SEARCH · PubMed Health

Results for “Functional genes”

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 91 records · Page 5Linked to original sources

PubMed2007

Methods for transient assay of gene function in floral tissues.

BACKGROUND: There is considerable interest in rapid assays or screening systems for assigning gene function. However, analysis of gene function in the flowers of some species is restricted due to the difficulty of producing stably transformed transgenic plants. As a result, experimental approaches based on transient gene expression assays are frequently used. Biolistics has long been used for transient over-expression of genes of interest, but has not been exploited for gene silencing studies. Agrobacterium-infiltration has also been used, but the focus primarily has been on the transient transformation of leaf tissue. RESULTS: Two constructs, one expressing an inverted repeat of the Antirrhinum majus (Antirrhinum) chalcone synthase gene (CHS) and the other an inverted repeat of the Antirrhinum transcription factor gene Rosea1, were shown to effectively induce CHS and Rosea1 gene silencing, respectively, when introduced biolistically into petal tissue of Antirrhinum flowers developing in vitro. A high-throughput vector expressing the Antirrhinum CHS gene attached to an inverted repeat of the nos terminator was also shown to be effective. Silencing spread systemically to create large zones of petal tissue lacking pigmentation, with transmission of the silenced state spreading both laterally within the affected epidermal cell layer and into lower cell layers, including the epidermis of the other petal surface. Transient Agrobacterium-mediated transformation of petal tissue of tobacco and petunia flowers in situ or detached was also achieved, using expression of the reporter genes GUS and GFP to visualise transgene expression. CONCLUSION: We demonstrate the feasibility of using biolistics-based transient RNAi, and transient transformation of petal tissue via Agrobacterium infiltration to study gene function in petals. We have also produced a vector for high throughput gene silencing studies, incorporating the option of using T-A cloning to insert the gene sequence of interest. These techniques should allow analysis of gene function in a much broader range of flower species.

Journal Article↗

PubMed1998

The sgp gene modulates stress responses of Streptococcus mutans: utilization of an antisense RNA strategy to investigate essential gene functions.

The sgp gene from Streptococcus mutans has been previously isolated, characterized, and demonstrated to encode a G-protein. In order to investigate the function of this gene, a novel antisense RNA strategy was developed. Expression of sgp antisense RNA in Escherichia coli led to transient inhibition of growth. In addition, sgp antisense RNA expression in S. mutans resulted in decreased growth under environmental stress conditions (44 degrees C, acidic pH, and high osmolarity). Therefore, these results suggest that the sgp gene plays a role in modulating the stress responses of S. mutans. This approach could be applicable for investigating the function of essential genes in other organisms for which mutants are not available.

Bacterial Proteins↗

PubMed1979

An adenovirus type 5 early gene function regulates expression of other early viral genes.

We have identified an adenovirus type 5(Ad5) early gene function located in early region 1 which is required for the production of early cytoplasmic mRNAs corresponding to early regions 2, 3, and 4. Mutant dl312 (lacks the segment between 1.5 and 4.5 map units) grows as well as wild-type virus in 293 cells (Ad5-transformed human embryonic kidney cells), but its growth is severely restricted in HeLa cells. We detect no viral RNAs in the cytoplasm of dl312-infected HeLa cells. Viral RNA sequences are present, however, in dl312-infected HeLa cell nuclei.

Adenoviruses, Human↗

PubMed2004

A probabilistic view of gene function.

Cells are controlled by the complex and dynamic actions of thousands of genes. With the sequencing of many genomes, the key problem has shifted from identifying genes to knowing what the genes do; we need a framework for expressing that knowledge. Even the most rigorous attempts to construct ontological frameworks describing gene function (e.g., the Gene Ontology project) ultimately rely on manual curation and are thus labor-intensive and subjective. But an alternative exists: the field of functional genomics is piecing together networks of gene interactions, and although these data are currently incomplete and error-prone, they provide a glimpse of a new, probabilistic view of gene function. We outline such a framework, which revolves around a statistical description of gene interactions derived from large, systematically compiled data sets. In this probabilistic view, pleiotropy is implicit, all data have errors and the definition of gene function is an iterative process that ultimately converges on the correct functions. The relationships between the genes are defined by the data, not by hand. Even this comprehensive view fails to capture key aspects of gene function, not least their dynamics in time and space, showing that there are limitations to the model that must ultimately be addressed.

Animals↗

PubMed2000

The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions.

