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At least 685 records · Page 38Linked to original sources
PubMed1999

Expression of messenger ribonucleic acid splice variants for vascular endothelial growth factor in the penis of adult rats and humans.

Erectile dysfunction is often associated with problems in vascular perfusion to the erectile components of the penis. In order to better understand the factors that control vascular formation and perfusion in the erectile tissues of the penis, we have begun to characterize the expression of vascular endothelial growth factor (VEGF) in penis tissues. VEGF is one of several polypeptides that have significant angiogenic activity in vitro and in vivo. Extensive characterization of the VEGF gene and its products has shown that several different mature mRNA transcripts exist, originating from alternative splicing of the basic VEGF transcript. These variant transcripts can encode peptides with different biological activities. Penile tissue was obtained from adult rats and from human patients undergoing penile prosthesis implantation. Analysis of the forms of VEGF transcripts was performed using a reverse transcription-polymerase chain reaction technique with primer pairs derived from the first and eighth exon of the VEGF gene. The expression levels of the various isoforms in the rat penis were then quantified using RNase protection assays. Four previously described splice variants of VEGF mRNA (VEGF 120, 144, 164, 188) were detected in rat and human penile tissues. In contrast to what is seen in the rat lung, where the most abundant form of VEGF mRNA is the 188 splice isoform, VEGF 164 is the most abundant transcript detected in the penis. Finally, sequence analysis of numerous VEGF cDNA clones obtained from the rat penis demonstrated the presence of a previously undescribed VEGF splice variant that could give rise to a protein of 110 amino acid residues (VEGF 110, GenBank accession no. AF080594). In summary, a number of VEGF mRNA isoforms are expressed in the rat and human penis, with the splice variant encoding a 164-amino acid protein present in greatest abundance. This study is a prelude to attempts to genetically manipulate VEGF expression in the penis as a therapy for erectile dysfunction.

Adult↗
PubMed2002

General statistics of stochastic process of gene expression in eukaryotic cells.

Thousands of genes are expressed at such very low levels (< or =1 copy per cell) that global gene expression analysis of rarer transcripts remains problematic. Ambiguity in identification of rarer transcripts creates considerable uncertainty in fundamental questions such as the total number of genes expressed in an organism and the biological significance of rarer transcripts. Knowing the distribution of the true number of genes expressed at each level and the corresponding gene expression level probability function (GELPF) could help resolve these uncertainties. We found that all observed large-scale gene expression data sets in yeast, mouse, and human cells follow a Pareto-like distribution model skewed by many low-abundance transcripts. A novel stochastic model of the gene expression process predicts the universality of the GELPF both across different cell types within a multicellular organism and across different organisms. This model allows us to predict the frequency distribution of all gene expression levels within a single cell and to estimate the number of expressed genes in a single cell and in a population of cells. A random "basal" transcription mechanism for protein-coding genes in all or almost all eukaryotic cell types is predicted. This fundamental mechanism might enhance the expression of rarely expressed genes and, thus, provide a basic level of phenotypic diversity, adaptability, and random monoallelic expression in cell populations.

Animals↗
PubMed2003

In vivo transcription of the Epstein-Barr virus (EBV) BamHI-A region without associated in vivo BARF0 protein expression in multiple EBV-associated disorders.

