bluuebunny/crossref_metadata_2025 huggingface dataset:
The Osmoregulatory and the Amino Acid-regulated Responses of System A Are Mediated by Different Signal Transduction Pathways
Authors: López-Fontanals Marta , Rodríguez-Mulero Silvia , Casado F. Javier , Dérijard Benoit , Pastor-Anglada Marçal
Published: June 2003

The osmotic response of system A for neutral amino acid transport has been related to the adaptive response of this transport system to amino acid starvation. In a previous study (Ruiz-Montasell, B., M. Gómez-Angelats, F.J. Casado, A. Felipe, J.D. McGivan, and M. Pastor-Anglada. 1994. Proc. Natl. Acad. Sci. USA. 91:9569–9573), a model was proposed in which both responses were mediated by different mechanisms. The recent cloning of several isoforms of system A as well as the elucidation of a variety of signal transduction pathways involved in stress responses allow to test this model. SAT2 mRNA levels increased after amino acid deprivation but not after hyperosmotic shock. Inhibition of p38 activity or transfection with a dominant negative p38 did not alter the response to amino acid starvation but partially blocked the hypertonicity response. Inhibition of the ERK pathway resulted in full inhibition of the adaptive response of system A and no increase in SAT2 mRNA levels, without modifying the response to hyperosmolarity. Similar results were obtained after transfection with a dominant negative JNK1. The CDK2 inhibitor peptide-II decreased the osmotic response in a dose-dependent manner but did not have any effect on the adaptive response of system A. In summary, the previously proposed model of up-regulation of system A after hypertonic shock or after amino acid starvation by separate mechanisms is now confirmed and the two signal transduction pathways have been identified. The involvement of a CDK–cyclin complex in the osmotic response of system A links the activity of this transporter to the increase in cell volume previous to the entry in a new cell division cycle.
Bimodal Action of Protons on ATP Currents of Rat PC12 Cells
Authors: Skorinkin Andrei , Nistri Andrea , Giniatullin Rashid
Published: June 2003

The mode of action of extracellular protons on ATP-gated P2X2 receptors remains controversial as either enhancement or depression of ATP-mediated currents has been reported. By investigating, at different pH, the electrophysiological effect of ATP on P2X2 receptors and complementing it with receptor modelling, the present study suggests a unified mechanism for both potentiation and inactivation of ATP receptors by protons. Our experiments on patch-clamped PC12 cells showed that, on the same cell, mild acidification potentiated currents induced by low ATP concentrations (<0.1 mM) and attenuated responses to high ATP concentrations (>1 mM) with emergence of current fading and rebound. To clarify the nature of the ATP/H+ interaction, we used the Ding and Sachs's “loop” receptor model which best describes the behavior of such receptors with two open states linked via one inactivated state. No effects by protons could be ascribed to H+-mediated open channel block. However, by assuming that protons facilitated binding of ATP to resting as well as open receptors, the model could closely replicate H+-induced potentiation of currents evoked by low ATP doses plus fading and rebound induced by high ATP doses. The latter phenomenon was due to receptor transition to the inactive state. The present data suggest that the high concentration of protons released with ATP (and catecholamines) from secretory vesicles may allow a dual action of H+ on P2X2 receptors. This condition might also occur on P2X2 receptors of central neurons exposed to low pH during ischemia.
Volumes of hyperbolic 3-manifolds. Notes on a paper of Gabai, Meyerhoff, and Milley
Authors: Marshall T. , Martin G.
Published: June 2003

We present a new approach and improvements to the recent results of Gabai, Meyerhoff and Milley concerning tubes and short geodesics in hyperbolic

3
3

-manifolds. We establish the following two facts: if a hyperbolic

3
3

-manifold admits an embedded tubular neighbourhood of radius

r
0

>
1.32

r_0>1.32

about any closed geodesic, then its volume exceeds that of the Weeks manifold. If the shortest geodesic of

M
M

has length less than

ℓ
0

>
0.1

\ell _0>0.1

, then its volume also exceeds that of the Weeks manifold.
Activity and Distribution of Paxillin, Focal Adhesion Kinase, and Cadherin Indicate Cooperative Roles during Zebrafish Morphogenesis
Authors: Crawford Bryan D. , Henry Clarissa A. , Clason Todd A. , Becker Amanda L. , Hille Merrill B.
Published: June 2003

We investigated the focal adhesion proteins paxillin and Fak, and the cell-cell adhesion protein cadherin in developing zebrafish (Danio rerio) embryos. Cadherins are expressed in presomitic mesoderm where they delineate cells. The initiation of somite formation coincides with an increase in the phosphorylation of Fak, and the accumulation of Fak, phosphorylated Fak, paxillin, and fibronectin at nascent somite boundaries. In the notochord, cadherins are expressed on cells during intercalation, and phosphorylated Fak accumulates in circumferential rings where the notochord cells contact laminin in the perichordal sheath. Subsequently, changes in the orientations of collagen fibers in the sheath suggest that Fak-mediated adhesion allows longitudinal expansion of the notochord, but not lateral expansion, resulting in notochord elongation. Novel observations showed that focal adhesion kinase and paxillin concentrate at sites of cell-cell adhesion in the epithelial enveloping layer and may associate with actin cytoskeleton at epithelial junctions containing cadherins. Fak is phosphorylated at these epithelial junctions but is not phosphorylated on Tyr397, implicating a noncanonical mechanism of regulation. These data suggest that Fak and paxillin may function in the integration of cadherin-based and integrin-based cell adhesion during the morphogenesis of the early zebrafish embryo.
A Novel Variant of Cardiac Myosin-binding Protein-C That Is Unable to Assemble into Sarcomeres Is Expressed in the Aged Mouse Atrium
Authors: Sato Naruki , Kawakami Tsutomu , Nakayama Ayako , Suzuki Hiroyuki , Kasahara Hideko , Obinata Takashi
Published: June 2003

