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At least 163 records · Page 9Linked to original sources

Genomic exclusion: a rapid means for inducing homozygous diploid lines in Tetrahymena pyriformis, syngen 1.

Genomic exclusion is an abnormal form of conjugation occurring between cells with defective micronuclei and normal cells with diploid micronuclei. The progeny are heterocaryons; each cell has an old macronucleus but a new diploid micronucleus derived from one meiotic product of the normal mate. Such cells express genes found in the old macronucleus, are sexually mature, and can be specifically selected. When inbred, they give rise to lines genetically homozygous at all known loci.

Genes↗

Conservative genome size and rapid chromosomal evolution in the South American tuco-tucos (Rodentia: Ctenomyidae).

Genome size (the amount of DNA per cell) was measured by flow-cytometric analysis in seven species of a chromosomally variable rodent genus: Ctenomys boliviensis, C. conoveri, C. frater, C. leucodon, C. lewisi, C. opimus, and C. steinbachi. The mean genome size of these species was 7.19 pg DNA and little inter- and intra-specific variation was observed. Genome size was not correlated with diploid number, suggesting that chromosomal evolution at this level is independent of total DNA content. A hypothetical taxonomic unit optimization procedure was carried out using genome size change on a Wagner tree derived from allozyme data. Allozyme evolution and genome size change are linked by a weak, but significant, negative correlation suggestive of preferential genic evolution in the absence of genome size evolution.

Animals↗

Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors.

Recent evidence indicates that many more genes than the currently known oncogenes may undergo amplification in tumors. We have developed a new technique, Comparative Genomic Hybridization (CGH), which allows rapid detection of DNA amplification anywhere in the tumor genome and maps the amplified sequences on normal chromosomes. CGH is based on a competitive in situ hybridization of differentially labeled tumor DNA and normal DNA to a normal human metaphase spread. Regions of gain of DNA sequences are seen as an increased color ratio of two fluorochromes used to detect the labeled DNAs. Over 20 different regions of amplification have been identified using CGH.

Chromosome Mapping↗

Arsenical resistance genes in Saccharomyces douglasii and other yeast species undergo rapid evolution involving genomic rearrangements and duplications.

We have isolated and characterized three adjacent Saccharomyces douglasii genes that share remarkable structural homology (97% amino acid sequence identity) with Saccharomyces cerevisiae ARR1 (ACR1), ARR2 (ACR2) and ARR3 (ACR3) genes involved in arsenical resistance. The ARR2 and ARR3 genes encoding the cytoplasmic arsenate reductase and the plasma membrane arsenite transporter are functionally interchangeable in both yeast species. In contrast, a single copy of S. douglasii ARR1 gene is not sufficient to complement the arsenic hypersensitivity of a S. cerevisiae mutant lacking the transcriptional activator Arr1p. This inability may be related to a deletion of a 35-bp sequence including the putative Yap-binding element in the ARR1 promoter of S. douglasii. Different mechanisms of regulation of ARR1 genes expression may therefore explain the increased tolerance of S. douglasii to arsenic in comparison with S. cerevisiae. The apparent duplication of the ARR gene cluster in the S. douglasii genome may constitute another factor contributing to the observed differences in arsenic sensitivity. Comparison of ARR genes from the genomes of several yeast species indicates that they are located in subtelomeric regions undergoing rapid evolution involving large-scale genomic rearrangements.

Amino Acid Sequence↗

Rapid accumulation of genome rearrangements in liver but not in brain of old mice.

Somatic mutations have long been considered a possible cause of ageing. To directly study mutational events in organs and tissues of ageing mammals, a transgenic mouse model has been generated that harbours lacZ reporter genes as part of chromosomally integrated plasmids. Using this model, we determined spontaneous mutant frequencies and spectra in mouse liver and brain as a function of age. In the liver, mutant frequencies increased with age from birth to 34 months; in the brain, an increase was observed only between birth and 4-6 months. Molecular characterization of the mutations showed that a substantial portion involved genome rearrangement events, with one breakpoint in a reporter gene and the other in the mouse flanking sequence. In the liver, these genome rearrangements did not increase with age until after 27 months, when they increased rapidly. In brain, the frequency of genome rearrangements was lower than in liver and did not increase with age.

Aging↗

A rapid, small scale method for characterization of plasmid insertions in the Dictyostelium genome.

