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At least 955 records · Page 53Linked to original sources
PubMed2006

Plant microsatellite genotyping with 4-color fluorescent detection using multiple-tailed primers.

We extended the concept of fluorescent microsatellite genotyping with a single-universal tailed primer to the simultaneous use of three different tailed primers to allow multiplexed 4-color detection for medium throughput genotyping of plant species. The method was tested on Eucalyptus DNA samples using three forward primer sequences of human microsatellite markers labeled with different fluorescent dyes. The robustness of the method was tested for the simultaneous detection and genetic analysis of microsatellites in a genetic mapping experiment. This method allows reliable and cost-effective genotyping with the same level of multiplexing attained in regular microsatellite fluorescent detection assays. Besides the enhanced quality of the genotypic data provided by the fluorescent detection method when compared to colorimetric ones, the economy brought about by this method becomes greater with an increasing number of microsatellite markers. This method has been particularly useful for genotyping populations of several tropical tree species addressing community-wide population genetics and conservation questions.

DNA Primers↗
PubMed2004

Use of genetic algorithms for neural networks to predict community-acquired pneumonia.

BACKGROUND: Genetic algorithms have been used to solve optimization problems for artificial neural networks (ANN) in several domains. We used genetic algorithms to search for optimal hidden-layer architectures, connectivity, and training parameters for ANN for predicting community-acquired pneumonia among patients with respiratory complaints. METHODS: Feed-forward back-propagation ANN were trained on sociodemographic, symptom, sign, comorbidity, and radiographic outcome data among 1044 patients from the University of Illinois (the training cohort), and were applied to 116 patients from the University of Nebraska (the testing cohort). Binary chromosomes with genes representing network attributes, including the number of nodes in the hidden layers, learning rate and momentum parameters, and the presence or absence of implicit within-layer connectivity using a competition algorithm, were operated on by various combinations of crossover, mutation, and probabilistic selection based on network mean-square error (MSE), and separately on average cross entropy (ENT). Predictive accuracy was measured as the area under a receiver-operating characteristic (ROC) curve. RESULTS: Over 50 generations, the baseline genetic algorithm evolved an optimized ANN with nine nodes in the first hidden layer, zero nodes in the second hidden layer, learning rate and momentum parameters of 0.5, and no within-layer competition connectivity. This ANN had an ROC area in the training cohort of 0.872 and in the testing cohort of 0.934 (P-value for difference, 0.181). Algorithms based on cross-generational selection, Gray coding of genes prior to mutation, and crossover recombination at different genetic levels, evolved optimized ANN identical to the baseline genetic strategy. Algorithms based on other strategies, including elite selection within generations (training ROC area 0.819), and inversions of genetic material during recombination (training ROC area 0.812), evolved less accurate ANN. CONCLUSION: ANN optimized by genetic algorithms accurately discriminated pneumonia within a training cohort, and within a testing cohort consisting of cases on which the networks had not been trained. Genetic algorithms can be used to implement efficient search strategies for optimal ANN to predict pneumonia.

Adolescent↗
PubMed1980

Schizophrenia: the testing of genetic models by pedigree analysis.

Simulated pedigrees of schizophrenia generally show a clear peak in their likelihood surface corresponding to analysis by the genetic models, which served as the basis for the simulation. The likelihood surface obtained with real data permits determination of the allelic frequency and the selection of an optimal one-locus, two-locus, and four-locus model. These three models have certain features in common, notably, a relatively high frequency of the allele predisposing to schizophrenia (about 20%) and a relatively low index of genetic determination (23%--34%). However, direct likelihood comparisons do not permit distinctions between the one-locus, two-locus, and four-locus models. The most likely interpretation of this finding is that the etiology of schizophrenia is heterogeneous or even nongenetic. However, a simple model with a single completely recessive locus and incomplete penetrance in the homozygote also produces a flat likelihood surface closely resembling that obtained with the real data. With reservation, this single-locus model may be put forward as a potentially useful working hypothesis.

Alleles↗
PubMed2002

Pharmacogenetics, pharmacogenomics, and cardiovascular therapeutics: the way forward.