Cardiac myosin-binding protein-C (MyBP-C), also known as C-protein, is one of the major myosin-binding proteins localizing at A-bands. MyBP-C has three isoforms encoded by three distinct genes: fast-skeletal, slow-skeletal, and cardiac type. Herein, we are reporting a novel alternative spliced form of cardiac MyBP-C, MyBP-C(+), which includes an extra 30 nucleotides, encoding 10 amino acids in the carboxyl-terminal connectin/titin binding region. This alternative spliced form of MyBP-C(+) has a markedly decreased binding affinity to myosin filaments and connectin/titin in vitro and does not localize to A-bands in cardiac myocytes. When MyBP-C(+) was expressed in chicken cardiac myocytes, sarcomere structure was markedly disorganized, suggesting it has possible dominant negative effects on sarcomere organization. Expression of MyBP-C(+) is hardly detected in ventricles through cardiac development, but its expression gradually increases in atria and becomes the dominant form after 6 mo of age. The present study demonstrates an age-induced new isoform of cardiac MyBP-C harboring possible dominant negative effects on sarcomere assembly.
CD1 and Major Histocompatibility Complex II Molecules Follow a Different Course during Dendritic Cell Maturation
Authors: van der Wel Nicole N. , Sugita Masahiko , Fluitsma Donna M. , Cao Xaiochun , Schreibelt Gerty , Brenner Michael B. , Peters Peter J.
Published: June 2003

The maturation of dendritic cells is accompanied by the redistribution of major histocompatibility complex (MHC) class II molecules from the lysosomal MHC class II compartment to the plasma membrane to mediate presentation of peptide antigens. Besides MHC molecules, dendritic cells also express CD1 molecules that mediate presentation of lipid antigens. Herein, we show that in human monocyte-derived dendritic cells, unlike MHC class II, the steady-state distribution of lysosomal CD1b and CD1c isoforms was unperturbed in response to lipopolysaccharide-induced maturation. However, the lysosomes in these cells underwent a dramatic reorganization into electron dense tubules with altered lysosomal protein composition. These structures matured into novel and morphologically unique compartments, here termed mature dendritic cell lysosomes (MDL). Furthermore, we show that upon activation mature dendritic cells do not lose their ability of efficient clathrin-mediated endocytosis as demonstrated for CD1b and transferrin receptor molecules. Thus, the constitutive endocytosis of CD1b molecules and the differential sorting of MHC class II from lysosomes separate peptide- and lipid antigen-presenting molecules during dendritic cell maturation.
The β1 Cytoplasmic Domain Regulates the Laminin-binding Specificity of the α7X1 Integrin
Authors: Yeh Ming-Guang , Ziober Barry L. , Liu Baomei , Lipkina Galina , Vizirianakis Ioannis S. , Kramer Randall H.
Published: June 2003

During muscle development, the laminin-specific α7 integrin is alternatively spliced in the putative ligand-binding domain to yield either the α7X1 or the α7X2 variant. The relative level of α7X1 and α7X2 is developmentally regulated. Similarly, the partner β1 integrin cytoplasmic domain is converted from the β1A to the β1D splice variant. To determine whether β1D modulates the activity of the α7 receptor, cells were transfected with α7X1 and β1D cDNA. α7X1 coupled with β1A failed to adhere to laminin-1, whereas cotransfectants expressing α7X1 and β1D showed strong adhesion. Interestingly, α7X1 complexed with β1A and β1D displayed the same level of poor adhesion to laminin-2/4 or strong adhesion to laminin-10/11. These findings indicate that α7 function is regulated not only by X1/X2 in its extracellular domain but also by β1 cytoplasmic splice variants. It is likely that expression of β1D alters α7X1 binding to laminin isoforms by a process related to ligand affinity modulation. Functional regulation of α7β1 by developmentally regulated splicing events may be important during myogenic differentiation and repair because the integrin mediates adhesion, motility, and cell survival.
Histone Hyperacetylation in Mitosis Prevents Sister Chromatid Separation and Produces Chromosome Segregation Defects
Authors: Cimini Daniela , Mattiuzzo Marta , Torosantucci Liliana , Degrassi Francesca
Published: June 2003