Sheltered from deleterious mutations, genes with overlapping or partially redundant functions may be important sources of novel gene functions. While most partially redundant genes originated in gene duplications, it is much less clear why genes with overlapping functions have been retained, in some cases for hundreds of millions of years. A case in point is the many partially redundant genes in vertebrates, the result of ancient gene duplications in primitive chordates. Their persistence and ubiquity become surprising when it is considered that duplicate and original genes often diversify very rapidly, especially if the action of natural selection is involved. Are overlapping gene functions perhaps maintained because of their protective role against otherwise deleterious mutations? There are two principal objections against this hypothesis, which are the main subject of this article. First, because overlapping gene functions are maintained in populations by a slow process of "second order" selection, population sizes need to be very high for this process to be effective. It is shown that even in small populations, pleiotropic mutations that affect more than one of a gene's functions simultaneously can slow the mutational decay of functional overlap after a gene duplication by orders of magnitude. Furthermore, brief and transient increases in population size may be sufficient to maintain functional overlap. The second objection regards the fact that most naturally occurring mutations may have much weaker fitness effects than the rather drastic "knock-out" mutations that lead to detection of partially redundant functions. Given weak fitness effects of most mutations, is selection for the buffering effect of functional overlap strong enough to compensate for the diversifying force exerted by mutations? It is shown that the extent of functional overlap maintained in a population is not only independent of the mutation rate, but also independent of the average fitness effects of mutation. These results are discussed with respect to experimental evidence on redundant genes in organismal development.

Animals↗

PubMed2004

Functional gene discovery using hybrid ribozyme libraries.

Hybrid ribozymes that couple the cleavage activity of hammerhead ribozymes with the unwinding activity of RNA helicases are powerful tools in the study of cell genetics and pharmaceutical drug development. They are useful for targeting a specific gene as well as screening functional genes to show phenotypic alterations. By randomizing the binding arms within the ribozymes, we can create a library of ribozymes that are capable of cleaving any mRNA. After introducing the library into cells and recovering the sequence information of ribozymes that alter the cell phenotype of interest, genes that are responsible for the specific phenotype can be identified. This chapter describes a method known as the gene-discovery system to identify novel functional genes related to a specific phenotype. Our gene-discovery system should be a powerful tool for post-genome research.

Base Sequence↗

PubMed2004

Synonymous codon usage and gene function are strongly related in Oryza sativa.

The relationship between codon usage and gene function was investigated while considering a dataset of 2106 nuclear genes of Oryza sativa. The results of standard chi(2) test and F-statistic showed that for every 59 synonymous codons, a strongly significant association with gene functional categories existed in rice, indicating that codon usage was generally coordinated with gene function whether it was at the level of individual amino acids or at the level of nucleotides. However, it could not be directly said that the use of every codons differed significantly between any two functional categories. Notably, there existed large difference both in selection for biased codons or selection intensity among functional categories. Therefore, we identified at least two classes of genes: one group of genes, mainly belonging to the "METABOLISM" category, was tended to use G- and/or C-ending codons while the other was more biased to choose codons ending with A and/or U. The latter group contained genes of various functions, especially those genes classified into the "Nuclear Structure" category. These observations will be more important for molecular genetic engineering and genome functional annotation.

Chromosome Mapping↗

PubMed1972

Organization of gene function in Bacillus subtilis bacteriophage SP82G.

A generalized assessment of the functions of 26 genes of SP82G, a bacteriophage of Bacillus subtilis, has been made. The production of phage-specific deoxyribonucleic acid (DNA), DNA-filled phage heads, completed phage particles, phage-specific antigen, and developmental aberrations has been examined in lysates of temperature-sensitive mutants grown under selective conditions. The genes show a tendency to occur on the genome in three groups of related function: genes involved with DNA synthesis, with tail synthesis, and with head synthesis.

Antigens, Viral↗

PubMed2003

From gene networks to gene function.

We propose a novel method to identify functionally related genes based on comparisons of neighborhoods in gene networks. This method does not rely on gene sequence or protein structure homologies, and it can be applied to any organism and a wide variety of experimental data sets. The character of the predicted gene relationships depends on the underlying networks;they concern biological processes rather than the molecular function. We used the method to analyze gene networks derived from genome-wide chromatin immunoprecipitation experiments, a large-scale gene deletion study, and from the genomic positions of consensus binding sites for transcription factors of the yeast Saccharomyces cerevisiae. We identified 816 functional relationships between 159 genes and show that these relationships correspond to protein-protein interactions, co-occurrence in the same protein complexes, and/or co-occurrence in abstracts of scientific articles. Our results suggest functions for seven previously uncharacterized yeast genes: KIN3 and YMR269W may be involved in biological processes related to cell growth and/or maintenance, whereas IES6, YEL008W, YEL033W, YHL029C, YMR010W, and YMR031W-A are likely to have metabolic functions.

