Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes

KAUST Repository

Moon, Robert; Hall, Joanna M.; Rangkuti, Farania; Ho, YungShwen; Almond, Neil M.; Mitchell, Graham Howard; Pain, Arnab; Holder, Anthony A.; Blackman, Michael J.

2012-01-01

Research into the aetiological agent of the most widespread form of severe malaria, Plasmodium falciparum, has benefitted enormously from the ability to culture and genetically manipulate blood-stage forms of the parasite in vitro. However, most malaria outside Africa is caused by a distinct Plasmodium species, Plasmodium vivax, and it has become increasingly apparent that zoonotic infection by the closely related simian parasite Plasmodium knowlesi is a frequent cause of life-threatening malaria in regions of southeast Asia. Neither of these important malarial species can be cultured in human cells in vitro, requiring access to primates with the associated ethical and practical constraints. We report the successful adaptation of P. knowlesi to continuous culture in human erythrocytes. Human-adapted P. knowlesi clones maintain their capacity to replicate in monkey erythrocytes and can be genetically modified with unprecedented efficiency, providing an important and unique model for studying conserved aspects of malarial biology as well as species-specific features of an emerging pathogen.

Analysis of tractable distortion metrics for EEG compression applications

International Nuclear Information System (INIS)

Bazán-Prieto, Carlos; Blanco-Velasco, Manuel; Cruz-Roldán, Fernando; Cárdenas-Barrera, Julián

2012-01-01

Coding distortion in lossy electroencephalographic (EEG) signal compression methods is evaluated through tractable objective criteria. The percentage root-mean-square difference, which is a global and relative indicator of the quality held by reconstructed waveforms, is the most widely used criterion. However, this parameter does not ensure compliance with clinical standard guidelines that specify limits to allowable noise in EEG recordings. As a result, expert clinicians may have difficulties interpreting the resulting distortion of the EEG for a given value of this parameter. Conversely, the root-mean-square error is an alternative criterion that quantifies distortion in understandable units. In this paper, we demonstrate that the root-mean-square error is better suited to control and to assess the distortion introduced by compression methods. The experiments conducted in this paper show that the use of the root-mean-square error as target parameter in EEG compression allows both clinicians and scientists to infer whether coding error is clinically acceptable or not at no cost for the compression ratio. (paper)

Drosophila growth cones: a genetically tractable platform for the analysis of axonal growth dynamics.

Science.gov (United States)

Sánchez-Soriano, Natalia; Gonçalves-Pimentel, Catarina; Beaven, Robin; Haessler, Ulrike; Ofner-Ziegenfuss, Lisa; Ballestrem, Christoph; Prokop, Andreas

2010-01-01

The formation of neuronal networks, during development and regeneration, requires outgrowth of axons along reproducible paths toward their appropriate postsynaptic target cells. Axonal extension occurs at growth cones (GCs) at the tips of axons. GC advance and navigation requires the activity of their cytoskeletal networks, comprising filamentous actin (F-actin) in lamellipodia and filopodia as well as dynamic microtubules (MTs) emanating from bundles of the axonal core. The molecular mechanisms governing these two cytoskeletal networks, their cross-talk, and their response to extracellular signaling cues are only partially understood, hindering our conceptual understanding of how regulated changes in GC behavior are controlled. Here, we introduce Drosophila GCs as a suitable model to address these mechanisms. Morphological and cytoskeletal readouts of Drosophila GCs are similar to those of other models, including mammals, as demonstrated here for MT and F-actin dynamics, axonal growth rates, filopodial structure and motility, organizational principles of MT networks, and subcellular marker localization. Therefore, we expect fundamental insights gained in Drosophila to be translatable into vertebrate biology. The advantage of the Drosophila model over others is its enormous amenability to combinatorial genetics as a powerful strategy to address the complexity of regulatory networks governing axonal growth. Thus, using pharmacological and genetic manipulations, we demonstrate a role of the actin cytoskeleton in a specific form of MT organization (loop formation), known to regulate GC pausing behavior. We demonstrate these events to be mediated by the actin-MT linking factor Short stop, thus identifying an essential molecular player in this context.

A Tractable Disequilbrium Framework for Integrating Computational Thermodynamics and Geodynamics

Science.gov (United States)

Spiegelman, M. W.; Tweed, L. E. L.; Evans, O.; Kelemen, P. B.; Wilson, C. R.

2017-12-01

The consistent integration of computational thermodynamics and geodynamics is essential for exploring and understanding a wide range of processes from high-PT magma dynamics in the convecting mantle to low-PT reactive alteration of the brittle crust. Nevertheless, considerable challenges remain for coupling thermodynamics and fluid-solid mechanics within computationally tractable and insightful models. Here we report on a new effort, part of the ENKI project, that provides a roadmap for developing flexible geodynamic models of varying complexity that are thermodynamically consistent with established thermodynamic models. The basic theory is derived from the disequilibrium thermodynamics of De Groot and Mazur (1984), similar to Rudge et. al (2011, GJI), but extends that theory to include more general rheologies, multiple solid (and liquid) phases and explicit chemical reactions to describe interphase exchange. Specifying stoichiometric reactions clearly defines the compositions of reactants and products and allows the affinity of each reaction (A = -Δ/Gr) to be used as a scalar measure of disequilibrium. This approach only requires thermodynamic models to return chemical potentials of all components and phases (as well as thermodynamic quantities for each phase e.g. densities, heat capacity, entropies), but is not constrained to be in thermodynamic equilibrium. Allowing meta-stable phases mitigates some of the computational issues involved with the introduction and exhaustion of phases. Nevertheless, for closed systems, these problems are guaranteed to evolve to the same equilibria predicted by equilibrium thermodynamics. Here we illustrate the behavior of this theory for a range of simple problems (constructed with our open-source model builder TerraFERMA) that model poro-viscous behavior in the well understood Fo-Fa binary phase loop. Other contributions in this session will explore a range of models with more petrologically interesting phase diagrams as well as

Non-Genetic Engineering Approaches for Isolating and Generating Novel Yeasts for Industrial Applications

Science.gov (United States)

Chambers, P. J.; Bellon, J. R.; Schmidt, S. A.; Varela, C.; Pretorius, I. S.

Generating novel yeast strains for industrial applications should be quite straightforward; after all, research into the genetics, biochemistry and physiology of Baker's Yeast, Saccharomyces cerevisiae, has paved the way for many advances in the modern biological sciences. We probably know more about this humble eukaryote than any other, and it is the most tractable of organisms for manipulation using modern genetic engineering approaches. In many countries, however, there are restrictions on the use of genetically-modified organisms (GMOs), particularly in foods and beverages, and the level of consumer acceptance of GMOs is, at best, variable. Thus, many researchers working with industrial yeasts use genetic engineering techniques primarily as research tools, and strain development continues to rely on non-GM technologies. This chapter explores the non-GM tools and strategies available to such researchers.

Capturing intracellular pH dynamics by coupling its molecular mechanisms within a fully tractable mathematical model.

Directory of Open Access Journals (Sweden)

Yann Bouret

Full Text Available We describe the construction of a fully tractable mathematical model for intracellular pH. This work is based on coupling the kinetic equations depicting the molecular mechanisms for pumps, transporters and chemical reactions, which determine this parameter in eukaryotic cells. Thus, our system also calculates the membrane potential and the cytosolic ionic composition. Such a model required the development of a novel algebraic method that couples differential equations for slow relaxation processes to steady-state equations for fast chemical reactions. Compared to classical heuristic approaches based on fitted curves and ad hoc constants, this yields significant improvements. This model is mathematically self-consistent and allows for the first time to establish analytical solutions for steady-state pH and a reduced differential equation for pH regulation. Because of its modular structure, it can integrate any additional mechanism that will directly or indirectly affect pH. In addition, it provides mathematical clarifications for widely observed biological phenomena such as overshooting in regulatory loops. Finally, instead of including a limited set of experimental results to fit our model, we show examples of numerical calculations that are extremely consistent with the wide body of intracellular pH experimental measurements gathered by different groups in many different cellular systems.

Marburg Virus Reverse Genetics Systems

Directory of Open Access Journals (Sweden)

Kristina Maria Schmidt

2016-06-01

Full Text Available The highly pathogenic Marburg virus (MARV is a member of the Filoviridae family and belongs to the group of nonsegmented negative-strand RNA viruses. Reverse genetics systems established for MARV have been used to study various aspects of the viral replication cycle, analyze host responses, image viral infection, and screen for antivirals. This article provides an overview of the currently established MARV reverse genetic systems based on minigenomes, infectious virus-like particles and full-length clones, and the research that has been conducted using these systems.

Comparative evaluation of 13 yeast species in the Yarrowia clade on lignocellulosic biomass hydrolysate and genetic engineering of inhibitor tolerant strains for lipid and biofuel production

Science.gov (United States)

Yarrowia lipolytica is an oleaginous yeast that has garnered interest for commercial production of single cell oil and other fatty acid-derived chemicals because of its GRAS status and genetic tractability. Three recent peer-reviewed studies have highlighted the possibility of lipid production by th...

Using genetic data to estimate diffusion rates in heterogeneous landscapes.

Science.gov (United States)

Roques, L; Walker, E; Franck, P; Soubeyrand, S; Klein, E K

2016-08-01

Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

Using Genetic Algorithms for Building Metrics of Collaborative Systems

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Cristian CIUREA

2011-01-01

Full Text Available he paper objective is to reveal the importance of genetic algorithms in building robust metrics of collaborative systems. The main types of collaborative systems in economy are presented and some characteristics of genetic algorithms are described. A genetic algorithm was implemented in order to determine the local maximum and minimum points of the relative complexity function associated to a collaborative banking system. The intelligent collaborative systems based on genetic algorithms, representing the new generation of collaborative systems, are analyzed and the implementation of auto-adaptive interfaces in a banking application is described.

The filamentous fungus Sordaria macrospora as a genetic model to study fruiting body development.

Science.gov (United States)

Teichert, Ines; Nowrousian, Minou; Pöggeler, Stefanie; Kück, Ulrich

2014-01-01

Filamentous fungi are excellent experimental systems due to their short life cycles as well as easy and safe manipulation in the laboratory. They form three-dimensional structures with numerous different cell types and have a long tradition as genetic model organisms used to unravel basic mechanisms underlying eukaryotic cell differentiation. The filamentous ascomycete Sordaria macrospora is a model system for sexual fruiting body (perithecia) formation. S. macrospora is homothallic, i.e., self-fertile, easily genetically tractable, and well suited for large-scale genomics, transcriptomics, and proteomics studies. Specific features of its life cycle and the availability of a developmental mutant library make it an excellent system for studying cellular differentiation at the molecular level. In this review, we focus on recent developments in identifying gene and protein regulatory networks governing perithecia formation. A number of tools have been developed to genetically analyze developmental mutants and dissect transcriptional profiles at different developmental stages. Protein interaction studies allowed us to identify a highly conserved eukaryotic multisubunit protein complex, the striatin-interacting phosphatase and kinase complex and its role in sexual development. We have further identified a number of proteins involved in chromatin remodeling and transcriptional regulation of fruiting body development. Furthermore, we review the involvement of metabolic processes from both primary and secondary metabolism, and the role of nutrient recycling by autophagy in perithecia formation. Our research has uncovered numerous players regulating multicellular development in S. macrospora. Future research will focus on mechanistically understanding how these players are orchestrated in this fungal model system. Copyright © 2014 Elsevier Inc. All rights reserved.

Genetically caused congenital anomalies of reproductive system

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L. F. Kurilo

2013-01-01

Full Text Available Classification of congenital disorders, their frequency of occurrence in populations, and some terminology questions discussed in the review. Genetically caused congenital anomalies of reproductive system are outlined. Full information about genetic syndromes is stated in the book: Kozlova S.I., Demikova N.S. Hereditary syndromes and genetic counseling. M., 2007.

An integrated system for genetic analysis

Directory of Open Access Journals (Sweden)

Duan Xiao

2006-04-01

Full Text Available Abstract Background Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use. Description We have developed an Integrated Genotyping System (IGS to meet this need. IGS securely stores, edits and analyses genotype and phenotype data. It stores information about DNA samples, plates, primers, markers and genotypes generated by a genotyping laboratory. Data are structured so that statistical genetic analysis of both case-control and pedigree data is straightforward. Conclusion IGS can model complex phenotypes and contain genotypes from whole genome association studies. The database makes it possible to integrate genetic analysis with data curation. The IGS web site http://bioinformatics.well.ox.ac.uk/project-igs.shtml contains further information.

Time-Delay System Identification Using Genetic Algorithm

DEFF Research Database (Denmark)

Yang, Zhenyu; Seested, Glen Thane

2013-01-01

Due to the unknown dead-time coefficient, the time-delay system identification turns to be a non-convex optimization problem. This paper investigates the identification of a simple time-delay system, named First-Order-Plus-Dead-Time (FOPDT), by using the Genetic Algorithm (GA) technique. The qual......Due to the unknown dead-time coefficient, the time-delay system identification turns to be a non-convex optimization problem. This paper investigates the identification of a simple time-delay system, named First-Order-Plus-Dead-Time (FOPDT), by using the Genetic Algorithm (GA) technique...

Optimal support arrangement of piping systems using genetic algorithm

International Nuclear Information System (INIS)

Chiba, T.; Okado, S.; Fujii, I.; Itami, K.

1996-01-01

The support arrangement is one of the important factors in the design of piping systems. Much time is required to decide the arrangement of the supports. The authors applied a genetic algorithm to find the optimum support arrangement for piping systems. Examples are provided to illustrate the effectiveness of the genetic algorithm. Good results are obtained when applying the genetic algorithm to the actual designing of the piping system

Cellular Clocks : Coupled Circadian Dispatch and Cell Division Cycles

NARCIS (Netherlands)

Merrow, Martha; Roenneberg, Till

2004-01-01

Gating of cell division by the circadian clock is well known, yet its mechanism is little understood. Genetically tractable model systems have led to new hypotheses and questions concerning the coupling of these two cellular cycles.

Evolution of genetic systems in filamentous ascomycetes

NARCIS (Netherlands)

Nauta, M.J.

1994-01-01

A great variety of genetic systems exist in filamentous ascomycetes. The transmission of genetic material does not only occur by (sexual or asexual) reproduction, but it can also follow vegetative fusion of different strains. In this thesis the evolution of this variability is studied,

Phage Genetic Engineering Using CRISPR–Cas Systems

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Asma Hatoum-Aslan

2018-06-01

Full Text Available Since their discovery over a decade ago, the class of prokaryotic immune systems known as CRISPR–Cas have afforded a suite of genetic tools that have revolutionized research in model organisms spanning all domains of life. CRISPR-mediated tools have also emerged for the natural targets of CRISPR–Cas immunity, the viruses that specifically infect bacteria, or phages. Despite their status as the most abundant biological entities on the planet, the majority of phage genes have unassigned functions. This reality underscores the need for robust genetic tools to study them. Recent reports have demonstrated that CRISPR–Cas systems, specifically the three major types (I, II, and III, can be harnessed to genetically engineer phages that infect diverse hosts. Here, the mechanisms of each of these systems, specific strategies used, and phage editing efficacies will be reviewed. Due to the relatively wide distribution of CRISPR–Cas systems across bacteria and archaea, it is anticipated that these immune systems will provide generally applicable tools that will advance the mechanistic understanding of prokaryotic viruses and accelerate the development of novel technologies based on these ubiquitous organisms.

Genetic optimization of steam multi-turbines system

International Nuclear Information System (INIS)

Olszewski, Pawel

2014-01-01

Optimization analysis of partially loaded cogeneration, multiple-stages steam turbines system was numerically investigated by using own-developed code (C++). The system can be controlled by following variables: fresh steam temperature, pressure, and flow rates through all stages in steam turbines. Five various strategies, four thermodynamics and one economical, which quantify system operation, were defined and discussed as an optimization functions. Mathematical model of steam turbines calculates steam properties according to the formulation proposed by the International Association for the Properties of Water and Steam. Genetic algorithm GENOCOP was implemented as a solving engine for non–linear problem with handling constrains. Using formulated methodology, example solution for partially loaded system, composed of five steam turbines (30 input variables) with different characteristics, was obtained for five strategies. The genetic algorithm found multiple solutions (various input parameters sets) giving similar overall results. In real application it allows for appropriate scheduling of machine operation that would affect equable time load of every system compounds. Also based on these results three strategies where chosen as the most complex: the first thermodynamic law energy and exergy efficiency maximization and total equivalent energy minimization. These strategies can be successfully used in optimization of real cogeneration applications. - Highlights: • Genetic optimization model for a set of five various steam turbines was presented. • Four various thermodynamic optimization strategies were proposed and discussed. • Operational parameters (steam pressure, temperature, flow) influence was examined. • Genetic algorithm generated optimal solutions giving the best estimators values. • It has been found that similar energy effect can be obtained for various inputs

A yeast screening system for simultaneously monitoring multiple genetic endpoints

International Nuclear Information System (INIS)

Dixon, M.L.; Mortimer, R.K.

1986-01-01

Mutation, recombination, and mitochondrial deficiencies have been proposed to have roles in the carcinogenic process. The authors describe a diploid strain of the yeast Saccharomyces cerevisiae capable of detecting this wide spectrum of genetic changes. The markers used for monitoring these events have been especially well characterized genetically. Ultraviolet light was chosen as a model carcinogenic agent to test this system. In addition to highly significant increases in the frequencies of each genetic change, increases in the absolute numbers of each change indicated induction and not selective survival. The relative amounts of each type of genetic change varied with dose. The wide spectrum of endpoints monitored in the XD83 yeast system may allow the detection of certain carcinogens and other genetically toxic agents which have escaped detection in more limited systems. Since only one strain is required to simultaneously monitor these genetic changes, this assay system should facilitate comparisons of the induced changes and be more efficient than using multiple strains to monitor the same endpoints. (Auth.)

Phenomics, Genomics and Genetics in Plasmodium vinckei

KAUST Repository

Ramaprasad, Abhinay

2017-11-01

Rodent malaria parasites (RMPs) serve as tractable models for experimental genetics, and as valuable tools to study malaria parasite biology and host-parasitevector interactions. Plasmodium vinckei, one of four RMPs adapted to laboratory mice, is the most geographically widespread species and displays considerable phenotypic and genotypic diversity amongst its subspecies and strains. The phenotypes and genotypes of P. vinckei isolates have been relatively less characterized compared to other RMPs, hampering its use as an experimental model for malaria. Here, we have studied the phenotypes and sequenced the genomes and transcriptomes of ten P. vinckei isolates including representatives of all five subspecies, all of which were collected from wild thicket rats (Thamnomys rutilans) in sub-Saharan Central Africa between the late 1940s and mid 1960s. We have generated a comprehensive resource for P. vinckei comprising of five high-quality reference genomes, growth profiles and genotypes of P. vinckei isolates, and expression profiles of genes across the intra-erythrocytic developmental stages of the parasite. We observe significant phenotypic and genotypic diversity among P. vinckei isolates, making them particularly suitable for classical genetics and genomics-driven studies on malaria parasite biology. As part of a proof of concept study, we have shown that experimental genetic crosses can be performed between P. vinckei parasites to potentially identify genotype-phenotype relationships. We have also shown that they are amenable to genetic manipulation in the laboratory.

Construction of a Recyclable Genetic Marker and Serial Gene Deletions in the Human Pathogenic Mucorales Mucor circinelloides.

Science.gov (United States)

Garcia, Alexis; Adedoyin, Gloria; Heitman, Joseph; Lee, Soo Chan

2017-07-05

Mucor circinelloides is a human pathogen, biofuel producer, and model system that belongs to a basal fungal lineage; however, the genetics of this fungus are limited. In contrast to ascomycetes and basidiomycetes, basal fungal lineages have been understudied. This may be caused by a lack of attention given to these fungi, as well as limited tools for genetic analysis. Nonetheless, the importance of these fungi as pathogens and model systems has increased. M. circinelloides is one of a few genetically tractable organisms in the basal fungi, but it is far from a robust genetic system when compared to model fungi in the subkingdom Dikarya. One problem is the organism is resistant to drugs utilized to select for dominant markers in other fungal transformation systems. Thus, we developed a blaster recyclable marker system by using the pyrG gene (encoding an orotidine-5'-phosphate decarboxylase, ortholog of URA3 in Saccharomyces cerevisiae ). A 237-bp fragment downstream of the pyrG gene was tandemly incorporated into the upstream region of the gene, resulting in construction of a pyrG-dpl237 marker. To test the functionality of the pyrG-dpl237 marker, we disrupted the carRP gene that is involved in carotenoid synthesis in pyrG - mutant background. The resulting carRP :: pyrG-dpl237 mutants exhibit a white colony phenotype due to lack of carotene, whereas wild type displays yellowish colonies. The pyrG marker was then successfully excised, generating carRP-dpl237 on 5-FOA medium. The mutants became auxotrophic and required uridine for growth. We then disrupted the calcineurin B regulatory subunit cnbR gene in the carRP :: dpl237 strain, generating mutants with the alleles carRP :: dpl237 and cnbR :: pyrG These results demonstrate that the recyclable marker system is fully functional, and therefore the pyrG-dpl237 marker can be used for sequential gene deletions in M. circinelloides . Copyright © 2017 Garcia et al.

Construction of a Recyclable Genetic Marker and Serial Gene Deletions in the Human Pathogenic Mucorales Mucor circinelloides

Directory of Open Access Journals (Sweden)

Alexis Garcia

2017-07-01

Full Text Available Mucor circinelloides is a human pathogen, biofuel producer, and model system that belongs to a basal fungal lineage; however, the genetics of this fungus are limited. In contrast to ascomycetes and basidiomycetes, basal fungal lineages have been understudied. This may be caused by a lack of attention given to these fungi, as well as limited tools for genetic analysis. Nonetheless, the importance of these fungi as pathogens and model systems has increased. M. circinelloides is one of a few genetically tractable organisms in the basal fungi, but it is far from a robust genetic system when compared to model fungi in the subkingdom Dikarya. One problem is the organism is resistant to drugs utilized to select for dominant markers in other fungal transformation systems. Thus, we developed a blaster recyclable marker system by using the pyrG gene (encoding an orotidine-5′-phosphate decarboxylase, ortholog of URA3 in Saccharomyces cerevisiae. A 237-bp fragment downstream of the pyrG gene was tandemly incorporated into the upstream region of the gene, resulting in construction of a pyrG-dpl237 marker. To test the functionality of the pyrG-dpl237 marker, we disrupted the carRP gene that is involved in carotenoid synthesis in pyrG− mutant background. The resulting carRP::pyrG-dpl237 mutants exhibit a white colony phenotype due to lack of carotene, whereas wild type displays yellowish colonies. The pyrG marker was then successfully excised, generating carRP-dpl237 on 5-FOA medium. The mutants became auxotrophic and required uridine for growth. We then disrupted the calcineurin B regulatory subunit cnbR gene in the carRP::dpl237 strain, generating mutants with the alleles carRP::dpl237 and cnbR::pyrG. These results demonstrate that the recyclable marker system is fully functional, and therefore the pyrG-dpl237 marker can be used for sequential gene deletions in M. circinelloides.

Steady-State-Preserving Simulation of Genetic Regulatory Systems

Directory of Open Access Journals (Sweden)

Ruqiang Zhang

2017-01-01

Full Text Available A novel family of exponential Runge-Kutta (expRK methods are designed incorporating the stable steady-state structure of genetic regulatory systems. A natural and convenient approach to constructing new expRK methods on the base of traditional RK methods is provided. In the numerical integration of the one-gene, two-gene, and p53-mdm2 regulatory systems, the new expRK methods are shown to be more accurate than their prototype RK methods. Moreover, for nonstiff genetic regulatory systems, the expRK methods are more efficient than some traditional exponential RK integrators in the scientific literature.

Population genetics models of local ancestry.

Science.gov (United States)

Gravel, Simon

2012-06-01

Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population structure and gene flow and interpret genomes of individuals that have ancestry from multiple source populations as mosaics of segments originating from each population. This article describes general and tractable models for local ancestry patterns with a focus on the length distribution of continuous ancestry tracts and the variance in total ancestry proportions among individuals. The models offer improved agreement with Wright-Fisher simulation data when compared to the state-of-the art and can be used to infer time-dependent migration rates from multiple populations. Considering HapMap African-American (ASW) data, we find that a model with two distinct phases of "European" gene flow significantly improves the modeling of both tract lengths and ancestry variances.

Different Parameters Support Generalization and Discrimination Learning in "Drosophila" at the Flight Simulator

Science.gov (United States)

Brembs, Bjorn; de Ibarra, Natalie Hempel

2006-01-01

We have used a genetically tractable model system, the fruit fly "Drosophila melanogaster" to study the interdependence between sensory processing and associative processing on learning performance. We investigated the influence of variations in the physical and predictive properties of color stimuli in several different operant-conditioning…

Robust reactor power control system design by genetic algorithm

Energy Technology Data Exchange (ETDEWEB)

Lee, Yoon Joon; Cho, Kyung Ho; Kim, Sin [Cheju National University, Cheju (Korea, Republic of)

1998-12-31

The H{sub {infinity}} robust controller for the reactor power control system is designed by use of the mixed weight sensitivity. The system is configured into the typical two-port model with which the weight functions are augmented. Since the solution depends on the weighting functions and the problem is of nonconvex, the genetic algorithm is used to determine the weighting functions. The cost function applied in the genetic algorithm permits the direct control of the power tracking performances. In addition, the actual operating constraints such as rod velocity and acceleration can be treated as design parameters. Compared with the conventional approach, the controller designed by the genetic algorithm results in the better performances with the realistic constraints. Also, it is found that the genetic algorithm could be used as an effective tool in the robust design. 4 refs., 6 figs. (Author)

Robust reactor power control system design by genetic algorithm

Energy Technology Data Exchange (ETDEWEB)

Lee, Yoon Joon; Cho, Kyung Ho; Kim, Sin [Cheju National University, Cheju (Korea, Republic of)

1997-12-31

The H{sub {infinity}} robust controller for the reactor power control system is designed by use of the mixed weight sensitivity. The system is configured into the typical two-port model with which the weight functions are augmented. Since the solution depends on the weighting functions and the problem is of nonconvex, the genetic algorithm is used to determine the weighting functions. The cost function applied in the genetic algorithm permits the direct control of the power tracking performances. In addition, the actual operating constraints such as rod velocity and acceleration can be treated as design parameters. Compared with the conventional approach, the controller designed by the genetic algorithm results in the better performances with the realistic constraints. Also, it is found that the genetic algorithm could be used as an effective tool in the robust design. 4 refs., 6 figs. (Author)

Mouse Chromosome Engineering for Modeling Human Disease

OpenAIRE

van der Weyden, Louise; Bradley, Allan

2006-01-01

Chromosomal rearrangements occur frequently in humans and can be disease-associated or phenotypically neutral. Recent technological advances have led to the discovery of copy-number changes previously undetected by cytogenetic techniques. To understand the genetic consequences of such genomic changes, these mutations need to be modeled in experimentally tractable systems. The mouse is an excellent organism for this analysis because of its biological and genetic similarity to humans, and the e...

Next-generation mammalian genetics toward organism-level systems biology.

Science.gov (United States)

Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

2017-01-01

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

Comparison between genetic fuzzy system and neuro fuzzy system to select oil wells for hydraulic fracturing; Comparacao entre genetic fuzzy system e neuro fuzzy system para selecao de pocos de petroleo para fraturamento hidraulico

Energy Technology Data Exchange (ETDEWEB)

Castro, Antonio Orestes de Salvo [PETROBRAS, Rio de Janeiro, RJ (Brazil); Ferreira Filho, Virgilio Jose Martins [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil)

2004-07-01

The hydraulic fracture operation is wide used to increase the oil wells production and to reduce formation damage. Reservoir studies and engineer analysis are made to select the wells for this kind of operation. As the reservoir parameters have some diffuses characteristics, Fuzzy Inference Systems (SIF) have been tested for this selection processes in the last few years. This paper compares the performance of a neuro fuzzy system and a genetic fuzzy system used for hydraulic Fracture well selection, with knowledge acquisition from an operational data base to set the SIF membership functions. The training data and the validation data used were the same for both systems. We concluded that, in despite of the genetic fuzzy system would be a younger process, it got better results than the neuro fuzzy system. Another conclusion was that, as the genetic fuzzy system can work with constraints, the membership functions setting kept the consistency of variables linguistic values. (author)

Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments.

Science.gov (United States)

McNamara, John M; Dall, Sasha R X; Hammerstein, Peter; Leimar, Olof

2016-10-01

There are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist. © 2016 John Wiley & Sons Ltd/CNRS.

Population genetics of Setaria viridis, a new model system.

Science.gov (United States)

Huang, Pu; Feldman, Maximilian; Schroder, Stephan; Bahri, Bochra A; Diao, Xianmin; Zhi, Hui; Estep, Matt; Baxter, Ivan; Devos, Katrien M; Kellogg, Elizabeth A

2014-10-01

An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a worldwide sample of more than 200 S. viridis accessions, using the genotyping-by-sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modelled demographic history and show signal of recent population decline in one subgroup. Finally, we show linkage disequilibrium decay is rapid (<45 kb) in our total sample and slow in genetic subgroups. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work including germplasm preservation, local adaptation, crossing designs and genomewide association studies. © 2014 John Wiley & Sons Ltd.

Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease.

Science.gov (United States)

Lyu, Zhe; Whitman, William B

2017-01-01

Current evolutionary models suggest that Eukaryotes originated from within Archaea instead of being a sister lineage. To test this model of ancient evolution, we review recent studies and compare the three major information processing subsystems of replication, transcription and translation in the Archaea and Eukaryotes. Our hypothesis is that if the Eukaryotes arose within the archaeal radiation, their information processing systems will appear to be one of kind and not wholly original. Within the Eukaryotes, the mammalian or human systems are emphasized because of their importance in understanding health. Biochemical as well as genetic studies provide strong evidence for the functional similarity of archaeal homologs to the mammalian information processing system and their dissimilarity to the bacterial systems. In many independent instances, a simple archaeal system is functionally equivalent to more elaborate eukaryotic homologs, suggesting that evolution of complexity is likely an central feature of the eukaryotic information processing system. Because fewer components are often involved, biochemical characterizations of the archaeal systems are often easier to interpret. Similarly, the archaeal cell provides a genetically and metabolically simpler background, enabling convenient studies on the complex information processing system. Therefore, Archaea could serve as a parsimonious and tractable host for studying human diseases that arise in the information processing systems.

Air data system optimization using a genetic algorithm

Science.gov (United States)

Deshpande, Samir M.; Kumar, Renjith R.; Seywald, Hans; Siemers, Paul M., III

1992-01-01

An optimization method for flush-orifice air data system design has been developed using the Genetic Algorithm approach. The optimization of the orifice array minimizes the effect of normally distributed random noise in the pressure readings on the calculation of air data parameters, namely, angle of attack, sideslip angle and freestream dynamic pressure. The optimization method is applied to the design of Pressure Distribution/Air Data System experiment (PD/ADS) proposed for inclusion in the Aeroassist Flight Experiment (AFE). Results obtained by the Genetic Algorithm method are compared to the results obtained by conventional gradient search method.

Stabilization of Electromagnetic Suspension System Behavior by Genetic Algorithm

Directory of Open Access Journals (Sweden)

Abbas Najar Khoda Bakhsh

2012-07-01

Full Text Available Electromagnetic suspension system with a nonlinear and unstable behavior, is used in maglev trains. In this paper a linear mathematical model of system is achieved and the state feedback method is used to improve the system stability. The control coefficients are tuned by two different methods, Riccati and a new method based on Genetic algorithm. In this new proposed method, we use Genetic algorithm to achieve the optimum values of control coefficients. The results of the system simulation by Matlab indicate the effectiveness of new proposed system. When a new reference of air gap is needed or a new external force is added, the proposed system could omit the vibration and shake of the train coupe and so, passengers feel more comfortable.

Optimization of Neuro-Fuzzy System Using Genetic Algorithm for Chromosome Classification

Directory of Open Access Journals (Sweden)

M. Sarosa

2013-09-01

Full Text Available Neuro-fuzzy system has been shown to provide a good performance on chromosome classification but does not offer a simple method to obtain the accurate parameter values required to yield the best recognition rate. This paper presents a neuro-fuzzy system where its parameters can be automatically adjusted using genetic algorithms. The approach combines the advantages of fuzzy logic theory, neural networks, and genetic algorithms. The structure consists of a four layer feed-forward neural network that uses a GBell membership function as the output function. The proposed methodology has been applied and tested on banded chromosome classification from the Copenhagen Chromosome Database. Simulation result showed that the proposed neuro-fuzzy system optimized by genetic algorithms offers advantages in setting the parameter values, improves the recognition rate significantly and decreases the training/testing time which makes genetic neuro-fuzzy system suitable for chromosome classification.

Strains and Stressors: An Analysis of Touchscreen Learning in Genetically Diverse Mouse Strains

Science.gov (United States)

Graybeal, Carolyn; Bachu, Munisa; Mozhui, Khyobeni; Saksida, Lisa M.; Bussey, Timothy J.; Sagalyn, Erica; Williams, Robert W.; Holmes, Andrew

2014-01-01

Touchscreen-based systems are growing in popularity as a tractable, translational approach for studying learning and cognition in rodents. However, while mouse strains are well known to differ in learning across various settings, performance variation between strains in touchscreen learning has not been well described. The selection of appropriate genetic strains and backgrounds is critical to the design of touchscreen-based studies and provides a basis for elucidating genetic factors moderating behavior. Here we provide a quantitative foundation for visual discrimination and reversal learning using touchscreen assays across a total of 35 genotypes. We found significant differences in operant performance and learning, including faster reversal learning in DBA/2J compared to C57BL/6J mice. We then assessed DBA/2J and C57BL/6J for differential sensitivity to an environmental insult by testing for alterations in reversal learning following exposure to repeated swim stress. Stress facilitated reversal learning (selectively during the late stage of reversal) in C57BL/6J, but did not affect learning in DBA/2J. To dissect genetic factors underlying these differences, we phenotyped a family of 27 BXD strains generated by crossing C57BL/6J and DBA/2J. There was marked variation in discrimination, reversal and extinction learning across the BXD strains, suggesting this task may be useful for identifying underlying genetic differences. Moreover, different measures of touchscreen learning were only modestly correlated in the BXD strains, indicating that these processes are comparatively independent at both genetic and phenotypic levels. Finally, we examined the behavioral structure of learning via principal component analysis of the current data, plus an archival dataset, totaling 765 mice. This revealed 5 independent factors suggestive of “reversal learning,” “motivation-related late reversal learning,” “discrimination learning,” “speed to respond,” and �

Dynamic modeling of genetic networks using genetic algorithm and S-system.

Science.gov (United States)

Kikuchi, Shinichi; Tominaga, Daisuke; Arita, Masanori; Takahashi, Katsutoshi; Tomita, Masaru

2003-03-22

The modeling of system dynamics of genetic networks, metabolic networks or signal transduction cascades from time-course data is formulated as a reverse-problem. Previous studies focused on the estimation of only network structures, and they were ineffective in inferring a network structure with feedback loops. We previously proposed a method to predict not only the network structure but also its dynamics using a Genetic Algorithm (GA) and an S-system formalism. However, it could predict only a small number of parameters and could rarely obtain essential structures. In this work, we propose a unified extension of the basic method. Notable improvements are as follows: (1) an additional term in its evaluation function that aims at eliminating futile parameters; (2) a crossover method called Simplex Crossover (SPX) to improve its optimization ability; and (3) a gradual optimization strategy to increase the number of predictable parameters. The proposed method is implemented as a C program called PEACE1 (Predictor by Evolutionary Algorithms and Canonical Equations 1). Its performance was compared with the basic method. The comparison showed that: (1) the convergence rate increased about 5-fold; (2) the optimization speed was raised about 1.5-fold; and (3) the number of predictable parameters was increased about 5-fold. Moreover, we successfully inferred the dynamics of a small genetic network constructed with 60 parameters for 5 network variables and feedback loops using only time-course data of gene expression.

Molecular marker systems for Oenothera genetics.

Science.gov (United States)

Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

2008-11-01

The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

Evolving rule-based systems in two medical domains using genetic programming.

Science.gov (United States)

Tsakonas, Athanasios; Dounias, Georgios; Jantzen, Jan; Axer, Hubertus; Bjerregaard, Beth; von Keyserlingk, Diedrich Graf

2004-11-01

To demonstrate and compare the application of different genetic programming (GP) based intelligent methodologies for the construction of rule-based systems in two medical domains: the diagnosis of aphasia's subtypes and the classification of pap-smear examinations. Past data representing (a) successful diagnosis of aphasia's subtypes from collaborating medical experts through a free interview per patient, and (b) correctly classified smears (images of cells) by cyto-technologists, previously stained using the Papanicolaou method. Initially a hybrid approach is proposed, which combines standard genetic programming and heuristic hierarchical crisp rule-base construction. Then, genetic programming for the production of crisp rule based systems is attempted. Finally, another hybrid intelligent model is composed by a grammar driven genetic programming system for the generation of fuzzy rule-based systems. Results denote the effectiveness of the proposed systems, while they are also compared for their efficiency, accuracy and comprehensibility, to those of an inductive machine learning approach as well as to those of a standard genetic programming symbolic expression approach. The proposed GP-based intelligent methodologies are able to produce accurate and comprehensible results for medical experts performing competitive to other intelligent approaches. The aim of the authors was the production of accurate but also sensible decision rules that could potentially help medical doctors to extract conclusions, even at the expense of a higher classification score achievement.

The Collaborative Cross Resource for Systems Genetics Research of Infectious Diseases.

Science.gov (United States)

Maurizio, Paul L; Ferris, Martin T

2017-01-01

An increasing body of evidence highlights the role of host genetic variation in driving susceptibility to severe disease following pathogen infection. In order to fully appreciate the importance of host genetics on infection susceptibility and resulting disease, genetically variable experimental model systems should be employed. These systems allow for the identification, characterization, and mechanistic dissection of genetic variants that cause differential disease responses. Herein we discuss application of the Collaborative Cross (CC) panel of recombinant inbred strains to study viral pathogenesis, focusing on practical considerations for experimental design, assessment and analysis of disease responses within the CC, as well as some of the resources developed for the CC. Although the focus of this chapter is on viral pathogenesis, many of the methods presented within are applicable to studies of other pathogens, as well as to case-control designs in genetically diverse populations.

Applications of Systems Genetics and Biology for Obesity Using Pig Models

DEFF Research Database (Denmark)

Kogelman, Lisette; Kadarmideen, Haja N.

2016-01-01

approach, a branch of systems biology. In this chapter, we will describe the state of the art of genetic studies on human obesity, using pig populations. We will describe the features of using the pig as a model for human obesity and briefly discuss the genetics of obesity, and we will focus on systems...

Immune System and Genetics: A Different Approach to the Diversity of Antibodies

International Nuclear Information System (INIS)

Matta Camacho, Nubia Estela

2011-01-01

It is common to find in immunology or genetic books a chapter entitled immune system and genetics; this association focuses on how the generation of antibodies broke the paradigm one gene, one protein, since in this case one gene generates millions of proteins. However, the immune system has many more links to genetics and heredity. For example, any substance or compound that an organism produces is a potential antigen, when it is recognized as foreign by the immune system of another organism from the same or different species. The proteins that are potentially antigenic are encoded by the individual's genotype. The ability of the immune system to respond to antigenic proteins, as well as the type and intensity of that response, are also correlated with the organism's genotype. In addition, deficiencies in the immune response may be associated with mutations or genetic polymorphisms, which result in susceptibility to infection diseases.

Time-Delay System Identification Using Genetic Algorithm

DEFF Research Database (Denmark)

Yang, Zhenyu; Seested, Glen Thane

2013-01-01

problem through an identification approach using the real coded Genetic Algorithm (GA). The desired FOPDT/SOPDT model is directly identified based on the measured system's input and output data. In order to evaluate the quality and performance of this GA-based approach, the proposed method is compared...

Genetic algorithms for adaptive real-time control in space systems

Science.gov (United States)

Vanderzijp, J.; Choudry, A.

1988-01-01

Genetic Algorithms that are used for learning as one way to control the combinational explosion associated with the generation of new rules are discussed. The Genetic Algorithm approach tends to work best when it can be applied to a domain independent knowledge representation. Applications to real time control in space systems are discussed.

Advances in faba bean genetics and genomics

Directory of Open Access Journals (Sweden)

Donal Martin O'Sullivan

2016-08-01

Full Text Available Vicia faba L, is a globally important grain legume whose main centres of diversity are the Fertile Crescent and Mediterranean basin. Because of its small number (six of exceptionally large and easily observed chromosomes it became a model species for plant cytogenetics the 70s and 80s. It is somewhat ironic therefore, that the emergence of more genomically tractable model plant species such as Arabidopsis and Medicago coincided with a marked decline in genome research on the formerly favoured plant cytogenetic model. Thus, as ever higher density molecular marker coverage and dense genetic and even complete genome sequence maps of key crop and model species emerged through the 1990s and early 2000s, genetic and genome knowledge of Vicia faba lagged far behind other grain legumes such as soybean, common bean and pea.However, cheap sequencing technologies have stimulated the production of deep transcriptome coverage from several tissue types and numerous distinct cultivars in recent years. This has permitted the reconstruction of the faba bean meta-transcriptome and has fuelled development of extensive sets of Simple Sequence Repeat and Single Nucleotide Polymorphism (SNP markers. Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic maps. A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance to a series of biotic and abiotic stresses were conducted during the 1990’s and early 2000s. More recently, SNP-based genetic maps have permitted chromosome intervals of interest to be aligned to collinear segments of sequenced legume genomes such as the model legume Medicago truncatula, which in turn opens up the possibility for hypotheses on gene content, order and function to be translated from model to crop. Some examples of where knowledge of gene content and function have already been productively exploited are

Mapping genetic influences on the corticospinal motor system in humans

DEFF Research Database (Denmark)

Cheeran, B J; Ritter, C; Rothwell, J C

2009-01-01

of the contribution of single nucleotide polymorphisms (SNP) and variable number tandem repeats. In humans, the corticospinal motor system is essential to the acquisition of fine manual motor skills which require a finely tuned coordination of activity in distal forelimb muscles. Here we review recent brain mapping......It is becoming increasingly clear that genetic variations account for a certain amount of variance in the acquisition and maintenance of different skills. Until now, several levels of genetic influences were examined, ranging from global heritability estimates down to the analysis...... studies that have begun to explore the influence of functional genetic variation as well as mutations on function and structure of the human corticospinal motor system, and also the clinical implications of these studies. Transcranial magnetic stimulation of the primary motor hand area revealed...