Posttranslational modifications of core histones contribute to driving changes in chromatin conformation and compaction. Herein, we investigated the role of histone deacetylation on the mitotic process by inhibiting histone deacetylases shortly before mitosis in human primary fibroblasts. Cells entering mitosis with hyperacetylated histones displayed altered chromatin conformation associated with decreased reactivity to the anti-Ser 10 phospho H3 antibody, increased recruitment of protein phosphatase 1-δ on mitotic chromosomes, and depletion of heterochromatin protein 1 from the centromeric heterochromatin. Inhibition of histone deacetylation before mitosis produced defective chromosome condensation and impaired mitotic progression in living cells, suggesting that improper chromosome condensation may induce mitotic checkpoint activation. In situ hybridization analysis on anaphase cells demonstrated the presence of chromatin bridges, which were caused by persisting cohesion along sister chromatid arms after centromere separation. Thus, the presence of hyperacetylated chromatin during mitosis impairs proper chromosome condensation during the pre-anaphase stages, resulting in poor sister chromatid resolution. Lagging chromosomes consisting of single or paired sisters were also induced by the presence of hyperacetylated histones, indicating that the less constrained centromeric organization associated with heterochromatin protein 1 depletion may promote the attachment of kinetochores to microtubules coming from both poles.
The Role of the 3′ Untranslated Region in mRNA Sorting to the Vicinity of Mitochondria Is Conserved from Yeast to Human Cells
Authors: Sylvestre J. , Margeot A. , Jacq C. , Dujardin G. , Corral-Debrinski M.
Published: June 2003

We recently demonstrated, using yeast DNA microarrays, that mRNAs of polysomes that coisolate with mitochondria code for a subset of mitochondrial proteins. The majority of these mRNAs encode proteins of prokaryotic origin. Herein, we show that a similar association occurs between polysomes and mitochondria in human cells. To determine whether mRNA transport machinery is conserved from yeast to human cells, we examined the subcellular localization of human OXA1 mRNA in yeast. Oxa1p is a key component in the biogenesis of mitochondrial inner membrane and is conserved from bacteria to eukaryotic organelles. The expression of human OXA1 cDNA partially restores the respiratory capacity of yeast oxa1–cells. In this study, we demonstrate that 1) OXA1 mRNAs are remarkably enriched in mitochondrion-bound polysomes purified from yeast and human cells; 2) the presence of the human OXA1 3′ untranslated region (UTR) is required for the function of the human Oxa1p inside yeast mitochondria; and 3) the accurate sorting of the human OXA1 mRNA to the vicinity of yeast mitochondria is due to the recognition by yeast proteins of the human 3′ UTR. Therefore, it seems that the recognition mechanism of OXA1 3′ UTR is conserved throughout evolution and is necessary for Oxa1p function.
Identification of Fer Tyrosine Kinase Localized on Microtubules as a Platelet Endothelial Cell Adhesion Molecule-1 Phosphorylating Kinase in Vascular Endothelial Cells
Authors: Kogata Naoko , Masuda Michitaka , Kamioka Yuji , Yamagishi Akiko , Endo Akira , Okada Masato , Mochizuki Naoki
Published: June 2003

Platelet endothelial adhesion molecule-1 (PECAM-1) is a part of intercellular junctions and triggers intracellular signaling cascades upon homophilic binding. The intracellular domain of PECAM-1 is tyrosine phosphorylated upon homophilic engagement. However, it remains unclear which tyrosine kinase phosphorylates PECAM-1. We sought to isolate tyrosine kinases responsible for PECAM-1 phosphorylation and identified Fer as a candidate, based on expression cloning. Fer kinase specifically phosphorylated PECAM-1 at the immunoreceptor tyrosine-based inhibitory motif. Notably, Fer induced tyrosine phosphorylation of SHP-2, which is known to bind to the immunoreceptor tyrosine-based inhibitory motif of PECAM-1, and Fer also induced tyrosine phosphorylation of Gab1 (Grb2-associated binder-1). Engagement-dependent PECAM-1 phosphorylation was inhibited by the overexpression of a kinase-inactive mutant of Fer, suggesting that Fer is responsible for the tyrosine phosphorylation upon PECAM-1 engagement. Furthermore, by using green fluorescent protein-tagged Fer and a time-lapse fluorescent microscope, we found that Fer localized at microtubules in polarized and motile vascular endothelial cells. Fer was dynamically associated with growing microtubules in the direction of cell-cell contacts, where p120catenin, which is known to associate with Fer, colocalized with PECAM-1. These results suggest that Fer localized on microtubules may play an important role in phosphorylation of PECAM-1, possibly through its association with p120catenin at nascent cell-cell contacts.
Ectopic Expression of atRSZ33 Reveals Its Function in Splicing and Causes Pleiotropic Changes in Development
Authors: Kalyna Maria , Lopato Sergiy , Barta Andrea
Published: June 2003

Splicing provides an additional level in the regulation of gene expression and contributes to proteome diversity. Herein, we report the functional characterization of a recently described plant-specific protein, atRSZ33, which has characteristic features of a serine/arginine-rich protein and the ability to interact with other splicing factors, implying that this protein might be involved in constitutive and/or alternative splicing. Overexpression of atRSZ33 leads to alteration of splicing patterns of atSRp30 and atSRp34/SR1, indicating that atRSZ33 is indeed a splicing factor. Moreover, atRSZ33 is a regulator of its own expression, as splicing of its pre-mRNA is changed in transgenic plants. Investigations by promoter-β-glucuronidase (GUS) fusion and in situ hybridization revealed that atRSZ33 is expressed during embryogenesis and early stages of seedling formation, as well as in flower and root development. Ectopic expression of atRSZ33 caused pleiotropic changes in plant development resulting in increased cell expansion and changed polarization of cell elongation and division. In addition, changes in activity of an auxin-responsive promoter suggest that auxin signaling is disturbed in these transgenic plants.
PIG-W Is Critical for Inositol Acylation but Not for Flipping of Glycosylphosphatidylinositol-Anchor
Authors: Murakami Yoshiko , Siripanyapinyo Uamporn , Hong Yeongjin , Kang Ji Young , Ishihara Sonoko , Nakakuma Hideki , Maeda Yusuke , Kinoshita Taroh
Published: June 2003

