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At least 217 records · Page 12Linked to original sources
PubMed2001

Genetic and physical mapping, expression analysis and partial sequence of porcine PER1.

The porcine PER1 gene was mapped to chromosome 12q1.4-->q1.5 using fluorescence in situ hybridisation. A polymorphic microsatellite marker (S0601) was isolated from a BAC clone shown to contain the PER1 gene. Linkage analysis assigned S0601 distal to ALOX12 on SSC12, providing further evidence for the conservation of synteny between HSA17 and SSC12. RT-PCR analysis demonstrated the expression of PER1 in all 11 tissues tested, consistent with the data from other mammalian species. Part of the PER1 gene was sequenced, homologous to exons 2-14 of the human gene and encoding the N-terminus of porcine PER1. The predicted amino acid sequence of the partial pig PER1 protein shares over 96% identity with its human orthologue.

Animals↗
PubMed2000

Identification and expression analysis of C3orf1, a novel human gene homologous to the Drosophila RP140-upstream gene.

We have isolated C3orf1, a novel gene on human chromosome 3 showing homology to the Drosophila RP140-upstream gene. When mutated, RP140-upstream causes lethality in flies through an unknown mechanism, perhaps by interfering with transcription of the RP140 RNA polymerase subunit. The human C3orf1 gene encodes a predicted membrane protein of 32.2 kDa with four transmembrane domains without any other known motifs. Northern blot analysis showed generalized expression of C3orf1, enhanced in heart and skeletal muscle. EST database searching revealed the existence of a homologue gene in mouse. Thus, the C3orf1 gene is conserved and may perform an essential function in all tissues in mammals.

Amino Acid Sequence↗
PubMed2002

Global gene expression analysis of developing neocortex using SAGE.

The mammalian brain is estimated to contain about a hundred billion neurons, making it the most complex biological structure on earth. Trying to understand the assembly and function of this elaborate organ is a formidable task. Yet the information to build a brain is encoded by no more than a subset of the 80,000 genes present in the genome, a more manageable number. This review describes the use of SAGE technology (Serial Analysis of Gene Expression) to decode the genetic repertoire of genes that are differentially expressed in time and in space during development of the neocortex, the part of the mammalian brain responsible for complex traits. We demonstrate that SAGE is not only powerful for generating comprehensive molecular portraits from the developing cortex but can also assist in discovering new genes.

Animals↗
PubMed2006

[Molecular cloning and expression analysis of swamp eel (Monopterus albus) Hprt].

The enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT) plays an important role in the purine salvage pathways. Full-length cDNA of swamp eel (Monopterus albus, the rice field eel) Hprt gene was obtained by the RACE method. The cDNA sequence was 1452 bp in length, which encoded a protein of 218 amino acids. Amino acid identities of Hprt between swamp eel and other vertebrates including human, mouse, chicken and zebrafish were more than 76.7%. Phylogenetic tree analysis based on the amino acid sequences showed that Hprt of swamp eel and zebrafish was in one clade. RT-PCR analysis showed ubiquitous expression pattern of swamp eel Hprt in adult tissues, suggesting that it has a constitutive function and is conserved during evolution.

Amino Acid Sequence↗
PubMed1995

Expression analysis of a Cucurbita cDNA encoding endonuclease.

The nuclear matrices of plant cell nuclei display intrinsic nuclease activity which consists in nicking supercoiled DNA. A cDNA encoding a 32 kDa endonuclease has been cloned and sequenced. The nucleotide and deduced amino-acid sequences show high homology to known 14-3-3 protein sequences from other sources. The amino-acid sequence shows agreement with consensus sequences for potential phosphorylation by protein kinase A and C and for calcium, lipid and membrane-binding sites. The nucleotide-binding site is also present within the conserved part of the sequence. By Northern blot analysis, the differential expression of the corresponding mRNA was detected; it was the strongest in sink tissues. The endonuclease activity found on DNA-polyacrylamide gel electrophoresis coincided with mRNA content and was the highest in tuber.

Amino Acid Sequence↗
PubMed2002

Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature.

