at which participants reported that they compared themselves with better‐off and worse‐off employees on several work‐related dimensions. Correlation and mediation analyses were conducted to test two complementary hypotheses. Firstly, upward comparison was expected to be positively related to perceived control and job satisfaction, and negatively related to health complaints and occupational burnout. Secondly, perceived control was expected to mediate the relationship between comparison direction and psychological outcomes such as burnout, health complaints, and job satisfaction. The results of both studies partially supported these predictions and showed that only the emotional component of burnout—emotional exhaustion—was affected by social comparison direction and mediated by perceived control.
Even the ‘Rich’ are Vulnerable: Multiple Shocks and Downward Mobility in Rural Uganda
Authors: Bird Kate , Shinyekwa Isaac
Published: January 2005

Poverty data rarely capture processes of change, limiting our ability to understand poverty trajectories at the individual or household levels. This article uses a household survey, village‐level participatory studies and indepth life‐history interviews to examine people's poverty trajectories and to identify what drives and maintains chronic poverty. Composite shocks can propel previously non‐poor households into severe and long‐term poverty. Poverty is hard to escape, and people born into chronically poor households find few opportunities for accumulation and wealth creation. The analysis highlights the importance of poverty interrupters, including the end of conflict and the re‐integration of internally displaced people, and suggests that state‐led interventions would be needed to provide real opportunities to the chronically poor.
Ownership and Incentives in Joint Forest Management: A Survey
Authors: Castrén Tuukka
Published: January 2005

The relationship between the state and communities has been an overriding issue in the development of forestry institutions globally. In many countries, the trend is for communities to become co‐managers of public forests. Meanwhile, in development co‐operation both poverty and multiple rural livelihoods have received increased attention. In this article, the potential of joint community‐state management of forests is discussed. Forest production has several characteristics that make it suitable for joint management where both parties benefit. Involving communities in management decreases the state's monitoring costs, while communities benefit from better access to market information. For this to take place, however, the state forest apparatus needs to be free from undue rent‐seeking. The most advantageous solutions are case‐ and context‐specific.
Taxation, Reranking and Equivalence Scales
Authors: Van De Ven Justin , Creedy John
Published: January 2005

It is conjectured that if the government has a distributional objective and formulates tax policy with a view to equitable treatment of households, then adopting the scale that is implicit in transfer policy should identify only reranking that has no equity foundation. This motivates the question: can the reranking‐minimizing scales be identified as those implicit in the transfer system? The analysis presented in this study suggests that the equivalence scale which minimizes reranking, while not necessarily equal to the tax implicit equivalence scale, is nevertheless in its vicinity.
Business-to-Business Virtual Collaboration of Aircraft Engine Combustor Design
Authors: Kao , Kevin J. , Seeley , Charles E. , Yin , Su , Kolonay Raymond M. , Rus Tony , Paradis Mike
Published: January 2005

In today’s fast-changing economy, product designs are becoming increasingly complex while demands for faster design cycles never cease. Tighter collaboration among business partners and streamlined integration of engineering processes are becoming essential elements to succeeding in the competitive global environment. Modern computer-aided design/engineering solutions and revolutionary Internet technologies facilitate such real-time business-to-business (B2B) design collaboration. This paper discusses various emerging technologies that enable a true B2B virtual collaboration of an aircraft engine combustor design between GE Aircraft Engines, a jet engine manufacturer, and Parker Hannifin, a gas turbine fuel nozzle supplier. A case study involving the collaborative design and analysis of a fuel nozzle is also presented, which demonstrates the realistic implementation of these new technologies.
The Management of Product Data in an Integrated Aircraft Analysis Environment
Authors: Lockett Helen , Bartholomew Peter , Gallop Julian
Published: January 2005

Today’s industry spends billions of dollars each year on generating engineering data as part of the product development process. This data is stored in the diverse proprietary formats of software vendors. These change rapidly and, particularly in aerospace projects, the lifecycle of the applications software is so short that the data will be inaccessible over much of the life of the associated product. This paper describes the work conducted in an EU collaborative research program to develop a standards-based approach to managing product data. The project used the EXPRESS language, as defined by Part 11 of the ISO10303 STEP standard, for data modeling 1. A principal focus of the project was the capture and exchange of product and analysis data in a multi-disciplinary optimization environment. Two separate approaches were investigated—first using a specialized EXPRESS schema that was developed specifically to meet the project requirements and, second, a generic approach based upon the STEP PDM Schema.
Waypoint: An Integrated Search and Retrieval System for Engineering Documents
Authors: McMahon Chris , Lowe , Alistair , Culley Steve , Corderoy Mark , Crossland Rose , Shah Tulan , Stewart Dave
Published: January 2005

