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Results for “differential expression”

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At least 361 records · Page 20Linked to original sources
PubMed2003

Differential expression of genes in the endometrium at implantation: upregulation of a novel member of the E2 class of ubiquitin-conjugating enzymes.

The process of embryo attachment and implantation is accompanied by dramatic cellular and functional changes in the endometrium, the control and mechanisms of which are not clearly understood. The cDNA cloning of differentially expressed genes, specifically at implantation sites in the rabbit endometrium, was used to identify genes controlling functional and remodeling changes. Tissue from the endometrium of Day 6(3/4) (preimplantation) and Day 8 (implantation initiation) pregnant rabbits was used to screen for differentially expressed genes by combined cDNA subtraction/suppressive hybridization. Twenty-nine differentially expressed genes were identified encoding protein modification enzymes, signaling proteins, structural proteins, and enzymes. One of these is a novel member of the E2 ubiquitin-conjugating enzyme family we have designated UBCi (i for implantation), which displayed dramatic nucleotide and deduced amino acid sequence conservation between rabbits, humans, and mice. In situ hybridization indicated UBCi expression exclusively in the luminal epithelium of the endometrium while glandular epithelium, trophoblast, and myometrium were negative. Expression was specific for epithelial cells at implantation sites and was not detected in non-implant-site endometrium. UBCi mRNA was detected in both the mesometrial and antimesometrial epithelial cells of the implantation sites, sites undergoing both differentiation and/or apoptosis. These results identify a group of differentially expressed genes in the endometrium including UBCi and provide new focal targets for studying processes controlling cellular remodeling during implantation. The important roles of ubiquitination in controlling the activities and turnover of key signaling proteins suggest potential roles in controlling critical aspects of implantation.

Amino Acid Sequence↗
PubMed1996

Detection of partial cDNA sequences differentially expressed in patients with myelodysplasia.

The most common chromosomal aberrations in myelodysplastic syndromes (MDS) are complete or partial loss of chromosomes 5 and 7, and trisomy 8. To identify genes important in the pathogenesis of this disease that could be associated with these gross chromosomal defects, we have employed the differential display PCR (DDPCR) procedure developed by Liang and Pardee. This method allows simultaneous comparison of several cDNA sources for the presence of differentially expressed genes. Polymorphonuclear cells (PMNs) from two MDS patients, containing a 5q deletion or a trisomy 8, and three healthy controls were used. Initial screening resulted in the identification of five and three partial cDNA sequences, respectively that were either differentially expressed in both patient samples or in individual patients, as compared with the controls. The authenticity of aberrant expression was verified by reanalyzing the same primer combinations on newly prepared cDNA. Differential expression of the three remaining fragments was subsequently checked on a larger panel of MDS patients, using amplicon-specific primer sets. These were obtained by cloning and sequencing of the fragments. For one partial cDNA (DC3), the original expression pattern, i.e., decreased expression in individual MDS patients, was confirmed. These results demonstrate the utility of the DDPCR procedure to isolate differentially expressed sequences in primary patient samples where the availability of cells is a limiting factor.

Adult↗
PubMed1996

[Cloning of genes, differentially expressed in the cerebellum during postnatal rat development].

To identify genes differentially expressed in the developing rat cerebellum, a subtractive cDNA cloning procedure, followed by differential screening, was used. Four novel genes, MB, MF, 3E7, and 3C6, the transcriptional activity of which changed by a factor of five during cerebellar development, were isolated. The genes obtained were differentially expressed in different regions of the central nervous system. Variations in the levels of corresponding transcripts in the brain cortex and cerebellum were also recorded during postnatal rat development.

Animals↗
PubMed2005

[Screening of differentially expressed genes in mouse hepatocarcinoma ascites cell line with high potential of lymphatic metastasis].

OBJECTIVE: To screen genes differentially expressed in mouse hepatocarcinoma ascites cell line with high potential of lymphatic metastasis. METHODS: A subtracted cDNA library of mouse hepatocarcinoma cell line with high potential of lymphatic metastasis Hca-F and its synogenetic cell line Hca-P with low metastatic potential was constructed by suppression subtractive hybridization (SSH) method. The screened clones of the subtracted library were sequenced and GenBank homology search was performed. RESULTS: Ten differentially expressed cDNA fragments of Hca-F with high potential of lymphatic spreading were obtained, two of which were newly identified ones. CONCLUSION: SSH is a useful technique to detect genes of differential expression and an effective method to clone novel genes.