The completion of sequencing of the human genome will be the vanguard for numerous advances in medicine. The first discernible application is likely to occur in pharmacogenomics, a field focused on the influence of genetic differences on the variability in patients' response to medications. While an inherited basis for drug response has been recognized for some time, it is the confluence of molecular biology, high-throughput genotyping, and bioinformatics that has made it practical to study the genetic basis of variability to medications on a large scale. Pharmacogenomics may enable clinicians to prospectively identify patients most likely to derive benefit from a drug, with minimal likelihood of adverse events. This DNA-based approach to predicting clinical drug efficacy and toxicity would shift the current prescribing paradigm from its empirical nature to a more patient-specific model, ushering in a new era of personalized medicine. Polymorphisms in drug metabolizing enzymes, drug targets, and disease pathogenesis genes are associated with therapeutic effect to cardiovascular pharmacotherapy. Moreover, pharmacogenomics and functional genomics are expected to have a profound impact on the process of drug discovery and development. Finally, pharmacogenomics is likely to transform the way clinical trials are conducted by allowing for the selection of a more homogeneous study population, thereby reducing the size and cost of clinical investigation.

Cardiovascular Agents↗
PubMed1976

Evaluation of the genetic effects induced by vinyl chloride monomer (VCM) under mammalian metabolic activation: studies in vitro and in vivo.

As part of a programme of investigations on the biological effects of the industrial compound vinyl chloride monomer (VCM), the raw material for the production of polyvinyl chloride (PVC), analyses on the genetic effects by this compound have been done by experiments (in vitro) which have taken mammalian metabolism into account. Vinyl chloride in the presence of purified microsomes (sedimented at 105,000 g) obtained from mouse liver was converted into an active metabolite(s) which produced gene mutations in the yeast Schizosaccharomyces pombe (forward mutation) and gene conversions in two loci of a diploid Saccharomyces cerevisiae. Moreover, the compound was active in the host-mediated assay, when mice were treated with an oral dose of 700 mg/kg. The role is discussed of mutagenicity tests for the prediction of both genetic and carcinogenic risks of chemical compounds in industrial use.

Animals↗
PubMed1999

Origins of individual differences in episodic memory in the oldest-old: a population-based study of identical and same-sex fraternal twins aged 80 and older.

The relative importance of genetic and environmental influences on episodic memory in very late life was studied using a quantitative genetic approach. Identical (n = 125) and same-sex fraternal (n = 157) twin pairs, aged 80 and older (mean age = 83.3; SD = 3.1) and without a diagnosis of dementia were tested with seven memory measures: (1-2) Digit Span Forward and Backwards, (3) Prose Recall, (4) Thurstone's picture memory test, and the Memory in Reality (MIR) test, including the subtasks of (5) free recall, (6) recognition, and (7) relocation. Heritabilities, estimated by structural equation modeling, ranged from .04 to .49. The digit span backward test showed the highest heritability (h2 = .49), while heritabilities were typically lower for the long-term memory measures. The results demonstrate genetic influences on memory in the oldest-old, but suggest that the magnitude of these effects differs across memory measures.

Aged↗
PubMed1977

Spontaneous forward mutation versus reversion frequencies for maize Adh1 in pollen.

Reliable quantitative data on spontaneous, specific gene mutation frequencies in higher plants and animals are few. Detergents include low natural frequencies and difficulty in obtaining in excess of 10(6) scorable organisms or gametophytes. The alcohol dehydrogenase-1 gene (Adh1 gene; ADH enzyme EC 1.1.1.1.), as expressed in pollen grains, is among the exceptionably suitable; much is known about the maize ADHs, Adh1 function is totally dispensible in an aerobic environment and maize pollen is a trinucleate gametophyte which expresses much of its haploid genome, including Adh1. In particular, there have been two recent methodological advances. First, I am able to cytochemically stain pollen, before or after in vitro germination, for the presence of above 5% normal ADH activity. And second, ADH1- pollen grains survive allyl alcohol (C=C-C-OH) vapour concentrations which kill ADH1+ grains; this selection scheme was developed for yeast by Megnet. My genetic resolution is approximately one mutant (Adh1+-->ADH-) per 10(7) chemically selected, viable gametophytes, and one (phenotypic) revertant (Adh1--->ADH+) per 10(8) unselected gatetophytes. In this note, I compare spontaneous forward mutant frequency with previously published revertant frequencies for one naturally occurring and six ethyl methanesulphonate-induced Adhl-deficient (Adh1-) alleles.