This paper describes the architecture and technical capabilities of an integrated engineering information search and retrieval system. The system is designed with a flexible architecture that allows it to be incorporated in other software systems and also to itself incorporate a variety of different software components. It provides uniform access to multiple heterogeneous information collections and an integrated access mechanism allowing both keyword searching and browsing of classification schemes interchangeably in a single information access session. Browsing using the system is based on a faceted classification approach in which continual feedback is given to the user on how the results of a search task may be refined, by updating browsable classifications to reflect previous user selections. The classification scheme is populated using an automatic constraint-based classifier. The article describes the rationale behind the choice of the system architecture and the incorporated technologies, and also describes three examples developed using the system.
A New ISO 10303 (STEP) Resource for Modeling Parameterization and Constraints
Authors: Pratt Michael J.
Published: January 2005

ISO 10303 (STEP) is a standard for the electronic exchange of product life-cycle data. It has been continually expanded by the addition of new capabilities since its first release by ISO in 1994. Until now, the standard has not been capable of exchanging models with parameterization and constraints such as those commonly generated by modern CAD systems. This makes it difficult to modify a model for any purpose following an exchange. However, new STEP resources have been developed to rectify this situation, and the paper reports on the the first of them to reach International Standard status. It provides the capability to associate explicitly represented parameterization and constraint information with CAD models. The primary application areas are in the 2D profiles or sketches that are inherent in many CAD model constructional procedures, in the positioning and orientation of features in 3D models and in the positioning and orientation of assembly components. Other complementary new STEP resources are briefly discussed at the end of the paper.
Ultrasound system to measure esophageal varix pressure: an in vitro validation study
Authors: Puckett James L. , Liu Jianmin , Bhalla Vikas , Kravetz David , Krinsky Mary Lee , Hassanein Tarek , Mittal Ravinder K.
Published: December 2004

We report our experience with an ultrasound system to measure esophageal varix pressure in an in vitro model. The ultrasound system consists of a 12.5 MHz frequency intraluminal ultrasound probe, a water infusion catheter, and a manometry catheter, all contained within a nondistensible latex bag. Esophagi and external jugular veins were harvested from five pigs. The vein and ultrasound system were placed inside the esophagus. One end of the vein was connected to a water reservoir to modulate its pressure; the other end was connected in two different ways to simulate hydrodynamic and hydrostatic flow conditions. The bag was inflated with water until vein occlusion was discernible on the ultrasound images. The influences of vein pressure, vein cross-sectional area and esophageal elasticity on the ultrasound measurement of vein pressure were assessed. A total of 108 trials were performed at nine different vein pressures. Complete vein occlusion occurred when the bag pressure was slightly greater (1.4 ± 0.7 mmHg) than the vein pressure. For a vein pressure of 25 mmHg, the average occlusion and opening pressures were 27 ± 0.2 and 25.7 ± 0.3 mmHg, respectively ( P < .05) suggesting that the vein opening pressure on the ultrasound images is more accurate than the vein closing pressure. In conclusion, the ultrasound technique can accurately measure intravariceal pressure in vitro. The bag pressure at the point of vein reopening is the best determinant of the vein pressure.
Decline in caveolin-1 expression and scaffolding of G protein receptor kinase-2 with age in Fischer 344 aortic vascular smooth muscle
Authors: Schutzer William E. , Reed John F. , Mader Scott L.
Published: December 2004

