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At least 847 records · Page 47Linked to original sources
PubMed2005

Phenotypic and functional analysis of EBV-specific memory CD8 cells in SLE.

T cell dysfunction has been described in systemic lupus erythematosus (SLE). However, the specific phenotype and function of antigen-specific CD8 cells is less clear. Here we determined phenotype and function of Epstein-Barr virus (EBV)-specific CD8 cells at the single-cell level in SLE. HLA-A2-restricted EBV-BMLF-1-specific CD8 cells were enumerated by flow cytometry using tetramers in SLE and healthy control subjects. Antigen-specific CD8 cells were analyzed for expression of differentiation, activation, proliferation, and anti-apoptotic markers. EBV-specific, other virus-specific (specific against a viral peptide pool consisting of cytomegalovirus, EBV and influenza virus peptides), and mitogen-induced CD8 cell function was assessed by INF-gamma ELISPOT assay. Frequencies of EBV-specific CD8 cells tended to be greater in SLE subjects than in healthy control subjects (p=0.07). While over 10% of EBV-specific CD8 cells were capable of producing IFN-gamma in four out of five healthy control subjects, such proportions of EBV-specific CD8 cells capable of IFN-gamma production were observed in only one out of six SLE subjects (p=0.04). In contrast, viral peptide pool-specific and mitogen-induced IFN-gamma-producing T cell function was intact in SLE subjects. Phenotypic analysis revealed EBV-specific CD8 cells to be in an early to intermediate differentiation and resting memory state in both groups. While EBV-specific CD8 cells are similar in phenotype, their frequency tends to be increased, and function appears to be decreased in SLE. Therefore, an impaired EBV-specific CD8 immune response may exist in SLE, potentially contributing to disease pathogenesis.

Adult↗
PubMed2000

Cloning and characterization of Echinococcus granulosus (Cestode) EgactI and EgactII actin gene promoters and their functional analysis in the NIH3T3 mouse cell line.

We report here for the first time the structure and function of a promoter from a cestode. The ability of DNA fragments respectively encompassing the 935-bp and 524-bp regions upstream from the ATG codon from the EgactI and EgactII actin genes of Echinococcus granulosus to promote transcription was studied in the NIH3T3 mouse cell line. The results of transfection assays showed that both regions have strong promoter activity in these cells. The fragments were tested in both orientations and the 524-bp fragment of EgactII presented a bidirectional promoter activity. Deletion analysis of EgactI and EgactII promoters indicated the presence of regulatory regions containing putative silencer elements. These results indicate that both EgactI and EgactII promoters are functional and that the preliminary functional evaluation of E. granulosus and possibly of other cestode promoters can be performed in heterologous cell lines.

3T3 Cells↗
PubMed2000

Oligodendrocytes as glucocorticoids target cells: functional analysis of the glycerol phosphate dehydrogenase gene.

Previous research has established that the development and function of oligodendrocytes are influenced by glucocorticoids. The enzyme glycerol phosphate dehydrogenase (E.C.1.1.1.8) has been used as a model to study glucocorticoid regulation of gene expression in oligodendrocytes and the C6 glial cell line. In the rat brain this enzyme is exclusively localized to oligodendrocytes. The sequence of the 5' flanking region for the rat gene encoding Glycerol Phosphate Dehydrogenase (GPDH; EC 1.1.1.8) was determined. 4 kb of sequence from the 5' flanking region, exon 1, and part of intron 1 of the rat GPDH gene was compared to the corresponding mouse sequence. Dotplot matrix comparison revealed that the rat sequence is more than 80% similar to the mouse sequence, but differs from the mouse sequence in two regions: the rat sequence is devoid of 200 bp of B1 repeat sequence that is present in the mouse, and the rat sequence has an excess 700 bp of B2 repeat sequence inserted between -0.7 kb and -1. 4 kb that is absent in the mouse. To determine the regulatory activity of the rat GPDH 5' flanking region, various portions of the rat GPDH 5' flanking region were placed in luciferase reporter constructs and tested for transcriptional activity. Transient transfection of reporter constructs into the C6 glial cell line revealed that the distal end of the 5' flanking region was glucocorticoid-inducible. A 385 bp Glucocorticoid Response Unit (GRU) was identified whose glucocorticoid induction was enhanced by dibutyryl-cAMP and reduced by phorbol esters. Sequence analysis of the GRU revealed the presence of four consensus GRE sequences and other putative consensus elements. Results here suggest that the 5' flanking region of the GPDH gene mediates the ligand-inducible regulation of GPDH, and that multiple signaling pathways converge at the 5' regulatory sequence to modulate GPDH gene expression in oligodendrocytes.