Global Optimization of a Periodic System using a Genetic Algorithm

Science.gov (United States)

Stucke, David; Crespi, Vincent

2001-03-01

We use a novel application of a genetic algorithm global optimizatin technique to find the lowest energy structures for periodic systems. We apply this technique to colloidal crystals for several different stoichiometries of binary and trinary colloidal crystals. This application of a genetic algorithm is decribed and results of likely candidate structures are presented.

A systems genetics approach provides a bridge from discovered genetic variants to biological pathways in rheumatoid arthritis.

Directory of Open Access Journals (Sweden)

Hirofumi Nakaoka

Full Text Available Genome-wide association studies (GWAS have yielded novel genetic loci underlying common diseases. We propose a systems genetics approach to utilize these discoveries for better understanding of the genetic architecture of rheumatoid arthritis (RA. Current evidence of genetic associations with RA was sought through PubMed and the NHGRI GWAS catalog. The associations of 15 single nucleotide polymorphisms and HLA-DRB1 alleles were confirmed in 1,287 cases and 1,500 controls of Japanese subjects. Among these, HLA-DRB1 alleles and eight SNPs showed significant associations and all but one of the variants had the same direction of effect as identified in the previous studies, indicating that the genetic risk factors underlying RA are shared across populations. By receiver operating characteristic curve analysis, the area under the curve (AUC for the genetic risk score based on the selected variants was 68.4%. For seropositive RA patients only, the AUC improved to 70.9%, indicating good but suboptimal predictive ability. A simulation study shows that more than 200 additional loci with similar effect size as recent GWAS findings or 20 rare variants with intermediate effects are needed to achieve AUC = 80.0%. We performed the random walk with restart (RWR algorithm to prioritize genes for future mapping studies. The performance of the algorithm was confirmed by leave-one-out cross-validation. The RWR algorithm pointed to ZAP70 in the first rank, in which mutation causes RA-like autoimmune arthritis in mice. By applying the hierarchical clustering method to a subnetwork comprising RA-associated genes and top-ranked genes by the RWR, we found three functional modules relevant to RA etiology: "leukocyte activation and differentiation", "pattern-recognition receptor signaling pathway", and "chemokines and their receptors".These results suggest that the systems genetics approach is useful to find directions of future mapping strategies to illuminate

Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida.

Science.gov (United States)

Lehnert, Erik M; Burriesci, Matthew S; Pringle, John R

2012-06-22

Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can lead to a breakdown of the essential symbiotic relationship between the coral host and its endosymbiotic dinoflagellates, a process known as coral bleaching. Although the environmental stresses causing this breakdown are largely known, the cellular mechanisms of symbiosis establishment, maintenance, and breakdown are still largely obscure. Investigating the symbiosis using an experimentally tractable model organism, such as the small sea anemone Aiptasia, should improve our understanding of exactly how the environmental stressors affect coral survival and growth. We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free) Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. We demonstrated that many of these contigs represent full-length or near-full-length transcripts that encode proteins similar to those from a diverse array of pathways in other organisms, including various metabolic enzymes, cytoskeletal proteins, and neuropeptide precursors. The contigs were annotated by sequence similarity, assigned GO terms, and scanned for conserved protein domains. We analyzed the frequency and types of single-nucleotide variants and estimated the size of the Aiptasia genome to be ~421 Mb. The contigs and annotations are available through NCBI (Transcription Shotgun Assembly database, accession numbers JV077153-JV134524) and at http://pringlelab.stanford.edu/projects.html. The availability of an extensive transcriptome assembly for A. pallida will facilitate analyses of gene-expression changes, identification of proteins of interest, and other studies in this important emerging model system.

Nuclear power control system design using genetic algorithm

International Nuclear Information System (INIS)

Lee, Yoon Joon; Cho, Kyung Ho

1996-01-01

The genetic algorithm(GA) is applied to the design of the nuclear power control system. The reactor control system model is described in the LQR configuration. The LQR system order is increased to make the tracking system. The key parameters of the design are weighting matrices, and these are usually determined through numerous simulations in the conventional design. To determine the more objective and optimal weightings, the improved GA is applied. The results show that the weightings determined by the GA yield the better system responses than those obtained by the conventional design method

US system of oversight for genetic testing: a report from the Secretary's Advisory Committee on Genetics, Health and Society.

Science.gov (United States)

Ferreira-Gonzalez, Andrea; Teutsch, Steven; Williams, Marc S; Au, Sylvia M; Fitzgerald, Kevin T; Miller, Paul Steven; Fomous, Cathy

2008-09-01

As genetic testing technology is integrated into healthcare, increasingly detailed information about individual and population genetic variation is available to patients and providers. Health professionals use genetic testing to diagnose or assess the risk of disease in individuals, families and populations and to guide healthcare decisions. Consumers are beginning to explore personalized genomic services in an effort to learn more about their risk for common diseases. Scientific and technological advances in genetic testing, as with any newly introduced medical technology, present certain challenges to existing frameworks of oversight. In addition, the growing use of genetic testing will require a significant investment in evidence-based assessments to understand the validity and utility of these tests in clinical and personal decisionmaking. To optimize the use of genetic testing in healthcare, all sectors of the oversight system need to be strengthened and yet remain flexible in order to adapt to advances that will inevitably increase the range of genetic tests and methodologies.

Multimodal sensorimotor system in unicellular zoospores of a fungus.

Science.gov (United States)

Swafford, Andrew J M; Oakley, Todd H

2018-01-19

Complex sensory systems often underlie critical behaviors, including avoiding predators and locating prey, mates and shelter. Multisensory systems that control motor behavior even appear in unicellular eukaryotes, such as Chlamydomonas , which are important laboratory models for sensory biology. However, we know of no unicellular opisthokonts that control motor behavior using a multimodal sensory system. Therefore, existing single-celled models for multimodal sensorimotor integration are very distantly related to animals. Here, we describe a multisensory system that controls the motor function of unicellular fungal zoospores. We found that zoospores of Allomyces arbusculus exhibit both phototaxis and chemotaxis. Furthermore, we report that closely related Allomyces species respond to either the chemical or the light stimuli presented in this study, not both, and likely do not share this multisensory system. This diversity of sensory systems within Allomyces provides a rare example of a comparative framework that can be used to examine the evolution of sensory systems following the gain/loss of available sensory modalities. The tractability of Allomyces and related fungi as laboratory organisms will facilitate detailed mechanistic investigations into the genetic underpinnings of novel photosensory systems, and how multisensory systems may have functioned in early opisthokonts before multicellularity allowed for the evolution of specialized cell types. © 2018. Published by The Company of Biologists Ltd.

[Reverse genetics system of rotaviruses: development and application for analysis of VP4 spike protein].

Science.gov (United States)

Komoto, Satoshi

2013-01-01

The rotavirus genome is composed of 11 gene segments of double-stranded (ds)RNA. Reverse genetics is the powerful and ideal methodology for the molecular analysis of virus biology, which enables the virus genome to be artificially manipulated. Although reverse genetics systems exist for nearly all major groups of RNA viruses, development of such a system for rotaviruses is more challenging owing in part to the technical complexity of manipulation of their multi-segmented genome. A breakthrough in the field of rotavirus reverse genetics came in 2006, when we established the first reverse genetics system for rotaviruses, which is a partially plasmid-based system that permits replacement of a viral gene segment with the aid of a helper virus. Although this helper virus-driven system is technically limited and gives low levels of recombinant viruses, it allows alteration of the rotavirus genome, thus contributing to our understanding of these medically important viruses. In this review, I describe the development and application of our rotavirus reverse genetics system, and its future perspectives.

The perceived impact of the European registration system for genetic counsellors and nurses.

Science.gov (United States)

Paneque, Milena; Moldovan, Ramona; Cordier, Christophe; Serra-Juhé, Clara; Feroce, Irene; Pasalodos, Sara; Haquet, Emmanuelle; Lambert, Debby; Bjørnevoll, Inga; Skirton, Heather

2017-09-01

The aim of the European Board of Medical Genetics has been to develop and promote academic and professional standards necessary in order to provide competent genetic counselling services. The aim of this study was to explore the impact of the European registration system for genetic nurses and counsellors from the perspectives of those professionals who have registered. Registration system was launched in 2013. A cross-sectional, online survey was used to explore the motivations and experiences of those applying for, and the effect of registration on their career. Fifty-five Genetic Nurses and Counsellors are registered till now, from them, thirty-three agreed to participate on this study. The main motivations for registering were for recognition of their work value and competence (30.3%); due to the absence of a registration system in their own country (15.2%) and the possibility of obtaining a European/international certification (27.3%), while 27.3% of respondents registered to support recognition of the genetic counselling profession. Some participants valued the registration process as an educational activity in its own right, while the majority indicated the greatest impact of the registration process was on their clinical practice. The results confirm that registrants value the opportunity to both confirm their own competence and advance the genetic counselling profession in Europe.

Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida

Directory of Open Access Journals (Sweden)

Lehnert Erik M

2012-06-01

Full Text Available Abstract Background Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can lead to a breakdown of the essential symbiotic relationship between the coral host and its endosymbiotic dinoflagellates, a process known as coral bleaching. Although the environmental stresses causing this breakdown are largely known, the cellular mechanisms of symbiosis establishment, maintenance, and breakdown are still largely obscure. Investigating the symbiosis using an experimentally tractable model organism, such as the small sea anemone Aiptasia, should improve our understanding of exactly how the environmental stressors affect coral survival and growth. Results We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. We demonstrated that many of these contigs represent full-length or near-full-length transcripts that encode proteins similar to those from a diverse array of pathways in other organisms, including various metabolic enzymes, cytoskeletal proteins, and neuropeptide precursors. The contigs were annotated by sequence similarity, assigned GO terms, and scanned for conserved protein domains. We analyzed the frequency and types of single-nucleotide variants and estimated the size of the Aiptasia genome to be ~421 Mb. The contigs and annotations are available through NCBI (Transcription Shotgun Assembly database, accession numbers JV077153-JV134524 and at http://pringlelab.stanford.edu/projects.html. Conclusions The availability of an extensive transcriptome assembly for A. pallida will facilitate analyses of gene-expression changes, identification of proteins of interest, and other studies in this

A Genetic Based Neuro-Fuzzy Controller System

International Nuclear Information System (INIS)

Mohamed, A.H.

2014-01-01

Recently, the mobile robots have great importance in the manufacturing processes. They are widely used for assembling processes, handling the dangerous components, moving the weighted things, etc. Designing the controller of the mobile robot is a very complex task. Many simple control systems used the neuro-fuzzy controller in the mobile robots. But, they faced with great complexity when moving in unstructured and dynamic environments. The proposed system introduces the uses of the genetic algorithm for optimizing the parameters of the neuro-fuzzy controller. So, the proposed system can improve the performance of the mobile robots. It has applied for a mobile robot used for moving the dangerous and critical materials in unstructured environment. Its results are compared with other traditional controller systems. The suggested system has proved its success for the real-time applications

Opposing Fat Metabolism Pathways Triggered by a Single Gene

OpenAIRE

Gilst, Marc R. Van; Hadjivassiliou, Haralambos; Jolly, Amber; Yamamoto, Keith R

2005-01-01

Mammalian nuclear hormone receptors (NHRs), such as liver X receptor, farnesoid X receptor, and peroxisome proliferator-activated receptors (PPARs), precisely control energy metabolism. Consequently, these receptors are important targets for the treatment of metabolic diseases, including diabetes and obesity. A thorough understanding of NHR fat regulatory networks has been limited, however, by a lack of genetically tractable experimental systems. Here we show that deletion of the Caenorhabdit...

Unfolding neutron spectra obtained from BS–TLD system using genetic algorithm

International Nuclear Information System (INIS)

Santos, J.A.L.; Silva, E.R.; Ferreira, T.A.E; Vilela, E.C.

2012-01-01

Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as a function of energy should be characterized. The precise information allows radiological quantities establishment related to that spectrum, but it is necessary that a spectrometric system covers a large interval of energy and an unfolding process is appropriate. This paper proposes use of a technique of Artificial Intelligence (AI) called genetic algorithm (GA), which uses bio-inspired mathematical models with the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a BS system to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enabling this technique to unfold neutron spectra with the BS–TLD system. - Highlights: ► The unfolding code used the artificial intelligence technique called genetic algorithms. ► A response matrix specific to the unfolding data obtained with the BS–TLD system is used by the AGLN. ► The observed results demonstrate the potential use of genetic algorithms in solving complex nuclear problems.

A New Selectable Marker System for Genetic Studies of Bacteria: Final Report

Energy Technology Data Exchange (ETDEWEB)

Parsons, D; Tolmasky, M; Chain, P; Segelke, B W

2011-03-18

Genetic manipulations in bacteria currently rely on the introduction of antibiotic resistance genes into a bacterial strain; for those organisms that will be used for commercial or industrial applications, the genetic cassette encoding the antibiotic resistance is sometimes removed after selection. it is clear that if alternative technologies could obviate the need to introduce antibiotic resistance into bacteria, they would most certainly become a standard tool in molecular micriobiology for commercial, industrial as well as research applications. Here, they present the development of a novel genetic engineering technology based on toxin-antitoxin systems to modify bacterial genomes without the use of antibiotic resistance in the mutagenesis process. The primary goal is to develop antibiotic-free selection for genetically altered select agent pathogens. They are adapting the toxinc-antitoxin system to enable gene replacement in select agent pathogens since the NIH restrictions introducing antibiotic resistance into select agent pathogens have hindered research with select agent pathogens.

Genetic coding and united-hypercomplex systems in the models of algebraic biology.

Science.gov (United States)

Petoukhov, Sergey V

2017-08-01

Structured alphabets of DNA and RNA in their matrix form of representations are connected with Walsh functions and a new type of systems of multidimensional numbers. This type generalizes systems of complex numbers and hypercomplex numbers, which serve as the basis of mathematical natural sciences and many technologies. The new systems of multi-dimensional numbers have interesting mathematical properties and are called in a general case as "systems of united-hypercomplex numbers" (or briefly "U-hypercomplex numbers"). They can be widely used in models of multi-parametrical systems in the field of algebraic biology, artificial life, devices of biological inspired artificial intelligence, etc. In particular, an application of U-hypercomplex numbers reveals hidden properties of genetic alphabets under cyclic permutations in their doublets and triplets. A special attention is devoted to the author's hypothesis about a multi-linguistic in DNA-sequences in a relation with an ensemble of U-numerical sub-alphabets. Genetic multi-linguistic is considered as an important factor to provide noise-immunity properties of the multi-channel genetic coding. Our results attest to the conformity of the algebraic properties of the U-numerical systems with phenomenological properties of the DNA-alphabets and with the complementary device of the double DNA-helix. It seems that in the modeling field of algebraic biology the genetic-informational organization of living bodies can be considered as a set of united-hypercomplex numbers in some association with the famous slogan of Pythagoras "the numbers rule the world". Copyright © 2017 Elsevier B.V. All rights reserved.

Integrative Functional Genomics for Systems Genetics in GeneWeaver.org.

Science.gov (United States)

Bubier, Jason A; Langston, Michael A; Baker, Erich J; Chesler, Elissa J

2017-01-01

The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems.

Science.gov (United States)

Croll, Daniel; McDonald, Bruce A

2017-04-01

Local adaptation plays a key role in the evolutionary trajectory of host-pathogen interactions. However, the genetic architecture of local adaptation in host-pathogen systems is poorly understood. Fungal plant pathogens in agricultural ecosystems provide highly tractable models to quantify phenotypes and map traits to corresponding genomic loci. The outcome of crop-pathogen interactions is thought to be governed largely by gene-for-gene interactions. However, recent studies showed that virulence can be governed by quantitative trait loci and that many abiotic factors contribute to the outcome of the interaction. After introducing concepts of local adaptation and presenting examples from wild plant pathosystems, we focus this review on a major pathogen of wheat, Zymoseptoria tritici, to show how a multitude of traits can affect local adaptation. Zymoseptoria tritici adapted to different thermal environments across its distribution range, indicating that thermal adaptation may limit effective dispersal to different climates. The application of fungicides led to the rapid evolution of multiple, independent resistant populations. The degree of colony melanization showed strong pleiotropic effects with other traits, including trade-offs with colony growth rates and fungicide sensitivity. The success of the pathogen on its host can be assessed quantitatively by counting pathogen reproductive structures and measuring host damage based on necrotic lesions. Interestingly, these two traits can be weakly correlated and depend both on host and pathogen genotypes. Quantitative trait mapping studies showed that the genetic architecture of locally adapted traits varies from single loci with large effects to many loci with small individual effects. We discuss how local adaptation could hinder or accelerate the development of epidemics in agricultural ecosystems. © 2016 John Wiley & Sons Ltd.

Symmetries in Genetic Systems and the Concept of Geno-Logical Coding

Directory of Open Access Journals (Sweden)

Sergey V. Petoukhov

2016-12-01

Full Text Available The genetic code of amino acid sequences in proteins does not allow understanding and modeling of inherited processes such as inborn coordinated motions of living bodies, innate principles of sensory information processing, quasi-holographic properties, etc. To be able to model these phenomena, the concept of geno-logical coding, which is connected with logical functions and Boolean algebra, is put forward. The article describes basic pieces of evidence in favor of the existence of the geno-logical code, which exists in p­arallel with the known genetic code of amino acid sequences but which serves for transferring inherited processes along chains of generations. These pieces of evidence have been received due to the analysis of symmetries in structures of molecular-genetic systems. The analysis has revealed a close connection of the genetic system with dyadic groups of binary numbers and with other mathematical objects, which are related with dyadic groups: Walsh functions (which are algebraic characters of dyadic groups, bit-reversal permutations, logical holography, etc. These results provide a new approach for mathematical modeling of genetic structures, which uses known mathematical formalisms from technological fields of noise-immunity coding of information, binary analysis, logical holography, and digital devices of artificial intellect. Some opportunities for a development of algebraic-logical biology are opened.

Identifying genetic variants that affect viability in large cohorts.

Directory of Open Access Journals (Sweden)

Hakhamanesh Mostafavi

2017-09-01

Full Text Available A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Adult Health and Aging (GERA cohort and to the parents of participants in the UK Biobank. Across the genome, we found only a few common variants with large effects on age-specific mortality: tagging the APOE ε4 allele and near CHRNA3. These results suggest that when large, even late-onset effects are kept at low frequency by purifying selection. Testing viability effects of sets of genetic variants that jointly influence 1 of 42 traits, we detected a number of strong signals. In participants of the UK Biobank of British ancestry, we found that variants that delay puberty timing are associated with a longer parental life span (P~6.2 × 10-6 for fathers and P~2.0 × 10-3 for mothers, consistent with epidemiological studies. Similarly, variants associated with later age at first birth are associated with a longer maternal life span (P~1.4 × 10-3. Signals are also observed for variants influencing cholesterol levels, risk of coronary artery disease (CAD, body mass index, as well as risk of asthma. These signals exhibit consistent effects in the GERA cohort and among participants of the UK Biobank of non-British ancestry. We also found marked differences between males and females, most notably at the CHRNA3 locus, and variants associated with risk of CAD and cholesterol levels. Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical data sets can be used to learn about selection effects in contemporary humans.

Optimal design of link systems using successive zooming genetic algorithm

Science.gov (United States)

Kwon, Young-Doo; Sohn, Chang-hyun; Kwon, Soon-Bum; Lim, Jae-gyoo

2009-07-01

Link-systems have been around for a long time and are still used to control motion in diverse applications such as automobiles, robots and industrial machinery. This study presents a procedure involving the use of a genetic algorithm for the optimal design of single four-bar link systems and a double four-bar link system used in diesel engine. We adopted the Successive Zooming Genetic Algorithm (SZGA), which has one of the most rapid convergence rates among global search algorithms. The results are verified by experiment and the Recurdyn dynamic motion analysis package. During the optimal design of single four-bar link systems, we found in the case of identical input/output (IO) angles that the initial and final configurations show certain symmetry. For the double link system, we introduced weighting factors for the multi-objective functions, which minimize the difference between output angles, providing balanced engine performance, as well as the difference between final output angle and the desired magnitudes of final output angle. We adopted a graphical method to select a proper ratio between the weighting factors.

Genetic learning in rule-based and neural systems

Science.gov (United States)

Smith, Robert E.

1993-01-01

The design of neural networks and fuzzy systems can involve complex, nonlinear, and ill-conditioned optimization problems. Often, traditional optimization schemes are inadequate or inapplicable for such tasks. Genetic Algorithms (GA's) are a class of optimization procedures whose mechanics are based on those of natural genetics. Mathematical arguments show how GAs bring substantial computational leverage to search problems, without requiring the mathematical characteristics often necessary for traditional optimization schemes (e.g., modality, continuity, availability of derivative information, etc.). GA's have proven effective in a variety of search tasks that arise in neural networks and fuzzy systems. This presentation begins by introducing the mechanism and theoretical underpinnings of GA's. GA's are then related to a class of rule-based machine learning systems called learning classifier systems (LCS's). An LCS implements a low-level production-system that uses a GA as its primary rule discovery mechanism. This presentation illustrates how, despite its rule-based framework, an LCS can be thought of as a competitive neural network. Neural network simulator code for an LCS is presented. In this context, the GA is doing more than optimizing and objective function. It is searching for an ecology of hidden nodes with limited connectivity. The GA attempts to evolve this ecology such that effective neural network performance results. The GA is particularly well adapted to this task, given its naturally-inspired basis. The LCS/neural network analogy extends itself to other, more traditional neural networks. Conclusions to the presentation discuss the implications of using GA's in ecological search problems that arise in neural and fuzzy systems.

Recent insights into the genetic basis of systemic lupus erythematosus

OpenAIRE

Moser, Kathy L.; Kelly, Jennifer A.; Lessard, Christopher J.; Harley, John B.

2009-01-01

Genetic variation was first shown to be part of the cause of systemic lupus erythematosus (SLE or lupus) in the 1970s with associations in the human leukocyte antigen (HLA) region. Almost four decades later, and with the help of increasingly powerful genetic approaches, more than 25 genes are now known to contribute to the mechanisms that predispose individuals to lupus. Over half of these loci have been discovered in the past two years, underscoring the extraordinary success of recent genome...

A Neuro-genetic Based Short-term Forecasting Framework for Network Intrusion Prediction System

Institute of Scientific and Technical Information of China (English)

Siva S. Sivatha Sindhu; S. Geetha; M. Marikannan; A. Kannan

2009-01-01

Information systems are one of the most rapidly changing and vulnerable systems, where security is a major issue. The number of security-breaking attempts originating inside organizations is increasing steadily. Attacks made in this way, usually done by "authorized" users of the system, cannot be immediately traced. Because the idea of filtering the traffic at the entrance door, by using firewalls and the like, is not completely successful, the use of intrusion detection systems should be considered to increase the defense capacity of an information system. An intrusion detection system (IDS) is usually working in a dynamically changing environment, which forces continuous tuning of the intrusion detection model, in order to maintain sufficient performance. The manual tuning process required by current IDS depends on the system operators in working out the tuning solution and in integrating it into the detection model. Furthermore, an extensive effort is required to tackle the newly evolving attacks and a deep study is necessary to categorize it into the respective classes. To reduce this dependence, an automatically evolving anomaly IDS using neuro-genetic algorithm is presented. The proposed system automatically tunes the detection model on the fly according to the feedback provided by the system operator when false predictions are encountered. The system has been evaluated using the Knowledge Discovery in Databases Conference (KDD 2009) intrusion detection dataset. Genetic paradigm is employed to choose the predominant features, which reveal the occurrence of intrusions. The neuro-genetic IDS (NGIDS) involves calculation of weightage value for each of the categorical attributes so that data of uniform representation can be processed by the neuro-genetic algorithm. In this system unauthorized invasion of a user are identified and newer types of attacks are sensed and classified respectively by the neuro-genetic algorithm. The experimental results obtained in this

Global structural optimizations of surface systems with a genetic algorithm

International Nuclear Information System (INIS)

Chuang, Feng-Chuan

2005-01-01

Global structural optimizations with a genetic algorithm were performed for atomic cluster and surface systems including aluminum atomic clusters, Si magic clusters on the Si(111) 7 x 7 surface, silicon high-index surfaces, and Ag-induced Si(111) reconstructions. First, the global structural optimizations of neutral aluminum clusters Al n (n up to 23) were performed using a genetic algorithm coupled with a tight-binding potential. Second, a genetic algorithm in combination with tight-binding and first-principles calculations were performed to study the structures of magic clusters on the Si(111) 7 x 7 surface. Extensive calculations show that the magic cluster observed in scanning tunneling microscopy (STM) experiments consist of eight Si atoms. Simulated STM images of the Si magic cluster exhibit a ring-like feature similar to STM experiments. Third, a genetic algorithm coupled with a highly optimized empirical potential were used to determine the lowest energy structure of high-index semiconductor surfaces. The lowest energy structures of Si(105) and Si(114) were determined successfully. The results of Si(105) and Si(114) are reported within the framework of highly optimized empirical potential and first-principles calculations. Finally, a genetic algorithm coupled with Si and Ag tight-binding potentials were used to search for Ag-induced Si(111) reconstructions at various Ag and Si coverages. The optimized structural models of √3 x √3, 3 x 1, and 5 x 2 phases were reported using first-principles calculations. A novel model is found to have lower surface energy than the proposed double-honeycomb chained (DHC) model both for Au/Si(111) 5 x 2 and Ag/Si(111) 5 x 2 systems

Setaria viridis as a model system to advance millet genetics and genomics

Directory of Open Access Journals (Sweden)

Pu Huang

2016-11-01

Full Text Available Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crop.

Setaria viridis as a Model System to Advance Millet Genetics and Genomics.

Science.gov (United States)

Huang, Pu; Shyu, Christine; Coelho, Carla P; Cao, Yingying; Brutnell, Thomas P

2016-01-01

Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail ( Setaria viridis ) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica . These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

Science.gov (United States)

Huang, Pu; Shyu, Christine; Coelho, Carla P.; Cao, Yingying; Brutnell, Thomas P.

2016-01-01

Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops. PMID:27965689

Genetic architecture of the Delis-Kaplan Executive Function System Trail Making Test: evidence for distinct genetic influences on executive function.

Science.gov (United States)

Vasilopoulos, Terrie; Franz, Carol E; Panizzon, Matthew S; Xian, Hong; Grant, Michael D; Lyons, Michael J; Toomey, Rosemary; Jacobson, Kristen C; Kremen, William S

2012-03-01

To examine how genes and environments contribute to relationships among Trail Making Test (TMT) conditions and the extent to which these conditions have unique genetic and environmental influences. Participants included 1,237 middle-aged male twins from the Vietnam Era Twin Study of Aging. The Delis-Kaplan Executive Function System TMT included visual searching, number and letter sequencing, and set-shifting components. Phenotypic correlations among TMT conditions ranged from 0.29 to 0.60, and genes accounted for the majority (58-84%) of each correlation. Overall heritability ranged from 0.34 to 0.62 across conditions. Phenotypic factor analysis suggested a single factor. In contrast, genetic models revealed a single common genetic factor but also unique genetic influences separate from the common factor. Genetic variance (i.e., heritability) of number and letter sequencing was completely explained by the common genetic factor while unique genetic influences separate from the common factor accounted for 57% and 21% of the heritabilities of visual search and set shifting, respectively. After accounting for general cognitive ability, unique genetic influences accounted for 64% and 31% of those heritabilities. A common genetic factor, most likely representing a combination of speed and sequencing, accounted for most of the correlation among TMT 1-4. Distinct genetic factors, however, accounted for a portion of variance in visual scanning and set shifting. Thus, although traditional phenotypic shared variance analysis techniques suggest only one general factor underlying different neuropsychological functions in nonpatient populations, examining the genetic underpinnings of cognitive processes with twin analysis can uncover more complex etiological processes.

Timing of gene expression from different genetic systems in shaping ...

Indian Academy of Sciences (India)

2011-12-16

Dec 16, 2011 ... different genetic systems, nutrition quality traits were mainly controlled by the accumulative or net ... pable of providing valuable information on the expression of ...... protein, carbohydrates, and dietary fiber components.

Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene.

Science.gov (United States)

Chintalapudi, Sumana R; Jablonski, Monica M

2017-01-01

Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Recently, γ-synuclein (SNCG) was shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the regulation of Sncg in RGCs, we used a systems genetics approach to identify a gene that modulates the expression of Sncg, followed by confirmatory studies in both healthy and diseased retinas. We found that chromosome 1 harbors an eQTL that modulates the expression of Sncg in the mouse retina and identified Pfdn2 as the candidate upstream modulator of Sncg expression. Downregulation of Pfdn2 in enriched RGCs causes a concomitant reduction in Sncg. In this chapter, we describe our strategy and methods for identifying and confirming a genetic modulation of a glaucoma-associated gene. A similar method can be applied to other genes expressed in other tissues.

Systems genetics of complex diseases using RNA-sequencing methods

DEFF Research Database (Denmark)

Mazzoni, Gianluca; Kogelman, Lisette; Suravajhala, Prashanth

2015-01-01

Next generation sequencing technologies have enabled the generation of huge quantities of biological data, and nowadays extensive datasets at different ‘omics levels have been generated. Systems genetics is a powerful approach that allows to integrate different ‘omics level and understand the bio...

Genetic Evaluation of Children with Global Developmental Delay—Current Status of Network Systems in Taiwan

Directory of Open Access Journals (Sweden)

Yong-Lin Foo

2015-08-01

Full Text Available This review article aims to introduce the screening and referral network of genetic evaluation for children with developmental delay in Taiwan. For these children, integrated systems provide services from the medical, educational, and social welfare sectors. All cities and counties in Taiwan have established a network for screening, detection, referral, evaluation, and intervention services. Increased awareness improves early detection and intervention. There remains a gap between supply and demand, especially with regard to financial resources and professional manpower. Genetic etiology has a major role in prenatal causes of developmental delay. A summary of reports on some related genetic disorders in the Taiwanese population is included in this review. Genetic diagnosis allows counseling with regard to recurrence risk and prevention. Networking with neonatal screening, laboratory diagnosis, genetic counseling, and orphan drugs logistics systems can provide effective treatment for patients. In Taiwan, several laboratories provide genetic tests for clinical diagnosis. Accessibility to advanced expensive tests such as gene chips or whole exome sequencing is limited because of funding problems; however, the service system in Taiwan can still operate in a relatively cost-effective manner. This experience in Taiwan may serve as a reference for other countries.

From Genetics to Genetic Algorithms

Indian Academy of Sciences (India)

artificial genetic system) string feature or ... called the genotype whereas it is called a structure in artificial genetic ... assigned a fitness value based on the cost function. Better ..... way it has produced complex, intelligent living organisms capable of ...

Periodontal disease associated to systemic genetic disorders.

Science.gov (United States)

Nualart Grollmus, Zacy Carola; Morales Chávez, Mariana Carolina; Silvestre Donat, Francisco Javier

2007-05-01

A number of systemic disorders increase patient susceptibility to periodontal disease, which moreover evolves more rapidly and more aggressively. The underlying factors are mainly related to alterations in immune, endocrine and connective tissue status. These alterations are associated with different pathologies and syndromes that generate periodontal disease either as a primary manifestation or by aggravating a pre-existing condition attributable to local factors. This is where the role of bacterial plaque is subject to debate. In the presence of qualitative or quantitative cellular immune alterations, periodontal disease may manifest early on a severe localized or generalized basis--in some cases related to the presence of plaque and/or specific bacteria (severe congenital neutropenia or infantile genetic agranulocytosis, Chediak-Higiashi syndrome, Down syndrome and Papillon-Lefévre syndrome). In the presence of humoral immune alterations, periodontal damage may result indirectly as a consequence of alterations in other systems. In connective tissue disorders, bacterial plaque and alterations of the periodontal tissues increase patient susceptibility to gingival inflammation and alveolar resorption (Marfan syndrome and Ehler-Danlos syndrome). The management of periodontal disease focuses on the control of infection and bacterial plaque by means of mechanical and chemical methods. Periodontal surgery and even extraction of the most seriously affected teeth have also been suggested. There are variable degrees of consensus regarding the background systemic disorder, as in the case of Chediak-Higiashi syndrome, where antibiotic treatment proves ineffective; in severe congenital neutropenia or infantile genetic agranulocytosis, where antibiotic prophylaxis is suggested; and in Papillon-Lefévre syndrome, where an established treatment protocol is available.

Efficient Feedforward Linearization Technique Using Genetic Algorithms for OFDM Systems

Directory of Open Access Journals (Sweden)

García Paloma

2010-01-01

Full Text Available Feedforward is a linearization method that simultaneously offers wide bandwidth and good intermodulation distortion suppression; so it is a good choice for Orthogonal Frequency Division Multiplexing (OFDM systems. Feedforward structure consists of two loops, being necessary an accurate adjustment between them along the time, and when temperature, environmental, or operating changes are produced. Amplitude and phase imbalances of the circuit elements in both loops produce mismatched effects that lead to degrade its performance. A method is proposed to compensate these mismatches, introducing two complex coefficients calculated by means of a genetic algorithm. A full study is carried out to choose the optimal parameters of the genetic algorithm applied to wideband systems based on OFDM technologies, which are very sensitive to nonlinear distortions. The method functionality has been verified by means of simulation.

Plant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure

Directory of Open Access Journals (Sweden)

Hardy Olivier J

2009-07-01

Full Text Available Abstract Background Understanding the mechanisms that control species genetic structure has always been a major objective in evolutionary studies. The association between genetic structure and species attributes has received special attention. As species attributes are highly taxonomically constrained, phylogenetically controlled methods are necessary to infer causal relationships. In plants, a previous study controlling for phylogenetic signal has demonstrated that Wright's FST, a measure of genetic differentiation among populations, is best predicted by the mating system (outcrossing, mixed-mating or selfing and that plant traits such as perenniality and growth form have only an indirect influence on FST via their association with the mating system. The objective of this study is to further outline the determinants of plant genetic structure by distinguishing the effects of mating system on gene flow and on genetic drift. The association of biparental inbreeding and inbreeding depression with population genetic structure, mating system and plant traits are also investigated. Results Based on data from 263 plant species for which estimates of FST, inbreeding (FIS and outcrossing rate (tm are available, we confirm that mating system is the main influencing factor of FST. Moreover, using an alternative measure of FST unaffected by the impact of inbreeding on effective population size, we show that the influence of tm on FST is due to its impact on gene flow (reduced pollen flow under selfing and on genetic drift (higher drift under selfing due to inbreeding. Plant traits, in particular perenniality, influence FST mostly via their effect on the mating system but also via their association with the magnitude of selection against inbred individuals: the mean inbreeding depression increases from short-lived herbaceous to long-lived herbaceous and then to woody species. The influence of perenniality on mating system does not seem to be related to

Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.

Science.gov (United States)

Coyne, Michael J; Roelofs, Kevin G; Comstock, Laurie E

2016-01-15

Type VI secretion systems (T6SSs) are contact-dependent antagonistic systems employed by Gram negative bacteria to intoxicate other bacteria or eukaryotic cells. T6SSs were recently discovered in a few Bacteroidetes strains, thereby extending the presence of these systems beyond Proteobacteria. The present study was designed to analyze in a global nature the diversity, abundance, and properties of T6SSs in the Bacteroidales, the most predominant Gram negative bacterial order of the human gut. By performing extensive bioinformatics analyses and creating hidden Markov models for Bacteroidales Tss proteins, we identified 130 T6SS loci in 205 human gut Bacteroidales genomes. Of the 13 core T6SS proteins of Proteobacteria, human gut Bacteroidales T6SS loci encode orthologs of nine, and an additional five other core proteins not present in Proteobacterial T6SSs. The Bacteroidales T6SS loci segregate into three distinct genetic architectures with extensive DNA identity between loci of a given genetic architecture. We found that divergent DNA regions of a genetic architecture encode numerous types of effector and immunity proteins and likely include new classes of these proteins. TheT6SS loci of genetic architecture 1 are contained on highly similar integrative conjugative elements (ICEs), as are the T6SS loci of genetic architecture 2, whereas the T6SS loci of genetic architecture 3 are not and are confined to Bacteroides fragilis. Using collections of co-resident Bacteroidales strains from human subjects, we provide evidence for the transfer of genetic architecture 1 T6SS loci among co-resident Bacteroidales species in the human gut. However, we also found that established ecosystems can harbor strains with distinct T6SS of all genetic architectures. This is the first study to comprehensively analyze of the presence and diversity of T6SS loci within an order of bacteria and to analyze T6SSs of bacteria from a natural community. These studies demonstrate that more than

Performance improvement of VAV air conditioning system through feedforward compensation decoupling and genetic algorithm

International Nuclear Information System (INIS)

Wang Jun; Wang Yan

2008-01-01

VAV (variable air volume) control system has the feature of multi-control loops. While all the control loops are working together, they interfere and influence each other. This paper designs the decoupling compensation unit in VAV system in the method of feedforward compensation. This paper also designs the controller parameters of VAV system by means of inverse deducing and the genetic algorithm. Experimental results demonstrate that the combination of the feedforward compensation decoupling and the controller optimization by genetic algorithm can improve the performance of the VAV control system

Towards systems metabolic engineering in Pichia pastoris.

Science.gov (United States)

Schwarzhans, Jan-Philipp; Luttermann, Tobias; Geier, Martina; Kalinowski, Jörn; Friehs, Karl

2017-11-01

The methylotrophic yeast Pichia pastoris is firmly established as a host for the production of recombinant proteins, frequently outperforming other heterologous hosts. Already, a sizeable amount of systems biology knowledge has been acquired for this non-conventional yeast. By applying various omics-technologies, productivity features have been thoroughly analyzed and optimized via genetic engineering. However, challenging clonal variability, limited vector repertoire and insufficient genome annotation have hampered further developments. Yet, in the last few years a reinvigorated effort to establish P. pastoris as a host for both protein and metabolite production is visible. A variety of compounds from terpenoids to polyketides have been synthesized, often exceeding the productivity of other microbial systems. The clonal variability was systematically investigated and strategies formulated to circumvent untargeted events, thereby streamlining the screening procedure. Promoters with novel regulatory properties were discovered or engineered from existing ones. The genetic tractability was increased via the transfer of popular manipulation and assembly techniques, as well as the creation of new ones. A second generation of sequencing projects culminated in the creation of the second best functionally annotated yeast genome. In combination with landmark physiological insights and increased output of omics-data, a good basis for the creation of refined genome-scale metabolic models was created. The first application of model-based metabolic engineering in P. pastoris showcased the potential of this approach. Recent efforts to establish yeast peroxisomes for compartmentalized metabolite synthesis appear to fit ideally with the well-studied high capacity peroxisomal machinery of P. pastoris. Here, these recent developments are collected and reviewed with the aim of supporting the establishment of systems metabolic engineering in P. pastoris. Copyright © 2017. Published

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

Science.gov (United States)

Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

1998-01-01

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Catecholaminergic systems in stress: structural and molecular genetic approaches.

Science.gov (United States)

Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

2009-04-01

Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

Reverse genetics with animal viruses. NSV reverse genetics

International Nuclear Information System (INIS)

Mebatsion, T.

2005-01-01

New strategies to genetically manipulate the genomes of several important animal pathogens have been established in recent years. This article focuses on the reverse genetics techniques, which enables genetic manipulation of the genomes of non-segmented negative-sense RNA viruses. Recovery of a negative-sense RNA virus entirely from cDNA was first achieved for rabies virus in 1994. Since then, reverse genetic systems have been established for several pathogens of medical and veterinary importance. Based on the reverse genetics technique, it is now possible to design safe and more effective live attenuated vaccines against important viral agents. In addition, genetically tagged recombinant viruses can be designed to facilitate serological differentiation of vaccinated animals from infected animals. The approach of delivering protective immunogens of different pathogens using a single vector was made possible with the introduction of the reverse genetics system, and these novel broad-spectrum vaccine vectors have potential applications in improving animal health in developing countries. (author)

Genetic Evaluation of Children with Global Developmental Delay--Current Status of Network Systems in Taiwan.

Science.gov (United States)

Foo, Yong-Lin; Chow, Julie Chi; Lai, Ming-Chi; Tsai, Wen-Hui; Tung, Li-Chen; Kuo, Mei-Chin; Lin, Shio-Jean

2015-08-01

This review article aims to introduce the screening and referral network of genetic evaluation for children with developmental delay in Taiwan. For these children, integrated systems provide services from the medical, educational, and social welfare sectors. All cities and counties in Taiwan have established a network for screening, detection, referral, evaluation, and intervention services. Increased awareness improves early detection and intervention. There remains a gap between supply and demand, especially with regard to financial resources and professional manpower. Genetic etiology has a major role in prenatal causes of developmental delay. A summary of reports on some related genetic disorders in the Taiwanese population is included in this review. Genetic diagnosis allows counseling with regard to recurrence risk and prevention. Networking with neonatal screening, laboratory diagnosis, genetic counseling, and orphan drugs logistics systems can provide effective treatment for patients. In Taiwan, several laboratories provide genetic tests for clinical diagnosis. Accessibility to advanced expensive tests such as gene chips or whole exome sequencing is limited because of funding problems; however, the service system in Taiwan can still operate in a relatively cost-effective manner. This experience in Taiwan may serve as a reference for other countries. Copyright © 2014. Published by Elsevier B.V.