The in vivo expression of the Epstein-Barr virus (EBV) BamHI-A rightward transcripts (BARTs) as well as the putative BART-encoded BARF0 and RK-BARF0 proteins in various EBV-associated malignancies was investigated. RT-PCRs specific for the different splice variants of the BARTs and both a nucleic acid sequence-based amplification assay and an RT-PCR specific for the BARF0 ORF were used. Abundant transcription of BARTs was found in EBV-associated Hodgkin's lymphomas, Burkitt's lymphomas (BL), T-cell non-Hodgkin's lymphomas, post-transplant lymphoproliferative disorders, AIDS-related lymphomas and gastric carcinomas. Using RNA in situ hybridization (RISH), BARTs were detected within the neoplastic cells of these malignancies. BARTs encoding RK-BARF0 were not detected. The BARTs detected were shown possibly to encode the RPMS1 and BARF0 proteins, based on their splicing. However, BARTs actually harbouring the BARF0 ORF were detected only in specimens containing a relatively large number of EBV-positive cells. New monoclonal antibodies against the BARF0 protein were generated that efficiently recognized prokaryotic and eukaryotic recombinant BARF0. However, the BARF0 protein was not detected in clinical samples, nor in EBV-positive cell lines, even though these were positive for BARTs by RISH and/or BARF0 RNA in vitro analysis. Using immunoblot analysis, no antibodies against baculovirus-expressed BARF0 protein were detected in the sera of nasopharyngeal carcinoma patients, BL patients and Hodgkin's disease patients, patients with chronic EBV infection, infectious mononucleosis patients or EBV-positive healthy donors. Thus, BARTs containing the BARF0 ORF are expressed in vivo but the BARF0 protein cannot be detected and may be expressed only marginally. It is concluded that the BARF0 protein is unlikely to play a role in vivo in EBV-positive malignancies.

Deoxyribonuclease BamHI↗
PubMed1992

Promoter fusions to the Activator transposase gene cause distinct patterns of Dissociation excision in tobacco cotyledons.

To explore the effects of altering the level of Activator (Ac) transposase (TPase) expression, a series of plasmids was constructed in which heterologous promoters were fused to the TPase gene. Promoters for the cauliflower mosaic virus (CaMV) 35S transcript and the octopine synthase (ocs) and nopaline synthase (nos) genes were tested. These fusions, and constructs expressing TPase from the wild-type Ac promoter, were introduced into tobacco, and their activity was monitored by crossing to a line carrying Dissociation (Ds) in a streptomycin phosphotransferase gene (Ds::SPT). The SPT marker provides a record of somatic excisions of Ds that occur during embryo development. The patterns of somatic variegation that resulted from transactivation by each fusion were distinct and strikingly different from the pattern triggered by the wild-type Ac constructs. Unlike wild-type Ac, which caused transposition throughout embryo development, each fusion gave rise to sectors of discrete size. Sectors triggered by the CaMV 35S fusion were largest, ocs sectors were intermediate, and nos were smallest. These patterns appear to indicate differential timing of the activation of these promoters during embryogeny. Measurement of transcript abundance for each transformant indicated that the CaMV 35S-transformed plants accumulated approximately 1000-fold more TPase mRNA than plants containing wild-type Ac, whereas ocs- and nos-transformed lines accumulated about 100-fold and 20-fold higher levels, respectively. Measurements of germinal excision frequencies driven by the chimeric TPase fusions, however, indicated that increasing transcription does not necessarily result in an increase in germinal excision. These measurements showed that the ocs and nos fusions have very low rates of germinal excision. Only the CaMV 35S fusion transformants were found to have higher rates than the Ac constructs, although significant pod-to-pod variation was observed. Gel blot analysis of DNA from progeny carrying germinal excision events resulting from the CaMV 35S fusion showed that excision is associated with reinsertion and that siblings sometimes carry the same transposition events. These findings suggest that in tobacco there is no direct proportionality between TPase expression and Ac-Ds transposition activity. This possibility has important implications for understanding the regulation of Ac transposition and for designing efficient gene tagging systems.

Base Sequence↗
PubMed2002

Enhanced cytokine mRNA levels in attack-free patients with familial Mediterranean fever.

Familial Mediterranean fever (FMF) is a recessively inherited inflammatory disorder, characterized by recurrent attacks of fever and serositis. Screening of mutations in the causing gene (MEFV) now allows accurate diagnosis of FMF among other inflammatory conditions. It is well documented that secreted levels of some pro-inflammatory cytokines are elevated in FMF. Here, we investigated cytokine expression at the transcriptional level, in patients that could be genetically ascertained. We have measured the transcript abundance of tumor necrosis factor alpha, interleukin-1beta, interleukin-6 and interleukin-8, in circulating leukocytes and shown that these were more elevated in attack-free FMF patients than in controls (P=0.01, P=0.008, P=0.02, P=0.001 respectively). There was no significant difference according to MEFV genotype or colchicine treatment. Our results suggest that cytokine transcriptional pathways are misregulated in attack-free FMF patients, and further supports the hypothesis that these patients have subclinical inflammation between attacks.

