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Results for “Genomic characterization”

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PubMed1997

Murine 86-kDa heat shock protein gene and promoter.

The class of 90 kDa heat shock proteins (Hsp90) is among the most abundant heat shock proteins (Hsps) in eukaryotic cells. In vertebrates, Hsp90 is encoded by two distinct gene families giving rise to products of 84 and 86 kDa. In mice the expression of these two genes, hsp84 and hsp86, vary with respect to each other in responses to stress, and also in response to signals for growth and development. Therefore, as a step towards understanding the molecular basis for the differential regulation of these two genes, we have isolated and characterized genomic clones of the murine hsp86 gene and its 5' flanking region. The gene is composed of eleven exons interrupted by 10 introns. The 5' region contains consensus TATA, several stimulatory protein-1 binding site (SP1) elements as well as six consensus heat shock elements (HSE) 5' of the transcription start site. An 806 bp fragment of the 5' promoter region conferred constitutive expression upon a reporter gene and this expression was increased upon heat shock.

Animals↗

PubMed2005

Molecular biology of the enzymes that degrade endocannabinoids.

Endocannabinoid circuits have been shown to regulate a number of important pathways including pain, feeding, memory and motor coordination. Direct manipulation of endocannabinoid tone, therefore, may relieve disease symptoms related to analgesia, obesity, Alzheimer's and Parkinson's in humans. The endocannabinoid circuit involves two cloned receptors: CB1 in the CNS and CB2 in the periphery; endogenously produced ligands including anandamide, 2-arachidonylglycerol and palmitoylethanolamide; and enzymes that degrade endocannabinoid ligands to terminate signaling. Currently, three enzymes have been characterized with the ability to hydrolyze endocannabinoids: fatty acid amide hydrolase (FAAH), monoglyceride lipase (MGL) and N-acylethanolamine-hydrolyzing acid amidase (NAAA). The purpose of this review is to examine the molecular biology for the enzymes that hydrolyze endocannabinoids covering the protein activity and expression, mRNA characterization, genomic locus organization, promoter analysis and knockout phenotypes.

Amidohydrolases↗

PubMed2004

[Clinical features and mutation analysis of a poly-(A)8 tract in M3 cholinergic receptor gene in Chinese HNPCC families].

OBJECTIVE: To characterize the clinical features of Chinese HNPCC families and to screen the mutations of a poly-(A)8 tract in M3 cholinergic receptor gene in these families. METHODS: The clinical features of 15 Chinese HNPCC families were characterized. Genomic DNAs from 15 probands were prepared. PCR and direct DNA sequencing analysis were employed to examine the mutations of a poly-(A)8 tract in exon 8 of M3 cholinergic receptor gene. RESULTS: Total 55 cancer patients were found in 15 families including 41 cases of colorectal carcinoma with an average of 2.73 colorectal carcinomas developed per family. Thirty out of forty-one (73%) patients were diagnosed before age of 50 years. Proximal colon was involved in 51% of patients, while anus and rectum were 40 %. Synchronous and metachronous multiple colorectal cancers developed in 5 patients (12%). Two thirds of families belonged to Lynch II syndrome, and total 18 extracolonic malignancies in 14 patients were identified. Gastric carcinoma was the most common extracolonic types. In 15 HNPCC probands, no mutation was detected in the poly-(A)8 tract of exon 8 of M3 cholinergic receptor gene. CONCLUSION: M3 cholinergic receptor gene might have little relation with HNPCC in Chinese population. The criteria for Chinese HNPCC are useful and practical in clinical application.

Adult↗

PubMed2000

Candidate gene analysis in Rett syndrome and the identification of 21 SNPs in Xq.

Rett syndrome (RTT) is an X-linked dominant neurodevelopmental disorder that affects females. Exclusion mapping studies using a new family with maternal inheritance of RTT defined Xq28 as the candidate region for the RTT gene. Six candidate genes were selected for mutation analysis based on their established expression patterns and known functions in the CNS. These are: Glutamate receptor subunit 3 (GLUR3), GABA receptor subunit alpha 3 (GABRA3), GABA receptor subunit e1 (GABRE1), Vacuolar ATPase subunit 1 (VATPS1, XAP3), the human homologue of plexin 3-SEX (XAP6) and the Synaptobrevin-like protein (SYBL1). Major rearrangements involving these genes were excluded by Southern analysis. No disease-causing mutations were found, but several single-nucleotide polymorphisms (SNPs) were detected. These SNPs will be useful in future linkage analysis and whole-genome association studies for other diseases. The genomic characterization of GLUR3 and GABRA3 will allow mutational analysis of these genes as candidates for other X-linked neurological disorders mapping to Xq25-Xq26 and Xq28.