A Hybrid Fuzzy Genetic Algorithm for an Adaptive Traffic Signal System

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S. M. Odeh

2015-01-01

Full Text Available This paper presents a hybrid algorithm that combines Fuzzy Logic Controller (FLC and Genetic Algorithms (GAs and its application on a traffic signal system. FLCs have been widely used in many applications in diverse areas, such as control system, pattern recognition, signal processing, and forecasting. They are, essentially, rule-based systems, in which the definition of these rules and fuzzy membership functions is generally based on verbally formulated rules that overlap through the parameter space. They have a great influence over the performance of the system. On the other hand, the Genetic Algorithm is a metaheuristic that provides a robust search in complex spaces. In this work, it has been used to adapt the decision rules of FLCs that define an intelligent traffic signal system, obtaining a higher performance than a classical FLC-based control. The simulation results yielded by the hybrid algorithm show an improvement of up to 34% in the performance with respect to a standard traffic signal controller, Conventional Traffic Signal Controller (CTC, and up to 31% in the comparison with a traditional logic controller, FLC.

Systems neuroscience in Drosophila: Conceptual and technical advantages.

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Kazama, H

2015-06-18

The fruit fly Drosophila melanogaster is ideally suited for investigating the neural circuit basis of behavior. Due to the simplicity and genetic tractability of the fly brain, neurons and circuits are identifiable across animals. Additionally, a large set of transgenic lines has been developed with the aim of specifically labeling small subsets of neurons and manipulating them in sophisticated ways. Electrophysiology and imaging can be applied in behaving individuals to examine the computations performed by each neuron, and even the entire population of relevant neurons in a particular region, because of the small size of the brain. Moreover, a rich repertoire of behaviors that can be studied is expanding to include those requiring cognitive abilities. Thus, the fly brain is an attractive system in which to explore both computations and mechanisms underlying behavior at levels spanning from genes through neurons to circuits. This review summarizes the advantages Drosophila offers in achieving this objective. A recent neurophysiology study on olfactory behavior is also introduced to demonstrate the effectiveness of these advantages. Copyright © 2014 IBRO. Published by Elsevier Ltd. All rights reserved.

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project.

Science.gov (United States)

Weston, David J; Turetsky, Merritt R; Johnson, Matthew G; Granath, Gustaf; Lindo, Zoë; Belyea, Lisa R; Rice, Steven K; Hanson, David T; Engelhardt, Katharina A M; Schmutz, Jeremy; Dorrepaal, Ellen; Euskirchen, Eugénie S; Stenøien, Hans K; Szövényi, Péter; Jackson, Michelle; Piatkowski, Bryan T; Muchero, Wellington; Norby, Richard J; Kostka, Joel E; Glass, Jennifer B; Rydin, Håkan; Limpens, Juul; Tuittila, Eeva-Stiina; Ullrich, Kristian K; Carrell, Alyssa; Benscoter, Brian W; Chen, Jin-Gui; Oke, Tobi A; Nilsson, Mats B; Ranjan, Priya; Jacobson, Daniel; Lilleskov, Erik A; Clymo, R S; Shaw, A Jonathan

2018-01-01

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses. © 2017 UT-Battelle New Phytologist © 2017 New Phytologist Trust.

Fault Diagnosis of Power System Based on Improved Genetic Optimized BP-NN

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Yuan Pu

2015-01-01

Full Text Available BP neural network (Back-Propagation Neural Network, BP-NN is one of the most widely neural network models and is applied to fault diagnosis of power system currently. BP neural network has good self-learning and adaptive ability and generalization ability, but the operation process is easy to fall into local minima. Genetic algorithm has global optimization features, and crossover is the most important operation of the Genetic Algorithm. In this paper, we can modify the crossover of traditional Genetic Algorithm, using improved genetic algorithm optimized BP neural network training initial weights and thresholds, to avoid the problem of BP neural network fall into local minima. The results of analysis by an example, the method can efficiently diagnose network fault location, and improve fault-tolerance and grid fault diagnosis effect.

Management of genetic resources in the nursery system of wild cherry (Prunus avium L.

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Proietti R

2006-01-01

Full Text Available Knowledge of genetic and adaptive traits of reproductive materials used in the nursery system of wild cherry, could be an useful instrument to improve ecological and economic sustainability of plantation ecosystems. This work reports results from a research which the objectives were: 1 to study the genetic variation of a Prunus avium L. Population, used for seed harvesting, through its multi-locus genotypes detected by starch gel electrophoresis; 2 to analyze the level of genetic variation within and among different steps in a commercial nursery system (basic population and sub-populations, seedlings aged S1T1 and S1T2, plantation. Results showed low genetic variation levels of the basic population, similar to a reference system of other 12 wild cherry Italian populations and to other French and Caucasian materials. The genetic distances among Monte Baldo and some closer Lombardy provenances (Area Garda, Bosco Fontana, Valtellina were smaller than the Venice Region populations (Monti Lessini and Asiago. Number of alleles and percentage of polymorphic loci within the complex of Monte Baldo provenance and multiplication materials were similar, whilst a variable value of Fis was noted. Indeed, along with the nursery system until the plantation, heterozygosis initially (S1T1 increased, then decreased proceeding to the plantation. This fluctuation of FIS values could be determined by seed lots characterized initially by higher levels of variation, due to self-incompatibility. In the following steps, a possible selection pressure can affect randomly the genotypic structure of wild cherry by increasing the homozygosity. There is not among population a well defined geographic characterization, as suggested by genetic distances, therefore homogeneous seed harvest could be established an area larger than geographic and administrative borders. On this way we could have reproductive material with a wide genetic base and environmental adaptability. To

Genetic variations in the serotoninergic system contribute to body-mass index in Chinese adolescents.

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Chunhui Chen

Full Text Available OBJECTIVE: Obesity has become a worldwide health problem in the past decades. Human and animal studies have implicated serotonin in appetite regulation, and behavior genetic studies have shown that body mass index (BMI has a strong genetic component. However, the roles of genes related to the serotoninergic (5-hydroxytryptamine,5-HT system in obesity/BMI are not well understood, especially in Chinese subjects. SUBJECTS AND DESIGN: With a sample of 478 healthy Chinese volunteers, this study investigated the relation between BMI and genetic variations of the serotoninergic system as characterized by 136 representative polymorphisms. We used a system-level approach to identify SNPs associated with BMI, then estimated their overall contribution to BMI by multiple regression and verified it by permutation. RESULTS: We identified 12 SNPs that made statistically significant contributions to BMI. After controlling for gender and age, four of these SNPs accounted for 7.7% additional variance of BMI. Permutation analysis showed that the probability of obtaining these findings by chance was low (p = 0.015, permuted for 1000 times. CONCLUSION: These results showed that genetic variations in the serotoninergic system made a moderate contribution to individual differences in BMI among a healthy Chinese sample, suggesting that a similar approach can be used to study obesity.

Computational Genetic Regulatory Networks Evolvable, Self-organizing Systems

CERN Document Server

Knabe, Johannes F

2013-01-01

Genetic Regulatory Networks (GRNs) in biological organisms are primary engines for cells to enact their engagements with environments, via incessant, continually active coupling. In differentiated multicellular organisms, tremendous complexity has arisen in the course of evolution of life on earth. Engineering and science have so far achieved no working system that can compare with this complexity, depth and scope of organization. Abstracting the dynamics of genetic regulatory control to a computational framework in which artificial GRNs in artificial simulated cells differentiate while connected in a changing topology, it is possible to apply Darwinian evolution in silico to study the capacity of such developmental/differentiated GRNs to evolve. In this volume an evolutionary GRN paradigm is investigated for its evolvability and robustness in models of biological clocks, in simple differentiated multicellularity, and in evolving artificial developing 'organisms' which grow and express an ontogeny starting fr...

PID-Controller Tuning Optimization with Genetic Algorithms in Servo Systems

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Arturo Y. Jaen-Cuellar

2013-09-01

Full Text Available Performance improvement is the main goal of the study of PID control and much research has been conducted for this purpose. The PID filter is implemented in almost all industrial processes because of its well-known beneficial features. In general, the whole system's performance strongly depends on the controller's efficiency and hence the tuning process plays a key role in the system's behaviour. In this work, the servo systems will be analysed, specifically the positioning control systems. Among the existent tuning methods, the Gain-Phase Margin method based on Frequency Response analysis is the most adequate for controller tuning in positioning control systems. Nevertheless, this method can be improved by integrating an optimization technique. The novelty of this work is the development of a new methodology for PID control tuning by coupling the Gain-Phase Margin method with the Genetic Algorithms in which the micro-population concept and adaptive mutation probability are applied. Simulations using a positioning system model in MATLAB and experimental tests in two CNC machines and an industrial robot are carried out in order to show the effectiveness of the proposal. The obtained results are compared with both the classical Gain-Phase Margin tuning and with a recent PID controller optimization using Genetic Algorithms based on real codification. The three methodologies are implemented using software.

Zebrafish neurotransmitter systems as potential pharmacological and toxicological targets.

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Rico, E P; Rosemberg, D B; Seibt, K J; Capiotti, K M; Da Silva, R S; Bonan, C D

2011-01-01

Recent advances in neurobiology have emphasized the study of brain structure and function and its association with numerous pathological and toxicological events. Neurotransmitters are substances that relay, amplify, and modulate electrical signals between neurons and other cells. Neurotransmitter signaling mediates rapid intercellular communication by interacting with cell surface receptors, activating second messenger systems and regulating the activity of ion channels. Changes in the functional balance of neurotransmitters have been implicated in the failure of central nervous system function. In addition, abnormalities in neurotransmitter production or functioning can be induced by several toxicological compounds, many of which are found in the environment. The zebrafish has been increasingly used as an animal model for biomedical research, primarily due to its genetic tractability and ease of maintenance. These features make this species a versatile tool for pre-clinical drug discovery and toxicological investigations. Here, we present a review regarding the role of different excitatory and inhibitory neurotransmitter systems in zebrafish, such as dopaminergic, serotoninergic, cholinergic, purinergic, histaminergic, nitrergic, glutamatergic, glycinergic, and GABAergic systems, and emphasizing their features as pharmacological and toxicological targets. The increase in the global knowledge of neurotransmitter systems in zebrafish and the elucidation of their pharmacological and toxicological aspects may lead to new strategies and appropriate research priorities to offer insights for biomedical and environmental research. Copyright © 2011 Elsevier Inc. All rights reserved.

Tractable flux-driven temperature, density, and rotation profile evolution with the quasilinear gyrokinetic transport model QuaLiKiz

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Citrin, J.; Bourdelle, C.; Casson, F. J.; Angioni, C.; Bonanomi, N.; Camenen, Y.; Garbet, X.; Garzotti, L.; Görler, T.; Gürcan, O.; Koechl, F.; Imbeaux, F.; Linder, O.; van de Plassche, K.; Strand, P.; Szepesi, G.; Contributors, JET

2017-12-01

Quasilinear turbulent transport models are a successful tool for prediction of core tokamak plasma profiles in many regimes. Their success hinges on the reproduction of local nonlinear gyrokinetic fluxes. We focus on significant progress in the quasilinear gyrokinetic transport model QuaLiKiz (Bourdelle et al 2016 Plasma Phys. Control. Fusion 58 014036), which employs an approximated solution of the mode structures to significantly speed up computation time compared to full linear gyrokinetic solvers. Optimisation of the dispersion relation solution algorithm within integrated modelling applications leads to flux calculations × {10}6-7 faster than local nonlinear simulations. This allows tractable simulation of flux-driven dynamic profile evolution including all transport channels: ion and electron heat, main particles, impurities, and momentum. Furthermore, QuaLiKiz now includes the impact of rotation and temperature anisotropy induced poloidal asymmetry on heavy impurity transport, important for W-transport applications. Application within the JETTO integrated modelling code results in 1 s of JET plasma simulation within 10 h using 10 CPUs. Simultaneous predictions of core density, temperature, and toroidal rotation profiles for both JET hybrid and baseline experiments are presented, covering both ion and electron turbulence scales. The simulations are successfully compared to measured profiles, with agreement mostly in the 5%-25% range according to standard figures of merit. QuaLiKiz is now open source and available at www.qualikiz.com.

Using Genetic Algorithm and MODFLOW to Characterize Aquifer System of Northwest Florida

Science.gov (United States)

By integrating Genetic Algorithm and MODFLOW2005, an optimizing tool is developed to characterize the aquifer system of Region II, Northwest Florida. The history and the newest available observation data of the aquifer system is fitted automatically by using the numerical model c...

Optimal Parameter Selection of Power System Stabilizer using Genetic Algorithm

Energy Technology Data Exchange (ETDEWEB)

Chung, Hyeng Hwan; Chung, Dong Il; Chung, Mun Kyu [Dong-AUniversity (Korea); Wang, Yong Peel [Canterbury Univeristy (New Zealand)

1999-06-01

In this paper, it is suggested that the selection method of optimal parameter of power system stabilizer (PSS) with robustness in low frequency oscillation for power system using real variable elitism genetic algorithm (RVEGA). The optimal parameters were selected in the case of power system stabilizer with one lead compensator, and two lead compensator. Also, the frequency responses characteristics of PSS, the system eigenvalues criterion and the dynamic characteristics were considered in the normal load and the heavy load, which proved usefulness of RVEGA compare with Yu's compensator design theory. (author). 20 refs., 15 figs., 8 tabs.

Neuro-genetic system for optimization of GMI samples sensitivity.

Science.gov (United States)

Pitta Botelho, A C O; Vellasco, M M B R; Hall Barbosa, C R; Costa Silva, E

2016-03-01

Magnetic sensors are largely used in several engineering areas. Among them, magnetic sensors based on the Giant Magnetoimpedance (GMI) effect are a new family of magnetic sensing devices that have a huge potential for applications involving measurements of ultra-weak magnetic fields. The sensitivity of magnetometers is directly associated with the sensitivity of their sensing elements. The GMI effect is characterized by a large variation of the impedance (magnitude and phase) of a ferromagnetic sample, when subjected to a magnetic field. Recent studies have shown that phase-based GMI magnetometers have the potential to increase the sensitivity by about 100 times. The sensitivity of GMI samples depends on several parameters, such as sample length, external magnetic field, DC level and frequency of the excitation current. However, this dependency is yet to be sufficiently well-modeled in quantitative terms. So, the search for the set of parameters that optimizes the samples sensitivity is usually empirical and very time consuming. This paper deals with this problem by proposing a new neuro-genetic system aimed at maximizing the impedance phase sensitivity of GMI samples. A Multi-Layer Perceptron (MLP) Neural Network is used to model the impedance phase and a Genetic Algorithm uses the information provided by the neural network to determine which set of parameters maximizes the impedance phase sensitivity. The results obtained with a data set composed of four different GMI sample lengths demonstrate that the neuro-genetic system is able to correctly and automatically determine the set of conditioning parameters responsible for maximizing their phase sensitivities. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development of a Laboratory Information Management System for Medical Genetic Investigations (LIMS)

OpenAIRE

Albers, K.

2006-01-01

Studying the genetic factor underlying a set of diseases with modern high- throughput techniques generates huge amounts of data, posing a challenge for data management. In this thesis a database management system called FIDB based on MySQL was developed to handle clinical and experimental genetic data. For the convenience of the users, a web interface was developed to insert, update, delete and display the data. In addition security aspects were taken care of. Currently FIDB is able to organi...

Optimization of redundancy by using genetic algorithm for reliability of plant protection system

International Nuclear Information System (INIS)

Yoo, D. W.; Seong, S. H.; Kim, D. H.; Park, H. Y.; Gu, I. S.

2000-01-01

The design and development of a reliable protection system has been becoming a key issue in industry field because the reliability of system is considered as an important factor to perform the system's function successfully. Plant Protection System(PPS) guarantees the safety of plant by accident detection and control action against the transient conditions of plant. This paper presents the analysis of PPS reliability and the formal problem statement about optimal redundancy based on the reliability of PPS. And the optimization problem is solved by genetic algorithm. The genetic algorithm is a useful tool to solve the problems, in the case of large searching, complex gradient, existence local minimum. The effectiveness of the proposed optimization technique is proved by the target reliability of one channel of PPS, using the failure rate based on the MIL-HDBK-217

A genetic fuzzy system for unstable angina risk assessment.

Science.gov (United States)

Dong, Wei; Huang, Zhengxing; Ji, Lei; Duan, Huilong

2014-02-18

Unstable Angina (UA) is widely accepted as a critical phase of coronary heart disease with patients exhibiting widely varying risks. Early risk assessment of UA is at the center of the management program, which allows physicians to categorize patients according to the clinical characteristics and stratification of risk and different prognosis. Although many prognostic models have been widely used for UA risk assessment in clinical practice, a number of studies have highlighted possible shortcomings. One serious drawback is that existing models lack the ability to deal with the intrinsic uncertainty about the variables utilized. In order to help physicians refine knowledge for the stratification of UA risk with respect to vagueness in information, this paper develops an intelligent system combining genetic algorithm and fuzzy association rule mining. In detail, it models the input information's vagueness through fuzzy sets, and then applies a genetic fuzzy system on the acquired fuzzy sets to extract the fuzzy rule set for the problem of UA risk assessment. The proposed system is evaluated using a real data-set collected from the cardiology department of a Chinese hospital, which consists of 54 patient cases. 9 numerical patient features and 17 categorical patient features that appear in the data-set are selected in the experiments. The proposed system made the same decisions as the physician in 46 (out of a total of 54) tested cases (85.2%). By comparing the results that are obtained through the proposed system with those resulting from the physician's decision, it has been found that the developed model is highly reflective of reality. The proposed system could be used for educational purposes, and with further improvements, could assist and guide young physicians in their daily work.

Males and females contribute unequally to offspring genetic diversity in the polygynandrous mating system of wild boar.

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Javier Pérez-González

Full Text Available The maintenance of genetic diversity across generations depends on both the number of reproducing males and females. Variance in reproductive success, multiple paternity and litter size can all affect the relative contributions of male and female parents to genetic variation of progeny. The mating system of the wild boar (Sus scrofa has been described as polygynous, although evidence of multiple paternity in litters has been found. Using 14 microsatellite markers, we evaluated the contribution of males and females to genetic variation in the next generation in independent wild boar populations from the Iberian Peninsula and Hungary. Genetic contributions of males and females were obtained by distinguishing the paternal and maternal genetic component inherited by the progeny. We found that the paternally inherited genetic component of progeny was more diverse than the maternally inherited component. Simulations showed that this finding might be due to a sampling bias. However, after controlling for the bias by fitting both the genetic diversity in the adult population and the number of reproductive individuals in the models, paternally inherited genotypes remained more diverse than those inherited maternally. Our results suggest new insights into how promiscuous mating systems can help maintain genetic variation.

Comorbidity of Alcohol Use Disorder and Chronic Pain: Genetic Influences on Brain Reward and Stress Systems.

Science.gov (United States)

Yeung, Ellen W; Craggs, Jason G; Gizer, Ian R

2017-11-01

Alcohol use disorder (AUD) is highly comorbid with chronic pain (CP). Evidence has suggested that neuroadaptive processes characterized by reward deficit and stress surfeit are involved in the development of AUD and pain chronification. Neurological data suggest that shared genetic architecture associated with the reward and stress systems may contribute to the comorbidity of AUD and CP. This monograph first delineates the prevailing theories of the development of AUD and pain chronification focusing on the reward and stress systems. It then provides a brief summary of relevant neurological findings followed by an evaluation of evidence documented by molecular genetic studies. Candidate gene association studies have provided some initial support for the genetic overlap between AUD and CP; however, these results must be interpreted with caution until studies with sufficient statistical power are conducted and replications obtained. Genomewide association studies have suggested a number of genes (e.g., TBX19, HTR7, and ADRA1A) that are either directly or indirectly related to the reward and stress systems in the AUD and CP literature. Evidence reviewed in this monograph suggests that shared genetic liability underlying the comorbidity between AUD and CP, if present, is likely to be complex. As the advancement in molecular genetic methods continues, future studies may show broader central nervous system involvement in AUD-CP comorbidity. Copyright © 2017 by the Research Society on Alcoholism.

An Interpretation of Part of Gilbert Gottlieb's Legacy: Developmental Systems Theory Contra Developmental Behavior Genetics

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Molenaar, Peter C. M.

2015-01-01

The main theme of this paper concerns the persistent critique of Gilbert Gottlieb on developmental behavior genetics and my reactions to this critique, the latter changing from rejection to complete acceptation. Concise characterizations of developmental behavior genetics, developmental systems theory (to which Gottlieb made essential…

Understanding mammalian genetic systems: the challenge of phenotyping in the mouse.

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Steve D M Brown

2006-08-01

Full Text Available Understanding mammalian genetic systems is predicated on the determination of the relationship between genetic variation and phenotype. Several international programmes are under way to deliver mutations in every gene in the mouse genome. The challenge for mouse geneticists is to develop approaches that will provide comprehensive phenotype datasets for these mouse mutant libraries. Several factors are critical to success in this endeavour. It will be important to catalogue assay and environment and where possible to adopt standardised procedures for phenotyping tests along with common environmental conditions to ensure comparable datasets of phenotypes. Moreover, the scale of the task underlines the need to invest in technological development improving both the speed and cost of phenotyping platforms. In addition, it will be necessary to develop new informatics standards that capture the phenotype assay as well as other factors, genetic and environmental, that impinge upon phenotype outcome.

Toward a generalized and high-throughput enzyme screening system based on artificial genetic circuits.

Science.gov (United States)

Choi, Su-Lim; Rha, Eugene; Lee, Sang Jun; Kim, Haseong; Kwon, Kilkoang; Jeong, Young-Su; Rhee, Young Ha; Song, Jae Jun; Kim, Hak-Sung; Lee, Seung-Goo

2014-03-21

Large-scale screening of enzyme libraries is essential for the development of cost-effective biological processes, which will be indispensable for the production of sustainable biobased chemicals. Here, we introduce a genetic circuit termed the Genetic Enzyme Screening System that is highly useful for high-throughput enzyme screening from diverse microbial metagenomes. The circuit consists of two AND logics. The first AND logic, the two inputs of which are the target enzyme and its substrate, is responsible for the accumulation of a phenol compound in cell. Then, the phenol compound and its inducible transcription factor, whose activation turns on the expression of a reporter gene, interact in the other logic gate. We confirmed that an individual cell harboring this genetic circuit can present approximately a 100-fold higher cellular fluorescence than the negative control and can be easily quantified by flow cytometry depending on the amounts of phenolic derivatives. The high sensitivity of the genetic circuit enables the rapid discovery of novel enzymes from metagenomic libraries, even for genes that show marginal activities in a host system. The crucial feature of this approach is that this single system can be used to screen a variety of enzymes that produce a phenol compound from respective synthetic phenyl-substrates, including cellulase, lipase, alkaline phosphatase, tyrosine phenol-lyase, and methyl parathion hydrolase. Consequently, the highly sensitive and quantitative nature of this genetic circuit along with flow cytometry techniques could provide a widely applicable toolkit for discovering and engineering novel enzymes at a single cell level.

The influence of genetic selection and feed system on the reproductive performance of spring-calving dairy cows within future pasture-based production systems.

Science.gov (United States)

Coleman, J; Pierce, K M; Berry, D P; Brennan, A; Horan, B

2009-10-01

Three genetic groups of Holstein-Friesian dairy cows were established from within the Moorepark (Teagasc, Ireland) dairy research herd: LowNA, indicative of the Irish national average-genetic-merit North American Holstein-Friesian; HighNA, high-genetic-merit North American Holstein-Friesian; HighNZ, high-genetic-merit New Zealand Holstein-Friesian. Genetic merit in this study was based on the Irish total merit index, the Economic Breeding Index. Animals from within each genetic group were randomly allocated to 1 of 2 possible post-European Union-milk-quota pasture-based feeding systems (FS): 1) The Moorepark (MP) pasture system (2.64 cows/ha and 500 kg of concentrate supplement per cow per lactation) and 2) a high output per hectare (HC) pasture system (2.85 cows/ha and 1,200 kg of concentrate supplement per cow per lactation). A total of 126, 128, and 140 spring-calving dairy cows were used during the years 2006, 2007, and 2008, respectively. Each group had an individual farmlet of 17 paddocks, and all groups were managed similarly throughout the study. The effects of genetic group, FS, and the interaction between genetic group and FS on reproductive performance, body weight, body condition score, and blood metabolite concentrations were studied using mixed models with factorial arrangements of genetic groups and FS. Odds ratios were used in the analysis of binary fertility traits, and survival analysis was used in the analysis of survival after first calving. When treatment means were compared, the HighNA and HighNZ genotypes (with greater genetic merit for fertility performance) had greater first-service pregnancy rates and had a greater proportion of cows pregnant after 42 d of the breeding season than the LowNA group. Both HighNA and HighNZ genotypes were submitted for artificial insemination earlier in the breeding season and had greater survival than the LowNA genotype. There was no significant FS or genotype by FS interactions for any of the reproductive

Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea

DEFF Research Database (Denmark)

Peng, Nan; Han, Wenyuan; Li, Yingjun

2017-01-01

Archaea represents the third domain of life, with the information-processing machineries more closely resembling those of eukaryotes than the machineries of the bacterial counterparts but sharing metabolic pathways with organisms of Bacteria, the sister prokaryotic phylum. Archaeal organisms also...

Evolving Rule-Based Systems in two Medical Domains using Genetic Programming

DEFF Research Database (Denmark)

Tsakonas, A.; Dounias, G.; Jantzen, Jan

2004-01-01

We demonstrate, compare and discuss the application of two genetic programming methodologies for the construction of rule-based systems in two medical domains: the diagnosis of Aphasia's subtypes and the classification of Pap-Smear Test examinations. The first approach consists of a scheme...

A Semantic Web-based System for Mining Genetic Mutations in Cancer Clinical Trials.

Science.gov (United States)

Priya, Sambhawa; Jiang, Guoqian; Dasari, Surendra; Zimmermann, Michael T; Wang, Chen; Heflin, Jeff; Chute, Christopher G

2015-01-01

Textual eligibility criteria in clinical trial protocols contain important information about potential clinically relevant pharmacogenomic events. Manual curation for harvesting this evidence is intractable as it is error prone and time consuming. In this paper, we develop and evaluate a Semantic Web-based system that captures and manages mutation evidences and related contextual information from cancer clinical trials. The system has 2 main components: an NLP-based annotator and a Semantic Web ontology-based annotation manager. We evaluated the performance of the annotator in terms of precision and recall. We demonstrated the usefulness of the system by conducting case studies in retrieving relevant clinical trials using a collection of mutations identified from TCGA Leukemia patients and Atlas of Genetics and Cytogenetics in Oncology and Haematology. In conclusion, our system using Semantic Web technologies provides an effective framework for extraction, annotation, standardization and management of genetic mutations in cancer clinical trials.

Genetic Algorithm-Based Identification of Fractional-Order Systems

Directory of Open Access Journals (Sweden)

Shengxi Zhou

2013-05-01

Full Text Available Fractional calculus has become an increasingly popular tool for modeling the complex behaviors of physical systems from diverse domains. One of the key issues to apply fractional calculus to engineering problems is to achieve the parameter identification of fractional-order systems. A time-domain identification algorithm based on a genetic algorithm (GA is proposed in this paper. The multi-variable parameter identification is converted into a parameter optimization by applying GA to the identification of fractional-order systems. To evaluate the identification accuracy and stability, the time-domain output error considering the condition variation is designed as the fitness function for parameter optimization. The identification process is established under various noise levels and excitation levels. The effects of external excitation and the noise level on the identification accuracy are analyzed in detail. The simulation results show that the proposed method could identify the parameters of both commensurate rate and non-commensurate rate fractional-order systems from the data with noise. It is also observed that excitation signal is an important factor influencing the identification accuracy of fractional-order systems.

Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis.

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Georgina M Cooke

Full Text Available Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum, where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.

Foundations of genetic algorithms 1991

CERN Document Server

1991-01-01

Foundations of Genetic Algorithms 1991 (FOGA 1) discusses the theoretical foundations of genetic algorithms (GA) and classifier systems.This book compiles research papers on selection and convergence, coding and representation, problem hardness, deception, classifier system design, variation and recombination, parallelization, and population divergence. Other topics include the non-uniform Walsh-schema transform; spurious correlations and premature convergence in genetic algorithms; and variable default hierarchy separation in a classifier system. The grammar-based genetic algorithm; condition

System control fuzzy neural sewage pumping stations using genetic algorithms

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Владлен Николаевич Кузнецов

2015-06-01

Full Text Available It is considered the system of management of sewage pumping station with regulators based on a neuron network with fuzzy logic. Linguistic rules for the controller based on fuzzy logic, maintaining the level of effluent in the receiving tank within the prescribed limits are developed. The use of genetic algorithms for neuron network training is shown.

Optimal Design of Pumped Pipeline Systems Using Genetic Algorithm and Mathematical Optimization

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Mohammadhadi Afshar

2007-12-01

Full Text Available In recent years, much attention has been paid to the optimal design of pipeline systems. In this study, the problem of pipeline system optimal design has been solved through genetic algorithm and mathematical optimization. Pipe diameters and their thicknesses are considered as decision variables to be designed in a manner that water column separation and excessive pressures are avoided in the event of pump failure. Capabilities of the genetic algorithm and the mathematical programming method are compared for the problem under consideration. For simulation of transient streams, explicit characteristic method is used in which devices such as pumps are defined as boundary conditions of the equations defining the hydraulic behavior of pipe segments. The problem of optimal design of pipeline systems is a constrained problem which is converted to an unconstrained optimization problem using an external penalty function approach. The efficiency of the proposed approaches is verified in one example and the results are presented.

System Response Analysis and Model Order Reduction, Using Conventional Method, Bond Graph Technique and Genetic Programming

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Lubna Moin

2009-04-01

Full Text Available This research paper basically explores and compares the different modeling and analysis techniques and than it also explores the model order reduction approach and significance. The traditional modeling and simulation techniques for dynamic systems are generally adequate for single-domain systems only, but the Bond Graph technique provides new strategies for reliable solutions of multi-domain system. They are also used for analyzing linear and non linear dynamic production system, artificial intelligence, image processing, robotics and industrial automation. This paper describes a unique technique of generating the Genetic design from the tree structured transfer function obtained from Bond Graph. This research work combines bond graphs for model representation with Genetic programming for exploring different ideas on design space tree structured transfer function result from replacing typical bond graph element with their impedance equivalent specifying impedance lows for Bond Graph multiport. This tree structured form thus obtained from Bond Graph is applied for generating the Genetic Tree. Application studies will identify key issues and importance for advancing this approach towards becoming on effective and efficient design tool for synthesizing design for Electrical system. In the first phase, the system is modeled using Bond Graph technique. Its system response and transfer function with conventional and Bond Graph method is analyzed and then a approach towards model order reduction is observed. The suggested algorithm and other known modern model order reduction techniques are applied to a 11th order high pass filter [1], with different approach. The model order reduction technique developed in this paper has least reduction errors and secondly the final model retains structural information. The system response and the stability analysis of the system transfer function taken by conventional and by Bond Graph method is compared and

Genetic autonomic disorders.

Science.gov (United States)

Axelrod, Felicia B

2013-03-01

Genetic disorders affecting the autonomic nervous system can result in abnormal development of the nervous system or they can be caused by neurotransmitter imbalance, an ion-channel disturbance or by storage of deleterious material. The symptoms indicating autonomic dysfunction, however, will depend upon whether the genetic lesion has disrupted peripheral or central autonomic centers or both. Because the autonomic nervous system is pervasive and affects every organ system in the body, autonomic dysfunction will result in impaired homeostasis and symptoms will vary. The possibility of genetic confirmation by molecular testing for specific diagnosis is increasing but treatments tend to remain only supportive and directed toward particular symptoms. Copyright © 2013 Elsevier Inc. All rights reserved.

Network-assisted crop systems genetics: network inference and integrative analysis.

Science.gov (United States)

Lee, Tak; Kim, Hyojin; Lee, Insuk

2015-04-01

Although next-generation sequencing (NGS) technology has enabled the decoding of many crop species genomes, most of the underlying genetic components for economically important crop traits remain to be determined. Network approaches have proven useful for the study of the reference plant, Arabidopsis thaliana, and the success of network-based crop genetics will also require the availability of a genome-scale functional networks for crop species. In this review, we discuss how to construct functional networks and elucidate the holistic view of a crop system. The crop gene network then can be used for gene prioritization and the analysis of resequencing-based genome-wide association study (GWAS) data, the amount of which will rapidly grow in the field of crop science in the coming years. Copyright © 2015 Elsevier Ltd. All rights reserved.

The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.

Science.gov (United States)

Shaw, Robyn E; Banks, Sam C; Peakall, Rod

2018-01-01

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure. © 2017 John Wiley & Sons Ltd.

Construction and characterisation of a complete reverse genetics system of dengue virus type 3

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Jefferson Jose da Silva Santos

2013-12-01

Full Text Available Dengue virulence and fitness are important factors that determine disease outcome. However, dengue virus (DENV molecular biology and pathogenesis are not completely elucidated. New insights on those mechanisms have been facilitated by the development of reverse genetic systems in the past decades. Unfortunately, instability of flavivirus genomes cloned in Escherichia coli has been a major problem in these systems. Here, we describe the development of a complete reverse genetics system, based on the construction of an infectious clone and replicon for a low passage DENV-3 genotype III of a clinical isolate. Both constructs were assembled into a newly designed yeast- E. coli shuttle vector by homologous recombination technique and propagated in yeast to prevent any possible genome instability in E. coli . RNA transcripts derived from the infectious clone are infectious upon transfection into BHK-21 cells even after repeated passages of the plasmid in yeast. Transcript-derived DENV-3 exhibited growth kinetics, focus formation size comparable to original DENV-3 in mosquito C6/36 cell culture. In vitro characterisation of DENV-3 replicon confirmed its identity and ability to replicate transiently in BHK-21 cells. The reverse genetics system reported here is a valuable tool that will facilitate further molecular studies in DENV replication, virus attenuation and pathogenesis.

Recent advances in genetic modification systems for Actinobacteria.

Science.gov (United States)

Deng, Yu; Zhang, Xi; Zhang, Xiaojuan

2017-03-01

Actinobacteria are extremely important to human health, agriculture, and forests. Because of the vast differences of the characteristics of Actinobacteria, a lot of genetic tools have been developed for efficiently manipulating the genetics. Although there are a lot of successful examples of engineering Actinobacteria, they are still more difficult to be genetically manipulated than other model microorganisms such as Saccharomyces cerevisiae, Escherichia coli, and Bacillus subtilis etc. due to the diverse genomics and biochemical machinery. Here, we review the methods to introduce heterologous DNA into Actinobacteria and the available genetic modification tools. The trends and problems existing in engineering Actinobacteria are also covered.

The Possibility to Use Genetic Algorithms and Fuzzy Systems in the Development of Tutorial Systems

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Anca Ioana ANDREESCU

2006-01-01

Full Text Available In this paper we are presenting state of the art information methods and techniques that can be applied in the development of efficient tutorial systems and also the possibility to use genetic algorithms and fuzzy systems in the construction of such systems. All this topics have been studied during the development of the research project INFOSOC entitled "Tutorial System based on Eduknowledge for Work Security and Health in SMEs According to the European Union Directives" accomplished by a teaching stuff from the Academy of Economic Studies, Bucharest, in collaboration with the National Institute for Research and Development in Work Security, the National Institute for Small and Middle Enterprises and SC Q’NET International srl.

Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria.

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Nozzi, Nicole E; Atsumi, Shota

2015-11-20

Cyanobacteria have gained popularity among the metabolic engineering community as a tractable photosynthetic host for renewable chemical production. However, though a number of successfully engineered production systems have been reported, long-term genetic stability remains an issue for cyanobacterial systems. The genetic engineering toolbox for cyanobacteria is largely lacking inducible systems for expression control. The characterization of tight regulation systems for use in cyanobacteria may help to alleviate this problem. In this work we explore the function of the IPTG inducible promoter P(L)lacO1 in the model cyanobacterium Synechococcus elongatus PCC 7942 as well as the effect of gene order within an operon on pathway expression. According to our experiments, P(L)lacO1 functions well as an inducible promoter in S. elongatus. Additionally, we found that gene order within an operon can strongly influence control of expression of each gene.

A tractable algorithm for the wellfounded model

NARCIS (Netherlands)

Jonker, C.M.; Renardel de Lavalette, G.R.

In the area of general logic programming (negated atoms allowed in the bodies of rules) and reason maintenance systems, the wellfounded model (first defined by Van Gelder, Ross and Schlipf in 1988) is generally considered to be the declarative semantics of the program. In this paper we present

Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms.

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J Matthew Mahoney

2015-01-01

Full Text Available Systemic sclerosis (SSc is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6-12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected

Using Genetic Algorithm and MODFLOW to Characterize Aquifer System of Northwest Florida (Published Proceedings)

Science.gov (United States)

By integrating Genetic Algorithm and MODFLOW2005, an optimizing tool is developed to characterize the aquifer system of Region II, Northwest Florida. The history and the newest available observation data of the aquifer system is fitted automatically by using the numerical model c...

Reduced scale PWR passive safety system designing by genetic algorithms

International Nuclear Information System (INIS)

Cunha, Joao J. da; Alvim, Antonio Carlos M.; Lapa, Celso Marcelo Franklin

2007-01-01

This paper presents the concept of 'Design by Genetic Algorithms (DbyGA)', applied to a new reduced scale system problem. The design problem of a passive thermal-hydraulic safety system, considering dimensional and operational constraints, has been solved. Taking into account the passive safety characteristics of the last nuclear reactor generation, a PWR core under natural circulation is used in order to demonstrate the methodology applicability. The results revealed that some solutions (reduced scale system DbyGA) are capable of reproducing, both accurately and simultaneously, much of the physical phenomena that occur in real scale and operating conditions. However, some aspects, revealed by studies of cases, pointed important possibilities to DbyGA methodological performance improvement

Thermodynamic laws in isolated systems.

Science.gov (United States)

Hilbert, Stefan; Hänggi, Peter; Dunkel, Jörn

2014-12-01

The recent experimental realization of exotic matter states in isolated quantum systems and the ensuing controversy about the existence of negative absolute temperatures demand a careful analysis of the conceptual foundations underlying microcanonical thermostatistics. Here we provide a detailed comparison of the most commonly considered microcanonical entropy definitions, focusing specifically on whether they satisfy or violate the zeroth, first, and second laws of thermodynamics. Our analysis shows that, for a broad class of systems that includes all standard classical Hamiltonian systems, only the Gibbs volume entropy fulfills all three laws simultaneously. To avoid ambiguities, the discussion is restricted to exact results and analytically tractable examples.

Recent insights into the genetic basis of systemic lupus erythematosus.

Science.gov (United States)

Moser, K L; Kelly, J A; Lessard, C J; Harley, J B

2009-07-01

Genetic variation was first shown to be important in systemic lupus erythematosus (SLE or lupus) in the 1970s with associations in the human leukocyte antigen region. Almost four decades later, and with the help of increasingly powerful genetic approaches, more than 25 genes are now known to contribute to the mechanisms that predispose individuals to lupus. Over half of these loci have been discovered in the past 2 years, underscoring the extraordinary success of genome-wide association approaches in SLE. Well-established risk factors include alleles in the major histocompatibility complex region (multiple genes), IRF5, ITGAM, STAT4, BLK, BANK1, PDCD1, PTPN22, TNFSF4, TNFAIP3, SPP1, some of the Fcgamma receptors, and deficiencies in several complement components, including C1q, C4 and C2. As reviewed here, many susceptibility genes fall into key pathways that are consistent with previous studies implicating immune complexes, host immune signal transduction and interferon pathways in the pathogenesis of SLE. Other loci have no known function or apparent immunological role and have the potential to reveal novel disease mechanisms. Certainly, as our understanding of the genetic etiology of SLE continues to mature, important new opportunities will emerge for developing more effective diagnostic and clinical management tools for this complex autoimmune disease.

Markov chains and entropy tests in genetic-based lithofacies analysis of deep-water clastic depositional systems

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Borka Szabolcs

2016-01-01

Full Text Available The aim of this study was to examine the relationship between structural elements and the so-called genetic lithofacies in a clastic deep-water depositional system. Process-sedimentology has recently been gaining importance in the characterization of these systems. This way the recognized facies attributes can be associated with the depositional processes establishing the genetic lithofacies. In this paper this approach was presented through a case study of a Tertiary deep-water sequence of the Pannonian-basin.

