Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Gene selection”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources
PubMed2002

Adaptive divergence and the balance between selection and gene flow: lake and stream stickleback in the Misty system.

We investigated the interplay between natural selection and gene flow in the adaptive divergence of threespine stickleback (Gasterosteus aculeatus) that reside parapatrically in lakes and streams. Within the Misty Lake system (Vancouver Island, British Columbia), stickleback from the inlet stream (flowing into the lake) have fewer gill rakers and deeper bodies than stickleback from the lake--differences thought to facilitate foraging (benthic macroinvertebrates in the stream vs. zooplankton in the open water of the lake). Common-garden experiments demonstrated that these differences have a genetic basis. Reciprocal transplant enclosure experiments showed that lake and inlet stickleback grow best in their home environments (although differences were subtle and often not significant). Release-recapture experiments in the inlet showed that lake fish are less well-suited than inlet fish for life in the stream (higher mortality or emigration in lake fish). Morphological divergence in the wild and under common rearing was greater between the lake and the inlet than between the lake and the outlet. Genetic divergence (mitochondrial DNA and microsatellites) was greatest between the lake and the upper inlet (1.8 km upstream from the lake), intermediate between the lake and the lower inlet (0.9 km upstream), and least between the lake and the outlet stream (1.2 km downstream). Relative levels of gene flow estimated from genetic data showed the inverse pattern. The negative association between morphological divergence and gene flow is consistent with the expectation that gene flow can constrain adaptation. Estimated absolute levels of gene flow also implied a constraint on adaptation in the outlet but not the inlet. Our results suggest that natural selection promotes the adaptive divergence of lake and stream stickleback. but that the magnitude of divergence can be constrained by gene flow.

Adaptation, Physiological↗
PubMed2003

T-DNA tagging in Brassica napus as an efficient tool for the isolation of new promoters for selectable marker genes.

A simple strategy to identify and isolate new promoters suitable for driving the expression of selectable marker genes is described. By employing a Brassica napus hypocotyl transformation protocol and a promoterless gus::nptII tagging construct, a series of 20 kanamycin-resistant tagged lines was produced. Most of the regenerated plants showed hardly any GUS activity in leaf, stem and root tissues. However, expression was readily restored in callus tissue induced on in vitro leaf segments. Genomic sequences upstream of the gus::nptII insertions were isolated via plasmid rescue. Three clones originating from single copy T-DNA lines were selected for further evaluation. The rescued plasmids were cloned as linear fragments in binary vectors and re-transformed to Brassica napus hypocotyl and Solanum tuberosum stem segments. The new sequences maintained their promoter activity, demonstrated by transient and stable GUS activity after transformation. Furthermore, the promoters provided sufficient expression of the nptII gene to yield transgenic plants when using kanamycin as selective agent. Database searching (BLASTN) revealed that the promoters have significant homology with three Arabidopsis BAC clones, one Arabidopsis cDNA and one Brassica napus cDNA. The results presented in this paper illustrate the strength of combined methods for identification, isolation and testing of new plant promoters.

Base Sequence↗
PubMed1982

Use of restriction fragment length polymorphisms for genetic counseling: population genetic considerations.

Two-locus population genetic models are analyzed to evaluate the utility of restriction fragment length polymorphisms for purposes of genetic counseling. It is shown that the linkage disequilibrium between a neutral marker and a tightly linked overdominant mutant will increase rapidly as the mutant moves to its polymorphic equilibrium. The linkage disequilibrium decays for deleterious recessive mutants. Two measures involving the linkage disequilibrium are investigated to determine how much information the transmission of the neutral marker provides about the transmission of the selected gene. In certain kinds of matings, where the parental two-locus genotypes and linkage phases are known, it is possible to determine whether or not a progeny is homozygous for the selected gene on the basis of the fetal genotype at the marker locus. A quantity of primary interest is the fraction of matings between individuals heterozygous for the selected gene in which exact diagnosis can be made in this way. The expected proportion of such matings, taken over all two-locus matings involving heterozygotes at the selected locus, is calculated as a function of the gene frequencies at the two loci and the linkage disequilibrium between them. This expected value is maximized when the linkage disequilibrium is at its maximum in absolute value. Fewer than half of all matings are informative if the linkage disequilibrium is small in magnitude or if the gene frequencies at the two loci are quite different. Consideration is also given to various conditional measures of association that may be useful when the parental two-locus genotypes are unknown. The results suggest that the utility of tightly linked neutral marker genes in predicting the transmission of a selected gene is generally less when selection acts against a recessive gene than for overdominant selection.