Computational Biology↗

PubMed1998

Sequence analysis of a variety of primate fertilin alpha genes: evidence for non-functional genes in the gorilla and man.

The sperm surface fertilin complex was first described in the guinea pig where it was found as a heterodimer of alpha and beta subunits, both of which were proposed to play a role in sperm-oolemma recognition and plasma membrane fusion during fertilisation. Whilst the beta subunit is apparently testis-specific, the finding of low levels of fertilin alpha in nonreproductive tissues has cast some doubt on a unique role in fertilisation. Moreover, the absence of a functional fertilin alpha gene in the human would imply that this gene product is not absolutely essential for fertilisation, although it could play a facilitatory role. We now describe the organisation and sequence of the fertilin alpha genes in a range of primates, including the great apes, and find that the gorilla gene, like that of the human, is non-functional.

ADAM Proteins↗

PubMedDate not supplied

Using RNAi to investigate orthologous homeotic gene function during development of distantly related insects.

Gene product distribution is often used to infer developmental similarities and differences in animals with evolutionarily diverse body plans. However, to address commonalties of developmental mechanisms, what is really needed is a method to assess and compare gene function in divergent organisms. This requires mutations eliminating gene function. Such mutations are often difficult to obtain, even in organisms amenable to genetic analysis. To address this issue we have investigated the use of double-stranded RNA interference to phenocopy null mutations. We show that RNA interference can be used to phenocopy mutations of the Deformed orthologues in Drosophila and Tribolium. We discuss the possible use of this technique for comparisons of developmental mechanisms in organisms with differing ontogenies.

Animals↗

PubMed2005

Design of long oligonucleotide probes for functional gene detection in a microbial community.

MOTIVATION: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes. RESULTS: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set. AVAILABILITY: http://brcapp.kribb.re.kr/HPD/

Algorithms↗

PubMed1995

Isolation and characterization of the functional gene encoding bovine cytochrome c oxidase subunit IV.

The structure and expression of the gene (COX4) encoding bovine cytochrome c oxidase subunit IV (COX IV) was studied in order to identify conserved DNA sequence elements involved in the control of mammalian nuclear respiratory genes. The functional bovine COX4 gene consists of five exons and four introns and is similar in organization to rat and mouse COX4. The domain encoded by exon 3 is the most highly conserved among the three species, suggesting it may encode a key functional domain of COX IV. Transcription of bovine COX4 begins at multiple sites, as has been seen previously for rat and mouse COX4 and other TATA-less genes. Comparative analysis of bovine, rat and mouse COX4 promoters identified multiple binding sites for the regulatory proteins Sp1 and GABP (NRF-2). The varied arrangements of multiple Sp1 and GABP sites in mammalian COX4 promoters suggests flexibility in the positioning of regulatory factors in controlling COX4 expression.

Amino Acid Sequence↗

PubMed2000

Use of large-scale expression cloning screens in the Xenopus laevis tadpole to identify gene function.

We have conducted an expression cloning screen of approximately 50, 000 cDNAs from a tadpole stage Xenopus laevis cDNA library to functionally identify genes affecting a wide range of cellular and developmental processes. Fifty-seven cDNAs were isolated for their ability to alter gross tadpole morphology or the expression patterns of tissue-specific markers. Thirty-seven of the cDNAs have not been previously described for Xenopus, and 15 of these show little or no similarity to sequences in the NCBI database. The screen and the identified genes are presented in this paper to demonstrate the power, ease, speed, and flexibility of expression cloning in the X. laevis embryo. Future screens such as this one can be done on a larger scale and will complement the sequence-based screens and genome-sequencing projects which are producing a large body of novel genes without ascribed functions.

Animals↗

PubMed2001

Ancestral MADS box genes in Sugi, Cryptomeria japonica D. Don (Taxodiaceae), homologous to the B function genes in angiosperms.