A rapid, simple method for characterization of plasmid insertions in the Dictyostelium discoideum genome was developed. It is based on the capability of linear plasmid multimers in the insertions to recircularize efficiently in Escherichia coli cells. This recombinational recircularization of plasmid multimers provides a highly sensitive and reliable tool for determining whether individual Dictyostelium transformants resulted from restriction enzyme-mediated integration (REMI) or from recombinational integration of plasmid (RIP). The method also reveals any rearrangements in RIP insertions and provides an estimate of the vector copy number in any particular transformant.

Animals↗

Rapid non-genomic inhibition of ATP-induced Cl- secretion by dexamethasone in human bronchial epithelium.

A non-genomic antisecretory role for dexamethasone at low concentrations (0.1 nM to1 microM) is described in monolayers of human bronchial epithelial cells in primary culture and in a continuous cell line (16HBE14o- cells). Dexamethasone produced a rapid decrease of [Ca(2+)](i) (measured with fura-2 spectrofluorescence) to a new steady-state concentration. After 15 min exposure to dexamethasone (1 nM), [Ca(2+)](i) was reduced by 32 +/- 11 nM (n = 7, P < 0.0001) from a basal value of 213 +/- 36 nM (n = 7). We have shown previously that aldosterone (1 nM) also produces a rapid fall in [Ca(2+)](i); however, after the decrease in [Ca(2+)](i) induced by dexamethasone, subsequent addition of aldosterone did not produced any further lowering of [Ca(2+)](i). The rapid response to dexamethasone was insensitive to pretreatment with cycloheximide and unaffected by the glucocorticoid type II and mineralocorticoid receptor antagonists RU486 and spironolactone, respectively. The rapid [Ca(2+)](i) decrease induced by dexamethasone was inhibited by the Ca(2+)-ATPase pump inhibitor thapsigargin (1 microM), the adenylate cyclase inhibitor MDL hydrochloride (500 microM) and the protein kinase A inhibitor Rp-adenosine 3',5'-cyclic monophosphorothioate (200 microM), but was not affected by the protein kinase C inhibitor, chelerythrine chloride (0.1 microM). Treatment of 16HBE14o- cell monolayers with dexamethasone (1 nM) inhibited the large and transient [Ca(2+)](i) increase induced by apical exposure to ATP (10(-4) M). Dexamethasone (1 nM) also reduced by 30 % the Ca(2+)-dependant Cl(-) secretion induced by apical exposure to ATP (measured as the Cl(-)-sensitive short-circuit current across monolayers mounted in Ussing chambers). Our results demonstrate, for the first time, that dexamethasone at low concentrations inhibits Cl(-) secretion in human bronchial epithelial cells. The rapid inhibition of Cl(-) secretion induced by the synthetic glucocorticoid is associated with a rapid decrease in [Ca(2+)](i) via a non-genomic mechanism that does not involve the classical glucocorticoid or mineralocorticoid receptor. Rather, it is a result of rapid non-genomic stimulation of thapsigargin-sensitive Ca(2+)-ATPase, via adenylate cyclase and protein kinase A signalling.

Adenosine Triphosphate↗

Estrogen receptor independent rapid non-genomic effects of environmental estrogens on [Ca2+]i in human breast cancer cells.

The aim of this study was to identify and characterize an alternative pathway through which environmental estrogenic compounds may mediate their intracellular effects. Three human breast cancer cell lines were employed including MCF-7 cells, which express both ERalpha and ERbeta; MDA-MB-231 cells, which express ERbeta but not ERalpha; and SKBR-3 cells, which express neither ERalpha nor ERbeta. The effect of environmental estrogenic compounds on intracellular calcium ion concentration ([Ca(2+)](i)) was measured and compared to that of 17beta-estradiol (E2). A rapid and maintained increase in [Ca(2+)](i) was observed following the application of nanomolar concentrations of environmental estrogens and E2 regardless of the expression of ERalpha and ERbeta. Removal of extracellular Ca(2+) completely abolished the steroid-induced [Ca(2+)](i) increase. Pre-treatment of cells with the estrogen receptor (ER) antagonist ICI 182,780 had no effect on either basal [Ca(2+)](i) or the steroid-triggered [Ca(2+)](i) response. In summary, we have demonstrated ER independent rapid non-genomic effects of environmental estrogenic compounds, at nanomolar concentrations, on [Ca(2+)](i). The results of this study demonstrate an alternative pathway to explain potent intracellular effects of endocrine disrupting chemicals.

