PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “gene function”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 271 records · Page 15Linked to original sources
PubMed1981

Translational regulation: identification of the site on bacteriophage T4 rIIB mRNA recognized by the regA gene function.

The bacteriophage T4 gene regA encodes a protein that diminishes the expression of many unlinked early T4 genes. Previous work demonstrated that regA-mediated repression occurs after transcription. We report here on the identification of the target site on one regA-sensitive mRNA, the message encoding the phage T4 rIIB protein. The target for regA-mediated action overlaps the translational initiation domain of the rIIB messenger. The regA protein may be a repressor that operates translationally on a significant and interesting set of early phage T4 mRNAs.

Base Sequence↗
PubMed1997

The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs.

The particulate methane monooxygenase gene pmoA, encoding the 27 kDa polypeptide of the membrane-bound particulate methane monooxygenase, was amplified by PCR from DNA isolated from a blanket peat bog and from enrichment cultures established, from the same environment, using methane as sole carbon and energy source. The resulting 525 bp PCR products were cloned and a representative number of clones were sequenced. Phylogenetic analysis of the derived amino acid sequences of the pmoA clones retrieved directly from environmental DNA samples revealed that they form a distinct cluster within representative PmoA sequences from type II methanotrophs and may originate from a novel group of acidophilic methanotrophs. The study also demonstrated the utility of the pmoA gene as a phylogenetic marker for identifying methanotroph-specific DNA sequences in the environment.

DNA Probes↗
PubMed1997

The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs.

The methanol dehydrogenase gene mxaF, encoding the large subunit of the enzyme, was amplified from the DNA of a number of representative methanotrophs, methyletrophs, and environmental samples by PCR using primers designed from regions of conserved amino acid sequence identified by comparison of three known sequences of the large subunit of methanol dehydrogenase. The resulting 550-bp PCR products were cloned and sequenced. Analysis of the predicted amino acid sequences corresponding to these mxaF genes revealed strong sequence conservation. Of the 172 amino acid residues, 47% were conserved among all 22 sequences obtained in this study. Phylogenetic analysis of these MxaF sequences showed that those from type I and type II methanotrophs form two distinct clusters and are separate from MxaF sequences of other gram-negative methylotrophs. MxaF sequences retrieved by PCR from DNA isolated from a blanket bog peat core sample formed a distinct phylogenetic cluster within the MxaF sequences of type II methanotrophs and may originate from a novel group of acidophilic methanotrophs which have yet to be cultured from this environment.

Alcohol Oxidoreductases↗
PubMed2004

Lack of association between angiotensin I-converting enzyme insertion/deletion gene functional polymorphism and panic disorder in humans.

Family and twin studies have indicated that genes influence susceptibility to panic disorder, but the genes involved remain unknown. The neuropeptide angiotensin II has been found to be involved in anxiety and regulation of respiration which are important in the pathophysiology of panic attacks. Assuming that angiotensins may be candidate genes in panic disorder, we analyzed the association between panic disorder and angiotensin I-converting enzyme (ACE) insertion (I)/deletion (D) gene functional polymorphism. We recruited 101 patients with panic disorder diagnosed according to DSM-IV criteria, and 184 control subjects in the study. No significant differences in the frequency of the genotype or allele in the polymorphism between patient and control groups were found (genotype, chi(2)=0.56, d.f.=2, P=0.77; allele, chi(2)=0.074, d.f.=1, P=0.78). This study suggests that the ACE I/D gene polymorphism is not directly associated with panic disorder in our Japanese patient group.

Adult↗
PubMed1990

Molecular structures and evolution of mouse isozyme genes functioning in the malate-aspartate shuttle.

To examine molecular mechanisms of transcription of mammalian isozyme genes functioning in the malate-aspartate shuttle and to observe structural and evolutionary relationships, we investigated gene organizations of cAspAT and mAspAT, and cMDH and mMDH, and isolated and characterized cDNAs and genomic DNAs for these isozymes in mice. The deduced amino acid sequences of mouse cAspAT and mAspAT showed about 47%, and those of mouse cMDH and mMDH, about 23% overall homology. Surprisingly, the homology between the mouse cMDH and thermophilic bacterial MDH, as well as the homology between the mouse mMDH and E. coli MDH, markedly exceeds the intraspecies sequence homology between mMDH and cMDH from mice. The first duplication of a common ancestral MDH gene should thus have occurred long before the emergence of the eukaryotic cells, and subsequently, the mammalian mMDH and E. coli MDH genes have evolved from one of the duplicates. The mammalian cMDH and Thermus flavus MDH genes have no doubt evolved from one of the other duplicates. Moreover, structural organizations of the two-pairs of isozyme genes indicated that introns antedate the divergence of these mitochondrial and cytosolic isozyme genes. The 5' ends of all four isozyme genes lacked the TATA and CAAT boxes characteristic of eukaryotic promoters but did contain G + C-rich sequences and multiple transcription-initiation sites. We found several highly conserved regions in the 5' flanking sequences between mAspAT and cAspAT, between mMDH and mAspAT, and between cMDH and cAspAT genes.

