bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drosophila melanogaster γ-TuRC is dispensable for targeting γ-tubulin to the centrosome and microtubule nucleation
Authors: Vérollet Christel , Colombié Nathalie , Daubon Thomas , Bourbon Henri-Marc , Wright Michel , Raynaud-Messina Brigitte 
Published: February 2006

In metazoans, γ-tubulin acts within two main complexes, γ-tubulin small complexes (γ-TuSCs) and γ-tubulin ring complexes (γ-TuRCs). In higher eukaryotes, it is assumed that microtubule nucleation at the centrosome depends on γ-TuRCs, but the role of γ-TuRC components remains undefined.
For the first time, we analyzed the function of all four γ-TuRC–specific subunits in Drosophila melanogaster: Dgrip75, Dgrip128, Dgrip163, and Dgp71WD. Grip-motif proteins, but not Dgp71WD, appear to be required for γ-TuRC assembly. Individual depletion of γ-TuRC components, in cultured cells and in vivo, induces mitotic delay and abnormal spindles. Surprisingly, γ-TuSCs are recruited to the centrosomes. These defects are less severe than those resulting from the inhibition of γ-TuSC components and do not appear critical for viability. Simultaneous cosilencing of all γ-TuRC proteins leads to stronger phenotypes and partial recruitment of γ-TuSC. In conclusion, γ-TuRCs are required for assembly of fully functional spindles, but we suggest that γ-TuSC could be targeted to the centrosomes, which is where basic microtubule assembly activities are maintained.
The DIMA web resource—exploring the protein domain network
Authors: Pagel Philipp , Oesterheld Matthias , Stümpflen Volker , Frishman Dmitrij 
Published: February 2006

Abstract
Summary: Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria.
Availability:
Contact: p.pagel@gsf.de
An ensemble of K-local hyperplanes for predicting protein–protein interactions
Authors: Nanni Loris , Lumini Alessandra 
Published: February 2006

Abstract
Prediction of protein–protein interaction is a difficult and important problem in biology. In this paper, we propose a new method based on an ensemble of K-local hyperplane distance nearest neighbor (HKNN) classifiers, where each HKNN is trained using a different physicochemical property of the amino acids. Moreover, we propose a new encoding technique that combines the amino acid indices together with the 2-Grams amino acid composition. A fusion of HKNN classifiers combined with the ‘Sum rule’ enables us to obtain an improvement over other state-of-the-art methods. The approach is demonstrated by building a learning system based on experimentally validated protein–protein interactions in human gastric bacterium Helicobacter pylori and in Human dataset.
Contact: lnanni@deis.unibo.it
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
Authors: Conesa Ana , Nueda María José , Ferrer Alberto , Talón Manuel 
Published: February 2006

Abstract
Motivation: Multi-series time-course microarray experiments are useful approaches for exploring biological processes. In this type of experiments, the researcher is frequently interested in studying gene expression changes along time and in evaluating trend differences between the various experimental groups. The large amount of data, multiplicity of experimental conditions and the dynamic nature of the experiments poses great challenges to data analysis.
Results: In this work, we propose a statistical procedure to identify genes that show different gene expression profiles across analytical groups in time-course experiments. The method is a two-regression step approach where the experimental groups are identified by dummy variables. The procedure first adjusts a global regression model with all the defined variables to identify differentially expressed genes, and in second a variable selection strategy is applied to study differences between groups and to find statistically significant different profiles. The methodology is illustrated on both a real and a simulated microarray dataset.
Availability: The method has been implemented in the statistical language R and is freely available from the Bioconductor contributed packages repository and from
Contact: aconesa@ivia.es; mj.nueda@ua.es
Second Language Acquisition of Variable Structures in Spanish by Portuguese Speakers
Authors: Geeslin Kimberly L. , Guijarro‐Fuentes Pedro 
Published: February 2006

