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PubMed2005

Developmental control of growth and cell cycle progression in Drosophila.

Drosophila melanogaster provides an outstanding experimental system to study the regulation of cell cycle progression during animal development. Sophisticated forward and reverse genetic techniques and the ability to observe detailed cell biological phenomena in vivo have allowed an unparalleled analysis of the cell cycle in the context of a whole animal. This chapter provides an overview of the diverse modes of cell cycle control that are utilized at different stages of Drosophila development.

Animals↗
PubMed2006

Electrophysiological analysis of neuronal and muscle function in C. elegans.

The nematode Caenorhabditis elegans provides numerous experimental advantages for the identification and characterization of genes required for the function of the nervous system. These advantages include forward and reverse genetic tractability, a relatively simple body plan with an invariant cellular lineage, and a fully sequenced and well-annotated genome. However, one limitation of C. elegans is the relative scarcity of electrophysiological data from excitable cells. To address this limitation, high-resolution cellular techniques for probing the roles of specific gene products in the C. elegans nervous system have been recently developed. This chapter will provide an overview of the technical requirements for patch-clamp electrophysiological analysis of C. elegans neurons and muscle cells, as well as provide some illustrative examples of insights gained from the pairing of electrophysiological techniques with molecular and genetic analysis.

Animals↗
PubMed2006

Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks.

Cellular events that execute life programs are ordered and reproducible, despite the noise and randomness underlying their biochemical reactions. The identification of the processes that ensure this robust operation is essential not only to uncover the salient design principles in organisms, but also to forward-engineer reliable genetic networks for biotechnological and therapeutic purposes. The use of feedback for noise reduction has been suggested as a recurring motif in genetic networks. In this work, we show that regulated degradation of proteins implements a negative feedback loop that enhances robustness against stochastic fluctuations and cellular noise. The analysis is carried out in the context of the bacterial heat shock response where the tight control of the amount of heat shock proteins is achieved through an intricate architecture of feedback loops involving the sigma(32)-factor. The sigma(32) regulates the transcription of heat shock proteins under normal and stress conditions. An essential feature of the heat shock response is a feedback loop regulating the degradation of sigma(32). We investigate the noise-rejection properties of this loop, therefore illustrating our point in a biologically plausible example.

Computer Simulation↗
PubMed2004

The Zuker collection: a resource for the analysis of autosomal gene function in Drosophila melanogaster.

The majority of genes of multicellular organisms encode proteins with functions that are not required for viability but contribute to important physiological functions such as behavior and reproduction. It is estimated that 75% of the genes of Drosophila melanogaster are nonessential. Here we report on a strategy used to establish a large collection of stocks that is suitable for the recovery of mutations in such genes. From approximately 72,000 F(3) cultures segregating for autosomes heavily treated with ethyl methanesulfonate (EMS), approximately 12,000 lines in which the treated second or third chromosome survived in homozygous condition were selected. The dose of EMS induced an estimated rate of 1.2-1.5 x 10(-3) mutations/gene and predicts five to six nonessential gene mutations per chromosome and seven to nine alleles per locus in the samples of 6000 second chromosomes and 6000 third chromosomes. Due to mosaic mutations induced in the initial exposure to the mutagen, many of the lines are segregating or are now fixed for lethal mutations on the mutagenized chromosome. The features of this collection, known as the Zuker collection, make it a valuable resource for forward and reverse genetic screens for mutations affecting a wide array of biological functions.

Alleles↗
PubMed2006

Fishing for gene function--endocrine modelling in the zebrafish.

The use of zebrafish (Danio rerio) in scientific research is growing rapidly. It initially became popular as a model of vertebrate development because zebrafish embryos develop rapidly and are transparent. In the past 5 years, the sequencing of the zebrafish genome has increased the profile of zebrafish research even further, expanding into other areas such as pharmacology, cancer research and drug discovery. The use of zebrafish in endocrine research has mainly been confined to the study of the development of endocrine organs. However, it is likely to be a useful model in other areas of endocrinology, as there are a wide variety of both forward and reverse genetic techniques that can be employed in the zebrafish to decipher gene function in disease states. In this review, we compare the endocrine system of the zebrafish to mouse and human, demonstrating that the systems are sufficiently similar for zebrafish to be employed as a model for endocrine research. We subsequently review the repertoire of genetic techniques commonly employed in the zebrafish model to understand gene function in vertebrate development and disease. We anticipate that the use of these techniques will make the zebrafish a prominent model in endocrine research in the coming years.

Animals↗
PubMed2003

High-throughput DNA extraction method suitable for PCR.