Many cell surface proteins are anchored to a membrane via a glycosylphosphatidylinositol (GPI), which is attached to the C termini in the endoplasmic reticulum. The inositol ring of phosphatidylinositol is acylated during biosynthesis of GPI. In mammalian cells, the acyl chain is added to glucosaminyl phosphatidylinositol at the third step in the GPI biosynthetic pathway and then is usually removed soon after the attachment of GPIs to proteins. The mechanisms and roles of the inositol acylation and deacylation have not been well clarified. Herein, we report derivation of human and Chinese hamster mutant cells defective in inositol acylation and the gene responsible, PIG-W. The surface expressions of GPI-anchored proteins on these mutant cells were greatly diminished, indicating the critical role of inositol acylation. PIG-W encodes a 504-amino acid protein expressed in the endoplasmic reticulum. PIG-W is most likely inositol acyltransferase itself because the tagged PIG-W affinity purified from transfected human cells had inositol acyltransferase activity and because both mutant cells were complemented with PIG-W homologs of Saccharomyces cerevisiae and Schizosaccharomyces pombe. The inositol acylation is not essential for the subsequent mannosylation, indicating that glucosaminyl phosphatidylinositol can flip from the cytoplasmic side to the luminal side of the endoplasmic reticulum.
Regulated Expression of the Centrosomal Protein DdCP224 Affects Microtubule Dynamics and Reveals Mechanisms for the Control of Supernumerary Centrosome Number
Authors: Gräf Ralph , Euteneuer Ursula , Ho Thi-Hieu , Rehberg Markus
Published: June 2003

The Dictyostelium XMAP215 family member DdCP224 is involved in centrosome duplication and cytokinesis and is concentrated at the centrosome and microtubule tips. Herein, we have created a DdCP224 promoter replacement mutant that allows both over- and underexpression. Overexpression led to supernumerary microtubule-organizing centers and, independently, an increase of the number of multinuclear cells. Electron microscopy demonstrated that supernumerary microtubule-organizing centers represented bona fide centrosomes. Live cell imaging of DdCP224-green fluorescent protein mutants also expressing green fluorescent protein-histone2B as a DNA label revealed that supernumerary centrosomes were also competent of cell cycle-dependent duplication. In contrast, underexpression of DdCP224 inhibited cell growth, reduced the number and length of astral microtubules, and caused nocodazole hypersensitivity. Moreover, microtubule regrowth after nocodazole removal was dependent on DdCP224. Underexpression also resulted in a striking disappearance of supernumerary centrosomes and multinuclear cells caused by previous overexpression. We show for the first time by live cell observation that the number of supernumerary centrosomes can be reduced either by centrosome fusion (coalescence) or by the formation of cytoplasts containing supernumerary centrosomes during cytokinesis.
Aberrant histone acetylation, altered transcription, and retinal degeneration in aDrosophilamodel of polyglutamine disease are rescued by CREB-binding protein
Authors: Taylor J. Paul , Taye Addis A. , Campbell Catherine , Kazemi-Esfarjani Parsa , Fischbeck Kenneth H. , Min Kyung-Tai
Published: June 2003

Sequestration of the transcriptional coactivator CREB-binding protein (CBP), a histone acetyltransferase, has been implicated in the pathogenesis of polyglutamine expansion neurodegenerative disease. We used aDrosophilamodel to demonstrate that polyglutamine-induced neurodegeneration is accompanied by a defect in histone acetylation and a substantial alteration in the transcription profile. Furthermore, we demonstrate complete functional and morphological rescue by up-regulation of endogenousDrosophilaCBP (dCBP). Rescue of the degenerative phenotype is associated with eradication of polyglutamine aggregates, recovery of histone acetylation, and normalization of the transcription profile. These findings suggest that histone acetylation is an early target of polyglutamine toxicity and indicate that transcriptional dysregulation is an important part of the pathogenesis of polyglutamine-induced neurodegeneration.
MAX4andRMS1are orthologous dioxygenase-like genes that regulate shoot branching inArabidopsisand pea
Authors: Sorefan Karim , Booker Jon , Haurogné Karine , Goussot Magali , Bainbridge Katherine , Foo Eloise , Chatfield Steven , Ward Sally , Beveridge Christine , Rameau Catherine , Leyser Ottoline
Published: June 2003

Shoot branching is inhibited by auxin transported down the stem from the shoot apex. Auxin does not accumulate in inhibited buds and so must act indirectly. We show that mutations in theMAX4gene ofArabidopsisresult in increased and auxin-resistant bud growth. Increased branching inmax4shoots is restored to wild type by grafting to wild-type rootstocks, suggesting thatMAX4is required to produce a mobile branch-inhibiting signal, acting downstream of auxin. A similar role has been proposed for the pea gene,RMS1. Accordingly,MAX4andRMS1were found to encode orthologous, auxin-inducible members of the polyene dioxygenase family.
Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis
Authors: Barczak Andrea , Rodriguez Madeleine Willkom , Hanspers Kristina , Koth Laura L. , Tai Yu Chuan , Bolstad Benjamin M. , Speed Terence P. , Erle David J.
Published: June 2003

