PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Expression analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources

Deletion and expression analysis of AZFa genes on the human Y chromosome revealed a major role for DBY in male infertility.

Three distinct regions, designated AZFa, b and c from proximal to distal Yq, are required for normal spermato-genesis in humans. Deletions involving AZFa (deletion interval 5C/D) seem to occur less frequently in infertile men and to be associated with a more severe testicular phenotype, with almost complete absence of germ cells. AZFa contains three genes, named USP9Y, DBY and UTY, and presents high homology with the mouse Delta Sxr (b) interval, deletion of which causes a severe spermatogenic impairment. However, the specific role of these genes in human spermatogenesis is still unknown and it is not clear which of them is responsible for the AZFa phenotype. Here we describe a complete sequence map of the AZFa region, the genomic structure of AZFa genes and their deletion analysis in a large number of infertile men characterized by well-defined spermatogenic alterations. Both USP9Y and DBY may cause severe testiculopathies, but DBY appears to be the major AZFa candidate. DBY is frequently deleted in infertile patients and its absence produces severe spermatogenic damage leading to a significant reduction of germ cells or even to their complete absence. Expression analysis of AZFa genes and their X-homologues revealed ubiquitous expression for all of them except DBY; this gene produces a long transcript which is ubiquitously expressed in addition to a shorter transcript which is only expressed in the testis, suggesting a specific role for DBY in the spermatogenic process. This hypothesis is further supported by the high similarity of DBY to other DEAD box proteins belonging to the PL10 subclass.

Animals↗

Expression analysis of ruminant alpha-lactalbumin in transgenic mice: developmental regulation and general location of important cis-regulatory elements.

The bovine alpha-lactalbumin transgene with 750 bp and 336 bp of the 5' and 3' flanking region, respectively, is developmentally regulated as its endogenous counterpart in transgenic mice. Comparative expression analysis of three 5'-shortened constructs suggests that the region -477/-220 contains important cis-acting transcriptional elements. The level of expression of a long caprine alpha-lactalbumin transgene encompassing 8.5 kb and 9.5 kb of the 5' and 3' flanking region, respectively, was higher but still unrelated to the copy number. Expression of the transgenes and of endogenous milk-protein genes was tissue-specific. In contrast with a recent report, only low amounts of the relevant mRNA were detected in some skin samples, which suggests a possible contamination by mammary tissue.

Animals↗

Gene expression analysis in mice with elevated glial fibrillary acidic protein and Rosenthal fibers reveals a stress response followed by glial activation and neuronal dysfunction.

Alexander disease is a fatal neurodegenerative disorder resulting from missense mutations of the intermediate filament protein, GFAP. The pathological hallmark of this disease is the formation of cytoplasmic protein aggregates within astrocytes known as Rosenthal fibers. Transgenic mice engineered to over-express wild-type human GFAP develop an encephalopathy with identical aggregates, suggesting that elevated levels of GFAP in addition to mutant protein contribute to the pathogenesis of this disorder. To study further the effects of elevated GFAP and Rosenthal fibers per se, independent of mutations, we performed gene expression analysis on olfactory bulbs of transgenic mice at two different ages to follow the progression of pathology. The expression profiles reveal a stress response that includes genes involved in glutathione metabolism, peroxide detoxification and iron homeostasis. Many of these genes are regulated by the transcription factor Nfe2l2, which is also increased in expression at 3 weeks. An immune-related response occurs with activation of cytokine and cytokine receptor genes, complement components and acute phase response genes. These transcripts are further elevated with age, with additional induction of macrophage-specific markers such as Mac1 and CD68, suggesting activation of microglia. At 4 months, decreased expression of genes for microtubule-associated proteins, vesicular trafficking proteins and neurotransmitter receptors becomes apparent. Interneuron-specific transcription factors including Dlx family members and Pax6 are downregulated as well as Gad1 and Gad2, suggesting impairment of GABAergic granule cells. Together, these data implicate an initial stress response by astrocytes, which results in the activation of microglia and compromised neuronal function.