β-Adrenergic receptor (β-AR)-mediated vasorelaxation declines with age in humans and animal models. This is not caused by changes in expression of β-AR, Gαs, adenylyl cyclase, or protein kinase A but is associated with decreased cAMP production. Expression and activity of G protein receptor kinase-2 (GRK-2), which phosphorylates and desensitizes the β-AR, increases with age in rat aortic tissue. Caveolin scaffolds the β-AR, GRK, and other proteins within “signaling pockets” and inhibits GRK activity when bound. We questioned the effect of age on caveolin-1 expression and interaction between caveolin-1 and GRK-2 in vascular smooth muscle (VSM) isolated from 2-, 6-, 12-, and 24-mo-old male Fischer 344 rat aorta. Western blot analysis found expression of caveolin-1 declined with age (6-, 12- and 24-mo-old rat aortas express 92, 50, and 42% of 2-mo-old rat aortas, respectively). Results from density-buoyancy analysis showed a lower percentage of GRK in caveolin-1-specific fractions with age (6-, 12- and 24-mo-old rat aortas express 95, 56, and 12% of 2-mo-old rat aortas, respectively). Coimmunoprecipitation confirmed this finding; density of GRK in caveolin-1 immunoprecipitates was 97, 30, and 21% of 2-mo-old aortas compared with 6-, 12- and 24-mo-old animals, respectively. Immunohistocytochemistry and confocal microscopy confirmed that GRK-2 and caveolin-1 colocalize in VSM. These results suggest that in nonoverexpressed, intact tissue, the decline in β-AR-mediated vasorelaxation may be caused by both a reduction in caveolin-1 expression and a reduction in binding of GRK-2 by caveolin-1. This could lead to an increase in the fraction of free GRK-2, which could phosphorylate and desensitize the β-AR.
cDNA microarray analysis of endothelial cells subjected to cyclic mechanical strain: importance of motion control
Authors: Frye Stacie R. , Yee Andrew , Eskin Suzanne G. , Guerra Rudy , Cong Xiuyu , McIntire Larry V.
Published: January 2005

Microarrays were utilized to determine gene expression of vascular endothelial cells (ECs) subjected to mechanical stretch for insight into the role of strain in vascular pathophysiology. Over 4,000 genes were screened for expression changes resulting from cyclic strain (10%, 1 Hz) of human umbilical vein ECs for 6 and 24 h. Comparison of t-statistics and adjusted P values identified genes having significantly different expression between strained and static cells but not between strained and motion control. Relative to static, 6 h of cyclic stretch upregulated two genes and downregulated two genes, whereas 24 h of cyclic stretch upregulated eight genes but downregulated no genes. However, incorporating the motion control revealed that fluid agitation over the cells, rather than strain, is the primary regulator of differential expression. Furthermore, no gene exceeded a threefold change when comparing cyclic strain to either static or motion control. Quantitative real-time polymerase chain reaction confirmed the dominance of fluid agitation in gene regulation with the exception of heat shock protein 10 at 24 h and plasminogen activator inhibitor 1 at 6 h. Taken together, the small number of differentially expressed genes and their low fold expression levels indicate that cyclic strain is a weak inducer of gene regulation in ECs. However, many of the differentially expressed genes possess antioxidant properties, suggesting that oxidative mechanisms direct EC adaptation to cyclic stretch.
Complete and overlapping congenics proving the existence of a quantitative trait locus for blood pressure on Dahl rat chromosome 17
Authors: Grondin Myrian , Eliopoulos Vasiliki , Lambert Raphaelle , Deng Yishu , Ariyarajah Anita , Moujahidine Myriam , Dutil Julie , Charron Sophie , Deng Alan Y.
Published: January 2005

Linkage studies suggested that a quantitative trait locus (QTL) for blood pressure (BP) was present in a region on chromosome 17 (Chr 17) of Dahl salt-sensitive (DSS) rats. A subsequent congenic strain targeting this QTL, however, could not confirm it. These conflicting results called into question the validity of localization of a QTL by linkage followed by the use of a congenic strain made with an incomplete chromosome coverage. To resolve this issue, we constructed five new congenic strains, designated C17S.L1 to C17S.L5, that completely spanned the ±2 LOD confidence interval supposedly containing the QTL. Each congenic strain was made by replacing a segment of the DSS rat by that of the normotensive Lewis (LEW) rat. The only section to be LL homozygous is the region on Chr 17 specified in a congenic strain, as evidenced by a total genome scan. The results showed that BPs of C17S.L1 and C17S.L2 were lower ( P < 0.04) than that of DSS rats. In contrast, BPs of C17S.L3, C17S.L4, and C17S.L5 were not different ( P > 0.6) from that of DSS rats. Consequently, a BP QTL must be located in an interval of ∼15 cM shared between C17S.L1 and C17S.L2 and unique to them both, as opposed to C17S.L3, C17S.L4, and C17S.L5. The present study illustrates the importance of thorough chromosome coverage, the necessity for a genome-wide screening, and the use of “negative” controls in physically mapping a QTL by congenic strains.