DNA microarrays produced by deposition (or `spotting')of a single long
oligonucleotide probe for each gene may be an attractive alternative to other
types of arrays. We produced spotted oligonucleotide arrays using two large
collections of ∼70-mer probes, and used these arrays to analyze gene
expression in two dissimilar human RNA samples. These samples were also
analyzed using arrays produced by in situ synthesis of sets of multiple short
(25-mer)oligonucleotides for each gene (Affymetrix GeneChips). We compared
expression measurements for 7344 genes that were represented in both long
oligonucleotide probe collections and the in situ-synthesized 25-mer arrays.
We found strong correlations (r = 0.8–0.9)between relative gene
expression measurements made with spotted long oligonucleotide probes and in
situ-synthesized 25-mer probe sets. Spotted long oligonucleotide arrays were
suitable for use with both unamplified cDNA and amplified RNA targets, and are
a cost-effective alternative for many functional genomics applications. Most
previously reported evaluations of microarray technologies have focused on
expression measurements made on a relatively small number of genes. The
approach described here involves far more gene expression measurements and
provides a useful method for comparing existing and emerging techniques for
genome-scale expression analysis.
Mechanisms of Thermal Adaptation Revealed From the Genomes of the AntarcticArchaea Methanogenium frigidumandMethanococcoides burtonii
Authors: Saunders Neil F.W. , Thomas Torsten , Curmi Paul M.G. , Mattick John S. , Kuczek Elizabeth , Slade Rob , Davis John , Franzmann Peter D. , Boone David , Rusterholtz Karl , Feldman Robert , Gates Chris , Bench Shellie , Sowers Kevin , Kadner Kristen , Aerts Andrea , Dehal Paramvir , Detter Chris , Glavina Tijana , Lucas Susan , Richardson Paul , Larimer Frank , Hauser Loren , Land Miriam , Cavicchioli Ricardo
Published: June 2003

We generated draft genome sequences for two cold-adaptedArchaea, Methanogenium frigidumandMethanococcoides burtonii, to identify genotypic characteristics that distinguish them fromArchaeawith a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adaptedArchaeaare characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15°–98°C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adaptedArchaeashowed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified inM. frigidum, two hypothetical proteins with CSD-folds inM. burtonii, and a unique winged helix DNA-binding domain protein inM. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adaptedArchaea. Structural analysis of tRNA sequences from theArchaeaindicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60°C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data fromArchaeaspanning the growth temperature extremes from psychrophiles to hyperthermophiles.
Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci
Authors: Wang Xiaosong , Le Roy Isabelle , Nicodeme Edwige , Li Renhua , Wagner Richard , Petros Christina , Churchill Gary A. , Harris Stephen , Darvasi Ariel , Kirilovsky Jorge , Roubertoux Pierre L. , Paigen Beverly
Published: June 2003

Mapping quantitative trait loci (QTLs)with high resolution facilitates
identification and positional cloning of the underlying genes. The novel
approach of advanced intercross lines (AILs) generates many more recombination
events and thus can potentially narrow QTLs significantly more than do
conventional backcrosses and F2 intercrosses. In this study, we
carried out QTL analyses in (C57BL/6J × NZB/BlNJ)× C57BL/6J
backcross progeny fed either chow or an atherogenic diet to detect QTLs that
regulate high-density lipoprotein cholesterol (HDL)concentrations, and in
(C57BL/6J × NZB/BlNJ)F11 AIL progeny to confirm and narrow
those QTLs. QTLs for HDL concentrations were found on chromosomes 1, 5, and
16. AIL not only narrowed the QTLs significantly more than did a conventional
backcross but also resolved a chromosome 5 QTL identified in the backcross
into two QTLs, the peaks of both being outside the backcross QTL region. We
tested 27 candidate genes and found significant mRNA expression differences
for 12 (Nr1i3, Apoa2, Sap, Tgfb2, Fgfbp1, Prom, Ppargc1, Tcf1, Ncor2,
Srb1, App, and Ifnar). Some of these underlay the same QTL,
indicating that expression differences are common and not sufficient to
identify QTL genes. All the major HDL QTLs in our study had homologous
counterparts in humans, implying that their underlying genes regulate HDL in
humans.
Systematic Cloning ofTreponema pallidumOpen Reading Frames for Protein Expression and Antigen Discovery
Authors: McKevitt Matthew , Patel Krupa , Smajs David , Marsh Michael , McLoughlin Melanie , Norris Steven J. , Weinstock George M. , Palzkill Timothy
Published: June 2003