Base Sequence↗

PubMedDate not supplied

Hepatitis C virus serotypes in Romanian patients with chronic hepatitis and cirrhosis.

OBJECTIVES: To determine the prevalence of hepatitis C virus (HCV) serotypes in Romanian patients with chronic hepatitis infections and the association between them and disease's severity. PATIENTS AND METHODS: Anti-HCV antibodies were first investigated by an indirect ELISA (Murex IIIrd generation). From 55 patients positive for anti-HCV, 22 patients (11 female and 11 male) with chronic active hepatitis (CAH--6 cases), chronic persistent hepatitis (CPH--11 cases) and cirrhosis (C--5 cases) were tested for HCV serotypes using an indirect ELISA (Murex HCV Serotypes 1-6 Assay). The average age for the selected group was 47.2 years (range 27 divided by 68). RESULTS: In the first study from our region concerning this subject we have found the following serotypes distribution: serotype 1--68.18% (6/11--CPH; 4/6--CAH; 5/5--C); serotypes 2, 3, 4, and 6--4.54% for each of them (all were CPH cases); untypable--13.65% (2 with CAH and 1 CPH respectively). CONCLUSIONS: (1) The serotype 1 seems to be predominant in our region in patients with chronic HCV infections and it is associated with the most severe cases. (2) The diversity of serotypes is higher compared with previous study group results (e.g. in haemodialized patients the serotype 1 was determined in almost 100% cases--unpublished data). (3) Untypable strains (13.65%) require the sequence analysis for HCV genome characterization.

Adult↗

PubMed1992

Early gene expression in lymphoma-associated hamster polyomavirus viral genomes.

Hamster polyomavirus (HaPV) is the causal agent of hair follicle epithelioma in hamsters belonging to a colony bred in Berlin-Buch. These tumors shed virus particles that are assembled in the keratinized layer of the epidermis. By contrast, HaPV induces lymphomas after inoculation into newborn hamsters from a distinct colony bred in Potsdam. These lymphoid tumors accumulate massive amounts of episomal viral genomes characterized by deletions that alter specifically the regulatory and the late coding sequences. Assuming that these alterations of the regulatory region may affect the transcription of the viral oncogenes in the tumor cells, the transcriptional activity of the wild-type and deleted early promoters have been studied in vitro in transient chloramphenicol acetyltransferase (CAT) expression assays. These assays performed in various cell types demonstrate that both versions of the HaPV early promoter carry a weak constitutive activity. Simultaneous expression of the HaPV early gene products leads to a strong stimulation of CAT activity with a concomitant activation of the replication of the plasmid constructs. The results obtained with origin-defective CAT vectors indicate that the replication contributes significantly to the stimulating effect of the early gene products. Indeed, transfection of massive amounts of CAT vectors that are unable to replicate can simulate the dosage effect of replication and also leads to measurable CAT activities. Under these conditions, the wild-type promoter is more active than the deleted version, indicating that sequences within the deletion carry a distinct stimulatory effect on transcription. This conclusion is supported by the observation that the lymphoma cells contain a low level of early transcripts, indicating that the deleted episomal viral templates accumulated in these tumors carry a weak transcriptional activity.

Animals↗

PubMed2003

Ferredoxin reductase: pharmacogenomic assessment in colorectal cancer.

Ferredoxin reductase (FDXR) is a putative contributor to TP53-mediated apoptosis from 5-fluorouracil chemotherapy through the generation of oxidative stress. With TaqMan real-time quantitative reverse transcription-PCR, this study established a significant difference in FDXR relative RNA expression level between tumor (median, 212.9 units) and normal tissues (median, 113.8 units) from 51 colorectal cancer patients (P < 0.001). Seven single nucleotide polymorphisms (SNPs) in the FDXR gene were discovered, with no significant difference in variant allele frequency between colon tumor and normal tissues (P > 0.05), and the common haplotypes for FDXR were not different between colon tumor and normal samples. No correlation was observed between FDXR genotype and RNA expression implying that the polymorphisms described in this study are not regulating FDXR expression in colon cancer. This genomic characterization provides the foundation for pharmacogenetic analysis of the impact of FDXR on chemotherapy for colorectal cancer.