Base Sequence↗
PubMed1995

Fluorescence-based selection of retrovirally transduced cells in the absence of a marker gene: direct selection of transduced type B Niemann-Pick disease cells and evidence for bystander correction.

Types A and B Niemann-Pick disease (NPD) are lysosomal storage disorders resulting from the deficient activity of acid sphingomyelinase (ASM). Type A NPD is characterized by the absence of residual ASM activity, massive accumulation of sphingomyelin and cholesterol within lysosomes, and a rapid, neurodegenerative course that leads to death by 3 years of age. In contrast, type B NPD patients have low, but detectable, levels of residual ASM activity and little or no neurologic disease. Thus, individuals with type B NPD may survive into late adolescence or adulthood and are considered excellent candidates for somatic cell gene therapy. To facilitate the development of gene therapy for this disorder, a novel procedure was devised to isolate metabolically corrected type B NPD cells in the absence of marker gene expression. Type B NPD cells were transduced with retroviral vectors expressing ASM, labeled with lissamine rhodamine sphingomyelin (LR-SPM), and subjected to preparative fluorescence-activated cell sorting (FACS). Two non-overlapping cell populations were isolated, corresponding to enzymatically corrected (i.e., low fluorescence) and noncorrected (i.e., high fluorescence) cells. Quantitative PCR analysis demonstrated that the enzymatically corrected cells were enriched for vector sequences. Moreover, the corrected cells could be regrown and continued to express high levels of ASM activity after numerous passages, consistent with the fact that they were stably transduced. Notably, coculture of FACS-sorted, overexpressing cells with untreated type B NPD fibroblasts resulted in a homogeneous cell population with low fluorescence whose FACS distribution overlapped that of the corrected cells. Computerized fluorescence microscopy confirmed that nearly all of these cocultured cells expressed ASM activity and could hydrolyze LR-SPM.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed2004

Tagging and mapping of a rice gall midge resistance gene, Gm8, and development of SCARs for use in marker-aided selection and gene pyramiding.

Using amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNAs (RAPDs), we have tagged and mapped Gm8, a gene conferring resistance to the rice gall midge (Orseolia oryzae), a major insect pest of rice, onto rice chromosome 8. Using AFLPs, two fragments, AR257 and AS168, were identified that were linked to the resistant and susceptible phenotypes, respectively. Another resistant phenotype-specific marker, AP19(587), was also identified using RAPDs. SCAR primers based on the sequence of the fragments AR257 and AS168 failed to reveal polymorphism between the resistant and the susceptible parents. However, PCR using primers based on the regions flanking AR257 revealed polymorphism that was phenotype-specific. In contrast, PCR carried out using primers flanking the susceptible phenotype-associated fragment AS168 produced a monomorphic fragment. Restriction digestion of these monomorphic fragments revealed polymorphism between the susceptible and resistant parents. Nucleotide BLAST searches revealed that the three fragments show strong homology to rice PAC and BAC clones that formed a contig representing the short arm of chromosome 8. PCR amplification using the above-mentioned primers on a larger population, derived from a cross between two indica rice varieties, Jhitpiti (resistant parent) and TN1 (susceptible parent), showed that there is a tight linkage between the markers and the Gm8 locus. These markers, therefore, have potential for use in marker-aided selection and pyramiding of Gm8 along with other previously tagged gall midge resistance genes [ Gm2, Gm4(t), and Gm7].

