Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “functional genetics”

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 829 records · Page 46Linked to original sources
PubMed2001

Polymorphisms in the ABC drug transporter gene MDR1.

In addition to genetically variable metabolic enzymes such as Cyp p450 proteins, blood and tissue levels of many drugs are influenced by controlled transport across compartmental boundaries. Major determinants in these transport processes are ATP-dependent efflux pumps such as P-glycoprotein and related proteins (eg MRPs), which can influence the bioavailability and CNS concentrations, as well as disposition of drugs. In addition to its recognized role in the development of multiple chemotherapy resistances, experimental evidence for the relevant influence of the MDR1 gene encoded P-glycoprotein, on the pharmacology of many other drugs has been gathered by the analyses of knockout mice, as well as in clinical studies. Recently, functional genetic polymorphisms in the MDR1 gene have been identified which influence the distribution and bioavailability of PGP substrates.

Animals↗
PubMed2004

DVL, a novel class of small polypeptides: overexpression alters Arabidopsis development.

Small polypeptides can act as important regulatory molecules that coordinate cellular responses required for differentiation, growth, and development. In a gain-of-function genetic screen for genes that influence fruit development in Arabidopsis, we identified a novel gene -DEVIL1 (DVL1) - encoding a small protein. Overexpression of DVL1 results in pleiotropic phenotypes featured by shortened stature, rounder rosette leaves, clustered inflorescences, shortened pedicles, and siliques with pronged tips. cDNA analysis indicates that DVL1 has a 153-nucleotide (nt) open-reading frame (ORF) encoding a 51-amino acid polypeptide that shares no significant similarity to previously identified proteins. Sequence alignment shows that DVL1 belongs to a family of related genes that are limited to angiosperm plants. Ectopic overexpression of each of the five closely related Arabidopsis DVL genes causes similar phenotypic changes, suggesting overlapping function in the DVL gene family. Point mutations of conserved amino acids in the C-terminal region of the DVL1 polypeptide reveal that these conserved residues are required for DVL1-overexpression phenotypes. Our results show that the DVL family is a novel class of small polypeptides and the overexpression phenotypes suggest that these polypeptides may have a role in plant development.

Amino Acid Sequence↗
PubMed2006

Three major haplotypes of the beta2 adrenergic receptor define psychological profile, blood pressure, and the risk for development of a common musculoskeletal pain disorder.

Adrenergic receptor beta(2) (ADRB2) is a primary target for epinephrine. It plays a critical role in mediating physiological and psychological responses to environmental stressors. Thus, functional genetic variants of ADRB2 will be associated with a complex array of psychological and physiological phenotypes. These genetic variants should also interact with environmental factors such as physical or emotional stress to produce a phenotype vulnerable to pathological states. In this study, we determined whether common genetic variants of ADRB2 contribute to the development of a common chronic pain condition that is associated with increased levels of psychological distress and low blood pressure, factors which are strongly influenced by the adrenergic system. We genotyped 202 female subjects and examined the relationships between three major ADRB2 haplotypes and psychological factors, resting blood pressure, and the risk of developing a chronic musculoskeletal pain condition-Temporomandibular Joint Disorder (TMD). We propose that the first haplotype codes for lower levels of ADRB2 expression, the second haplotype codes for higher ADRB2 expression, and the third haplotype codes for higher receptor expression and rapid agonist-induced internalization. Individuals who carried one haplotype coding for high and one coding for low ADRB2 expression displayed the highest positive psychological traits, had higher levels of resting arterial pressure, and were about 10 times less likely to develop TMD. Thus, our data suggest that either positive or negative imbalances in ADRB2 function increase the vulnerability to chronic pain conditions such as TMD through different etiological pathways that imply the need for tailored treatment options.

Adolescent↗
PubMed2004

Small interfering RNA production by enzymatic engineering of DNA (SPEED).

Small interfering RNAs (siRNAs) potently silence expression of target genes. In principle siRNA libraries can be used to perform effective genome-scale functional genetic screens in mammalian cells, but their development has been hampered by the need to chemically synthesize thousands of oligonucleotides and to incorporate them into expression vectors. We have developed a technology to efficiently convert a double-stranded cDNA library into a retroviral siRNA library in which 21-base siRNAs are produced in infected cells at high levels and efficiently block expression of their target genes. The key steps are the generation of random cDNA fragments that are fused to a hairpin linker, cleavage with the MmeI endonuclease that creates 20- to 21-bp cDNA fragments, conversion to a double-stranded DNA that contains two copies of the cDNA insert in a head-to-head palindrome, and insertion of the construct downstream of a polymerase III promoter. We constructed a siRNA library with 3 x 10(6) clones from a mouse embryo cDNA library; siRNAs were found against many different genes; and multiple siRNAs can be generated from a single mRNA. We further showed that specific siRNAs were efficiently produced in stably infected mammalian cells and resulted in significant and specific reduction of their target mRNAs. Because no prior knowledge about target transcripts is needed, a cDNA-derived siRNA library will generate siRNAs against unknown transcripts and genes. Finally, cDNA-derived siRNA libraries can be readily generated from any cell type or species, enabling genome-wide functional screens in many biological systems.