Animals↗
PubMed2000

Identification by functional analysis of the gene encoding alpha-isopropylmalate synthase II (LEU9) in Saccharomyces cerevisiae.

The function of the open reading frame (ORF) YOR108w of Saccharomyces cerevisiae has been analysed. The deletion of this ORF from chromosome XV did not give an identifiable phenotype. A mutant in which both ORF YOR108w and LEU4 gene have been deleted proved to be leucine auxotrophic and alpha-isopropylmalate synthase (alpha-IPMS)-negative. This mutant recovered alpha-IPMS activity and a Leu(+) phenotype when transformed with a plasmid copy of YOR108w. These data and the sequence homology indicated that YOR108w is the structural gene for alpha-IPMS II, responsible for the residual alpha-IPMS activity found in a leu4Delta strain. The leu4Delta strain appeared to be very sensitive to the leucine analogue trifluoroleucine. In the absence of leucine, its growth was not much impaired in glucose but more on non-fermentable carbon sources.

2-Isopropylmalate Synthase↗
PubMed2006

Functional analysis of ori1 and repA of the R-plasmid pSJ5.6 from Neisseria gonorrhoeae.

The functional ori1 of the 5.6kb gonococcal R-plasmid pSJ5.6 contains an A-T rich region followed by four 22bp direct repeats and one 19bp inverted repeat. The replication region of the plasmid also contains a gene encoding for a 39kD RepA protein. We have further assessed the functionality of the replication region in pSJ5.6, an-iteron type plasmid, using in vivo complementation assays in Escherichia coli. A 2.1kb PstI-RsaI fragment containing the ori1 and repA gene of pSJ5.6 was cloned into vector pZErO -2 to obtain pZA-MRR. The pUC origin in pZA-MRR was deleted to render the plasmid dependable on the cis-acting ori1 for replication. The resulting plasmid, pMRR, was capable of replication and maintenance in E. coli. We also cloned the ori1 and repA gene separately to obtain pA-Ori and pZG-Rep, respectively. Using in vivo complementation assays, we demonstrated that the ori1(+) plasmid (pA-Ori) was maintained only when the RepA protein was supplied in trans by the high copy number plasmid pZG-Rep.

Bacterial Proteins↗
PubMed2005

Plant secondary metabolism glycosyltransferases: the emerging functional analysis.

Glycosylation is a widespread modification of plant secondary metabolites. It is involved in various functions, including the regulation of hormone homeostasis, the detoxification of xenobiotics and the biosynthesis and storage of secondary compounds. In plants, these reactions are controlled by a specific subclass of the ubiquitous glycosyltransferase family. Although these enzymes have been studied intensively for many years, to date only a handful have been characterized in planta. Plant genome projects have uncovered unsuspected complexity within this family that is hindering the characterization of single genes. However, genome information also paves the way for the development of functional genomic approaches. Here, we highlight recent progress and the outcomes of novel strategies developed to uncover the physiological roles of these glycosyltransferases.

Genome, Plant↗
PubMed2002

[Clinical and functional analysis of long-term results of uvulopalatopharyngoplasty].

In order to evaluate the clinical and functional effectiveness of uvulopalatopharyngoplasty (UPPP) in chronic roncopathy, we studied the subjective improvement of operated patients and compared to pulsioximetry findings before and after surgery. A follow-up was made on 72 patients entitled of chronic roncopathy--51 with obstructive sleep apnea syndrome (OSAS) and 21 with simple snoring-, for a mean period of time of 41 months. Preoperatory study included on ENT exploration, fibre optic endoscopy, Müller maneuver, pharyngeal CT, value of daytime sleepiness with Epworth's scale, espirometry and pulsioximetry, and the postoperatory study included of pulsioximetry and a health questionnaire over snoring and daytime sleepiness. Snoring improved or disappeared in 13 of 21 patients (61.8%), and daytime sleepiness did it in 26 of 39 (66.6%). Therapeutic failure in snoring was mainly due to an increase in the body mass index. After UPPP in OSAS, only 21 patients (41.1%) showed all positive response criteria (decrease into ODI > or = 50% or in absolute values < 6, CT 90% < 1%, and SaO2 Min > or = 85%). UPPP failed in long term evaluation in the rest of individuals. Patient selection is mandatory to optimize clinical response of UPPP for snoring, without OSAS success depends on body mass index, respiratory disturbances ratios and the eventual presence of another upper airways collapses below velopharyngeal segment.