Animals↗
PubMed1997

Leptin receptor mRNA is expressed in ewe anterior pituitary and adipose tissues and is differentially expressed in hypothalamic regions of well-fed and feed-restricted ewes.

Infertility associated with suboptimal nutrition is a major concern among livestock producers. Recently, much effort has been put into understanding the role of the protein leptin in regulating feed intake and reproduction. Leptin, produced by adipocytes, has receptors in the hypothalamus, but more precise locations of leptin receptor-expressing cell bodies have not been reported in a livestock species. The leptin receptor transcript has several splice variants in the mouse and human, but only the "long-form" product (OBRL) is capable of signal transduction. A partial ovine long-form leptin receptor cDNA was cloned and used to evaluate OBRL mRNA expression within hypothalamic, anterior pituitary, and adipose tissues of ovariectomized adult ewes. Expression was detected in reverse transcription-polymerase chain reaction products of all tissues examined. OBRL mRNA was detected by in situ hybridization in the ventromedial and arcuate nuclei of the hypothalamus. In ewes that had been feed restricted for 3 wk before tissue collection, the expression of OBRL mRNA in these areas was greater (P < 0.05) than that found in well-fed ewes. These findings provide evidence that the full-length leptin receptor is expressed in hypothalamic, anterior pituitary, and adipose tissue (the latter proffering an autoregulatory mechanisms for leptin) and that within the hypothalamus, this receptor form is differentially expressed in well-fed vs. feed-restricted animals.

Adipose Tissue↗
PubMed2006

Differential expression of phospholipases D1 and D2 in mouse tissues.

The differential expression of phospholipase D (PLD) isozymes, which include PLD1 and PLD2, was examined in various murine tissues, including the cerebrum, cerebellum, heart, lung, liver, spleen, stomach, pancreas, ileum, colon, adrenal gland, kidneys, testes, ovaries, and uterus. In Western blot analysis, only PLD1 was detected in the heart and ovary, while only PLD2 was detected in the pancreas and ileum. Both PLD1 and PLD2 were strongly expressed in the cerebrum, cerebellum, and lung, and both were also expressed in the liver, spleen, stomach, colon, kidney, testes, and uterus. Immunohistochemistry showed intense PLD immunostaining in the cerebrum, cerebellum, lungs, intestines, and testis, and weak PLD immunostaining in the liver, kidneys, spleen, and heart. These findings suggest that PLD1 and PLD2 are differentially expressed in the various organs of mice, and that each PLD isozyme plays a distinct role in each organ.

Animals↗
PubMed2002

Within the fold: assessing differential expression measures and reproducibility in microarray assays.

BACKGROUND: 'Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed between query and reference samples. More accurate measures of differential expression and effective data-normalization strategies are required to identify high-confidence sets of genes with biologically meaningful changes in transcription. Further, the analysis of a large number of expression profiles is facilitated by a common reference sample, the construction of which must be carefully addressed. RESULTS: We carried out a series of 'self-self' hybridizations in which aliquots of the same RNA sample were labeled separately with Cy3 and Cy5 fluorescent dyes and co-hybridized to the same microarray. From this, we can analyze the intensity-dependent behavior of microarray data, define a statistically significant measure of differential expression that exploits the structure of the fluorescent signals, and measure the inherent reproducibility of the technique. We also devised a simple procedure for identifying and eliminating low-quality data for replicates within and between slides. We examine the properties required of a universal reference RNA sample and show how pooling a small number of samples with a diverse representation of expressed genes can outperform more complex mixtures as a reference sample. CONCLUSION: Analysis of cell-line samples can identify systematic structure in measured gene-expression levels. A general procedure for analyzing cDNA microarray data is proposed and validated. We show that pooled reference samples should be based not only on the expression of individual genes in each cell line but also on the expression levels of genes within cell lines.

Brain Neoplasms↗
PubMed1997

High mobility group proteins cHMG1a, cHMG1b, and cHMGI are distinctly distributed in chromosomes and differentially expressed during ecdysone dependent cell differentiation.