PCR has become one of the most popular techniques in functional genomics. Projects in both forward and reverse genetics routinely require PCR amplification of thousands of samples. Processing samples to extract DNA of sufficient purity for PCR is often a limiting step. We have developed a simple 96-well plate-based high-throughput DNA extraction method that is applicable to many plant species. The method involves a simple incubation of plant tissue samples in a DNA extraction buffer followed by a neutralization step. With the addition of a modified PCR buffer, the extracted DNA enabled the robust amplification of genomic fragments from samples of Arabidopsis, tobacco, sorghum, cotton, moss, and even pine needles. Several thousand DNA samples can be economically processed in a single day by one person without the use of robotics. This procedure will facilitate many technologies including high-throughput genotyping, map-based cloning, and identification of T-DNA or transposon-tagged mutants for known gene sequences.

Algorithms↗
PubMed2004

Zebrafish as a genomics research model.

The zebrafish (Danio rerio) is a recent addition to the genomic scientists' repertoire of vertebrate animal model systems. Unlike simple invertebrates such as the fly or the nematode, this teleost maintains the biological and genomic complexity found in higher vertebrates. Furthermore, the zebrafish has many advantageous technical and genomic properties that open the door to experimental approaches not practical using more classical models. The zebrafish genome can be functionally accessed using both forward and reverse genetics based approaches. A notable recent addition to the zebrafish genomics toolbox is the development of morpholino-based antisense gene inhibition for sequence-based 'knockdown' screening. This method offers the opportunity to examine the role of significant subsets of the vertebrate genome for specific gene function in vivo. The zebrafish embryo can rapidly provide critical information for drug target discovery purposes when examined with an emphasis on clinically-relevant biological processes. Finally, the advent of chemical genetics in zebrafish suggests that, in addition to the identification and understanding of drug targets and their biology, this system will be a powerful tool in the direct development of novel pharmaceuticals in the near future.

Animals↗
PubMed1987

[Saccharomyces cerevisiae mutants characterized by increased induced mutagenesis. II. Genetic analysis of mutants].

Induction of forward adenine-dependent (Ade+----Ade-) mutations by HAP was used to analyse genetically yeast mutants with enhanced induced mutagenesis. Three mutations studied in detail segregated as a single mendelian trait and composed independent complementation groups (HIM1, HIM2, HIM3). the him1-1 mutation was centromere-linked, the him3-1 and him2-1 mutations being not. All three mutations did not show any cross-linkage. Uracil-DNA glycosylase activity was determined in crude cell extract from wild type strain and him mutants; no detectable differences were observed.

Adenine↗
PubMed2005

Looking forward in geriatric anxiety and depression: implications of basic science for the future.

Major depression and anxiety are common psychiatric illnesses whose etiology remains incompletely understood. This review highlights progress in understanding the etiology of these illnesses through genetic strategies and looks forward to their impact on geriatric psychiatry. We briefly address three broad domains of progress, namely 1) genetic approaches to etiology, including linkage and association studies, pharmacogenetics ("personalized medicine"), and gene x environment interactions; 2) mechanisms of thyroid and testosterone action via nuclear receptors, given these hormones' status as possible augmenters of antidepressants; and 3) the role of the neuroimmune system as a contributor to the stress response. Genetic strategies offer one path for converting correlational findings into causal pathways while complementing studies of a gene's function at the molecular, cellular, network, and whole-organismal levels. Neuroendocrine supplementation (thyroid and testosterone) has a long history and tradition. A molecular understanding of nuclear receptor pathways and their coactivators, the mediator complex proteins, provides a rationale for improved targeting of hormonal action in a tissue-selective manner, yielding drugs with improved safety and efficacy. Neural-immune interactions in psychiatric illness remain tantalizing topics. Research suggests that cytokine pathways may contribute to the maintenance or susceptibility to stress, anxiety, and depressive disorders. The reciprocal and recursive interactions among basic science, drug discovery, and clinical science will continue to provide hopeful themes for improving the lives of patients with treatment-refractive psychiatric illness.

Aged↗
PubMed2005

Biotechnology and the domestication of forest trees.

Wood is one of the major renewable materials. To compensate for the ever-increasing demand for wood and to reduce pressure on native forests, more wood of higher quality will need to be produced on less land by planting highly productive trees. Biotechnology has shown great promise for forest tree improvement and over the past 10 years this field has flourished. Not only has the potential of transgenic trees with optimized yield and quality traits been demonstrated in field trials, but progress in genetical genomics and association genetics promise quantum leaps forward for tree improvement.

Alleles↗
PubMed2002

Hierarchical genetic algorithm for near optimal feedforward neural network design.

