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 289 records · Page 16Linked to original sources

Bacteriophage T4 unf (=alc) gene function is required for late replication in the presence of plasmid pR386.

The bacteriophage T4 unf gene, known to be involved in the arrest of transcription from cytosine-containing DNA, is unessential except in Escherichia coli strains containing plasmid pR386. Comparative genetic and biochemical analyses of parameters of unf+ and unf- phage growth in host cells isogenic except for the presence or absence of plasmid pR386 have shown that unf gene function is required for late phage DNA synthesis in the presence of the plasmid. Shutoff of host DNA, RNA, and protein syntheses, degradation of host DNA, adsorption, injection, and early phage DNA, RNA, and protein syntheses all occurred with normal or near-normal kinetics in unf- infections, even in the presence of the plasmid. The switch from early to late protein synthesis occurred in plasmid pR386-containing cells infected with unf+ or unf- phage. However, this switchover was slow in both cases and may be slower in unf- infections than in unf+ infections. Net incorporation of [3H]thymidine terminated at about 30 min after infection of pR386-containing cells with unf- phage at 30 degrees C. Alkaline sucrose gradient studies of the intracellular pools of replicative DNA in unf-infected plasmid pR386-containing cells indicated that this DNA is not detectably nickel or cleaved at the time that DNA synthesis aborts. The addition of chloramphenicol subsequent to early enzyme synthesis prevented the arrest of DNA synthesis in plasmid-containing cells infected with unf-phage.

Centrifugation, Density Gradient↗

Predicting gene function by conserved co-expression.

We show that gene co-expression, which generally provides only a very weak signal for the prediction of functional interactions, can provide a reliable signal by exploiting evolutionary conservation. The encoded proteins of conserved co-expressed gene pairs are highly likely to be part of the same pathway not only after speciation (98%), but also after parallel gene duplication (97%). Conserved co-expression combined with homology data enables us to predict specific gene functions. The use of conservation between parallel duplicated gene pairs to predict function is especially promising given that gene duplication is common in eukaryotes, and that data from only a single organism can be used.

Animals↗

Diversification of gene function: homologs of the floral regulator FLO/LFY control the first zygotic cell division in the moss Physcomitrella patens.

After fertilization, the zygote undergoes dynamic changes in chromosomal and cytoplasmic organization, and begins the cell cycles that eventually lead to formation of the multicellular embryo. Specific transcription factors that initiate this cascade of events in land plants have not been identified. We have identified two FLO/LFY genes, PpLFY1 and PpLFY2, that regulate the first cell division after formation of the zygote in the moss Physcomitrella patens. The deduced amino acid sequences of the two PpLFY genes are 94.8% identical to each other and show similar expression patterns. While fertilization occurred in the PpLFY disruptants, the development of double disruptant zygotes was arrested at the single-cell stage. When the double disruptants, as the female parent, were crossed with the wild type, as the male parent, normal sporophytes were formed, supporting the notion that the PpLFY genes function after fertilization to regulate the first mitotic cell division in zygotes. The rare sporophytes that formed on the PpLFY double disruptants showed mostly normal organogenesis, but had abnormalities in the pattern of cell division, supporting a role of PpLFY genes in regulating cell division. The FLO/LFY genes in angiosperms are conserved master regulators of floral identity without any obvious effects on cell division. By contrast, our study suggests that FLO/LFY genes have functions throughout sporophyte development in the basal land plant lineages.