Alcohol Dehydrogenase↗
PubMed2006

Begomovirus genetic diversity in the native plant reservoir Solanum nigrum: Evidence for the presence of a new virus species of recombinant nature.

We examined the native plant host Solanum nigrum as reservoir of genetic diversity of begomoviruses that cause the tomato yellow leaf curl disease (TYLCD) emerging in southern Spain. Presence of isolates of all the species and strains found associated with TYLCD in this area was demonstrated. Mixed infections were common, which is a prerequisite for recombination to occur. In fact, presence of a novel recombinant begomovirus was demonstrated. Analysis of an infectious clone showed that it resulted from a genetic exchange between isolates of the ES strain of Tomato yellow leaf curl Sardinia virus and of the type strain of Tomato yellow leaf curl virus. The novel biological properties suggested that it is a step forward in the ecological adaptation to the invaded area. This recombinant represents an isolate of a new begomovirus species for which the name Tomato yellow leaf curl Axarquia virus is proposed. Spread into commercial tomatoes is shown.

Base Sequence↗
PubMed2000

Brassinosteroid signal transduction: still casting the actors.

Significant advances in the genetic dissection of brassinosteroid biosynthesis and signaling have been made during the past few years. Genetic and biochemical data have helped to elucidate the pathways of biosynthesis of brassinolide, the most active brassinosteroid. In addition, several models have been put forward for the perception of brassinolide by its putative receptor, BRI1, a ubiquitously expressed plasma membrane localized protein kinase. These studies provide the basic framework for future analysis of brassinosteroid signaling.

Brassinosteroids↗
PubMed1994

Genotoxicity of the flame retardant tris(2,3-dibromopropyl)phosphate in the rat and Drosophila: effects of deuterium substitution.

Formation of 2-bromoacrolein (2BA) from tris(2,3-dibromopropyl)phosphate (Tris-BP) by cytochrome P450 (cyt. P450) activity is most likely responsible for the high mutagenicity of Tris-BP for bacteria in vitro when rat liver microsomes are used for metabolic activation. As yet, it has not been established whether cyt. P450 plays a role in the formation of genotoxic metabolites from Tris-BP in higher organisms in vivo. This was studied by comparing the effects of completely deuterated Tris-BP (D15-Tris-BP) with normal Tris-BP in various in vivo test systems for genotoxicity: deuterium substitution should decrease cyt. P450-dependent bioactivation of Tris-BP. Three test systems in Drosophila were used to measure different types of genetic damage: (I) the ring-X chromosome loss (CL) test to detect clastogenicity, (II) the sex-linked recessive lethal (RL) test to detect forward mutations and deletions and (III) the white/white+ (w/w+) eye mosaic assay to detect predominantly mitotic recombination. Tris-BP was positive in all test systems, while D15-Tris-BP was without effect. The relative clastogenic efficiency of a compound, defined as the ratio of CL over RL, can be used to distinguish monofunctional agents (CL/RL ratio < or = 1) from those having cross-linking potential (CL/RL ratio > 2). The CL/RL ratio of Tris-BP was 2.4, indicating that Tris-BP has cross-linking potential. No CL/RL ratio for D15-Tris-BP could be determined, because it was negative in both tests. The putative Tris-BP metabolite 2BA was also tested in the Drosophila test systems. 2BA was positive in the CL test at a high dose, but it showed no response in the RL test. The relative clastogenic efficiency (the ratio of CL/RL) could not be determined accurately, but the data nevertheless argue in favour of cross-linking properties of 2BA. Further, 2BA was clearly positive in the w/w+ eye mosaic test system, which indicates that it is a recombinagen. Genotoxicity of Tris-BP in rats was determined by the induction of micronuclei in hepatocytes. Tris-BP administered intraperitoneally 17 h after 2/3 partial hepatectomy (PH), induced a high frequency of micronuclei at days 2 and 3 after injection (26% and 22%, respectively). D15-Tris-BP, however did not increase the micronuclei frequency.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1987

Etoposide (VP16) and teniposide (VM26): novel anticancer drugs, strongly mutagenic in mammalian but not prokaryotic test systems.