A topoisomerase-based method was used to clone PCR products encoding 991 of the 1041 open reading frames identified in the genome sequence of the bacterium that causes syphilis,Treponema pallidumsubsp.pallidum. Cloning the open reading frames into the univector plasmid system permitted the rapid conversion of the original clone set to other functional vectors containing a variety of promoters or tag sequences. A computational prediction of signal sequences identified 248T. pallidumproteins that are potentially secreted from the cell. These clones were systematically converted into vectors designed to express the encoded proteins as glutathione-S-transferase fusion proteins. To test the potential of the clone set for novel antigen discovery, 85 of these fusion proteins were expressed fromEscherichia coli, partially purified, and tested for antigenicity by using sera from rabbits infected withT. pallidum. Twelve of the 85 proteins bound significant levels of antibody. Of these 12 proteins, seven had previously been identified asT. pallidumantigens, and the remaining five represent novel antigens. These results demonstrate the potential of theT. pallidumclone set for antigen discovery and, more generally, for advancing the biology of this enigmatic spirochete.
Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay
Authors: Khambata-Ford Shirin , Liu Yueyi , Gleason Christopher , Dickson Mark , Altman Russ B. , Batzoglou Serafim , Myers Richard M.
Published: June 2003

Attempts to identify regulatory sequences in the human genome have involved
experimental and computational methods such as cross-species sequence
comparisons and the detection of transcription factor binding-site motifs in
coexpressed genes. Although these strategies provide information on which
genomic regions are likely to be involved in gene regulation, they do not give
information on their functions. We have developed a functional selection for
promoter regions in the human genome that uses a retroviral plasmid
library-based system. This approach enriches for and detects promoter function
of isolated DNA fragments in an in vitro cell culture assay. By using this
method, we have discovered likely promoters of known and predicted genes, as
well as many other putative promoter regions based on the presence of features
such as CpG islands. Comparison of sequences of 858 plasmid clones selected by
this assay with the human genome draft sequence indicates that a significantly
higher percentage of sequences align to the 500-bp segment upstream of the
transcription start sites of known genes than would be expected from random
genomic sequences. We also observed enrichment for putative promoter regions
of genes predicted in at least two annotation databases and for clones
overlapping with CpG islands. Functional validation of randomly selected
clones enriched by this method showed that a large fraction of these putative
promoters can drive the expression of a reporter gene in transient
transfection experiments. This method promises to be a useful genome-wide
function-based approach that can complement existing methods to look for
promoters.
Analysis of mRNA With Microsomal Fractionation Using a SAGE-Based DNA Microarray System Facilitates Identification of the Genes Encoding Secretory Proteins
Authors: Toyoda Nobuaki , Nagai Shigenori , Terashima Yuya , Motomura Kazushi , Haino Makoto , Hashimoto Shin-ichi , Takizawa Hajime , Matsushima Kouji
Published: June 2003

In the regulation of host defense responses such as inflammation and
immunity, the secretory proteins, including membrane proteins, play central
roles. Although many secretory proteins have been identified by using methods
such as differential display, random screening, or the signal sequence trap
method, each method suffers from poor reproducibility, low sensitivity, or
time-consuming or laborious work. Therefore, the strategy for facilitating the
selection of the genes encoding the secretory proteins is desired. In this
paper, we describe a system for isolating the genes encoding secretory
proteins by analyzing mRNAs with microsomal fractionation on serial analysis
of gene expression (SAGE)–based DNA microarray system. This system
succeeded in discriminating the genes encoding secretory proteins from ones
encoding nonsecretory proteins with 80% accuracy. We applied this system to
human T lymphocytes. As a result, we were able to identify the genes that are
not only encoding secretory proteins but also expressing selectively in a
specific subset of T lymphocytes. The SAGE-based DNA microarray system is a
promising system to identify the genes encoding specific secretory
proteins.
An Active Non-LTR Retrotransposon With Tandem Structure in the Compact
Genome of the Pufferfish Tetraodon nigroviridis
Authors: Bouneau Laurence , Fischer Cécile , Ozouf-Costaz Catherine , Froschauer Alexander , Jaillon Olivier , Coutanceau Jean-Pierre , Körting Cornelia , Weissenbach Jean , Bernot Alain , Volff Jean-Nicolas
Published: June 2003

The fish retrotransposable element Zebulon encodes a reverse
transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and
is related phylogenetically to site-specific non-LTR retrotransposons from
nematodes. Zebulon was detected in the pufferfishes Tetraodon
nigroviridis and Takifugu rubripes, as well as in the zebrafish
Danio rerio. Structural analysis suggested that Zebulon, in
contrast to most non-LTR retrotransposons, might be able to retrotranspose as
a partial tandem array. Zebulon was active relatively recently in the
compact genome of T. nigroviridis, in which it contributed to the
extension of intergenic and intronic sequences, and possibly to the formation
of genomic rearrangements. Accumulation of Zebulon together with
other retrotransposons was observed in some heterochromatic chromosomal
regions of the genome of T. nigroviridis that might serve as
reservoirs for active elements. Hence, pufferfish compact genomes are not
evolutionarily inert and contain active retrotransposons, suggesting the
presence of mechanisms allowing accumulation of retrotransposable elements in
heterochromatin, but minimizing their impact on euchromatic regions.
Homologous recombination between partial tandem sequences eliminating active
copies of Zebulon and reducing the size of insertions in intronic and
intragenic regions might represent such a mechanism.
Genetic Variation Among World Populations: Inferences From 100
Alu Insertion Polymorphisms
Authors: Watkins W. Scott , Rogers Alan R. , Ostler Christopher T. , Wooding Steve , Bamshad Michael J. , Brassington Anna-Marie E. , Carroll Marion L. , Nguyen Son V. , Walker Jerilyn A. , Prasad B.V. Ravi , Reddy P. Govinda , Das Pradipta K. , Batzer Mark A. , Jorde Lynn B.
Published: June 2003

