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At least 973 records · Page 54Linked to original sources
PubMed2005

MSight: an image analysis software for liquid chromatography-mass spectrometry.

Images obtained from high-throughput mass spectrometry (MS) contain information that remains hidden when looking at a single spectrum at a time. Image processing of liquid chromatography-MS datasets can be extremely useful for quality control, experimental monitoring and knowledge extraction. The importance of imaging in differential analysis of proteomic experiments has already been established through two-dimensional gels and can now be foreseen with MS images. We present MSight, a new software designed to construct and manipulate MS images, as well as to facilitate their analysis and comparison.

Chromatography, Liquid↗
PubMed2002

Evaluation of cadmium-induced transcriptome alterations by three color cDNA labeling microarray analysis on a T-cell line.

Beside heavy metals, cadmium (Cd(2+)) is a ubiquitous toxic metal with a well established apoptotic and genotoxic effect, chronic exposure of which has been involved in a variety of pathological conditions. In the present study, we investigated by 1455 genes cDNA microarrays the toxic and apoptotic effect of Cd(2+), on the T-cell line CCRF-CEM, applying a three laser differential analysis, on the same microarray slide. The cells were cultured for 6 and 24 h in the absence (control) or presence of Cd(2+) (10 or 20 microM), RNAs were extracted and the produced cDNAs were labeled with rhodamine derivatives fluorescent dyes. A microarray slide was simultaneously hybridized by the labeled cDNAs and analyzed. We found that, in relation to control, treatment of the cells for 6 h with 10 and 20 microM Cd(2+), induces up-regulation in 20 and 34 genes, respectively. Treatment for 24 h with 10 and 20 microM Cd(2+) induces up-regulation in 22 and 84 genes, respectively. Twenty-eight genes were found down-regulated only after treatment for 24 h with Cd(2+) 10 microM. These data suggest that Cd(2+) produces a time- and dose-dependent molecular cascade, induces disturbances in different subcellular compartments, influencing thereafter the normal cellular functions, the differentiation process, the malignant transformation and the cell death.

Apoptosis↗
PubMed1994

Evaluation of c-erbB-2 amplification in breast carcinoma by differential polymerase chain reaction.

Previous studies have found that amplification and overexpression of the c-erbB-2 oncogene in mammary ductal adenocarcinomas predicts decreased disease-free or overall survival. Information regarding the prognostic and pathogenetic significance of oncogene amplification has been limited by difficulty obtaining sufficient quantities of high molecular weight DNA for Southern blot analysis. Differential polymerase chain reaction (PCR) has been suggested as an alternative method for evaluating gene amplification and can be performed using formalin-fixed paraffin-embedded specimens. The authors of this study used differential PCR to detect c-erbB-2 gene amplification and immunohistochemistry to evaluate c-erbB-2 expression. A highly significant degree of concordance (P < .002) between c-erbB-2 amplification and expression was observed. Abnormalities of c-erbB-2 copy number or expression were more common in tumors with higher histologic grade, and trends were noted toward association with other prognostically unfavorable biologic markers, such as reduced progesterone receptor content and DNA aneuploidy.

Base Sequence↗
PubMed1999

[Rheumatic diseases of the ankle joint and tarsus].

Diseases of the hindfoot are associated with considerable functional impairment and therefore may hamper patients' movements during gait considerably. Because of biomechanical overload, articular structures, tendons and ligaments are prone to early degenerative changes during the course of rheumatic diseases as visible with plain film radiography, sonography (US), or magnetic resonance imaging (MRI). Findings may occur as arthritis of major joints or in the form of fibroostitis and bursitis of the os calcis. Despite the progressive course of rheumatic diseases and characteristic imaging findings, high variability of X-ray signs may occur. Plain film radiograms and high-resolution ultrasonography play a key role in imaging rheumatic diseases of the hindfoot. MRI supports imaging diagnosis in selected cases. The principal goals of diagnostic imaging are precise and reproducible documentation of morphologic abnormalities and differentiated analysis for planning proper conservative or surgical treatment.

Ankle↗
PubMed2006

Statistical search space reduction and two-dimensional data display approaches for UPLC-MS in biomarker discovery and pathway analysis.