Animals↗
PubMed2000

Effects of exercise training on cardiac function, gene expression, and apoptosis in rats.

This study determined the effects of exercise training on cardiac function, gene expression, and apoptosis. Rats exposed to a regimen of treadmill exercise for 13 wk had a significant increase in cardiac index and stroke volume index and a concomitant decrease in systemic vascular resistance compared with both age-matched and body weight-matched sedentary controls in the conscious state at rest. In exercise-trained animals, there was no change in the expression of several marker genes known to be associated with pathological cardiac adaptation, including atrial natriuretic factor, beta-myosin heavy chain, alpha-skeletal and smooth muscle actins, and collagens I and III. Exercise training, however, produced a significant induction of alpha-myosin heavy chain, which was not observed in rats with myocardial infarction. No histological features of cardiac apoptosis were observed in the treadmill-trained rats. In contrast, apoptotic myocytes were detected in animals with myocardial infarction. In summary, exercise training improves cardiac function without evidence of cardiac apoptosis and produces a pattern of cardiac gene expression distinct from pathological cardiac adaptation.

Actins↗
PubMed2004

Applications and advantages of virus-induced gene silencing for gene function studies in plants.

Virus-induced gene silencing (VIGS) is a recently developed gene transcript suppression technique for characterizing the function of plant genes. The approach involves cloning a short sequence of a targeted plant gene into a viral delivery vector. The vector is used to infect a young plant, and in a few weeks natural defense mechanisms of the plant directed at suppressing virus replication also result in specific degradation of mRNAs from the endogenous plant gene that is targeted for silencing. VIGS is rapid (3-4 weeks from infection to silencing), does not require development of stable transformants, allows characterization of phenotypes that might be lethal in stable lines, and offers the potential to silence either individual or multiple members of a gene family. Here we briefly review the discoveries that led to the development of VIGS and what is known about the experimental requirements for effective silencing. We describe the methodology of VIGS and how it can be optimized and used for both forward and reverse genetics studies. Advantages and disadvantages of VIGS compared with other loss-of-function approaches available for plants are discussed, along with how the limitations of VIGS might be overcome. Examples are reviewed where VIGS has been used to provide important new insights into the roles of specific genes in plant development and plant defense responses. Finally, we examine the future prospects for VIGS as a powerful tool for assessing and characterizing the function of plant genes.

Gene Silencing↗
PubMed2000

Functional gene testing of the Glu298Asp polymorphism of the endothelial NO synthase.

OBJECTIVES: To test whether the Glu298Asp polymorphism of the endothelial nitric oxide synthase (eNOS) gene is of functional relevance in humans by altering endothelium-dependent vasodilation. BACKGROUND: The Asp298 variant of the eNOS gene product has been associated with arterial hypertension, coronary artery disease and myocardial infarction. The pathogenetic mechanism has not yet been elucidated. Since endothelium-dependent vasodilation has been shown to be impaired in these disorders, we hypothesized that the Glu298Asp polymorphism of the eNOS gene influences endothelium-dependent vasodilation. METHODS: In 80 patients with normal or elevated cholesterol, endothelium-dependent and -independent vasodilation was assessed. Forearm blood flow was measured by plethysmography in response to intra-arterial (i.a.) infusion of 12 and 48 microg/min acetylcholine and 3.2 and 12.8 microg/min nitroprusside, respectively. NG-monomethyl-L-arginine (L-NMMA) in doses of 4, 8 and 16 micromol/min was infused to test basal nitric oxide (NO) production and release. Genomic DNA was extracted from blood samples to determine the Glu298Asp polymorphism of the eNOS gene at position 1917 G/T after BanII restriction. RESULTS: Baseline parameters (age, gender, blood pressure, body mass index, cholesterol level) were similar across the genotypes. Genotype frequencies did not deviate from the Hardy-Weinberg equilibrium. No differences in forearm blood flow to i.a. acetylcholine (average increase: + 554 +/- 371%), nitroprusside or L-NMMA infusion were found across the eNOS genotypes, neither for endothelium-dependent or endothelium-independent vasodilation, nor for basal NO production and release. Our sample size of n = 80 had a power of > 80% (beta = 0.20) with a P value < 0.05 (alpha = 0.05) to detect a 200% difference in forearm blood flow response to 48 microg/min acetylcholine. CONCLUSIONS: At a power of 80%, we can exclude a relevant effect on endothelium-dependent vasodilation due to the eNOS Glu298Asp polymorphism. Thus, our functional genetic study does not suggest any biological effect of the eNOS Glu298Asp genotype on the cardiovascular system via an influence on endothelium-dependent vasodilation.