Adult↗

PubMed2005

Chronic hepatitis C and genotyping: the clinical significance of determining HCV genotypes.

Chronic hepatitis C, attributed to infection with hepatitis C virus (HCV), is a global health problem. The overall prevalence of viral hepatitis worldwide is estimated to be 3-5% with over 175 million people infected with HCV. Clinically, HCV can establish a persistent, chronic infection contributing to progressive liver disease, including cirrhosis and hepatocellular carcinoma (HCC), requiring intensive treatment regimens, possible liver transplantation and long-term care. Due to the chronic nature of HCV infection and the tremendous burden on healthcare resources, clinicians and laboratorians have looked for key epidemiological, pathological and viral characteristics that may provide insight into disease progression, severity and response to therapy to permit the administration of effective therapeutic regimens as well as long-term management of infected individuals. Determination of viral genotype has been identified as one parameter that could provide direction in the clinical management of patients with chronic HCV infections. The following review provides background on determination of HCV genotypes and the relevance of viral genome characterization in the current clinical setting.

Algorithms↗

PubMedDate not supplied

[Use of the restriction analysis in the quality control of the strain of Cuban biolarvicide BACTIVEC].

The genomic characterization of the strain used in manufacturing biolarvicide BACTIVET was shown in this paper. Digestion patterns of Bacillus thuringiensis reference strain 266 from the collection of Pushkin Institute located in former Leningrad and of two strains isolated from 2 batches of biolarvicide were compared. Chromosomal DNA digestion was performed by enzymes Hindlll and EcoRI. The same restriction pattern was observed in all cases, which is indicative of genetic stability of the active ingredient of biolarvicide BACTIVET.

Bacillus thuringiensis↗

PubMed1990

CD14 is a member of the family of leucine-rich proteins and is encoded by a gene syntenic with multiple receptor genes.

We have isolated and characterized genomic and cDNA clones encoding the murine homolog of the human monocyte/granulocyte cell surface glycoprotein, CD14. As in man, the expression of murine CD14 is limited to the myeloid lineage. The murine and human CD14 genes are highly conserved in their intron-exon organization and nucleotide sequence. Their deduced protein sequences show 66% amino acid identity. In both mouse and man, the CD14 protein contains a repeating (10 times) leucine-rich motif (LXXLXLX) that is also found in a group of heterogeneous proteins from phylogenetically distant species. The CD14 gene has been mapped to mouse chromosome 18 which also contains at least five genes encoding receptors (Pdgfr, Adrb2r, li, Grl-1, Fms). Thus CD14 and the receptor genes form a conserved syntenic group localized on mouse chromosome 18 and human chromosome 5. The inclusion of CD14 in the family of leucine-rich proteins, its expression profile and the murine chromosomal localization support the hypothesis that CD14 may function as a receptor.

Amino Acid Sequence↗

PubMed1991

Structure of the rabbit phospholamban gene, cloning of the human cDNA, and assignment of the gene to human chromosome 6.

We have isolated and characterized genomic DNA clones encoding rabbit phospholamban. Only a single gene for phospholamban was detected in the rabbit genome. The phospholamban gene of 13.2 kilobases contains only one 10.5-kilobase intron, which separates exonic sequences located in the 5'-untranslated region. Two potential transcription initiation sites were mapped to 335 and 185 nucleotides upstream from the translation initiation site in the mRNA or 239 and 89 nucleotides upstream from the exon/intron boundary. Phospholamban gene expression in various smooth muscle tissues, as well as in cardiac and slow twitch skeletal muscle, was detected by Northern blotting. The phospholamban gene was mapped to human chromosome 6, using a human phospholamban cDNA.

Adenosine Triphosphatases↗

PubMed1990

Mouse opsin. Gene structure and molecular basis of multiple transcripts.

