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At least 649 records · Page 36Linked to original sources
PubMed2001

Molecular cloning and expression analysis of the turkey vasoactive intestinal peptide receptor.

Vasoactive intestinal peptide (VIP) is a prolactin (PRL)-releasing factor whose activity in avian species is believed to be mediated by a specific VIP receptor (VIP-R). Circulating PRL levels are closely related to hypothalamic VIP immunoreactivity, hypothalamic VIP mRNA content, and hypophysial-portal blood VIP concentrations in turkeys. In the present study, a turkey VIP-R (tVIP-R) cDNA was cloned and its mRNA abundance was quantified in various tissues during different reproductive stages. The 2347-bp tVIP-R cDNA encoded a 457 amino acid protein, with a predicted Mr of 52 kDa. The full-length cDNA shares approximately 55% similarity with the mammalian VIP receptor-1. Northern blot analysis revealed that a major 2.7-kb transcript was expressed in laying hen pituitaries. Furthermore, two minor tVIP-R transcripts of 3.7 and 3.4 kb were observed. Semiquantitative reverse transcription polymerase chain reaction (RT-PCR) was performed using RNA from various turkey brain and peripheral tissues throughout the reproductive cycle. The steady-state levels of pituitary tVIP-R mRNA changed during the reproductive cycle, whereas mRNA expression in other tissues was not affected. The steady-state levels of tVIP-R mRNA were only affected in the pituitary, whereas mRNA expression in any of the other tissues examined following the immunization of turkeys against VIP were not affected.

Amino Acid Sequence↗
PubMed2006

An mRNA expression analysis of stimulation and blockade of 5-HT7 receptors during memory consolidation.

Despite the compelling support for 5-hydroxytryptamine (5-HT) receptors participation in learning and memory in mammal species, the molecular basis had been largely absent from any discussion of its mechanistic underpinnings. Here, we report that reverse transcriptase-polymerase chain reaction (RT-PCR) analysis revealed that there was a higher level of expression of the investigated 5-HT receptor mRNAs in autoshaping-trained relative to untrained groups. Actually, pharmacological naïve untrained and autoshaping-trained rats showed significant differences, the latter groups expressing, in decreasing order, 5-HT1A < 5-HT6 < 5-HT4 < or = 5-HT7 receptors mRNA in prefrontal cortex and hippocampus. In order to determine more precisely mRNA expression and memory consolidation, we combined selective 5-HT7 receptors stimulation or blockade in the same animals, and brain areas individually analyzed. 5-HT7 receptors were strongly expressed in all the three brain areas of vehicle-trained rats relative to untrained group. The potential selective 5-HT7 receptor agonist AS 19 enhanced memory consolidation, attenuated mRNA receptors expression, and the facilitatory memory effect was reversed by SB-269970. Finally, pharmacological stimulation of 5-HT7 receptors reversed scopolamine- or dizocilpine-induced amnesia and receptor down-regulation.

Animals↗
PubMed1999

Cloning and expression analysis of a Petunia hybrida flower specific mitotic-like cyclin.

A cyclin cDNA clone (Pethy;CycB1;1) was isolated from a Petunia hybrida ovary specific cDNA library. Sequence comparison revealed that Pethy;CYCB1;1 protein is highly homologous to mitotic B1 cyclins. Northern analysis and in situ hybridisation experiments showed that its expression is developmentally regulated and restricted to flower organs. We have attempted to define some of the cell division patterns which contribute to shaping each floral organ by analysing Pethy;CycB1;1 expression on Petunia flower sections. While in sepals, epidermis and parenchyma cell division patterns were comparable, there were two distinct cell division patterns in petals. In the epidermis, Pethy;CYCB1;1 expression was found both at the petal tip and along epidermis, whereas in the parenchyma only at the petal tips. In reproductive organs cell divisions were detected only in sporophytic tissues. No signals were detected inside meiotic cells.

Cloning, Molecular↗
PubMed2006

Protein expression analysis of Halobacillus dabanensis D-8T subjected to salt shock.