In this paper, we propose a genetic algorithm based design procedure for a multi layer feed forward neural network. A hierarchical genetic algorithm is used to evolve both the neural networks topology and weighting parameters. Compared with traditional genetic algorithm based designs for neural networks, the hierarchical approach addresses several deficiencies, including a feasibility check highlighted in literature. A multi objective cost function is used herein to optimize the performance and topology of the evolved neural network simultaneously. In the prediction of Mackey Glass chaotic time series, the networks designed by the proposed approach prove to be competitive, or even superior, to traditional learning algorithms for the multi layer Perceptron networks and radial basis function networks. Based upon the chosen cost function, a linear weight combination decision making approach has been applied to derive an approximated Pareto optimal solution set. Therefore, designing a set of neural networks can be considered as solving a two objective optimization problem.

Algorithms↗
PubMed2004

Genetics of photosensitivity (photoparoxysmal response): a review.

We present a review of phenotype-genotype correlation and the genetics of photosensitivity. The photoparoxysmal response in EEG (PPR) is still one of the best paradigms for exogenously triggered brain responses based on a genetic predisposition. The definition of the PPR phenotype requires multiple, precise methodologic guidelines. Individual factors such as age and gender but also other, unknown factors influence the expression of the PPR. For example, PPRs occur during adolescence and can disappear at a later age. As a consequence, it is difficult to assign nonaffected disease status correctly. Autosomal dominant inheritance has been found in clinical studies of relatives of PPR-positive epilepsy and nonepilepsy subjects. Genetic heterogeneity of the PPR is obvious because the PPR also can be evoked in a number of autosomal recessive diseases. PPR is most commonly associated with idiopathic generalized epilepsies (IGEs) such as juvenile myoclonic epilepsy (JME). This comorbidity suggests that a genetic factor involved in photosensitivity also may influence the susceptibility for JME. Finding the gene for PPR also might represent a step forward in unraveling the genetic background of JME. The search for the genetic factors causing PPRs should focus on the genes affected in such epilepsies, such as genes (coding) for ion channels and neurotransmitters and their receptors. The expression of defined proteins with as-yet-undetermined functions, is changed in a few types of epilepsies with a mendelian mode of inheritance. These additional genes and the human equivalents of the genes found to be mutated in animal models also are candidates for molecular genetic studies of the PPR.

Animals↗
PubMed2001

Heterosis in two closely related species of earthworm (Eisenia fetida and E. andrei).

The importance of heterosis, and in particular allozyme-associated heterosis, in natural populations remains unclear. Much of the scepticism that surrounds allozyme-associated heterosis comes from inconsistent and unreliable detection of the relationship. Thus, evaluating the genetic mechanisms that may cause allozyme-associated heterosis in natural populations has proven difficult. The most prevalent hypotheses that have been put forward to explain the genetic basis of heterosis are the general dominance and the local overdominance hypotheses. A factorial crossing design was used to survey eight polymorphic allozyme loci in the parent and offspring generations of two species of earthworms in order to evaluate possible mechanisms of allozyme-associated heterosis for growth rate. Significant heritable variation for growth rate was detected only within a single cross. Allozyme-associated heterosis for growth rate was detected only within this cross. This relationship did not persist after the effects of interfamily variation were removed. These results indicate that simple heritability of a fitness-related trait may be necessary for predictive power and repeatability of allozyme-associated heterosis, and that the allozyme-associated heterosis detected in this study was the result of general dominant genetic effects.

Animals↗
PubMed2001

Fast realistic modeling in bioelectromagnetism using lead-field interpolation.

The practical use of realistic models in bioelectromagnetism is limited by the time-consuming amount of numerical calculations. We propose a method leading to much higher speed than currently available, and compatible with any kind of numerical methods (boundary elements (BEM), finite elements, finite differences). Illustrated with the BEM for EEG and MEG, it applies to ECG and MCG as well. The principle is two-fold. First, a Lead-Field matrix is calculated (once for all) for a grid of dipoles covering the brain volume. Second, any forward solution is interpolated from the pre-calculated Lead-Fields corresponding to grid dipoles near the source. Extrapolation is used for shallow sources falling outside the grid. Three interpolation techniques were tested: trilinear, second-order Bézier (Bernstein polynomials), and 3D spline. The trilinear interpolation yielded the highest speed gain, with factors better than x10,000 for a 9,000-triangle BEM model. More accurate results could be obtained with the Bézier interpolation (speed gain approximately 1,000), which, combined with a 8-mm step grid, lead to intrinsic localization and orientation errors of only 0.2 mm and 0.2 degrees. Further improvements in MEG could be obtained by interpolating only the contribution of secondary currents. Cropping grids by removing shallow points lead to a much better estimation of the dipole orientation in EEG than when solving the forward problem classically, providing an efficient alternative to locally refined models. This method would show special usefulness when combining realistic models with stochastic inverse procedures (simulated annealing, genetic algorithms) requiring many forward calculations.

