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Results for “Expression analysis”

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At least 307 records · Page 17Linked to original sources

PubMed2005

[Molecular cloning and expression analysis of a novel human gene ZNF18].

The zinc-finger motif found in many transcription factors is thought to be important for human heart development and diseases. This study reports cloning and expression analysis of a novel human zinc finger protein ZNF18 cDNA. The ZNF18 cDNA is 2,767 bp in length encoding a 549-amino-acid protein that contains a SCAN-box, a KRAB box and five consecutive C2H2 zinc finger motifs. ZNF18 shows high similarity with mouse Zfp535 (identity 77%). The ZNF18 gene is located on human chromosome 17p12-p13 with 9 exons and 8 introns. ZNF18 was ubiquitously expressed in adult mouse tissues except heart as revealed by Northern blot. Whole-mount in situ hybridization showed that expression of ZNF18 in mouse embryos was very dynamic. Expression was predominantly in extraembryonic tissues of E7.5 mouse embryo. By E8.5, ZNF18 began to express in anterior of trunk, and became abundant in tail and heart at E9.0, especially in the embryo heart at E10.5. These expression results suggest that ZNF18 may play an important role in the development of embryo heart.

Amino Acid Sequence↗

PubMed2005

Complementary DNA cloning, genomic characterization and expression analysis of a mammalian gene encoding histidine-rich calcium binding protein.

A protein complex present at the junctional sarcoplasmic reticulum (SR) membrane is implicated in the Ca(2+) release process during muscle contraction. The histidine-rich Ca(2+)-binding protein (HRC) is an emerging component associated into the SR protein complex. We cloned cDNAs for rat and monkey HRCs, showing a conserved sequence organization in common with other mammalian HRCs. Genomic analysis revealed that each mammalian HRC gene is present as a single copy in the genome, consisting of 6 exons and 5 introns. Developmental expression analysis using mouse embryos and postnatal hearts demonstrated that Hrc transcription begins at 12.5 days postcoitum and its level increases gradually, reaching an adult level in the range 5-20 days after birth. Comparing the Hrc gene and other SR genes, we found that the timing and pattern of gene expression vary among the SR genes and the full-level expression of these genes is achieved in the heart after postnatal day 20. Collectively, our study provides comprehensive information about the structure and expression of the mammalian HRC gene, together with the comparative expression data of the related SR genes.

Amino Acid Sequence↗

PubMed2002

Long oligonucleotide arrays on nylon for large-scale gene expression analysis.

To date, most studies of multigenic expression patterns by long DNA array have used DNA fragments as probes. These probes are usually obtained as PCR products, and this represents a time-consuming and error-prone approach, requiring strict quality control. The present study examines the use of 40- and 70-mer synthetic oligonucleotides as probes for DNA array analysis with radioactive labeled targets. Design, spotting onto nylon filters, and hybridization conditions were determined and optimized. In this approach, the sensitivity and the specificity of the hybridization appear comparable to the conventional long DNA probes assay, permitting the analysis of small samples of approximately 1 microg total RNA. The long oligonucleotide array thus provides a very convenient method for the analysis of gene expression patterns in biological specimens and in clinical research.

Arabidopsis↗

PubMed2001

Protein expression analysis: from "tip of the iceberg" to a global method.

In this review I will describe the advances that have recently been made in "traditional" two-dimensional gel based protein expression analysis. A major jump has been made toward the automation of gel image analysis and comparison, one of the major bottlenecks in the analysis chain as well as the automation of spot excision and preparation for mass spectrometric analysis. Currently the gel-based "proteome mapping" approach is highly effective and 300 gels and over 10,000 spots a week can be analysed. Very recently, viable alternatives to the use of two-dimensional gel electrophoresis have emerged and these approaches are discussed here. In combination with the recently developed stable isotopic tagging methods for peptide quantitation and new mass spectrometers, this emerging technology will be a rapid and highly effective alternative to gel-based methods with few of the latter's shortcomings.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2006

Oleosin gene family of Coffea canephora: quantitative expression analysis of five oleosin genes in developing and germinating coffee grain.