Colchicine↗
PubMed1998

Light-regulated transcription of genes encoding peridinin chlorophyll a proteins and the major intrinsic light-harvesting complex proteins in the dinoflagellate amphidinium carterae hulburt (Dinophycae). Changes In cytosine methylation accompany photoadaptation

In the dinoflagellate Amphidinium carterae, photoadaptation involves changes in the transcription of genes encoding both of the major classes of light-harvesting proteins, the peridinin chlorophyll a proteins (PCPs) and the major a/c-containing intrinsic light-harvesting proteins (LHCs). PCP and LHC transcript levels were increased up to 86- and 6-fold higher, respectively, under low-light conditions relative to cells grown at high illumination. These increases in transcript abundance were accompanied by decreases in the extent of methylation of CpG and CpNpG motifs within or near PCP- and LHC-coding regions. Cytosine methylation levels in A. carterae are therefore nonstatic and may vary with environmental conditions in a manner suggestive of involvement in the regulation of gene expression. However, chemically induced undermethylation was insufficient in activating transcription, because treatment with two methylation inhibitors had no effect on PCP mRNA or protein levels. Regulation of gene activity through changes in DNA methylation has traditionally been assumed to be restricted to higher eukaryotes (deuterostomes and green plants); however, the atypically large genomes of dinoflagellates may have generated the requirement for systems of this type in a relatively "primitive" organism. Dinoflagellates may therefore provide a unique perspective on the evolution of eukaryotic DNA-methylation systems.

Journal Article↗
PubMed2004

Cloning of apoptosis-related genes by representational difference analysis of cDNA.

Apoptosis is frequently triggered by events that alter the expression of key target genes. Under these circumstances, the genes involved can be identified by techniques that analyze gene expression. Researchers now have a choice of reliable and effective methods for differential gene expression analysis. Comparative approaches, including gene microarray analysis, serial analysis of gene expression, and differential display provide global information about expression levels. Subtractive approaches like complementary DNA representational difference analysis (cDNA RDA) and suppression subtraction polymerase chain reaction identify a focused set of differentially expressed genes. The most suitable technique to apply depends on individual circumstances. cDNA RDA is particularly useful in nonstandard model organisms for which comprehensive gene microarrays are not available and is best used for the identification of genes with a large difference in expression levels between two populations. The technique involves the generation of amplified mixtures of cDNA fragments that are typically smaller than 1000 base pairs and represent >86% of mRNA species from each starting population. Transcriptional differences between two populations can then be identified by subtraction of cDNA amplicons followed by further polymerase chain reaction amplification. The technique is capable of detecting differences for genes expressed at less than one copy per cell and is achievable using standard laboratory apparatus. cDNA RDA can identify genes not previously described in the database, can detect low abundance transcripts (e.g., from mixed cell populations), and is best applied in experiments where relatively few differentially expressed genes are expected. Here, we describe the application of cDNA RDA to the identification of apoptosis-related genes.

Animals↗
PubMed2005

Characterization of the c-type lysozyme gene family in Anopheles gambiae.

Seven new c-type lysozyme genes were found using the Anopheles gambiae genome sequence, increasing to eight the total number of genes in this family identified in this species. The eight lysozymes in An. gambiae have considerable variation in gene structure and expression patterns. Lys c-6 has the most unusual primary amino acid structure as the predicted protein consists of five lysozyme-like domains. Transcript abundance of each c-type lysozyme was determined by semiquantitative RT-PCR. Lys c-1, c-6 and c-7 are expressed constitutively in all developmental stages from egg to adult. Lys c-2 and c-4 also are found in all stages, but with relatively much higher levels in adults. Conversely, Lys c-3 and c-8 transcripts are highest in larvae. Lys c-1, c-6 and c-7 transcripts are found in nearly all the adult tissue samples examined while Lys c-2 and Lys c-4 are more restricted in their expression. Lys c-1 and c-2 transcripts are clearly immune responsive and are increased significantly 6-12 h post challenge with bacteria. The functional adaptive changes that may have evolved during the expansion of this gene family are briefly discussed in terms of the expression patterns, gene and protein structures.