This study provides a model for examining the second language (L2) acquisition of structures where the first language (L1) and L2 are similar, and where native speaker (NS) use varies. Research on the copula contrast in Spanish (ser and estar mean “to be”) has shown that an assessment of learner choice cannot rely on an error analysis (Geeslin, 2001, 2003a; Geeslin & Guijarro‐Fuentes, 2004). Obligatory contexts are difficult to identify because norms for copula use with adjectives are changing (Silva‐Corvalán, 1994; Guijarro‐Fuentes & Geeslin, in press) and NSs vary in their choices for a given context (Geeslin, 2003a). A more effective approach to assessing the acquisition of variable structures incorporates statistical models that identify features of the discourse that best predict copula choice for NSs and nonnative speakers (NNSs). Our research design, which incorporates semantic and discourse‐pragmatic constraints, is the first to apply this approach to the acquisition of L2 Spanish by Portuguese‐speaking learners. Because Portuguese also possesses copula choice, unlike previously researched L1s, our research also shows that the L2 and the L1 can be compared through analyses based on discourse features and the degree to which each predicts copula choice.Three participant groups were studied: NSs of Spanish (N = 19), Portuguese‐speaking NNSs of Spanish (N = 11), and NSs of Portuguese (N = 11). Thus, our definition of NS targets comes from two separate sociolinguistic studies in addition to our study of L2 data. The data elicited using a 28‐item contextualized preference task were coded and analyzed according to seven discourse features present in each [copula + adjective] context. Results show that both groups of NSs share the same four predictors, differing only in the level of significance of each. In contrast, the Portuguese NNSs of Spanish are different from each of the other two groups. Our study connects work on the acquisition of Spanish by Portuguese learners to the growing body of research on L2 variation.
The Effect of Crossing‐Network Trading on Dealer Market's Bid‐Ask Spreads
Authors: Gresse Carole 
Published: February 2006

Abstract This article provides new insights into market competition between traditional exchanges and alternative trading systems in Europe. It investigates the relationship between the trading activity of a crossing network (CN) and the liquidity of a traditional dealer market (DM) by comparing data from the SEAQ quote‐driven segment of the London Stock Exchange (LSE) and internal data from the POSIT crossing network. A cross‐sectional analysis of bid‐ask spreads shows that DM spreads are negatively related to CN executions. Risk‐sharing benefits from CN trading dominate fragmentation and cream‐skimming costs. Further, risk‐sharing gains are found to be related to dealer trading in the CN.
Adoptive transfer of nontransgenic mesenteric lymph node cells induces colitis in athymic HLA-B27 transgenic nude rats
Authors: Hoentjen F , Tonkonogy S L , Liu B , Sartor R B , Taurog J D , Dieleman L A 
Published: February 2006

SummaryHLA-B27 transgenic (TG) rats develop spontaneous colitis when colonized with intestinal bacteria, whereas athymic nude (rnu/rnu) HLA-B27 TG rats remain disease free. The present study was designed to determine whether or not HLA-B27 expression on T cells is required for development of colitis after transfer of mesenteric lymph node (MLN) cells into rnu/rnu HLA-B27 recipients. Athymic nontransgenic (non-TG) and HLA-B27 TG recipients received MLN cells from either TG or non-TG rnu/+ heterozygous donor rats that contain T cells. HLA-B27 TG rnu/rnu recipients receiving either non-TG or TG MLN cells developed severe colitis and had higher caecal MPO and IL-1β levels, and their MLN cells produced more IFN-γ and less IL-10 after in vitro stimulation with caecal bacterial lysate compared to rnu/rnu non-TG recipients that remained disease free after receiving either TG or non-TG cells. Interestingly, proliferating donor TG T cells were detectable one week after adoptive transfer into rnu/rnu TG recipients but not after transfer into non-TG recipients. T cells from either non-TG or TG donors induce colitis in rnu/rnu TG but not in non-TG rats, suggesting that activation of effector T cells by other cell types that express HLA-B27 is pivotal for the pathogenesis of colitis in this model.
Specific messenger RNA expression for signal transduction molecules by lipopolysaccharide in intestinal macrophages
Authors: Nakata K , Inagawa H , Nishizawa T , Kohchi C , Soma G-I 
Published: February 2006