Arabidopsis↗

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

BACKGROUND: The expression of gene batteries, genomic units of functionally linked genes which are activated by similar sets of cis- and trans-acting regulators, has been proposed as a major determinant of cell specialization in metazoans. We developed a predictive procedure to screen the mouse and human genomes and transcriptomes for cases of gene-battery-like regulation. RESULTS: In a screen that covered approximately 40 percent of all annotated protein-coding genes, we identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory sequence elements. 66 predicted cases of over-represented transcription factor binding motifs were validated against the literature and fell into three categories: (i) previously described cases of gene battery-like regulation, (ii) previously unreported cases of gene battery-like regulation with some support in a limited number of genes, and (iii) predicted cases that currently lack experimental support. The novel predictions include for example Sox 17 and RFX transcription factor binding sites that were detected in approximately 10% of all testis specific genes, and HNF-1 and 4 binding sites that were detected in approximately 30% of all kidney specific genes respectively. The results are publicly available at http://www.wlab.gu.se/lindahl/genebatteries. CONCLUSION: 21 co-expressed gene clusters were enriched for a total of 66 shared cis-regulatory sequence elements. A majority of these predictions represent novel cases of potential co-regulation of functionally coupled proteins. Critical technical parameters were evaluated, and the results and the methods provide a valuable resource for future experimental design.

Amino Acid Motifs↗

Antisense oligonucleotides: a systematic high-throughput approach to target validation and gene function determination.

Antisense technology provides a high-throughput and systematic approach to drug target validation and gene function discovery. In combination with other emerging technologies (such as microarrays), this technology will enable efficient evaluation of the sequence data generated by the Human Genome Project. The authors review recent advances in the antisense field and discuss the potential use of antisense technology for functional genomics.

Journal Article↗

[Molecular pharmacogenetic studies of drug responses to obsessive-compulsive disorder and six functional genes].

OBJECTIVE: To investigate the associations between the drug responses to obsessive -pulsive disorder (OCD) and six functional genes related with serotonin and dopamine. METHODS: One hundred and thirteen OCD nuclear families were collected. The OCD patients were treated with serotonin reuptake inhibitors (SRIs) for 8 weeks and the drug responses were assessed using the Yale-Brown obsessive-compulsive scale (Y-BOCS). The patients were divided into drug responders group and non-responders group according to the reducing rate of Y-BOCS score. The genotypes of six genes were determined with the Amp-FLP and Amp-RFLP techniques and analyzed by transmission disequilibrium test (TDT). The six genes are serotonin 2A receptor (5-HT2A), serotonin transporter (5-HTT), dopamine D2 receptor ( DRD2), dopamine D4 receptor (DRD4), catechol-O- methyltransferase (COMT) and monoamine oxidase A (MAOA). RESULTS: No association was found between the six genes and different drug responses groups. However, there was significant difference between the drug responders and non-responders in homozygosity at the 5-HT2A -1438G/A locus (chi(2)=4.69, P=0.03). CONCLUSION: The results suggested that the 5-HT2A may play some roles in the effects of drug treatment on OCD.

Adolescent↗

PEP4 gene function is required for expression of several vacuolar hydrolases in Saccharomyces cerevisiae.

The pep4-3 mutation results in a 90-95% reduction in the levels of five vacuolar hydrolases in yeast, including proteinases A and B, carboxypeptidase Y, RNase(s) and the repressible alkaline phosphatase. The mutation is without effect on two secreted glycoproteins, on an enzyme of the vacuolar membrane, and on a proteinase located outside of the vacuole. Mutations at the PEP4 locus exhibit a dosage effect on the levels of some, but not all, of the enzymes whose expression requires the function of the gene.

Alkaline Phosphatase↗

Paralogous Hox genes: function and regulation.

The Hox homeobox gene family plays a pivotal role in regulating patterning and axial morphogenesis in vertebrates. Molecular characterization of the four Hox clusters has shown that they are evolutionarily related with respect to sequence, organization, and expression, suggesting they arose by duplication and divergence. Transgenic analysis has clearly demonstrated the functional roles of individual genes in a broad range of embryonic tissues, and in compound mutants has addressed the issues of cooperativity and redundancy. There is an emerging picture of the cis-regulatory elements underlying Hox expression, and for the 3' members of the clusters there is a considerable degree of conservation between paralogous genes with respect to their functional roles and regulatory control.