Amino Acid Sequence↗
PubMed2005

The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo.

Maternal and zygotic activities of the homeodomain protein PAL-1 specify the identity and maintain the development of the multipotent C blastomere lineage in the C. elegans embryo. To identify PAL-1 regulatory target genes, we used microarrays to compare transcript abundance in wild-type embryos with mutant embryos lacking a C blastomere and to mutant embryos with extra C blastomeres. pal-1-dependent C-lineage expression was verified for select candidate target genes by reporter gene analysis, though many of the target genes are expressed in additional lineages as well. The set of validated target genes includes 12 transcription factors, an uncharacterized wingless ligand and five uncharacterized genes. Phenotypic analysis demonstrates that the identified PAL-1 target genes affect specification, differentiation and morphogenesis of C-lineage cells. In particular, we show that cell fate-specific genes (or tissue identity genes) and a posterior HOX gene are activated in lineage-specific fashion. Transcription of targets is initiated in four temporal phases, which together with their spatial expression patterns leads to a model of the regulatory network specified by PAL-1.

Analysis of Variance↗
PubMed2003

RNA amplification and transcriptional profiling for analysis of stem cell populations.

As stem cells constitute a rare cell pool, a global analysis of gene expression is typically not possible. Here, we use a T7-based RNA amplification method combined with high-density oligonucleotide array technology to analyze gene expression. We isolated RNA from ES cells (100-100,000 cells), subjected them to two rounds of amplification, and compared each sample using microarray analysis. RNA isolation and amplification was highly reproducible and sensitive for the analysis of low abundant transcripts. Greater than 93% of the transcripts expressed were changed less than 2-fold when comparing the results of amplified RNA (100 cells to 100,000 cells) to unamplified RNA (isolated from 1,000,000 cells). This transcriptional analysis resulted in minimal skewing of gene expression. Using this technology, we analyzed the genetic programs of ES cells, STO feeder cells, and adult cardiomyocytes. We conclude that these technologies can be applied to the analysis of the genetic programs of rare cell populations and ultimately this analysis will enhance our understanding of the regulatory mechanisms of stem cell populations.

Animals↗
PubMed1990

Distinct regional expression of nicotinic acetylcholine receptor genes in chick brain.

Four genes (alpha 2, alpha 3, alpha 4 and beta 2) have been reported as encoding subunits of the nicotinic acetylcholine receptor (nAChR) in chicken brain. The mRNAs transcribed from these genes have here been localised to particular regions using in situ hybridisation histochemistry. The beta 2 mRNA was clearly the most abundant transcript, being widely distributed throughout the chick brain. In the cerebellum, all four mRNA species were present, although they showed different cellular patterns of distribution. Only alpha 2 mRNA and beta 2 mRNA were found in significant amounts in the optic tectum. In the lateral spiriform nucleus, while alpha 2 mRNA, alpha 4 mRNA and beta 2 mRNA were all very abundant, the alpha 4 mRNA was localised to a subgroup of neurons containing alpha 2 mRNA and beta 2 mRNA. This represents the first evidence that individual cells may express two different nAChR alpha subunit genes in vivo. The distributions of the 4 mRNA species showed few common features. This suggests that other neuronal nAChR genes remain to be identified, and that these 4 genes are not generally expressed in the same cells to constitute a single macromolecular complex. The results therefore provide evidence for nAChR heterogeneity in the central nervous system.

Animals↗
PubMed2005

Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid HR-specific downregulation of photosynthesis.