A new analytical strategy for biomarker recovery from directly coupled ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC Tof MS) data on biofluids is presented and exemplified using a study on hydrazine-induced liver toxicity. A key step in the strategy involves a novel procedure for reducing the spectroscopic search space by differential analysis of cohorts of normal and pathological samples using an orthogonal projection to latent structures discriminant analysis (O-PLS-DA). This efficiently sorts principal discriminators of toxicity from the background of thousands of metabolic features commonly observed in data sets generated by UPLC-MS analysis of biological fluids and is thus a powerful tool for biomarker discovery.

Animals↗
PubMed2003

Activation induced differential regulation of stem cell antigen-1 (Ly-6A/E) expression in murine B cells.

Expression of stem cell antigen-1 (Ly-6A/E) is developmentally regulated in murine B cells. However, little is known about its modulation during B cell activation. We report here the differential regulation of Ly-6A/E expression in response to diverse activation signals in mature B cells. Stimulation of resting B cells through the antigen receptor (BCR) inhibited, Ly-6A/E surface expression in dose dependent manner. Activation induced downregulation of Ly-6A/E is specific to BCR mediated signaling events as stimulation of B cells with anti-CD40, lipopolysaccharide or interferon-gamma induced upregulation of Ly-6A/E surface expression. The activation induced differential modulation of Ly-6A/E expression is mediated at the mRNA levels. A role for BCR signaling in inhibition of Ly-6A/E expression was further confirmed using STAT-1(-/-) B cells, which expressed constitutive, but not inducible Ly-6A/E. The BCR induced inhibition of Ly-6A/E RNA and surface expression was mimicked by ionomycin, but not phorbol myristate acetate, indicating a role for calcium but not protein kinase C dependent signaling events. Inhibition of calcineurin reversed the BCR or ionomycin inhibited Ly-6A/E expression. Interestingly, in vitro differentiation analysis of Ly-6A/E(+) and Ly-6A/E(-) splenic B cells revealed the Ly-6A/E(+) cells to be the major source of antibody production, suggesting a potential role for Ly-6A/E in B cell differentiation. These studies provide the first evidence for activation induced differential modulation and differentiation of Ly-6A/E(+) B cells.

Animals↗
PubMed2004

Gene expression profiling identifies matriptase overexpression in malignant mesothelioma.

STUDY OBJECTIVE: We investigated the gene expression profiles of malignant pleural mesothelioma (MPM) specimens to identify novel genes that are potentially involved in the oncogenic transformation of human pleural cells. DESIGN: Complementary DNA (cDNA) microarray transcriptional profiling studies of 10 MPM cell lines and 4 MPM primary tumor specimens were performed using hierarchic clustering. To confirm microarray data, we used real-time polymerase chain reaction and immunoblotting. RESULTS: Cluster analysis differentiated among epithelial (E), sarcomatoid, and biphasic MPM variants. Expression profiling identified common overexpressed or underexpressed genes in MPM. Notably, matriptase messenger RNA was found to be overexpressed by 826-fold in E MPM, with protein expression subsequently confirmed by immunoblot analysis. This recently characterized trypsin-like serine protease has been implicated in tumor invasion and metastasis of E-derived cancers, but has not been described until now in MPM. We also identified other novel genes, such as insulin-like growth factor binding protein 5 and a cDNA clone similar to proteolipid MAL2. CONCLUSIONS: Thus, further large-scale profiling of MPM may elucidate previously unrecognized molecular mechanisms by identifying novel genes that are involved in malignant transformation. Our study has now found matriptase to be one of these mesothelioma-associated genes, with potential pathogenic and therapeutic significance.

Cell Line, Tumor↗
PubMed1997

Differentiation between bacterial species and sub-species by pyrolysis mass spectrometry of extracted DNA.

Whole cell samples from cultures of Staphylococcus aureus, S. hominis, S. epidermidis and Streptococcus pyogenes were analysed by pyrolysis mass spectrometry and the results were compared with Py-MS-derived analyses of samples of DNA extracted from the same organisms. Py-MS analysis differentiated the four organisms in both circumstances. These results challenge previous assumptions that Py-MS is restricted to detecting phenotypic differences, although the basis for the differentiation of the DNA extracts has yet to be determined.