Mouse forward genetics in the study of the peripheral nervous system and human peripheral neuropathy

Science.gov (United States)

Douglas, Darlene S.; Popko, Brian

2009-01-01

Forward genetics, the phenotype-driven approach to investigating gene identity and function, has a long history in mouse genetics. Random mutations in the mouse transcend bias about gene function and provide avenues towards unique discoveries. The study of the peripheral nervous system is no exception; from historical strains such as the trembler mouse, which led to the identification of PMP22 as a human disease gene causing multiple forms of peripheral neuropathy, to the more recent identification of the claw paw and sprawling mutations, forward genetics has long been a tool for probing the physiology, pathogenesis, and genetics of the PNS. Even as spontaneous and mutagenized mice continue to enable the identification of novel genes, provide allelic series for detailed functional studies, and generate models useful for clinical research, new methods, such as the piggyBac transposon, are being developed to further harness the power of forward genetics. PMID:18481175

Optimal Design of Wind-PV-Diesel-Battery System using Genetic Algorithm

Science.gov (United States)

Suryoatmojo, Heri; Hiyama, Takashi; Elbaset, Adel A.; Ashari, Mochamad

Application of diesel generators to supply the load demand on isolated islands in Indonesia has widely spread. With increases in oil price and the concerns about global warming, the integration of diesel generators with renewable energy systems have become an attractive energy sources for supplying the load demand. This paper performs an optimal design of integrated system involving Wind-PV-Diesel-Battery system for isolated island with CO2 emission evaluation by using genetic algorithm. The proposed system has been designed for the hybrid power generation in East Nusa Tenggara, Indonesia-latitude 09.30S, longitude 122.0E. From simulation results, the proposed system is able to minimize the total annual cost of the system under study and reduce CO2 emission generated by diesel generators.

Seeding-inspired chemotaxis genetic algorithm for the inference of biological systems.

Science.gov (United States)

Wu, Shinq-Jen; Wu, Cheng-Tao

2014-09-18

A large challenge in the post-genomic era is to obtain the quantitatively dynamic interactive information of the important constitutes of underlying systems. The S-system is a dynamic and structurally rich model that determines the net strength of interactions between genes and/or proteins. Good generation characteristics without the need for prior information have allowed S-systems to become one of the most promising canonical models. Various evolutionary computation technologies have recently been developed for the identification of system parameters and skeletal-network structures. However, the gaps between the truncated and preserved terms remain too small. Additionally, current research methods fail to identify the structures of high dimensional systems (e.g., 30 genes with 1800 connections). Optimization technologies should converge fast and have the ability to adaptively adjust the search. In this study, we propose a seeding-inspired chemotaxis genetic algorithm (SCGA) that can force evolution to adjust the population movement to identify a favorable location. The seeding-inspired training strategy is a method to achieve optimal results with limited resources. SCGA introduces seeding-inspired genetic operations to allow a population to possess competitive power (exploitation and exploration) and a winner-chemotaxis-induced population migration to force a population to repeatedly tumble away from an attractor and swim toward another attractor. SCGA was tested on several canonical biological systems. SCGA not only learned the correct structure within only one to three pruning steps but also ensures pruning safety. The values of the truncated terms were all smaller than 10 -14 , even for a thirty-gene system. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Genetics factors in pathogenesis and clinical genetics of binge eating disorder].

Science.gov (United States)

Kibitov, А О; Мazo, G E

2016-01-01

Genetic studies have shown that binge eating disorder (ВЕD) aggregates in families, heritability was estimated as about 60% and additive genetic influences on BED up to 50%. Using a genetic approach has proved useful for verifying the diagnostic categories of BED using DSM-IV criteria and supporting the validity of considering this pathology as a separate nosological category. The results confirmed the genetic and pathogenic originality of BED as a separate psychopathological phenomenon, but not a subtype of obesity. It seems fruitful to considerate BED as a disease with hereditary predisposition with significant genetic influence and a complex psychopathological syndrome, including not only eating disorders, but also depressive and addictive component. A possible mechanism of pathogenesis of BED may be the interaction of the neuroendocrine and neurotransmitters systems including the active involvement of the reward system in response to a variety of chronic stress influences with the important modulatory role of specific personality traits. The high level of genetic influence on the certain clinical manifestations of BED confirms the ability to identify the subphenotypes of BED on genetic basis involving clinical criteria. It can not only contribute to further genetic studies, taking into account more homogeneous samples, but also help in finding differentiated therapeutic approaches.

Can the reproductive system of a rare and narrowly endemic plant species explain its high genetic diversity?

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Daniele M. Rodrigues

2018-01-01

Full Text Available ABSTRACT The reproductive system of flowering plants can be highly variable, affecting their biology, gene flow and genetic variability among populations. Petunia secreta is a rare annual endemic species of Pedra do Segredo, located in the municipality of Caçapava do Sul, state of Rio Grande do Sul, Brazil. Although rare, the species possesses a high level of genetic variability. We investigated the reproductive system of P. secreta, including fruit production and seed germinability, in order to determine if its reproductive system can explain its genetic diversity. We sampled five populations and conducted five greenhouse hand-pollination treatments: 1 autonomous apomixis; 2 self-pollination; 3 hand self-pollination; 4 geitonogamy; and 5 cross-pollination. We analysed a total of 40 plants, 468 flowers, and 6,500 seeds. Only autonomous apomixis and self-pollination did not produce fruit. No differences in fruit weight were observed among pollination treatments (P > 0.05. Seeds of two colours were produced, with no differences in germinability. Considering all plants, populations, and treatments, the average germinability was 73 % (range 9 % to 100 %. These results, along with other previous studies, indicate that the reproductive systems of P. secreta, and its large effective population size, can explain its high genetic diversity.

Application of genetic algorithm in electrical system optimization for offshore wind farms

DEFF Research Database (Denmark)

Chen, Zhe; Zhao, M.; Blaabjerg, Frede

2008-01-01

Genetic Algorithm (GA) has been widely used in solving optimization problem in different areas. This paper illustrates the application of GA in the electrical system design for offshore wind farms, where the main components of a wind farm and key technical specifications are used as input...

The genetic architecture of the human immune system: a bioresource for autoimmunity and disease pathogenesis.

Science.gov (United States)

Roederer, Mario; Quaye, Lydia; Mangino, Massimo; Beddall, Margaret H; Mahnke, Yolanda; Chattopadhyay, Pratip; Tosi, Isabella; Napolitano, Luca; Terranova Barberio, Manuela; Menni, Cristina; Villanova, Federica; Di Meglio, Paola; Spector, Tim D; Nestle, Frank O

2015-04-09

Despite recent discoveries of genetic variants associated with autoimmunity and infection, genetic control of the human immune system during homeostasis is poorly understood. We undertook a comprehensive immunophenotyping approach, analyzing 78,000 immune traits in 669 female twins. From the top 151 heritable traits (up to 96% heritable), we used replicated GWAS to obtain 297 SNP associations at 11 genetic loci, explaining up to 36% of the variation of 19 traits. We found multiple associations with canonical traits of all major immune cell subsets and uncovered insights into genetic control for regulatory T cells. This data set also revealed traits associated with loci known to confer autoimmune susceptibility, providing mechanistic hypotheses linking immune traits with the etiology of disease. Our data establish a bioresource that links genetic control elements associated with normal immune traits to common autoimmune and infectious diseases, providing a shortcut to identifying potential mechanisms of immune-related diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease.

Science.gov (United States)

Johnson, Michael R; Shkura, Kirill; Langley, Sarah R; Delahaye-Duriez, Andree; Srivastava, Prashant; Hill, W David; Rackham, Owen J L; Davies, Gail; Harris, Sarah E; Moreno-Moral, Aida; Rotival, Maxime; Speed, Doug; Petrovski, Slavé; Katz, Anaïs; Hayward, Caroline; Porteous, David J; Smith, Blair H; Padmanabhan, Sandosh; Hocking, Lynne J; Starr, John M; Liewald, David C; Visconti, Alessia; Falchi, Mario; Bottolo, Leonardo; Rossetti, Tiziana; Danis, Bénédicte; Mazzuferi, Manuela; Foerch, Patrik; Grote, Alexander; Helmstaedter, Christoph; Becker, Albert J; Kaminski, Rafal M; Deary, Ian J; Petretto, Enrico

2016-02-01

Genetic determinants of cognition are poorly characterized, and their relationship to genes that confer risk for neurodevelopmental disease is unclear. Here we performed a systems-level analysis of genome-wide gene expression data to infer gene-regulatory networks conserved across species and brain regions. Two of these networks, M1 and M3, showed replicable enrichment for common genetic variants underlying healthy human cognitive abilities, including memory. Using exome sequence data from 6,871 trios, we found that M3 genes were also enriched for mutations ascertained from patients with neurodevelopmental disease generally, and intellectual disability and epileptic encephalopathy in particular. M3 consists of 150 genes whose expression is tightly developmentally regulated, but which are collectively poorly annotated for known functional pathways. These results illustrate how systems-level analyses can reveal previously unappreciated relationships between neurodevelopmental disease-associated genes in the developed human brain, and provide empirical support for a convergent gene-regulatory network influencing cognition and neurodevelopmental disease.

Comprehensive allelotype and genetic anaysis of 466 human nervous system tumors

DEFF Research Database (Denmark)

von Deimling, A; Fimmers, R; Schmidt, M C

2000-01-01

Brain tumors pose a particular challenge to molecular oncology. Many different tumor entities develop in the nervous system and some of them appear to follow distinct pathogenic routes. Molecular genetic alterations have increasingly been reported in nervous system neoplasms. However......, a considerable number of affected genes remain to be identified. We present here a comprehensive allelotype analysis of 466 nervous system tumors based on loss of heterozygosity (LOH) studies with 129 microsatellite markers that span the genome. Specific alterations of the EGFR, CDK4, CDKN2A, TP53, DMBT1, NF2...... may provide a valuable framework for future studies to delineate molecular pathways in many types of human central nervous system tumors....

Genetic structure, mating system, and long-distance gene flow in heart of palm (Euterpe edulis Mart.).

Science.gov (United States)

Gaiotto, F A; Grattapaglia, D; Vencovsky, R

2003-01-01

We report a detailed analysis of the population genetic structure, mating system, and gene flow of heart of palm (Euterpe edulis Mart.-Arecaceae) in central Brazil. This palm is considered a keystone species because it supplies fruits for birds and rodents all year and is intensively harvested for culinary purposes. Two populations of this palm tree were examined, using 18 microsatellite loci. The species displays a predominantly outcrossed mating system (tm = 0.94), with a probability of full sibship greater than 70% within open-pollinated families. The following estimates of interpopulation genetic variation were calculated and found significant: FIT = 0.17, FIS = 0.12, FST = 0.06, and RST = 0.07. This low but significant level of interpopulation genetic variation indicates high levels of gene flow. Two adult trees were identified as likely seed parents (P > 99.9%) of juveniles located at a distance of 22 km. Gene flow over such distances has not been reported before for tropical tree species. The establishment and management of in situ genetic reserves or ex situ conservation and breeding populations for E. edulis should contemplate the collection of several hundreds open-pollinated maternal families from relatively few distant populations to maximize the genetic sampling of a larger number of pollen parents.

Optimisation of Refrigeration System with Two-Stage and Intercooler Using Fuzzy Logic and Genetic Algorithm

Directory of Open Access Journals (Sweden)

Bayram Kılıç

2017-04-01

Full Text Available Two-stage compression operation prevents excessive compressor outlet pressure and temperature and this operation provides more efficient working condition in low-temperature refrigeration applications. Vapor compression refrigeration system with two-stage and intercooler is very good solution for low-temperature refrigeration applications. In this study, refrigeration system with two-stage and intercooler were optimized using fuzzy logic and genetic algorithm. The necessary thermodynamic characteristics for optimization were estimated with Fuzzy Logic and liquid phase enthalpy, vapour phase enthalpy, liquid phase entropy, vapour phase entropy values were compared with actual values. As a result, optimum working condition of system was estimated by the Genetic Algorithm as -6.0449 oC for evaporator temperature, 25.0115 oC for condenser temperature and 5.9666 for COP. Morever, irreversibility values of the refrigeration system are calculated.

Development of a BWR loading pattern design system based on modified genetic algorithms and knowledge

International Nuclear Information System (INIS)

Martin-del-Campo, Cecilia; Francois, Juan Luis; Avendano, Linda; Gonzalez, Mario

2004-01-01

An optimization system based on Genetic Algorithms (GAs), in combination with expert knowledge coded in heuristics rules, was developed for the design of optimized boiling water reactor (BWR) fuel loading patterns. The system was coded in a computer program named Loading Pattern Optimization System based on Genetic Algorithms, in which the optimization code uses GAs to select candidate solutions, and the core simulator code CM-PRESTO to evaluate them. A multi-objective function was built to maximize the cycle energy length while satisfying power and reactivity constraints used as BWR design parameters. Heuristic rules were applied to satisfy standard fuel management recommendations as the Control Cell Core and Low Leakage loading strategies, and octant symmetry. To test the system performance, an optimized cycle was designed and compared against an actual operating cycle of Laguna Verde Nuclear Power Plant, Unit I

A Genetic Algorithm Approach to the Optimization of a Radioactive Waste Treatment System

International Nuclear Information System (INIS)

Yang, Yeongjin; Lee, Kunjai; Koh, Y.; Mun, J.H.; Kim, H.S.

1998-01-01

This study is concerned with the applications of goal programming and genetic algorithm techniques to the analysis of management and operational problems in the radioactive waste treatment system (RWTS). A typical RWTS is modeled and solved by goal program and genetic algorithm to study and resolve the effects of conflicting objectives such as cost, limitation of released radioactivity to the environment, equipment utilization and total treatable radioactive waste volume before discharge and disposal. The developed model is validated and verified using actual data obtained from the RWTS at Kyoto University in Japan. The solution by goal programming and genetic algorithm would show the optimal operation point which is to maximize the total treatable radioactive waste volume and minimize the released radioactivity of liquid waste even under the restricted resources. The comparison of two methods shows very similar results. (author)

Interspecific sex in grass smuts and the genetic diversity of their pheromone-receptor system.

Directory of Open Access Journals (Sweden)

Ronny Kellner

2011-12-01

Full Text Available The grass smuts comprise a speciose group of biotrophic plant parasites, so-called Ustilaginaceae, which are specifically adapted to hosts of sweet grasses, the Poaceae family. Mating takes a central role in their life cycle, as it initiates parasitism by a morphological and physiological transition from saprobic yeast cells to pathogenic filaments. As in other fungi, sexual identity is determined by specific genomic regions encoding allelic variants of a pheromone-receptor (PR system and heterodimerising transcription factors. Both operate in a biphasic mating process that starts with PR-triggered recognition, directed growth of conjugation hyphae, and plasmogamy of compatible mating partners. So far, studies on the PR system of grass smuts revealed diverse interspecific compatibility and mating type determination. However, many questions concerning the specificity and evolutionary origin of the PR system remain unanswered. Combining comparative genetics and biological approaches, we report on the specificity of the PR system and its genetic diversity in 10 species spanning about 100 million years of mating type evolution. We show that three highly syntenic PR alleles are prevalent among members of the Ustilaginaceae, favouring a triallelic determination as the plesiomorphic characteristic of this group. Furthermore, the analysis of PR loci revealed increased genetic diversity of single PR locus genes compared to genes of flanking regions. Performing interspecies sex tests, we detected a high potential for hybridisation that is directly linked to pheromone signalling as known from intraspecies sex. Although the PR system seems to be optimised for intraspecific compatibility, the observed functional plasticity of the PR system increases the potential for interspecific sex, which might allow the hybrid-based genesis of newly combined host specificities.

Evaluation of a 13-loci STR multiplex system for Cannabis sativa genetic identification.

Science.gov (United States)

Houston, Rachel; Birck, Matthew; Hughes-Stamm, Sheree; Gangitano, David

2016-05-01

Marijuana (Cannabis sativa) is the most commonly used illicit substance in the USA. The development of a validated method using Cannabis short tandem repeats (STRs) could aid in the individualization of samples as well as serve as an intelligence tool to link multiple cases. For this purpose, a modified 13-loci STR multiplex method was optimized and evaluated according to ISFG and SWGDAM guidelines. A real-time PCR quantification method for C. sativa was developed and validated, and a sequenced allelic ladder was also designed to accurately genotype 199 C. sativa samples from 11 U.S. Customs and Border Protection seizures. Distinguishable DNA profiles were generated from 127 samples that yielded full STR profiles. Four duplicate genotypes within seizures were found. The combined power of discrimination of this multilocus system is 1 in 70 million. The sensitivity of the multiplex STR system is 0.25 ng of template DNA. None of the 13 STR markers cross-reacted with any of the studied species, except for Humulus lupulus (hops) which generated unspecific peaks. Phylogenetic analysis and case-to-case pairwise comparison of 11 cases using F st as genetic distance revealed the genetic association of four groups of cases. Moreover, due to their genetic similarity, a subset of samples (N = 97) was found to form a homogeneous population in Hardy-Weinberg and linkage equilibrium. The results of this research demonstrate the applicability of this 13-loci STR system in associating Cannabis cases for intelligence purposes.

Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform

NARCIS (Netherlands)

Lee, Sung Sik; Avalos Vizcarra, Ima; Huberts, Daphne H E W; Lee, Luke P; Heinemann, Matthias

2012-01-01

Important insights into aging have been generated with the genetically tractable and short-lived budding yeast. However, it is still impossible today to continuously track cells by high-resolution microscopic imaging (e.g., fluorescent imaging) throughout their entire lifespan. Instead, the field

Genetic mating systems and reproductive natural histories of fishes: lessons for ecology and evolution.

Science.gov (United States)

Avise, John C; Jones, Adam G; Walker, DeEtte; DeWoody, J Andrew

2002-01-01

Fish species have diverse breeding behaviors that make them valuable for testing theories on genetic mating systems and reproductive tactics. Here we review genetic appraisals of paternity and maternity in wild fish populations. Behavioral phenomena quantified by genetic markers in various species include patterns of multiple mating by both sexes; frequent cuckoldry by males and rare cuckoldry by females in nest-tending species; additional routes to surrogate parentage via nest piracy and egg-thievery; egg mimicry by nest-tending males; brood parasitism by helper males in cooperative breeders; clutch mixing in oral brooders; kinship in schooling fry of broadcast spawners; sperm storage by dams in female-pregnant species; and sex-role reversal, polyandry, and strong sexual selection on females in some male-pregnant species. Additional phenomena addressed by genetic parentage analyses in fishes include clustered mutations, filial cannibalism, and local population size. All results are discussed in the context of relevant behavioral and evolutionary theory.

Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

Directory of Open Access Journals (Sweden)

Sascha van der Meer

Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

The Relationship between Mating System and Genetic Diversity in Diploid Sexual Populations of Cyrtomium falcatum in Japan.

Directory of Open Access Journals (Sweden)

Ryosuke Imai

Full Text Available The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation in gametophytes: mixed (M type and separate (S type. We examined whether there is variation in the selfing rate among populations of this species, and evaluated the relationship between mating system, genetic diversity and effective population size using microsatellites. In this study, we developed eight new microsatellite markers and evaluated genetic diversity and structure of seven populations (four M-type and three S-type. Past effective population sizes (Ne were inferred using Approximate Bayesian computation (ABC. The values of fixation index (FIS, allelic richness (AR and gene diversity (h differed significantly between the M-type (FIS: 0.626, AR: 1.999, h: 0.152 and the S-type (FIS: 0.208, AR: 2.718, h: 0.367 populations (when admixed individuals were removed from two populations. Although evidence of past bottleneck events was detected in all populations by ABC, the current Ne of the M-type populations was about a third of that of the S-type populations. These results suggest that the M-type populations have experienced more frequent bottlenecks, which could be related to their higher colonization ability via gametophytic selfing. Although high population differentiation among populations was detected (FST = 0.581, F'ST = 0.739, there was no clear genetic differentiation between the M- and S-types. Instead, significant isolation by distance was detected among all populations. These results suggest that mating system variation in this species is generated by the selection for single spore colonization during local extinction and recolonization events and there is no genetic structure due to mating system.

A study on maintenance reliability allocation of urban transit brake system using hybrid neuro-genetic technique

International Nuclear Information System (INIS)

Bae, Chul Ho; Kim, Hyun Jun; Lee, Jung Hwan; Suh, Myung Won; Chu, Yul

2007-01-01

For reasonable establishing of maintenance strategies, safety security and cost limitation must be considered at the same time. In this paper, the concept of system reliability introduces and optimizes as the key of reasonable maintenance strategies. This study aims at optimizing component's reliability that satisfies the target reliability of brake system in the urban transit. First of all, constructed reliability evaluation system is used to predict and analyze reliability. This data is used for the optimization. To identify component reliability in a system, a method is presented in this paper which uses hybrid neuro-genetic technique. Feed-forward multi-layer neural networks trained by back propagation are used to find out the relationship between component reliability (input) and system reliability (output) of a structural system. The inverse problem can be formulated by using neural network. Genetic algorithm is used to find the minimum square error. Finally, this paper presents reasonable maintenance cycle of urban transit brake system by using optimal system reliability

The STAT4 gene influences the genetic predisposition to systemic sclerosis phenotype.

NARCIS (Netherlands)

Rueda, B.; Broen, J.; Simeon, C.; Hesselstrand, R.; Diaz, B.; Suarez, H.; Ortego-Centeno, N.; Riemekasten, G.; Fonollosa, V.; Vonk, M.C.; Hoogen, F.H.J. van den; Sanchez-Roman, J.; Aguirre-Zamorano, M.A.; Garcia-Portales, R.; Pros, A.; Camps, M.T.; Gonzalez-Gay, M.A.; Coenen, M.J.H.; Airo, P.; Beretta, L.; Scorza, R.; Laar, J. van; Gonzalez-Escribano, M.F.; Nelson, J.L.; Radstake, T.R.D.J.; Martin, J.

2009-01-01

The aim of this study was to investigate the possible role of STAT4 gene in the genetic predisposition to systemic sclerosis (SSc) susceptibility or clinical phenotype. A total of 1317 SSc patients [896 with limited cutaneous SSc (lcSSc) and 421 with diffuse cutaneous SSc (dcSSc)] and 3113 healthy

Felling-system and regeneration of pine forests on ecological-genetic-geographical basis

Directory of Open Access Journals (Sweden)

S. N. Sannikov

2015-12-01

Full Text Available A conception of the adaptation of Scots pine populations to the natural regeneration on open sites with the mosaic retained stand and mineralized soil surface on the basis of the ecological-genetic-geographical investigations in the forests of the Russia and the theory of petropsammofitness-pyrofitness (Sannikov S. N., 1983 has been substantiated. The methods of clear cuts with the seeding from surrounding forest, seed curtains and sufficiently extent of the substrate preparation for the pine selfsown have been selected and elaborated as a main organization principle of the system «felling-regeneration» in the plains pine forests of the forest zone. High regeneration efficiency of this system with the application of original aggregate for the optimal mineralization of the soil substrate (with its synchronous loosing has been shown on the example of dominating pine forest types in the subzone for-forest-steppe of the Western Siberia. The silvicultural-ecological and reproductive-genetic advantages of retaining seed curtains instead of separate seed trees have been substantiated. The basic parameters of the system «felling-regeneration», which guarantee a sufficient success of the following pine regeneration in the for-forest-steppe subzone, have been determined with the help of the methods of the mathematical imitation modeling of the pine selfsown density depending on the area and localization of seed curtains, surrounding forest and the extent of the substrate mineralization. The zonal differentiated system of the fellings and measures for the regeneration optimization in the climatically substituting pine forest types in the Western Siberia has been elaborated according to the parameters, studied earlier, on the ecological-genetic-geographical basis. The principles of this system in forest zone come to the clear strip-fellings with insemination of cuts from the seed curtains and forest walls, and to the hollow-fellings with the

Automatic Tuning of PID Controller for a 1-D Levitation System Using a Genetic Algorithm

DEFF Research Database (Denmark)

Yang, Zhenyu; Pedersen, Gerulf K.m.

2006-01-01

The automatic PID control design for a onedimensional magnetic levitation system is investigated. The PID controller is automatically tuned using the non-dominated sorting genetic algorithm (NSGA-II) based on a nonlinear system model. The developed controller is digitally implemented and tested...

Preservation of the genetic diversity of a local common carp in the agricultural heritage rice–fish system

Science.gov (United States)

Ren, Weizheng; Hu, Liangliang; Guo, Liang; Zhang, Jian; Tang, Lu; Zhang, Entao; Zhang, Jiaen; Luo, Shiming; Tang, Jianjun; Chen, Xin

2018-01-01

We examined how traditional farmers preserve the genetic diversity of a local common carp (Cyprinus carpio), which is locally referred to as “paddy field carp” (PF-carp), in a “globally important agricultural heritage system” (GIAHS), i.e., the 1,200-y-old rice–fish coculture system in Zhejiang Province, China. Our molecular and morphological analysis showed that the PF-carp has changed into a distinct local population with higher genetic diversity and diverse color types. Within this GIAHS region, PF-carps exist as a continuous metapopulation, although three genetic groups could be identified by microsatellite markers. Thousands of small farmer households interdependently obtained fry and parental carps for their own rice–fish production, resulting in a high gene flow and large numbers of parent carps distributing in a mosaic pattern in the region. Landscape genetic analysis indicated that farmers’ connectivity was one of the major factors that shaped this genetic pattern. Population viability analysis further revealed that the numbers of these interconnected small farmer households and their connection intensity affect the carps’ inherent genetic diversity. The practice of mixed culturing of carps with diverse color types helped to preserve a wide range of genetic resources in the paddy field. This widespread traditional practice increases fish yield and resource use, which, in return, encourages famers to continue their practice of selecting and conserving diverse color types of PF-carp. Our results suggested that traditional farmers secure the genetic diversity of PF-carp and its viability over generations in this region through interdependently incubating and mixed-culturing practices within the rice−fish system. PMID:29295926

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems.

Science.gov (United States)

Araújo, Luciano V; Malkowski, Simon; Braghetto, Kelly R; Passos-Bueno, Maria R; Zatz, Mayana; Pu, Calton; Ferreira, João E

2011-12-22

Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

Estimation of countries’ interdependence in plant genetic resources provisioning national food supplies and production systems

OpenAIRE

Khoury, C.K.; Achicanoy, H.A.; Bjorkman, A.D.; Navarro-Racines, C.; Guarino, L.; Flores-Palacios, X.; Engels, J.M.M.; Wiersema, J.H.; Dempewolf, H.; Ramirez-Villegas, J.; Castaneda-Alvarez, N.P.; Fowler, C.; Jarvis, A.; Rieseberg, L.H.; Struik, P.C.

2015-01-01

The Contracting Parties of the International Treaty recognize that plant genetic resources for food and agriculture are a common concern of all countries, in that all countries depend largely on plant genetic resources for food and agriculture that originated elsewhere. Nearly 20 years ago, an initial research on interdependence mong countries on crop diversity provided information helpful for countries to establish the Treaty, and in particular its Multilateral System of Access and Benefit-s...

Network reconfiguration for loss reduction in electrical distribution system using genetic algorithm

International Nuclear Information System (INIS)

Adail, A.S.A.A.

2012-01-01

Distribution system is a critical links between the utility and the nuclear installation. During feeding electricity to that installation there are power losses. The quality of the network depends on the reduction of these losses. Distribution system which feeds the nuclear installation must have a higher quality power. For example, in Inshas site, electrical power is supplied to it from two incoming feeders (one from new abu-zabal substation and the other from old abu-zabal substation). Each feeder is designed to carry the full load, while the operator preferred to connect with a new abu-zabal substation, which has a good power quality. Bad power quality affects directly the nuclear reactor and has a negative impact on the installed sensitive equipment's of the operation. The thesis is Studying the electrical losses in a distribution system (causes and effected factors), feeder reconfiguration methods, and applying of genetic algorithm in an electric distribution power system. In the end, this study proposes an optimization technique based on genetic algorithms for distribution network reconfiguration to reduce the network losses to minimum. The proposed method is applied to IEEE test network; that contain 3 feeders and 16 nodes. The technique is applied through two groups, distribution have general loads, and nuclear loads. In the groups the technique applied to seven cases at normal operation state, system fault condition as well as different loads conditions. Simulated results are drawn to show the accuracy of the technique.

Long-Term Adult Feline Liver Organoid Cultures for Disease Modeling of Hepatic Steatosis

NARCIS (Netherlands)

Kruitwagen, Hedwig S.; Oosterhoff, Loes A.; Vernooij, Ingrid G.W.H.; Schrall, Ingrid M.; van Wolferen, Monique E.; Bannink, Farah; Roesch, Camille; van Uden, Lisa; Molenaar, Martijn R.; Helms, J. Bernd; Grinwis, Guy C.M.; Verstegen, Monique M.A.; van der Laan, Luc J.W.; Huch, Meritxell; Geijsen, Niels; Vries, Robert G.; Clevers, Hans; Rothuizen, Jan; Schotanus, Baukje A.; Penning, Louis C.; Spee, Bart

2017-01-01

Hepatic steatosis is a highly prevalent liver disease, yet research is hampered by the lack of tractable cellular and animal models. Steatosis also occurs in cats, where it can cause severe hepatic failure. Previous studies demonstrate the potential of liver organoids for modeling genetic diseases.

A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host

DEFF Research Database (Denmark)

Lyngsø, C.; Kjaerulff, S.; Muller, S.

2010-01-01

in vivo selection system for folded proteins. It is based on genetic complementation of the Schizosaccharomyces pombe growth marker gene invertase fused C-terminally to a protein library. The fusion proteins are directed to the secretion system, utilizing the ability of the eukaryotic protein quality...

Genetics for the ophthalmologist

Directory of Open Access Journals (Sweden)

Karthikeyan A Sadagopan

2012-01-01

Full Text Available The eye has played a major role in human genomics including gene therapy. It is the fourth most common organ system after integument (skin, hair and nails, nervous system, and musculoskeletal system to be involved in genetic disorders. The eye is involved in single gene disorders and those caused by multifactorial etiology. Retinoblastoma was the first human cancer gene to be cloned. Leber hereditary optic neuropathy was the first mitochondrial disorder described. X-Linked red-green color deficiency was the first X-linked disorder described. The eye, unlike any other body organ, allows directly visualization of genetic phenomena such as skewed X-inactivation in the fundus of a female carrier of ocular albinism. Basic concepts of genetics and their application to clinical ophthalmological practice are important not only in making a precise diagnosis and appropriate referral, but also in management and genetic counseling.

Genetic secrets: Protecting privacy and confidentiality in the genetic era

Energy Technology Data Exchange (ETDEWEB)

Rothstein, M.A. [ed.

1998-07-01

Few developments are likely to affect human beings more profoundly in the long run than the discoveries resulting from advances in modern genetics. Although the developments in genetic technology promise to provide many additional benefits, their application to genetic screening poses ethical, social, and legal questions, many of which are rooted in issues of privacy and confidentiality. The ethical, practical, and legal ramifications of these and related questions are explored in depth. The broad range of topics includes: the privacy and confidentiality of genetic information; the challenges to privacy and confidentiality that may be projected to result from the emerging genetic technologies; the role of informed consent in protecting the confidentiality of genetic information in the clinical setting; the potential uses of genetic information by third parties; the implications of changes in the health care delivery system for privacy and confidentiality; relevant national and international developments in public policies, professional standards, and laws; recommendations; and the identification of research needs.

Automatic Laser Pointer Detection Algorithm for Environment Control Device Systems Based on Template Matching and Genetic Tuning of Fuzzy Rule-Based Systems

Directory of Open Access Journals (Sweden)

F.

2012-04-01

Full Text Available In this paper we propose a new approach for laser-based environment device control systems based on the automatic design of a Fuzzy Rule-Based System for laser pointer detection. The idea is to improve the success rate of the previous approaches decreasing as much as possible the false offs and increasing the success rate in images with laser spot, i.e., the detection of a false laser spot (since this could lead to dangerous situations. To this end, we propose to analyze both, the morphology and color of a laser spot image together, thus developing a new robust algorithm. Genetic Fuzzy Systems have also been employed to improve the laser spot system detection by means of a fine tuning of the involved membership functions thus reducing the system false offs, which is the main objective in this problem. The system presented in this paper, makes use of a Fuzzy Rule-Based System adjusted by a Genetic Algorithm, which, based on laser morphology and color analysis, shows a better success rate than previous approaches.

The genetic algorithm for the nonlinear programming of water pollution control system

Energy Technology Data Exchange (ETDEWEB)

Wei, J.; Zhang, J. [China University of Geosciences (China)

1999-08-01

In the programming of water pollution control system the combined method of optimization with simulation is used generally. It is not only laborious in calculation, but also the global optimum of the obtained solution is guaranteed difficult. In this paper, the genetic algorithm (GA) used in the nonlinear programming of water pollution control system is given, by which the preferred conception for the programming of waste water system is found in once-through operation. It is more succinct than the conventional method and the global optimum of the obtained solution could be ensured. 6 refs., 4 figs., 3 tabs.

The effectiveness of argumentation in tutorial dialogues with an Intelligent Tutoring System for genetic risk of breast cancer

Science.gov (United States)

Cedillos-Whynott, Elizabeth M.; Wolfe, Christopher R.; Widmer, Colin L.; Brust-Renck, Priscila G.; Weil, Audrey; Reyna, Valerie F.

2017-01-01

BRCA Gist is an Intelligent Tutoring System that helps women understand issues related to genetic testing and breast cancer risk. In two laboratory experiments and a field experiment with community and web-based samples, an avatar asked 120 participants to produce arguments for and against genetic testing for breast cancer risk. Two raters assessed the number of argumentation elements (claim, reason, backing, etc.) found in response to prompts soliciting arguments for and against genetic testing for breast cancer risk (IRR=.85). When asked to argue for genetic testing, 53.3 % failed to meet the minimum operational definition of making an argument, a claim supported by one or more reasons. When asked to argue against genetic testing, 59.3 % failed to do so. Of those who failed to generate arguments most simply listed disconnected reasons. However, participants who provided arguments against testing (40.7 %) performed significantly higher on a posttest of declarative knowledge. In each study we found positive correlations between the quality of arguments against genetic testing (i.e., number of argumentation elements) and genetic risk categorization scores. Although most interactions did not contain two or more argument elements, when more elements of arguments were included in the argument against genetic testing interaction, participants had greater learning outcomes. Apparently, many participants lack skills in making coherent arguments. These results suggest an association between argumentation ability (knowing how to make complex arguments) and subsequent learning. Better education in developing arguments may be necessary for people to learn from generating arguments within Intelligent Tutoring Systems and other settings. PMID:26511370

Application of genetic algorithm for optimization the safety system of the nuclear reactor

International Nuclear Information System (INIS)

El-Sayed Wahed, M.; Ibrahim, W.Z.; Effat, A.M.

2009-01-01

The purpose of this paper is to present an approach to optimization in which every target is considered as a separate objective to be optimized. Multi-objective optimization is a powerful tool for resolving conflicting objectives in engineering design and numerous other fields. One approach to solve multi-objective optimization problems is the non-dominated sorting genetic algorithm (NSGA). Genetic algorithm (GA) was applied in regarding the choice of the time intervals for the periodic testing of the components of the chimney water injection system (CWIS) of the 22 MW open pool multipurpose reactor (MPR), ETRR-2, at the Egyptian Atomic Energy Authority, has been used as a case study. (authors)

A fuzzy genetic approach for network reconfiguration to enhance voltage stability in radial distribution systems

International Nuclear Information System (INIS)

Sahoo, N.C.; Prasad, K.

2006-01-01

This paper presents a fuzzy genetic approach for reconfiguration of radial distribution systems (RDS) so as to maximize the voltage stability of the network for a specific set of loads. The network reconfiguration involves a mechanism for selection of the best set of branches to be opened, one from each loop, such that the reconfigured RDS possesses desired performance characteristics. This discrete solution space is better handled by the proposed scheme, which maximizes a suitable optimizing function (computed using two different approaches). In the first approach, this function is chosen as the average of a voltage stability index of all the buses in the RDS, while in the second approach, the complete RDS is reduced to a two bus equivalent system and the optimizing function is the voltage stability index of this reduced two bus system. The fuzzy genetic algorithm uses a suitable coding and decoding scheme for maintaining the radial nature of the network at every stage of genetic evolution, and it also uses a fuzzy rule based mutation controller for efficient search of the solution space. This method, tested on 69 bus and 33 bus RDSs, shows promising results for the both approaches. It is also observed that the network losses are reduced when the voltage stability is enhanced by the network reconfiguration

Genetic Programming for Medicinal Plant Family Identification System

Directory of Open Access Journals (Sweden)

Indra Laksmana

2014-11-01

Full Text Available Information about medicinal plants that is available in text documents is generally quite easy to access, however, one needs some efforts to use it. This research was aimed at utilizing crucial information taken from a text document to identify the family of several species of medicinal plants using a heuristic approach, i.e. genetic programming. Each of the species has its unique features. The genetic program puts the characteristics or special features of each family into a tree form. There are a number of processes involved in the investigated method, i.e. data acquisition, booleanization, grouping of training and test data, evaluation, and analysis. The genetic program uses a training process to select the best individual, initializes a generate-rule process to create several individuals and then executes a fitness evaluation. The next procedure is a genetic operation process, which consists of tournament selection to choose the best individual based on a fitness value, the crossover operation and the mutation operation. These operations have the purpose of complementing the individual. The best individual acquired is the expected solution, which is a rule for classifying medicinal plants. This process produced three rules, one for each plant family, displaying a feature structure that distinguishes each of the families from each other. The genetic program then used these rules to identify the medicinal plants, achieving an average accuracy of 86.47%.

A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi

DEFF Research Database (Denmark)

Nødvig, Christina Spuur; Nielsen, Jakob Blæsbjerg; Kogle, Martin Engelhard

2015-01-01

there is a demand for developing versatile methods that can be used to genetically manipulate non-model filamentous fungi. To facilitate this, we have developed a CRISPR-Cas9 based system adapted for use in filamentous fungi. The system is simple and versatile, as RNA guided mutagenesis can be achieved...... by transforming a target fungus with a single plasmid. The system currently contains four CRISPR- Cas9 vectors, which are equipped with commonly used fungal markers allowing for selection in a broad range of fungi. Moreover, we have developed a script that allows identification of protospacers that target gene...... used our CRISPR Cas9 system to generate a strain that contains an AACU_pyrG marker and demonstrated that the resulting strain can be used for iterative gene targeting....

Tissue P Systems With Channel States Working in the Flat Maximally Parallel Way.

Science.gov (United States)

Song, Bosheng; Perez-Jimenez, Mario J; Paun, Gheorghe; Pan, Linqiang

2016-10-01

Tissue P systems with channel states are a class of bio-inspired parallel computational models, where rules are used in a sequential manner (on each channel, at most one rule can be used at each step). In this work, tissue P systems with channel states working in a flat maximally parallel way are considered, where at each step, on each channel, a maximal set of applicable rules that pass from a given state to a unique next state, is chosen and each rule in the set is applied once. The computational power of such P systems is investigated. Specifically, it is proved that tissue P systems with channel states and antiport rules of length two are able to compute Parikh sets of finite languages, and such P systems with one cell and noncooperative symport rules can compute at least all Parikh sets of matrix languages. Some Turing universality results are also provided. Moreover, the NP-complete problem SAT is solved by tissue P systems with channel states, cell division and noncooperative symport rules working in the flat maximally parallel way; nevertheless, if channel states are not used, then such P systems working in the flat maximally parallel way can solve only tractable problems. These results show that channel states provide a frontier of tractability between efficiency and non-efficiency in the framework of tissue P systems with cell division (assuming P ≠ NP ).

Genomic conflict in scale insects : The causes and consequences of bizarre genetic systems

NARCIS (Netherlands)

Ross, Laura; Pen, Ido; Shuker, David M.

2010-01-01

It is now clear that mechanisms of sex determination are extraordinarily labile, with considerable variation across all taxonomic levels. This variation is often expressed through differences in the genetic system (XX-XY, XX-XO, haplodiploidy, and so on). Why there is so much variation in such a

Integrated genetic analysis microsystems

International Nuclear Information System (INIS)

Lagally, Eric T; Mathies, Richard A

2004-01-01

With the completion of the Human Genome Project and the ongoing DNA sequencing of the genomes of other animals, bacteria, plants and others, a wealth of new information about the genetic composition of organisms has become available. However, as the demand for sequence information grows, so does the workload required both to generate this sequence and to use it for targeted genetic analysis. Microfabricated genetic analysis systems are well poised to assist in the collection and use of these data through increased analysis speed, lower analysis cost and higher parallelism leading to increased assay throughput. In addition, such integrated microsystems may point the way to targeted genetic experiments on single cells and in other areas that are otherwise very difficult. Concomitant with these advantages, such systems, when fully integrated, should be capable of forming portable systems for high-speed in situ analyses, enabling a new standard in disciplines such as clinical chemistry, forensics, biowarfare detection and epidemiology. This review will discuss the various technologies available for genetic analysis on the microscale, and efforts to integrate them to form fully functional robust analysis devices. (topical review)

Y-chromosomal insights into the genetic impact of the caste system in India.

Science.gov (United States)

Zerjal, Tatiana; Pandya, Arpita; Thangaraj, Kumarasamy; Ling, Edmund Y S; Kearley, Jennifer; Bertoneri, Stefania; Paracchini, Silvia; Singh, Lalji; Tyler-Smith, Chris

2007-03-01

The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86 from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger effective population sizes, or less strict isolation, or both.

Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

Directory of Open Access Journals (Sweden)

Sarel Halachmi

2007-01-01

Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

Contribution to Control of an Elastic Two-Mass System by Means of Genetic Algorithm

Directory of Open Access Journals (Sweden)

Zelmira Ferkova

2007-01-01

Full Text Available Oscillations of an elastic two-mass system with all known parameters may be suppressed by suitable feedback signal. An observer enables to estimate this feedback without measurement of load mechanism speed. This article contains application of genetic algorithms for identification of elastic system parameters and determination of corresponding observer feedback coefficients. Design correctness is verified by simulation.

