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Results for “Gene selection”

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At least 217 records · Page 12Linked to original sources
PubMed1995

Human calgizzarin; one colorectal cancer-related gene selected by a large scale random cDNA sequencing and northern blot analysis.

A cDNA library was constructed from COLO 205 and 1056 clones randomly selected from this library were partially sequenced. Two hundred and two (38.4%) out of 526 independent genes had more than 80% similarity to the genes reported in GenBank. In Northern blot analysis, 96 out of 98 genes were shown to be expressed at the same level in colon and lung carcinoma cell lines and control fibroblasts. Only two clones, including human synovial phospholipase A-2 and a homologue to rabbit calgizzarin, were expressed at different levels among these cell lines. The full sequence of human calgizzarin was determined and its expression was remarkably elevated in colorectal cancers compared with that in normal colorectal mucosa.

Amino Acid Sequence↗
PubMed1999

NK lytic-associated molecule: a novel gene selectively expressed in cells with cytolytic function.

NK cells are most effective in killing a broad spectrum of primary tumor cells after stimulation with cytokines. We have cloned a novel gene, designated NKLAM (for NK lytic-associated molecule), whose expression is associated with this cytokine-enhanced process. NKLAM expression is up-regulated in NK cells by IL-2 and IFN-beta. NKLAM is also selectively expressed by activated macrophages and CTL. Treatment of NK cells and CTL with NKLAM antisense oligonucleotides specifically decreases their cytolytic activity, while having no effect on cell growth. The NKLAM gene encodes a 62-kDa ring finger-containing protein that localizes to the cytoplasmic granules in NK cells. Further study of this gene may add to our understanding of cytotoxic processes common to NK cells, CTL, and activated macrophages.

Amino Acid Sequence↗
PubMed1990

Expression of selected genes in differentiated HL-60 cells and primary cells from human leukemias.

Expression of three clones (6-1E, 7-3G and 9-5C) selected from a chronic lymphocytic leukemia cDNA library was studied by nucleic acid hybridization in human promyelocytic leukemia cells (HL-60) treated with chemical inducers of cell differentiation and in primary cells derived from 27 patients with leukemia or myelodysplastic syndrome. The differentiation of HL-60 cells into macrophage-like cells upon induction by 12-0-tetradecanoyl phorbol-13-acetate (TPA) was accompanied by rapid induction of the expression of 6-1E and 7-3G genes. The levels of expression of the 9-5C gene were not altered during macrophage-monocytic or granulocytic differentiation of HL-60 cells. The expression of the 6-1E and/or 7-3G gene was induced by TPA in four of 6 samples derived from patients who achieved complete remission, but not in any of the acute nonlymphocytic leukemia samples from patients who failed to achieve complete remission. These findings suggest that expression of the 6-1E and 7-3G genes is related to macrophage-monocytic differentiation and that alterations of these gene expressions in fresh leukemia cells after one hour of TPA treatment are of prognostic significance in predicting the response to therapy.

Base Sequence↗
PubMed2002

Molecular analysis of constitutively expressed erm(C) genes selected in vitro by incubation in the presence of the noninducers quinupristin, telithromycin, or ABT-773.

A Staphylococcus aureus strain that harbored a plasmid-borne inducibly expressed erm(C) gene was cultivated in the presence of the noninducers quinupristin, telithromycin, and ABT-773. After overnight incubation, 78 mutants that displayed combined resistance to macrolides, lincosamides, streptogramin B antibiotics, and ketolides were analyzed for the genetic basis of this altered resistance phenotype. Because this resistance phenotype is indicative for constitutively expressed erm(C) genes, the erm(C) regulatory regions of all mutants were sequenced. All 78 mutants showed sequence alterations in the erm(C) translational attenuator. Seventeen different types of sequence deletions ranging from 5 bp to 121 bp and nine different types of tandem duplications of 13-100 bp, all causing constitutive erm(C) gene expression, were detected. These sequence deletions or tandem duplications either favored the formation of mRNA secondary structures in the erm(C) translational attenuator, which did not inhibit translation of the erm(C) transcripts, or completely prevented the formation of any mRNA secondary structures in the erm(C) translational attenuator. The mean frequencies of 10-6 to 10-8 by which constitutive mutants were obtained, strongly suggest that telithromycin and ABT-773 not be recommended for the treatment of staphylococci that exhibit the inducible MLSB phenotype.

Anti-Bacterial Agents↗
PubMed2005

Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress.