To investigate the mechanism of salt tolerance of gram-positive moderately halophilic bacteria, two-dimensional gel electrophoresis (2-D PAGE) was employed to achieve high resolution maps of proteins of Halobacillus dabanensis D-8T. Approximately 700 spots of proteins were identified from these 2-D PAGE maps. The majority of these proteins had molecular weights between 17.5 and 66 kDa, and most of them were distributed between the isoelectric points (pI) 4.0 and 5.9. Some protein spots were distributed in the more acidic region of the 2-D gel (pI <4.0). This pattern indicated that a number of proteins in the strain D-8T are acidic. To understand the adaptation mechanisms of moderately halophilic bacteria in response to sudden environmental changes, differential protein profiles of this strain were investigated by 2-D PAGE and Imagemaster 2D Platinum software after the cells were subjected to salt shock of 1 to 25% salinity for 5 and 50 min. Analysis showed 59 proteins with an altered level of expression as the result of the exposure to salt shock. Eighteen proteins had increased expression, 8 proteins were induced, and the expression of 33 proteins was down-regulated. Eight of the up-regulated proteins were identified using MALDI-TOF/MS and MASCOT, and were similar to proteins involved in signal transduction, proteins participating in energy metabolism pathways and proteins involved in stress.

Bacillaceae↗
PubMed2004

Gene expression analysis on biochemical networks using the Potts spin model.

MOTIVATION: Microarray technology allows us to profile the expression of a large subset or all genes of a cell. Biochemical research over the last three decades has elucidated an increasingly complete image of the metabolic architecture. For less complex organisms, such as Escherichia coli, the biochemical network has been described in much detail. Here, we investigate the clustering of such networks by applying gene expression data that define edge lengths in the network. RESULTS: The Potts spin model is used as a nearest neighbour based clustering algorithm to discover fragmentation of the network in mutants or in biological samples when treated with drugs. As an example, we tested our method with gene expression data from E.coli treated with tryptophan excess, starvation and trpyptophan repressor mutants. We observed fragmentation of the tryptophan biosynthesis pathway, which corresponds well to the commonly known regulatory response of the cells.

Algorithms↗
PubMed2006

Full-length sequence and expression analysis of Toll-like receptor 9 in the gilthead seabream (Sparus aurata L.).

Toll-Like Receptors (TLRs) have recently emerged as key sensors of invading microbes, acting through recognition of pathogen-associated molecular patterns. It has been demonstrated that TLR9 is involved in the recognition of unmethylated CpG motifs in mice, humans, and pigs. We report here the full-length sequence of TLR9 cDNA in the gilthead sea bream (Sparus aurata L.). The predicted protein (1063 amino acids) was similar to mammalian TLR9s, showing 21 leucine-rich repeats in the extracellular region and a typical Toll/IL-1R (TIR) domain in the intracellular region. Comparative analysis of TLR9 sequences indicated that critical residues for ligand-binding are conserved across vertebrate lineages, although evidence of functional divergence was observed. Analysis of the genomic structure of sea bream TLR9 gene revealed the presence of two intervening sequences. Retention of the second intron produced an alternatively spliced mRNA (TLR9B) showing differential expression among tissues or developmental stages compared to the wild-type isoform (TLR9A). RT-PCR analysis indicated a broad expression of TLR9A, especially in immune-related organs (spleen, head-kidney) and mucosal-epithelial barriers (gills, gut, skin). Using quantitative Real-Time RT-PCR, no statistically significant variation was observed for TLR9 mRNAs expression in the spleen of experimentally infected animals compared to healthy controls. Comparing sequence and expression profile of sea bream TLR9 with mammalian TLR9s suggested that the main function of TLR9 might be conserved across vertebrates, although species-specific features are present (modulation of ligand-binding specificity, alternative splicing).

Amino Acid Sequence↗
PubMed2006

Expression analysis of LacZ gene placed in the locus of Cnot7 exhibits its activity in osteoblasts in vivo and in mineralized nodules in vitro.

CCR4-NOT complex 7 (Cnot7) was identified as a regulator of gene expression in yeast and evolutionally conserved in mammals. Cnot7 deficient male mice exhibit abnormality in spermatogenesis. As these mice contained construct to express LacZ, we followed the expression patterning in these animals. LacZ was expressed in osteoblasts located in the primary spongiosa in adult mice. Cellular analysis indicated that LacZ is expressed in osteoblasts but not in osteoclasts. In the mineralized nodules formed in the culture of bone marrow cells obtained from Cnot7 +/- mice, LacZ expression was mainly observed in the cells forming mineralized nodules but not in un-mineralized area scattered around the periphery of the nodules. LacZ blue positive cells were gradually depositing minerals along its time course of the in vitro mineralization assay. Cnot7 expression was enhanced by the treatment with BMP. These data suggest that Cnot7 is expressed in osteoblasts and is associated with mineralization.

3T3 Cells↗
PubMed2002

Linear amplification coupled with controlled extension as a means of probe amplification in a cDNA array and gene expression analysis during cold acclimation in alfalfa (Medicago sativa L.).