The mutagenic effect of the antineoplastic drugs VP16 (etoposide; 4'-demethylepipodophyllotoxin-ethylidene-beta-D-glucopyranoside) and VM26 (teniposide; 4'-demethylepipodophyllotoxin-thenylidene-beta-D-glucopyr ano side) in mammalian and prokaryotic test systems have been compared. Both VP16 and VM26 which interact with mammalian DNA topoisomerase II, are strongly mutagenic in Chinese hamster ovary cells as indicated by the induction of mutations at the hypoxanthine-guanine phosphoribosyl transferase and adenosine kinase loci, and production of DNA strand breaks and sister-chromatid exchanges. Mouse L cells treated with these drugs also show a large dose-dependent (0.05-0.2 microgram/ml for VM26 and 0.5-1.5 micrograms/ml for VP16) increase in the frequency of 6-thioguanine-resistant mutants and extensive fragmentation of cellular DNA. In contrast to the results obtained with mammalian cells, VP16, which was extensively investigated, showed no increase in revertant frequencies in the Salmonella typhimurium strains TA98 and TA100 at concentrations up to greater than 500 micrograms/plate, in either the absence or presence of an exogenous rat liver activation system. However, a very weak mutagenic response to VP16 and VM26 (less than 2-fold increase in revertant frequency) at very high drug concentrations was observed in the strain TA102. VP16 also failed to show any mutagenic response (up to greater than 500 micrograms/ml) in an excision repair-proficient Escherichia coli strain 113/143 employing two different forward mutation detection systems [viz. ability to grow in galactose (Gal+) or in presence of 5-methyltryptophan], which are capable of detecting various types of genetic lesions.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Polymerase chain reaction for identification of human and porcine spirochaetes recovered from cases of intestinal spirochaetosis.

A polymerase chain reaction (PCR) amplification of 16S rDNA was developed to identify spirochaetes recovered from cases of intestinal spirochaetosis in humans and pigs; these bacteria belong to a distinct genetic group of spirochaetes, with the proposed name 'Anguillina coli'. The PCR incorporated a universal eubacterial 16S rDNA sequencing primer (1492r), and a 21-base forward primer designed to include a nucleotide sequence specific for 'A. coli'. The PCR was used to correctly identify DNA extracted from 43 isolates of 'A. coli' from humans and pigs, whilst no product was produced from Escherichia coli, or from other intestinal spirochaetes, including 38 isolates of Serpulina spp., and one each of Treponema succinifaciens and Brachyspira aalborgi. The amplification provided a rapid and simple means of identifying DNA from isolates of 'A. coli', and could be used on boiled whole 'A. coli' cells, with a detection limit equivalent to 2.5 x 10(2) cells. The reaction was used to detect and identify these spirochaetes from selective agar plates inoculated with stool specimens from infected pigs.

Animals↗
PubMed2005

Parental smoking and childhood asthma: clinical implications.

Environmental tobacco smoke and constituents are global risks for human health. Considerable evidence shows that environmental tobacco smoke exposure contributes to, and exacerbates, respiratory disorders. This review assesses the causal role of environmental tobacco smoke exposure for childhood respiratory disorders, and in particular asthma. Tobacco smoke and environmental tobacco smoke exposure during pregnancy have an effect upon lung function in newborn infants; exposure after birth also has an effect upon lung function. An effect upon bronchial responsiveness has been suggested but the evidence is not as strong as for lung function. From 1997 to 1999 a comprehensive set of systematic reviews concerning the relationship between exposure to environmental tobacco smoke and respiratory health in children summarized the results from hundreds of published papers. The evidence for a causal relationship between environmental tobacco smoke exposure and asthmatic symptoms on the one hand, and between environmental tobacco smoke exposure and reduction in lung function on the other hand, was quite strong, whereas the evidence between environmental tobacco smoke exposure and development of allergy was much weaker. Here we present an overview of the effects of environmental tobacco smoke exposure on lung health in children. A hypothesis has been put forward regarding upregulation of pulmonary neuroendocrine cells in relationship to mechanisms of tobacco smoke products (TSP)-induced pulmonary disease. It has also been reported that genetic variation makes part of the population especially vulnerable to environmental tobacco smoke exposure during pregnancy. Furthermore, there is a need for intervention to reduce environmental tobacco smoke exposure in young children, by educating parents and adolescents about the health effects of environmental tobacco smoke exposure. Studies are needed to identify possible critical periods when environmental tobacco smoke exposure is more likely to induce harmful effects on lung health in young children in order to implement effective preventive strategies.