Plant stress studies are more and more based on gene expression. The analysis of gene expression requires sensitive, precise, and reproducible measurements for specific mRNA sequences. Real-time RT-PCR is at present the most sensitive method for the detection of low abundance mRNA. To avoid bias, real-time RT-PCR is referred to one or several internal control genes, which should not fluctuate during treatments. Here, the non-regulation of seven housekeeping genes (beta-tubulin, cyclophilin, actin, elongation factor 1-alpha (ef1alpha), 18S rRNA, adenine phosphoribosyl transferase (aprt), and cytoplasmic ribosomal protein L2) during biotic (late blight) and abiotic stresses (cold and salt stress) was tested on potato plants using geNorm software. Results from the three experimental conditions indicated that ef1alpha was the most stable among the seven tested. The expression of the other housekeeping genes tested varied upon stress. In parallel, a study of the variability of expression of hsp20.2, shown to be implicated in late blight stress, was realized. The relative quantification of the hsp20.2 gene varied according to the internal control and the number of internal controls used, thus highlighting the importance of the choice of internal controls in such experiments.

Cold Temperature↗
PubMed1986

Stable expression of selectable genes introduced into human hematopoietic stem cells by electric field-mediated DNA transfer.

The successful introduction of DNA into human bone marrow cells by electric field-mediated transfer was initially demonstrated by the detection of transient chloramphenicol acetyltransferase (acetyl-CoA:chloramphenicol O3-acetyltransferase, EC 2,3.1.28) activity in marrow cell extracts. To determine whether DNA was transferred into hematopoietic stem cells, human nucleated marrow cells were subjected to electroporation in the presence of a plasmid construct containing the bacterial genes conferring resistance to the neomycin analogue G418 (neo) and to mycophenolic acid (gpt). The growth of granulocyte/macrophage colonies in selective media, followed by hybridization analyses of resistant cells, established that DNA was transferred into human granulopoietic progenitor cells and was stably maintained and expressed in their differentiated progeny. Electroporation, therefore, offers the opportunity to transfer genes effectively into human hematopoietic stem cells and avoids some of the disadvantages associated with other methods of gene transfer.

Bone Marrow↗
PubMed2004

Selective gene expression in magnocellular neurons in rat supraoptic nucleus.

Oxytocin- and vasopressin-producing magnocellular neurons (MCNs) of the hypothalamo-neurohypophysial system are the only neuronal phenotypes present in the rat supraoptic nucleus (SON). Laser microdissection of the SON, extraction and T7-based amplification of its RNAs, and analysis of the resulting cDNAs by hybridization on a 35, 319 element DNA microarray have provided a detailed composite view of the gene expression profile of the MCNs. The genes expressed in the SON were compared with those expressed in a reference tissue consisting of total hypothalamus, and this "expression ratio" indicated which genes were preferentially expressed in the SON. Of the 26,000 unique genes on the array, 1385 were found to be expressed in the SON at levels more than two times greater than in the hypothalamus as a whole. Of these, 123 were expressed > or =3.4-fold higher in the SON versus hypothalamus. Most of these preferentially expressed genes were not previously known to be expressed in the MCNs. Quantitative and double-label in situ hybridization histochemistry was used selectively to confirm a number of these microarray observations and to evaluate the osmotic regulation and cell-specific expression of these genes, respectively.

Animals↗
PubMed1989

Identification of sequences regulating the transcription of a Dictyostelium gene selectively expressed in prespore cells.

There has been considerable debate about the relative contributions of transcriptional and post-transcriptional mechanisms to the regulation of prespore gene expression in Dictyostelium. We have determined the DNA sequence upstream of D19, the Dictyostelium gene encoding PsA, a prespore-specific, cell surface protein of unknown function. Our analysis of gene fusions, in which D19 upstream sequences are placed adjacent to a heterologous reporter gene, indicates that transcriptional signals alone are sufficient for the correct temporal and cell-type specific expression of this gene. We also show that the 5' and 3' boundaries of the minimal sequences necessary for correct developmental regulation lie within the region 338 to 122 nucleotides upstream of the start site of transcription but that flanking sequences seem to be necessary for optimal expression.

Base Sequence↗
PubMed1977

Somatic nuclei in amphibian oocytes: evidence for selective gene expression.