This study describes a rapid and simple way to amplify limited amounts of probes used for cDNA array hybridization while maintaining the original representation of transcripts in the samples. The approach is based on linear amplification of cDNA-coupled controlled extension of amplified products and yielded a 50-75-fold increases in hybridization signal intensity. Controlled extension of products is achieved either by adjusting the amplification conditions or by using a digested template. Linear amplification with controlled extension generates a population of fragments consisting mainly of 3'-end portions of original transcripts and ranging in length from 200 to 800 nucleotides. cDNA array analysis revealed that amplified and non-amplified probes generate expression profiles with correlations ranging from r=0.857 to 0.895. Up to 90% of cDNA clones, differentially expressed during cold acclimation in alfalfa, could be detected with both types of probes. This amplification method should increase the utility of cDNA arrays for identifying novel differentially expressed genes as well as expression profiling in specialized tissues or cells when the amount of analysed material is limited. The possibility of diminishing cross-hybridization of long genes sharing high sequence homology and improving the hybridization kinetics of complex probes after amplification is also discussed.

Acclimatization↗
PubMed2004

Expression analysis of the SG-SSPN complex in smooth muscle and endothelial cells of human umbilical cord vessels.

Recently, participation of the sarcoglycan (SG)-sarcospan (SSPN) complex in the development of cardiomyopathy in patients with limb-girdle muscular dystrophy has been shown, and presence of the complex in smooth muscle may be important for the contraction/dilation process of vessels. However, there are few studies determining the SG-SSPN complex in vascular smooth muscle and endothelial cells of vessels. In this study, we analyzed by reverse transcriptase-polymerase chain reaction and immunofluorescence the expression of different components of the complex in vein/artery smooth muscle and endothelial cells of the human umbilical cord. By RNA analysis, we observed expression of alpha-, beta-, gamma-, delta-, epsilon-SG, and SSPN in smooth muscle cells. In endothelial cells, RNA expression was restricted to beta-, delta-, epsilon-SG, and SSPN. At protein level, we observed in smooth muscle the presence of beta-, delta-, epsilon-SG, and SSPN. In endothelial cells, immunostaining only evidenced the presence of epsilon-SG and SSPN. However, colocalization of SGs and SSPN with dystrophin and utrophin was noted. These results, interestingly, suggest that the SG-SSPN complex may either form with dystrophin or utrophin in smooth muscle cells, and with utrophin in endothelial cells. Additionally, we also observed in some smooth muscle regions the colocalization of the SG-SSPN complex with caveolin, with colocalization being more pronounced between epsilon-SG-SSPN and caveolin in endothelial cells.

Carrier Proteins↗
PubMed2001

Gene expression analysis of an H(2)O(2)-resistant lens epithelial cell line.

Gene expression patterns were examined in lens epithelial cells conditioned to grow in 125 microM hydrogen peroxide in order to define the protective mechanisms that may be involved in survival during oxidative stress. RNA was extracted from normal and hydrogen peroxide-resistant alphaTN4 mouse lens epithelial cells. Gene expression was evaluated using Differential Display (DD) and RT-PCR. Upregulation of mRNAs for antioxidant and cellular defense enzymes was observed. The highest elevation detected was a 14-fold increase in catalase in the hydrogen peroxide-resistant cells. Glutathione peroxidase, ferritin, and alphaB-crystallin were upregulated 2-fold, and reticulocalbin was upregulated 6-fold in the resistant cells. alphaA-crystallin was downregulated 5-fold, while aldose reductase and mitochondrial gene products were unchanged. Thus, in the alphaTN4 mouse lens cell line, long-term exposure to high levels of hydrogen peroxide elicited an upregulation of transcripts for enzymes involved in hydrogen peroxide degradation, metal binding, and chaperone function. Since mitochondrial gene transcription is sensitive to hydrogen peroxide, the presence of normal levels of mitochondrial transcripts, in this study, demonstrates the effectiveness of the antioxidant defense systems.

Animals↗
PubMed2001

Cloning and expression analysis of chicken Lix1, a founding member of a novel gene family.

Limb Expression 1 (Lix1), a founding member of a novel gene family, was identified in a screen for genes transiently and locally expressed during early chicken limb development. Most prominently, Lix1 is transiently expressed in the nascent hindlimb bud between Hamburger-Hamilton stages 15 and 19. Chicken Lix1 transcripts are also found in the basal plate of rhombomeres 3 and 5, in pharyngeal and in foregut mesenchyme and in all facial primordia except for the mandibular arches. Homologs of chick Lix1 exist in human, mouse and Drosophila.