Animals↗
PubMed2025

Genetic mapping in the red mason bee implicates ANTSR as an ancient sex-determining locus in bees and ants.

Haplodiploid inheritance, in which females are diploid and males are haploid, is found in all species of Hymenoptera. Sex in haplodiploids is commonly determined by the alleles present at a complementary sex determination (CSD) locus, with heterozygosity triggering the female developmental pathway. The identity of this locus differs among taxa and is only known in a few species. Here, we map a single CSD locus to a 2 kbp region in the genome of the red mason bee Osmia bicornis. It overlaps the long noncoding RNA ANTSR, which has been identified as the sex-determining gene in the invasive ant Linepithema humile. This locus is homozygous in diploid males and exhibits extremely high levels of haplotype diversity, consistent with the action of frequency-dependent selection. The elevated levels of heterozygosity in the CSD locus enable us to fine-map potentially functional genetic variation within it. We also identify elevated levels of genetic diversity in the ortholog of the CSD locus in five other bee and ant genera, suggesting that it may govern sex determination widely in Hymenoptera. Our data are consistent with the hypothesis that ANTSR evolved a role in sex determination over 150 million years ago and is the ancestral sex-determination locus of bees and ants.

Animals↗
PubMed2004

[Morphochemical analysis of hippocampus of rats predisposed (August) or resistant (Wistar) to emotional stress].

The aim of this work was the comparative cytochemical study of some parameters of neurotransmitter and protein metabolism in the hippocampus (CA3 field) of August and Wistar rats, which were used as genetic-functional models demonstrating different brain organization, in particular, in respect to an emotional stress. Using quantitative cytochemical methods it was demonstrated that the activities of aminopeptidase, monoaminooxidase (substrates--tryptamine and serotonin), and glutamate dehydrogenase, were lower in the hippocampus of August rats (predisposed to emotional stress) as compared to that one in Wistar rats (resistant to emotional stress). August rats were also characterized by smaller sizes of neuronal cytoplasm and nuclei and by their lower protein content and concentration. The analysis of the data obtained has shown the existence of neurons with different modalities within the limits of CA3 hippocampal field, and these characteristics are thought to define the morphochemical differences in the hippocampus (CA3 field) of genetically different rats.

Aminopeptidases↗
PubMed2002

Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast.

Maturation of the large subunit rRNAs includes a series of cleavages that result in removal of the internal transcribed spacer (ITS2) that separates mature 5.8S and 25/28S rRNAs. Previous work demonstrated that formation of higher order secondary structure within the assembling pre-ribosomal particle is a prerequisite for accurate and efficient pre-rRNA processing. To date, it is not clear which specific sequences or secondary structures are required for processing. Two alternative secondary structure models exist for Saccharomyces cerevisiae ITS2. Chemical and enzymatic structure probing and phylogenetic comparisons resulted in one structure (Yeh & Lee, J Mol Biol, 1990, 211:699-712) referred to here as the "hairpin model." More recently, an alternate folded structure was proposed (Joseph et al., Nucleic Acids Res, 1999, 27:4533-4540), called here the "ring model." We have used a functional genetic assay to examine the potential significance of these predicted structures in processing. Our data indicate that elements of both structural models are important in efficient processing. Mutations that prevent formation of ring-specific structures completely blocked production of mature 25S rRNA, whereas those that primarily disrupt hairpin elements resulted in reduced levels of mature product. Based on these results, we propose a dynamic conformational model for the role of ITS2 in processing: Initial formation of the ring structure may be required for essential, early events in processing complex assembly and may be followed by an induced transition to the hairpin structure that facilitates subsequent processing events. In this model, yeast ITS2 elements may provide in cis certain of the functions proposed for vertebrate U8 snoRNA acting in trans.

Base Sequence↗
PubMed2003

Use of Sindbis virus-mediated RNA interference to demonstrate a conserved role of Broad-Complex in insect metamorphosis.