Coffee grains have an oil content between 10% and 16%, with these values associated with Coffea canephora (robusta) and C. arabica (arabica), respectively. As the majority of the oil stored in oil seeds is contained in specific structures called oil bodies, we were interested in determining whether there are any differences in the expression of the main oil body proteins, the oleosins, between the robusta and arabica varieties. Here, we present the isolation, characterization and quantitative expression analysis of six cDNAs representing five genes of the coffee oleosin family (CcOLE-1 to CcOLE-5) and one gene of the steroleosin family (CcSTO-1). Each coffee oleosin cDNA encodes for the signature structure for oleosins, a long hydrophobic central sequence containing a proline KNOT motif. Sequence analysis also indicates that the C-terminal domain of CcOLE-1, CcOLE-3 and CcOLE-5 contain an 18-residue sequence typical of H-form oleosins. Quantitative RT-PCR showed that the transcripts of all five oleosins were predominantly expressed during grain maturation in robusta and arabica grain, with CcOLE-1 and CcOLE-2 being more highly expressed. While the relative expression levels of the five oleosins were similar for robusta and arabica, significant differences in the absolute levels of expression were found between the two species. Quantitative analysis of oleosin transcripts in germinating arabica grain generally showed that the levels of these transcripts were lower in the grain after drying, and then further decreased during germination, except for a small spike of expression for CcOLE-2 early in germination. In contrast, the levels of CcSTO-1 transcripts remained relatively constant during germination, in agreement with suggestions that this protein is actively involved in the process of oil body turnover. Finally, we discuss the implications of the coffee oleosin expression data presented relative to the predicted roles for the different coffee oleosins during development and germination.

Amino Acid Sequence↗

PubMed1997

The phosphoenolpyruvate carboxylase (ppc) gene family of Flaveria trinervia (C4) and F. pringlei (C3): molecular characterization and expression analysis of the ppcB and ppcC genes.

Phosphoenolpyruvate carboxylase (PEPC) is a central enzyme of C4 and CAM photosynthesis but plants, in addition, contain various non-photosynthetic isoforms with characteristic and variable functions. The partial sequence and a detailed expression analysis of the PpcB and PpcC genes which encode non-photosynthetic PEPC isoforms in the C4 plant Flaveria trinervia and the C3 species F. pringlei is presented. Southern analyses showed that PpcB and PpcC sequences are most probably of single-copy in the genomes of F. trinervia and F. pringlei. With gene-specific probes the various ppc transcripts could be distinguished unequivocally from one another and the expression patterns of all ppc genes were compared. PpcB and PpcC transcripts of both F. trinervia and F. pringlei were detected preferentially in roots and stems and at low levels in leaves. Their accumulation patterns are thus similar to each other, but different from that of the PpcA genes which in F. trinervia encode the C4 isoform of PEPC. Transgenic analysis of the 5'-flanking regions of the PpcB genes of both F. trinervia and F. pringlei in tobacco revealed that the PpcB promoter/beta-glucuronidase reporter genes were preferentially expressed in the phloem and the roots. Comparison of the PpcB promoter/reporter gene with the accumulation pattern of the PpcB transcripts in F. trinervia and F. pringlei suggests that the expression of the PpcB genes is predominantly controlled by transcription.

Base Sequence↗

PubMedDate not supplied

Identification of genes associated with ovarian cancer metastasis using microarray expression analysis.

Although the transition from early- to advanced-stage ovarian cancer is a critical determinant of survival, little is known about the molecular underpinnings of ovarian metastasis. We hypothesize that microarray analysis of global gene expression patterns in primary ovarian cancer and metastatic omental implants can identify genes that underlie the metastatic process in epithelial ovarian cancer. We utilized Affymetrix U95Av2 microarrays to characterize the molecular alterations that underlie omental metastasis from 47 epithelial ovarian cancer samples collected from multiple sites in 20 patients undergoing primary surgical cytoreduction for advanced-stage (IIIC/IV) serous ovarian cancer. Fifty-six genes demonstrated differential expression between ovarian and omental samples (P < 0.01), and twenty of these 56 differentially expressed genes have previously been implicated in metastasis, cell motility, or cytoskeletal function. Ten of the 56 genes are involved in p53 gene pathways. A Bayesian statistical tree analysis was used to identify a 27-gene expression pattern that could accurately predict the site of tumor (ovary versus omentum). This predictive model was evaluated using an external data set. Nine of the 27 predictive genes have previously been shown to be involved in oncogenesis and/or metastasis, and 10/27 genes have been implicated in p53 pathways. Microarray findings were validated by real-time quantitative PCR. We conclude that gene expression patterns that distinguish omental metastasis from primary epithelial ovarian cancer can be identified and that many of the genes have functions that are biologically consistent with a role in oncogenesis, metastasis, and p53 gene networks.