Breast Neoplasms↗

Toxoplasma gondii: a rapid method for the isolation of pure tachyzoites. Preliminary characterization of its genome.

A rapid and simple technique for the purification of Toxoplasma gondii tachyzoites was developed. Highly purified parasites were obtained from the peritoneal exudates of infected mice by means of two consecutive discontinuous sucrose gradients run at low speed (10,000xg, 30 min). Parasites obtained by this method conserved its biological activity. Hybridization studies with DNA from healthy mice and from purified tachyzoites preparations demonstrated that Toxoplasma gondii tachyzoites DNA could be obtained with better than 90% purity. Preliminary studies with DNA endonucleases showed the presence in the tachyzoites genome of highly repetitive sequences.

Animals↗

Pyrimidine dimer induction and removal in the epidermis of hairless mice: inefficient repair in the genome overall and rapid repair in the H-ras sequence.

Excision repair of pyrimidine dimers was examined at the genome overall in three strains of hairless (hr/hr) and congenic wild-type mice, as well as in the expressed H-ras gene in hairless mice. The assay used a pyrimidine dimer-specific endonuclease from Micrococcus luteus and alkaline agarose gel electrophoresis. From 0 to 25% of endonuclease-sensitive sites were removed at the genome level in either hairy or hairless mice but about 50% were removed in the H-ras gene in hairless mice by 24 h after exposure to 5.4 J/cm2 UV (290-400 nm) irradiation. No differences were observed in the repair capacity between hairy and hairless mice, thus eliminating defective DNA repair as the explanation for the greater susceptibility to UV carcinogenesis in hairless mice.

Animals↗

Rapid isolation of genomic DNA from animal tissues.

A simple technique for the isolation of very high molecular weight genomic DNA from animal tissues and cells is described. The method involves rapid isolation of nuclei and their embedding in agarose beads followed by extraction of lipids and proteins with SDS. The protocol does not require proteolytic digestion and the whole procedure can be completed in 1 day. The isolated DNA is digestible by restriction enzymes and free of ligase inhibitors.

Animals↗

Rapid non-genomic and genomic responses to progestogens, estrogens, and glucocorticoids in the endocrine pancreatic B cell, the adipocyte and other cell types.

Rapid biologic responses to injected steroids were described as early as 60 years ago. More recently, evidence has been presented that 17beta-estradiol given i.v. will double the uterine cAMP activity within 15 s (Proc Natl Acad Sci USA 1967;58:1711-8), and also that estrogens will bind to the outer surfaces of endometrial cells (Nature 1977;265:69-72), suggesting that these steroids can both engage and direct intracellular events. Unfortunately, studies of such rapid membrane effects of steroids have languished due to the accumulation of compelling data for the more slowly manifest actions of these compounds at the level of nuclear DNA. We report a number of observations in women, in experimental animals, and in isolated organ or cell systems using 17beta-estradiol, progesterone or glucocorticoids which provide ample evidence for rapid intracellular metabolic responses to these steroids, mediated by their actions at the cellular plasma membrane. Such rapid responses have been shown in various classic targets or not, such as the B cell of the endocrine pancreas and the fat cell. They involve plasma membrane binding, changes in membrane electrical activity, Ca2+ handling, G and Ras proteins, cAMP, cGMP, IP(3), DAG, phosphodiesterases, protein kinases, tyrosine kinases, ER kinases, and mitogen activated protein kinases (MAPks) and nitric oxide synthase. These recent findings are discussed in detail and should lead to a fuller understanding of the cellular effects of the steroid hormones.

Adipocytes↗

Rapid isolation of genomic clones for individual members of human multigene families: identification and localisation of UBE2L4, a novel member of a ubiquitin conjugating enzyme dispersed gene family.

We describe a rapid, PCR-based, screening procedure for the isolation of human genomic clones in lambda bacteriophage, containing sequences coding for individual homologous members of a multigene family. The approach is based upon the identification, by dilution, of sub-pools of the genomic library that contain members of the gene family, prior to phage isolation. The presence of specific genes is established by PCR of aliquots of individually amplified library pools, using consensus primers and subsequent sequencing. We have used the approach to isolate a fourth member of the UBE2L gene family, UBE2L4, and located it on chromosome 19q13.1-->q13.2. This PCR-based approach to library screening has wider applicability in that it could be used to isolate alternate-spliced products from cDNA libraries.