Previous work has shown that multiple HeLa nuclei injected into Xenopus oocytes remain transcriptionally active for many days and that the expression of HeLa genes in oocytes can be detected by 2-D gel electrophoresis. We show here that of 25 proteins which have the electrophoretic properties of HeLa gene products, only 3 are expressed in injected oocytes. To test that these proteins are products of HeLa genes, and not products of activated oocyte genes, we have injected HeLa nuclei into enucleated oocytes. Three days later, several HeLa proteins were synthesized. The turning off of most HeLa genes in injected oocytes is apparently not at the translational level. This is indicated by the fact that adenovirus mRNA is efficiently translated when injected into Xenopus oocytes. When adenovirus-infected HeLa cells nuclei are injected into oocytes the adenovirus genes are not expressed, although some HeLa genes are expressed by the same nuclei. The same HeLa genes as are expressed or switched off in injected Xenopus oocytes are also preferentially expressed or switched off in injected oocytes of a Urodele amphibian, Pleurodeles. This suggests that conditions or molecules may exist in oocytes which selectively impose on injected nuclei a new programme of gene expression.

Adenoviridae↗
PubMed1991

Selective gene expression in failing human heart. Quantification of steady-state levels of messenger RNA in endomyocardial biopsies using the polymerase chain reaction.

BACKGROUND: Evaluation of gene expression in failing human heart has been limited by the availability of cardiac tissue. METHODS AND RESULTS: We used the polymerase chain reaction (PCR) to assess gene expression in small quantities of failing and nonfailing human heart. PCR is a powerful new molecular biological tool that allows a small quantity of DNA to be amplified as much as 1 million-fold. Total RNA was extracted from 3-5 mg samples of human heart and reverse-transcribed to complementary DNA (cDNA). With selected oligonucleotide primers, we used PCR to amplify cDNAs encoding atrial natriuretic peptide, beta-myosin heavy chain, phospholamban, and cytoskeletal beta-actin. To quantify the relative levels of messenger RNA (mRNA) in human heart, a known amount of a control RNA was present in the reverse transcription and PCR reactions. The amount of mRNA in the sample could therefore be assessed in relation to the amount of control product. The control RNA was transcribed from a synthetic DNA template containing primers complementary to those used to amplify the cDNAs of interest. Atrial natriuretic factor mRNA could not be detected in nonfailing human heart but was abundant in ventricular myocardium from failing human heart. In contrast, steady-state levels of phospholamban mRNA decreased, whereas levels of beta-myosin heavy-chain mRNA were unchanged with heart failure. CONCLUSIONS: Alterations in gene expression in the failing human heart appear to be selective. In addition, the present study suggests that PCR provides a rapid and economical way to quantify the expression of multiple genes of interest in endomyocardial biopsy specimens and may therefore be used to advance our understanding of heart muscle disease.

Biopsy↗
PubMed1998

Inverse targeting of retroviral vectors: selective gene transfer in a mixed population of hematopoietic and nonhematopoietic cells.

We previously reported that retroviral vectors displaying epidermal growth factor (EGF) as part of a chimeric envelope glycoprotein are sequestered upon binding to EGF receptor (EGFR)-positive target cells, leading to loss of infectivity. In the current study, we have displayed stem cell factor (SCF) on beta-galactosidase-transducing ecotropic and amphotropic retroviral vector particles as a factor Xa protease-cleavable N-terminal extension of the envelope glycoprotein. Viral incorporation of the SCF chimeric envelopes was demonstrated by immunoblotting of pelleted virions and their specific attachment to Kit receptors was demonstrated by flow cytometry. Gene transfer studies showed that when SCF was displayed on an amphotropic envelope, the infectivity of the SCF-displaying vectors was selectively inhibited on Kit-expressing cells, but could be restored by adding soluble SCF to block the Kit receptors or by cleaving the displayed SCF domain from the vector particles with factor Xa protease. The host range properties of EGF-displaying and SCF-displaying vectors were then compared in cell mixing experiments. When EGFR-positive cancer cells and Kit-positive hematopoietic cells were mixed and exposed to the different engineered vector particles, the cancer cells were selectively transduced by the SCF-displaying vector and the hematopoietic cells were selectively transduced by the EGF-displaying vector. Retroviral display of polypeptide growth factors can therefore provide the basis for a novel inverse targeting strategy with potential use for selective transduction of hematopoietic or nonhematopoietic cells (eg, cancer cells) in a mixed cell population.

3T3 Cells↗
PubMed2005

Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus, Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections.