The mammalian high mobility group proteins HMGI/Y and HMG1/2 are thought to play an architectural role in assembly of nucleoprotein structures. Counterparts to these proteins have recently been found in the cells of the Dipteran insect Chironomus. In this report we investigate the distribution of three abundant HMG proteins in interphase giant chromosomes of the midge, Chironomus. By means of the indirect immunofluorescence technique the cHMG1b and cHMGI proteins were localized in chromosomal puffs, suggesting their involvement in the organization of transcriptionally active chromatin. In contrast, the highly abundant protein cHMG1a was rather uniformly distributed in the chromosomes. The cHMGI protein, but not cHMG1a or cHMG1b, was detected in nucleoli, which may indicate a role in the transcription of ribosomal genes. The regions of the interphase chromosomes containing AT-rich DNA did not contain higher levels of the cHMGI and cHMG1b proteins. A correlation between the specific location of these proteins in chromatin and their synthesis and turnover rates was observed.

Amino Acid Sequence↗
PubMed2005

Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray.

Microarray analyses have contributed greatly to the rapid understanding of functional genomics through the identification of gene networks as well as gene discovery. To facilitate functional genomics of the inner ear, we have developed a mouse inner-ear-pertinent custom microarray chip (CMA-IE1). Nonredundant cDNA clones were obtained from two cDNA library resources: the RIKEN subtracted inner ear set and the NIH organ of Corti library. At least 2000 cDNAs unique to the inner ear were present on the chip. Comparisons were performed to examine the relative expression levels of these unique cDNAs within the organ of Corti, lateral wall, and spiral ganglion. Total RNA samples were obtained from the three cochlear-dissected fractions from adult CF-1 mice. The total RNA was linearly amplified, and a dendrimer-based system was utilized to enhance the hybridization signal. Differentially expressed genes were verified by comparison to known gene expression patterns in the cochlea or by correlation with genes and gene families deduced to be present in the three tissue types. Approximately 22-25% of the genes on the array had significant levels of expression. A number of differentially expressed genes were detected in each tissue fraction. These included genes with known functional roles, hypothetical genes, and various unknown or uncharacterized genes. Four of the differentially expressed genes found in the organ of Corti are linked to deafness loci. None of these are hypothetical or unknown genes.

Animals↗
PubMed2000

Identification and characterization of differentially expressed genes in denervated muscle.

Denervation results in a series of changes in skeletal muscle. To elucidate the molecular basis underlying these changes, it is important to identify the profile of altered gene expression in skeletal muscle following nerve injury. In the present study, we have examined the differentially expressed genes in denervated gastrocnemius muscle using RNA fingerprinting by arbitrarily primed PCR. Eight differentially expressed mRNA transcripts have been identified. A bilateral regulatory profile can be observed for the up-regulated genes in both denervated and contralateral control muscle following unilateral sciatic nerve injury. The temporal expression profiles of the denervation-regulated genes in muscle during development, together with their dependency on nerve activity, suggest potential functional roles following nerve injury in vivo. In particular, the identification of two apoptosis-related genes in denervated muscle provides molecular evidence that the apoptotic process is likely to be involved in the intricate changes that lead to muscle atrophy. Our findings not only allow the identification of novel genes, but also suggest possible functions for some known genes in muscle following nerve injury. Taken together, these findings provide important insights into our understanding of the molecular events in denervated muscle and suggest that the differentially expressed genes may play potential roles during muscle denervation and regeneration.

Animals↗
PubMed2005

[Differential expression of mitochondrial proteins in hepatoma cells analyzed using two-dimensional electrophoresis].

BACKGROUND & OBJECTIVE: Mitochondria play a key role in cell apoptosis. Proteomic analysis of mitochondria will contribute to the discovery of tumorigenic mechanism, early detection of cancer, and findings of anticarcinogens. This study was to identify the differentially expressed mitochondrial proteins in hepatoma cells using two-dimensional gel electrophoresis (2-DE). METHODS: Mitochondria were isolated from normal hepatocytes L02, and hepatoma QGY-7703 cells before and after treatment of epirubicin by density gradient centrifugation; the proteins of mitochondrial samples were analyzed with 2-DE. RESULTS: After density gradient centrifugation, the mitochondrial marker enzyme activities were increased by 11.8, 13.8, and 10.2 times, respectively, for L02 cells, untreated QGY-7703 cells, and epirubicin-treated QGY-7703 cells, and the 2-DE profiles identified 206, 217, and 214 protein spots, respectively, from the 3 samples. Compared L02 cells and QGY-7703 cells, 49 differentially expressed protein spots were identified; compared QGY-7703 cells before and after treatment of epirubicin, 29 differentially expressed protein spots were identified. CONCLUSION: A set of differentially expressed protein spots are detected in mitochondria of QGY-7703 cells with density gradient centrifugation and 2-DE.