Systems genetic analysis of brown adipose tissue function

Czech Academy of Sciences Publication Activity Database

Pravenec, Michal; Saba, L. M.; Zídek, Václav; Landa, Vladimír; Mlejnek, Petr; Šilhavý, Jan; Šimáková, Miroslava; Strnad, Hynek; Trnovská, J.; Škop, V.; Hüttl, M.; Marková, I.; Oliyarnyk, O.; Malínská, H.; Kazdová, L.; Smith, H.; Tabakoff, B.

2018-01-01

Roč. 50, č. 1 (2018), s. 52-66 ISSN 1094-8341 R&D Projects: GA ČR(CZ) GA13-04420S Institutional support: RVO:67985823 Keywords : brown adipose tissue * coexpression modules * quantitative trait locus * recombinant inbred strains * spontaneously hypertensive rat Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Human genetics Impact factor: 3.044, year: 2016

Cryptic Genetic Variation in Evolutionary Developmental Genetics

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Annalise B. Paaby

2016-06-01

Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

An injectable spheroid system with genetic modification for cell transplantation therapy.

Science.gov (United States)

Uchida, Satoshi; Itaka, Keiji; Nomoto, Takahiro; Endo, Taisuke; Matsumoto, Yu; Ishii, Takehiko; Kataoka, Kazunori

2014-03-01

The new methodology to increase a therapeutic potential of cell transplantation was developed here by the use of three-dimensional spheroids of transplanting cells subsequent to the genetic modification with non-viral DNA vectors, polyplex nanomicelles. Particularly, spheroids in regulated size of 100-μm of primary hepatocytes transfected with luciferase gene were formed on the micropatterned culture plates coated with thermosensitive polymer, and were recovered in the form of injectable liquid suspension simply by cooling the plates. After subcutaneously transplanting these hepatocyte spheroids, efficient transgene expression was observed in host tissue for more than a month, whereas transplantation of a single-cell suspension from a monolayer culture resulted in an only transient expression. The spheroid system contributed to the preservation of innate functions of transplanted hepatocytes in the host tissue, such as albumin expression, thereby possessing high potential for expressing transgene. Intravital observation of transplanted cells showed that those from spheroid cultures had a tendency to localize in the vicinity of blood vessels, making a favorable microenvironment for preserving cell functionality. Furthermore, spheroids transfected with erythropoietin-expressing DNA showed a significantly higher hematopoietic effect than that of cell suspensions from monolayer cultures, demonstrating high potential of this genetically-modified spheroid transplantation system for therapeutic applications. Copyright © 2013 Elsevier Ltd. All rights reserved.

Optimisation of electrical system for offshore wind farms via genetic algorithm

DEFF Research Database (Denmark)

Chen, Zhe; Zhao, Menghua; Blaabjerg, Frede

2009-01-01

An optimisation platform based on genetic algorithm (GA) is presented, where the main components of a wind farm and key technical specifications are used as input parameters and the electrical system design of the wind farm is optimised in terms of both production cost and system reliability....... The power losses, wind power production, initial investment and maintenance costs are considered in the production cost. The availability of components and network redundancy are included in the reliability evaluation. The method of coding an electrical system to a binary string, which is processed by GA......, is developed. Different GA techniques are investigated based on a real example offshore wind farm. This optimisation platform has been demonstrated as a powerful tool for offshore wind farm design and evaluation....

Fanconi anemia: correlating central nervous system malformations and genetic complementation groups.

Science.gov (United States)

Johnson-Tesch, Benjamin A; Gawande, Rakhee S; Zhang, Lei; MacMillan, Margaret L; Nascene, David R

2017-06-01

Congenital central nervous system abnormalities in children with Fanconi anemia are poorly characterized, especially with regard to specific genetic complementation groups. To characterize the impact of genetic complementation groups on central nervous system anatomy. Through chart review we identified 36 patients with Fanconi anemia with available brain MRIs at the University of Minnesota (average age, 11.3 years; range, 1-43 years; M:F=19:17), which we reviewed and compared to 19 age- and sex-matched controls (average age, 7.9 years; range, 2-18 years; M:F=9:10). Genotypic information was available for 27 patients (15 FA-A, 2 FA-C, 3 FA-G, and 7 FA-D1 [biallelic mutations in BRCA2 gene]). Of the 36 patients, 61% had at least one congenital central nervous system or skull base abnormality. These included hypoplastic clivus (n=12), hypoplastic adenohypophysis (n=11), platybasia (n=8), pontocerebellar hypoplasia (n=7), isolated pontine hypoplasia (n=4), isolated vermis hypoplasia (n=3), and ectopic neurohypophysis (n=6). Average pituitary volume was significantly less in patients with Fanconi anemia (PFanconi anemia patients (P=0.006), but the basal angle of those with FA-D1 was not significantly different from controls (P=0.239). Clivus length was less in the Fanconi anemia group (P=0.002), but significance was only observed in the FA-D1 subgroup (PFanconi anemia have higher incidences of ectopic neurohypophysis, adenohypophysis hypoplasia, platybasia and other midline central nervous system skull base posterior fossa abnormalities than age- and sex-matched controls. Patients with posterior fossa abnormalities, including pontocerebellar hypoplasia, are more likely to have biallelic BRCA2 mutations.

Genetic algorithm based optimization on modeling and design of hybrid renewable energy systems

International Nuclear Information System (INIS)

Ismail, M.S.; Moghavvemi, M.; Mahlia, T.M.I.

2014-01-01

Highlights: • Solar data was analyzed in the location under consideration. • A program was developed to simulate operation of the PV hybrid system. • Genetic algorithm was used to optimize the sizes of the hybrid system components. • The costs of the pollutant emissions were considered in the optimization. • It is cost effective to power houses in remote areas with such hybrid systems. - Abstract: A sizing optimization of a hybrid system consisting of photovoltaic (PV) panels, a backup source (microturbine or diesel), and a battery system minimizes the cost of energy production (COE), and a complete design of this optimized system supplying a small community with power in the Palestinian Territories is presented in this paper. A scenario that depends on a standalone PV, and another one that depends on a backup source alone were analyzed in this study. The optimization was achieved via the usage of genetic algorithm. The objective function minimizes the COE while covering the load demand with a specified value for the loss of load probability (LLP). The global warming emissions costs have been taken into account in this optimization analysis. Solar radiation data is firstly analyzed, and the tilt angle of the PV panels is then optimized. It was discovered that powering a small rural community using this hybrid system is cost-effective and extremely beneficial when compared to extending the utility grid to supply these remote areas, or just using conventional sources for this purpose. This hybrid system decreases both operating costs and the emission of pollutants. The hybrid system that realized these optimization purposes is the one constructed from a combination of these sources

Parameter identification of the glazed photovoltaic thermal system using Genetic Algorithm–Fuzzy System (GA–FS) approach and its comparative study

International Nuclear Information System (INIS)

Singh, Sonveer; Agrawal, Sanjay

2015-01-01

Highlights: • Optimization using Genetic Algorithm–Fuzzy System approach. • Overall exergy efficiency has been evaluated with different optimization tools. • Comparative analysis has been done. • GA–FS is very efficient and fast technique. • Overall exergy efficiency has been improved. - Abstract: In this paper, Genetic Algorithm–Fuzzy System (GA–FS) approach is used to identify the optimized parameters of the glazed photovoltaic thermal (PVT) system and to improve its overall exergy efficiency. The fuzzy knowledge base is used to improve the efficiency of Genetic Algorithm (GA). It is observed that three GA parameters, namely: (i) crossover probability (P cross ), (ii) mutation probability (P mut ) and (iii) population size are changing dynamically during the program, according to fuzzy knowledge base to maximize the efficiency of the GA. Here, overall exergy efficiency is considered as an objective function during the optimization process for GA–FS approach. The effort has been made to identify the different optimized parameters like; length and depth of the channel, velocity of flowing fluid, overall heat transfer coefficient from solar cell to ambient and flowing fluid and overall back loss heat transfer coefficient from flowing fluid to the ambient to maximize the overall exergy efficiency using GA–FS approach. Performance of glazed PVT using GA–FS approach has been compared with performance using GA approach and without GA. It has also been observed that the GA–FS approach is a better approach as compared to GA approach because it converges faster as compare to GA because the use of the fuzzy knowledge base with GA and take less time for identification of optimized system parameters.

A Decision Support System Based on Genetic Algorithm (Case Study: Scheduling in Supply Chain

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Mohammad Ali Beheheshtinia

2016-10-01

Full Text Available Nowadays, the application of effective and efficient decisions on complex issues require the use of decision support systems. This Paper provided a decision support system based on the genetic algorithm for production and transportation scheduling problem in a supply chain. It is assumed that there are number of orders that should be produced by suppliers and should be transported to the plant by a transportation fleet. The aim is to assign orders to the suppliers, specify the order of their production, allocate processed orders to the vehicles for transport and to arrange them in a way that minimizes the total delivery time. It has been shown that the complexity of the problem was related to Np-hard and there was no possibility of using accurate methods to solve the problem in a reasonable time. So, the genetic algorithm was used in this paper to solve the problem. By using this decision support system, a new approach to supply chain management was proposed. The analysis of the approach proposed in this study compared to the conventional approaches by the decision support system indicated the preference of our proposed approach

Optimization of Wind-Marine Hybrid Power System Configuration Based on Genetic Algorithm

Institute of Scientific and Technical Information of China (English)

SHI Hongda; LI Linna; ZHAO Chenyu

2017-01-01

Multi-energy power systems can use energy generated from various sources to improve power generation reliability.This paper presents a cost-power generation model of a wind-tide-wave energy hybrid power system for use on a remote island,where the configuration is optimized using a genetic algorithm.A mixed integer programming model is used and a novel object function,including cost and power generation,is proposed to solve the boundary problem caused by existence of two goals.Using this model,the final optimized result is found to have a good fit with local resources.

Genetic Variation in the Dopamine System Influences Intervention Outcome in Children with Cerebral Palsy

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Rochellys Diaz Heijtz

2018-02-01

Interpretation: Naturally occurring genetic variation in the dopamine system can influence treatment outcomes in children with cerebral palsy. A polygenic dopamine score might be valid for treatment outcome prediction and for designing individually tailored interventions for children with cerebral palsy.

Evidence for transgenerational metabolic programming in Drosophila

Directory of Open Access Journals (Sweden)

Jessica L. Buescher

2013-09-01

Worldwide epidemiologic studies have repeatedly demonstrated an association between prenatal nutritional environment, birth weight and susceptibility to adult diseases including obesity, cardiovascular disease and type 2 diabetes. Despite advances in mammalian model systems, the molecular mechanisms underlying this phenomenon are unclear, but might involve programming mechanisms such as epigenetics. Here we describe a new system for evaluating metabolic programming mechanisms using a simple, genetically tractable Drosophila model. We examined the effect of maternal caloric excess on offspring and found that a high-sugar maternal diet alters body composition of larval offspring for at least two generations, augments an obese-like phenotype under suboptimal (high-calorie feeding conditions in adult offspring, and modifies expression of metabolic genes. Our data indicate that nutritional programming mechanisms could be highly conserved and support the use of Drosophila as a model for evaluating the underlying genetic and epigenetic contributions to this phenomenon.

A Genetic System for the Thermophilic Acetogenic Bacterium Thermoanaerobacter kivui.

Science.gov (United States)

Basen, Mirko; Geiger, Irina; Henke, Laura; Müller, Volker

2018-02-01

urgent need to understand the carbon and electron flows through the Wood-Ljungdahl pathway and their links to energy conservation, which requires genetic manipulations such as deletion or overexpression of genes encoding putative key enzymes. Unfortunately, genetic systems have been reported for only a few acetogenic bacteria. Here, we demonstrate proof of concept for the genetic modification of the thermophilic acetogenic species Thermoanaerobacter kivui The genetic system will be used to study genes involved in biosynthesis and energy metabolism, and may further be applied to metabolically engineer T. kivui to produce fuels and chemicals. Copyright © 2018 American Society for Microbiology.

Application of genetic algorithms to tuning fuzzy control systems

Science.gov (United States)

Espy, Todd; Vombrack, Endre; Aldridge, Jack

1993-01-01

Real number genetic algorithms (GA) were applied for tuning fuzzy membership functions of three controller applications. The first application is our 'Fuzzy Pong' demonstration, a controller that controls a very responsive system. The performance of the automatically tuned membership functions exceeded that of manually tuned membership functions both when the algorithm started with randomly generated functions and with the best manually-tuned functions. The second GA tunes input membership functions to achieve a specified control surface. The third application is a practical one, a motor controller for a printed circuit manufacturing system. The GA alters the positions and overlaps of the membership functions to accomplish the tuning. The applications, the real number GA approach, the fitness function and population parameters, and the performance improvements achieved are discussed. Directions for further research in tuning input and output membership functions and in tuning fuzzy rules are described.

A fuzzy genetic approach for network reconfiguration to enhance voltage stability in radial distribution systems

Energy Technology Data Exchange (ETDEWEB)

Sahoo, N.C. [Faculty of Engineering and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450 Melaka (Malaysia); Prasad, K. [Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450 Melaka (Malaysia)

2006-11-15

This paper presents a fuzzy genetic approach for reconfiguration of radial distribution systems (RDS) so as to maximize the voltage stability of the network for a specific set of loads. The network reconfiguration involves a mechanism for selection of the best set of branches to be opened, one from each loop, such that the reconfigured RDS possesses desired performance characteristics. This discrete solution space is better handled by the proposed scheme, which maximizes a suitable optimizing function (computed using two different approaches). In the first approach, this function is chosen as the average of a voltage stability index of all the buses in the RDS, while in the second approach, the complete RDS is reduced to a two bus equivalent system and the optimizing function is the voltage stability index of this reduced two bus system. The fuzzy genetic algorithm uses a suitable coding and decoding scheme for maintaining the radial nature of the network at every stage of genetic evolution, and it also uses a fuzzy rule based mutation controller for efficient search of the solution space. This method, tested on 69 bus and 33 bus RDSs, shows promising results for the both approaches. It is also observed that the network losses are reduced when the voltage stability is enhanced by the network reconfiguration. (author)

Integrating a Genetic Algorithm Into a Knowledge-Based System for Ordering Complex Design Processes

Science.gov (United States)

Rogers, James L.; McCulley, Collin M.; Bloebaum, Christina L.

1996-01-01

The design cycle associated with large engineering systems requires an initial decomposition of the complex system into design processes which are coupled through the transference of output data. Some of these design processes may be grouped into iterative subcycles. In analyzing or optimizing such a coupled system, it is essential to be able to determine the best ordering of the processes within these subcycles to reduce design cycle time and cost. Many decomposition approaches assume the capability is available to determine what design processes and couplings exist and what order of execution will be imposed during the design cycle. Unfortunately, this is often a complex problem and beyond the capabilities of a human design manager. A new feature, a genetic algorithm, has been added to DeMAID (Design Manager's Aid for Intelligent Decomposition) to allow the design manager to rapidly examine many different combinations of ordering processes in an iterative subcycle and to optimize the ordering based on cost, time, and iteration requirements. Two sample test cases are presented to show the effects of optimizing the ordering with a genetic algorithm.

Desktop Genetics

OpenAIRE

Hough, Soren H; Ajetunmobi, Ayokunmi; Brody, Leigh; Humphryes-Kirilov, Neil; Perello, Edward

2016-01-01

Desktop Genetics is a bioinformatics company building a gene-editing platform for personalized medicine. The company works with scientists around the world to design and execute state-of-the-art clustered regularly interspaced short palindromic repeats (CRISPR) experiments. Desktop Genetics feeds the lessons learned about experimental intent, single-guide RNA design and data from international genomics projects into a novel CRISPR artificial intelligence system. We believe that machine learni...

Genetic Modification in Human Pluripotent Stem Cells by Homologous Recombination and CRISPR/Cas9 System.

Science.gov (United States)

Xue, Haipeng; Wu, Jianbo; Li, Shenglan; Rao, Mahendra S; Liu, Ying

2016-01-01

Genetic modification is an indispensable tool to study gene function in normal development and disease. The recent breakthrough of creating human induced pluripotent stem cells (iPSCs) by defined factors (Takahashi et al., Cell 131:861-872, 2007) provides a renewable source of patient autologous cells that not only retain identical genetic information but also give rise to many cell types of the body including neurons and glia. Meanwhile, the rapid advancement of genome modification tools such as gene targeting by homologous recombination (Capecchi, Nat Rev Genet 6:507-512, 2005) and genome editing tools such as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system, TALENs (Transcription activator-like effector nucleases), and ZFNs (Zinc finger nucleases) (Wang et al., Cell 153:910-918, 2013; Mali et al., Science 339:823-826, 2013; Hwang et al., Nat Biotechnol 31:227-229, 2013; Friedland et al., Nat Methods 10(8):741-743, 2013; DiCarlo et al., Nucleic Acids Res 41:4336-4343, 2013; Cong et al., Science 339:819-823, 2013) has greatly accelerated the development of human genome manipulation at the molecular level. This chapter describes the protocols for making neural lineage reporter lines using homologous recombination and the CRISPR/Cas system-mediated genome editing, including construction of targeting vectors, guide RNAs, transfection into hPSCs, and selection and verification of successfully targeted clones. This method can be applied to various needs of hPSC genetic engineering at high efficiency and high reliability.

Genetic counseling and the ethical issues around direct to consumer genetic testing.

Science.gov (United States)

Hawkins, Alice K; Ho, Anita

2012-06-01

Over the last several years, direct to consumer(DTC) genetic testing has received increasing attention in the public, healthcare and academic realms. DTC genetic testing companies face considerable criticism and scepticism,particularly from the medical and genetic counseling community. This raises the question of what specific aspects of DTC genetic testing provoke concerns, and conversely,promises, for genetic counselors. This paper addresses this question by exploring DTC genetic testing through an ethic allens. By considering the fundamental ethical approaches influencing genetic counseling (the ethic of care and principle-based ethics) we highlight the specific ethical concerns raised by DTC genetic testing companies. Ultimately,when considering the ethics of DTC testing in a genetic counseling context, we should think of it as a balancing act. We need careful and detailed consideration of the risks and troubling aspects of such testing, as well as the potentially beneficial direct and indirect impacts of the increased availability of DTC genetic testing. As a result it is essential that genetic counselors stay informed and involved in the ongoing debate about DTC genetic testing and DTC companies. Doing so will ensure that the ethical theories and principles fundamental to the profession of genetic counseling are promoted not just in traditional counseling sessions,but also on a broader level. Ultimately this will help ensure that the public enjoys the benefits of an increasingly genetic based healthcare system.

The Parameters Optimization of MCR-WPT System Based on the Improved Genetic Simulated Annealing Algorithm

Directory of Open Access Journals (Sweden)

Sheng Lu

2015-01-01

Full Text Available To solve the problem of parameter selection during the design of magnetically coupled resonant wireless power transmission system (MCR-WPT, this paper proposed an improved genetic simulated annealing algorithm. Firstly, the equivalent circuit of the system is analysis in this study and a nonlinear programming mathematical model is built. Secondly, in place of the penalty function method in the genetic algorithm, the selection strategy based on the distance between individuals is adopted to select individual. In this way, it reduces the excess empirical parameters. Meanwhile, it can improve the convergence rate and the searching ability by calculating crossover probability and mutation probability according to the variance of population’s fitness. At last, the simulated annealing operator is added to increase local search ability of the method. The simulation shows that the improved method can break the limit of the local optimum solution and get the global optimum solution faster. The optimized system can achieve the practical requirements.

The influence of health care policies and health care system distrust on willingness to undergo genetic testing.

Science.gov (United States)

Armstrong, Katrina; Putt, Mary; Halbert, Chanita Hughes; Grande, David; Schwartz, Jerome Sanford; Liao, Kaijun; Marcus, Noora; Demeter, Mirar Bristol; Shea, Judy

2012-05-01

As the potential role of genetic testing in disease prevention and management grows, so does concern about differences in uptake of genetic testing across social and racial groups. Characteristics of how genetic tests are delivered may influence willingness to undergo testing and, if they affect population subgroups differently, alter disparities in testing. Conjoint analysis study of the effect of 3 characteristics of genetic test delivery (ie, attributes) on willingness to undergo genetic testing for cancer risk. Data were collected using a random digit dialing survey of 128 African American and 209 white individuals living in the United States. Measures included conjoint scenarios, the Revised Health Care System Distrust Scale (including the values and competence subscales), health insurance coverage, and sociodemographic characteristics. The 3 attributes studied were disclosure of test results to the health insurer, provision of the test by a specialist or primary care doctor, and race-specific or race-neutral marketing. In adjusted analyses, disclosure of test results to insurers, having to get the test from a specialist, and race-specific marketing were all inversely associated with willingness to undergo the genetic test, with the greatest effect for the disclosure attribute. Racial differences in willingness to undergo testing were not statistically significant (P=0.07) and the effect of the attributes on willingness to undergo testing did not vary by patient race. However, the decrease in willingness to undergo testing with insurance disclosure was greater among individuals with high values distrust (P=0.03), and the decrease in willingness to undergo testing from specialist access was smaller among individuals with high competence distrust (P=0.03). Several potentially modifiable characteristics of how genetic tests are delivered are associated with willingness to undergo testing. The effect of 2 of these characteristics vary according to the level of

Multiprocessor scheduling for real-time systems

CERN Document Server

Baruah, Sanjoy; Buttazzo, Giorgio

2015-01-01

This book provides a comprehensive overview of both theoretical and pragmatic aspects of resource-allocation and scheduling in multiprocessor and multicore hard-real-time systems.  The authors derive new, abstract models of real-time tasks that capture accurately the salient features of real application systems that are to be implemented on multiprocessor platforms, and identify rules for mapping application systems onto the most appropriate models.  New run-time multiprocessor scheduling algorithms are presented, which are demonstrably better than those currently used, both in terms of run-time efficiency and tractability of off-line analysis.  Readers will benefit from a new design and analysis framework for multiprocessor real-time systems, which will translate into a significantly enhanced ability to provide formally verified, safety-critical real-time systems at a significantly lower cost.

Refining and defining riverscape genetics: How rivers influence population genetic structure

Science.gov (United States)

Chanté D. Davis; Clinton W. Epps; Rebecca L. Flitcroft; Michael A. Banks

2018-01-01

Traditional analysis in population genetics evaluates differences among groups of individuals and, in some cases, considers the effects of distance or potential barriers to gene flow. Genetic variation of organisms in complex landscapes, seascapes, or riverine systems, however, may be shaped by many forces. Recent research has linked habitat heterogeneity and landscape...

Using probability modelling and genetic parentage assignment to test the role of local mate availability in mating system variation.

Science.gov (United States)

Blyton, Michaela D J; Banks, Sam C; Peakall, Rod; Lindenmayer, David B

2012-02-01

The formal testing of mating system theories with empirical data is important for evaluating the relative importance of different processes in shaping mating systems in wild populations. Here, we present a generally applicable probability modelling framework to test the role of local mate availability in determining a population's level of genetic monogamy. We provide a significance test for detecting departures in observed mating patterns from model expectations based on mate availability alone, allowing the presence and direction of behavioural effects to be inferred. The assessment of mate availability can be flexible and in this study it was based on population density, sex ratio and spatial arrangement. This approach provides a useful tool for (1) isolating the effect of mate availability in variable mating systems and (2) in combination with genetic parentage analyses, gaining insights into the nature of mating behaviours in elusive species. To illustrate this modelling approach, we have applied it to investigate the variable mating system of the mountain brushtail possum (Trichosurus cunninghami) and compared the model expectations with the outcomes of genetic parentage analysis over an 18-year study. The observed level of monogamy was higher than predicted under the model. Thus, behavioural traits, such as mate guarding or selective mate choice, may increase the population level of monogamy. We show that combining genetic parentage data with probability modelling can facilitate an improved understanding of the complex interactions between behavioural adaptations and demographic dynamics in driving mating system variation. © 2011 Blackwell Publishing Ltd.

Fanconi anemia: correlating central nervous system malformations and genetic complementation groups

International Nuclear Information System (INIS)

Johnson-Tesch, Benjamin A.; Gawande, Rakhee S.; Nascene, David R.; Zhang, Lei; MacMillan, Margaret L.

2017-01-01

Congenital central nervous system abnormalities in children with Fanconi anemia are poorly characterized, especially with regard to specific genetic complementation groups. To characterize the impact of genetic complementation groups on central nervous system anatomy. Through chart review we identified 36 patients with Fanconi anemia with available brain MRIs at the University of Minnesota (average age, 11.3 years; range, 1-43 years; M:F=19:17), which we reviewed and compared to 19 age- and sex-matched controls (average age, 7.9 years; range, 2-18 years; M:F=9:10). Genotypic information was available for 27 patients (15 FA-A, 2 FA-C, 3 FA-G, and 7 FA-D1 [biallelic mutations in BRCA2 gene]). Of the 36 patients, 61% had at least one congenital central nervous system or skull base abnormality. These included hypoplastic clivus (n=12), hypoplastic adenohypophysis (n=11), platybasia (n=8), pontocerebellar hypoplasia (n=7), isolated pontine hypoplasia (n=4), isolated vermis hypoplasia (n=3), and ectopic neurohypophysis (n=6). Average pituitary volume was significantly less in patients with Fanconi anemia (P<0.0001) than in controls. Basal angle was significantly greater in Fanconi anemia patients (P=0.006), but the basal angle of those with FA-D1 was not significantly different from controls (P=0.239). Clivus length was less in the Fanconi anemia group (P=0.002), but significance was only observed in the FA-D1 subgroup (P<0.0001). Of the seven patients meeting criteria for pontocerebellar hypoplasia, six belonged to the FA-D1 group. Patients with Fanconi anemia have higher incidences of ectopic neurohypophysis, adenohypophysis hypoplasia, platybasia and other midline central nervous system skull base posterior fossa abnormalities than age- and sex-matched controls. Patients with posterior fossa abnormalities, including pontocerebellar hypoplasia, are more likely to have biallelic BRCA2 mutations. (orig.)

Fanconi anemia: correlating central nervous system malformations and genetic complementation groups

Energy Technology Data Exchange (ETDEWEB)

Johnson-Tesch, Benjamin A. [University of Minnesota, Department of Radiology, Minneapolis, MN (United States); Gawande, Rakhee S.; Nascene, David R. [University of Minnesota, Department of Radiology, Neuroradiology Section, Minneapolis, MN (United States); Zhang, Lei [University of Minnesota, Biostatistical Design and Analysis Centre, Minneapolis, MN (United States); MacMillan, Margaret L. [University of Minnesota, Blood and Marrow Transplant Program, Department of Pediatrics, Minneapolis, MN (United States)

2017-06-15

Congenital central nervous system abnormalities in children with Fanconi anemia are poorly characterized, especially with regard to specific genetic complementation groups. To characterize the impact of genetic complementation groups on central nervous system anatomy. Through chart review we identified 36 patients with Fanconi anemia with available brain MRIs at the University of Minnesota (average age, 11.3 years; range, 1-43 years; M:F=19:17), which we reviewed and compared to 19 age- and sex-matched controls (average age, 7.9 years; range, 2-18 years; M:F=9:10). Genotypic information was available for 27 patients (15 FA-A, 2 FA-C, 3 FA-G, and 7 FA-D1 [biallelic mutations in BRCA2 gene]). Of the 36 patients, 61% had at least one congenital central nervous system or skull base abnormality. These included hypoplastic clivus (n=12), hypoplastic adenohypophysis (n=11), platybasia (n=8), pontocerebellar hypoplasia (n=7), isolated pontine hypoplasia (n=4), isolated vermis hypoplasia (n=3), and ectopic neurohypophysis (n=6). Average pituitary volume was significantly less in patients with Fanconi anemia (P<0.0001) than in controls. Basal angle was significantly greater in Fanconi anemia patients (P=0.006), but the basal angle of those with FA-D1 was not significantly different from controls (P=0.239). Clivus length was less in the Fanconi anemia group (P=0.002), but significance was only observed in the FA-D1 subgroup (P<0.0001). Of the seven patients meeting criteria for pontocerebellar hypoplasia, six belonged to the FA-D1 group. Patients with Fanconi anemia have higher incidences of ectopic neurohypophysis, adenohypophysis hypoplasia, platybasia and other midline central nervous system skull base posterior fossa abnormalities than age- and sex-matched controls. Patients with posterior fossa abnormalities, including pontocerebellar hypoplasia, are more likely to have biallelic BRCA2 mutations. (orig.)

Indoor high precision three-dimensional positioning system based on visible light communication using modified genetic algorithm

Science.gov (United States)

Chen, Hao; Guan, Weipeng; Li, Simin; Wu, Yuxiang

2018-04-01

To improve the precision of indoor positioning and actualize three-dimensional positioning, a reversed indoor positioning system based on visible light communication (VLC) using genetic algorithm (GA) is proposed. In order to solve the problem of interference between signal sources, CDMA modulation is used. Each light-emitting diode (LED) in the system broadcasts a unique identity (ID) code using CDMA modulation. Receiver receives mixed signal from every LED reference point, by the orthogonality of spreading code in CDMA modulation, ID information and intensity attenuation information from every LED can be obtained. According to positioning principle of received signal strength (RSS), the coordinate of the receiver can be determined. Due to system noise and imperfection of device utilized in the system, distance between receiver and transmitters will deviate from the real value resulting in positioning error. By introducing error correction factors to global parallel search of genetic algorithm, coordinates of the receiver in three-dimensional space can be determined precisely. Both simulation results and experimental results show that in practical application scenarios, the proposed positioning system can realize high precision positioning service.

Exploring Relationships Among Belief in Genetic Determinism, Genetics Knowledge, and Social Factors

Science.gov (United States)

Gericke, Niklas; Carver, Rebecca; Castéra, Jérémy; Evangelista, Neima Alice Menezes; Marre, Claire Coiffard; El-Hani, Charbel N.

2017-12-01

Genetic determinism can be described as the attribution of the formation of traits to genes, where genes are ascribed more causal power than what scientific consensus suggests. Belief in genetic determinism is an educational problem because it contradicts scientific knowledge, and is a societal problem because it has the potential to foster intolerant attitudes such as racism and prejudice against sexual orientation. In this article, we begin by investigating the very nature of belief in genetic determinism. Then, we investigate whether knowledge of genetics and genomics is associated with beliefs in genetic determinism. Finally, we explore the extent to which social factors such as gender, education, and religiosity are associated with genetic determinism. Methodologically, we gathered and analyzed data on beliefs in genetic determinism, knowledge of genetics and genomics, and social variables using the "Public Understanding and Attitudes towards Genetics and Genomics" (PUGGS) instrument. Our analyses of PUGGS responses from a sample of Brazilian university freshmen undergraduates indicated that (1) belief in genetic determinism was best characterized as a construct built up by two dimensions or belief systems: beliefs concerning social traits and beliefs concerning biological traits; (2) levels of belief in genetic determination of social traits were low, which contradicts prior work; (3) associations between knowledge of genetics and genomics and levels of belief in genetic determinism were low; and (4) social factors such as age and religiosity had stronger associations with beliefs in genetic determinism than knowledge. Although our study design precludes causal inferences, our results raise questions about whether enhancing genetic literacy will decrease or prevent beliefs in genetic determinism.

Genetic secrets: Protecting privacy and confidentiality in the genetic era. Final report

Energy Technology Data Exchange (ETDEWEB)

Rothstein, M.A. [ed.

1998-09-01

Few developments are likely to affect human beings more profoundly in the long run than the discoveries resulting from advances in modern genetics. Although the developments in genetic technology promise to provide many additional benefits, their application to genetic screening poses ethical, social, and legal questions, many of which are rooted in issues of privacy and confidentiality. The ethical, practical, and legal ramifications of these and related questions are explored in depth. The broad range of topics includes: the privacy and confidentiality of genetic information; the challenges to privacy and confidentiality that may be projected to result from the emerging genetic technologies; the role of informed consent in protecting the confidentiality of genetic information in the clinical setting; the potential uses of genetic information by third parties; the implications of changes in the health care delivery system for privacy and confidentiality; relevant national and international developments in public policies, professional standards, and laws; recommendations; and the identification of research needs.

Association of systemic lupus erythematosus clinical features with European population genetic substructure.

Directory of Open Access Journals (Sweden)

Elisa Alonso-Perez

Full Text Available Systemic Lupus Erythematosus (SLE is an autoimmune disease with a very varied spectrum of clinical manifestations that could be partly determined by genetic factors. We aimed to determine the relationship between prevalence of 11 clinical features and age of disease onset with European population genetic substructure. Data from 1413 patients of European ancestry recruited in nine countries was tested for association with genotypes of top ancestry informative markers. This analysis was done with logistic regression between phenotypes and genotypes or principal components extracted from them. We used a genetic additive model and adjusted for gender and disease duration. Three clinical features showed association with ancestry informative markers: autoantibody production defined as immunologic disorder (P = 6.8×10(-4, oral ulcers (P = 6.9×10(-4 and photosensitivity (P = 0.002. Immunologic disorder was associated with genotypes more common in Southern European ancestries, whereas the opposite trend was observed for photosensitivity. Oral ulcers were specifically more common in patients of Spanish and Portuguese self-reported ancestry. These results should be taken into account in future research and suggest new hypotheses and possible underlying mechanisms to be investigated. A first hypothesis linking photosensitivity with variation in skin pigmentation is suggested.

Association of Systemic Lupus Erythematosus Clinical Features with European Population Genetic Substructure

Science.gov (United States)

Calaza, Manuel; Witte, Torsten; Papasteriades, Chryssa; Marchini, Maurizio; Migliaresi, Sergio; Kovacs, Attila; Ordi-Ros, Josep; Bijl, Marc; Santos, Maria Jose; Ruzickova, Sarka; Pullmann, Rudolf; Carreira, Patricia; Skopouli, Fotini N.; D'Alfonso, Sandra; Sebastiani, Gian Domenico; Suarez, Ana; Blanco, Francisco J.; Gomez-Reino, Juan J.; Gonzalez, Antonio

2011-01-01

Systemic Lupus Erythematosus (SLE) is an autoimmune disease with a very varied spectrum of clinical manifestations that could be partly determined by genetic factors. We aimed to determine the relationship between prevalence of 11 clinical features and age of disease onset with European population genetic substructure. Data from 1413 patients of European ancestry recruited in nine countries was tested for association with genotypes of top ancestry informative markers. This analysis was done with logistic regression between phenotypes and genotypes or principal components extracted from them. We used a genetic additive model and adjusted for gender and disease duration. Three clinical features showed association with ancestry informative markers: autoantibody production defined as immunologic disorder (P = 6.8×10−4), oral ulcers (P = 6.9×10−4) and photosensitivity (P = 0.002). Immunologic disorder was associated with genotypes more common in Southern European ancestries, whereas the opposite trend was observed for photosensitivity. Oral ulcers were specifically more common in patients of Spanish and Portuguese self-reported ancestry. These results should be taken into account in future research and suggest new hypotheses and possible underlying mechanisms to be investigated. A first hypothesis linking photosensitivity with variation in skin pigmentation is suggested. PMID:22194982

Artificially Expanded Genetic Information Systems for New Aptamer Technologies

Directory of Open Access Journals (Sweden)

Elisa Biondi

2018-05-01

Full Text Available Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS that adds independently replicating nucleotide “letters” to the evolving “alphabet”.

Development of enzymes and enzyme systems by genetic engineering to convert biomass to sugars

Science.gov (United States)

TITLE Development of Enzymes and Enzyme Systems by Genetic Engineering to Convert Biomass to Sugars ABSTRACT Plant cellulosic material is one of the most viable renewable resources for the world’s fuel and chemical feedstock needs. Currently ethanol derived from corn starch is the most common li...

DHLAS: A web-based information system for statistical genetic analysis of HLA population data.

Science.gov (United States)

Thriskos, P; Zintzaras, E; Germenis, A

2007-03-01

DHLAS (database HLA system) is a user-friendly, web-based information system for the analysis of human leukocyte antigens (HLA) data from population studies. DHLAS has been developed using JAVA and the R system, it runs on a Java Virtual Machine and its user-interface is web-based powered by the servlet engine TOMCAT. It utilizes STRUTS, a Model-View-Controller framework and uses several GNU packages to perform several of its tasks. The database engine it relies upon for fast access is MySQL, but others can be used a well. The system estimates metrics, performs statistical testing and produces graphs required for HLA population studies: (i) Hardy-Weinberg equilibrium (calculated using both asymptotic and exact tests), (ii) genetics distances (Euclidian or Nei), (iii) phylogenetic trees using the unweighted pair group method with averages and neigbor-joining method, (iv) linkage disequilibrium (pairwise and overall, including variance estimations), (v) haplotype frequencies (estimate using the expectation-maximization algorithm) and (vi) discriminant analysis. The main merit of DHLAS is the incorporation of a database, thus, the data can be stored and manipulated along with integrated genetic data analysis procedures. In addition, it has an open architecture allowing the inclusion of other functions and procedures.

Stochastic resonances in a distributed genetic broadcasting system: the NFκB/IκB paradigm.

Science.gov (United States)

Wang, Zhipeng; Potoyan, Davit A; Wolynes, Peter G

2018-01-01

Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of information not to one but to many genes carrying out distinct functions whose dynamical binding and unbinding characteristics are widely distributed. In such broadcasting networks, the intended target sites are also often dwarfed in number by the even more numerous non-functional binding sites. Taking the genetic regulatory network of NF κ B as an exemplary system we explore the impact of having numerous distributed sites on the stochastic dynamics of oscillatory broadcasting genetic networks pointing out how resonances in binding cycles control the network's specificity and performance. We also show that active kinetic regulation of binding and unbinding through molecular stripping of DNA bound transcription factors can lead to a higher coherence of gene-co-expression and synchronous clearance. © 2018 The Author(s).

Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems

OpenAIRE

Chen, Yvonne Y.; Jensen, Michael C.; Smolke, Christina D.

2010-01-01

RNA molecules perform diverse regulatory functions in natural biological systems, and numerous synthetic RNA-based control devices that integrate sensing and gene-regulatory functions have been demonstrated, predominantly in bacteria and yeast. Despite potential advantages of RNA-based genetic control strategies in clinical applications, there has been limited success in extending engineered RNA devices to mammalian gene-expression control and no example of their application to functional res...

OCSEGen: Open Components and Systems Environment Generator

Science.gov (United States)

Tkachuk, Oksana

2014-01-01

To analyze a large system, one often needs to break it into smaller components.To analyze a component or unit under analysis, one needs to model its context of execution, called environment, which represents the components with which the unit interacts. Environment generation is a challenging problem, because the environment needs to be general enough to uncover unit errors, yet precise enough to make the analysis tractable. In this paper, we present a tool for automated environment generation for open components and systems. The tool, called OCSEGen, is implemented on top of the Soot framework. We present the tool's current support and discuss its possible future extensions.

Community acquired pneumonia: genetic variants influencing systemic inflammation.

Science.gov (United States)

Ferrer Agüero, J M; Millán, S; Rodríguez de Castro, F; Martín-Loeches, I; Solé Violán, J

2014-01-01

The inflammatory response depends on several factors, including pathogenicity and duration of the stimulus, and also on the balance between inflammatory and antiinflammatory response. Several studies have presented evidence of the importance of genetic factors in severe infections. The innate immune response prevents the invasion and spread of pathogens during the first hours after infection. Each of the different processes involved in innate immunity may be affected by genetic polymorphisms, which can result in susceptibility or resistance to infection. The results obtained in the different studies do not irrefutably prove the role or function of a gene in the pathogenesis of respiratory infections. However, they can generate new hypotheses, suggest new candidate genes based on their role in the inflammatory response, and constitute a first step in understanding the underlying genetic factors. Copyright © 2013 Elsevier España, S.L. and SEMICYUC. All rights reserved.

Human genetics of diabetic vascular complications

Indian Academy of Sciences (India)

Diabetic vascular complications (DVC) affecting several important organ systems of human body such as the cardiovascular system constitute a major public health problem. There is evidence demonstrating that genetic factors contribute to the risk of DVC genetic variants, structural variants, and epigenetic changes play ...

Sex Determination, Sex Ratios, and Genetic Conflict

NARCIS (Netherlands)

Werren, John H.; Beukeboom, Leo W.

1998-01-01

Genetic mechanisms of sex determination are unexpectedly diverse and change rapidly during evolution. We review the role of genetic conflict as the driving force behind this diversity and turnover. Genetic conflict occurs when different components of a genetic system are subject to selection in

The role of genetic variants in genes regulating the oxytocin-vasopressin neurohumoral system in childhood-onset aggression.

Science.gov (United States)

Malik, Ayesha I; Zai, Clement C; Berall, Laura; Abu, Zihad; Din, Farah; Nowrouzi, Behdin; Chen, Sheng; Beitchman, Joseph H

2014-10-01

The genetic etiology of aggressive behaviors remains elusive, but growing evidence suggests that they are heritable, and certain genetic variants have been implicated as contributing factors. The oxytocin-vasopressin (OXT-AVP) neurohumoral system has recently been implicated in social behaviors. Oxytocin, especially, has been linked to prosocial behaviors such as trust and social bonds. Hence, the aim of this study was to determine whether genes regulating this system were also associated with childhood-onset aggressive behaviors. Our sample included 182 White children showing extreme, persistent, and pervasive aggressive behavior. These cases were matched with 182 White controls on the basis of sex and age. We used PCR to determine the genotype for 28 single nucleotide polymorphisms within eight genes regulating the OXT-AVP system, including CD38 polymorphisms. Genotypic analyses were carried out using STATA, whereas differences in haplotypic and allelic frequencies were analyzed using Unphased. None of the results reached significance after correction for multiple testing. However, nominally significant allelic effects were observed for OXTR rs6770632T (P=0.028) and AVPR1A rs11174811G (P=0.040) in females, and OXTR rs237898A (P=0.006), rs237902C (P=0.007), and AVP rs3761249A (P=0.008) in males. Genetic variants regulating the OXT-AVP system may be associated with childhood-onset aggression.