The transcription factor Broad-Complex (BR-C) is required for differentiation of adult structures as well as for the programmed death of obsolete larval organs during metamorphosis of the fruit fly Drosophila melanogaster. Whether BR-C has a similar role in other holometabolous insects could not be proven without a loss-of-function genetic test, performed in a non-drosophilid species. Here we use a recombinant Sindbis virus as a tool to silence BR-C expression in the silkmoth Bombyx mori. The virus expressing a BR-C antisense RNA fragment reduced endogenous BR-C mRNA levels in infected tissues (adult wing and leg primordia) via RNA interference (RNAi). The RNAi knock-down of BR-C resulted in the failure of animals to complete the larval-pupal transition or in later morphogenetic defects, including differentiation of adult compound eyes, legs, and wings from their larval progenitors. BR-C RNAi also perturbed the programmed cell death of larval silk glands. These developmental defects correspond to loss-of-function phenotypes of BR-C Drosophila mutants in both the morphogenetic and degenerative aspects, suggesting that the critical role of BR-C in metamorphosis is evolutionarily conserved. We also demonstrate that the Sindbis virus is a useful vehicle for silencing of developmental genes in new insect models.

Animals↗
PubMed2006

Postgenomic bioinformatic analysis of yeast artificial chromosome sequence.

The free availability of multiple genomic sequences represents one of the greatest advances in biology of the new millennium, and promises to revolutionize our ability to determine and treat the causes of human disease. This chapter highlights a number of basic, freely available, and user-friendly bioinformatic techniques that can be used to predict the functional genetic contents of specific yeast artificial chromosome (YAC) clones. The content of this chapter is written for the level of graduate students, who may be relatively inexperienced with the use of computers for analyzing DNA sequences. The basic instructions that allow the identification of the genomic sequence of interest and to download this sequence onto a personal computer from an online database are presented. Simple instructions are also given on how to perform basic sequence manipulations, how to use online tools to design polymerase chain reaction primers, and how to map restriction sites. Also described are more complicated programs that rapidly and efficiently perform genome alignments that, in addition to predicting the location of protein coding sequences, allow the prediction of functional genomic sequences, such as cis regulatory elements and scaffold/matrix attachment sites. The availability of genomic sequences and the rapidly expanding numbers of predictive programs that allow the predictive analysis of these sequences promises to greatly facilitate the use of YAC clones in the search for the causes of disease.

Chromosomes, Artificial, Yeast↗
PubMed1979

Transcription maps of mtDNAs of two strains of saccharomyces: transcription of strain-specific insertions; Complex RNA maturation and splicing.

We have developed a two-dimensional method for simultaneously mapping on the yeast mtDNA genome all the transcripts representing more than 0.01% of mtRNA. In two yeast strains, Saccharomyces carlsbergensis NCYC-74 and Saccharomyces cerevisiae KL14-4A, about 25 discrete transcripts were found apart from tRNAs. The mtDNAs of these strains differ by the absence (NCYC-74) or presence (KL 14-4A) of various large insertions located within genetically active regions. The transcripts can all be related to known loci on the genetic map. In nearly all cases the RNAs are much longer than required to specify the known protein product of the locus concerned. The organization of the transcripts is similar in the two strains except at the positions of the large insertions (500-3300 bp) in the oxi-3 and cob loci. The sequences of these insertions are present in RNA species larger than 25S, but are absent from smaller transcripts of the same regions. This is probably due to splicing, since the coding sequences for most of these smaller transcripts are noncontiguous. The smaller transcripts of other loci also seem to arise from processing of larger RNA species. The oxi-3 locus, containing the structural gene for cytochrome c oxidase subunit l, is transcribed in a very complex fashion that suggests differential splicing into partially overlapping transcripts. This may indicate that oxi-3 has additional genetic functions, including possible control of the biosynthesis of cytochrome c oxidase holoenzyme or its assembly into the mitochondrial inner membrane. As in the case of the eucaryote nucleus, the regulation of mitochondrial gene expression seems to occur more at the level of RNA processing than has been recognized thus far.

Chromosome Mapping↗
PubMed2003

Functional screening of genes suppressing TRAIL-induced apoptosis: distinct inhibitory activities of Bcl-XL and Bcl-2.