Bacteriophage lambda↗

Restriction endonuclease analysis of the genome of Campylobacter pylori with a rapid extraction method: evidence for considerable genomic variation.

We developed a rapid extraction method to analyze the chromosomal DNA of 84 isolates of Campylobacter pylori (formerly Campylobacter pyloridis) from 70 individuals. Only three of the nine endonucleases tested gave satisfactory digestions: HindIII, EcoRI, and SacI. The latter two produced mostly larger bands, whereas HindIII produced smaller bands, which allowed clearer comparisons between isolates. The isolates from 69 Australian subjects and one from England each had a unique profile. Isolates from a husband and wife were different, as were those from a brother and sister. In pairs of isolates from 11 individuals, the second isolate was markedly different in six subjects. The profile changes were not associated with changes in antibiotic susceptibility or with loss of catalase or urease activity, which can occur during storage of C. pylori. These restriction endonuclease profiles suggest considerable subspecies variation in C. pylori. Plasmid bands were found in undigested DNA from 40 of the 84 C. pylori isolates.

Campylobacter↗

Rapid non-genomic vasodilator actions of oestrogens and sex steroids.

There is now convincing experimental evidence documenting acute and transient actions of steroid hormones in the vasculature. Steroids can rapidly activate signalling cascades within endothelial and smooth muscle cells that seem to bypass the classical, genomic receptor. Activation of these signalling cascades, involving alterations in intracellular Ca2+ and MAPK activity, leads to changes in membrane potential and/or Ca2+ fluxes through L-type channels. In addition to stimulating NO production acutely in endothelial cells, chronic exposure to 17beta-oestradiol may activate expression of eNOS via a genomic receptor(s).

Animals↗

Systematic use of automated fluorescence-based sequence analysis of amplified genomic DNA for rapid detection of point mutations.

Several approaches are now available for screening populations for known mutations in a given gene. However, for detection of multiple mutations in a population that has not been characterized or for detection of new mutations, the value and efficiency of these screening procedures decreases. Although more than 100 different beta-thalassemia mutations have so far been described, the spectrum of mutations in the Eastern Mediterranean and Israel has not been defined in detail. We have used automated fluorescence-based DNA sequence analysis of PCR-amplified genomic DNA employing a cycle-sequencing strategy coupled with advanced analysis software to rapidly detect beta-thalassemia mutations in Israeli patients. This method enabled rapid identification of eight different mutations in 10 patients, including two rare mutations, one of which has never been described in this geographic region. Our results show that automated fluorescence-based DNA sequence analysis of amplified genomic DNA is a rapid and reliable method for detection of point mutations and small deletions or insertions in both heterozygous and homozygous states. This approach is particularly effective for a relatively small gene such as beta-globin, but it can also be used for rapid detection of mutations in large genes by first sequencing clusters of exons and intron/exon borders.

Automation↗

Rapid evolution of genomic Acp complement in the melanogaster subgroup of Drosophila.

Unusual properties of molecular evolution in reproduction-related Drosophila genes, including atypically rapid rates of protein evolution, support the idea that natural selection plays an important role in divergence of reproductive function in Drosophila. We used subtractive hybridization to investigate another potential side of evolution of the male reproductive transcriptome. We carried out a screen for genes with much greater transcript abundance in Drosophila simulans reproductive tracts than in Drosophila melanogaster reproductive tracts. Such genes could be present in both species but diverged dramatically in transcript abundance or could be present in D. simulans but absent from D. melanogaster. Here we report data from melanogaster subgroup species for three previously unknown accessory gland protein genes (Acps) identified in this screen. We found multiple Acps that were present in some lineages yet absent from other closely related melanogaster subgroup lineages, representing several losses of genes. An Acp that may have been lost in D. melanogaster and Drosophila erecta is segregating a null allele in Drosophila yakuba, yet shows evidence of adaptive protein evolution in contrasts of polymorphism and divergence within and between D. yakuba and its close relative, Drosophila teissieri. These data suggest that turnover of Acps occurs rapidly in Drosophila, consistent with rapid evolution of seminal fluid function.

Amino Acid Sequence↗