Animals↗
PubMed1995

Ectopic integration of transforming DNA is rare among neurospora transformants selected for gene replacement.

In a variety of organisms, DNA-mediated transformation experiments commonly produce transformants with multiple copies of the transforming DNA, including both selected and unselected molecules. Such "cotransformants" are much more common than expected from the individual transformation frequencies, suggesting that subpopulations of cells, or nuclei, are particularly competent for transformation. We found that Neurospora crassa transformants selected for gene replacement at the am gene had not efficiently incorporated additional DNA, suggesting that nuclei that undergo transformation by homologous recombination are not highly competent at integration of DNA by illegitimate recombination. Spheroplasts were treated with DNA fragments homologous to am and with an Escherichia coli hph plasmid. Transformants were initially selected for hph (hygromycinR), allowed to conidiate to generate homokaryons and then selected for either Am- (gene replacements) or hph. Surprisingly, most am replacement strains were hygromycinS (124/140) and carried no extraneous DNA (116/140). Most transformants selected for hph also had ectopic copies of am DNA and/or multiple copies of hph sequences (32/35), generally at multiple sites, confirming that efficient cotransformation could occur. To test the implication that cotransformation involving gene replacement and ectopic integration is rare, we compared the yields of am replacement strains with or without prior selection for hph. The initial selection did not appreciably help (or hinder) recovery of strains with replacements.

Blotting, Southern↗
PubMed2003

Directed indices for exploring gene expression data.

MOTIVATION: Large expression studies with clinical outcome data are becoming available for analysis. An important goal is to identify genes or clusters of genes where expression is related to patient outcome. While clustering methods are useful data exploration tools, they do not directly allow one to relate the expression data to clinical outcome. Alternatively, methods which rank genes based on their univariate significance do not incorporate gene function or relationships to genes that have been previously identified. In addition, after sifting through potentially thousands of genes, summary estimates (e.g. regression coefficients or error rates) algorithms should address the potentially large bias introduced by gene selection. RESULTS: We developed a gene index technique that generalizes methods that rank genes by their univariate associations to patient outcome. Genes are ordered based on simultaneously linking their expression both to patient outcome and to a specific gene of interest. The technique can also be used to suggest profiles of gene expression related to patient outcome. A cross-validation method is shown to be important for reducing bias due to adaptive gene selection. The methods are illustrated on a recently collected gene expression data set based on 160 patients with diffuse large cell lymphoma (DLCL).

Algorithms↗
PubMed1991

The prokaryotic neomycin-resistance-encoding gene acts as a transcriptional silencer in eukaryotic cells.

The gene encoding neomycin resistance (neo) mediates a cis-acting negative effect on expression from promoters in transient and stable transfectants of mammalian cell lines. Inserting the neo gene either into retroviral vectors or into plasmids containing reporter genes results in a five- to tenfold decrease of expression from proximal promoters like the simian virus 40 early or the retroviral myeloproliferative sarcoma virus promoter. The silencing effect is not dependent on the insertion site or the orientation of the fragment. The neo gene is frequently used in eukaryotic vectors as a dominant selectable gene. Other selectable genes were tested for potential cis-activity. We found that the gene conferring resistance to puromycin from Streptomyces alboniger does not influence adjacent promoters.

Base Sequence↗
PubMed2001

Efficient elimination of selectable marker genes from the plastid genome by the CRE-lox site-specific recombination system.