SummaryIntestinal macrophages are known to display profound inflammatory anergy in response to lipopolysacchraide (LPS). To study the mechanisms of unresponsiveness of intestinal macrophages to LPS, we compared the mRNA expression of molecules associated with signal transduction of intestinal macrophages with those of other tissue macrophages. Also cellular localization of CD14 protein was examined. Intestinal, alveolar and peritoneal macrophages were isolated from rats or mice. The expression of mRNA was assessed by real-time PCR, and cellular localization of CD14 protein was examined by flow cytometry. Cellular responses to LPS were examined by production of TNF and NO. The expression of CD14 mRNA in intestinal macrophages was lower than for peritoneal macrophages but higher than for alveolar macrophages. The mRNA expression of other molecules corresponding to intracellular signal transduction in intestinal macrophages was similar with alveolar and peritoneal macrophages. Despite the presence of CD14 mRNA, proteins of CD14 were not detected on cell surfaces of intestinal macrophages, and induction of TNF or NO responding to LPS were not detected. Flow cytometric analysis demonstrated that CD14 protein was not expressed on the cell surface but was expressed inside intestinal macrophages. The unresponsiveness of intestinal macrophages after LPS exposure is considered to be largely attributed to the lack of CD14 protein on their cell surfaces. However, CD14 protein was expressed inside of the cells, suggesting that post-transcriptional regulation rather than transcriptional suppression may play a dominant role in determining the phenotype of the intestinal macrophages.
Comparative studies on the roles of mediator molecules in expression of the suppressor activity ofMycobacterium aviumcomplex-induced immunosuppressive macrophages against T cell and B cell mitogenic responses
Authors: Cai S , Shimizu T , Tomioka H 
Published: February 2006

SummaryMycobacterium avium complex-induced immunosuppressive macrophages (MAC-MΦs) exhibit suppressor activity against concanavalin A-induced T cell mitogenesis (T cell Con A mitogenesis). We examined the profiles of the MAC-MΦ-mediated suppression of lipopolysaccharide-induced B cell mitogenesis (B cell LPS mitogenesis) and found the following. First, although NG-monomethyl-L-arginine and carboxy-PTIO effectively blocked the MAC-MΦ’s suppressor activity against T cell Con A mitogenesis, MAC-MΦ’s action against B cell LPS mitogenesis was only weakly affected by these NO-reducing agents. Second, B cell LPS mitogenesis was remarkably more susceptible to MAC-MΦ-derived reactive oxygen intermediates than T cell Con A mitogenesis. Third, B cell LPS mitogenesis was less susceptible to the inhibitory effects of the other MAC-MΦ-derived suppressor mediators, including free fatty acids, TGF-β and prostaglandin E2, than T cell Con A mitogenesis. Fourth, MAC-MΦ’s suppressor activity was strongly dependent on B7-1 like molecule-mediated cell contact with target cells only in the case of T cell Con A mitogenesis. Therefore, there are significant differences in the modes of suppressor action of MAC-MΦs against T cell and B cell mitogenesis.
T cell-mediated oral tolerance is intact in germ-free mice
Authors: Walton K L W , Galanko J A , Balfour Sartor R , Fisher N C 
Published: February 2006

SummaryCommensal enteric bacteria stimulate innate immune cells and increase numbers of lamina propria and mesenteric lymph node (MLN) T and B lymphocytes. However, the influence of luminal bacteria on acquired immune function is not understood fully. We investigated the effects of intestinal bacterial colonization on T cell tolerogenic responses to oral antigen compared to systemic immunization. Lymphocytes specific for ovalbumin–T cell receptor (OVA–TCR Tg+) were transplanted into germ-free (GF) or specific pathogen-free (SPF) BALB/c mice. Recipient mice were fed OVA or immunized subcutaneously with OVA peptide (323–339) in complete Freund’s adjuvant (CFA). Although the efficiency of transfer was less in GF recipients, similar proportions of cells from draining peripheral lymph node (LN) or MLN were proliferating 3–4 days later in vivo in GF and SPF mice. In separate experiments, mice were fed tolerogenic doses of OVA and then challenged with an immunogenic dose of OVA 4 days later. Ten days after immunization, lymphocytes were restimulated with OVA in vitro to assess antigen-specific proliferative responses. At both high and low doses of OVA, cells from both SPF and GF mice fed OVA prior to immunization had decreased proliferation compared to cells from control SPF or GF mice. In addition, secretion of interferon (IFN)-γ and interleukin (IL)-10 by OVA–TCR Tg+ lymphocytes was reduced in both SPF and GF mice fed OVA compared to control SPF or GF mice. Unlike previous reports indicating defective humoral responses to oral antigen in GF mice, our results indicate that commensal enteric bacteria do not enhance the induction of acquired, antigen-specific T cell tolerance to oral OVA.
Association of rheumatoid factor production with FcγRIIIa polymorphism in Taiwanese rheumatoid arthritis
Authors: Chen J-Y , Wang C-M , Wu J-M , Ho H-H , Luo S-F 
Published: February 2006