Animals↗

Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation in pulp and paper mill effluent treatment systems.

The relationship between the abundance of three functional genes and their corresponding biochemical reaction rates was investigated in several activated sludge and mill effluent microbial communities. Gene probes were prepared for two key denitrification genes (nirS and nirK) and for one nitrogen-fixation gene (nifH) and were validated using a variety of strains of known nir and nif genotype. ATP-based measures of viable cell numbers were used to provide total population sizes. In certain microbial communities (activated sludge enrichment cultures and multiple samples taken from the same mill primary clarifier), a strong correlation was observed between gene abundance and biochemical activity rates. However, when comparing several different nonenriched activated sludge bioreactors and separate primary clarifier microbial communities, the ratio of specific gene abundance to biochemical activity rates varied widely. These results suggest that in cases where a microbial community is not fully induced for a given biochemical activity or when very different communities are compared, quantitative gene probing can give a better measure of a community's potential to carry out the encoded function than can the relevant biochemical assay. However, the gene quantitation method employed here probably underestimated the true number of probed genes present in the microbial communities due to nirS and nifH genes in the communities having reduced DNA sequence similarity with the probes used.

Adenosine Triphosphate↗

Targeted DNA integration within different functional gene domains in yeast reveals ORF sequences as recombinational cold-spots.

The efficiency of gene targeting within different segments of genes in yeast was estimated by transforming yeast cells with double-stranded integrative plasmids, bearing functional gene domains [promoter (P), ORF (O) and terminator (T)] derived from the common genetic markers HIS3, LEU2, TRP1 and URA3. Transformation experiments with circular plasmids carrying a single gene domain demonstrated that the 5' and 3' flanking DNA regions (P and T) of the HIS3 and URA3 genes are preferred as sites for plasmid integration by several fold over the corresponding ORFs. Moreover, when plasmids bearing combinations of two or three regions were linearized to target them to a specific site of integration, three of the ORFs were found to be less preferred as sites for plasmid integration than their corresponding flanking regions. Surprisingly, in up to 50% of the transformants obtained with plasmids that had been linearized within coding sequences, the DNA actually integrated into neighbouring regions. Almost the same frequencies of ORF mis-targeting were obtained with plasmid vectors containing only two functional domains ("PO" or "OT") of the gene URA3, demonstrating that this event is not the consequence of competition between homologous DNA regions distal to the ORF. Therefore, we suggest that coding sequences could be considered to be "cold spots" for plasmid integration in yeast.

Aldose-Ketose Isomerases↗

MHC class I-subversive gene functions of cytomegalovirus and their regulation by interferons-an intricate balance.

Multiple glycoproteins of human cytomegalovirus (HCMV) encoded by the genes US2, US3, US6 and US11 interrupt the MHC class I pathway of antigen presentation at distinct checkpoints to avoid recognition of infected cells by cytotoxic CD8+ T lymphocytes. The action of cytokines like interferon (IFN)-gamma, IFN-alpha/beta and tumour necrosis factor alpha (TNF-alpha) compensate for the viral inhibition and restore antigen presentation in HCMV-infected cells. This finding was explained by their effects on cellular rather than viral genes and reflected by an increase in the production, assembly and maturation of MHC class I molecules resulting in an escape of MHC I from viral control. Here we reproduce the IFN-gamma-mediated effect when MHC I-subversive gene functions of HCMV are tested in isolation, but the efficacy of IFN-gamma to restore MHC I surface expression in US2-, US6- and US11-transfectants differs significantly. In addition, in HCMV-infected cells IFN-gamma strongly affects the synthesis of the US6-encoded glycoprotein. Despite the capability of HCMV to block the interferon signaling pathway the IFN-gamma driven enhancement of MHC class I and class II expression remains effective provided that cells are exposed to IFN-gamma before infection. Our findings illustrate a complex interplay between host immune factors and viral immune evasion functions.