Incorporation of a selectable marker gene during transformation is essential to obtain transformed plastids. However, once transformation is accomplished, having the marker gene becomes undesirable. Here we report on adapting the P1 bacteriophage CRE-lox site-specific recombination system for the elimination of marker genes from the plastid genome. The system was tested by the elimination of a negative selectable marker, codA, which is flanked by two directly oriented lox sites (>codA>). Highly efficient elimination of >codA> was triggered by introduction of a nuclear-encoded plastid-targeted CRE by Agrobacterium transformation or via pollen. Excision of >codA> in tissue culture cells was frequently accompanied by a large deletion of a plastid genome segment which includes the tRNA-ValUAC gene. However, the large deletions were absent when cre was introduced by pollination. Thus pollination is our preferred protocol for the introduction of cre. Removal of the >codA> coding region occurred at a dramatic speed, in striking contrast to the slow and gradual build-up of transgenic copies during plastid transformation. The nuclear cre gene could subsequently be removed by segregation in the seed progeny. The modified CRE-lox system described here will be a highly efficient tool to obtain marker-free transplastomic plants.

Base Sequence↗
PubMed2004

Molecular signature in three types of hepatocellular carcinoma with different viral origin by oligonucleotide microarray.

Chronic infection with hepatitis B or C virus (HBV or HCV) is the most clearly established risk factor for hepato-cellular carcinoma (HCC). One type of HCC (non-B, non-C HCC) also appears to develop in patients negative for both HBV and HCV. Using a supervised learning method, we investigated gene expression in 11 non-B, non-C HCCs with high-density oligonucleotide microarrays, and compared the patterns of gene expression with those of HBV-infected HCCs (B-type HCCs) and HCV-infected HCCs (C-type HCCs) in the previous dataset. Our gene selection identified 112 and 64 genes that were differentially expressed in non-B, non-C HCC in comparison with B- and C-type HCCs, respectively. In both gene selections, we found that the false discovery rate, the percentage of genes identified by chance, was less than 5%. Additionally, in combination with the previous data, our present data revealed a set of genes specific to each type of B- and C-type HCCs and non-B, non-C HCC. Among these, an interferon-induced gene, IFI27, was differentially expressed among all three types of HCCs, and this result was confirmed by RT-PCR. Thus, our present study provides a framework to characterize the molecular features in the three subtypes of HCC with different viral origin.

Carcinoma, Hepatocellular↗
PubMed1986

Development of new methods in human gene mapping: selection for fragments of the human Y chromosome after chromosome-mediated gene transfer.

Chromosome-mediated gene transfer (CMGT) can be used to generate fragments of human chromosomes and chromosomal maps can be constructed using these fragments. In previous experiments CMGT techniques have been limited to those regions of the genome which encode biochemically selectable markers. We have extended the regions of the human genome which can be subjected to CMGT methods by employing a cell surface antigen as a selectable marker. These experiments have been facilitated by the discovery that co-transformation of chromosomes with a plasmid bearing a biochemically selectable marker followed by selection for the marker pre-selects for cells which have incorporated chromosomal fragments. The plasmid may also integrate into the donor chromosomes and this provides, in some cases, an additional selectable marker in the chromosome fragment of interest. Using these methods we have isolated for the first time cells containing varying portions of the human Y chromosome.

Cell Line↗
PubMed2004

Effective production of marker-free transgenic strawberry plants using inducible site-specific recombination and a bifunctional selectable marker gene.

Public concerns about the issue of the environmental safety of genetically modified plants have led to a demand for technologies allowing the production of transgenic plants without selectable (antibiotic resistance) markers. We describe the development of an effective transformation system for generating such marker-free transgenic plants, without the need for repeated transformation or sexual crossing. This system combines an inducible site-specific recombinase for the precise elimination of undesired, introduced DNA sequences with a bifunctional selectable marker gene used for the initial positive selection of transgenic tissue and subsequent negative selection for fully marker-free plants. The described system can be generally applied to existing transformation protocols, and was tested in strawberry using a model vector in which site-specific recombination leads to a functional combination of a cauliflower mosaic virus 35S promoter and a GUS encoding sequence, thereby enabling the histochemical monitoring of recombination events. Fully marker-free transgenic strawberry plants were obtained following two different selection/regeneration strategies.

Journal Article↗
PubMed2006

Selecting normalization genes for small diagnostic microarrays.