Asthma↗
PubMed1995

Triethylenemelamine: induction of specific-locus mutations in the ad-3 region of heterokaryon 12 of Neurospora crassa.

The mutagenicity of the trifunctional alkylating (or cross-linking) agent TEM (triethylenemelamine or 2,4,6-tris(1-aziridinyl)-1,3,5-triazine) in the adenine-3 (ad-3) region was studied with a two-component heterokaryon (H-12) of Neurospora crassa. The objective was to characterize the genetic damage produced by this chemical to determine the spectrum of specific-locus mutations induced in a lower eukaryotic organism and to compare this spectrum with that induced in the mouse. Specific-locus mutations in the ad-3 region of strain H-12 result from gene/point mutations, multiple-locus mutations, and multilocus deletion mutations at the closely linked ad-3A and ad-3B loci. These loci control two sequential biochemical reactions in the purine biosynthetic pathway. A 0.1 M solution of TEM was used to treat conidial suspensions of H-12 for 20, 40, 80, 120, or 170 min to obtain dose-response curves for (1) inactivation of conidia, and (2) the induction of specific-locus mutations in the ad-3 region. These experiments demonstrated that TEM is a strong mutagen (maximum forward-mutation frequency between 100 and 1000 ad-3 mutations per 10(6) survivors) for the induction of specific-locus mutations in the ad-3 region. Both biochemical and classical genetic tests were used to characterize the TEM-induced ad-3 mutations from each of the five treatment groups to distinguish between the different genotypic classes and subclasses. The overall data base from these genetic studies demonstrates that TEM-induced ad-3 mutations result predominantly (95.5% [769/805]) from gene/point mutations at the ad-3A and ad-3B loci, and from a low percentage (4.5% [36/805) of multilocus deletion mutations. In addition, TEM induces an unusually high frequency of multiple-locus mutations with sites of recessive lethal damage closely linked with the ad-3 region. Comparison of the dose-response curves for the major classes and subclasses of TEM-induced ad-3 mutations demonstrates (1) that gene/point mutations and multilocus deletion mutations increase as the 1.4 power of TEM treatment time, and (2) that the two classes of TEM-induced multiple-locus ad-3 mutations consisting of gene/point mutations with separate sites of recessive lethal damage increase at about the 1.96 power of TEM treatment time. When the data from the present specific-locus studies are compared with those in the mouse, we find, insofar as such comparisons are possible, that a similar spectrum of specific-locus mutations has been induced by TEM in each assay system.

Animals↗
PubMed1999

The expected number of alleles in a gene conversion model with mutation.

Gene conversions and mutations affect the number of different alleles in a population as it evolves. Here these effects are studied for a sample of r individuals represented by one chromosome, each with n loci. The long-term evolution of the sample is modelled with the coalescent. Gene conversions can only occur within a chromosome between a pair of loci. Recombination is not included in the model. Mutations occur according to the infinitely many alleles model. A new expression for the expected number of alleles is derived using the Backward time approach. It is then possible to simulate the expectation for various sample paths. The new estimator is computationally inexpensive and has a lower variance than the conventional, forward time, approximation by simulation.

Alleles↗
PubMed2006

Employing epigenetics to augment the expression of therapeutic proteins in mammalian cells.

Recombinant proteins form an increasingly large part of the portfolio of biopharmaceutical companies. Production of these often complex transgenic proteins is achieved predominantly in mammalian cell lines but the process is hampered by low yields and unstable expression. Some of these problems are caused by gene silencing at the level of chromatin - so-called epigenetic gene silencing. Here, we describe approaches, which have emerged during the past few years, designed to interfere with epigenetic gene silencing with the aim of enhancing and stabilizing transgene expression. These include targeting histones, the inclusion of specific DNA elements and targeting sites of high gene-expression. We conclude that employing epigenetic gene regulation tools, in combination with further process optimization, might represent the next step forward in the production of therapeutic proteins.

Animals↗
PubMed1999

CAP3: A DNA sequence assembly program.

We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 5' and 3' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints.

Algorithms↗
PubMed2001

Integration: farm and environment.

At a time when GM crops are being planted all around the globe, Europe appears to favour a more primitive and less productive agricultural system. Is the abandonment of 50 years of agricultural development the way forward or is there a rational alternative?

Agriculture↗