Transcript profiling during susceptible (S) and hypersensitive response-associated resistance (R) interactions was determined in soybean (Glycine max). Pseudomonas syringae pv. glycinea carrying or lacking the avirulence gene avrB, was infiltrated into cultivar Williams 82. Leaf RNA was sampled at 2, 8, and 24 h postinoculation (hpi). Significant changes in transcript abundance were observed for 3,897 genes during the experiment at P < or = 0.000005. Many of the genes showed a similar direction of increase or decrease in abundance in both the S and R responses, but the R response generally showed a significantly greater degree of differential expression. More than 25% of these responsive genes had not been previously reported as being associated with pathogen interactions, as 704 had no functional annotation and 378 had no homolog in National Center for Biotechnology Information databases. The highest number of transcriptional changes was noted at 8 hpi, including the downregulation of 94 chloroplast-associated genes specific to the R response. Photosynthetic measurements were consistent with an R-specific reduction in photosystem II operating efficiency (phiPSII) that was apparent at 8 hpi for the R response with little effect in the S or control treatments. Imaging analyses suggest that the decreased phiPSII was a result of physical damage to PSII reaction centers.

Analysis of Variance↗
PubMed1998

Transcription of the human cytomegalovirus natural killer decoy gene, UL18, in vitro and in vivo.

Multiplex RT-PCR analysis of human cytomegalovirus (HCMV) replication in human fibroblasts showed transcription of the natural killer (NK) cell decoy gene, UL18, from 72 h onwards. Transcription of glycoprotein B (gpUL55; a late gene) occurred from early time-points and peaked at 24 h post-infection. UL18 mRNA was also detected in the peripheral blood mononuclear cells of organ transplant recipients with HCMV viraemia, especially those with HCMV DNA virus loads greater than 10(5) genomes/ml whole blood. Thus, UL18 is produced via a low abundance transcript late during the infectious cycle at a time coincidental with the increased risk of NK cell lysis as a consequence of class I HLA down-regulation.

Base Sequence↗
PubMed2005

Differentially expressed transcripts from phenotypically identified olfactory sensory neurons.

In comparing purified mouse olfactory sensory neurons (OSNs) with neighboring cells, we identified 54 differentially expressed transcripts. One-third of the transcripts encode proteins with no known function, but the others have functions that correlate with challenges faced by OSNs. The OSNs expressed a diversity of signaling protein genes, including stomatin (Epb7.2), S100A5, Ddit3, Sirt2, CD81, Sdc2, Omp, and Ptpla. The elaboration of dendrites, cilia, and axons that places OSNs in contact with diverse cell types and signals presumably also requires large investments in cytoskeletal-associated proteins, lipid biosynthesis, and energy production. Several of the genes encode proteins that participate in these biological processes, including ATP5g3, Ndufa9, Sqrdl, Mdh1, Got1, beta-2 tubulin, Capza1, Bin3, Tom1, Acl6, and similar to O-MACS. Three transcripts had restricted expression patterns. Similar to O-MACS and Gstm2 had zonally restricted expression patterns in OSNs and sustentacular cells but not in Bowman's glands, suggesting that zonality can be differentially regulated by cell type. The mosaic expression pattern of S100A5 in approximately 70% of OSNs predicts that it is coexpressed with a subset of odorant receptors. We captured four abundant transcripts, Cyp2a4, similar to Cyp2g1, Gstm2, and Cbr2, that encode xenobiotic metabolizing enzymes expressed by sustentacular cells or Bowman's glands, reinforcing the interpretation that clearance of xenobiotic compounds is a major function of these cells. Within the olfactory epithelium, Cbr2 is a new anatomical marker for sustentacular cells. We also discovered that Reg3g is a marker for respiratory epithelium.

Animals↗
PubMed1988

Isolation and characterization of cDNA clones encoding epitopes shared with Alzheimer neurofibrillary tangles.