Amino Acid Sequence↗
PubMed2006

[Identification of the rice (Oryza sativa L.) mutant msp1-4 and expression analysis of its UDT1 and GAMYB genes].

A rice male-sterile mutant msp1-4 (MULTIPLE SPOROCYTE) with japonica cultivar '9522' background, was obtained in M(3) population treated with (60)Co gamma-ray. Results of genetic analysis indicated that the male-sterile phenotype was controlled by a single recessive locus. To map this locus, an F(2) population was constructed from the cross between the msp1-4 (japonica) and 'LongTeFu B' (indica). This locus was mapped between the two InDel markers, WY-4 and WY-8, with physical distance of 247 kb. A deletion with 10 base pairs between 758 bp and 767 bp in MSP1 open reading frame was confirmed by sequence analysis, which led to pre-termination of MSP1 translation. Phenotype analysis of msp1-4 indicated that it was similar to the msp1 mutant. To insight the expression change of rice anther developmental genes in this mutant, semi-quantitative RT-PCR analysis was carried out. The results showed that the expression level of rice UDT1 and GAMYB were reduced in msp1-4, implying that UDT1 and GAMYB are possibly the downstream genes of MSP1 gene in rice pollen development.

Flowers↗
PubMed2004

Comparative uterine gene expression analysis after dioxin and estradiol administration.

The environmental pollutant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) adversely affects many organisms. TCDD exposure is known to be associated with abnormal development, hepatotoxicity and endocrine effects. It has also been reported to have antiestrogenic activity in addition to estrogenic activity. In order to clarify the effects of TCDD in the uterus, we evaluated the patterns of gene expression after TCDD and estradiol administration. Of the 10 000 arrayed genes, only a few were affected by both estradiol and TCDD. Although the subset of genes that responded to estrogen was also activated by TCDD, the response to TCDD was more limited than that observed in response to estradiol. Therefore, according to our analysis of gene expression patterns, TCDD had partial and weak estrogenic activity in the uterus.

Animals↗
PubMed2006

Expression analysis of mammaglobin A (SCGB2A2) and lipophilin B (SCGB1D2) in more than 300 human tumors and matching normal tissues reveals their co-expression in gynecologic malignancies.

BACKGROUND: Mammaglobin A (SCGB2A2) and lipophilin B (SCGB1D2), two members of the secretoglobin superfamily, are known to be co-expressed in breast cancer, where their proteins form a covalent complex. Based on the relatively high tissue-specific expression pattern, it has been proposed that the mammaglobin A protein and/or its complex with lipophilin B could be used in breast cancer diagnosis and treatment. In view of these clinical implications, the aim of the present study was to analyze the expression of both genes in a large panel of human solid tumors (n = 309), corresponding normal tissues (n = 309) and cell lines (n = 11), in order to evaluate their tissue specific expression and co-expression pattern. METHODS: For gene and protein expression analyses, northern blot, dot blot hybridization of matched tumor/normal arrays (cancer profiling arrays), quantitative RT-PCR, non-radioisotopic RNA in situ hybridization and immunohistochemistry were used. RESULTS: Cancer profiling array data demonstrated that mammaglobin A and lipophilin B expression is not restricted to normal and malignant breast tissue. Both genes were abundantly expressed in tumors of the female genital tract, i.e. endometrial, ovarian and cervical cancer. In these four tissues the expression pattern of mammaglobin A and lipophilin B was highly concordant, with both genes being down-, up- or not regulated in the same tissue samples. In breast tissue, mammaglobin A expression was down-regulated in 49% and up-regulated in 12% of breast tumor specimens compared with matching normal tissues, while lipophilin B was down-regulated in 59% and up-regulated in 3% of cases. In endometrial tissue, expression of mammaglobin A and lipophilin B was clearly up-regulated in tumors (47% and 49% respectively). Both genes exhibited down-regulation in 22% of endometrial tumors. The only exceptions to this concordance of mammaglobin A/lipophilin B expression were normal and malignant tissues of prostate and kidney, where only lipophilin B was abundantly expressed and mammaglobin A was entirely absent. RNA in situ hybridization and immunohistochemistry confirmed expression of mammaglobin A on a cellular level in endometrial and cervical cancer and their corresponding normal tissues. CONCLUSION: Altogether, these data suggest that expression of mammaglobin A and lipophilin B might be controlled in different tissues by the same regulatory transcriptional mechanisms. Diagnostic assays based on mammaglobin A expression and/or the mammaglobin A/lipophilin B complex appear to be less specific for breast cancer, but with a broader spectrum of potential applications, which includes gynecologic malignancies.