Amino Acid Sequence↗

Fluorescent tagged analysis of neural gene function using mosaics in zebrafish and Xenopus laevis.

An important question in the neurosciences is the role of specific gene expression in the control of neural morphology and connectivity. To address this question, methods are needed for expression of exogenous genes in a subset of neurons. This limited and mosaic expression allows the assessment of gene expression in a cell autonomous fashion without environmental contributions from neighboring expressing cells. These methods must also label neurons so that detailed morphology and neural connections can be evaluated. The labeling method should label only a subset of neurons so that neuronal morphology can be viewed upon a non-stained background, in a Golgi staining fashion. Here, we report methods using plasmids called pTAGUM (tagged analysis of genes using mosaics) that accomplish these goals. These methods should prove useful for the analysis of neural gene function in two important model organisms, the zebrafish and Xenopus laevis.

Animals↗

EST derived PCR-based markers for functional gene homologues in cotton.

We investigated the utility of the Gossypium arboreum EST sequences in the GenBank database for developing PCR-based markers targeting known-function genes in cultivated tetraploid cottons, G. hirsutum and G. barbadense. Four hundred sixty-five randomly selected ESTs from this library were subjected to BLASTn search against all GenBank databases, of which putative function was assigned to 93 ESTs based on high nucleotide homology to previously studied genes. PCR primers were synthesized for 89 of the known-function ESTs. A total of 57 primer pairs amplified G. arboreum genomic DNA, but only 39 amplified in G. hirsutum and G. barbadense, suggesting that sequence divergence may be a factor causing non-amplification for some sites. DNA sequence analysis showed that most primer pairs were targeting the expected homologous loci. While the amplified products that were of larger size than the corresponding EST sequences contain introns, the primer pairs with a smaller amplicon than predicted from the flanking EST sequences did not amplify the expected orthologous gene sequences. Among the 39 primer pairs that amplified tetraploid cotton DNA, 3 detected amplicon size polymorphisms and 10 detected polymorphisms after digestion with one of six restriction enzymes. Ten of the polymorphic loci were subsequently mapped to an anchor RFLP map. Digestion of PCR-amplified sequences offers one means by which cotton genes can be mapped to their chromosomal locations more quickly and economically than by RFLP analysis.

Base Sequence↗

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes.

An important element of the developing field of proteomics is to understand protein-protein interactions and other functional links amongst genes. Across-species correlation methods for detecting functional links work on the premise that functionally linked proteins will tend to show a common pattern of presence and absence across a range of genomes. We describe a maximum likelihood statistical model for predicting functional gene linkages. The method detects independent instances of the correlated gain or loss of pairs of proteins on phylogenetic trees, reducing the high rates of false positives observed in conventional across-species methods that do not explicitly incorporate a phylogeny. We show, in a dataset of 10,551 protein pairs, that the phylogenetic method improves by up to 35% on across-species analyses at identifying known functionally linked proteins. The method shows that protein pairs with at least two to three correlated events of gain or loss are almost certainly functionally linked. Contingent evolution, in which one gene's presence or absence depends upon the presence of another, can also be detected phylogenetically, and may identify genes whose functional significance depends upon its interaction with other genes. Incorporating phylogenetic information improves the prediction of functional linkages. The improvement derives from having a lower rate of false positives and from detecting trends that across-species analyses miss. Phylogenetic methods can easily be incorporated into the screening of large-scale bioinformatics datasets to identify sets of protein links and to characterise gene networks.

Journal Article↗

Epigenetic regulation of chromatin structure and gene function by biotin.