Adult↗
PubMed1982

Influence of phage T3 and T7 gene functions on a type III(EcoP1) DNA restriction-modification system in vivo.

The ocr+ gene function (gp 0.3) of bacteriophages T3 and T7 not only counteracts type I (EcoB, EcoK) but also type III restriction endonucleases (EcoP1). Despite the presence of recognition sites, phage DNA as well as simultaneously introduced plasmid DNA are protected by ocr+ expression against both the endonucleolytic and the methylating activities of the EcoP1 enzyme. Nevertheless, the EcoP1 protein causes the exclusion of T3 and T7 in P1-lysogenic cells, apparently by exerting a repressor-like effect on phage gene expression. T3 which induces an S-adenosylmethionine hydrolase is less susceptible to the repressor effect of the SAM-stimulated EcoP1 enzyme. The abundance of EcoP1 recognition sites in the T7 genome is explained by their near identity with the T7 DNA primase recognition site.

DNA Replication↗
PubMed1995

The age-1 and daf-2 genes function in a common pathway to control the lifespan of Caenorhabditis elegans.

Recessive mutations in two genes, daf-2 and age-1, extend the lifespan of Caenorhabditis elegans significantly. The daf-2 gene also regulates formation of an alternative developmental state called the dauer. Here we asked whether these two genes function in the same or different lifespan pathways. We found that the longevity of both age-1 and daf-2 mutants requires the activities of the same two genes, daf-16 and daf-18. In addition, the daf-2(e1370); age-1(hx546) double mutant did not live significantly longer than the daf-2 single mutant. We also found that, like daf-2 mutations, the age-1(hx546) mutation affects certain aspects of dauer formation. These findings suggest that age-1 and daf-2 mutations do act in the same lifespan pathway and extend lifespan by triggering similar if not identical processes.

Animals↗
PubMed2004

Applying Support Vector Machines for Gene Ontology based gene function prediction.

BACKGROUND: The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However, these methods can either only be applied for specific subsets, or their results are not formalised, or they do not provide precise confidence estimates for their predictions. RESULTS: We have developed a large-scale annotation system that tackles all of these shortcomings. In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. The general performance of the system was benchmarked with a large dataset. An organism-wise cross-validation was performed to define confidence estimates, resulting in an average precision of 80% for 74% of all test sequences. The validation results show that the prediction performance was organism-independent and could reproduce the annotation of other automated systems as well as high-quality manual annotations. We applied our trained classification system to Xenopus laevis sequences, yielding functional annotation for more than half of the known expressed genome. Compared to the currently available annotation, we provided more than twice the number of contigs with good quality annotation, and additionally we assigned a confidence value to each predicted GO term. CONCLUSIONS: We present a complete automated annotation system that overcomes many of the usual problems by applying a controlled vocabulary of Gene Ontology and an established classification method on large and well-described sequence data sets. In a case study, the function for Xenopus laevis contig sequences was predicted and the results are publicly available at ftp://genome.dkfz-heidelberg.de/pub/agd/gene_association.agd_Xenopus.

Animals↗
PubMed2004

A primer on using in ovo electroporation to analyze gene function.

The chicken embryo has served as a classic model system for developmental studies due to its easy access for surgical manipulations and a wealth of data about chicken embryogenesis. Notably, the mechanisms controlling limb development have been explored best in the chick. Recently, the method of in ovo electroporation has been used successfully to transfect particular cells/tissues during embryonic development, without the production or infectivity associated with retroviruses. With the sequencing of the chicken genome near completion, this approach will provide a powerful opportunity to examine the function of chicken genes and their counterparts in other species. In ovo electroporation has been most effectively used to date for ectopic or overexpression analyses. However, recent studies indicate that this approach can be used successfully for loss-of-function analyses, including protein knockdown experiments with morpholinos and RNAi. Here, I will discuss parameters for using in ovo electroporation successfully to study developmental processes.