The single copy mouse opsin gene produces five major transcripts, varying in size from 1.7 to 5.1 kilobases. The mRNAs are present at levels that vary over 2 orders of magnitude and can be detected as early as postnatal day 1. Each of the transcripts is polyadenylated and can be identified in polysome-bound RNA, suggesting that each is translated in vivo. To elucidate the molecular basis of this complex transcription pattern, we have characterized genomic fragments covering the entire mouse opsin gene, including several kilobases of 5'- and 3'-flanking regions. Transcription initiates at a single site 97 base pairs upstream of the translation start codon. Northern hybridization with exon- and intron-specific probes demonstrated that the various transcripts are not generated by partial or alternative splicing. Sequence analysis of the 3' end of the gene showed the presence of multiple polyadenylation signals. Analysis by polymerase chain reaction of the 3' end of opsin cDNA demonstrated that the complex transcription pattern originated from the selective use of these polyadenylation sites, generating transcripts that differ only in the length of the 3'-untranslated region. Transcript heterogeneity similar to that observed in mouse was also found in rat and, to a lesser degree, in human and frog opsin mRNAs.

Amino Acid Sequence↗

PubMed1991

Organization and expression of two tandemly oriented genes encoding ribulosebisphosphate carboxylase/oxygenase activase in barley.

We have isolated and structurally characterized genomic DNA and cDNA sequences encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rbu-P2 carboxylase) activase from barley (Hordeum vulgare L.). Three Rbu-P2 carboxylase activase (Rca) polypeptides are encoded in the barley genome by two closely linked, tandemly oriented nuclear genes (RcaA and RcaB); cDNAs encoding each of the three Rbu-P2 carboxylase activase polypeptides were isolated from cDNA libraries of barley leaf mRNA. RcaA produces two mRNAs, which encode polypeptides of 42 and 46 kDa, by an alternative splicing mechanism identical to that previously reported for spinach and Arabidopsis Rca genes (Werneke, J.M., Chatfield, J.M., and Ogren, W. L. (1989) Plant Cell 1, 815-825). RcaB is transcribed to produce a single mRNA, which encodes a mature peptide of 42 kDa. Genomic Southern blots indicate that RcaA and RcaB represent the entire Rbu-P2 carboxylase activase gene family in barley. The genes share 80% nucleotide sequence identity, and the 42-kDa polypeptides encoded by RcaA and RcaB share 87% amino acid sequence identity. Coding regions of the two barley Rca genes are separated by 1 kilobase pair of flanking DNA. DNA sequence motifs similar to those thought to control light-regulated gene expression in other nuclear-encoded plastid polypeptide genes are found at the 5' end of both barley Rca genes. Probes specific to three mRNAs were used to determine the relative contribution each species makes to the total Rca mRNA pool.

Amino Acid Sequence↗

PubMed1990

The Neurospora crassa arg-2 locus. Structure and expression of the gene encoding the small subunit of arginine-specific carbamoyl phosphate synthetase.

We have characterized genomic and cDNA clones for arg-2, the gene encoding the small subunit of the Neurospora crassa arginine-specific carbamoyl phosphate synthetase (CPS-A), and examined its transcriptional regulation. The polypeptide's predicted amino acid sequence (453 residues) is 56% and 36% identical with the sequences of the homologous polypeptides of Saccharomyces cerevisiae and Escherichia coli, respectively. The ARG2 polypeptide has an additional amino-terminal domain with the hallmark features of a mitochondrial signal sequence. The arg-2 mRNA also encodes a 24-residue peptide in the segment upstream of the coding region for the ARG2 polypeptide. This upstream open reading frame (uORF) strongly resembles the uORF in the homologous S. cerevisiae transcript. Northern analyses indicate that arg-2 mRNA levels are reduced by arginine supplementation and increased by amino acid limitation. The large increase in arg-2 mRNA levels that occurs in response to amino acid limitation is not observed in a strain containing the cpc-1 mutation, indicating that the cross-pathway control system participates in arg-2 regulation. Four copies of the sequence TGACTC, the binding site for the CPC1 regulatory protein, are found in the arg-2 genetic region. Two copies are located upstream of the mRNA start sites, and two are present within introns in the arg-2 uORF.

Amino Acid Sequence↗

PubMed1983

Prostatic steroid-binding protein. Isolation and characterization of C3 genes.