Adult↗
PubMed2004

Molecular and functional analysis of the dictyostelium centrosome.

The centrosome is a nonmembranous, nucleus-associated organelle that functions not only as the main microtubule-organizing center but also as a cell cycle control unit. How the approximately 100 different proteins that make up a centrosome contribute to centrosome function is still largely unknown. Considerable progress in the understanding of centrosomal functions can be expected from comparative cell biology of morphologically different centrosomal structures fulfilling conserved functions. Dictyostelium is an alternative model organism for centrosome research in addition to yeast and animal cells. With the elucidation of morphological changes and dynamics of centrosome duplication, the establishment of a centrosome isolation protocol, and the identification of many centrosomal components, there is a solid basis for understanding the biogenesis and function of this fascinating organelle. Here we give an overview of the prospective protein inventory of the Dictyostelium centrosome based on database searches. Moreover, we focus on the comparative cell biology of known components of the Dictyostelium centrosome including the gamma-tubulin complex and the homologues of centrin, Nek2, XMAP215, and EB1.

Animals↗
PubMed2002

Structural-functional analysis of bacteriophage T7 RNA polymerase.

This review summarizes our results of the structural and functional studies of bacteriophage T7 DNA-dependent RNA polymerase (T7 RNAP). Particular features of this enzyme (the single-subunit composition, relatively low molecular weight) make it the most convenient model for investigating the physicochemical aspects of transcription. The review discusses the main properties of T7 RNAP, interaction between the enzyme and promoter, principle stages of T7-transcription, and also the results of structural and functional studies by affinity modification and both random and site-directed mutagenesis techniques.

Amino Acid Sequence↗
PubMed2000

Specificity and functional analysis of the pH-responsive element within renal glutaminase mRNA.

The specificity and the functional significance of the binding of a specific cytosolic protein to a direct repeat of an eight-base AU sequence within the 3'-nontranslated region of the glutaminase (GA) mRNA were characterized. Competition experiments established that the protein that binds to this sequence is not an AUUUA binding protein. When expressed in LLC-PK(1)-F(+) cells, the half-life of a beta-globin reporter construct, betaG-phosphoenolpyruvate carboxykinase, was only slightly affected (1.3-fold) by growth in acidic (pH 6.9, 10 mM HCO(-)(3)) vs. normal (pH 7.4, 25 mM HCO(-)(3)) medium. However, insertion of short segments of GA mRNA containing the direct repeat or a single eight-base AU sequence was sufficient to impart a fivefold pH-responsive stabilization to the chimeric mRNA. Furthermore, site-directed mutation of the direct repeat of the 8-base AU sequence in a betaG-GA mRNA, which contains 956 bases of the 3'-nontranslated region of the GA mRNA, completely abolished the pH-responsive stabilization of the wild-type betaG-GA mRNA. Thus either the direct repeat or a single eight-base AU sequence is both sufficient and necessary to create a functional pH-response element.

Acidosis↗
PubMed1979

Functional analysis of organic sphincter systems by elastance-measurement. Evaluation of a new method.

The function of organic sphincter systems cannot be described by measuring a static pressure, but only by applying a dynamic procedure of measurement that takes into account the characteristics of smooth muscles. Therefore, the elastance-method has been developed. Experiences with this method and its clinical value are demonstrated when one applies this procedure to measurements in the lower oesophagus, the duodenal papilla and the anal canal.

Ampulla of Vater↗
PubMed1995

Functional analysis of human MT and related visual cortical areas using magnetic resonance imaging.