A pool of ten monoclonal antibodies to SDS-insoluble epitopes of Alzheimer neurofibrillary tangles (NFT) was used to screen an adult human brain cDNA expression library. Fourteen clones were isolated, two of which are described. The largest of the clones encodes 80 kD, or approximately 600 amino acids, of microtubule-associated protein 2 (MAP 2). The MAP 2 region encoded by the clone shares at least two epitopes with human tau, another microtubule-associated protein which cross-reacts with NFT. In rat brain mRNA, the MAP 2 cDNA hybridizes to a single transcript of 9.5 kb. In human neuroblastoma mRNA, the MAP 2 cDNA hybridizes, at high stringency, to two transcripts of 9.5 kb and 6 kb. The 6-kb transcript comigrates with the transcript for tau, as detected by a human tau cDNA. The properties of the MAP 2 cDNA suggest that, in humans, MAP 2 and tau have a common domain which may play a role in NFT formation. Another clone isolated with the anti-NFT antibodies shares epitopes, but not nucleic acid homology, with the MAP 2 cDNA. This clone detects a single abundant transcript of 1 kb present in RNA from human neuroblastoma and from several non-neuronal human cell lines. The properties of this cDNA suggest that it encodes a protein other than those previously reported to cross-react with NFT.

Adult↗
PubMed1994

Mosaic suppressor, a gene in Drosophila that modifies retrotransposon expression and interacts with zeste.

A newly identified locus in Drosophila melanogaster, Mosaic suppressor (Msu), is described. This gene modifies the expression of white-apricot (wa), which is a copia retrotransposon-induced allele of the white gene. In addition to suppressing wa in a mosaic fashion, this mutation suppresses or enhances the expression of several other retrotransposon induced white alleles. Mutations in Msu alter copia transcript abundance and may regulate the expression of several other retrotransposons. While each of the two Msu isolates is homozygous lethal, heteroallelic escapers occur at a low frequency. These escapers act not only as strong suppressors of wa, but also as a recessive enhancer of synaptic-dependent gene expression at white. The mutation described here suggests a connection between the regulation of specific transcriptional units such as retrotransposons and more global synapsis dependent regulatory effects.

Alleles↗
PubMed1992

Genomic structure and alternative splicing of 519, a gene expressed late after T cell activation.

Relatively little is known about the transcriptional control of genes expressed late after T cell activation. We have identified four genes expressed 3 to 5 days after T cell activation by alloantigen or mitogen. Here we report the genomic organization of 519, one of these late T cell activation Ag. Analysis of the genomic clone revealed that 519 consists of six exons. Ribonuclease protection experiments indicated that the most abundant transcript arising from this region is an alternatively spliced form of 519, referred to as 520, which lacks exon 2 and is similar in sequence to NKG5, a cDNA identified in NK cells. These experiments also revealed the existence of two other alternatively spliced RNA transcripts, with heterogeneity in exon 2. Primer extension analysis and ribonuclease protection assays demonstrated that there are two prominent start sites for transcription; however, there is no evidence for the NKG5 transcript in T cells, indicating that NKG5 may represent a NK cell-specific form of 520. The 5' flanking region of this gene contains several previously identified sequences involved in transcriptional regulation, as well as some potentially interesting novel conserved motifs.

Antigens, Differentiation, T-Lymphocyte↗
PubMed1998

Up-regulation of CD44 variant exon expression in endometrial carcinomas: analysis of mRNA and protein isoforms, and relation to clinicopathological factors.

In order to clarify the relation between expression of individual CD44 variant exons and tumor progression, 34 endometrial carcinomas (endometrioid type) were investigated, as well as 27 samples of normal endometrium, using a combination of reverse transcription-polymerase chain reaction (RT-PCR) and Southern blot hybridization (SBH). Western blotting was also performed for comparison of protein levels with the results of the RT-PCR/SBH methods. Analysis of gross CD44 splicing patterns demonstrated high-level expression of variant isoforms in endometrial carcinomas as compared with normal endometrium. Exon-specific RT-PCR/SBH assays revealed large, abundant transcripts of individual variant exons in particular v3, v4, and v5, in tumors, but these isoforms were also expressed in normal endometria, suggesting a lack of tumor-specificity. No individual CD44 variant transcripts were associated with any of the prognostic factors investigated. Parallel observations showed variant CD44 transcripts to be more readily detectable than protein isoforms in the same samples. These findings indicate that in endometrial carcinomas, expression of individual variant CD44 exons is markedly up-regulated, but this molecule may not be useful as a consistent indicator of tumor progression.

Endometrial Neoplasms↗