We performed genome-wide expression analysis to determine genetic responses in Saccharomyces cerevisiae to a low temperature environment using a cDNA microarray. Approximately 25% of the genes in the yeast genome were found to be involved in the response of yeast to low temperature. This finding of a large number of genes being involved in the response to low temperature enabled us to give a functional interpretation to the genetic responses to the stimulus. Functional and clustering analyses of temporal changes in gene expression revealed that global states of the expressions of up-regulated genes could be characterized as having three phases (the early, middle, and late phases). In each phase, genes related to rRNA synthesis, ribosomal proteins, or several stress responses are time-dependently up-regulated, respectively. Through these phases, yeast cells may improve reduced efficiency of translation and enhance cell protection mechanisms to survive under a low temperature condition. Furthermore, these time-dependent regulations of these genes would be controlled by the cAMP-protein kinase A pathway. The results of our study provide a global description of transcriptional response for adaptation to low temperature in yeast cells.

Cyclic AMP↗
PubMed2003

Gene expression analysis of thymocyte selection in vivo.

Self versus non-self discrimination is a key feature of immunorecognition. Through TCR-activated apoptotic mechanisms, autoreactive thymocytes are purged at the CD4(+)CD8(+) double-positive (DP) precursor stage prior to maturation to CD4(+) or CD8(+) single-positive (SP) thymocytes. To investigate this selection process in vivo, gene expression analysis by oligonucleotide array was performed in TCR transgenic mice. In total, 244 differentially expressed DP thymocyte genes induced or repressed by TCR triggering in vivo were identified. Genes involved in the biological processes of apoptosis, DNA recombination, antigen processing and adhesion are coordinately engaged. Moreover, analysis of gene expression in thymocyte subsets revealed that TCR ligand-induced expression profiles vary according to their developmental stage, with 48 genes showing DP preference and nine showing SP thymocyte preference. Finally, our data suggest that both the extrinsic and the intrinsic apoptosis pathways are operating in thymic selection.

Animals↗
PubMed2003

Cloning and expression analysis of the pcbAB-pcbC beta-lactam genes in the marine fungus Kallichroma tethys.

Here we report the identification of the beta-lactam biosynthesis genes pcbAB and pcbC from a cosmid genomic DNA library of the marine fungus Kallichroma tethys. A BLAST homology search showed that they share high sequence identity with the delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) synthetases and isopenicillin N synthases, respectively, of various fungal and bacterial beta-lactam producers, while phylogenetic analysis indicated a close relationship with homologous genes of the cephalosporin-producing pyrenomycete Acremonium chrysogenum. Expression analysis by reverse transcription-PCR suggested that both genes are highly regulated and are expressed in the late growth phase of K. tethys cultures. Complementation of an Aspergillus nidulans strain deficient in ACV synthetase suggested that at least pcbAB is functional, although attempts to isolate active antibiotic from K. tethys were unsuccessful.

Base Sequence↗
PubMed2003

Cloning and embryonic expression analysis of the mouse Gbx1 gene.

We report the cloning of a cDNA encoding the complete mouse Gbx1 coding region as well as a comparative expression analysis of Gbx1 and Gbx2 during murine development. Gbx1 is expressed first during gastrulation and later in a dynamic pattern in the central nervous system, including rhombomeres 3 and 5, optic vesicles, and the medial ganglionic eminence. Gbx1 expression is not upregulated in Gbx2 null homozygotes. Therefore, the only regions of potential genetic redundancy are where Gbx1 and 2 are normally coexpressed: the primitive streak, regions of the ventricular zone of the neural tube and the medial ganglionic eminence. Finally, we demonstrate that neither Gbx1 nor Gbx2 require FGF8 for expression during gastrulation, contrary to previous published reports.

Amino Acid Sequence↗
PubMed2002

cDNA cloning and expression analysis of a novel human F-box only protein.

F-box proteins are an expanding family of eukaryotic proteins that are characterized by an approximately 40 amino acid motif. Some F-box proteins are critical for the controlled degradation of cellular regulatory proteins. During a large-scale sequencing analysis of a human fetal brain cDNA library, we isolated a cDNA clone that encodes a novel F-box protein. It showed a 90.0% identity with the previously isolated mouse F-box protein16 at the amino acid level. Northern blot analysis showed no detectable expression, while reverse transcription-polymerase chain reaction analysis indicated that FBXO16 was expressed in the heart, spleen, and colon. By mapping, we localized the FBXO16 gene to the human chromosome 8p12. The FBXO16 gene consisted of 9 exons that spanned 67,816 bp of human genomic DNA.