We examine the distribution and structure of human genetic diversity for
710 individuals representing 31 populations from Africa, East Asia, Europe,
and India using 100 Alu insertion polymorphisms from all 22
autosomes. Alu diversity is highest in Africans (0.349) and lowest in
Europeans (0.297). Alu insertion frequency is lowest in Africans
(0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans
(0.559). Large genetic distances are observed among African populations and
between African and non-African populations. The root of a neighbor-joining
network is located closest to the African populations. These findings are
consistent with an African origin of modern humans and with a bottleneck
effect in the human populations that left Africa to colonize the rest of the
world. Genetic distances among all pairs of populations show a significant
product-moment correlation with geographic distances (r = 0.69,
P < 0.00001). FST, the proportion of genetic diversity
attributable to population subdivision is 0.141 for Africans/E.
Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31
populations. Resampling analyses show that ∼50 Alu polymorphisms
are sufficient to obtain accurate and reliable genetic distance estimates.
These analyses also demonstrate that markers with higher FST values
have greater resolving power and produce more consistent genetic distance
estimates.
How intangibility affects perceived risk: the moderating role of knowledge and involvement
Authors: Laroche Michel , Bergeron Jasmin , Goutaland Christine
Published: June 2003

The marketing literature suggests that product intangibility is positively associated with perceived risk and the intangibility construct encompasses three dimensions: physical intangibility, mental intangibility, and generality. The purpose of this research is to test which dimension of the intangibility construct is the most correlated with perceived risk. A survey was conducted and structural equation modeling analyses were used to test the proposed model. Results show that the mental dimension of intangibility accounts for more variance in the perceived risk construct than the other two dimensions, even when knowledge and involvement are included as moderators. Hence, the challenge for marketers might not be so much to reduce risk by physically tangibilizing goods and services, as has been advised for the past two decades, as rather to mentally tangibilize their offerings.
Exploring managers’ implicit theories of atmospheric music: comparing academic analysis to industry insight
Authors: Areni Charles S.
Published: June 2003

A total of 90 hotel, restaurant, and pub managers completed unstructured telephone interviews exploring their implicit theories of how atmospheric music affects consumer behavior. Many of the implicit theories emerging in the interviews were grounded in previous research, but others had no obvious counterparts in the literature. The more novel theories suggested that atmospheric music: must follow circadian rhythms to be effective; encourages or discourages anti‐social behavior; and blocks out annoying and intrusive background noise. Each of the 14 industry‐based explanations of the effects of music is compared with results reported in the academic literature, and directions for future research on the effects of atmospheric music are identified.
An empirical examination of factors influencing the internationalization of service firms
Authors: Javalgi Rajshekhar (Raj) G. , Griffith David A. , Steven White D.
Published: June 2003

The internationalization of service firms is expanding dramatically, fueled by recent technological innovations and reductions of trade barriers. Drawing upon Dunning’s eclectic theory, firm‐ and location‐specific factors which have been found to be antecedents of internationalization of manufacturing firms are extended to determine their applicability to the internationalization of service firms. The hypotheses are empirically examined through a survey of 228 business‐to‐business service firms. Findings indicate that the firm‐specific factor of firm size and the location‐specific factor of market characteristics influence management attitudes toward operating internationally, which in turn influence the degree of internationalization of service firms. Practical implications, drawn from the results, are offered for managers of service firms who are facing the task of internationalizing.
The relationship of differential loci with perceived quality and behavioral intentions
Authors: Swanson Scott R. , Charlene Davis J.
Published: June 2003

This paper suggests that he/she whom the customer holds most responsible for a service experience may influence which service quality dimensions take precedence in customer satisfaction, word‐of‐mouth intentions, and repurchase intentions. Results indicate that, when consumers find the contact employee more responsible for the experience, what is delivered is most important to evaluations of service quality, satisfaction, and behavioral intentions. When management is thought to be more responsible, how the service is delivered is essential to consumers’ evaluations. When responsibility is perceived as shared between the contact employee and management, the physical environment may play a larger role in influencing consumers’ satisfaction with the service experience.
Cause‐related marketing: how generation Y responds
Authors: Cui Yanli , Trent Elizabeth S. , Sullivan Pauline M. , Matiru Grace N.
Published: June 2003

Generation Y, children born to baby‐boomers, is widely considered to be the next big generation. Businesses are therefore struggling to find ways to capture a piece of this market. Could cause‐related marketing be the answer? Employs an experimental design to examine how college‐age Generation Y consumers respond to a cause‐related marketing (CRM) offer based on four structural elements. Also examines the potential impacts of socio‐demographic characteristics of participants. The results indicate that a CRM offer is more likely to elicit a more positive response to a disaster cause than an ongoing cause when businesses use non‐transaction‐based and long‐term/frequent support. Finds that females, social science majors, parents’ annual income and previous donation activity have significant impact on the evaluation of a CRM offer. There is a positive relationship between evaluation of a CRM offer and purchase intent toward the offer.
Student perceptions of retailing as a destination career
Authors: Broadbridge Adelina
Published: June 2003