Using noninvasive functional magnetic resonance imaging (fMRI) technique, we analyzed the responses in human area MT with regard to visual motion, color, and luminance contrast sensitivity, and retinotopy. As in previous PET studies, we found that area MT responded selectively to moving (compared to stationary) stimuli. The location of human MT in the present fMRI results is consistent with that of MT in earlier PET and anatomical studies. In addition we found that area MT has a much higher contrast sensitivity than that in several other areas, including primary visual cortex (V1). Functional MRI half-amplitudes in V1 and MT occurred at approximately 15% and 1% luminance contrast, respectively. High sensitivity to contrast and motion in MT have been closely associated with magnocellular stream specialization in nonhuman primates. Human psychophysics indicates that visual motion appears to diminish when moving color-varying stimuli are equated in luminance. Electrophysiological results from macaque MT suggest that the human percept could be due to decreases in firing of area MT cells at equiluminance. We show here that fMRI activity in human MT does in fact decrease at and near individually measured equiluminance. Tests with visuotopically restricted stimuli in each hemifield produced spatial variations in fMRI activity consistent with retinotopy in human homologs of macaque areas V1, V2, V3, and VP. Such activity in area MT appeared much less retinotopic, as in macaque. However, it was possible to measure the interhemispheric spread of fMRI activity in human MT (half amplitude activation across the vertical meridian = approximately 15 degrees).

Animals↗
PubMed2004

Density and wave function analysis of actinide complexes: what can fuzzy atom, atoms-in-molecules, Mulliken, Lowdin, and natural population analysis tell us?

Recent advances in computational methods have made it possible to calculate the wave functions for a wide variety of simple actinide complexes. Equally important is the ability to analyze the information contained therein and produce a chemically meaningful understanding of the electronic structure. Yet the performance of the most common wave function analyses for the calculation of atomic charge and bond order has not been thoroughly investigated for actinide systems. This is particularly relevant because the calculation of charge and bond order even in transition metal complexes is known to be fraught with difficulty. Here we use Mulliken, Lowdin, natural population analysis, atoms-in-molecules (AIM), and fuzzy atom techniques to determine the charges and bond orders of UO(2)(2+), PuO(2)(2+), UO(2), UO(2)Cl(4)(2-), UO(2)(CO)(5)(2+), UO(2)(CO)(4)(2+), UO(2)(CN)(5)(3-), UO(2)(CN)(4)(2-), UO(2)(OH)(5)(3-), and UO(2)(OH)(4)(2-). This series exhibits a clear experimental and computational trend in bond lengths and vibrational frequencies. The results indicate that Mulliken and Lowdin populations and bond orders are unreliable for the actinyls. Natural population analysis performs well after modification of the partitioning of atomic orbitals to include the 6d in the valence space. The AIM topological partitioning is insensitive to the electron donating ability of the equatorial ligands and the relative atomic volume of the formally U(VI) center is counterintuitively larger than that of O(2-) in the UO(2)(2+) core. Lastly, the calibrated fuzzy atom method yields reasonable bond orders for the actinyls at significantly reduced computational cost relative to the AIM analysis.

Journal Article↗
PubMed2001

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data.

Upon the completion of the SACCHAROMYCES: cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) NATURE:, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the SACCHAROMYCES: Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at genome-www.stanford. edu/Saccharomyces/.

Databases, Factual↗
PubMed2004

Optimizing donor heart outcome after prolonged storage with endothelial function analysis and continuous perfusion.

BACKGROUND: By minimizing tissue ischemia, continuous perfusion (CP) during organ transport may increase the safety of "marginal donors." My colleagues and I investigated whether an analysis of donor heart viability predicts recovery of grafts challenged with a 24-hour preservation interval. METHODS: Dog hearts underwent cold static storage (CS) for 8 hours (n = 8) or 24 hours (n = 2) or CP for 24 hours with cold asanguinous, oxygenated solution (n = 8). Myocardial systolic and diastolic function and oxygen and lactate consumption were assessed at base line, during CP, and after Langendorff blood reperfusion. Base line endothelial function was evaluated by the percentage transcoronary change ([coronary sinus - aorta]/aorta) in myeloperoxidase and by platelet function and coronary flow reserve after 20 seconds of coronary artery occlusion. During CP, the endothelium was assessed by transcoronary protein release and coronary resistance. Edema was assessed by weight gain and histology. RESULTS: Base line systolic and metabolic functions showed no relation to post-Langendorff function. Compared with CS, CP resulted in a greater recovery in systolic function (87% +/- 35% vs 65% +/- 15% of baseline; p = 0.05) and a shorter interval required for lactate consumption to exceed production (7.0 +/- 6.8 minutes vs 15.0 +/- 8.9 minutes; p = 0.06). Endothelial function was heterogeneous: coronary flow reserve, 2.7 +/- 0.7; percentage change in myeloperoxidase, -8.4% +/- 6.8%; and change in platelet function, 4.3% +/- 3.5%, as determined by thromboelastography angle at base line. Protein release during CP for 24 hours was 8.3 +/- 7.1 g. Two factors predicted more than 75% systolic pressure generation recovery: use of CP and normal endothelial function (p = 0.05; Fisher's exact test). However, CP led to edema according to histology, weight gain (72 +/- 29 g), and impaired diastolic function versus CS (end-diastolic pressure-volume relationship, 1.4 +/- 0.4 mm Hg/mL vs 0.8 +/- 0.3 mm Hg/mL; p = 0.08). CONCLUSIONS: Better systolic function despite 16 hours' more preservation than cold storage corroborates the idea that CP supports aerobic metabolism at physiologically important levels. Viability analysis focused on endothelial function and identified organs that were able to tolerate this 24-hour preservation interval.