In flowering plants, flower organ identity is controlled by the ABC genes, including several MADS box genes. We present two MADS box genes of a conifer, Cryptomeria japonica D. Don. The genes, CjMADS1 and CjMADS2, were related to the angiosperm B function genes which determine the identities of petals and stamens. A phylogenetic analysis showed that these genes form a new clade outside the angiosperm B group, that is, PISTILLATA (PI) and APETALA3 (AP3) lineages. CjMADS1 had a PI-group specific motif and CjMADS2 had AP3-group specific motifs at the C terminal end, respectively. CjMADS1 was expressed in male strobili (or cones) throughout its development, while CjMADS2 was transiently expressed during male strobilus development. The specific expression in the male reproductive organ indicated that the B function is maintained in gymnosperms. Our cladistic analysis suggests that the gene duplication event which generated B function gene lineages predates the divergence of angiosperms and gymnosperms and that the gene duplication which produced the two genes of C. japonica occurred in an ancestral conifer species.

Amino Acid Sequence↗

PubMed1998

Mouse mutagenesis-systematic studies of mammalian gene function.

The mouse will play a pivotal role in mammalian gene function studies as we enter the post-genomics era. The challenge is to develop systematic, genome-wide mutagenesis approaches to the study of gene function. The current mouse mutant resource has been an important source of human genetic disease models. However, despite an apparently large catalogue of mouse mutations, we have access to mutations at only a small fraction of the likely total number of mammalian genes-there is a phenotype gap that needs to be filled by the establishment of new mutagenesis programmes. Two routes, genotype- and phenotype-driven, can be used for the recovery of novel mouse mutations. For the former, gene trap embryonic stem cell libraries appear set to deliver a large number of mutations around the mouse genome. The advantage of genotype-driven approaches is the ease of identification of the mutated locus; the disadvantage that a priori assumptions have to be made concerning the function and likely phenotype of the mutated gene. In contrast, phenotype-driven mutagenesis emphasizes the recovery of novel phenotypes. One phenotype-driven approach that will play an important role in expanding the mouse mutant resource employs the mutagen N-ethyl-N-nitrosourea (ENU). The phenotype-driven route makes no assumptions about the underlying genes involved, and ENU mutagenesis programmes can be expected to play a significant role in uncovering novel pathways and genes; the disadvantage is that the identification of the mutant gene is still not trivial. Together, the complementary routes of genotype- and phenotype-driven mutagenesis will provide a much enlarged catalogue of mouse mutations and phenotypes for future gene function studies.

Animals↗

PubMed2002

Specific interference with gene expression and gene function mediated by long dsRNA in neural cells.

Double-stranded (ds) RNA-induced sequence-specific interference with gene expression, RNA interference (RNAi), has been extensively used in invertebrates, allowing for efficient and high-throughput gene silencing and gene function analysis. In vertebrates, however, use of RNAi to study gene function has been limited due to non-specific effects induced by double-stranded RNA (dsRNA)-dependent protein kinase and interferon activation. dsRNA-induced specific inhibition of vertebrate gene expression has only been shown in embryonic and non-differentiated mammalian cells. In this report, we demonstrate dsRNA-induced specific interference of gene expression and gene function in partially as well as fully differentiated mouse neuroblastoma cells. Specific silencing was observed in the expression of an integrated transgene coding for green fluorescent protein and a variety of endogenous genes. Moreover, we show that RNAi-mediated inhibition of poly (ADP-ribose) polymerase (PARP) expression induced cellular resistance to oxygen-glucose deprivation, consistent with the role of PARP in ischemia-induced brain damage. Our results indicate that RNAi can be used as a powerful tool to study gene function in neural cells.

Animals↗

PubMed2004

Predicting gene function through systematic analysis and quality assessment of high-throughput data.

MOTIVATION: Determining gene function is an important challenge arising from the availability of whole genome sequences. Until recently, approaches based on sequence homology were the only high-throughput method for predicting gene function. Use of high-throughput generated experimental data sets for determining gene function has been limited for several reasons. RESULTS: Here a new approach is presented for integration of high-throughput data sets, leading to prediction of function based on relationships supported by multiple types and sources of data. This is achieved with a database containing 125 different high-throughput data sets describing phenotypes, cellular localizations, protein interactions and mRNA expression levels from Saccharomyces cerevisiae, using a bit-vector representation and information content-based ranking. The approach takes characteristic and qualitative differences between the data sets into account, is highly flexible, efficient and scalable. Database queries result in predictions for 543 uncharacterized genes, based on multiple functional relationships each supported by at least three types of experimental data. Some of these are experimentally verified, further demonstrating their reliability. The results also generate insights into the relative merits of different data types and provide a coherent framework for functional genomic datamining. AVAILABILITY: Free availability over the Internet. CONTACT: f.c.p.holstege@med.uu.nl SUPPLEMENTARY INFORMATION: http://www.genomics.med.uu.nl/pub/pk/comb_gen_network.

Computer Simulation↗