Summary
Fcγ receptors (FcγR) impact upon the development of inflammatory arthritis through immune complex stimulation and proinflammatory cytokine production. FcγRIIa, FcγRΙΙΙa and FcRγIIIb polymorphisms were genotyped in 212 rheumatoid arthritis (RA) patients and 371 healthy control subjects using an allelic-specific polymerase chain reaction (PCR). No significant skewing in the distribution of FcγRIIa H/R131, FcγRIIIa F/V158 and FcγRIIIb NA1/NA2 was found between RA patients and healthy control subjects. However, a significant skewing distribution of the FcγRIIIa F/V158 polymorphism was observed between rheumatoid factor (RF)-positive versus RF-negative RA patients (P = 0·01). The low-affinity FcγRIIIa F158 allele seems to have a protective role in RF production, in comparison with the FcγRIIIa V158 allele (P = 0·004; OR = 0·485; 95% CI: 0·293–0·803). A high frequency of FcγRIIIa F/F158 was identified in RA patients with negative RF compared with RF-positive patients (for FF158 versus FV158 + VV158; P = 0·002; OR = 0·372; 95% CI: 0·194–0·713). In addition, no association was found between FcγRIIa H/R131, FcγΡIIIa F/V158 and FcγRIIIb NA1/NA2 polymorphisms and other clinical parameters. The results of this study suggest that three activating FcγRs polymorphisms lack association with RA but FcγIIIa F/V158 polymorphism may influence RF production and IgG RF immune complex handling in Taiwanese RA patients.
CD127 expression and regulation are altered in the memory CD8 T cells of HIV-infected patients − reversal by highly active anti-retroviral therapy (HAART)
Authors: Colle J-H , Moreau J-L , Fontanet A , Lambotte O , Joussemet M , Delfraissy J-F , Thèze J 
Published: February 2006

Summary
HIV infection activates abnormally the immune system and the chronic phase is accompanied by marked alterations in the CD8 compartment. The expression of CD127 (IL-7R alpha chain) by memory CD8 T lymphocytes in HIV-infected patients is analysed and reported. The memory CD8 T cell subset was characterized by expression of CD45RA and CD27 markers, and CD127 cell surface expression was measured ex vivo by four-colour flow cytometry. HIV infection was associated with a fall in the proportion of CD127+ cells among memory CD8 lymphocytes that resulted in a higher CD127– CD45RA–CD27+ CD8 T cell count in HIV-infected patients. Diminished CD127 cell surface expression [mean fluorescence intensity (MFI)] by positive cells was also observed in this subset. The data suggest that these defects were reversed by highly active anti-retroviral therapy (HAART). The regulation of CD127 expression was also studied in vitro. Down-regulation of CD127 by interkeukin (IL)-7 was observed in memory CD8 lymphocytes from healthy donors and HAART patients. Expression of CD127 by memory CD8 lymphocytes cultured in the absence of IL-7 confirmed that IL-7R regulation is altered in viraemic patients. Under the same experimental conditions, memory CD8 lymphocytes from HAART patients were shown to express CD127 at levels comparable to cells from healthy individuals. Altered CD127 cell surface expression and defective CD127 regulation in the memory CD8 T lymphocytes of HIV-infected patients are potential mechanisms by which these cells may be impeded in their physiological response to endogenous IL-7 stimulatory signals. Our data suggest that these defects are reversed during the immune reconstitution that follows HAART.
Increased expression and secretion of interleukin-6 in human parvovirus B19 non-structural protein (NS1) transfected COS-7 epithelial cells
Authors: Hsu T-C , Tzang B-S , Huang C-N , Lee Y-J , Liu G-Y , Chen M-C , Tsay G J 
Published: February 2006