Biomarkers, Tumor↗
PubMed2001

Molecular cloning and functional expression analysis of a cDNA for human hepassocin, a liver-specific protein with hepatocyte mitogenic activity.

By means of differential cDNA expression cloning, we earlier isolated a novel rat cDNA and its protein, named hepassocin, which is upregulated during liver regeneration. Using the rat cDNA as a probe, we have now isolated human hepassocin cDNA encoding a protein of 312 amino acids, which has 81.4% and 83.8% identity, respectively, to rat hepassocin before and after elimination of its signal peptide. Dot blot analysis revealed that hepassocin mRNA was strongly expressed in adult liver, fairly strongly in fetal liver, and weakly in pancreas, but not in other tissues. Recombinant human hepassocin produced in Chinese hamster ovary (CHO) cells by the dihydrofolate reductase-methotrexate (DHFR--MTX) gene amplification method is a homodimer (68 kDa) and has mitogenic activities in hepatocytes of various animal species including rat, mouse, rabbit and dog, and the activity was lost with 2-mercaptoethanol treatment. These results suggest that hepassocin is a potent regulator in liver cell growth not only in rats but also in humans. Computer searches revealed that human hepassocin as well as rat hepassocin has a characteristic disulfide structure close to that of fibrinogen-gamma. We assume that this newly identified growth factor exerts functions in association with an extracellular matrix such as fibrinogen.

Amino Acid Sequence↗
PubMed2002

Classification and expression analysis of Arabidopsis F-box-containing protein genes.

F-box proteins regulate diverse cellular processes, including cell cycle transition, transcriptional regulation and signal transduction, by playing roles in Skp1p-cullin-F-box protein (SCF) complexes or non-SCF complexes. F-box proteins are encoded by a large gene family. Our database search revealed that at least 568 F-box protein genes are present in the Arabidopsis thaliana (Arabidopsis) genome. Domain search analysis using SMART and Pfam-A databases revealed that 67 of the F-box proteins contained Kelch repeats and 29 contained leucine-rich repeats (LRRs). Interestingly only two F-box proteins contained WD40 repeats that are found in many F-box proteins of other organisms. Kelch repeats, LRRs and WD40 repeats are implicated in protein-protein interactions. This analysis also resulted in the finding of several unique functional domains; however, 448 of the F-box proteins did not contain any known domains. Therefore, these proteins were used to search the Pfam-B database to find novel domains, and three putative ones were found. These domain search analyses led us to classify the Arabidopsis F-box proteins into at least 19 groups based on their domain structures. Macro array analysis showed that several F-box protein genes are expressed in a tissue-specific manner.

Arabidopsis↗
PubMed2005

Locating a blood pressure quantitative trait locus within 117 kb on the rat genome: substitution mapping and renal expression analysis.

Previously, a blood pressure (BP) quantitative trait locus (QTL) on rat chromosome 9 (RNO9) was localized to a <2.4 cM interval using congenic strains generated by introgressing segments of RNO9 from the Dahl salt-resistant (R) rat into the background of the Dahl salt-sensitive (S) rat. Renal gene expression using Affymetrix gene chips was profiled on S and a congenic strain spanning the 2.4-cM BP QTL interval. This analysis identified 20 differentially expressed genes/expressed sequence tags. Of these, the locus with the greatest differential expression (30- to 35-fold) was regulated endocrine-specific protein 18 (Resp18), which also mapped in the 2.4-cM BP QTL interval. Additional substitution mapping located the QTL to <0.4 cM or approximately 493 kb. This newly defined QTL region still included Resp18. Nucleotide variants were identified between S and R genomic DNA of Resp18 in the coding, 5' regulatory and 3' untranslated regions. The coding sequence variation (T/C) occurs in exon 2 and predicts an amino acid change (Ile/Val) in the protein product. Resp18 was considered a differentially expressed positional candidate for the QTL. To fine-map the BP QTL, we constructed a congenic strain with a smaller introgressed region. Compared with the S rat, this strain (1) had significantly lower BP, (2) did not contain the R form of Resp18, and (3) did not retain the rather spectacular differential expression of Resp18. Together, these results demonstrate that a BP QTL independent of Resp18 exists within the newly defined 117-kb QTL region on RNO9.

Animals↗