Ten potential reference genes were compared for their use in experiments investigating cellular mRNA expression of virus infected cells. Human cell lines were infected with Cytomegalovirus, Human Herpesvirus-6, Camelpox virus, SARS coronavirus or Yellow fever virus. The expression levels of these genes and the viral replication were determined by real-time PCR. Genes were ranked by the BestKeeper tool, the GeNorm tool and by criteria we reported previously. Ranking lists of the genes tested were tool dependent. However, over all, beta-actin is an unsuitable as reference gene, whereas TATA-Box binding protein and peptidyl-prolyl-isomerase A are stable reference genes for expression studies in virus infected cells.

Cell Line↗
PubMed2004

Allelic variation of the Tas1r3 taste receptor gene selectively affects behavioral and neural taste responses to sweeteners in the F2 hybrids between C57BL/6ByJ and 129P3/J mice.

Recent studies have shown that the T1R3 receptor protein encoded by the Tas1r3 gene is involved in transduction of sweet taste. To assess ligand specificity of the T1R3 receptor, we analyzed the association of Tas1r3 allelic variants with taste responses in mice. In the F2 hybrids between the C57BL/6ByJ (B6) and 129P3/J (129) inbred mouse strains, we determined genotypes of markers on chromosome 4, where Tas1r3 resides, measured consumption of taste solutions presented in two-bottle preference tests, and recorded integrated responses of the chorda tympani gustatory nerve to lingual application of taste stimuli. For intakes and preferences, significant linkages to Tas1r3 were found for the sweeteners sucrose, saccharin, and D-phenylalanine but not glycine. For chorda tympani responses, significant linkages to Tas1r3 were found for the sweeteners sucrose, saccharin, D-phenylalanine, D-tryptophan, and SC-45647 but not glycine, L-proline, L-alanine, or L-glutamine. No linkages to distal chromosome 4 were detected for behavioral or neural responses to non-sweet quinine, citric acid, HCl, NaCl, KCl, monosodium glutamate, inosine 5'-monophosphate, or ammonium glutamate. These results demonstrate that allelic variation of the Tas1r3 gene affects gustatory neural and behavioral responses to some, but not all, sweeteners. This study describes the range of ligand sensitivity of the T1R3 receptor using an in vivo approach and, to our knowledge, is the first genetic mapping study of activity in gustatory nerves.

Alleles↗
PubMed1983

An approach to the cloning of cell surface protein genes. Selection by cell sorting of mouse L-cells that express HLA or 4F2 antigens after transformation with total human DNA.

We describe an approach to the cloning of cell surface proteins that is independent of messenger RNA isolation. Mouse Ltk- cells are cotransformed with the thymidine kinase gene from Herpes Simplex Virus and total human DNA. Transformants expressing the human surface antigens of interest are isolated by two selection steps, consisting of treatment with hypoxanthine/aminopterin/thymidine and fluorescence-activated cell sorting. Using this procedure, we isolated seven transformants expressing HLA-A,B,C antigens and 12 transformants expressing the 4F2 antigen. We have so far failed to identify any OKT-10 antigen expressing L-cell transformants. Three independent secondary 4F2 transformants were obtained after identical cotransformation of fresh Ltk- cells with DNA from primary transformants. Analysis of their genome by hybridization with human DNA revealed a shared set of human restriction fragments in all three cell lines. This 32 X 10(3) base-pair segment of DNA codes for the human 4F2 antigen, thereby offering the opportunity to clone the gene. To substantiate this hypothesis, we analyzed the seven HLA-expressing cell lines, and we found that all of them had acquired an HLA-coding sequence concomitant to its expression.

Animals↗
PubMed1976

The theory of neutral and weakly selected genes.

The controversy over whether a major fraction of evolutionary allele substitutions and protein polymorphisms in natural populations is due to random drift of neutral mutations remains unresolved; but the discussion has led to extensions of population genetic theory, particularly in stochastic models. The work of Maruyama in seeking quantities that are not strongly dependent on assumptions about population structure is particularly discussed. Under some circumstances, and perhaps quite generally, the probability of eventual fixation of a mutant gene, the total number of heterozygotes in which the gene is involved before its fixation or less, and the total number of heterozygotes during the time the gene has a specified frequency in the entire population have this desirable property. Whether there are many mutants that are so nearly neutral as to be unaffected by selective forces or not, it is clear that there are many loci at which selection is very weak and some of the evolutionary consequences of this are discussed briefly.

Amino Acid Sequence↗