Antibiotics, Antineoplastic↗
PubMed1998

Infectivity of Trypanosoma cruzi strains is associated with differential expression of surface glycoproteins with differential Ca2+ signalling activity.

Mammalian cell invasion assays, using metacyclic trypomastigotes of Trypanosoma cruzi G and CL strains, showed that the CL strain enters target cells in several-fold higher numbers as compared with the G strain. Analysis of expression of surface glycoproteins in metacyclic forms of the two strains by iodination, immunoprecipitation and FACS, revealed that gp90, undetectable in the CL strain, is one of the major surface molecules in the G strain, that expression of gp82 is comparable in both strains and that gp35/50 is expressed at lower levels in the CL strain. Purified gp90 and gp35/50 bound more efficiently than gp82 to cultured HeLa cells. However, the intensity of the Ca2+ response triggered in HeLa cells by gp82 was significantly higher than that induced by gp35/50 or gp90. Most of the Ca2+ signalling activity of the metacyclic extract towards HeLa cells was due to gp82 and was inhibitable by gp82-specific monoclonal antibody 3F6. Ca2+ mobilization was also triggered in metacyclic trypomastigotes by host-cell components; it was mainly gp82-mediated and more intense in the CL than in the G strain. We propose that expression of gp90 and gp35/50 at high levels impairs binding of metacyclic forms to host cells through productive gp82-mediated interaction, which leads to the target-cell and parasite Ca2+ mobilization required for invasion. Analysis of metacyclic forms of eight additional T. cruzi strains corroborated the inverse correlation between infectivity and expression of gp90 and gp35/50.

Animals↗
PubMed2004

The three sorCS genes are differentially expressed and regulated by synaptic activity.

We have isolated the murine sorCS3 gene, a new member of the family of receptors containing a Vps10p-domain. Receptors of this family facilitate rapid endocytosis and are thought to be involved in intracellular sorting. SorCS3 and the highly homologous sorCS1 and sorCS2 genes were expressed in a combinatorial, mostly non-overlapping pattern in both the developing and mature central nervous system. During development, distribution and abundancy of their transcripts was regulated. Moreover, their expression was differentially influenced by neuronal activity in the hippocampus of adult mice. Although kainic acid-induced seizures had no effect on sorCS2 mRNA levels, they dramatically increased the expression of sorCS1 and sorCS3. The activity-dependent induction of sorCS1 expression required de novo protein synthesis, whereas that of sorCS3 did not. Our results imply that the three sorCS genes have diverse, but partly overlapping functions in the developing and mature central nervous system.

Animals↗
PubMed2001

[Cloning and identifying renal cell carcinoma differentially expressed genes and their significance].

OBJECTIVE: To Clone study the differentially expressed new genes in renal cell carcinoma (RCC). METHODS: Using a technique known as suppression subtractive hybridization to construct the library which contains the differently expressing cDNAs between RCC and normal kidney cells. Then the RCC specifically expressed genes were cloned. RESULTS: Human RCC subtractive library with high subtractive efficiency was set up successfully. The amplified library contained 350 positive clones. Sequence analysis were performed for 5 clones. All the sequences were unknown previously and the cDNA insert GYLZ-RCC18 had three copies. Northern blot analysis showed that GYLZ-RCC18 cDNA expressed highly in RCC, but no signal could be detected in normal kidney. Using SMART RACE technique, the full length of novel gene of GYLZ-RCC18 was obtained. CONCLUSIONS: The highly efficient cDNA subtractive library may have formed solid foundation for screening and cloning new and specific oncogenes or tumor suppressor genes of RCC. The novel differentially expressed genes may provide an important clue for studying the mechanism of occurrence and development of RCC.

Carcinoma, Renal Cell↗
PubMed1991

Differential expression of Raf-1 protooncogene in resting and activated human leukocyte populations.