Summary
Human parvovirus B19 (B19) has been associated with a variety of autoimmune diseases, including rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). We have demonstrated previously that B19 non-structural protein (NS1) induced apoptosis through the mitochondria cell death pathway in COS-7 epithelial cells and that B19 NS1 may play a role in the pathogenesis of autoimmune diseases. In order to examine the expression profiles of cytokines and chemokines in B19 NS1 transfected COS-7 cells, we constructed the NS1 gene in the pEGFP-C1 vector named enhanced green fluorescence protein gene (EGFP)-NS1. COS-7 cells were transfected with EGFP or EGFP-NS1 plasmid. The expression profiles of cytokines and chemokines, including interleukin (IL)-1β, IL-5, IL-6, IL-8, IL-10, tumour necrosis factor (TNF)-α, transforming growth factor (TGF)-β, granulocyte–macrophage colony-stimulating factor (GM-CSF), growth-related oncogene α (GROα), interferon gamma-inducible protein (IP)-10, stromal cell derived factor (SDF)-1, macrophage inflammatory protein (MIP)-1β, monocyte chemoattractant protein (MCP)-1, regulated upon activation normal T cell expressed and secreted (RANTES), Fractalkine, CX3CR1, CCR2, CCR5 and CCR11 were examined in COS-7 cells, EGFP and EGFP-NS1 transfected cells using enzyme-linked immunosorbent assay (ELISA) or reverse transcription–polymerase chain reaction (RT–PCR). Increased expression and levels of IL-6 were found in EGFP-NS1 transfected cells using RT–PCR and ELISA. There were no significant increases in the expression of IL-1β, IL-8, IP-10, SDF-1, RANTES, Fractalkine, CX3CR-1, CCR2, CCR5, CCR11, TNF-α, GM-CSF and TGF-β using RT–PCR. There were no significantly increased levels of IL-5, IL-10, TNF-α, TGF-β, GROα, MIP-1β and MCP-1 found by ELISA in this study. Our results show that increased expression and secretion of IL-6 in B19 NS1 transfected epithelial cells may play a role in the pathogenesis of autoimmune diseases.
A role for CD4+CD25+ T cells in regulation of the immune response during human tuberculosis
Authors: Ribeiro-Rodrigues R , Resende Co T , Rojas R , Toossi Z , Dietze R , Boom W H , Maciel E , Hirsch C S 
Published: February 2006

Summary
Active tuberculosis (TB) is associated with prolonged suppression of Mycobacterium tuberculosis (MTB)-specific immune responses, but mechanisms involved are understood incompletely. We investigated a potential role for CD4+CD25+ regulatory T cells in depressed anti-MTB immunity by evaluating serially CD4 cell phenotype and interferon (IFN)-γ production by mononuclear cells from patients with TB. At diagnosis, frequencies of CD4+CD25+ T cells were increased in blood from TB patients compared to healthy purified protein derivative (PPD)-positive controls (with a history of prior TB exposure), and remained elevated at completion of therapy (6 months). By contrast, expression of another activation marker, CD69, by CD4 T cells was increased at diagnosis, but declined rapidly to control levels with treatment. Among CD4+CD25+ T cells from TB patients at diagnosis those expressing high levels of CD25, probably representing regulatory T cells, were increased 2·9-fold when compared to control subjects, while MTB-stimulated IFN-γ levels in whole blood supernatants were depressed. A role for CD4+CD25+ T cells in depressed IFN-γ production during TB was substantiated in depletion experiments, where CD25+-depleted CD4 T cells produced increased amounts of IFN-γ upon MTB stimulation compared to unseparated T cells. At follow-up, IFN-γ production improved most significantly in blood from TB patients with high baseline frequencies of CD4+CD25+ T cells (more than threefold higher than controls for both total and CD25hi+ CD4 T cells), who also had a significant drop in frequencies of both total and ‘regulatory’ CD4+CD25+ T cells in response to treatment. Expansion of CD4+CD25+ regulatory T cells during active TB may play a role in depressed T cell IFN-γ production.