Algorithms↗
PubMed1997

The social and economic origins of genetic determinism: a case history of the American Eugenics Movement, 1900-1940 and its lessons for today.

Eugenics, the attempt to improve the genetic quality of the human species by 'better breeding', developed as a worldwide movement between 1900 and 1940. It was particularly prominent in the United States, Britain and Germany, and in those countries was based on the then-new science of Mendelian genetics. Eugenicists developed research programs to determine the degree in which traits such as Huntington's chorea, blindness, deafness, mental retardation (feeblemindedness), intelligence, alcoholism, schizophrenia, manic depression, rebelliousness, nomadism, prostitution and feeble inhibition were genetically determined. Eugenicists were also active in the political arena, lobbying in the United States for immigration restriction and compulsory sterilization laws for those deemed genetically unfit; in Britain they lobbied for incarceration of genetically unfit and in Germany for sterilization and eventually euthanasia. In all these countries one of the major arguments was that of efficiency: that it was inefficient to allow genetic defects to be multiplied and then have to try and deal with the consequences of state care for the offspring. National socialists called genetically defective individuals 'useless eaters' and argued for sterilization or euthanasia on economic grounds. Similar arguments appeared in the United States and Britain as well. At the present time (1997) much research and publicity is being given to claims about a genetic basis for all the same behaviors (alcoholism, manic depression, etc.), again in an economic context--care for people with such diseases is costing too much. There is an important lesson to learn from the past: genetic arguments are put forward to mask the true--social and economic--causes of human behavioral defects.

Eugenics↗
PubMed1992

Genetic toxicology evaluation of commercial beers, III. SCE, chromosome aberrations, and forward mutation (HGPRT) of commercial beer products in CHO cells.

Concentrated organic residues extracted from 5 blended aliquots of commercial beers were evaluated for their ability to induce sister chromatid exchange (SCE), chromosomal aberrations and forward mutation in Chinese hamster ovary (CHO) cells. Each extract was prepared by blending 4 commercial beers of similar ingredients and brewing method, passing the beer pool over XAD-2 resin, extracting the resin and concentrating the extract. Studies were performed both with and without metabolic activation using variable amounts of reconstituted residues from 225-fold concentrates of the blended samples. CHO cultures were treated with 0.75 microliters/ml through 10.0 microliters/ml of the concentrates in the SCE assays, 1.0 microliters/ml through 10.0 microliters/ml of the extracts in the aberration assays and 2.5 microliters/ml up to 20 microliters/ml for forward mutation assays. In preliminary screening for SCE as an indicator of potential DNA damage, a significant increase was observed for 3 of 5 concentrated samples; however, no increase in SCE was induced by any of the 5 samples when S9 was added as a source of exogenous metabolic activation. More definitive tests for induction of genetic events, i.e., chromosome aberrations and forward HGPRT mutations, were negative for all 5 extracts whether or not S9 mix was present. Since SCE were not induced in tests with metabolic activation and since there was no concordant aberration or point mutation induction, the preliminary indication of potential DNA damage shown by elevated SCE under conditions without metabolic activation appears to have little biological significance.

Animals↗
PubMed2003

Recombinant Newcastle disease virus as a vaccine vector.

Veterinary vaccines remained conventional for more than fifty years. Recent advances in the recombinant genetic engineering techniques brought forward a leap in designing vaccines for veterinary use. A novel approach of delivering protective immunogens of many different pathogens in a single virus vector was made possible with the introduction of a "reverse genetics" system for nonsegmented negative-sense RNA viruses. Newcastle disease virus (NDV), a nonsegmented negative-sense virus, is one of the major viruses of economic importance in the poultry industry throughout the world. Despite the availability of live virus vaccines of good potency, the intrinsic ability of attenuated strains to revert in virulence makes control of this disease by vaccination difficult. Armed with the knowledge of virulence factors of this virus, it is now possible to produce genetically stable vaccines and to engineer mutations that enhance immunogenicity. The modular nature of the genome of this virus facilitates engineering additional genes from several different pathogens or tumor-specific antigens to design contemporary vaccines for animals and humans. This review will summarize the developments in using NDV as a vaccine vector and the potential of this approach in designing next generation vaccines for veterinary use.

Animals↗