DNA, Bacterial↗
PubMed1994

Structural and ultrastructural characteristics of human pineal gland, and pineal parenchymal tumors.

We have studied 20 pineal parenchymal tumors (PPT) and 4 normal or cystic pineal glands both by light and electron microscopy and immunohistochemistry with antibodies against glial markers [glial fibrillary acidic protein (GFAP) and protein S-100] or neural/neuroendocrine markers [neurofilaments (NF), synaptophysin and chromogranin A]. Light microscopy revealed the cellular organization of pinealocytes in the normal gland and in different morphological types of pineal tumors (typical pineocytomas, PPT with intermediate differentiation, mixed PPT exhibiting elements of both pineocytoma and pineoblastoma and pineoblastomas). Immunohistochemistry showed the presence of GFAP and protein S-100 in interstitial cells in non-neoplastic pineal gland. Cell processes were labeled with anti-synaptophysin and anti-NF antibodies. No immunoreactivity was found for chromogranin A in non-neoplastic pineal gland. In pineocytomas, GFAP and protein S-100 were observed in interstitial cells. Synaptophysin and NF were present in the large rosettes of pineocytomas. Synaptophysin, NF and chromogranin A were present in pineocytomas with a lobular arrangement of cells. Anti-chromogranin A immunoreactivity was also seen in lobular areas of some PPT with intermediate differentiation. Analysis of normal human pineal gland by electron microscopy showed the presence of vesicle-crowned rodlets (VCR or synaptic ribbons), fibrous filaments (F), paired twisted filaments but few dense-core vesicles (DCV) in normal pinealocytes. Tumoral pineal cells appeared to differentiate either towards a neurosensory pathway characterized by the presence of sensory cells elements (VCR and F), or towards a neuroendocrine pathway, with the occurrence of many DCV. Immunogold labeling demonstrated the presence of chromogranin A in neurosecretory granules.

Adolescent↗
PubMed1985

[Madness in Zola's writing. II. Interactions of insanity in La Joie de Vivre. 1. Situations and psychopathologic types].

In The gladness of life (1884: La joie de vivre) d'E. Zola, madness in full interaction call to a psychopathological analysis which is doing in three parts: The situations and psychopathological types; the psychopathological and anthropological relationship; The text's unconscious and the work of mourning. This part, proposes the analysis of the psychopathological types (cyclic psychosis of Lazare, the "typus melancholicus" of Véronique, the paranoia of madam Chanteau, the "crack" and masochism of Pauline) and the pathogenic-situations in the most narrow interaction ("in" and "out" of the personages). A differential analysis is proposed between the pessimist position and the nihilist one, in a therapeutic perspective.

France↗
PubMed1996

Codon usage and base composition in Rickettsia prowazekii.

Codon usage and base composition in sequences from the A + T-rich genome of Rickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21 R. prowazekii proteins with that of a homologous set of proteins from Escherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests that R. prowazekii has around 800 genes and that 60-70% of the genome may be coding.

Base Composition↗
PubMed2001

Beta-catenin dysregulation in thyroid neoplasms: down-regulation, aberrant nuclear expression, and CTNNB1 exon 3 mutations are markers for aggressive tumor phenotypes and poor prognosis.