Aerobiosis↗
PubMed2003

Characterization, localization and functional analysis of Gpr1p, a protein affecting sensitivity to acetic acid in the yeast Yarrowia lipolytica.

Adaptation of cells to acetic acid requires a hitherto unknown number of proteins. Studies on the GPR1 gene and its encoded protein in the ascomycetous fungus Yarrowia lipolytica have revealed an involvement of this protein in the molecular processes of adaptation to acetic acid. Gpr1p belongs to a novel family of conserved proteins in prokaryotic and eukaryotic organisms that is characterized by the two motifs (A/G)NPAPLGL and SYG(X)FW (GPR1_FUN34_YaaH protein family). Analysis of four trans-dominant mutations and N-terminal deletion analysis of Gpr1p identified the amino acid sequence FGGTLN important for function of this protein in Y. lipolytica. Deletion of GPR1 slowed down adaptation to acetic acid, but had no effect on growth in the presence of acetic acid. Expression of GPR1 is induced by acetic acid and moderately repressed by glucose. It was shown by subcellular fractionation that Gpr1p is an integral membrane protein, which is also suggested by the presence of five to six putative transmembrane spanning regions. Fluorescence microscopy confirmed a localization to the plasma membrane. A model is presented describing a hypothetical function of Gpr1p during adaptation to acetic acid.

Acetic Acid↗
PubMed2004

Bayesian integrated functional analysis of microarray data.

MOTIVATION: The statistical analysis of microarray data usually proceeds in a sequential manner, with the output of the previous step always serving as the input of the next one. However, the methods currently used in such analyses do not properly account for the fact that the intermediate results may not always be correct, then leading to cumulating error in the inferences drawn based on such steps. RESULTS: Here we show that, by an application of hierarchical Bayesian methodology, this sequential procedure can be replaced by a single joint analysis, while systematically accounting for the uncertainties in this process. Moreover, we can also integrate relevant functional information available from databases into such an analysis, thereby increasing the reliability of the biological conclusions that are drawn. We illustrate these points by analysing real data and by showing that the genes can be divided into categories of interest, with the defining characteristic depending on the biological question that is considered. We contend that the proposed method has advantages at two levels. First, there are gains in the statistical and biological results from the analysis of this particular dataset. Second, it opens up new possibilities in analysing microarray data in general.

Algorithms↗
PubMed2006

Multiscale probability density function analysis: non-Gaussian and scale-invariant fluctuations of healthy human heart rate.

For a detailed characterization of intermittency and non-Gaussianity of human heart rate, we introduce an analysis method to investigate the deformation process of the probability density function (PDF) of detrended increments when going from fine to coarse scales. To characterize the scale dependence of the multiscale PDF, we use two methods: 1) calculation of Kullback-Leibler relative entropy; 2) parameter estimation based on Castaing's equation (B. Castaing et al, 1990). We compare scale-dependence of the increment PDFs between actual heart rate fluctuations and artificially generated Gaussian and non-Gaussian noise, including a widely used autoregressive model and a recently proposed multifractal model based on a random cascade process. Our analysis highlights an essential difference between heart rate fluctuations and those generated by other models. The outstanding feature of human heart rate is the robust scale-invariance of the non-Gaussian PDF, which is preserved not only in a quiescent condition, but also in a dynamic state during waking hours, in which the mean level of heart rate is dramatically changing. Our results strongly suggest the need for revising existing models of heart rate variability to incorporate the scale-invariance in the PDF.

Adult↗