Development and application of genetic sexing systems for the Mediterranean fruit fly based on a temperature sensitive lethal mutation

International Nuclear Information System (INIS)

Franz, G.; Willhoeft, U.; Kerremans, P.; Hendrichs, J.; Rendon, P.

1997-01-01

The present status in genetic sexing for the Mediterranean fruit fly is discussed. This includes the selection of the appropriate sexing gene (which determines the feasibility and practical applicability of the sexing system) as well as the selection of the appropriate Y-autosome translocation (which determines the stability of the sexing system). A temperature sensitive lethal mutation is used to eliminate females during the egg stage. This mutation in combination with new Y-autosome translocations allowed the construction of a genetic sexing strain, named VIENNA-42, that is stable enough for large scale mass rearing. Also described are the analysis of this strain under field cage and field conditions and, in preparation for large scale tests in Guatemala, the outcrossing of VIENNA-42 with genetic material from the target area. (author)

Genetic diversity in a crop metapopulation

NARCIS (Netherlands)

Heerwaarden, van J.; Eeuwijk, van F.A.; Ross-Ibarra, J.

2010-01-01

The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that

Discourse and tractable morality

NARCIS (Netherlands)

de Graaf, G.; Lütge, C.

2013-01-01

When managerial decisions are examined, somehow the business context must be included in the analysis. In this chapter, causalities that transcend individuals are promoted as unit of analysis in empirical moral research, namely, discourse. Studying managerial decisions in their discursive context is

Mob/oriT, a mobilizable site-specific recombination system for unmarked genetic manipulation in Bacillus thuringiensis and Bacillus cereus.

Science.gov (United States)

Wang, Pengxia; Zhu, Yiguang; Zhang, Yuyang; Zhang, Chunyi; Xu, Jianyi; Deng, Yun; Peng, Donghai; Ruan, Lifang; Sun, Ming

2016-06-10

Bacillus thuringiensis and Bacillus cereus are two important species in B. cereus group. The intensive study of these strains at the molecular level and construction of genetically modified bacteria requires the development of efficient genetic tools. To insert genes into or delete genes from bacterial chromosomes, marker-less manipulation methods were employed. We present a novel genetic manipulation method for B. thuringiensis and B. cereus strains that does not leave selection markers. Our approach takes advantage of the relaxase Mob02281 encoded by plasmid pBMB0228 from Bacillus thuringiensis. In addition to its mobilization function, this Mob protein can mediate recombination between oriT sites. The Mob02281 mobilization module was associated with a spectinomycin-resistance gene to form a Mob-Spc cassette, which was flanked by the core 24-bp oriT sequences from pBMB0228. A strain in which the wild-type chromosome was replaced with the modified copy containing the Mob-Spc cassette at the target locus was obtained via homologous recombination. Thus, the spectinomycin-resistance gene can be used to screen for Mob-Spc cassette integration mutants. Recombination between the two oriT sequences mediated by Mob02281, encoded by the Mob-Spc cassette, resulted in the excision of the Mob-Spc cassette, producing the desired chromosomal alteration without introducing unwanted selection markers. We used this system to generate an in-frame deletion of a target gene in B. thuringiensis as well as a gene located in an operon of B. cereus. Moreover, we demonstrated that this system can be used to introduce a single gene or an expression cassette of interest in B. thuringiensis. The Mob/oriT recombination system provides an efficient method for unmarked genetic manipulation and for constructing genetically modified bacteria of B. thuringiensis and B. cereus. Our method extends the available genetic tools for B. thuringiensis and B. cereus strains.

Genetic and epigenetic control of gene expression by CRISPR–Cas systems

Science.gov (United States)

Lo, Albert; Qi, Lei

2017-01-01

The discovery and adaption of bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems has revolutionized the way researchers edit genomes. Engineering of catalytically inactivated Cas variants (nuclease-deficient or nuclease-deactivated [dCas]) combined with transcriptional repressors, activators, or epigenetic modifiers enable sequence-specific regulation of gene expression and chromatin state. These CRISPR–Cas-based technologies have contributed to the rapid development of disease models and functional genomics screening approaches, which can facilitate genetic target identification and drug discovery. In this short review, we will cover recent advances of CRISPR–dCas9 systems and their use for transcriptional repression and activation, epigenome editing, and engineered synthetic circuits for complex control of the mammalian genome. PMID:28649363

Founder effects and genetic population structure of brown trout (Salmo trutta) in a Danish river system

DEFF Research Database (Denmark)

Hansen, Michael Møller; Mensberg, Karen-Lise Dons

1996-01-01

The influence of founder effects on the genetic population structure of brown trout (Salmo trutta) was studied in a small Danish river system. Samples of trout from seven locations were analysed by allozyme electrophoresis and mitochondrial DNA restriction fragment length polymorphism analysis....... For comparison, allozyme data from other Danish trout populations and mtDNA data from two hatchery strains were included. Genetic differentiation among populations was found to be small but significant. Pairwise tests for homogeneity of allele and haplotype frequencies between samples showed that significance...... simulations of the influence of founder effects on mitochondrial DNA differentiation and variability showed that the observed divergence could be due either to natural founder effects or to a genetic contribution by hatchery trout. However, the allozyme results pointed towards natural founder effects...

Point Genetics: A New Concept to Assess Neutron Kinetics

International Nuclear Information System (INIS)

Klein Meulekamp, R.; Kuijper, J.C.; Schikorr, M.

2005-01-01

Point genetic equations are introduced. These equations are similar to the well-known point kinetic equations but characterize and couple individual fission generations in subcritical systems. Point genetic equations are able to describe dynamic behavior of source-driven subcritical systems on shorter timescales than is possible with point kinetic equations. Point genetic parameters can be used as a first-order characterization of the system and can be calculated using standard Monte Carlo techniques; the implementation in other calculational schemes seems straightforward. A Godiva sphere is considered to show the applicability of the point genetic equations in describing a detector response on short timescales. For this system the point genetic parameters are calculated and compared with reference calculations. Typical dynamic source behavior is considered by studying a transient in which the neutron source energy decreases from 20 to 1 MeV. For all cases studied, the point genetic equations are compared to full space-time kinetic solutions, and it is shown that point genetics performs well

DTREEv2, a computer-based support system for the risk assessment of genetically modified plants

NARCIS (Netherlands)

Pertry, I.; Nothegger, C.; Sweet, J.; Kuiper, H.A.; Davies, H.; Iserentant, D.; Hull, R.; Mezzetti, B.; Messens, K.; Loose, De M.; Oliveira, de D.; Burssens, S.; Gheysen, G.; Tzotzos, G.

2014-01-01

Risk assessment of genetically modified organisms (GMOs) remains a contentious area and a major factor influencing the adoption of agricultural biotech. Methodologically, in many countries, risk assessment is conducted by expert committees with little or no recourse to databases and expert systems

Water Curtain System Pre-design for Crude Oil Storage URCs : A Numerical Modeling and Genetic Programming Approach

NARCIS (Netherlands)

Ghotbi Ravandi, Ebrahim; Rahmannejad, Reza; Karimi-Nasab, Saeed; Sarrafi, Amir; Raoof, Amir

In this paper the main criteria of the water curtain system for unlined rock caverns (URCs) is described. By the application of numerical modeling and genetic programming (GP), a method for water curtain system pre-design for Iranian crude oil storage URCs (common dimension worldwide) is presented.

The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics.

Directory of Open Access Journals (Sweden)

Jason A Corwin

2016-02-01

Full Text Available The most established model of the eukaryotic innate immune system is derived from examples of large effect monogenic quantitative resistance to pathogens. However, many host-pathogen interactions involve many genes of small to medium effect and exhibit quantitative resistance. We used the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B. cinerea, we identified a total of 2,982 genes associated with quantitative resistance using lesion area and 3,354 genes associated with camalexin production as measures of the interaction. Most genes were associated with resistance to a specific Botrytis isolate, which demonstrates the influence of pathogen genetic variation in analyzing host quantitative resistance. While known resistance genes, such as receptor-like kinases (RLKs and nucleotide-binding site leucine-rich repeat proteins (NLRs, were found to be enriched among associated genes, they only account for a small fraction of the total genes associated with quantitative resistance. Using publically available co-expression data, we condensed the quantitative resistance associated genes into co-expressed gene networks. GO analysis of these networks implicated several biological processes commonly connected to disease resistance, including defense hormone signaling and ROS production, as well as novel processes, such as leaf development. Validation of single gene T-DNA knockouts in a Col-0 background demonstrate a high success rate (60% when accounting for differences in environmental and Botrytis genetic variation. This study shows that the genetic architecture underlying host innate immune system is extremely complex and is likely able to sense and respond to differential virulence among pathogen

Developmental system at the crossroads of system theory, computer science, and genetic engineering

CERN Document Server

Węgrzyn, Stefan; Vidal, Pierre

1990-01-01

Many facts were at the origin of the present monograph. The ftrst is the beauty of maple leaves in Quebec forests in Fall. It raised the question: how does nature create and reproduce such beautiful patterns? The second was the reading of A. Lindenmayer's works on L systems. Finally came the discovery of "the secrets of DNA" together with many stimulating ex­ changes with biologists. Looking at such facts from the viewpoint of recursive numerical systems led to devise a simple model based on six elementary operations organized in a generating word, the analog of the program of a computer and of the genetic code of DNA in the cells of a living organism. It turned out that such a model, despite its simplicity, can account for a great number of properties of living organisms, e.g. their hierarchical structure, their ability to regenerate after a trauma, the possibility of cloning, their sensitivity to mutation, their growth, decay and reproduction. The model lends itself to analysis: the knowledge of the genera...

Genetics of aggression.

Science.gov (United States)

Anholt, Robert R H; Mackay, Trudy F C

2012-01-01

Aggression mediates competition for food, mating partners, and habitats and, among social animals, establishes stable dominance hierarchies. In humans, abnormal aggression is a hallmark of neuropsychiatric disorders and can be elicited by environmental factors acting on an underlying genetic susceptibility. Identifying the genetic architecture that predisposes to aggressive behavior in people is challenging because of difficulties in quantifying the phenotype, genetic heterogeneity, and uncontrolled environmental conditions. Studies on mice have identified single-gene mutations that result in hyperaggression, contingent on genetic background. These studies can be complemented by systems genetics approaches in Drosophila melanogaster, in which mutational analyses together with genome-wide transcript analyses, artificial selection studies, and genome-wide analysis of epistasis have revealed that a large segment of the genome contributes to the manifestation of aggressive behavior with widespread epistatic interactions. Comparative genomic analyses based on the principle of evolutionary conservation are needed to enable a complete dissection of the neurogenetic underpinnings of this universal fitness trait.

A New System of Automated Eco-genetic Database and Modern Conception of Prognosis of Bronchial Asthma

National Research Council Canada - National Science Library

Karseladze, Rusudan; Lia, Zhorzholiani; Goderdzishvili, Liza

2004-01-01

.... There is a need for an integrative study of the eco-genetic characteristics of BA. However, a unified assessment system for the cumulative impact of ecological and endogenous factors in BA does not yet exist...

Parallel island genetic algorithm applied to a nuclear power plant auxiliary feedwater system surveillance tests policy optimization

International Nuclear Information System (INIS)

Pereira, Claudio M.N.A.; Lapa, Celso M.F.

2003-01-01

In this work, we focus the application of an Island Genetic Algorithm (IGA), a coarse-grained parallel genetic algorithm (PGA) model, to a Nuclear Power Plant (NPP) Auxiliary Feedwater System (AFWS) surveillance tests policy optimization. Here, the main objective is to outline, by means of comparisons, the advantages of the IGA over the simple (non-parallel) genetic algorithm (GA), which has been successfully applied in the solution of such kind of problem. The goal of the optimization is to maximize the system's average availability for a given period of time, considering realistic features such as: i) aging effects on standby components during the tests; ii) revealing failures in the tests implies on corrective maintenance, increasing outage times; iii) components have distinct test parameters (outage time, aging factors, etc.) and iv) tests are not necessarily periodic. In our experiments, which were made in a cluster comprised by 8 1-GHz personal computers, we could clearly observe gains not only in the computational time, which reduced linearly with the number of computers, but in the optimization outcome

Alternative Watson-Crick Synthetic Genetic Systems.

Science.gov (United States)

Benner, Steven A; Karalkar, Nilesh B; Hoshika, Shuichi; Laos, Roberto; Shaw, Ryan W; Matsuura, Mariko; Fajardo, Diego; Moussatche, Patricia

2016-11-01

In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa.

Science.gov (United States)

Kyndt, Tina; Assogbadjo, Achille E; Hardy, Olivier J; Glele Kakaï, Romain; Sinsin, Brice; Van Damme, Patrick; Gheysen, Godelieve

2009-05-01

This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.

Linear filtering of systems with memory and application to finance

Directory of Open Access Journals (Sweden)

2006-01-01

Full Text Available We study the linear filtering problem for systems driven by continuous Gaussian processes V ( 1 and V ( 2 with memory described by two parameters. The processes V ( j have the virtue that they possess stationary increments and simple semimartingale representations simultaneously. They allow for straightforward parameter estimations. After giving the semimartingale representations of V ( j by innovation theory, we derive Kalman-Bucy-type filtering equations for the systems. We apply the result to the optimal portfolio problem for an investor with partial observations. We illustrate the tractability of the filtering algorithm by numerical implementations.

Desktop Genetics.

Science.gov (United States)

Hough, Soren H; Ajetunmobi, Ayokunmi; Brody, Leigh; Humphryes-Kirilov, Neil; Perello, Edward

2016-11-01

Desktop Genetics is a bioinformatics company building a gene-editing platform for personalized medicine. The company works with scientists around the world to design and execute state-of-the-art clustered regularly interspaced short palindromic repeats (CRISPR) experiments. Desktop Genetics feeds the lessons learned about experimental intent, single-guide RNA design and data from international genomics projects into a novel CRISPR artificial intelligence system. We believe that machine learning techniques can transform this information into a cognitive therapeutic development tool that will revolutionize medicine.

Increasing milk solids production across lactation through genetic selection and intensive pasture-based feed system.

Science.gov (United States)

Coleman, J; Pierce, K M; Berry, D P; Brennan, A; Horan, B

2010-09-01

The objective of the study was to quantify the effect of genetic improvement using the Irish total merit index, the Economic Breeding Index (EBI), on overall performance and lactation profiles for milk, milk solids, body weight (BW), and body condition score (BCS) within 2 pasture-based systems of milk production likely to be used in the future, following abolition of the European Union's milk quota system. Three genotypes of Holstein-Friesian dairy cattle were established from within the Moorepark dairy research herd: LowNA, indicative of animals with North American origin and average or lower genetic merit at the time of the study; HighNA, North American Holstein-Friesians of high genetic merit; and HighNZ, New Zealand Holstein-Friesians of high genetic merit. Animals from within each genotype were randomly allocated to 1 of 2 possible pasture-based feeding systems (FS): 1) The Moorepark pasture (MP) system (2.64 cows/ha and 344 kg of concentrate supplement per cow per lactation) and 2) a high output per hectare (HC) system (2.85 cows/ha and 1,056 kg of concentrate supplement per cow per lactation). Pasture was allocated to achieve similar postgrazing residual sward heights for both treatments. A total of 126, 128, and 140 spring-calving dairy cows were used during the years 2006, 2007, and 2008, respectively. Each group had an individual farmlet of 17 paddocks and all groups were managed similarly throughout the study. The effects of genotype, FS, and the interaction between genotype and FS on milk production, BW, and BCS across lactation were studied using mixed models with factorial arrangements of genotype and FS accounting for the repeated cow records across years. No significant genotype by FS interaction was observed for any of the variables measured. Results show that milk solids production of the national average dairy cow can be increased across lactation through increased EBI. High EBI genotypes (HighNA and HighNZ) produced more milk solids per cow and

A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination

NARCIS (Netherlands)

van Beurden, Steven J; Berends, Alinda J; Krämer-Kühl, Annika; Spekreijse, Dieuwertje; Chénard, Gilles; Philipp, Hans-Christian; Mundt, Egbert; Rottier, Peter J M; Verheije, M Hélène

2017-01-01

BACKGROUND: Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens that causes severe economic losses in the poultry industry worldwide. Major advances in the study of the molecular biology of IBV have resulted from the development of reverse genetics systems for

Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN system.

Directory of Open Access Journals (Sweden)

Axel Hausmann

Full Text Available BACKGROUND: The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN system of BOLD (Barcode of Life Datasystems, a method that supports automated, rapid species delineation and identification. METHODOLOGY/PRINCIPAL FINDINGS: This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88% in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93% were found to possess diagnostic barcode sequences at the European level while only three species pairs (3% were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads shared BINs, while specimens from the remaining species (18% were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies. CONCLUSIONS/SIGNIFICANCE: This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed

Genetic improvement of vegetables

International Nuclear Information System (INIS)

Jaramillo Vasquez, J.G.

2001-01-01

Some genetic bases of the improvement of vegetables are given. The objectives of the genetic improvement and the fundamental stages of this process are done. The sources of genetic variation are indicated and they are related the reproduction systems of the main horticultural species. It is analyzed the concept of genetic inheritance like base to determine the procedures more appropriate of improvement. The approaches are discussed, has more than enough phenotypic value, genetic action and genotypic variance; Equally the heredability concepts and value of improvement. The conventional methods of improvement are described, like they are: the introduction of species or varieties, the selection, the pure line, the pedigree method, the selection for families, the recurrent selection, the selection for unique seed, the haploids method, the selection for heterosis and the synthetic varieties

Genetic prion disease: no role for the immune system in disease pathogenesis?

Science.gov (United States)

Friedman-Levi, Yael; Binyamin, Orli; Frid, Kati; Ovadia, Haim; Gabizon, Ruth

2014-08-01

Prion diseases, which can manifest by transmissible, sporadic or genetic etiologies, share several common features, such as a fatal neurodegenerative outcome and the aberrant accumulation of proteinase K (PK)-resistant PrP forms in the CNS. In infectious prion diseases, such as scrapie in mice, prions first replicate in immune organs, then invade the CNS via ascending peripheral tracts, finally causing death. Accelerated neuroinvasion and death occurs when activated prion-infected immune cells infiltrate into the CNS, as is the case for scrapie-infected mice induced for experimental autoimmune encephalomyelitis (EAE), a CNS inflammatory insult. To establish whether the immune system plays such a central role also in genetic prion diseases, we induced EAE in TgMHu2ME199K mice, a line mimicking for late onset genetic Creutzfeldt Jacob disease (gCJD), a human prion disease. We show here that EAE induction of TgMHu2ME199K mice neither accelerated nor aggravated prion disease manifestation. Concomitantly, we present evidence that PK-resistant PrP forms were absent from CNS immune infiltrates, and most surprisingly also from lymph nodes and spleens of TgMHu2ME199K mice at all ages and stages of disease. These results imply that the mechanism of genetic prion disease differs widely from that of the infectious presentation, and that the conversion of mutant PrPs into PK resistant forms occurs mostly/only in the CNS. If the absence of pathogenic PrP forms form immune organs is also true for gCJD patients, it may suggest their blood is devoid of prion infectivity. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The STAT4 gene influences the genetic predisposition to systemic sclerosis phenotype.

Science.gov (United States)

Rueda, B; Broen, J; Simeon, C; Hesselstrand, R; Diaz, B; Suárez, H; Ortego-Centeno, N; Riemekasten, G; Fonollosa, V; Vonk, M C; van den Hoogen, F H J; Sanchez-Román, J; Aguirre-Zamorano, M A; García-Portales, R; Pros, A; Camps, M T; Gonzalez-Gay, M A; Coenen, M J H; Airo, P; Beretta, L; Scorza, R; van Laar, J; Gonzalez-Escribano, M F; Nelson, J L; Radstake, T R D J; Martin, J

2009-06-01

The aim of this study was to investigate the possible role of STAT4 gene in the genetic predisposition to systemic sclerosis (SSc) susceptibility or clinical phenotype. A total of 1317 SSc patients [896 with limited cutaneous SSc (lcSSc) and 421 with diffuse cutaneous SSc (dcSSc)] and 3113 healthy controls, from an initial case-control set of Spanish Caucasian ancestry and five independent cohorts of European ancestry (The Netherlands, Germany, Sweden, Italy and USA), were included in the study. The rs7574865 polymorphism was selected as STAT4 genetic marker. We observed that the rs7574865 T allele was significantly associated with susceptibility to lcSSc in the Spanish population [P = 1.9 x 10(-5) odds ratio (OR) 1.61 95% confidence intervals (CI) 1.29-1.99], but not with dcSSc (P = 0.41 OR 0.84 95% CI 0.59-1.21). Additionally, a dosage effect was observed showing individuals with rs7574865 TT genotype higher risk for lcSSc (OR 3.34, P = 1.02 x 10(-7) 95% CI 2.11-5.31). The association of the rs7574865 T allele with lcSSc was confirmed in all the replication cohorts with different effect sizes (OR ranging between 1.15 and 1.86), as well as the lack of association of STAT4 with dcSSc. A meta-analysis to test the overall effect of the rs7574865 polymorphism showed a strong risk effect of the T allele for lcSSc susceptibility (pooled OR 1.54 95% CI 1.36-1.74; P < 0.0001). Our data show a strong and reproducible association of the STAT4 gene with the genetic predisposition to lcSSc suggesting that this gene seems to be one of the genetic markers influencing SSc phenotype.

Systems, methods and apparatus for modeling, specifying and deploying policies in autonomous and autonomic systems using agent-oriented software engineering

Science.gov (United States)

Hinchey, Michael G. (Inventor); Penn, Joaquin (Inventor); Sterritt, Roy (Inventor)

2011-01-01

Systems, methods and apparatus are provided through which in some embodiments, an agent-oriented specification modeled with MaCMAS, is analyzed, flaws in the agent-oriented specification modeled with MaCMAS are corrected, and an implementation is derived from the corrected agent-oriented specification. Described herein are systems, method and apparatus that produce fully (mathematically) tractable development of agent-oriented specification(s) modeled with methodology fragment for analyzing complex multiagent systems (MaCMAS) and policies for autonomic systems from requirements through to code generation. The systems, method and apparatus described herein are illustrated through an example showing how user formulated policies can be translated into a formal mode which can then be converted to code. The requirements-based programming systems, method and apparatus described herein may provide faster, higher quality development and maintenance of autonomic systems based on user formulation of policies.

FY 1999 project on the development of new industry support type international standards. Standardization of evaluation method of the genetic testing system (Separate volume); 1999 nendo shinki sangyo shiengata kokusai hyojunka kaihatsu jigyo seika hokokusho. Idenshi kensa system no hyoka hoho no hyojunka (bessatsu)

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

The separate volume included the proceedings of the re-consignee joint meeting on the standardization of evaluation method of the genetic testing system, the proceedings/data of the meeting of the committee of the standardization of evaluation method of the genetic testing system, etc. The data of the meeting are about a plan to execute the standardization of evaluation method of the genetic testing system, standardization of forms for reporting the results of the genetic test, a trial guideline for standardization of the genetic testing, standardization of evaluation method of the genetic testing system, etc. Moreover, the volume included 11 literature papers overseas on the above-mentioned themes, 'reports on the surveys in Europe and the U.S. on the standardization of evaluation method of the genetic testing system,' etc. (NEDO)

FY 1999 project on the development of new industry support type international standards. Standardization of evaluation method of the genetic testing system (Separate volume); 1999 nendo shinki sangyo shiengata kokusai hyojunka kaihatsu jigyo seika hokokusho. Idenshi kensa system no hyoka hoho no hyojunka (bessatsu)

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

The separate volume included the proceedings of the re-consignee joint meeting on the standardization of evaluation method of the genetic testing system, the proceedings/data of the meeting of the committee of the standardization of evaluation method of the genetic testing system, etc. The data of the meeting are about a plan to execute the standardization of evaluation method of the genetic testing system, standardization of forms for reporting the results of the genetic test, a trial guideline for standardization of the genetic testing, standardization of evaluation method of the genetic testing system, etc. Moreover, the volume included 11 literature papers overseas on the above-mentioned themes, 'reports on the surveys in Europe and the U.S. on the standardization of evaluation method of the genetic testing system,' etc. (NEDO)

Genetic analysis of fertility restoration under CGMS system in rice ...

Indian Academy of Sciences (India)

restore complete fertility of a certain CMS line by various restorer lines (Tan et ... Keywords. rice; heterosis; three-way test cross; fertility restoration genetics. Journal of ..... plants indicating a strong genetic load of maintenance in. DE2. Table 8.

Molecular genetic studies on obligate anaerobic bacteria

International Nuclear Information System (INIS)

Woods, D.R.

1982-01-01

Molecular genetic studies on obligate anaerobic bacteria have lagged behind similar studies in aerobes. However, the current interest in biotechnology, the involvement of anaerobes in disease and the emergence of antibioticresistant strains have focused attention on the genetics of anaerobes. This article reviews molecular genetic studies in Bacteroides spp., Clostridium spp. and methanogens. Certain genetic systems in some anaerobes differ from those in aerobes and illustrate the genetic diversity among bacteria

Development of an improved genetic algorithm and its application in the optimal design of ship nuclear power system

International Nuclear Information System (INIS)

Jia Baoshan; Yu Jiyang; You Songbo

2005-01-01

This article focuses on the development of an improved genetic algorithm and its application in the optimal design of the ship nuclear reactor system, whose goal is to find a combination of system parameter values that minimize the mass or volume of the system given the power capacity requirement and safety criteria. An improved genetic algorithm (IGA) was developed using an 'average fitness value' grouping + 'specified survival probability' rank selection method and a 'separate-recombine' duplication operator. Combining with a simulated annealing algorithm (SAA) that continues the local search after the IGA reaches a satisfactory point, the algorithm gave satisfactory optimization results from both search efficiency and accuracy perspectives. This IGA-SAA algorithm successfully solved the design optimization problem of ship nuclear power system. It is an advanced and efficient methodology that can be applied to the similar optimization problems in other areas. (authors)

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system.

Science.gov (United States)

Raimondo, Joseph V; Joyce, Bradley; Kay, Louise; Schlagheck, Theresa; Newey, Sarah E; Srinivas, Shankar; Akerman, Colin J

2013-01-01

Within the nervous system, intracellular Cl(-) and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission, and network excitability. Cl(-) and pH are often co-regulated, and network activity results in the movement of both Cl(-) and H(+). Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl(-) and pH sensors have been described previously, these either lack ion specificity or are unsuitable for neuronal use. Here we present ClopHensorN-a new genetically-encoded ratiometric Cl(-) and pH sensor that is optimized for the nervous system. We demonstrate the ability of ClopHensorN to dissociate and simultaneously quantify Cl(-) and H(+) concentrations under a variety of conditions. In addition, we establish the sensor's utility by characterizing activity-dependent ion dynamics in hippocampal neurons.

Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.

Science.gov (United States)

Sharma, Vishakha; Nandineni, Madhusudan R

2014-04-01

Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485-0.971) as compared to IRAP (0.69-0.911) and REMAP (0.713-0.947). A Mantel's matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0

Genetic aspects of pathological gambling: a complex disorder with shared genetic vulnerabilities.

Science.gov (United States)

Lobo, Daniela S S; Kennedy, James L

2009-09-01

To summarize and discuss findings from genetic studies conducted on pathological gambling (PG). Searches were conducted on PubMed and PsychInfo databases using the keywords: 'gambling and genes', 'gambling and family' and 'gambling and genetics', yielding 18 original research articles investigating the genetics of PG. Twin studies using the Vietnam Era Twin Registry have found that: (i) the heritability of PG is estimated to be 50-60%; (ii) PG and subclinical PG are a continuum of the same disorder; (iii) PG shares genetic vulnerability factors with antisocial behaviours, alcohol dependence and major depressive disorder; (iv) genetic factors underlie the association between exposure to traumatic life-events and PG. Molecular genetic investigations on PG are at an early stage and published studies have reported associations with genes involved in the brain's reward and impulse control systems. Despite the paucity of studies in this area, published studies have provided considerable evidence of the influence of genetic factors on PG and its complex interaction with other psychiatric disorders and environmental factors. The next step would be to investigate the association and interaction of these variables in larger molecular genetic studies with subphenotypes that underlie PG. Results from family and genetic investigations corroborate further the importance of understanding the biological underpinnings of PG in the development of more specific treatment and prevention strategies.

Drug-induced and genetic alterations in stress-responsive systems: Implications for specific addictive diseases.

Science.gov (United States)

Zhou, Yan; Proudnikov, Dmitri; Yuferov, Vadim; Kreek, Mary Jeanne

2010-02-16

From the earliest work in our laboratory, we hypothesized, and with studies conducted in both clinical research and animal models, we have shown that drugs of abuse, administered or self-administered, on a chronic basis, profoundly alter stress-responsive systems. Alterations of expression of specific genes involved in stress responsivity, with increases or decreases in mRNA levels, receptor, and neuropeptide levels, and resultant changes in hormone levels, have been documented to occur after chronic intermittent exposure to heroin, morphine, other opiates, cocaine, other stimulants, and alcohol in animal models and in human molecular genetics. The best studied of the stress-responsive systems in humans and mammalian species in general is undoubtedly the HPA axis. In addition, there are stress-responsive systems in other parts in the brain itself, and some of these include components of the HPA axis, such as CRF and CRF receptors, along with POMC gene and gene products. Several other stress-responsive systems are known to influence the HPA axis, such as the vasopressin-vasopressin receptor system. Orexin-hypocretin, acting at its receptors, may effect changes which suggest that it should be properly categorized as a stress-responsive system. However, less is known about the interactions and connectivity of some of these different neuropeptide and receptor systems, and in particular, about the possible connectivity of fast-acting (e.g., glutamate and GABA) and slow-acting (including dopamine, serotonin, and norepinephrine) neurotransmitters with each of these stress-responsive components and the resultant impact, especially in the setting of chronic exposure to drugs of abuse. Several of these stress-responsive systems and components, primarily based on our laboratory-based and human molecular genetics research of addictive diseases, will be briefly discussed in this review. Copyright 2009 Elsevier B.V. All rights reserved.

Intellectual property right in genetic resources

Directory of Open Access Journals (Sweden)

Milošević Mirjana

2017-01-01

Full Text Available Plant genetic resources for food and agriculture are necessary in food production and biodiversity conservation. These are the most important natural resources, in addition to air, water and soil. Unfortunately, during the evolution large number of plant genetic resources has been lost. The biggest negative impact on loss of plant genetic resources had been made by humans through the modernization of agriculture and the creation of varieties of high genetic uniformity. FAO and its operation through international mechanisms, such as the adoption of the Convention on Biological Diversity, the first legal act which regulates all levels of biodiversity: ecosystems, species and genetic resources, biotechnology, including the Cartagena Protocol on Biosafety (regulates the transfer of genetic material across the border, contributed to the conservation of plant genetic resources for food and agriculture. In addition to the Convention on Biological Diversity, FAO has been defined by the International Treaty on Plant Genetic Resources for Food and Agriculture in more specific and detailed way, the preservation of genetic resources. The objectives of the International Treaty on Plant Genetic Resources for Food and Agriculture are the conservation and sustainable use of all plant genetic resources for food and agriculture and the fair and equitable sharing of the benefits arising out of their use. There are four basic pillars which form the substance of the Contract, Sustainable use of plant genetic resources, Farmers' Rights, the Multilateral System and the Global Information System. Two organizations, the International Biodiversity and the International Union for the Protection of New Varieties of Plants trying to solve the issues of protection of the population and old varieties as intellectual property.

Systems genetics identifies a role for Cacna2d1 regulation in elevated intraocular pressure and glaucoma susceptibility.

Science.gov (United States)

Chintalapudi, Sumana R; Maria, Doaa; Di Wang, Xiang; Bailey, Jessica N Cooke; Hysi, Pirro G; Wiggs, Janey L; Williams, Robert W; Jablonski, Monica M

2017-11-24

Glaucoma is a multi-factorial blinding disease in which genetic factors play an important role. Elevated intraocular pressure is a highly heritable risk factor for primary open angle glaucoma and currently the only target for glaucoma therapy. Our study helps to better understand underlying genetic and molecular mechanisms that regulate intraocular pressure, and identifies a new candidate gene, Cacna2d1, that modulates intraocular pressure and a promising therapeutic, pregabalin, which binds to CACNA2D1 protein and lowers intraocular pressure significantly. Because our study utilizes a genetically diverse population of mice with known sequence variants, we are able to determine that the intraocular pressure-lowering effect of pregabalin is dependent on the Cacna2d1 haplotype. Using human genome-wide association study (GWAS) data, evidence for association of a CACNA2D1 single-nucleotide polymorphism and primary open angle glaucoma is found. Importantly, these results demonstrate that our systems genetics approach represents an efficient method to identify genetic variation that can guide the selection of therapeutic targets.

Causation of nervous system tumors in children: insights from traditional and genetically engineered animal models

International Nuclear Information System (INIS)

Rice, Jerry M.

2004-01-01

Pediatric neurogenic tumors include primitive neuroectodermal tumors (PNETs), especially medulloblastoma; ependymomas and choroid plexus papillomas; astrocytomas; retinoblastoma; and sympathetic neuroblastoma. Meningiomas and nerve sheath tumors, although uncommon in childhood, are also significant because they can result from exposures of children to ionizing radiation. Specific chromosomal loci and specific genes are related to each of these tumor types. Virtually all these genes appear to act as tumor suppressor genes, which are inactivated in tumor cells by mutations or by chromosomal loss. In genetically engineered mice, some genes that are clearly associated with specific human tumors (e.g., RB1 in retinoblastoma and NF2 in meningiomas and schwannomas) have no such effect. Other genetic constructs in mice involving the genes p53, ptc1, and Nf1 have produced tumors remarkably similar to some of the human pediatric neoplasms. Some of these tumors become clinically apparent after only a few weeks, while the mice are still juveniles, especially when two or more tumor suppressor genes are inactivated in the same genetic construct. Conversely, at least one genetic pathway in rodents involving point mutation in the coding region of a transforming gene (neu in malignant schwannomas) does not appear to operate in any human tumors. The nervous system is markedly susceptible to experimental carcinogenesis during early life in rodents, dogs, primates, and other nonhuman species, and there is no obvious reason why this generalization should not also apply to humans. However, except for therapeutic ionizing radiation, no physical, chemical, or biological cause of human pediatric nervous system tumors is known. The failure of experimental transplacental carcinogenesis to mirror human pediatric experience more closely may reflect the need for multiple mutational events in target cells, and for experimental carcinogens that are capable of causing the full spectrum of

Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens

DEFF Research Database (Denmark)

Timms, Richard T.; Menzies, Sam A.; Tchasovnikarova, Iva A.

2016-01-01

The application of forward genetic screens to cultured human cells represents a powerful method to study gene function. The repurposing of the bacterial CRISPR/Cas9 system provides an effective method to disrupt gene function in mammalian cells, and has been applied to genome-wide screens. Here, we...... compare the efficacy of genome-wide CRISPR/Cas9-mediated forward genetic screens versus gene-trap mutagenesis screens in haploid human cells, which represent the existing ‘gold standard’ method. This head-to-head comparison aimed to identify genes required for the endoplasmic reticulum....../3-associated disulphide reductase. Genome-wide CRISPR/Cas9-mediated screens together with haploid genetic screens provide a powerful addition to the forward genetic toolbox....

Differential Genetic Associations for Systemic Lupus Erythematosus Based on Anti–dsDNA Autoantibody Production

Science.gov (United States)

Chung, Sharon A.; Taylor, Kimberly E.; Graham, Robert R.; Nititham, Joanne; Lee, Annette T.; Ortmann, Ward A.; Jacob, Chaim O.; Alarcón-Riquelme, Marta E.; Tsao, Betty P.; Harley, John B.; Gaffney, Patrick M.; Moser, Kathy L.; Petri, Michelle; Demirci, F. Yesim; Kamboh, M. Ilyas; Manzi, Susan; Gregersen, Peter K.; Langefeld, Carl D.; Behrens, Timothy W.; Criswell, Lindsey A.

2011-01-01

Systemic lupus erythematosus (SLE) is a clinically heterogeneous, systemic autoimmune disease characterized by autoantibody formation. Previously published genome-wide association studies (GWAS) have investigated SLE as a single phenotype. Therefore, we conducted a GWAS to identify genetic factors associated with anti–dsDNA autoantibody production, a SLE–related autoantibody with diagnostic and clinical importance. Using two independent datasets, over 400,000 single nucleotide polymorphisms (SNPs) were studied in a total of 1,717 SLE cases and 4,813 healthy controls. Anti–dsDNA autoantibody positive (anti–dsDNA +, n = 811) and anti–dsDNA autoantibody negative (anti–dsDNA –, n = 906) SLE cases were compared to healthy controls and to each other to identify SNPs associated specifically with these SLE subtypes. SNPs in the previously identified SLE susceptibility loci STAT4, IRF5, ITGAM, and the major histocompatibility complex were strongly associated with anti–dsDNA + SLE. Far fewer and weaker associations were observed for anti–dsDNA – SLE. For example, rs7574865 in STAT4 had an OR for anti–dsDNA + SLE of 1.77 (95% CI 1.57–1.99, p = 2.0E-20) compared to an OR for anti–dsDNA – SLE of 1.26 (95% CI 1.12–1.41, p = 2.4E-04), with pheterogeneity<0.0005. SNPs in the SLE susceptibility loci BANK1, KIAA1542, and UBE2L3 showed evidence of association with anti–dsDNA + SLE and were not associated with anti–dsDNA – SLE. In conclusion, we identified differential genetic associations with SLE based on anti–dsDNA autoantibody production. Many previously identified SLE susceptibility loci may confer disease risk through their role in autoantibody production and be more accurately described as autoantibody propensity loci. Lack of strong SNP associations may suggest that other types of genetic variation or non-genetic factors such as environmental exposures have a greater impact on susceptibility to anti–dsDNA – SLE. PMID

Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.

Directory of Open Access Journals (Sweden)

Sharon A Chung

2011-03-01

Full Text Available Systemic lupus erythematosus (SLE is a clinically heterogeneous, systemic autoimmune disease characterized by autoantibody formation. Previously published genome-wide association studies (GWAS have investigated SLE as a single phenotype. Therefore, we conducted a GWAS to identify genetic factors associated with anti-dsDNA autoantibody production, a SLE-related autoantibody with diagnostic and clinical importance. Using two independent datasets, over 400,000 single nucleotide polymorphisms (SNPs were studied in a total of 1,717 SLE cases and 4,813 healthy controls. Anti-dsDNA autoantibody positive (anti-dsDNA +, n = 811 and anti-dsDNA autoantibody negative (anti-dsDNA -, n = 906 SLE cases were compared to healthy controls and to each other to identify SNPs associated specifically with these SLE subtypes. SNPs in the previously identified SLE susceptibility loci STAT4, IRF5, ITGAM, and the major histocompatibility complex were strongly associated with anti-dsDNA + SLE. Far fewer and weaker associations were observed for anti-dsDNA - SLE. For example, rs7574865 in STAT4 had an OR for anti-dsDNA + SLE of 1.77 (95% CI 1.57-1.99, p = 2.0E-20 compared to an OR for anti-dsDNA - SLE of 1.26 (95% CI 1.12-1.41, p = 2.4E-04, with p(heterogeneity<0.0005. SNPs in the SLE susceptibility loci BANK1, KIAA1542, and UBE2L3 showed evidence of association with anti-dsDNA + SLE and were not associated with anti-dsDNA - SLE. In conclusion, we identified differential genetic associations with SLE based on anti-dsDNA autoantibody production. Many previously identified SLE susceptibility loci may confer disease risk through their role in autoantibody production and be more accurately described as autoantibody propensity loci. Lack of strong SNP associations may suggest that other types of genetic variation or non-genetic factors such as environmental exposures have a greater impact on susceptibility to anti-dsDNA - SLE.

Robust Management of Combined Heat and Power Systems via Linear Decision Rules

DEFF Research Database (Denmark)

Zugno, Marco; Morales González, Juan Miguel; Madsen, Henrik

2014-01-01

The heat and power outputs of Combined Heat and Power (CHP) units are jointly constrained. Hence, the optimal management of systems including CHP units is a multicommodity optimization problem. Problems of this type are stochastic, owing to the uncertainty inherent both in the demand for heat and...... linear decision rules to guarantee both tractability and a correct representation of the dynamic aspects of the problem. Numerical results from an illustrative example confirm the value of the proposed approach....

A Systems Genetic Approach to Identify Low Dose Radiation-Induced Lymphoma Susceptibility/DOE2013FinalReport

Energy Technology Data Exchange (ETDEWEB)

Balmain, Allan [University of California, San Francisco; Song, Ihn Young [University of California, San Francisco

2013-05-15

The ultimate goal of this project is to identify the combinations of genetic variants that confer an individual's susceptibility to the effects of low dose (0.1 Gy) gamma-radiation, in particular with regard to tumor development. In contrast to the known effects of high dose radiation in cancer induction, the responses to low dose radiation (defined as 0.1 Gy or less) are much less well understood, and have been proposed to involve a protective anti-tumor effect in some in vivo scientific models. These conflicting results confound attempts to develop predictive models of the risk of exposure to low dose radiation, particularly when combined with the strong effects of inherited genetic variants on both radiation effects and cancer susceptibility. We have used a Systems Genetics approach in mice that combines genetic background analysis with responses to low and high dose radiation, in order to develop insights that will allow us to reconcile these disparate observations. Using this comprehensive approach we have analyzed normal tissue gene expression (in this case the skin and thymus), together with the changes that take place in this gene expression architecture a) in response to low or high- dose radiation and b) during tumor development. Additionally, we have demonstrated that using our expression analysis approach in our genetically heterogeneous/defined radiation-induced tumor mouse models can uniquely identify genes and pathways relevant to human T-ALL, and uncover interactions between common genetic variants of genes which may lead to tumor susceptibility.