Prostatic steroid-binding protein, whose expression is stimulated by androgens, consists of two subunits, one containing the polypeptides C1 and C3 and the other containing the polypeptides C2 and C3. We have isolated and sequenced cDNA clones specific for C3 mRNA and used them to isolate and characterize genomic clones for two C3 genes. Both genes are 3.2 kilobases with identical exon/intron arrangements, which is similar to the organization of the C1 and C2 genes, suggesting that they may have arisen by duplications of an ancestral gene. Finally, homologous human genes have not been detected.

Amino Acid Sequence↗

PubMed1995

[Acute myocardial infarction without elevation of CK activity: analysis of CK-MM protein and gene of CK-MM].

A 56 year old female patient had acute myocardial infarction which was confirmed by autopsy. However the patient showed no elevation of CK activity in the serum. We proved the deficiency of CK-MM protein in her serum as well as in the myocardial tissues. To further elucidate the molecular mechanism we isolated and characterized genomic DNA and cDNA of CK-MM from the myocardial tissue of the patient and demonstrated the depression of mRNA of CK-MM which might be related with the deficiency of CK-MM protein. Point mutation at codon 54 [Exon 2, GAC (Asp)-->GGC(Gly)] was also demonstrated on the beta-sheet of CK-MM. Association of point mutation with depressed CK-MM is to be clarified.

Base Sequence↗

PubMed1994

Structure of the gene encoding the alpha subunit of the human granulocyte-macrophage colony stimulating factor receptor. Implications for the evolution of the cytokine receptor superfamily.

The receptor for granulocyte-macrophage colony-stimulating factor (GM-CSF) is composed of at least two subunits, alpha and beta. In addition to the conserved cysteine residues and a "WSxWS" motif, the extracellular segments of both subunits have domains that are structurally related to a fibronectin type III domain. This structure is conserved in all members of the cytokine receptor superfamily. We isolated and characterized genomic DNA clones containing the entire coding sequences of the alpha subunit of the human GM-CSF receptor (hGMR alpha). The gene spans approximately 44 kilobases and has 13 exons. The major transcription initiation site was determined to be 195 base pairs upstream of the translation initiation site. The putative promoter region lacks a typical TATA motif and an Sp1 binding site, but contains a purine-rich stretch about 30 base pairs upstream of the transcription initiation site. This stretch is also found in the human interleukin 2 receptor gamma subunit and granulocyte colony-stimulating factor receptor genes. We compared the exon-intron organization of the hGMR alpha gene with other members of the cytokine receptor superfamily and found the genomic organizations to be remarkably well conserved. On the basis of these observations, we propose a model for evolution of this gene family.

Base Sequence↗

PubMed1993

Separate nuclear genes encode cytosolic and mitochondrial nucleoside diphosphate kinase in Dictyostelium discoideum.

We have previously isolated cDNA clones for the gip17 gene encoding the cytosolic nucleoside diphosphate (NDP) kinase from Dictyostelium discoideum, and partial cDNAs for guk, a second member of the NDP kinase gene family (Wallet, V., Mutzel, R., Troll, H., Barzu, O., Wurster, B., Véron, M., and Lacombe, M. L. (1990) J. Natl. Cancer Inst. 80, 1199-1202). We now characterize genomic DNA clones for both NDP kinase genes, and we show that guk defines a nuclear-encoded mitochondrial NDP kinase. Isolated D. discoideum mitochondria contain 3% of the total cellular NDP kinase activity. Antibodies which specifically recognize and inhibit the activity of either cytosolic or mitochondrial NDP kinase unambiguously distinguish between these activities. The nascent mitochondrial NDP kinase contains a presequence of 57 amino acids that is removed during import into the organelle as shown by determination of the NH2 terminus of the mature protein from mitochondria. The genes for mitochondrial and cytosolic NDP kinases contain four and two introns, respectively. The positions of the of the introns in the gene for the cytosolic enzyme match exactly the positions of the second and fourth introns in the coding region of its mitochondrial homologue. From these results we conclude that the isozymes diverged from a common ancestor, and we discuss possible phylogenetic pathways for the evolution of cytosolic and organelle NDP kinases.

Amino Acid Sequence↗