Animals↗
PubMed2002

Analysis of gene function in somatic mammalian cells using small interfering RNAs.

RNA interference (RNAi) is a highly conserved gene silencing mechanism that uses double-stranded RNA (dsRNA) as a signal to trigger the degradation of homologous mRNA. The mediators of sequence-specific mRNA degradation are 21- to 23-nt small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs. Twenty-one-nucleotide siRNA duplexes trigger specific gene silencing in mammalian somatic cells without activation of the unspecific interferon response. Here we provide a collection of protocols for siRNA-mediated knockdown of mammalian gene expression. Because of the robustness of the siRNA knockdown technology, genomewide analysis of human gene function in cultured cells has now become possible.

Animals↗
PubMed1995

Analysis of gene function in Dictyostelium.

Over the past ten years, powerful molecular genetic techniques have been developed to analyze gene function in Dictyostelium. DNA-mediated transformation using a variety of selections and vectors has allowed the introduction of wild-type or modified genes that are under various forms of transcriptional control. Homologous recombination is efficient and can be used to modify the genome in precise ways. In addition, it is now possible to clone genes based on their mutant phenotype alone, either by insertional mutagenesis, or by screening antisense expression cDNA libraries. Finally, a nearly complete physical map of the genome is available and so genes are easily mapped by physical techniques. We discuss many of these advances within the context of major research problems presently under study.

Animals↗
PubMed2005

RNAi in mice: a promising approach to decipher gene functions in vivo.

RNA interference (RNAi) is a simple and powerful tool widely used to study gene functions in many species. Vector-based systems using RNA polymerase III promoters have been developed to achieve stable expression of small interfering RNA (siRNA) or small hairpin RNA (shRNA) in mammalian cells. Recent investigations demonstrated that when, combined with the Cre-loxP system, the vector-based RNAi can be used to achieve conditional or tissue specific knockdown of endogenous genes with high efficiency in mice. Here, we review these recent progresses and discuss the advantages, limitations and future development of this emerging technology.

Animals↗
PubMed2006

Olig gene function in CNS development and disease.

Olig1 and Olig2 encode basic helix-loop-helix (bHLH) transcription factors that are expressed in both the developing and mature vertebrate central nervous system. While numerous studies have established critical functions for Olig genes during the formation of motor neurons and oligodendrocytes of the ventral neural tube, their roles at later stages of development and in adulthood have remained relatively obscure. Recent studies, however, reveal that in the fetal dorsal spinal cord and neural progenitor cells of the adult brain, Olig expression continues to mark, and may regulate, the formation of oligodendroglia. Studies of Olig expression in human brain tumors and repair of demyelinating lesions suggest the possibility of additional functions in a variety of neurological diseases.

Animals↗
PubMed2006

Establishment of a patterned GAL4-VP16 transactivation system for discovering gene function in rice.

A binary GAL4-VP16-UAS transactivation system has been established in rice (Oryza sativa L.) in this study for the discovery of gene functions. This binary system consists of two types of transgenic lines, pattern lines and target lines. The pattern lines were produced by transformation of Zhonghua 11, a japonica cultivar, with a construct consisting of the transactivator gene GAL4-VP16 controlled by a minimal promoter and the GUSplus reporter controlled by the upstream activation sequence (UAS; cis-element to GAL4). Target lines were generated by transformation of Zhonghua 11 with constructs carrying the EGFP reporter and target genes of interest, both controlled by the UAS but in opposite directions. Hybrid plants were obtained by crossing target lines of 10 putative transcription factor genes from rice with six pattern lines showing expression in anther, stigma, palea, lemma and leaves. The EGFP and target genes perfectly co-expressed in hybrid plants with the same expression patterns as in the pattern lines. Various phenotypic changes, such as delayed flowering, multiple pistils, dwarfism, narrow and droopy leaves, reduced tillers, growth retardation and sterility, were induced as a result of the expression of the target genes. It is concluded that this transactivation system can provide a useful tool in rice to unveil latent functions of unknown or known genes.

DNA-Binding Proteins↗