Amino Acid Sequence↗
PubMed2000

Characterization and expression analysis of the yellow lupin (Lupinus luteus L.) gene coding for nodule specific proline-rich protein.

The LlPRP2 gene coding for a proline-rich protein shows a high level of similarity to, as well as significant differences from the family of ENOD2 nodule-specific genes. Several sequence motifs with putative regulatory function were identified in the 5' and 3' noncoding regions of the LlPRP2 gene. Northern blot analysis revealed that the expression of the LlPRP2 gene begins 9 days after inoculation of yellow lupin roots with Bradyrhizobium sp. (Lupinus); the expression is restricted to symbiotic nodules and is not detected in other tissues or organs. Detailed hybridization analysis showed that, when expression is activated, the LlPRP2 transcript is modified so as to produce at least three bands and a continuous distribution of decay intermediates. The modification of the LlPRP2 transcript probably involves degradation from the 5'- and/or 3'-ends of the RNA molecules. Southern blot analysis indicates that only one gene is present in the yellow lupin genome. The presence of genes homologous to the LlPRP2 gene was confirmed for three cultivars of yellow lupin and for Lupinus angustifolius. However, LlPRP2 homologues were not detected in Lupinus albus cv. Bac, indicating that this plant may lack the ENOD2 sequence.

3' Untranslated Regions↗
PubMed1996

Cloning and expression analysis of human bleomycin hydrolase, a cysteine proteinase involved in chemotherapy resistance.

A cDNA encoding human bleomycin hydrolase, a member of the cysteine proteinase family of proteins, has been cloned from a human brain cDNA library. The isolated cDNA contains an open reading frame coding for a polypeptide of 456 amino acids that contains all of the structural features characteristic of cysteine proteinases, including the cysteine, histidine, and asparagine residues that are essential for the catalytic properties of these enzymes. The deduced amino acid sequence for human bleomycin hydrolase shows 92, 40, and about 35% of identities with those determined for rabbit bleomycin hydrolase, yeast bleomycin hydrolase, and bacterial aminopeptidase C, respectively. Northern blot analysis of poly(A)+ RNAs isolated from a variety of human tissues demonstrated that human bleomycin hydrolase is expressed in all examined tissues, which is consistent with a putative role of this protein as a proteolytic enzyme involved in norman cellular protein degradation and turnover. Preliminary expression analysis of bleomycin hydrolase in different human tumors showed increased expression of the enzyme in a series of head and neck carcinomas when compared with paired adjacent normal mucosa. We also observed a variable degree of bleomycin hydrolase expression in different types of lymphoma, with low or undetectable levels in Hodgkin's disease samples and higher levels in Burkitt's lymphomas. These results are consistent with a proposed role for human bleomycin hydrolase in resistance of some tumor to bleomycin chemotherapy.

Amino Acid Sequence↗
PubMed2003

Gene expression analysis using single molecule detection.

Recent developments of single molecule detection techniques and in particular the introduction of fluorescence correlation spectroscopy (FCS) led to a number of important applications in biological research. We present a unique approach for the gene expression analysis using dual-color cross-correlation. The expression assay is based on gene-specific hybridization of two dye-labeled DNA probes to a selected target gene. The counting of the dual-labeled molecules within the solution allows the quantification of the expressed gene copies in absolute numbers. As detection and analysis by FCS can be performed at the level of single molecules, there is no need for any type of amplification. We describe the gene expression assay and present data demonstrating the capacity of this novel technology. In order to prove the gene specificity, we performed experiments with gene-depleted total cDNA. The biological application was demonstrated by quantifying selected high, medium and low abundant genes in cDNA prepared from HL-60 cells.

Actins↗
PubMedDate not supplied

[Differential gene expression analysis by DNA microarrays technology and its application in molecular oncology].