TNF-related apoptosis-inducing ligand (TRAIL) is known to selectively induce apoptosis in various tumour cells. However, downstream-signalling of TRAIL-receptor is not well defined. A functional genetic screening was performed to isolate genes interfering with TRAIL-induced apoptosis using cDNA retroviral library. Bcl-X(L) and FLIP were identified after DNA sequencing analysis of cDNA rescued from TRAIL-resistant clones. We found that increased expression of Bcl-X(L), but not Bcl-2, suppressed TRAIL-induced apoptosis in tumour cells. Western blot and immunohistochemical analyses showed that expression of Bcl-X(L), but not Bcl-2, was highly increased in human breast cancer tissues. Exposure of MDA-MB-231 breast tumour cells to TRAIL induced apoptosis accompanied by dissipation of mitochondrial membrane potential and enzymatic activation of caspase-3, -8, and -9. However, SK-BR-3 breast tumour cells exhibiting increased expression level of Bcl-X(L) were resistant to TRAIL, though upon exposure to TRAIL, caspase-8 and Bid were activated. Forced expression of Bcl-X(L), but not Bcl-2, desensitised TRAIL-sensitive MDA-MB-231 cells to TRAIL. Similar inhibitory effects were also observed in other tumour cells such as HeLa and Jurkat cells stably expressing Bcl-X(L), but not Bcl-2. These results are indicative of the crucial and distinct function of Bcl-X(L) and Bcl-2 in the modulation of TRAIL-induced apoptosis.

Antineoplastic Agents↗
PubMed2005

Molecular genetics of adult-type hypolactasia.

Adult-type hypolactasia (lactase non-persistence; primary lactose malabsorption) is characterized by the down-regulation of the lactase enzyme activity in the intestinal wall after weaning. The down-regulation is genetically determined and a mutation has occurred that has made part of mankind tolerate milk (lactase persistence). A DNA-variant, single nucleotide polymorphism C/T-13910 located 13 910 base pairs (bp) upstream of the lactase gene (LCT) at chromosome 2q21-22 has been shown to associate with the lactase persistence/non-persistence trait both in family and case-control studies. The C/T-13910 variant is located in a non-coding region in the genome in intron 13 of the minichromosome maintenance type 6 gene (MCM6). Significant correlation between the C/T-13910-variant and lactase activity in the intestinal biopsy specimens has been demonstrated. Molecular epidemiological studies on the prevalence of the C/C-13910 genotype associated with low lactase activity are in agreement with the prevalence figures for adult type hypolactasia in>70 diverse ethnic groups studied. Recent functional studies have suggested that this variant has an enhancer effect over the lactase gene. Based on the biochemical, functional, genetic and molecular epidemiological studies of the C/T-13910 variant, genetic testing for adult type hypolactasia has been introduced into clinical practice in Finland. Identification of the genetic change has highlighted the role of non-coding variants in the regulation of common genes and created new tools to study the mechanism of lactase enzyme activation.

Adult↗
PubMed1997

High genetic instability of heterochromatin after transposition of the LINE-like I factor in Drosophila melanogaster.

In the present work, we have asked whether a group of 13 essential genes mapping to the heterochromatin of Drosophila melanogaster chromosome 2 are mutable following transposition of the I factor during I-R hybrid dysgenesis. We found that the frequency of lethal events mapping to chromosome 2 heterochromatin is surprisingly high, despite the low density of genetic functions identified in this region compared with euchromatin. Cytogenetic and molecular analyses indicated that the recovered mutations correspond either to insertions or to rearrangements. Moreover, chromosomes bearing specific heterochromatic lethal mutations were generated by recombination in the heterochromatin. Together, these data indicate that I factors transpose with high frequency into pericentric regions of chromosome 2 and may play a role in the evolution of constitutive heterochromatin.

Animals↗
PubMed1984

Isolation and characterization of the RNA2+, RNA4+, and RNA11+ genes of Saccharomyces cerevisiae.

We used genetic complementation to isolate DNA fragments that encode the Saccharomyces cerevisiae genes RNA2+, RNA4+, and RNA11+ and to localize the genes on the cloned DNA fragments. RNA blot-hybridization analyses coupled with genetic analyses indicated the RNA2+ is coded by a 3.0-kilobase (kb) transcript, RNA4+ is coded by a 1.6-kb transcript, and RNA11+ is coded by a 1.3-kb or a 1.7-kb transcript or both; none of the cloned genes contains detectable introns. All three genes were transcribed into messages of very low abundance (approximately 20 times lower than a ribosomal protein message). DNA blot-hybridization revealed that all cloned genes are represented only once in the yeast chromosome. mRNA for RNA2+ and RNA4+ is produced in approximate proportion to gene dosage, whereas RNA11+ transcription appears to be not nearly so dependent on gene dosage. On a medium-copy plasmid (5 to 10 copies per cell), each cloned gene complemented mutations only in its own gene, indicating that each gene encodes a unique function. Genetic analysis by integrative transformation indicated that we cloned the RNA2+, RNA4+, and RNA11+ structural genes and not second-site suppressors.