Adolescent↗

Cloning and expression analysis of a mouse gene related to Drosophila odd-skipped.

The Drosophila pair-rule gene odd-skipped (odd) and two related genes, sister of odd (sob) and bowel (bowl), encode zinc finger containing proteins, two of which play important roles in embryonic development probably functioning as transcription factors. Here we report the cloning and expression analysis of a mouse gene related to odd, odd-skipped related 1 (Osr1). During early embryogenesis Osr1 is expressed in the intermediate mesoderm and in a dynamic pattern during limb and branchial arch development.

5' Untranslated Regions↗

Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae.

The Saccharomyces cerevisiae Snf/Swi complex has been previously demonstrated to control transcription and chromatin structure of particular genes in vivo and to remodel nucleosomes in vitro. We have performed whole-genome expression analysis, using DNA microarrays, to study mutants deleted for a gene encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi component. This analysis was performed on cells grown in both rich and minimal media. The microarray results, combined with Northern blot, computational, and genetic analyses, show that snf2Delta and swi1Delta mutations cause similar effects on mRNA levels, that Snf/Swi controls some genes differently in rich and minimal media, and that Snf/Swi control is exerted at the level of individual genes rather than over larger chromosomal domains. In addition, this work shows that Snf/Swi controls mRNA levels of MATalpha-specific genes, likely via controlling transcription of the regulators MATalpha1 and MCM1. Finally, we provide evidence that Snf/Swi acts both as an activator and as a repressor of transcription, and that neither mode of control is an indirect effect of the other.

Acid Phosphatase↗

[Towards the identification of new markers of pancreatic cancer by gene expression analysis].

The poor prognosis of pancreatic cancer has remained unchanged for many years, with a 5-year survival of less than 5 %. Current methods for diagnosing pancreatic cancer are inadequate at identifying small tumors that can be resected by surgery. Characterization of gene expression patterns in pancreatic cancer provided a list of genes that are specifically overexpressed in cancer cells. These genes are putative novel markers for the diagnosis and the prognosis of pancreatic cancer and for the development of targeted therapies. Gene expression analysis should lead to the discovery of molecular markers for early detection of pancreatic cancer that could benefit patients at high risk of developing pancreatic cancer.

Antigens, Neoplasm↗

Characterization and expression analysis of an ancestor-type Pax gene in the hydrozoan jellyfish Podocoryne carnea.

We characterized a Pax gene from the hydrozoan Podocoryne carnea. It is most similar to cnidarian Pax-B genes and encodes a paired domain, a homeodomain and an octapeptide. Expression analysis demonstrates the presence of Pax-B transcripts in eggs, the ectoderm of the planula larva and in a few scattered cells in the apical polyp ectoderm. In developing and mature medusae, Pax-B is localized in particular endodermal cells, oriented toward the outside. Pax-B is not expressed in muscle cells. However, if isolated striated muscle tissue is activated for transdifferentiation, the gene is expressed within 1 h, before new cell types, such as smooth muscle and nerve cells, have formed. The expression data indicate that Pax-B is involved in nerve cell differentiation.

Amino Acid Sequence↗

Expression analysis of the yersiniabactin receptor gene fyuA and the heme receptor hemR of Yersinia enterocolitica in vitro and in vivo using the reporter genes for green fluorescent protein and luciferase.