BACKGROUND: Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normalization strategies to diagnostic microarrays causes new normalization problems. RESULTS: In this paper we point out the differences of normalizing large microarrays and small diagnostic microarrays. We suggest to include additional normalization genes on the small diagnostic microarrays and propose two strategies for selecting them from genomewide microarray studies. The first is a data driven univariate selection of normalization genes. The second is multivariate and based on finding a balanced diagnostic signature. Finally, we compare both methods to standard normalization protocols known from large microarrays. CONCLUSION: Not including additional genes for normalization on small microarrays leads to a loss of diagnostic information. Using house keeping genes from the literature for normalization fails to work for certain datasets. While a data driven selection of additional normalization genes works well, the best results were obtained using a balanced signature.

Algorithms↗
PubMed2004

Gene expression profiling in two morphologically different uterine cervical carcinoma cell lines derived from a single donor using a human cancer cDNA array.

PURPOSE: To examine the differentially expressed cancer-related genes in two morphologically different uterine cervical carcinoma cell lines derived from the same patient by an Affymetrix Human Cancer G110 Array carrying 1700 cancer-associated genes. In addition, to investigate specific gene expression depending on histological type, we examined expression of the selected genes in a panel of established cervical carcinoma cell lines derived from cervical adenocarcinoma and squamous cell carcinoma (SCC). EXPERIMENTAL DESIGN: Two distinct human uterine cervical carcinoma cell lines SKG-IIIa and SKG-IIIb derived from a single donor were screened using a cDNA microarray. The array results were additionally validated using semiquantitative RT-PCR. Expressions of the 10 selected genes were analyzed in the nine established cervical carcinoma cell lines using RT-PCR. RESULTS: The cDNA microarray analysis showed that 16 genes in SKG-IIIa were upregulated more than 10-fold compared to SKG-IIIb, and seven genes in SKG-IIIb were upregulated. Semiquantitative RT-PCR analysis of a subset of these differentially expressed genes gave results consistent with microarray findings. Among the 10 selected genes, insulin-like growth factor-binding protein-3, inhibitor of apoptosis protein 1, and cadherin-13 were more frequently expressed in SCC cell lines. 1-8D gene of interferon-inducible genes, Sno oncogenes, and transforming growth factor-beta II receptor were expressed in both SCC and adenocarcinoma cell lines. CONCLUSIONS: Our experimental data demonstrated that multiple genes are differentially expressed in uterine cervical carcinoma cell lines. It is suggested that these genes are involved with the differences in morphological characteristics and carcinogenesis of cervical carcinoma.

Adenocarcinoma↗
PubMed2003

Evolutionary dynamics of oncogenes and tumor suppressor genes: higher intensities of purifying selection than other genes.

Oncogenes and tumor suppressor genes (hereafter referred to as "cancer genes") result in cancer when they experience substitutions that prevent or distort their normal function. We examined evolutionary pressures acting on cancer genes and other classes of disease-related genes and compared our results to analyses of genes without known association to disease. We compared synonymous and nonsynonymous substitution rates in 3,035 human genes-approximately 10% of the genome-measuring the intensity of purifying selection on 311 human disease genes, including 122 cancer-related genes. Although the genes examined are similar to nondisease genes in product, expression, function, and pathway affiliation, we found intriguing differences in the selective pressures experienced by cancer genes relative to other (noncancer) disease-related and non-disease-related genes. We found a statistically significant increase in the intensity of purifying selection exerted on cancer genes (the average ratio of nonsynonymous to synonymous substitutions, omega, was 0.079) relative to all other disease-related genes groups (omega = 0.101) and non-disease-related genes (omega = 0.100). This difference indicates a striking increase in selection against nonsynonymous substitutions in oncogenes and tumor suppressor genes. This finding provides insight into the etiology of cancer and the differences between genes involved in cancer and those implicated in other human diseases. Specifically, we found a significant overlap between human oncogenes and tumor suppressor genes and "essential genes," human homologs of mouse lethal genes identified by knockout experiments. This insight may improve our ability to identify cancer-related genes and enhances our understanding of the nature of these genes.