Accumulation of genetic and epigenetic aberrations leads to malignant transformation of normal cells. Functional studies of cancer using genomic and proteomic tools will help to reveal the true complexity of the processes leading to cancer development in humans. Until recently, diagnosis and prognosis of cancer was based on conventional pathologic criteria and epidemiological evidence. Certain tumors were divided only into relatively broad histological and morphological subcategories. Rapidly developing methods of differential gene expression analysis promote the search for clinically relevant genes changing their expression levels during malignant transformation. DNA microarrays offer a unique possibility to rapidly assess the global expression picture of thousands genes in any given time point and compare the detailed combinatory analysis results of global expression profiles for normal and malignant cells at various functional stages or separate experimental conditions. Acquisition of such "genetic portraits" allows searching for regularity and difference in expression patterns of certain genes, understanding their function and pathological importance, and ultimately developing the "molecular nosology" of cancer. This review describes the basis of DNA microarray technology and methodology, and focuses on their applications in molecular classification of tumors, drug sensitivity and resistance studies, and identification of biological markers of cancer.

Biomarkers, Tumor↗
PubMed2004

A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.).

To elucidate the roles of the isogenes encoding starch synthase (EC 2.4.1.21) in rice (Oryza sativa L.), a comprehensive expression analysis of the gene family was conducted. Extensive searches for starch synthase genes were done in the databases of both the whole genome and full-length cDNAs of rice, and ten genes were revealed to comprise the starch synthase gene family. Multi-sequence alignment analysis of the starch synthase proteins from rice and other plant species suggested that they were grouped into five classes, soluble starch synthase I (SSI), SSII, SSIII, SSIV and granule-bound starch synthase (GBSS). In rice, there was one gene for SSI, three for SSII and two each for SSIII, IV and GBSS. The expression pattern of the ten genes in the developing caryopsis was examined by semi-quantitative RT-PCR analysis. Based on the temporal expression patterns, the ten genes could be divided into three groups: (i) early expressers ( SSII-2, III-1, GBSSII), which are expressed in the early stage of grain filling; (ii) late expressers ( SSII-3, III-2, GBSSI), which are expressed in the mid to later stage of grain filling; and (iii) steady expressers ( SSI, II-1, IV-1, IV-2), which are expressed relatively constantly during grain filling. Within a caryopsis, the three gene groups spatially share their expression, i.e. "early expressers" in the pericarp, the "late expressers" in the endosperm" and the "steady expressers" in both tissues. In addition, this grouping was reflected in the expression pattern of various rice tissues: expression in non-endosperm, endosperm or all tissues examined. The implications in this spatio-temporal work sharing of starch synthesis isogenes are discussed.

DNA Primers↗
PubMed2000

Molecular cloning and expression analysis of 3-ketoacyl-ACP synthases in the immature seeds of Perilla frutescens.

We report the isolation and expression analysis of two cDNAs encoding 3-ketoacyl-acyl carrier protein synthases (KAS) that are involved in the de novo synthesis of fatty acids in plastids of perilla (Perilla frutescens L.). The cDNAs, designated PfFAB1 and PfFAB24, encoded polypeptides with high sequence identities to those of KAS I and KAS II/IV, respectively, of various plants. Genomic Southern blots revealed that there was a single PfFAB1 gene but two PfFAB24 genes in the perilla genome. Of interest is that the expression of both genes was developmentally regulated in seeds. Their mRNA expression patterns in seeds were also discussed in comparison with the profile of fatty acid accumulation.

3-Oxoacyl-(Acyl-Carrier-Protein) Synthase↗
PubMed2005

Expression analysis of a human hepatic cell line in response to palmitate.

Saturated fat plays a role in common debilitating diseases such as obesity, type 2 diabetes, and coronary heart disease. It is also clear that certain fatty acids act as regulators of metabolism via both direct and indirect signalling of target tissues. As the molecular mechanisms of saturated fatty acid signalling in the liver are poorly defined, hepatic gene expression analysis was undertaken in a human hepatocyte cell line after incubation with palmitate. Profiling of mRNA expression using cDNA microarray analysis revealed that 162 of approximately 18,000 genes tested were differentially expressed after incubation with palmitate for 48 h. Altered transcription profiles were observed in a wide variety of genes, including genes involved in lipid and cholesterol transport, cholesterol catabolism, cell growth and proliferation, cell signalling, beta-oxidation, and oxidative stress response. While palmitate signalling has been examined in pancreatic beta-cells, this is the first report showing that palmitate regulates expression of numerous genes via direct molecular signalling mechanisms in liver cells.

Cell Line↗