Reports on the results of a questionnaire survey into the perceptions of retailing as a destination career. While some students are attracted to the industry, overall a neutral or negative perception prevails. This is conveyed from a general ignorance as to what a retail management job involves or the variety of career opportunities it provides. Often, students have only their experiences as consumers or as part‐time employees in forming their perception of it as a future career. Personal, and word of mouth, work experience can help either to persuade or to dissuade the perceptions of retailing as a destination career. Reports on the work of various bodies such as BIR, CORTCO and CRU in fostering the partnership between industry and educational providers in order to raise the image of retailing as a graduate career. Also provides recommendations on how to raise the profile of the industry.
“Not in my neighborhood”: resistance to chain drug‐stores
Authors: Lavin Marilyn
Published: June 2003

The present paper compares the protests that CVS, a leading chain retailer, experienced as it attempted to establish a new drug‐store on the Upper West Side of New York City’s borough of Manhattan with those Walgreen, another major chain pharmacy, encountered as it attempted to enter a neighborhood shopping area in Madison, Wisconsin, a medium‐sized city in the mid‐western region of the USA. It finds that well‐educated, affluent residents in both locations believe that they should have input regarding the retail composition of local shopping areas, and that their resistance to new stores can be successful. It also reveals that such consumers may be protective of small retailers and may harbor strong anti‐chain‐store sentiments.
Kiosks in retailing: the quiet revolution
Authors: Rowley Jennifer , Slack Frances
Published: June 2003

Kiosks have the potential to be a significant application of information technology in retailing, information provision and service delivery. This article discusses and analyses the application of kiosks as a channel for in‐store service delivery. For these kiosks a taxonomy that characterises kiosks by their function – inform, interact, transact and relate – is proposed. Eight case study examples of in‐store kiosks are analysed in using a framework that includes environment, task, audience, and technology. Included are kiosks used by Halifax, Daewoo, Argos, Ikea, Debenhams, GNER, Sainsburys and Boots. Both the taxonomy and the framework provide a basis for further analysis of the role of kiosks in service delivery, by allowing analysis and discussion of individual kiosks to be contextualised within a wider framework.
Using ZMET to explore barriers to the adoption of 3G mobile banking services
Authors: Lee Morna S.Y. , McGoldrick Peter J. , Keeling Kathleen A. , Doherty Joanne
Published: June 2003

Telecommunications companies world‐wide are developing 3G mobile phones and applications. In the UK, mobile banking is considered to be one of the most value‐added and important mobile services available. However, the adoption rate of using 3G mobile phones for financial services is yet to be determined. The current research examined both innovative attributes and customers’ perceived risk in order to understand customers’ behaviour and motivation toward this innovation. It has advanced the theoretical frameworks of innovation and customers’ risk perception as new attributes and risk dimensions were identified. The findings provide banking executives with a better understanding of what are the perceived advantages and disadvantages of 3G mobile banking services, helping them to plan marketing strategies and promotion approaches for 3G mobile banking services in the future.
Knowledge management in the emerging strategic business process: information, complexity and imagination
Authors: Bueno Campos Eduardo , Paz Salmador Sánchez Ma
Published: June 2003

This article features a descriptive proposal that examines the different conceptual dimensions of knowledge (basically the epistemological, ontological, systemic and strategic dimensions) that are involved in the emerging strategic process of organizations. Included in this process are aspects of information, complexity and imagination that make up the spirals of knowledge. In this study we aim to shed light on knowledge management in strategy‐making so that the different categories of knowledge may emerge and develop their potential within an organization and interact among each other. The goal is to create sustainable competitive advantages or essential competencies that help a business to succeed. Considering a constructionist approach to knowledge – specifically, the theory of knowledge creation developed by Nonaka and Takeuchi – we conclude that the formation of the strategy is a double‐loop knowledge creating process. Finally, we outline some of the main practical implications of our position.
A framework to create key performance indicators for knowledge management solutions
Authors: del‐Rey‐Chamorro Francisco M. , Roy Rajkumar , van Wegen Bert , Steele Andy
Published: June 2003

Knowledge management (KM) is popular within the engineering industry. With increasing investment in KM projects, companies are looking for ways to justify their effort. This research develops a framework to assess the contribution of KM solutions within a business against its corporate objectives. The framework uses a set of key performance indicators (KPIs) as lead indicators. The lead indicators are developed in line with the lag indicators at the strategic level. A number of templates is developed to implement the framework within a company. A real life case study is presented where the templates are used to identify KPIs for a manufacturing solution. The paper also gives guidelines on using the templates effectively.
Managing knowledge in a software organization
Authors: Mathiassen Lars , Pourkomeylian Pouya
Published: June 2003

This paper explores the practical usage of insights on knowledge management (KM) to support innovation in a software organization. The organization has for some time engaged in software process improvement (SPI) initiatives to improve its operation. The paper applies two complementary approaches to KM, the codified and the personalized, to evaluate current KM practices and to improve its SPI practices. Based on the insights from the case we review key principles within SPI and evaluate the applied KM approaches. We conclude that it is advisable for SPI efforts to explicitly address KM issues. Each software organization has to find its own balance between personalized and codified approaches, this balance needs to be dynamically adjusted as the organization matures, and the adopted KM approach should differentiate between different types of SPI services.