beta-catenin has a role in cell adhesion and Wnt signaling. It is mutated or otherwise dysregulated in a variety of human cancers. In this study we assess beta-catenin alteration in 145 thyroid tumors samples from 127 patients. beta-catenin was localized using immunofluorescence and mutational analysis was performed by single-strand conformational polymorphism. Membrane beta-catenin expression was decreased in eight of 12 (66%) adenomas and in all 115 carcinomas (P: < 0.0001). Among carcinomas, reduced membrane beta-catenin was associated with progressive loss of tumor differentiation (P: < 0.0001). CTNNB1 exon 3 mutations and nuclear beta-catenin localization were restricted to poorly differentiated [7 of 28 (25%) and 6 of 28 cases (21.4%), respectively] or undifferentiated carcinomas [19 of 29 (65.5%) and 14 of 29 (48.3%) cases, respectively]. Poorly differentiated tumors always featured mutations involving Ser and Thr residues and were characterized by Thr to Ile amino acid substitutions (P: = 0.0283). The association between CTNNB1 exon 3 mutations and aberrant nuclear immunoreactivity (P: = 0.0020) is consistent with Wnt activation because of stabilizing beta-catenin mutations. Low membrane beta-catenin expression as well as its nuclear localization or CTNNB1 exon 3 mutations are significantly associated with poor prognosis, independent of conventional prognostic indicators for thyroid cancer but not of tumor differentiation. Analysis of beta-catenin dysregulation may be useful to objectively subtype thyroid neoplasms and more accurately predict outcomes.

Adenoma↗
PubMed1997

Differentiation of Arthroderma spp. by random amplification of polymorphic DNA (RAPD) and Southern hybridization.

To develop the molecular differentiation analysis of dermatophytes, we carried out RAPD and Southern hybridization analyses using genomic DNAs of six Arthroderma species, including A. fulvum, A. grubyi, A. gypseum, A. incurvatum, A. otae and A. racemosum. The RAPD analysis gave different band patterns specific to each of the six Arthroderma fungi. However, minor differences in the banding patterns were observed between the strains of plus (+) and minus (-) mating types of A. gypseum, A. fulvum and A. incurvatum. Southern blot analysis using a probe (1S) obtained from A. grubyi DNA gave specific bands only in the DNA samples of A. grubyi and A. incurvatum. On the other hand, Southern blot analysis using a probe (C3) obtained from A. otae DNA gave specific bands in all six Arthroderma species examined, and the size of the bands were specific to each species. These findings indicate that RAPD and Southern hybridization analyses are useful in the differentiation of these Arthroderma species.

Amino Acid Sequence↗
PubMed1970

Place and modality analysis in nucleus of posterior commissure.

1. Single units (157) responsive to somatic stimulation in the nucleus of the posterior commissure were examined in the cat under chloralose anaesthesia. 87.3% responded to stimulation of all four limbs, 2.4% to three limbs, 8.7% to two limbs and 2% to one limb.2. 44.7% of units could be activated by phasic hair movement; 52.4% responded additionally to auditory stimuli and 34.6% to visual stimuli, although there are marked differences in degree of heterosensory convergence between hair-sensitive units and others.3. Analysis by spike numbers and latencies show marked preference for contralateral limbs.4. Results are compared with those obtained under identical experimental conditions from units of the gigantocellular bulbar reticular formation, and show that anatomically discrete areas of the reticular formation are capable of differential analysis of afferent input.

Animals↗
PubMed2001

Identification of differentially expressed genes in mouse development using differential display and in situ hybridization.

A common problem in developmental biology is the isolation of genes that are expressed differentially between two closely matched tissue populations, for example, between wild-type and mutant mouse embryos generated by targeted gene disruption. Typically, the applicable experimental methodologies are limited by the amount of mRNA that can be obtained for cDNA library construction and/or expression analysis. Differential display is a polymerase chain reaction (PCR)-based RNA fingerprinting technique that is ideally suited for the identification of differentially expressed transcripts when only limiting amounts of tissue are available, as is frequently encountered in studies of vertebrate development. Here, I describe protocols for differential display using arbitrarily primed reverse transcription PCR and for the subsequent verification of differential gene expression that are adapted for molecular genetic studies of mouse embryogenesis. The overall strategy involves two steps: First, RNA samples isolated from two nearly identical populations of embryos or microdissected embryonic tissues are compared by differential display, and candidate differentially expressed transcripts are identified. Second, these candidate transcripts are analyzed for differential expression in vivo using nonradioactive whole-mount or section in situ hybridization. In principle, this strategy permits the efficient isolation of genes that are differentially expressed during early mouse embryogenesis.

Animals↗
PubMed1994

Relaxin influences growth, differentiation and cell-cell adhesion of human breast-cancer cells in culture.