Evolution, Molecular↗
PubMed1995

A strategy for cloning the hereditary hemochromatosis gene.

Selective hybridization of small intestine and liver cDNA libraries was carried out using yeast artificial chromosomes (YACs) surrounding D6S105, the microsatellite that appears to be close to the gene for hereditary hemochromatosis (HFE). Of 14 candidate probes hybridizing with these YACs, only one, designated. LD5-1, detected abnormalities in southern blots of patients with hemochromatosis. Two different abnormalities. were detected in 3 of 55 patients with hemochromatosis with the LD5-1 probe, and one of these was detected in one of 44 normal subjects. The gene that hybridizes with this probe is located about 300-400 kb centromeric of D6S105. It is transcribed into mRNA that is about 8.5 kb in length in many tissues, including peripheral blood leukocytes. The available sequence indicates tha it codes for a zinc finger protein. We propose that there is a reasonable probability that LD5-1 hybridizes with the gene for hereditary hemochromatosis.

Base Sequence↗
PubMed2000

Distribution and sequence variations of selected virulence genes among group A streptococcal isolates from western Norway.

In order to compare the distribution of selected virulence genes among group A streptococci recovered from invasive disease and superficial infections, 42 isolates were screened for mga, speB, speA, ssa and ska, by PCR. The isolates were predominantly of the sequence types emm1, emm3 and emm6, but also included a few of the types emm22, emm28, emm75 and emm78. The phage-mediated speA seemed to be prevalent in emm types 1 and 3, and its distribution was not related to disease severity. The other genes were present in all isolates. The mga, speB and speA were further studied by sequence analysis. Although allotypic associations with invasiveness were not found, allelic specificity to the emm sequence type was observed. In addition, the mga sequences indicated two lineages, related to opacity factor production. A possible recombination between these two main divergent mga genes was observed in isolates of the types emm22 and emm75. A logical nomenclature of the alleles of mga and speB is suggested.

Alleles↗
PubMed1999

Selective neointimal gene transfer in an avian model of vascular injury.

Avian models of atherosclerosis helped pioneer the study of vascular biology, and offer economic and technical advantages over mammalian models. As an initial step towards investigating important molecular pathways involved in avian atherogenesis and restenosis, we developed a recombinant adenovirus (Ad) which expresses the reporter gene beta-galactosidase (beta-gal), and applied it to cultured chicken vascular smooth muscle cells (SMCs) and a rooster model of acute vascular injury. In cultured chicken SMCs, recombinant gene expression increased as a function of multiplicity of infection (MOI) and incubation time. Maximal expression occurred at an MOI of 10(4) plaque-forming units (pfu)/cell with approximately 50% of quiescent and non-quiescent chicken SMCs expressing beta-gal. Human aorta SMCs had two- to four-fold increased beta-gal expression compared with chicken SMCs at all MOI and incubation times. In vivo instillation of recombinant Ad into uninjured rooster femoral artery segments revealed low efficiency endothelial cell expression of the reporter gene. In contrast, recombinant Ad infection of rooster femoral artery segments 3-21 days after balloon injury revealed up to 60% of luminal surface beta-gal expression, confined predominantly to the neointimal layer. Peak reporter gene expression efficiencies occurred in arterial segments infected 3 days after balloon injury. Uninfected and control Ad infected arteries had no detectable beta-gal expression. Rooster neointimal cells targeted by the recombinant Ad were identified as alpha-smooth muscle actin containing cells by immunohistochemistry. We conclude that Ad-mediated gene transfer is efficient and selective for the neointima in the rooster acute vascular injury model, and offers the potential to efficiently introduce exogenous genes that may impact on the injury response. This model of acute vascular injury may also be manipulated into more established avian models of atherosclerosis, permitting the investigation of acute injury progression to chronic injury.

Adenoviridae↗