Optimization of fog inlet air cooling system for combined cycle power plants using genetic algorithm

International Nuclear Information System (INIS)

Ehyaei, Mehdi A.; Tahani, Mojtaba; Ahmadi, Pouria; Esfandiari, Mohammad

2015-01-01

In this research paper, a comprehensive thermodynamic modeling of a combined cycle power plant is first conducted and the effects of gas turbine inlet fogging system on the first and second law efficiencies and net power outputs of combined cycle power plants are investigated. The combined cycle power plant (CCPP) considered for this study consist of a double pressure heat recovery steam generator (HRSG) to utilize the energy of exhaust leaving the gas turbine and produce superheated steam to generate electricity in the Rankine cycle. In order to enhance understanding of this research and come up with optimum performance assessment of the plant, a complete optimization is using a genetic algorithm conducted. In order to achieve this goal, a new objective function is defined for the system optimization including social cost of air pollution for the power generation systems. The objective function is based on the first law efficiency, energy cost and the external social cost of air pollution for an operational system. It is concluded that using inlet air cooling system for the CCPP system and its optimization results in an increase in the average output power, first and second law efficiencies by 17.24%, 3.6% and 3.5%, respectively, for three warm months of year. - Highlights: • To model the combined cycle power plant equipped with fog inlet air cooling method. • To conduct both exergy and economic analyses for better understanding. • To conduct a complete optimization using a genetic algorithm to determine the optimal design parameters of the system

Cyanobacteria as a platform for biofuel production

Directory of Open Access Journals (Sweden)

Nicole E Nozzi

2013-09-01

Full Text Available Cyanobacteria have great potential as a platform for biofuel production because of their fast growth, ability to fix carbon dioxide gas, and their genetic tractability. Furthermore they do not require fermentable sugars or arable land for growth and so competition with cropland would be greatly reduced. In this perspective we discuss the challenges and areas for improvement most pertinent for advancing cyanobacterial fuel production, including: improving genetic parts, carbon fixation, metabolic flux, nutrient requirements on a large scale, and photosynthetic efficiency using natural light.

A Double-Deck Elevator Group Supervisory Control System with Destination Floor Guidance System Using Genetic Network Programming

Science.gov (United States)

Yu, Lu; Zhou, Jin; Mabu, Shingo; Hirasawa, Kotaro; Hu, Jinglu; Markon, Sandor

The Elevator Group Supervisory Control Systems (EGSCS) are the control systems that systematically manage three or more elevators in order to efficiently transport the passengers in buildings. Double-deck elevators, where two elevators are connected with each other, serve passengers at two consecutive floors simultaneously. Double-deck Elevator systems (DDES) become more complex in their behavior than conventional single-deck elevator systems (SDES). Recently, Artificial Intelligence (AI) technology has been used in such complex systems. Genetic Network Programming (GNP), a graph-based evolutionary method, has been applied to EGSCS and its advantages are shown in some papers. GNP can obtain the strategy of a new hall call assignment to the optimal elevator when it performs crossover and mutation operations to judgment nodes and processing nodes. Meanwhile, Destination Floor Guidance System (DFGS) is installed in DDES, so that passengers can also input their destinations at elevator halls. In this paper, we have applied GNP to DDES and compared DFGS with normal systems. The waiting time and traveling time of DFGS are all improved because of getting more information from DFGS. The simulations showed the effectiveness of the double-deck elevators with DFGS in different building traffics.

Genetic variation of the ghrelin signalling system in individuals with amphetamine dependence.

Science.gov (United States)

Suchankova, Petra; Jerlhag, Elisabet; Jayaram-Lindström, Nitya; Nilsson, Staffan; Toren, Kjell; Rosengren, Annika; Engel, Jörgen A; Franck, Johan

2013-01-01

The development of amphetamine dependence largely depends on the effects of amphetamine in the brain reward systems. Ghrelin, an orexigenic peptide, activates the reward systems and is required for reward induced by alcohol, nicotine, cocaine and amphetamine in mice. Human genetic studies have shown that polymorphisms in the pre-proghrelin (GHRL) as well as GHS-R1A (GHSR) genes are associated with high alcohol consumption, increased weight and smoking in males. Since the heritability factor underlying drug dependence is shared between different drugs of abuse, we here examine the association between single nucleotide polymorphisms (SNPs) and haplotypes in the GHRL and GHSR, and amphetamine dependence. GHRL and GHSR SNPs were genotyped in Swedish amphetamine dependent individuals (n = 104) and controls from the general population (n = 310). A case-control analysis was performed and SNPs and haplotypes were additionally tested for association against Addiction Severity Interview (ASI) composite score of drug use. The minor G-allele of the GHSR SNP rs2948694, was more common among amphetamine dependent individuals when compared to controls (pc  = 0.02). A significant association between the GHRL SNP rs4684677 and ASI composite score of drug use was also reported (pc  = 0.03). The haplotype analysis did not add to the information given by the individual polymorphisms. Although genetic variability of the ghrelin signalling system is not a diagnostic marker for amphetamine dependence and problem severity of drug use, the present results strengthen the notion that ghrelin and its receptor may be involved in the development of addictive behaviours and may thus serve as suitable targets for new treatments of such disorders.

Genetic variation of the ghrelin signalling system in individuals with amphetamine dependence.

Directory of Open Access Journals (Sweden)

Petra Suchankova

Full Text Available The development of amphetamine dependence largely depends on the effects of amphetamine in the brain reward systems. Ghrelin, an orexigenic peptide, activates the reward systems and is required for reward induced by alcohol, nicotine, cocaine and amphetamine in mice. Human genetic studies have shown that polymorphisms in the pre-proghrelin (GHRL as well as GHS-R1A (GHSR genes are associated with high alcohol consumption, increased weight and smoking in males. Since the heritability factor underlying drug dependence is shared between different drugs of abuse, we here examine the association between single nucleotide polymorphisms (SNPs and haplotypes in the GHRL and GHSR, and amphetamine dependence. GHRL and GHSR SNPs were genotyped in Swedish amphetamine dependent individuals (n = 104 and controls from the general population (n = 310. A case-control analysis was performed and SNPs and haplotypes were additionally tested for association against Addiction Severity Interview (ASI composite score of drug use. The minor G-allele of the GHSR SNP rs2948694, was more common among amphetamine dependent individuals when compared to controls (pc  = 0.02. A significant association between the GHRL SNP rs4684677 and ASI composite score of drug use was also reported (pc  = 0.03. The haplotype analysis did not add to the information given by the individual polymorphisms. Although genetic variability of the ghrelin signalling system is not a diagnostic marker for amphetamine dependence and problem severity of drug use, the present results strengthen the notion that ghrelin and its receptor may be involved in the development of addictive behaviours and may thus serve as suitable targets for new treatments of such disorders.

Methods of orbit correction system optimization

International Nuclear Information System (INIS)

Chao, Yu-Chiu.

1997-01-01

Extracting optimal performance out of an orbit correction system is an important component of accelerator design and evaluation. The question of effectiveness vs. economy, however, is not always easily tractable. This is especially true in cases where betatron function magnitude and phase advance do not have smooth or periodic dependencies on the physical distance. In this report a program is presented using linear algebraic techniques to address this problem. A systematic recipe is given, supported with quantitative criteria, for arriving at an orbit correction system design with the optimal balance between performance and economy. The orbit referred to in this context can be generalized to include angle, path length, orbit effects on the optical transfer matrix, and simultaneous effects on multiple pass orbits

Chromosome-based genetic complementation system for Xylella fastidiosa.

Science.gov (United States)

Matsumoto, Ayumi; Young, Glenn M; Igo, Michele M

2009-03-01

Xylella fastidiosa is a xylem-limited, gram-negative bacterium that causes Pierce's disease of grapevine. Here, we describe the construction of four vectors that facilitate the insertion of genes into a neutral site (NS1) in the X. fastidiosa chromosome. These vectors carry a colE1-like (pMB1) replicon and DNA sequences from NS1 flanking a multiple-cloning site and a resistance marker for one of the following antibiotics: chloramphenicol, erythromycin, gentamicin, or kanamycin. In X. fastidiosa, vectors with colE1-like (pMB1) replicons have been found to result primarily in the recovery of double recombinants rather than single recombinants. Thus, the ease of obtaining double recombinants and the stability of the resulting insertions at NS1 in the absence of selective pressure are the major advantages of this system. Based on in vitro and in planta characterizations, strains carrying insertions within NS1 are indistinguishable from wild-type X. fastidiosa in terms of growth rate, biofilm formation, and pathogenicity. To illustrate the usefulness of this system for complementation analysis, we constructed a strain carrying a mutation in the X. fastidiosa cpeB gene, which is predicted to encode a catalase/peroxidase, and showed that the sensitivity of this mutant to hydrogen peroxide could be overcome by the introduction of a wild-type copy of cpeB at NS1. Thus, this chromosome-based complementation system provides a valuable genetic tool for investigating the role of specific genes in X. fastidiosa cell physiology and virulence.

Forecasting systems reliability based on support vector regression with genetic algorithms

International Nuclear Information System (INIS)

Chen, K.-Y.

2007-01-01

This study applies a novel neural-network technique, support vector regression (SVR), to forecast reliability in engine systems. The aim of this study is to examine the feasibility of SVR in systems reliability prediction by comparing it with the existing neural-network approaches and the autoregressive integrated moving average (ARIMA) model. To build an effective SVR model, SVR's parameters must be set carefully. This study proposes a novel approach, known as GA-SVR, which searches for SVR's optimal parameters using real-value genetic algorithms, and then adopts the optimal parameters to construct the SVR models. A real reliability data for 40 suits of turbochargers were employed as the data set. The experimental results demonstrate that SVR outperforms the existing neural-network approaches and the traditional ARIMA models based on the normalized root mean square error and mean absolute percentage error

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system

Science.gov (United States)

Raimondo, Joseph V.; Joyce, Bradley; Kay, Louise; Schlagheck, Theresa; Newey, Sarah E.; Srinivas, Shankar; Akerman, Colin J.

2013-01-01

Within the nervous system, intracellular Cl− and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission, and network excitability. Cl− and pH are often co-regulated, and network activity results in the movement of both Cl− and H+. Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl− and pH sensors have been described previously, these either lack ion specificity or are unsuitable for neuronal use. Here we present ClopHensorN—a new genetically-encoded ratiometric Cl− and pH sensor that is optimized for the nervous system. We demonstrate the ability of ClopHensorN to dissociate and simultaneously quantify Cl− and H+ concentrations under a variety of conditions. In addition, we establish the sensor's utility by characterizing activity-dependent ion dynamics in hippocampal neurons. PMID:24312004

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system

Directory of Open Access Journals (Sweden)

Joseph Valentino Raimondo

2013-11-01

Full Text Available Within the nervous system, intracellular Cl- and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission and network excitability. Cl- and pH are often co-regulated, and network activity results in the movement of both Cl- and H+. Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl- and pH sensors have been described previously, these either lack ion specificity or are unsuitable for neuronal use. Here we present ClopHensorN - a new genetically-encoded ratiometric Cl- and pH sensor that is optimized for the nervous system. We demonstrate the ability of ClopHensorN to dissociate and simultaneously quantify Cl- and H+ concentrations under a variety of conditions. In addition, we establish the sensor’s utility by characterizing activity-dependent ion dynamics in hippocampal neurons.

Optimization of linear consecutive-k-out-of-n system with a Birnbaum importance-based genetic algorithm

International Nuclear Information System (INIS)

Cai, Zhiqiang; Si, Shubin; Sun, Shudong; Li, Caitao

2016-01-01

The optimization of linear consecutive-k-out-of-n (Lin/Con/k/n) is to find an optimal component arrangement where n components are assigned to n positions to maximize the system reliability. With the interchangeability of components in practical systems, the optimization of Lin/Con/k/n systems is becoming widely applied in engineering practice, which is also a typical component assignment problem concerned by many researchers. This paper proposes a Birnbaum importance-based genetic algorithm (BIGA) to search the near global optimal solution for Lin/Con/k/n systems. First, the operation procedures and corresponding execution methods of BIGA are described in detail. Then, comprehensive simulation experiments are implemented on both small and large systems to evaluate the performance of the BIGA by comparing with the Birnbaum importance-based two-stage approach and Birnbaum importance-based genetic local search algorithm. Thirdly, further experiments are provided to discuss the applicability of BIGA for Lin/Con/k/n system with different k and n. Finally, the case study on oil transportation system is implemented to demonstrate the application of BIGA in the optimization of Lin/Con/k/n system. - Highlights: • BIGA integrates BI and GA to solve the Lin/Con/k/n systems optimization problems. • The experiment results show that the BIGA performs well in most conditions. • Suggestions are given for the application of BIGA and BITA with different k and n. • The application procedure of BIGA is demonstrated by the oil transportation system.

Integrated analysis of genetic data with R

Directory of Open Access Journals (Sweden)

Zhao Jing

2006-01-01

Full Text Available Abstract Genetic data are now widely available. There is, however, an apparent lack of concerted effort to produce software systems for statistical analysis of genetic data compared with other fields of statistics. It is often a tremendous task for end-users to tailor them for particular data, especially when genetic data are analysed in conjunction with a large number of covariates. Here, R http://www.r-project.org, a free, flexible and platform-independent environment for statistical modelling and graphics is explored as an integrated system for genetic data analysis. An overview of some packages currently available for analysis of genetic data is given. This is followed by examples of package development and practical applications. With clear advantages in data management, graphics, statistical analysis, programming, internet capability and use of available codes, it is a feasible, although challenging, task to develop it into an integrated platform for genetic analysis; this will require the joint efforts of many researchers.

Advances in the genetically complex autoinflammatory diseases.

Science.gov (United States)

Ombrello, Michael J

2015-07-01

Monogenic diseases usually demonstrate Mendelian inheritance and are caused by highly penetrant genetic variants of a single gene. In contrast, genetically complex diseases arise from a combination of multiple genetic and environmental factors. The concept of autoinflammation originally emerged from the identification of individual, activating lesions of the innate immune system as the molecular basis of the hereditary periodic fever syndromes. In addition to these rare, monogenic forms of autoinflammation, genetically complex autoinflammatory diseases like the periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome, chronic recurrent multifocal osteomyelitis (CRMO), Behçet's disease, and systemic arthritis also fulfill the definition of autoinflammatory diseases-namely, the development of apparently unprovoked episodes of inflammation without identifiable exogenous triggers and in the absence of autoimmunity. Interestingly, investigations of these genetically complex autoinflammatory diseases have implicated both innate and adaptive immune abnormalities, blurring the line between autoinflammation and autoimmunity. This reinforces the paradigm of concerted innate and adaptive immune dysfunction leading to genetically complex autoinflammatory phenotypes.

Sex-biased dispersal creates spatial genetic structure in a parthenogenetic ant with a dependent-lineage reproductive system.

Science.gov (United States)

Kuhn, A; Bauman, D; Darras, H; Aron, S

2017-10-01

Reproduction and dispersal are key aspects of species life history that influence spatial genetic structure in populations. Several ant species in the genus Cataglyphis have evolved a unique breeding system in which new reproductives (that is, queens and males) are produced asexually by parthenogenesis; in contrast, non-reproductives (that is, workers) are produced via sexual reproduction by mates from distinct genetic lineages. We investigated how these two coexisting reproductive methods affect population-level spatial genetic structure using the ant Cataglyphis mauritanica as a model. We obtained genotypes for queens and their male mates from 338 colonies, and we found that the two lineages present in the study population occurred with equal frequency. Furthermore, analysis of spatial genetic structure revealed strong sex-biased dispersal. Because queens were produced by parthenogenesis and because they dispersed over short distances, there was an extreme level of spatial structuring: a mosaic of patches composed of clonal queens was formed. Males, on the other hand, dispersed over several hundred metres and, thus, across patches, ensuring successful interlineage mating.

Hybrid Genetic Algorithm Optimization for Case Based Reasoning Systems

International Nuclear Information System (INIS)

Mohamed, A.H.

2008-01-01

The success of a CBR system largely depen ds on an effective retrieval of useful prior case for the problem. Nearest neighbor and induction are the main CBR retrieval algorithms. Each of them can be more suitable in different situations. Integrated the two retrieval algorithms can catch the advantages of both of them. But, they still have some limitations facing the induction retrieval algorithm when dealing with a noisy data, a large number of irrelevant features, and different types of data. This research utilizes a hybrid approach using genetic algorithms (GAs) to case-based induction retrieval of the integrated nearest neighbor - induction algorithm in an attempt to overcome these limitations and increase the overall classification accuracy. GAs can be used to optimize the search space of all the possible subsets of the features set. It can deal with the irrelevant and noisy features while still achieving a significant improvement of the retrieval accuracy. Therefore, the proposed CBR-GA introduces an effective general purpose retrieval algorithm that can improve the performance of CBR systems. It can be applied in many application areas. CBR-GA has proven its success when applied for different problems in real-life

Beyond dual systems: A genetically-informed, latent factor model of behavioral and self-report measures related to adolescent risk-taking

Directory of Open Access Journals (Sweden)

K. Paige Harden

2017-06-01

Full Text Available The dual systems model posits that adolescent risk-taking results from an imbalance between a cognitive control system and an incentive processing system. Researchers interested in understanding the development of adolescent risk-taking use a diverse array of behavioral and self-report measures to index cognitive control and incentive processing. It is currently unclear whether different measures commonly interpreted as indicators of the same psychological construct do, in fact, tap the same underlying dimension of individual differences. In a diverse sample of 810 adolescent twins and triplets (M age = 15.9 years, SD = 1.4 years from the Texas Twin Project, we investigated the factor structure of fifteen self-report and task-based measures relevant to adolescent risk-taking. These measures can be organized into four factors, which we labeled premeditation, fearlessness, cognitive dyscontrol, and reward seeking. Most behavioral measures contained large amounts of task-specific variance; however, most genetic variance in each measure was shared with other measures of the corresponding factor. Behavior genetic analyses further indicated that genetic influences on cognitive dyscontrol overlapped nearly perfectly with genetic influences on IQ (rA = −0.91. These findings underscore the limitations of using single laboratory tasks in isolation, and indicate that the study of adolescent risk taking will benefit from applying multimethod approaches.

Machine Learning in Production Systems Design Using Genetic Algorithms

OpenAIRE

Abu Qudeiri Jaber; Yamamoto Hidehiko Rizauddin Ramli

2008-01-01

To create a solution for a specific problem in machine learning, the solution is constructed from the data or by use a search method. Genetic algorithms are a model of machine learning that can be used to find nearest optimal solution. While the great advantage of genetic algorithms is the fact that they find a solution through evolution, this is also the biggest disadvantage. Evolution is inductive, in nature life does not evolve towards a good solution but it evolves aw...

Systems genetics analysis of pharmacogenomics variation during antidepressant treatment

DEFF Research Database (Denmark)

Madsen, Majbritt Busk; Kogelman, L J A; Kadarmideen, H N

2016-01-01

Selective serotonin reuptake inhibitors (SSRIs) are the most widely used antidepressants, but the efficacy of the treatment varies significantly among individuals. It is believed that complex genetic mechanisms play a part in this variation. We have used a network based approach to unravel the in...... genes involved in calcium homeostasis. In conclusion, we suggest a difference in genetic interaction networks between initial and subsequent SSRI response.The Pharmacogenomics Journal advance online publication, 18 October 2016; doi:10.1038/tpj.2016.68....

Comparison between an exclusive in vitro-produced embryo transfer system and artificial insemination for genetic, technical, and financial herd performance.

Science.gov (United States)

Kaniyamattam, K; Block, J; Hansen, P J; De Vries, A

2017-07-01

The objective of this study was to implement an in vitro-produced embryo transfer (IVP-ET) system in an existing stochastic dynamic dairy simulation model with multitrait genetics to evaluate the genetic, technical, and financial performance of a dairy herd implementing an exclusive IVP-ET or artificial insemination (AI) system. In the AI system, sexed semen was used on the genetically best heifers only. In the IVP-ET system, all of the animals in the herd were impregnated with female sexed embryos created through in vitro fertilization of oocytes collected from animals of superior genetics for different traits of interest. Each donor was assumed to yield on average 4.25 transferable embryos per collection. The remaining animals in the herd were used as recipients and received either a fresh embryo or a frozen embryo when fresh embryos were not available. Selection of donors was random or based on the greatest estimated breeding value (EBV) of lifetime net merit (NM$), milk yield, or daughter pregnancy rate. For both the IVP-ET and AI systems, culling of surplus heifer calves not needed to replace culled cows was based on the lowest EBV for the same traits. A herd of 1,000 milking cows was simulated 15 yr over time after the start of the IVP-ET system. The default cost to produce and transfer 1 embryo was set at $165. Prices of fresh embryos at which an exclusive IVP-ET system financially breaks even with the comparable AI system in yr 15 and for an investment period of 15 yr were also estimated. More surplus heifer calves were sold from the IVP-ET systems than from the comparable AI systems. The surplus calves from the IVP-ET systems were also genetically superior to the surplus calves from the comparable AI systems, which might be reflected in their market value as a premium price. The most profitable scenario among the 4 IVP-ET scenarios in yr 15 was the one in which NM$ was maximized in the herd. This scenario had an additional profit of $8/cow compared with a

Biochemical genetic variation between four populations of ...

African Journals Online (AJOL)

system) to 0.093 in the Spekboom River population (Limpopo River system). The genetic distance, FST and NEM values, as well as pair-wise contingency c2 analyses indicate a lack of gene flow between populations, as expected for isolated fish. Evidence of foreign genetic material in one population was also observed.

Reverse genetics of avian metapneumoviruses

Science.gov (United States)

An overview of avian metapneumovirus (aMPV) infection in turkeys and development of a reverse genetics system for aMPV subgroup C (aMPV-C) virus will be presented. By using reverse genetics technology, we generated recombinant aMPV-C viruses containing a different length of glycoprotein (G) gene or...

Genetic and biochemical changes of the serotonergic system in migraine pathobiology.

Science.gov (United States)

Gasparini, Claudia Francesca; Smith, Robert Anthony; Griffiths, Lyn Robyn

2017-12-01

Migraine is a brain disorder characterized by a piercing headache which affects one side of the head, located mainly at the temples and in the area around the eye. Migraine imparts substantial suffering to the family in addition to the sufferer, particularly as it affects three times more women than men and is most prevalent between the ages of 25 and 45, the years of child rearing. Migraine typically occurs in individuals with a genetic predisposition and is aggravated by specific environmental triggers. Attempts to study the biochemistry of migraine began as early as the 1960s and were primarily directed at serotonin metabolism after an increase of 5-hydroxyindoleacetic acid (5-HIAA), the main metabolite of serotonin was observed in urine of migraineurs. Genetic and biochemical studies have primarily focused on the neurotransmitter serotonin, considering receptor binding, transport and synthesis of serotonin and have investigated serotonergic mediators including enzymes, receptors as well as intermediary metabolites. These studies have been mainly assayed in blood, CSF and urine as the most accessible fluids. More recently PET imaging technology integrated with a metabolomics and a systems biology platform are being applied to study serotonergic biology. The general trend observed is that migraine patients have alterations of neurotransmitter metabolism detected in biological fluids with different biochemistry from controls, however the interpretation of the biological significance of these peripheral changes is unresolved. In this review we present the biology of the serotonergic system and metabolic routes for serotonin and discuss results of biochemical studies with regard to alterations in serotonin in brain, cerebrospinal fluid, saliva, platelets, plasma and urine of migraine patients.

Availability allocation to repairable systems with genetic algorithms: a multi-objective formulation

International Nuclear Information System (INIS)

Elegbede, Charles; Adjallah, Kondo

2003-01-01

This paper describes a methodology based on genetic algorithms (GA) and experiments plan to optimize the availability and the cost of reparable parallel-series systems. It is a NP-hard problem of multi-objective combinatorial optimization, modeled with continuous and discrete variables. By using the weighting technique, the problem is transformed into a single-objective optimization problem whose constraints are then relaxed by the exterior penalty technique. We then propose a search of solution through GA, whose parameters are adjusted using experiments plan technique. A numerical example is used to assess the method

Ruminant Nutrition Symposium: a systems approach to integrating genetics, nutrition, and metabolic efficiency in dairy cattle.

Science.gov (United States)

McNamara, J P

2012-06-01

The role of the dairy cow is to help provide high-quality protein and other nutrients for humans. We must select and manage cows with the goal of reaching the greatest possible efficiency for any given environment. We have increased efficiency tremendously over the years, yet the variation in productive and reproductive efficiency among animals is still quite large. In part this is because of a lack of full integration of genetic, nutritional, and reproductive biology into management decisions. However, integration across these disciplines is increasing as biological research findings show more specific control points at which genetics, nutrition, and reproduction interact. An ordered systems biology approach that focuses on why and how cells regulate energy and N use and on how and why organs interact by endocrine and neurocrine mechanisms will speed improvements in efficiency. More sophisticated dairy managers will demand better information to improve the efficiency of their animals. Using genetic improvement and proper animal management to improve milk productive and reproductive efficiency requires a deeper understanding of metabolic processes during the transition period. Using existing metabolic models, we can design experiments specifically to integrate new data from transcriptional arrays into models that describe nutrient use in farm animals. A systems modeling approach can help focus our research to make faster and large advances in efficiency and show directly how this can be applied on the farms.

Rapid-throughput skeletal phenotyping of 100 knockout mice identifies 9 new genes that determine bone strength.

Directory of Open Access Journals (Sweden)

J H Duncan Bassett

Full Text Available Osteoporosis is a common polygenic disease and global healthcare priority but its genetic basis remains largely unknown. We report a high-throughput multi-parameter phenotype screen to identify functionally significant skeletal phenotypes in mice generated by the Wellcome Trust Sanger Institute Mouse Genetics Project and discover novel genes that may be involved in the pathogenesis of osteoporosis. The integrated use of primary phenotype data with quantitative x-ray microradiography, micro-computed tomography, statistical approaches and biomechanical testing in 100 unselected knockout mouse strains identified nine new genetic determinants of bone mass and strength. These nine new genes include five whose deletion results in low bone mass and four whose deletion results in high bone mass. None of the nine genes have been implicated previously in skeletal disorders and detailed analysis of the biomechanical consequences of their deletion revealed a novel functional classification of bone structure and strength. The organ-specific and disease-focused strategy described in this study can be applied to any biological system or tractable polygenic disease, thus providing a general basis to define gene function in a system-specific manner. Application of the approach to diseases affecting other physiological systems will help to realize the full potential of the International Mouse Phenotyping Consortium.

Functional relevance for associations between genetic variants and systemic lupus erythematosus.

Directory of Open Access Journals (Sweden)

Fei-Yan Deng

Full Text Available Systemic lupus erythematosus (SLE is a serious prototype autoimmune disease characterized by chronic inflammation, auto-antibody production and multi-organ damage. Recent association studies have identified a long list of loci that were associated with SLE with relatively high statistical power. However, most of them only established the statistical associations of genetic markers and SLE at the DNA level without supporting evidence of functional relevance. Here, using publically available datasets, we performed integrative analyses (gene relationship across implicated loci analysis, differential gene expression analysis and functional annotation clustering analysis and combined with expression quantitative trait loci (eQTLs results to dissect functional mechanisms underlying the associations for SLE. We found that 14 SNPs, which were significantly associated with SLE in previous studies, have cis-regulation effects on four eQTL genes (HLA-DQA1, HLA-DQB1, HLA-DQB2, and IRF5 that were also differentially expressed in SLE-related cell groups. The functional evidence, taken together, suggested the functional mechanisms underlying the associations of 14 SNPs and SLE. The study may serve as an example of mining publically available datasets and results in validation of significant disease-association results. Utilization of public data resources for integrative analyses may provide novel insights into the molecular genetic mechanisms underlying human diseases.

Genetic Algorithm (GA Method for Optimization of Multi-Reservoir Systems Operation

Directory of Open Access Journals (Sweden)

Shervin Momtahen

2006-01-01

Full Text Available A Genetic Algorithm (GA method for optimization of multi-reservoir systems operation is proposed in this paper. In this method, the parameters of operating policies are optimized using system simulation results. Hence, any operating problem with any sort of objective function, constraints and structure of operating policy can be optimized by GA. The method is applied to a 3-reservoir system and is compared with two traditional methods of Stochastic Dynamic Programming and Dynamic Programming and Regression. The results show that GA is superior both in objective function value and in computational speed. The proposed method is further improved using a mutation power updating rule and a varying period simulation method. The later is a novel procedure proposed in this paper that is believed to help in solving computational time problem in large systems. These revisions are evaluated and proved to be very useful in converging to better solutions in much less time. The final GA method is eventually evaluated as a very efficient procedure that is able to solve problems of large multi-reservoir system which is usually impossible by traditional methods. In fact, the real performance of the GA method starts where others fail to function.

Predictive Control of Hydronic Floor Heating Systems using Neural Networks and Genetic Algorithms

DEFF Research Database (Denmark)

Vinther, Kasper; Green, Torben; Østergaard, Søren

2017-01-01

This paper presents the use a neural network and a micro genetic algorithm to optimize future set-points in existing hydronic floor heating systems for improved energy efficiency. The neural network can be trained to predict the impact of changes in set-points on future room temperatures. Additio...... space is not guaranteed. Evaluation of the performance of multiple neural networks is performed, using different levels of information, and optimization results are presented on a detailed house simulation model....

Genetic variants of genital mycoplasmas and their relation to the clinical course of inflammatory diseases of the urogenital system in women

Directory of Open Access Journals (Sweden)

M. R. Rakhmatulina

2014-01-01

Full Text Available Goal of the study. To study genetic variability of M. hominis (based on the vaa gene and M. genitalium (based on the mg192 gene derived from biological material samples taken from women with different clinical manifestations of inflammatory diseases of the urogenital system and clinically healthy women (for M. hominis. Materials and methods. Genetic variability of twenty M. hominis samples taken from patients with inflammatory diseases of the urogenital system and twenty M. hominis samples taken from patients without clinical and laboratory signs of inflammatory processes of the urogenital system was studied by the sequence analysis method. Genetic variability of eight M. genitalium samples taken from patients with different clinical signs of inflammatory diseases of the urogenital system was also examined by the sequence analysis method. Results. Three genetic variants of M. hominis based on the vaa gene were found; variant I was revealed more often in patients with clinical manifestations of inflammatory diseases (65.0%, and variant II - in clinically healthy women (60.0%. Three phylogenetic M. gentium groups based on the mg192 gene were revealed; two samples were referred to Groups I and II, and four samples were referred to Group III. Samples from each phylogenetic groups were taken from patients with clinical and laboratory manifestations of cervicitis and urethritis. Conclusion. The study data demonstrate a potential effect of the VAA surface protein on the virulence of opportunistic M. hominis pathogens.

Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network and pathway analyses

DEFF Research Database (Denmark)

Kogelman, Lisette; Pant, Sameer Dinkar; Fredholm, Merete

2014-01-01

.g. metabolic processes. WISH networks based on genotypic correlations allowed further identification of various gene ontology terms and pathways related to obesity and related traits, which were not identified by the GWA study. In conclusion, this is the first study to develop a (genetic) obesity index...... investigations focusing on single genetic variants have achieved limited success, and the importance of including genetic interactions is becoming evident. Here, the aim was to perform an integrative genomic analysis in an F2 pig resource population that was constructed with an aim to maximize genetic variation...... of obesity-related phenotypes and genotyped using the 60K SNP chip. Firstly, Genome Wide Association (GWA) analysis was performed on the Obesity Index to locate candidate genomic regions that were further validated using combined Linkage Disequilibrium Linkage Analysis and investigated by evaluation...

Genetic characterization of the inducible SOS-like system of Bacillus subtilis

Energy Technology Data Exchange (ETDEWEB)

Love, P.E.; Yasbin, R.E.

1984-12-01

The SOS-like system of Bacillus subtilis consists of several coordinately induced phenomena which are expressed after cellular insult such as DNA damage of inhibition of DNA replication. Mutagenesis of the bacterial chromosomes and the development of maintenance of competence also appear to be involved in the SOS-like response in this bacterium. The genetic characterization of the SOS-like system has involved an analysis of (i) the effects of various DNA repair mutations on the expression of inducible phenomena and (ii) the tsi-23 mutation, which renders host strains thermally inducible for each of the SOS-like functions. Bacterial filamentation was unaffected by any of the DNA repair mutations studied. In contrast, the induction of prophage after thermal or UV pretreatment was abolished in strains carrying the recE4, recA1, recB2, or recG13 mutation. The Weigle reactivation of UV-damaged bacteriophage was also inhibited by the recE4, recA1, recB2, or recG13 mutation, whereas levels of Weigle reactivation were lower in strains which carried the uvrA42, polA5, or rec-961 mutation than in the DNA repair-proficient strain. Strains which carried the recE4 mutation were incapable of chromosomal DNA-mediated transformation, and the frequency of this event was decreased in strains carrying recA1, recB2, or tsi-23 mutation. Plasmid DNA transformation efficiency was decreased only in strains carrying the tsi-23 mutation in addition to the recE4, recA1, or recB2 mutation. The results indicate that the SOS-like system of B. subtilis is regulated at different levels by two or more gene products. In this report, the current data regarding the genetic regulation of inducible phenomena are summarized, and a model is proposed to explain the mechanism of SOS-like induction in B. subtillis. 50 references, 3 figures, 6 tables.

The New Genetics and Natural versus Artificial Genetic Modification

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Mae-Wan Ho

2013-11-01

Full Text Available The original rationale and impetus for artificial genetic modification was the “central dogma” of molecular biology that assumed DNA carries all the instructions for making an organism, which are transmitted via RNA to protein to biological function in linear causal chains. This is contrary to the reality of the “fluid genome” that has emerged since the mid-1970s. In order to survive, the organism needs to engage in natural genetic modification in real time, an exquisitely precise molecular dance of life with RNA and DNA responding to and participating in “downstream” biological functions. Artificial genetic modification, in contrast, is crude, imprecise, and interferes with the natural process. It drives natural systems towards maximum biosemiotic entropy as the perturbations are propagated and amplified through the complex cascades of interactions between subsystems that are essential for health and longevity.

Multifactorial diseases and risk estimations: special reference of mutation component

International Nuclear Information System (INIS)

Yasuda, Norikazu

1995-01-01

Genetic effects of radiation in man have been tractable such aspects as genes, chromosomes, genomes, individuals and populations. In spite of enormous interest from an academic view point on the mechanism studies, it is rather a little study on incidence or prevalence of genetic diseases as hereditary effects when human population in general have been exposed by radiation. Such studies are valuable for radiation protection as well as radiation public health. In this review, I have attempted to reconcile some fragments evidences to derive an important conclusion: the hereditary effects of radiation could not be detected from examination of disease incidence (or prevalence) for the genetic risk. (J.P.N.)

Drosophila olfactory memory: single genes to complex neural circuits.

Science.gov (United States)

Keene, Alex C; Waddell, Scott

2007-05-01

A central goal of neuroscience is to understand how neural circuits encode memory and guide behaviour. Studying simple, genetically tractable organisms, such as Drosophila melanogaster, can illuminate principles of neural circuit organization and function. Early genetic dissection of D. melanogaster olfactory memory focused on individual genes and molecules. These molecular tags subsequently revealed key neural circuits for memory. Recent advances in genetic technology have allowed us to manipulate and observe activity in these circuits, and even individual neurons, in live animals. The studies have transformed D. melanogaster from a useful organism for gene discovery to an ideal model to understand neural circuit function in memory.

Medical Genetics Is Not Eugenics

Science.gov (United States)

Cowan, Ruth Schwartz

2008-01-01

The connection that critics make between medical genetics and eugenics is historically fallacious. Activists on the political right are as mistaken as activists on the political left: Genetic screening was not eugenics in the past, is not eugenics in the present, and, unless its technological systems become radically transformed, will not be…

National Genetic Evaluation (System of Hanwoo (Korean Native Cattle

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B. Park

2013-02-01

practically contributed to the improvement in aspects of quality and quantity. In sum, the current selection system is good enough to accommodate circumstances where fewer sires are used on many more cows. Although progeny tests take longer and cost more, they seem to be appropriate under the circumstances of the domestic market with its higher requirement for better meat quality. Consequently, accumulative data collection, genetic evaluation model development, revision of selection indices, as well as cooperation among farms, associations, National Agricultural Cooperative Federation, universities, research institutes, and government agencies must be applied to the Hanwoo selection program. All these efforts will assist the domestic market to secure a competitive position against imported beef under Free Trade Agreement trade system and will provide farmers with higher profits as well as the public with a higher quality of beef.

Genetic design of interpolated non-linear controllers for linear plants

International Nuclear Information System (INIS)

Ajlouni, N.

2000-01-01

The techniques of genetic algorithms are proposed as a means of designing non-linear PID control systems. It is shown that the use of genetic algorithms for this purpose results in highly effective non-linear PID control systems. These results are illustrated by using genetic algorithms to design a non-linear PID control system and contrasting the results with an optimally tuned linear PID controller. (author)

Quantum dynamics in open quantum-classical systems.

Science.gov (United States)

Kapral, Raymond

2015-02-25

Often quantum systems are not isolated and interactions with their environments must be taken into account. In such open quantum systems these environmental interactions can lead to decoherence and dissipation, which have a marked influence on the properties of the quantum system. In many instances the environment is well-approximated by classical mechanics, so that one is led to consider the dynamics of open quantum-classical systems. Since a full quantum dynamical description of large many-body systems is not currently feasible, mixed quantum-classical methods can provide accurate and computationally tractable ways to follow the dynamics of both the system and its environment. This review focuses on quantum-classical Liouville dynamics, one of several quantum-classical descriptions, and discusses the problems that arise when one attempts to combine quantum and classical mechanics, coherence and decoherence in quantum-classical systems, nonadiabatic dynamics, surface-hopping and mean-field theories and their relation to quantum-classical Liouville dynamics, as well as methods for simulating the dynamics.

Genetic fuzzy system modeling and simulation of vascular behaviour

DEFF Research Database (Denmark)

Tang, Jiaowei; Boonen, Harrie C.M.

Background: The purpose of our project is to identify the rule sets and their interaction within the framework of cardiovascular function. By an iterative process of computational simulation and experimental work, we strive to mimic the physiological basis for cardiovascular adaptive changes in c...... the pressure change of different blood vessels. Conclusion: Genetic fuzzy system is one of potential modeling methods in modeling and simulation of vascular behavior.......Background: The purpose of our project is to identify the rule sets and their interaction within the framework of cardiovascular function. By an iterative process of computational simulation and experimental work, we strive to mimic the physiological basis for cardiovascular adaptive changes...... in cardiovascular disease and ultimately improve pharmacotherapy. For this purpose, novel computational approaches incorporating adaptive properties, auto-regulatory control and rule sets will be assessed, properties that are commonly lacking in deterministic models based on differential equations. We hypothesize...

A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements

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Astrid D. Haase

2016-01-01

Full Text Available Transposons are mobile genetic elements that threaten the survival of species by destabilizing the germline genomes. Limiting the spread of these selfish elements is imperative. Germ cells employ specialized small regulatory RNA pathways to restrain transposon activity. PIWI proteins and Piwi-interacting RNAs (piRNAs silence transposons at the transcriptional and posttranscriptional level with loss-of-function mutant animals universally exhibiting sterility often associated with germ cell defects. This short review aims to illustrate basic strategies of piRNA-guided defense against transposons. Mechanisms of piRNA silencing are most readily studied in Drosophila melanogaster, which serves as a model to delineate molecular concepts and as a reference for mammalian piRNA systems. PiRNA pathways utilize two major strategies to handle the challenges of transposon control: (1 the hard-wired molecular memory of prior transpositions enables recognition of mobile genetic elements and discriminates transposons from host genes; (2 a feed-forward adaptation mechanism shapes piRNA populations to selectively combat the immediate threat of transposon transcripts. In flies, maternally contributed PIWI-piRNA complexes bolster both of these lines of defense and ensure transgenerational immunity. While recent studies have provided a conceptual framework of what could be viewed as an ancient immune system, we are just beginning to appreciate its many molecular innovations.

Generalizing genetical genomics: getting added value from environmental perturbation.

Science.gov (United States)

Li, Yang; Breitling, Rainer; Jansen, Ritsert C

2008-10-01

Genetical genomics is a useful approach for studying the effect of genetic perturbations on biological systems at the molecular level. However, molecular networks depend on the environmental conditions and, thus, a comprehensive understanding of biological systems requires studying them across multiple environments. We propose a generalization of genetical genomics, which combines genetic and sensibly chosen environmental perturbations, to study the plasticity of molecular networks. This strategy forms a crucial step toward understanding why individuals respond differently to drugs, toxins, pathogens, nutrients and other environmental influences. Here we outline a strategy for selecting and allocating individuals to particular treatments, and we discuss the promises and pitfalls of the generalized genetical genomics approach.

Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus.