In this study we examined by Northern blot analysis the expression of Raf-1 protooncogene in normal human peripheral blood leukocytes. Unlike thymocytes, circulating lymphocytes did not express appreciable levels of Raf-1 mRNA. In contrast, polymorphonuclear cells (PMN) had high levels of Raf-1 transcripts. Also density gradient separated monocytes showed Raf-1 mRNA but at lower levels compared to PMN. Expression of Raf-1 was constitutive inasmuch as it was not induced by the purification procedure. The half-life of Raf-1 mRNA in PMN was greater than 4 h. Functional activation of PMN and monocytes with various stimuli (phorbol esters, tumor necrosis factor, colony stimulating factors, LPS) did not affect Raf-1 expression. By contrast, density gradient purified monocytes allowed to adhere to plastic for 1 h expressed augmented levels of Raf-1. Monocytes cultivated in suspension or allowed to adhere to plastic showed an half-life of Raf-1 transcripts of, respectively, more than 4 h and less than 30 min. Circulating lymphocytes stimulated with mitogens (PHA, conA, anti-CD3 antibodies, and Staphylococcus aureus) also expressed high levels of transcripts of this protooncogene. PHA-induced transcripts in lymphocytes had an half-life greater than 4 h. The pattern of expression of Raf-1 in resting and activated leukocytes suggests that this protooncogene may play a role in expression of differentiated functions and activation of these cells.

Cell Line↗
PubMed1995

[cDNA clones of differential expression between human normal liver tissue and hepatocarcinoma].

Using mRNA differential display technique, we studied the interesting cDNA clones of differential expression between human normal liver and hepatocarcinoma. mRNA extracted from normal liver tissue and hepatocarcinoma cell line Hep3B were subjected to RT-PCR reaction with ten combinations of two 3' primers and five 5' primers. After subjecting these PCR products to labelling with 35S(a)-dATP, PAGE and autoradiography, we obtained a lot of cDNA clones of differential expression. Thirty-one of these clones were partially sequenced. It was shown that 30 clones had no sequences matched with GenBank except one. Dot hybridization showed that 2 cDNA clones were overexpressed in liver cancer tissue and 1 cDNA clone was overexpressed in normal liver tissue. The further characterization of these cDNA clones is in progress.

Carcinoma, Hepatocellular↗
PubMed2006

Differential expression of insulin-like growth factor binding protein-5 in pancreatic adenocarcinomas: identification using DNA microarray.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by its aggressiveness and resistance to both radiation and chemotherapeutic treatment. To better understand the molecular pathogenesis of pancreatic cancer, DNA array technology was employed to identify genes differentially expressed in pancreatic tumors when compared to non-malignant pancreatic tissues. RNA isolated from 11 PDACs and 14 non-malignant bulk pancreatic duct specimens was used to probe Affymetrix U95A DNA arrays. Genes that displayed at least a fourfold differential expression were identified and real-time quantitative PCR was used to verify the differential expression of selected upregulated genes. Interrogation of the DNA array revealed that 73 genes were upregulated in PDACs and 77 genes were downregulated. The majority of the 150 genes identified have not been previously reported to be differentially expressed in pancreatic tumors, although a number of the upregulated transcripts have been reported previously. Immunohistochemistry was used to correlate calponin and insulin-like growth factor binding protein-5 (IGFBP-5) RNA levels with protein expression in PDACs and revealed peritumoral calponin staining in the reactive stroma and intense focal staining of islets cells expressing IGFBP-5 at the edge of tumors; thus implicating the interplay of various cell types to promote neoplastic cell growth within pancreatic carcinomas. As a potential modulator of cell proliferation, the overexpression of IGFBP-5 may, therefore, play a significant role in the malignant transformation of normal pancreatic epithelial cells.

Adenocarcinoma↗
PubMed2006

Empirical comparison of tests for differential expression on time-series microarray experiments.

Methods for identifying differentially expressed genes were compared on time-series microarray data simulated from artificial gene networks. Select methods were further analyzed on existing immune response data of Boldrick et al. (2002, Proc. Natl. Acad. Sci. USA 99, 972-977). Based on the simulations, we recommend the ANOVA variants of Cui and Churchill. Efron and Tibshirani's empirical Bayes Wilcoxon rank sum test is recommended when the background cannot be effectively corrected. Our proposed GSVD-based differential expression method was shown to detect subtle changes. ANOVA combined with GSVD was consistent on background-normalized simulation data. GSVD with empirical Bayes was consistent without background correction. Based on the Boldrick et al. data, ANOVA is best suited to detect changes in temporal data, while GSVD and empirical Bayes effectively detect individual spikes or overall shifts, respectively. For methods tested on simulation data, lowess after background correction improved results. On simulation data without background correction, lowess decreased performance compared to median centering.

Gene Expression Profiling↗