Base Sequence↗
PubMed2000

National Institute of Mental Health goals for behavioral science.

Because all health conditions for which the National Institute of Mental Health (NIMH) is responsible manifest at the level of behavior, and all interventions must have an impact at the behavioral level, NIMH is firmly committed to the support of behavioral science. In an era in which research in areas that some view as reductionist--for example, genomics, genetics, functional genomics and proteomics, and molecular science--is especially promising, NIMH is striving to maintain a balance in its portfolio with studies that explore integrative aspects of biology, including behavior. Without this perspective, new information about fundamental processes will prove ultimately to be shallow. This commentary discusses how understanding of brain and behavior in mental illness and health calls for integrating bottom-up research that studies brain and behavior through genes and molecules, with top-down research that examines the impact of environment.

Behavioral Sciences↗
PubMed1997

Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins.

Mutations in the Arabidopsis ETHYLENE-INSENSITIVE3 (EIN3) gene severely limit a plant's response to the gaseous hormone ethylene. ein3 mutants show a loss of ethylene-mediated effects including gene expression, the triple response, cell growth inhibition, and accelerated senescence. EIN3 acts downstream of the histidine kinase ethylene receptor, ETR1, and the Raf-like kinase, CTR1. The EIN3 gene encodes a novel nuclear-localized protein that shares sequence similarity, structural features, and genetic function with three EIN3-LIKE (EIL) proteins. In addition to EIN3, EIL1 orEIL2 were able to complement ein3, suggesting their participation in the ethylene signaling pathway. Overexpression of EIN3 or EIL1 in wild-type or ethylene-insensitive2 plants conferred constitutive ethylene phenotypes, indicating their sufficiency for activation of the pathway in the absence of ethylene.

Alleles↗
PubMed1982

Amplification of the uvrA gene product of Escherichia coli to 7% of cellular protein by linkage to the pL promoter of pKC30.

We have constructed a hybrid pKC30-uvrA plasmid (pGHY5003) in which transcription of the uvrA gene can be induced under pL control to amplify the uvrA gene product to 7% of cellular protein. To construct pGHY5003, we developed a genetic selection using the basal level of expression (30 degrees C) from pL in thermosensitive cI857 lysogens to isolate appropriately tailored repair genes inserted at the Hpa I site of pKC30 from recombinant DNA mixtures with a variety of products. In addition, a post-UV-irradiation radiolabeling method was adapted to screen inserts for temperature-inducible polypeptide synthesis directed by transcription under pL control rapidly. This should prove generally useful for isolating genes inserted at the Hpa I site of plasmid pKC30 with the following characteristics: (i) genetically functional hybrid plasmids selected from a large population of exonucleolytically tailored fragments ligated into Hpa I of pKC30 and (ii) production of high-level amplification for the gene product of interest by screening for post-UV-irradiation temperature inducibility of polypeptides synthesized from hybrid plasmids. The level of amplification obtained for the uvrA gene product from pGHY5003 is approximately 10,000-fold higher than estimates of the level of uvrA protein in logarithmic phase Escherichia coli.

Bacterial Proteins↗
PubMed2000

Characterization of Drosophila OVO protein DNA binding specificity using random DNA oligomer selection suggests zinc finger degeneration.

The Drosophila melanogaster ovo locus codes for several tissue- and stage-specific proteins that all possess a common C-terminal array of four C(2)H(2)zinc fingers. Three fingers conform to the motif framework and are evolutionarily conserved; the fourth diverges considerably. The ovo genetic function affects germ cell viability, sex identity and oogenesis, while the overlapping svb function is a key selector for epidermal structures under the control of wnt and EGF receptor signaling. We isolated synthetic DNA oligomers bound by the OVO zinc finger array from a high complexity starting population and derived a statistically significant 9 bp long DNA consensus sequence, which is nearly identical to a consensus derived from several Drosophila genes known or suspected of being regulated by the ovo function in vivo. The DNA consensus recognized by Drosophila OVO protein is atypical for zinc finger proteins in that it does not conform to many of the 'rules' for the interaction of amino acid contact residues and DNA bases. Additionally, our results suggest that only three of the OVO zinc fingers contribute to DNA-binding specificity.

Amino Acid Sequence↗