The effects of different concentrations of relaxin (RLX) on growth and differentiation of a human breast-cancer cell line (MCF-7) have been studied after various times of exposure. The cells were cultured for 4 and 7 days in the absence (control) and the presence of highly purified porcine RLX at concentrations of 10(-9) M and 10(-6) M. (3H)-Thymidine uptake assay was used to evaluate cell proliferation. Electron microscopy and immunocytochemistry for the cell-cell adhesion molecule E-cadherin were carried out to evaluate cell differentiation. Analysis of DNA changes associated with apoptosis was performed to clarify whether RLX induces active cell death in the MCF-7 cells. The findings obtained show that RLX, when applied at micromolar concentrations, or even at nanomolar concentrations for long exposure times, suppresses proliferation, stimulates differentiation, and enhances expression of the surface molecule E-cadherin. Growth inhibition is not accompanied by apoptosis. The results of this study show that RLX can be recognized as a novel agent active in influencing growth and differentiation of MCF-7 breast-cancer cells. When applied at appropriate concentrations and exposure times, the peptide has a growth-inhibitory action, thus reversing the growth-stimulatory effect exerted at low concentrations for short exposure times, and promotes differentiation and cell-cell adhesion. These last-mentioned properties might result in a decrease in invasiveness of breast adenocarcinoma cells.

Adenocarcinoma↗
PubMed2026

Exploring the treatment of liver cancer with Gehua Hugan Gao based on bioinformatics, network pharmacology, and molecular docking.

Gehua Hugan Gao (GHHGG) is a traditional Chinese medicine paste that is chiefly used to treat liver cancer. However, the potential impact of GHHGG on liver cancer remains unclear. We explored how GHHGG treats liver cancer using bioinformatics, network pharmacology, and molecular docking. Network pharmacology included GHHGG active ingredients, predicted targets, predicted targets for liver cancer, and differential gene collection. A protein-protein interaction network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database, and crucial targets were ranked according to their degree values. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of liver cancer targets were followed by survival, differential analysis, and molecular docking. Venn diagrams show 123 predicted GHHGG targets for the treatment of hepatocellular carcinoma (HCC). Enrichment analysis showed that GHHGG treats HCC through multiple targets and pathways. We also found that estrogen receptor 1, cytochrome P450 3A4, cyclin-dependent kinase 4, type IIA topoisomerase, aurora kinase A, and cyclin E1 targets were closely associated with HCC development through survival and differential analyses. Molecular docking confirmed GHHGG's strong affinity for liver cancer targets. This study helps us understand GHHGG ingredients and targets for liver cancer treatment. To a certain extent, the molecular mechanism of GHHGG in the treatment of liver cancer has been elucidated, thus providing a theoretical basis.

Molecular Docking Simulation↗
PubMed2005

Evidence for genetic drift in the diversification of a geographically isolated population of the hyperthermophilic archaeon Pyrococcus.

Genetic drift is a mechanism of population divergence that is important in the evolution of plants and animals but is thought to be rare in free-living microorganisms because of their typically large population sizes and unrestricted means of dispersal. We used both phylogenetic and insertion sequence (IS) element analyses in hyperthermophilic archaea of the genus Pyrococcus to test the hypothesis that genetic drift played an important role in the diversification of these microorganisms. Multilocus sequence typing of a collection of 36 isolates of Pyrococcus, from different hydrothermal systems in the Pacific Ocean and the Mediterranean Sea, revealed that Pyrococcus populations from different geographic locations are genetically differentiated. Analysis of IS elements in these isolates exposed their presence in all individuals of only one geographically isolated lineage, that of Vulcano Island in the Mediterranean Sea. Detailed sequence analysis of six selected IS elements in the Vulcano population showed that these elements cause deleterious genomic alterations, including inactivation of gene function. The high frequency of IS elements in the sampled population together with their observed harmful effects in the genome of Pyrococcus provide molecular evidence that the Vulcano Island population of Pyrococcus is geographically isolated and that those genetic mobile elements have been brought up to high frequency by genetic drift. Thus, genetic drift resulting from physical isolation should be considered as a factor influencing differentiation in prokaryotes.

Base Sequence↗