Covalent modifications of histones are a crucial component of epigenetic events that regulate chromatin structures and gene function. Evidence exists that distinct lysine residues in histones are modified by covalent attachment of the vitamin biotin, catalyzed by biotinidase and holocarboxylase synthetase. Biotinylation of histones appears to be conserved across species. The following biotinylation sites were identified using both MS and enzymatic biotinylation of synthetic peptides: K9, K13, K125, K127, and K129 in histone H2A; K4, K9, and K18 in histone H3; and K8 and K12 in histone H4. Evidence was provided that biotinylated histone H4 is enriched in pericentromeric heterochromatin, and that biotinylation of histone H4 participates in gene silencing, mitotic condensation of chromatin, and the cellular response to DNA damage. Biotinylation of histones is a reversible process and depends on the exogenous biotin supply, but the identities of histone debiotinylases remain uncertain. We propose that some effects of biotin deficiency can be attributed to abnormal chromatin structures.

Biotin↗

[Target delivery of functional genes in gene therapy using carbohydrate containing vectors].

Various aspects of use of specific interactions with a participation of carbohydrate and oligosaccharide ligands to increase an efficiency of gene transfer into eukaryotic cells (including in vivo experiments) are considered in details. Data on addressed gene delivery with applying carbohydrate-containing ligands (such as asialoglycoproteins and galactosides) are discussed in the paper. Results on the usage of glycoside ligands, containing lactose, mannose, glucose residues, for receptor-mediated gene transfer, are analysed. Special attention is paid to application of chitosans for functional gene transfer into eukaryotic cells, which is considered by authors as a case of receptor-mediated gene transfer. It is notice that neo-oligosaccharide vectors, recognizing surface lectins, represent very perspective type of gene delivery systems.

Animals↗

Intravenously administered short interfering RNA accumulates in the kidney and selectively suppresses gene function in renal proximal tubules.

Different gene-silencing methods, like antisense and short interfering RNA (siRNA), are widely used as experimental tools to inhibit gene expression. In the present study, the in vivo behavior of siRNA in rats and siRNA-mediated silencing of genes in the renal proximal tubule were investigated. To study the biodistribution of siRNA, rats were injected i.v. with radiolabeled siRNA or radiolabel alone (control), and scintigraphic images were acquired at different time intervals postinjection. The siRNA preferentially accumulated in the kidneys and was excreted in the urine. One hour after injection, the amount of siRNA present in both kidneys (1.7 +/- 0.3% of injected dose/g tissue) was on average 40 times higher than in other tissues (liver, brain, intestine, muscle, lung, spleen, and blood). Besides the biodistribution, the effect of siRNA on multidrug resistance protein isoform 2 (Mrp2/Abcc2, siRNAMrp2) in renal proximal tubules was investigated. Mrp2 function was assessed by measuring the excretion of its fluorescent substrate calcein in the isolated perfused rat kidney. Four days after administration, siRNAMrp2 reduced the urinary calcein excretion rate significantly (35% inhibition over the period 80-150 min of perfusion). This down-regulation was specific because another siRNA sequence directed against a different transporter in the proximal tubule, Mrp4 (Abcc4, siRNAMrp4), did not alter the Mrp2-mediated excretion of calcein. In conclusion, siRNA accumulates spontaneously in the kidney after i.v. injection, where it selectively suppresses gene function in the proximal tubules. Therefore, i.v. administered siRNA provides a novel experimental and potential therapeutic tool for gene silencing in the kidney.

ATP-Binding Cassette Transporters↗

Escherichia coli 4.5S RNA gene function can be complemented by heterologous bacterial RNA genes.

The essential 4.5S RNA gene of Escherichia coli can be complemented by 4.5S RNA-like genes from three other eubacteria, including both gram-positive and gram-negative organisms. Two of the genes encode RNAs similar in size to the E. coli species; the third, from Bacillus subtilis, specifies an RNA more than twice as large. The heterologous genes are expressed efficiently in E. coli, and the product RNAs resemble those produced by cognate cells. We conclude that the heterologous RNAs can replace E. coli 4.5S RNA and that the essential function of 4.5S RNA is evolutionarily conserved. A consensus structure is presented for the functionally related 4.5S RNA homologs.

Base Sequence↗