The enteropathogenic Yersinia enterocolitica strains have several systems for scavenging iron from their environment. We have studied the expression of the fyuA gene, which encodes the outer membrane receptor for the siderophore yersiniabactin (Ybt), and the hemR gene, which encodes the receptor for heme, using the reporter genes gfp (encoding green fluorescent protein) and luc (encoding firefly luciferase). To study gene expression in vitro as well as in vivo, we have constructed several translational reporter gene fusions to monitor simultaneously expression of fyuA and hemR or expression of one gene by a gfp-luc tandem reporter. Results of the in vitro expression analysis (liquid media) indicated that fyuA and hemR are strongly derepressed under iron starvation conditions, resulting in strong fluorescence and/or luminescence at 27 degrees C. In the in vivo BALB/C mouse infection model, tissue-specific expression of fyuA and hemR reporter fusions was observed. Surprisingly, fyuA and hemR reporter constructs were weakly expressed by yersiniae located in the liver and intestinal lumen, whereas strong expression was found for yersiniae in the peritoneal cavity and moderate expression was found in the spleen. Strikingly, yersiniae carrying fyuA or hemR reporter fusions exhibited threefold-stronger signals when grown in the peritoneal cavity of mice than those growing under iron derepression in vitro. This hyperexpression suggests that besides Fur derepression, additional activators may be involved in the enhanced expression of fyuA and hemR under peritoneal growth conditions. Differential expression of the fyuA and hemR reporter fusions could not be observed, suggesting similar regulation of fyuA and hemR in the mouse infection model.

Animals↗

Microgenomics: gene expression analysis at the tissue-specific and single-cell levels.

Plant organs are composed of many different cell types and the analysis of 'bulk' material results in the average of all information in these cells. Therefore, this does not reflect any individuality of the tissues present in plants. This review briefly summarizes different sampling methods which provide tissue- and cell-specific samples, respectively. In addition, gene expression analysis tools that allow the analysis of transcripts in minute samples are discussed in detail. The combination of both approaches results in high resolution gene expression data, which increases understanding of plant physiology in such diverse areas as primary and secondary metabolism, plant defence or stress response.

Base Sequence↗

[Prediction of response to neoadjuvant chemotherapy in Barrett's carcinoma by quantitative gene expression analysis].

The potential of gene expression profiles to predict the response to neoadjuvant chemotherapy in patients with advanced adenocarcinoma of the esophagus was analyzed. Paraffin-embedded endoscopic esophageal tumor biopsies of 38 patients with advanced esophageal adenocarcinoma (Barrett's adenocarcinoma) were included. All patients underwent two cycles of cisplatin and fluorouracil (5-FU) therapy with or without additional paclitaxel (taxol) followed by abdominothoracal esophagectomy. RNA expression levels of 5-FU-metabolism associated genes thymidylate synthase (TS), thymidine phosphorylase (TP), dihydropyrimidine dehydrogenase (DPD), methylenetetrahydrofolate reductase (MTHFR), MAP7, ELF3, as well as of platinum and taxane associated related genes caldesmon, excision cross-complementing genes (ERCC1 and ERCC4) HER2-neu, DNA damage-inducible gene 45 (GADD45) and multidrug resistance genes (MDR1, MRP1) were determined using real-time RT-PCR. Expression levels were correlated with the histopathological response to chemotherapy assessed in surgically resected specimens. Responding patients showed significantly higher pretherapeutic expression levels of MTHFR (p = 0.012), Caldesmon (p = 0.016), MRP1 (p = 0.007) and MDR1 (p = 0.025). In addition, patients with high pretherapeutic MTHFR and MRP1 levels had a survival benefit after surgery (p = 0.013 and p = 0.015, respectively). Additionally, intratumoral heterogeneity of gene expression of selected genes (TP, DPD, MTHFR, HER2-neu, Caldesmon, ERCC4, MRP1) was additionally verified in 9 untreated Barrett's adenocarcinoma by examination of 5 distinct tumor areas and was observed in 12.7% (5.6%-23.5%, CI 95%) of all cases analyzed. Our results indicate that determination of mRNA levels of a few genes may be useful for the prediction of the success of neoadjuvant chemotherapy in individual cancer patients with advanced adenocarcinoma of the esophagus.

Adenocarcinoma↗

Cloning and expression analysis of goldfish (Carassius auratus L.) prominin.