Bayes Theorem↗

PubMed2004

Gene expression analysis of human prostate carcinoma during hormonal therapy identifies androgen-responsive genes and mechanisms of therapy resistance.

The androgen-signaling pathway is critical to the development and progression of prostate cancer and androgen ablation is a mainstay of therapy for this disease. We performed a genome-wide expression analysis of human prostate cancer during androgen ablation therapy to identify genes regulated by androgen and genes differentially expressed after the development of resistance. Six hundred and fifty-four of 63,175 probe sets detected significant expression changes after 3 months of treatment with goserelin and flutamide. This included 149 genes that were also differentially expressed 36 hours after androgen withdrawal in LNCaP cells. These genes reflect the physiological changes that occur in treated tumors and include potential direct targets of the androgen receptor. Expression profiles of androgen ablation-resistant tumors demonstrated that many of the gene expression changes detected during therapy were no longer present suggesting a reactivation of the androgen response pathway in the absence of exogenous hormone. Therapy resistance was associated with differential expression of a unique set of genes that reflect potential mechanisms of reactivation. Specifically an up-regulation of the androgen receptor and key enzymes for steroid biosynthesis suggest that resistant tumors have increased sensitivity to and endogenous synthesis of androgenic hormones. The specific pathways of reactivation provide opportunities for classification of resistant tumors and targeted therapies.

Algorithms↗

PubMed2004

Gene expression analysis following hypoxia-reoxygenation in rat gastric epithelial cells using a high-density oligonucleotide array.

Recent investigations have demonstrated that the signaling of hypoxia-re-oxygenation is a major contributing pathway leading to gastric mucosal injury induced by stress, non-steroidal anti-inflammatory drugs, and Helicobacter pylori. The aim of the present study was to perform a gene expression analysis on the gastric mucosal cellular response to hypoxia-reoxygenation using a high-density oligonucleotide array. Cells were subjected to hypoxia with 95% N(2) and 5% CO(2) at 37 degrees C for 2 h. Reoxygenation was initiated by placing the cells in an environment of normoxia for 2 h. Total RNA was extracted, and differences in gene expression profiles between the normoxia and hypoxia-reoxygenation groups were investigated using a GeneChip of Rat Toxicology U34 array (Affymetrix). Hypoxia-reoxygenation up-regulated the stress-related genes (heat shock protein-70 [HSP-70], catalase). The enhanced expression of HSP-70 was confirmed by Western blot analysis. In conclusion, these results suggest that up-regulation of the HSP-70 gene after reoxygenation may play a role in maintaining cell survival and supporting cell function as a molecular chaperone.

Animals↗

PubMed2005

Characterization and expression analysis of the chicken interleukin-11 receptor alpha chain.

Interleukin-11 (IL-11) is a multifunctional cytokine involved in various pathways in blood cells, their precursors and many other cell types in vitro and in vivo. The effects of IL-11 are largely mediated by the IL-11 receptor alpha-chain (IL-11Ralpha). In this study, a putative cDNA sequence encoding the 414 amino acid propeptide of chicken IL-11R (chIL-11R) was identified. The predicted 414 amino acid sequence showed 42-43% sequence identity with mammalian homologues. In a domain search of the molecule, two fibronectin (FN) type-III domains were identified in the C- terminal portion. On comparison with mammalian IL-11R, 4 conserved cysteine residues and a WSXWS motif were observed within the FN type-III domains. Expression analysis revealed that chIL-11Ralpha is strongly expressed in brain, heart, lung, liver, glandular stomach, kidney, the immature testis, ovary and chicken blastodermal cells (CBCs) after 1-day-cultivation. These findings strongly indicate that the identified chicken cDNA sequence encodes chIL-11R alpha-chain homologue.

Amino Acid Sequence↗

PubMed1993

Characterization and expression analysis of the murine rck gene: a protein kinase with a potential function in sensory cells.