The integral membrane protein known as prominin was first identified on the apical surface of mouse neural epithelial cells as well as on the surface of human haematopoietic progenitor cells. This report describes a prominin-like sequence and expression analysis of the prominin in the goldfish. The predicted amino acid sequence for goldfish prominin shares all of the hallmark structural characteristics of the prominin family, however the relatedness assessed using the percent amino acid identity indicated that goldfish prominin cannot be placed into the current mammalian dichotomy of type 1 or 2. The real time PCR analyses indicated that prominin was broadly expressed in different tissues with particularly high levels observed in the kidney and gill of the goldfish. Goldfish prominin was also found to be differentially expressed in subpopulations of in vitro-derived goldfish macrophages, with the highest expression observed in progenitor cells.

AC133 Antigen↗

Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana.

The ionotropic glutamate receptor (iGluR) gene family has been widely studied in animals and is determined to be important in excitatory neurotransmission and other neuronal processes. We have previously identified ionotropic glutamate receptor-like genes (GLRs) in Arabidopsis thaliana, an organism that lacks a nervous system. Upon the completion of the Arabidopsis genome sequencing project, a large family of GLR genes has been uncovered. A preliminary phylogenetic analysis divides the AtGLR gene family into three clades and is used as the basis for the recently established nomenclature for the AtGLR gene family. We performed a phylogenetic analysis with extensive annotations of the iGluR gene family, which includes all 20 Arabidopsis GLR genes, the entire iGluR family from rat (except NR3), and two prokaryotic iGluRs, Synechocystis GluR0 and Anabaena GluR. Our analysis supports the division of the AtGLR gene family into three clades and identifies potential functionally important amino acid residues that are conserved in both prokaryotic and eukaryotic iGluRs as well as those that are only conserved in AtGLRs. To begin to investigate whether the three AtGLR clades represent different functional classes, we performed the first comprehensive mRNA expression analysis of the entire AtGLR gene family. On the basis of RT-PCR, all AtGLRs are expressed genes. The three AtGLR clades do not show distinct clade-specific organ expression patterns. All 20 AtGLR genes are expressed in the root. Among them, five of the nine clade-II genes are root-specific in 8-week-old Arabidopsis plants.

Animals↗

Molecular cloning of cDNA encoding a ubiquitin-activating enzyme (E1) from goldfish (Carassius auratus) and expression analysis of the cloned gene.

Destruction of cyclin B is required to the mitotic and meiotic cycles. A cyclin-specific ubiquitinating system, including ubiquitin-activating enzyme (E1), is thought to be responsible for cyclin B destruction. Here we present the cloning, sequencing and expression analysis of goldfish, Carassius auratus, E1 from goldfish ovary. The cloned cDNA is 4069 bp long and encodes 1059 amino acids. The deduced amino acid sequence is highly homologous to E1 from other species. Recombinant goldfish E1 could transfer ubiquitin to cyclin-selective ubiquitin-conjugating enzyme. Tissue distribution revealed a single 4.0-kb message ubiquitous among tissues.

Amino Acid Sequence↗

Cloning and expression analysis of a potato cDNA that encodes branching enzyme: evidence for co-expression of starch biosynthetic genes.

One of the key enzymes involved in the formation of amylopectin, which is the major component of starch, is branching enzyme. A cDNA for potato branching enzyme was cloned by screening a tuber-specific cDNA expression library using an antiserum directed against a denatured preparation of the protein. Complementation of an Escherichia coli strain deficient in branching enzyme was achieved using a construct derived from this clone. Analysis of the expression of the gene in potato revealed a close association with conditions favouring starch biosynthesis. The expression pattern of the gene coding for potato branching enzyme, as analyzed at the mRNA level, closely resembles that of AGPase S, a gene coding for one of the subunits of ADP-glucose pyrophosphorylase, which is the key regulatory enzyme in the starch biosynthetic pathway. This raises the possibility that enzymes involved in the pathway are coordinately regulated at the transcriptional level.

1,4-alpha-Glucan Branching Enzyme↗

Molecular cloning of cDNA encoding a cyclin-selective ubiquitin carrier protein (E2-C) from Carassius auratus (goldfish) and expression analysis of the cloned gene.

Destruction of cyclin B is required for exit from mitosis and meiosis. A cyclin-specific ubiquitinating system, including cyclin-selective ubiquitin carrier protein (E2-C), is thought to be responsible for cyclin B destruction. Here we present the cloning, sequencing and expression analysis of goldfish, Carassius auratus, E2-C which encodes the cyclin-selective ubiquitin carrier protein from goldfish ovary. The cloned cDNA is 677 bp long and encodes 172 amino acids. The deduced amino acid sequence is highly homologous to E2-C from other species. Recombinant goldfish E2-C possesses ubiquitinating activity against cyclin B. The expression of mRNA for E2-C was similar to that of mRNA for cyclin B, occurring at very high level in the ovary. The similarity of the expression pattern of E2-C and cyclin B suggests that E2-C mediates a cyclin-specific ubiquitination.

Amino Acid Sequence↗

Emotion recognition through facial expression analysis based on a neurofuzzy network.

Extracting and validating emotional cues through analysis of users' facial expressions is of high importance for improving the level of interaction in man machine communication systems. Extraction of appropriate facial features and consequent recognition of the user's emotional state that can be robust to facial expression variations among different users is the topic of this paper. Facial animation parameters (FAPs) defined according to the ISO MPEG-4 standard are extracted by a robust facial analysis system, accompanied by appropriate confidence measures of the estimation accuracy. A novel neurofuzzy system is then created, based on rules that have been defined through analysis of FAP variations both at the discrete emotional space, as well as in the 2D continuous activation-evaluation one. The neurofuzzy system allows for further learning and adaptation to specific users' facial expression characteristics, measured though FAP estimation in real life application of the system, using analysis by clustering of the obtained FAP values. Experimental studies with emotionally expressive datasets, generated in the EC IST ERMIS project indicate the good performance and potential of the developed technologies.

Adaptation, Psychological↗

Gene expression analysis of tumor spheroids reveals a role for suppressed DNA mismatch repair in multicellular resistance to alkylating agents.

Drug resistance is a major obstacle in the successful treatment of cancer. Thus, elucidation of the mechanisms responsible is a critical first step in trying to prevent or delay such manifestations of resistance. In this regard, three-dimensional multicellular tumor cell spheroids are intrinsically more resistant to virtually all anticancer cytotoxic drugs than conventional monolayer cultures. We have employed the EMT-6 subline PC5T, which forms highly compact spheroids, and differential display to identify candidate genes whose expression differs between monolayer and spheroids. Approximately 5,000 bands were analyzed, revealing 26 to be differentially expressed. Analysis of EMT-6 tumor variants selected in vivo for acquired resistance to alkylating agents identified eight genes whose expression correlated with drug resistance in tumor spheroids. Four genes (encoding Nop56, the NADH SDAP subunit, and two novel sequences) were found to be down-regulated in EMT-6 spheroids and four (encoding 2-oxoglutarate carrier protein, JTV-1, and two novel sequences) were up-regulated. Analysis of the DNA mismatch repair-associated PMS2 gene, which overlaps at the genomic level with the JTV-1 gene, revealed PMS2 mRNA to be down-regulated in tumor spheroids, which was confirmed at the protein level. Analysis of PMS2(-/-) mouse embryo fibroblasts confirmed a role for PMS2 in sensitivity to cisplatin, and DNA mismatch repair activity was found to be reduced in EMT-6 spheroids compared to monolayers. Dominant negative PMS2 transfection caused increased resistance to cisplatin in EMT-6 and CHO cells. Our results implicate reduced DNA mismatch repair as a determinant factor of reversible multicellular resistance of tumor cells to alkylating agents.

Alkylating Agents↗

Expression analysis of classic and non-classic HLA molecules before interferon alfa-2b treatment of melanoma.

Individual predictive clinical, immunological, or molecular features for definition of patients with lymph-node-positive melanoma who do not benefit from adjuvant postsurgery high-dose interferon alpha treatment are lacking. Expression analysis of classic and non-classic HLA molecules on melanoma cells metastatic to the locoregional lymph node may help select these patients before treatment.

Antineoplastic Agents↗