We have characterized a murine protein kinase gene, rck, which was identified by crosshybridization with sequences from the v-ros tyrosine kinase gene under conditions of reduced stringency. cDNA analysis indicated that rck encodes a putative protein kinase related to the cdc2 subclass of the gene family and that the gene is identical to mak identified previously in the rat. An extensive expression analysis in the mouse performed by a combination of in situ hybridization and RNase protection revealed a novel and restricted pattern of expression: rck transcripts are found in two cell types involved in sensory transduction, photoreceptors and olfactory receptors as well as in epithelia of the respiratory tract and choroid plexus. Specific transcripts are also found in pre- and postmeiotic male germ cells. We suggest therefore that rck participates in signalling pathways important in a distinct set of cells, remarkably among them cells involved in sensory signal transduction.

Amino Acid Sequence↗

PubMed2005

cDNA cloning, genomic structure and expression analysis of the goose (Anser cygnoides) MHC class I gene.

To provide data for studies on avian disease resistance, goose MHC class I cDNA (Ancy-MHC I) was cloned from a goose cDNA library, it's genomic structure and expression analysis were investigated. The mature peptides of Ancy-MHC I cDNA encoded 333 amino acids. The genomic organization is composed of eight exons and seven introns. Based on the genetic distance, six Ancy-MHC I genes from six individuals can be classified into four lineages. A total of nineteen amino acid positions in peptide-binding domain showed high scores by Wu-kabat index analysis. The Ancy-MHC I amino acid sequence displayed seven critical HLA-A2 amino acids that bind with antigen polypeptides, and have an 85.4-98.9% amino acid homology with each genes, and a 59.8-66.0% amino acid homology with chicken MHC class I. Expression analyses using Q-RT-PCR to detect the tissue-specific expression of Ancy-MHC I mRNA in an adult goose. The result appeared that Ancy-MHC I cDNA was expressed in the liver, spleen, intestine, kidney, lung, pancreas, heart, brain, and skin. The phylogenetic tree appears to branch in an order consistent with accepted evolutionary pathways.

Amino Acid Sequence↗

PubMed2005

Characterization and expression analysis of a chicken interleukin-6 receptor alpha.

Interleukin-6 (IL-6) is a multifunctional cytokine that plays roles in regulating immune responses, acute phase reactions and hematopoiesis. IL-6 signaling is regulated by two receptors, a specific alpha chain (IL-6Ralpha) and a signal transducer, gp130. In this study, cDNA encoding the 445 amino acid propeptide of chicken IL-6Ralpha (chIL-6Ralpha) was identified. The predicted 445 amino acids showed approximately 40% sequence identity with mammalian homologues. In a domain search, chIL-6Ralpha had a signal peptide of 20 residues, an immunoglobulin-like (IG) domain of 71 residues and a fibronectin-type III (FN III) domain of 85 residues. On comparison with mammalian homologues, four conserved cysteine residues and the WSXWS motif were observed in the N- and C-terminal regions of the FN III domain, respectively. Expression analysis revealed that chIL-6Ralpha is strongly expressed in liver and the chicken hepatoma cell line LMH. These findings indicate that the identified chicken cDNA sequence encodes a chIL-6Ralpha homologue.

Amino Acid Sequence↗

PubMed2003

Identification and expression analysis of a novel splice variant of human Sprouty1 gene.

Sprouty (SPRY) was first identified in a genetic screen in Drosophila to be an antagonist of fibroblast growth factor (FGF) and epidermal growth factor (EGF) signaling, seemingly by inhibiting the Ras/MAP kinase pathway. During large scale DNA sequencing of the human fetal brain cDNA library, we cloned a novel splice variant of human Sprouty1 gene, and termed it human Sprouty1b (SPRY1b). It has the same deduced protein as Sprouty1a, which has been reported. And like other members of Sprouty family, SPRY1b deduced protein also has a C-terminal cysteine-rich region. According to the search against human genome database, SPRY1b was mapped to 4q25-28. Expression analysis of SPRY1a and SPRY1b shows that they are hardly expressed in adult human, but have different expression patterns in fetus, which confirmed that SPRY1 is an important gene during fetal development.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Spotted long oligonucleotide arrays for human gene expression analysis.

DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression in two dissimilar human RNA samples. These samples were also analyzed using arrays produced by in situ synthesis of sets of multiple short (25-mer) oligonucleotides for each gene (Affymetrix GeneChips). We compared expression measurements for 7344 genes that were represented in both long oligonucleotide probe collections and the in situ-synthesized 25-mer arrays. We found strong correlations (r = 0.8-0.9) between relative gene expression measurements made with spotted long oligonucleotide probes and in situ-synthesized 25-mer probe sets. Spotted long oligonucleotide arrays were suitable for use with both unamplified cDNA and amplified RNA targets, and are a cost-effective alternative for many functional genomics applications. Most previously reported evaluations of microarray technologies have focused on expression measurements made on a relatively small number of genes. The approach described here involves far more gene expression measurements and provides a useful method for comparing existing and emerging techniques for genome-scale expression analysis.

Cell Line↗

PubMed2005

Utilization of tomato microarrays for comparative gene expression analysis in the Solanaceae.

Transcriptional profiling allows for the assessment and comparison of cross-species gene activity and function on a comprehensive scale. The Solanaceae is a large, diverse dicot family, with well-established genetic relationships between major crop species (tomato, potato, pepper, eggplant, and tobacco). Although Arabidopsis thaliana is often the model of choice for anchoring comparative studies, certain biological processes are better examined in other plants. The ripening of fleshy fruits is not tractable in Arabidopsis; however, it has received considerable attention in tomato. As a member of the Solanaceae, tomato provides a well-characterized system to anchor transcriptional profiles of fruit ripening and development in related species. By utilizing different stages of tomato, pepper, and eggplant fruit, the use of tomato microarrays for expression analysis has been demonstrated in closely related heterologous species, and groups of candidate expressed sequence tags, which are useful as orthologous markers, have been identified, as well as genes implicated in fruit ripening and development in the Solanaceae.

Fruit↗

PubMed2005

Porcine SPLUNC1: molecular cloning, characterization and expression analysis.

SPLUNC1, originally named PLUNC for palate, lung and nasal epithelium clone, is a small protein which is secreted from the epithelial cells of the nasal cavity and the upper respiratory tract in humans, mice, rats and cows. SPLUNC1 is structurally homologous to the two key mediators of host defense against Gram-negative bacteria, lipopolysaccharide binding protein (LBP) and bactericidal permeability increasing protein (BPI). SPLUNC1 is therefore believed to play a role in the innate immune system. This work reports the cloning and analysis of the porcine (Sus scrofa) homologue of SPLUNC1. The SPLUNC1 cDNA was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) using oligonucleotide primers derived from in silico sequences. The porcine cDNA codes for a protein of 249 amino acids which shows a high similarity to bovine (74%) and to human (69%) SPLUNC1. The predicted S. scrofa SPLUNC1, SsSPLUNC1, polypeptide contains a putative signal peptide of 19 residues. A similar signal sequence is also found in all other members of the PLUNC family. Expression analysis by RT-PCR demonstrated a very high expression level of the porcine SPLUNC1 homologue in trachea and lung tissue only. This airway-specific expression might be of particular interest in the study of airborne diseases in pig.

Amino Acid Sequence↗

PubMed2004

Cloning and expression analysis of the mouse stroma marker Snep encoding a novel nidogen domain protein.

The vertebrate kidney develops through a series of mesenchymal-epithelial interactions between the ureteric bud and the metanephrogenic mesenchyme to form nephrons and the collecting system, which are both embedded in the renal interstitium. The interstitial stromal cells are an essential prerequisite for regular kidney development, but their origin and function is poorly understood. They are found in the kidney periphery and the medulla and are likely derived from the kidney mesenchyme and/or from migrating neural crest cells. During late kidney development, stromal cells are lost through massive apoptosis. We have identified a novel marker of kidney stroma cells, Snep (stromal nidogen extracellular matrix protein), that is additionally expressed in mesenchymal cells of other embryonic tissues and within the nervous system. Of interest, Snep transcripts are also found at sites of embryonic apoptosis. Furthermore, comparative expression analysis of kidney stroma markers suggests that Snep is expressed in a specific subpopulation of stromal cells and may provide environmental cues to support regular development.

Animals↗