Science.gov (United States)

Park, Joo Youn; Moon, Bo Youn; Park, Juw Won; Thornton, Justin A; Park, Yong Ho; Seo, Keun Seok

2017-03-21

Discovery of clustered, regularly interspaced, short palindromic repeats and the Cas9 RNA-guided nuclease (CRISPR/Cas9) system provides a new opportunity to create programmable gene-specific antimicrobials that are far less likely to drive resistance than conventional antibiotics. However, the practical therapeutic use of CRISPR/Cas9 is still questionable due to current shortcomings in phage-based delivery systems such as inefficient delivery, narrow host range, and potential transfer of virulence genes by generalized transduction. In this study, we demonstrate genetic engineering strategies to overcome these shortcomings by integrating CRISPR/Cas9 system into a temperate phage genome, removing major virulence genes from the host chromosome, and expanding host specificity of the phage by complementing tail fiber protein. This significantly improved the efficacy and safety of CRISPR/Cas9 antimicrobials to therapeutic levels in both in vitro and in vivo assays. The genetic engineering tools and resources established in this study are expected to provide an efficacious and safe CRISPR/Cas9 antimicrobial, broadly applicable to Staphylococcus aureus.

Optimal Design of Gravity Pipeline Systems Using Genetic Algorithm and Mathematical Optimization

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maryam rohani

2015-03-01

Full Text Available In recent years, the optimal design of pipeline systems has become increasingly important in the water industry. In this study, the two methods of genetic algorithm and mathematical optimization were employed for the optimal design of pipeline systems with the objective of avoiding the water hammer effect caused by valve closure. The problem of optimal design of a pipeline system is a constrained one which should be converted to an unconstrained optimization problem using an external penalty function approach in the mathematical programming method. The quality of the optimal solution greatly depends on the value of the penalty factor that is calculated by the iterative method during the optimization procedure such that the computational effort is simultaneously minimized. The results obtained were used to compare the GA and mathematical optimization methods employed to determine their efficiency and capabilities for the problem under consideration. It was found that the mathematical optimization method exhibited a slightly better performance compared to the GA method.

Genetic analysis of eight population groups living in Taiwan using a 13 X-chromosomal STR loci multiplex system.

Science.gov (United States)

Hwa, Hsiao-Lin; Lee, James Chun-I; Chang, Yih-Yuan; Yin, Hsiang-Yi; Chen, Ya-Hui; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

2011-01-01

A 13 X-chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, and DXS7423) was tested on 1,037 DNA samples from eight population groups currently living in Taiwan. Different distributions of the allelic frequencies in different populations were presented. DXS8377 and DXS101 were the two most polymorphic loci in these eight populations, whereas DXS7423 was the least informative marker in most of the populations studied. The genetic distances between the populations and the constructed phylogenetic tree revealed a long genetic distance between Asian and Caucasian populations as well as isolation of the Tao population. The phylogenetic tree grouped populations into clusters compatible with their ethnogeographic relationships. This 13 X-chromosomal short tandem repeat multiplex system offers a considerable number of polymorphic patterns in different populations. This system can be useful in forensic identification casework and ethnogeographic research.

Possible genetic damage from diagnostic x irradiation. A review

International Nuclear Information System (INIS)

Withrow, T.J.; Andersen, F.A.; Yao, K.T.S.; Stratmeyer, M.E.

1980-08-01

Although it is known that x irradiation is capable of producing mutations and chromosomal abnormalities in experimental systems, there is little or no direct evidence of such phenomena in humans. This report reviews some human genetic diseases and chromosomal abnormalities as well as the evidence for x-ray induced mutations and chromosomal abnormalities in experimental systems. The examination of these areas reveals that spontaneous chromosomal abnormalities and genetic diseases are associated with the same type of DNA damage that x irradiation produces in experimental systems. Therefore, it is concluded that genetic radiation damage in humans may mainfest itself as an increase in the spontaneous genetic diseases rather than as any unique disease

The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model.

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Gilberto Bento

2017-02-01

Full Text Available Negative frequency-dependent selection (NFDS is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. We fine-map one locus associated with D. magna resistance to P. ramosa and genetically characterize two haplotypes of the Pasteuria resistance (PR- locus using de novo genome and transcriptome sequencing. Sequence comparison of PR-locus haplotypes finds dramatic structural polymorphisms between PR-locus haplotypes including a large portion of each haplotype being composed of non-homologous sequences resulting in haplotypes differing in size by 66 kb. The high divergence of PR-locus haplotypes suggest a history of multiple, diverse and repeated instances of structural mutation events and restricted recombination. Annotation of the haplotypes reveals striking differences in gene content. In particular, a group of glycosyltransferase genes that is present in the susceptible but absent in the resistant haplotype. Moreover, in natural populations, we find that the PR-locus polymorphism is associated with variation in resistance to different P. ramosa genotypes, pointing to the PR-locus polymorphism as being responsible for the matching-allele interactions that have been previously described for this system. Our results conclusively identify a genetic basis for the matching-allele interaction observed in a coevolving host-parasite system and provide a first insight into

The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model.

Science.gov (United States)

Bento, Gilberto; Routtu, Jarkko; Fields, Peter D; Bourgeois, Yann; Du Pasquier, Louis; Ebert, Dieter

2017-02-01

Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa. We fine-map one locus associated with D. magna resistance to P. ramosa and genetically characterize two haplotypes of the Pasteuria resistance (PR-) locus using de novo genome and transcriptome sequencing. Sequence comparison of PR-locus haplotypes finds dramatic structural polymorphisms between PR-locus haplotypes including a large portion of each haplotype being composed of non-homologous sequences resulting in haplotypes differing in size by 66 kb. The high divergence of PR-locus haplotypes suggest a history of multiple, diverse and repeated instances of structural mutation events and restricted recombination. Annotation of the haplotypes reveals striking differences in gene content. In particular, a group of glycosyltransferase genes that is present in the susceptible but absent in the resistant haplotype. Moreover, in natural populations, we find that the PR-locus polymorphism is associated with variation in resistance to different P. ramosa genotypes, pointing to the PR-locus polymorphism as being responsible for the matching-allele interactions that have been previously described for this system. Our results conclusively identify a genetic basis for the matching-allele interaction observed in a coevolving host-parasite system and provide a first insight into its molecular basis.

Scientific discovery using genetic programming

DEFF Research Database (Denmark)

Keijzer, Maarten

2001-01-01

programming paradigm. The induction of mathematical expressions based on data is called symbolic regression. In this work, genetic programming is extended to not just fit the data i.e., get the numbers right, but also to get the dimensions right. For this units of measurement are used. The main contribution......Genetic Programming is capable of automatically inducing symbolic computer programs on the basis of a set of examples or their performance in a simulation. Mathematical expressions are a well-defined subset of symbolic computer programs and are also suitable for optimization using the genetic...... in this work can be summarized as: The symbolic expressions produced by genetic programming can be made suitable for analysis and interpretation by using units of measurements to guide or restrict the search. To achieve this, the following has been accomplished: A standard genetic programming system...

System network planning expansion using mathematical programming, genetic algorithms and tabu search

International Nuclear Information System (INIS)

Sadegheih, A.; Drake, P.R.

2008-01-01

In this paper, system network planning expansion is formulated for mixed integer programming, a genetic algorithm (GA) and tabu search (TS). Compared with other optimization methods, GAs are suitable for traversing large search spaces, since they can do this relatively rapidly and because the use of mutation diverts the method away from local minima, which will tend to become more common as the search space increases in size. GA's give an excellent trade off between solution quality and computing time and flexibility for taking into account specific constraints in real situations. TS has emerged as a new, highly efficient, search paradigm for finding quality solutions to combinatorial problems. It is characterized by gathering knowledge during the search and subsequently profiting from this knowledge. The attractiveness of the technique comes from its ability to escape local optimality. The cost function of this problem consists of the capital investment cost in discrete form, the cost of transmission losses and the power generation costs. The DC load flow equations for the network are embedded in the constraints of the mathematical model to avoid sub-optimal solutions that can arise if the enforcement of such constraints is done in an indirect way. The solution of the model gives the best line additions and also provides information regarding the optimal generation at each generation point. This method of solution is demonstrated on the expansion of a 10 bus bar system to 18 bus bars. Finally, a steady-state genetic algorithm is employed rather than generational replacement, also uniform crossover is used

Genetic Algorithm-Based Model Order Reduction of Aeroservoelastic Systems with Consistant States

Science.gov (United States)

Zhu, Jin; Wang, Yi; Pant, Kapil; Suh, Peter M.; Brenner, Martin J.

2017-01-01

This paper presents a model order reduction framework to construct linear parameter-varying reduced-order models of flexible aircraft for aeroservoelasticity analysis and control synthesis in broad two-dimensional flight parameter space. Genetic algorithms are used to automatically determine physical states for reduction and to generate reduced-order models at grid points within parameter space while minimizing the trial-and-error process. In addition, balanced truncation for unstable systems is used in conjunction with the congruence transformation technique to achieve locally optimal realization and weak fulfillment of state consistency across the entire parameter space. Therefore, aeroservoelasticity reduced-order models at any flight condition can be obtained simply through model interpolation. The methodology is applied to the pitch-plant model of the X-56A Multi-Use Technology Testbed currently being tested at NASA Armstrong Flight Research Center for flutter suppression and gust load alleviation. The present studies indicate that the reduced-order model with more than 12× reduction in the number of states relative to the original model is able to accurately predict system response among all input-output channels. The genetic-algorithm-guided approach exceeds manual and empirical state selection in terms of efficiency and accuracy. The interpolated aeroservoelasticity reduced order models exhibit smooth pole transition and continuously varying gains along a set of prescribed flight conditions, which verifies consistent state representation obtained by congruence transformation. The present model order reduction framework can be used by control engineers for robust aeroservoelasticity controller synthesis and novel vehicle design.

Genetic variability in elite barley genotypes based on the agro-morphological characteristics evaluated under irrigated system

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Renato Fernando Amabile

Full Text Available ABSTRACT Recently, researches have shown that the Brazilian savannah has a great potential to supply the demand for barley grains. The purpose of this study was to assess the genetic variability in 39 elite barley (Hordeum vulgare L. genotypes based on the agro-morphological traits of a crop irrigated in the savannah system. An irrigation experiment in the design of complete randomized block with four replicates was conducted at Federal District - Brazil. The evaluated traits were: distance from the last knot to the rachis, distance from the flag leaf to rachis, spike length, number of grains by ear, flag leaf area, plant height, silking, lodging, grain yield, thousand-seed weight, protein content and grain commercial classification. After using analysis of variance the means were used to estimate the genetic dissimilarity among all genotypes pairs based on the Mahalanobis’ generalized distance. Cluster analysis using genetic distance matrix was performed having Unweighted Pair Group Method using Arithmetic Means method (UPGMA as the criteria. Highly significant differences were found among the genotypes for all traits evaluated. The high coefficient of genetic variation indicates the possibility of having genetic gains for all traits. The traits that most contributed to the variability were the flag leaf area and silking, while the protein content and lodging were the traits that contributed the least. Based on the cluster analysis, at least three major groups of similarity were found. There was a clustering trend of two and six-rowed materials. The most divergent genotypes were PFC 2005123, Antártica-1, Nandi and FM 404.

Genetic analysis of Schizosaccharomyces pombe

DEFF Research Database (Denmark)

Ekwall, Karl; Thon, Genevieve

2017-01-01

In this introduction we discuss some basic genetic tools and techniques that are used with the fission yeast Schizosaccharomyces pombe. Genes commonly used for selection or as reporters are discussed, with an emphasis on genes that permit counterselection, intragenic complementation, or colony......-color assays. S. pombe is most stable as a haploid organism. We describe its mating-type system, how to perform genetic crosses and methods for selecting and propagating diploids. We discuss the relative merits of tetrad dissection and random spore preparation in strain construction and genetic analyses...

A niching genetic algorithm applied to a nuclear power plant auxiliary feedwater system surveillance tests policy optimization

International Nuclear Information System (INIS)

Sacco, W.F.; Lapa, Celso M.F.; Pereira, C.M.N.A.; Oliveira, C.R.E. de

2006-01-01

This article extends previous efforts on genetic algorithms (GAs) applied to a nuclear power plant (NPP) auxiliary feedwater system (AFWS) surveillance tests policy optimization. We introduce the application of a niching genetic algorithm (NGA) to this problem and compare its performance to previous results. The NGA maintains a populational diversity during the search process, thus promoting a greater exploration of the search space. The optimization problem consists in maximizing the system's average availability for a given period of time, considering realistic features such as: (i) aging effects on standby components during the tests; (ii) revealing failures in the tests implies on corrective maintenance, increasing outage times; (iii) components have distinct test parameters (outage time, aging factors, etc.) and (iv) tests are not necessarily periodic. We find that the NGA performs better than the conventional GA and the island GA due to a greater exploration of the search space

Recombinase-driver rat lines: tools, techniques, and optogenetic application to dopamine-mediated reinforcement.

Science.gov (United States)

Witten, Ilana B; Steinberg, Elizabeth E; Lee, Soo Yeun; Davidson, Thomas J; Zalocusky, Kelly A; Brodsky, Matthew; Yizhar, Ofer; Cho, Saemi L; Gong, Shiaoching; Ramakrishnan, Charu; Stuber, Garret D; Tye, Kay M; Janak, Patricia H; Deisseroth, Karl

2011-12-08

Currently there is no general approach for achieving specific optogenetic control of genetically defined cell types in rats, which provide a powerful experimental system for numerous established neurophysiological and behavioral paradigms. To overcome this challenge we have generated genetically restricted recombinase-driver rat lines suitable for driving gene expression in specific cell types, expressing Cre recombinase under the control of large genomic regulatory regions (200-300 kb). Multiple tyrosine hydroxylase (Th)::Cre and choline acetyltransferase (Chat)::Cre lines were produced that exhibited specific opsin expression in targeted cell types. We additionally developed methods for utilizing optogenetic tools in freely moving rats and leveraged these technologies to clarify the causal relationship between dopamine (DA) neuron firing and positive reinforcement, observing that optical stimulation of DA neurons in the ventral tegmental area (VTA) of Th::Cre rats is sufficient to support vigorous intracranial self-stimulation (ICSS). These studies complement existing targeting approaches by extending the generalizability of optogenetics to traditionally non-genetically-tractable but vital animal models. Copyright © 2011 Elsevier Inc. All rights reserved.

ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants.

Science.gov (United States)

Patel, Ronak Y; Shah, Neethu; Jackson, Andrew R; Ghosh, Rajarshi; Pawliczek, Piotr; Paithankar, Sameer; Baker, Aaron; Riehle, Kevin; Chen, Hailin; Milosavljevic, Sofia; Bizon, Chris; Rynearson, Shawn; Nelson, Tristan; Jarvik, Gail P; Rehm, Heidi L; Harrison, Steven M; Azzariti, Danielle; Powell, Bradford; Babb, Larry; Plon, Sharon E; Milosavljevic, Aleksandar

2017-01-12

The success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through practice guidelines, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have published standards and guidelines for the interpretation of sequence variants. However, manual application of the guidelines is tedious and prone to human error. Web-based tools and software systems may not only address this problem but also document reasoning and supporting evidence, thus enabling transparency of evidence-based reasoning and resolution of discordant interpretations. In this report, we describe the design, implementation, and initial testing of the Clinical Genome Resource (ClinGen) Pathogenicity Calculator, a configurable system and web service for the assessment of pathogenicity of Mendelian germline sequence variants. The system allows users to enter the applicable ACMG/AMP-style evidence tags for a specific allele with links to supporting data for each tag and generate guideline-based pathogenicity assessment for the allele. Through automation and comprehensive documentation of evidence codes, the system facilitates more accurate application of the ACMG/AMP guidelines, improves standardization in variant classification, and facilitates collaborative resolution of discordances. The rules of reasoning are configurable with gene-specific or disease-specific guideline variations (e.g. cardiomyopathy-specific frequency thresholds and functional assays). The software is modular, equipped with robust application program interfaces (APIs), and available under a free open source license and as a cloud-hosted web service, thus facilitating both stand-alone use and integration with existing variant curation and interpretation systems. The Pathogenicity Calculator is accessible at http

Genetic Variations and their Association with Diseases among ...

African Journals Online (AJOL)

genetics plays in disease, death and infections. The mode of study involved a combination of a retrospective study and the analysis of genetic variation among Kenyan ethnic populations using ABO blood group system. The results showed that there was association between allele frequencies of ABO system and disease ...

Genetic modification and genetic determinism

Science.gov (United States)

Resnik, David B; Vorhaus, Daniel B

2006-01-01

In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions. PMID:16800884

Genetic modification and genetic determinism

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Vorhaus Daniel B

2006-06-01

Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

Genetic Learning of Fuzzy Expert Systems for Decision Support in the Automated Process of Wooden Boards Cutting

Directory of Open Access Journals (Sweden)

Yaroslav MATSYSHYN

2014-03-01

Full Text Available Sawing solid wood (lumber, wooden boards into blanks is an important technological operation, which has significant influence on the efficiency of the woodworking industry as a whole. Selecting a rational variant of lumber cutting is a complex multicriteria problem with many stochastic factors, characterized by incomplete information and fuzzy attributes. About this property by currently used automatic optimizing cross-cut saw is not always rational use of wood raw material. And since the optimization algorithms of these saw functions as a “black box”, their improvement is not possible. Therefore topical the task of developing a new approach to the optimal cross-cutting that takes into account stochastic properties of wood as a material from biological origin. Here we propose a new approach to the problem of lumber optimal cutting in the conditions of uncertainty of lumber quantity and fuzziness lengths of defect-free areas. To account for these conditions, we applied the methods of fuzzy sets theory and used a genetic algorithm to simulate the process of human learning in the implementation the technological operation. Thus, the rules of behavior with yet another defect-free area is defined in fuzzy expert system that can be configured to perform specific production tasks using genetic algorithm. The author's implementation of the genetic algorithm is used to set up the parameters of fuzzy expert system. Working capacity of the developed system verified on simulated and real-world data. Implementation of this approach will make it suitable for the control of automated or fully automatic optimizing cross cutting of solid wood.

A genetic replacement system for selection-based engineering of essential proteins

Science.gov (United States)

2012-01-01

Background Essential genes represent the core of biological functions required for viability. Molecular understanding of essentiality as well as design of synthetic cellular systems includes the engineering of essential proteins. An impediment to this effort is the lack of growth-based selection systems suitable for directed evolution approaches. Results We established a simple strategy for genetic replacement of an essential gene by a (library of) variant(s) during a transformation. The system was validated using three different essential genes and plasmid combinations and it reproducibly shows transformation efficiencies on the order of 107 transformants per microgram of DNA without any identifiable false positives. This allowed for reliable recovery of functional variants out of at least a 105-fold excess of non-functional variants. This outperformed selection in conventional bleach-out strains by at least two orders of magnitude, where recombination between functional and non-functional variants interfered with reliable recovery even in recA negative strains. Conclusions We propose that this selection system is extremely suitable for evaluating large libraries of engineered essential proteins resulting in the reliable isolation of functional variants in a clean strain background which can readily be used for in vivo applications as well as expression and purification for use in in vitro studies. PMID:22898007

Engaging nurses in genetics: the strategic approach of the NHS National Genetics Education and Development Centre.

Science.gov (United States)

Kirk, Maggie; Tonkin, Emma; Burke, Sarah

2008-04-01

The UK government announced the establishment of an NHS National Genetics Education and Development Centre in its Genetics White Paper. The Centre aims to lead and coordinate developments to enhance genetics literacy of health professionals. The nursing program takes a strategic approach based on Ajzen's Theory of Planned Behavior, using the UK nursing genetics competences as the platform for development. The program team uses innovative approaches to raise awareness of the relevance of genetics, working collaboratively with policy stakeholders, as key agents of change in promoting competence. Providing practical help in preparing learning and teaching resources lends further encouragement. Evaluation of the program is dependent on gathering baseline data, and the program has been informed by an education needs analysis. The challenges faced are substantial and necessitate international collaboration where expertise and resources can be shared to produce a global system of influence to facilitate the engagement of non-genetic nurses.

NeuroChip: a microfluidic electrophysiological device for genetic and chemical biology screening of Caenorhabditis elegans adult and larvae.

Directory of Open Access Journals (Sweden)

Chunxiao Hu

Full Text Available Genetic and chemical biology screens of C. elegans have been of enormous benefit in providing fundamental insight into neural function and neuroactive drugs. Recently the exploitation of microfluidic devices has added greater power to this experimental approach providing more discrete and higher throughput phenotypic analysis of neural systems. Here we make a significant addition to this repertoire through the design of a semi-automated microfluidic device, NeuroChip, which has been optimised for selecting worms based on the electrophysiological features of the pharyngeal neural network. We demonstrate this device has the capability to sort mutant from wild-type worms based on high definition extracellular electrophysiological recordings. NeuroChip resolves discrete differences in excitatory, inhibitory and neuromodulatory components of the neural network from individual animals. Worms may be fed into the device consecutively from a reservoir and recovered unharmed. It combines microfluidics with integrated electrode recording for sequential trapping, restraining, recording, releasing and recovering of C. elegans. Thus mutant worms may be selected, recovered and propagated enabling mutagenesis screens based on an electrophysiological phenotype. Drugs may be rapidly applied during the recording thus permitting compound screening. For toxicology, this analysis can provide a precise description of sub-lethal effects on neural function. The chamber has been modified to accommodate L2 larval stages showing applicability for small size nematodes including parasitic species which otherwise are not tractable to this experimental approach. We also combine NeuroChip with optogenetics for targeted interrogation of the function of the neural circuit. NeuroChip thus adds a new tool for exploitation of C. elegans and has applications in neurogenetics, drug discovery and neurotoxicology.

Functional Metagenomic Investigations of the Human Intestinal Microbiota

DEFF Research Database (Denmark)

Moore, Aimee M.; Munck, Christian; Sommer, Morten Otto Alexander

2011-01-01

The human intestinal microbiota encode multiple critical functions impacting human health, including metabolism of dietary substrate, prevention of pathogen invasion, immune system modulation, and provision of a reservoir of antibiotic resistance genes accessible to pathogens. The complexity...... microorganisms, but relatively recently applied to the study of the human commensal microbiota. Metagenomic functional screens characterize the functional capacity of a microbial community, independent of identity to known genes, by subjecting the metagenome to functional assays in a genetically tractable host....... Here we highlight recent work applying this technique to study the functional diversity of the intestinal microbiota, and discuss how an approach combining high-throughput sequencing, cultivation, and metagenomic functional screens can improve our understanding of interactions between this complex...

Soft computing techniques in engineering applications

CERN Document Server

Zhong, Baojiang

2014-01-01

The Soft Computing techniques, which are based on the information processing of biological systems are now massively used in the area of pattern recognition, making prediction & planning, as well as acting on the environment. Ideally speaking, soft computing is not a subject of homogeneous concepts and techniques; rather, it is an amalgamation of distinct methods that confirms to its guiding principle. At present, the main aim of soft computing is to exploit the tolerance for imprecision and uncertainty to achieve tractability, robustness and low solutions cost. The principal constituents of soft computing techniques are probabilistic reasoning, fuzzy logic, neuro-computing, genetic algorithms, belief networks, chaotic systems, as well as learning theory. This book covers contributions from various authors to demonstrate the use of soft computing techniques in various applications of engineering.  

Lipid Uptake, Metabolism, and Transport in the Larval Zebrafish

Directory of Open Access Journals (Sweden)

Vanessa H. Quinlivan

2017-11-01

Full Text Available The developing zebrafish is a well-established model system for studies of energy metabolism, and is amenable to genetic, physiological, and biochemical approaches. For the first 5 days of life, nutrients are absorbed from its endogenous maternally deposited yolk. At 5 days post-fertilization, the yolk is exhausted and the larva has a functional digestive system including intestine, liver, gallbladder, pancreas, and intestinal microbiota. The transparency of the larval zebrafish, and the genetic and physiological similarity of its digestive system to that of mammals make it a promising system in which to address questions of energy homeostasis relevant to human health. For example, apolipoprotein expression and function is similar in zebrafish and mammals, and transgenic animals may be used to examine both the transport of lipid from yolk to body in the embryo, and the trafficking of dietary lipids in the larva. Additionally, despite the identification of many fatty acid and lipid transport proteins expressed by vertebrates, the cell biological processes that mediate the transport of dietary lipids from the intestinal lumen to the interior of enterocytes remain to be elucidated. Genetic tractability and amenability to live imaging and a range of biochemical methods make the larval zebrafish an ideal model in which to address open questions in the field of lipid transport, energy homeostasis, and nutrient metabolism.

Generalizing genetical genomics : getting added value from environmental perturbation

NARCIS (Netherlands)

Li, Yang; Breitling, Rainer; Jansen, Ritsert C.

2008-01-01

Genetical genomics is a useful approach for studying the effect of genetic perturbations on biological systems at the molecular level. However, molecular networks depend on the environmental conditions and, thus, a comprehensive understanding of biological systems requires studying them across

Development of Web-Based Menu Planning Support System and its Solution Using Genetic Algorithm

Science.gov (United States)

Kashima, Tomoko; Matsumoto, Shimpei; Ishii, Hiroaki

2009-10-01

Recently lifestyle-related diseases have become an object of public concern, while at the same time people are being more health conscious. As an essential factor for causing the lifestyle-related diseases, we assume that the knowledge circulation on dietary habits is still insufficient. This paper focuses on everyday meals close to our life and proposes a well-balanced menu planning system as a preventive measure of lifestyle-related diseases. The system is developed by using a Web-based frontend and it provides multi-user services and menu information sharing capabilities like social networking services (SNS). The system is implemented on a Web server running Apache (HTTP server software), MySQL (database management system), and PHP (scripting language for dynamic Web pages). For the menu planning, a genetic algorithm is applied by understanding this problem as multidimensional 0-1 integer programming.

Genetic programming theory and practice XII

CERN Document Server

Riolo, Rick; Kotanchek, Mark

2015-01-01

These contributions, written by the foremost international researchers and practitioners of Genetic Programming (GP), explore the synergy between theoretical and empirical results on real-world problems, producing a comprehensive view of the state of the art in GP. Topics in this volume include: gene expression regulation, novel genetic models for glaucoma, inheritable epigenetics, combinators in genetic programming, sequential symbolic regression, system dynamics, sliding window symbolic regression, large feature problems, alignment in the error space, HUMIE winners, Boolean multiplexer funct

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

Science.gov (United States)

Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S.; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P.; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E.

2018-01-01

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

Directory of Open Access Journals (Sweden)

Guillermo Sánchez-de la Vega

2018-03-01

Full Text Available Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma. Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango. We detected low

Author's Response to Commentaries on: "An Interpretation of Part of Gilbert Gottlieb's Legacy: Developmental Systems Theory Contra Developmental Behavior Genetics"

Science.gov (United States)

Molenaar, Peter C. M.

2015-01-01

In this article, Peter Molenaar responds to three commentaries (this issue) on his article, "An Interpretation of Part of Gilbert Gottlieb's Legacy: Developmental Systems Theory Contra Developmental Behavior Genetics." He addresses aspects of relational developmental systems (RDS) mentioned and questions raised in each of the…

Genetic variation in the endocannabinoid system and response to Cognitive Behavior Therapy for child anxiety disorders

Science.gov (United States)

Coleman, Jonathan R. I.; Roberts, Susanna; Keers, Robert; Breen, Gerome; Bögels, Susan; Creswell, Cathy; Hudson, Jennifer L.; McKinnon, Anna; Nauta, Maaike; Rapee, Ronald M.; Schneider, Silvia; Silverman, Wendy K.; Thastum, Mikael; Waite, Polly; Wergeland, Gro Janne H.; Eley, Thalia C.

2016-01-01

Extinction learning is an important mechanism in the successful psychological treatment of anxiety. Individual differences in response and relapse following Cognitive Behavior Therapy may in part be explained by variability in the ease with which fears are extinguished or the vulnerability of these fears to re‐emerge. Given the role of the endocannabinoid system in fear extinction, this study investigates whether genetic variation in the endocannabinoid system explains individual differences in response to CBT. Children (N = 1,309) with a primary anxiety disorder diagnosis were recruited. We investigated the relationship between variation in the CNR1, CNR2, and FAAH genes and change in primary anxiety disorder severity between pre‐ and post‐treatment and during the follow‐up period in the full sample and a subset with fear‐based anxiety disorder diagnoses. Change in symptom severity during active treatment was nominally associated (P < 0.05) with two SNPs. During the follow‐up period, five SNPs were nominally associated with a poorer treatment response (rs806365 [CNR1]; rs2501431 [CNR2]; rs2070956 [CNR2]; rs7769940 [CNR1]; rs2209172 [FAAH]) and one with a more favorable response (rs6928813 [CNR1]). Within the fear‐based subset, the effect of rs806365 survived multiple testing corrections (P < 0.0016). We found very limited evidence for an association between variants in endocannabinoid system genes and treatment response once multiple testing corrections were applied. Larger, more homogenous cohorts are needed to allow the identification of variants of small but statistically significant effect and to estimate effect sizes for these variants with greater precision in order to determine their potential clinical utility. © 2016 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc. PMID:27346075

Screening for genetically modified organisms sequences in food ...

African Journals Online (AJOL)

We used the Allin 2.0 GMO screening system from Biosmart, Switzerland to screen for the presence of genetically modified food sequences in maize meal samples, fresh fruit and vegetables from some retailers around Gaborone, Botswana. The Allin 2.0 is a multiplex PCR system for the detection of genetically modified ...

Application of genetic algorithms to the maintenance scheduling optimization in a nuclear system basing on reliability

International Nuclear Information System (INIS)

Lapa, Celso M. Franklin; Pereira, Claudio M.N.A.; Mol, Antonio C. de Abreu

1999-01-01

This paper presents a solution based on genetic algorithm and probabilistic safety analysis that can be applied in the optimization of the preventive maintenance politic of nuclear power plant safety systems. The goal of this approach is to improve the average availability of the system through the optimization of the preventive maintenance scheduling politic. The auxiliary feed water system of a two loops pressurized water reactor is used as a sample case, in order to demonstrate the effectiveness of the proposed method. The results, when compared to those obtained by some standard maintenance politics, reveal quantitative gains and operational safety levels. (author)

Somatic and genetic effects

International Nuclear Information System (INIS)

Broerse, J.J.; Barendsen, G.W.; Kal, H.B.; Kogel, A.J. van der

1983-01-01

This book contains the extended abstracts of the contributions of the poster workshop sessions on somatic and genetic effects of the 7th international congress of radiation research. They cover the following main topics: haematopoietic and immune systems, mechanisms of late effects in various tissues, endogenous and exogenous factors in radiation carcinogenesis, teratogenic effects, genetic effects, in vitro transformation, tumour induction in different tissues, carcinogenesis in incorporated tissues, cancer epidemology and risk assessment. refs.; figs.; tabs

Bacillus subtilis as a Platform for Molecular Characterisation of Regulatory Mechanisms of Enterococcus faecalis Resistance against Cell Wall Antibiotics

OpenAIRE

Fang, Chong; Stiegeler, Emanuel; Cook, Gregory M.; Mascher, Thorsten; Gebhard, Susanne

2014-01-01

To combat antibiotic resistance of Enterococcus faecalis, a better understanding of the molecular mechanisms, particularly of antibiotic detection, signal transduction and gene regulation is needed. Because molecular studies in this bacterium can be challenging, we aimed at exploiting the genetically highly tractable Gram-positive model organism Bacillus subtilis as a heterologous host. Two fundamentally different regulators of E. faecalis resistance against cell wall antibiotics, the bacitra...

Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion

OpenAIRE

Lawton, Thomas J.; Rosenzweig, Amy C.

2016-01-01

Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in tradi...

Multicolor bleach-rate imaging enlightens in vivo sterol transport

DEFF Research Database (Denmark)

Wüstner, Daniel; Sage, Daniel

2011-01-01

, dehydroergosterol (DHE) in the genetically tractable model organism Caenorhabditis elegans (C. elegans). DHE is structurally very similar to cholesterol and ergosterol, two sterols used by the sterol-auxotroph nematode. We developed a new computational method measuring fluorophore bleaching kinetics at every pixel...... with a lysosomal marker, GFP-LMP1. Our new methods hold great promise for further studies on endosomal sterol transport in C. elegans....

Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges.

Science.gov (United States)

Kanthaswamy, S

2015-10-01

This review highlights the importance of domestic animal genetic evidence sources, genetic testing, markers and analytical approaches as well as the challenges this field is facing in view of the de facto 'gold standard' human DNA identification. Because of the genetic similarity between humans and domestic animals, genetic analysis of domestic animal hair, saliva, urine, blood and other biological material has generated vital investigative leads that have been admitted into a variety of court proceedings, including criminal and civil litigation. Information on validated short tandem repeat, single nucleotide polymorphism and mitochondrial DNA markers and public access to genetic databases for forensic DNA analysis is becoming readily available. Although the fundamental aspects of animal forensic genetic testing may be reliable and acceptable, animal forensic testing still lacks the standardized testing protocols that human genetic profiling requires, probably because of the absence of monetary support from government agencies and the difficulty in promoting cooperation among competing laboratories. Moreover, there is a lack in consensus about how to best present the results and expert opinion to comply with court standards and bear judicial scrutiny. This has been the single most persistent challenge ever since the earliest use of domestic animal forensic genetic testing in a criminal case in the mid-1990s. Crime laboratory accreditation ensures that genetic test results have the courts' confidence. Because accreditation requires significant commitments of effort, time and resources, the vast majority of animal forensic genetic laboratories are not accredited nor are their analysts certified forensic examiners. The relevance of domestic animal forensic genetics in the criminal justice system is undeniable. However, further improvements are needed in a wide range of supporting resources, including standardized quality assurance and control protocols for sample

Artificial activation of toxin-antitoxin systems as an antibacterial strategy.

Science.gov (United States)

Williams, Julia J; Hergenrother, Paul J

2012-06-01

Toxin-antitoxin (TA) systems are unique modules that effect plasmid stabilization via post-segregational killing of the bacterial host. The genes encoding TA systems also exist on bacterial chromosomes, and it has been speculated that these are involved in a variety of cellular processes. Interest in TA systems has increased dramatically over the past 5 years as the ubiquitous nature of TA genes on bacterial genomes has been revealed. The exploitation of TA systems as an antibacterial strategy via artificial activation of the toxin has been proposed and has considerable potential; however, efforts in this area remain in the early stages and several major questions remain. This review investigates the tractability of targeting TA systems to kill bacteria, including fundamental requirements for success, recent advances, and challenges associated with artificial toxin activation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multi-Objective Optimization Design for a Hybrid Energy System Using the Genetic Algorithm

Directory of Open Access Journals (Sweden)

Myeong Jin Ko

2015-04-01

Full Text Available To secure a stable energy supply and bring renewable energy to buildings within a reasonable cost range, a hybrid energy system (HES that integrates both fossil fuel energy systems (FFESs and new and renewable energy systems (NRESs needs to be designed and applied. This paper presents a methodology to optimize a HES consisting of three types of NRESs and six types of FFESs while simultaneously minimizing life cycle cost (LCC, maximizing penetration of renewable energy and minimizing annual greenhouse gas (GHG emissions. An elitist non-dominated sorting genetic algorithm is utilized for multi-objective optimization. As an example, we have designed the optimal configuration and sizing for a HES in an elementary school. The evolution of Pareto-optimal solutions according to the variation in the economic, technical and environmental objective functions through generations is discussed. The pair wise trade-offs among the three objectives are also examined.

Powertrain Matching and Optimization of Dual-Motor Hybrid Driving System for Electric Vehicle Based on Quantum Genetic Intelligent Algorithm

Directory of Open Access Journals (Sweden)

Yong Wang

2014-01-01

Full Text Available In order to increase the driving range and improve the overall performance of all-electric vehicles, a new dual-motor hybrid driving system with two power sources was proposed. This system achieved torque-speed coupling between the two power sources and greatly improved the high performance working range of the motors; at the same time, continuously variable transmission (CVT was achieved to efficiently increase the driving range. The power system parameters were determined using the “global optimization method”; thus, the vehicle’s dynamics and economy were used as the optimization indexes. Based on preliminary matches, quantum genetic algorithm was introduced to optimize the matching in the dual-motor hybrid power system. Backward simulation was performed on the combined simulation platform of Matlab/Simulink and AVL-Cruise to optimize, simulate, and verify the system parameters of the transmission system. Results showed that quantum genetic algorithms exhibited good global optimization capability and convergence in dealing with multiobjective and multiparameter optimization. The dual-motor hybrid-driving system for electric cars satisfied the dynamic performance and economy requirements of design, efficiently increasing the driving range of the car, having high performance, and reducing energy consumption of 15.6% compared with the conventional electric vehicle with single-speed reducers.

Effect of selective logging on genetic diversity and gene flow in Cariniana legalis sampled from a cacao agroforestry system.

Science.gov (United States)

Leal, J B; Santos, R P; Gaiotto, F A

2014-01-28

The fragments of the Atlantic Forest of southern Bahia have a long history of intense logging and selective cutting. Some tree species, such as jequitibá rosa (Cariniana legalis), have experienced a reduction in their populations with respect to both area and density. To evaluate the possible effects of selective logging on genetic diversity, gene flow, and spatial genetic structure, 51 C. legalis individuals were sampled, representing the total remaining population from the cacao agroforestry system. A total of 120 alleles were observed from the 11 microsatellite loci analyzed. The average observed heterozygosity (0.486) was less than the expected heterozygosity (0.721), indicating a loss of genetic diversity in this population. A high fixation index (FIS = 0.325) was found, which is possibly due to a reduction in population size, resulting in increased mating among relatives. The maximum (1055 m) and minimum (0.095 m) distances traveled by pollen or seeds were inferred based on paternity tests. We found 36.84% of unique parents among all sampled seedlings. The progenitors of the remaining seedlings (63.16%) were most likely out of the sampled area. Positive and significant spatial genetic structure was identified in this population among classes 10 to 30 m away with an average coancestry coefficient between pairs of individuals of 0.12. These results suggest that the agroforestry system of cacao cultivation is contributing to maintaining levels of diversity and gene flow in the studied population, thus minimizing the effects of selective logging.

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

Science.gov (United States)

Kim, Sun; Chatr-aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer; Wilbur, W. John; Comeau, Donald C.; Dolinski, Kara; Tyers, Mike

2017-01-01

A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information. Computational text-mining methods offer the potential to augment and accelerate manual curation. To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task. This was a non-competitive, cooperative task in which the participants worked together to build BioC-compatible modules into an integrated pipeline to assist BioGRID curators. As an integral part of this task, a test collection of full text articles was developed that contained both biological entity annotations (gene/protein and organism/species) and molecular interaction annotations (protein–protein and genetic interactions (PPIs and GIs)). This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two major model organisms, namely budding yeast and human. The BioC-BioGRID corpus contains annotations for 6409 mentions of genes and their Entrez Gene IDs, 186 mentions of organism names and their NCBI Taxonomy IDs, 1867 mentions of PPIs and 701 annotations of PPI experimental evidence statements, 856 mentions of GIs and 399 annotations of GI evidence statements. The purpose, characteristics and possible future

Genetic influence on prolonged gestation

DEFF Research Database (Denmark)

Laursen, Maja; Bille, Camilla; Olesen, Annette Wind

2004-01-01

OBJECTIVE: The purpose of this study was to test a possible genetic component to prolonged gestation. STUDY DESIGN: The gestational duration of single, first pregnancies by both female and male twins was obtained by linking the Danish Twin Registry, The Danish Civil Registration System, and the D...... factors. CONCLUSION: Maternal genes influence prolonged gestation. However, a substantial paternal genetic influence through the fetus was not found....

Environmental chemical mutagens and genetic risks: Lessons from radiation genetics

International Nuclear Information System (INIS)

Sankaranarayanan, K.

1996-01-01

The last three decades have witnessed substantial progress in the development and use of a variety of in vitro and in vivo assay systems for the testing of environmental chemicals which may pose a mutagenic hazard to humans. This is also true of basic studies in chemical mutagenesis on mechanisms, DNA repair, molecular dosimetry, structure-activity relationships, etc. However, the field of quantitative evaluation of genetic risks of environmental chemicals to humans is still in it infancy. This commentary addresses the question of how our experience in estimating genetic risks of exposure to ionizing radiation can be helpful in similar endeavors with environmental chemical mutagens. 24 refs., 3 tabs

Quantum Genetics in terms of Quantum Reversible Automata and Quantum Computation of Genetic Codes and Reverse Transcription

CERN Document Server

Baianu,I C

2004-01-01

The concepts of quantum automata and quantum computation are studied in the context of quantum genetics and genetic networks with nonlinear dynamics. In previous publications (Baianu,1971a, b) the formal concept of quantum automaton and quantum computation, respectively, were introduced and their possible implications for genetic processes and metabolic activities in living cells and organisms were considered. This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu,1971b; 1977; 1987; 2004; Baianu et al, 2004). The notions of topological semigroup, quantum automaton, or quantum computer, were then suggested with a view to their potential applications to the analogous simulation of biological systems, and especially genetic activities and nonlinear dynamics in genetic networks. Further, detailed studies of nonlinear dynamics in genetic networks were carried out in categories of n-valued, Lukasiewicz Logic Algebra...

Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks

Directory of Open Access Journals (Sweden)

Zarnescu Daniela C

2008-11-01

Full Text Available Abstract Background In Drosophila, the genes sticky and dFmr1 have both been shown to regulate cytoskeletal dynamics and chromatin structure. These genes also genetically interact with Argonaute family microRNA regulators. Furthermore, in mammalian systems, both genes have been implicated in neuronal development. Given these genetic and functional similarities, we tested Drosophila sticky and dFmr1 for a genetic interaction and measured whole genome expression in both mutants to assess similarities in gene regulation. Results We found that sticky mutations can dominantly suppress a dFmr1 gain-of-function phenotype in the developing eye, while phenotypes produced by RNAi knock-down of sticky were enhanced by dFmr1 RNAi and a dFmr1 loss-of-function mutation. We also identified a large number of transcripts that were misexpressed in both mutants suggesting that sticky and dFmr1 gene products similarly regulate gene expression. By integrating gene expression data with a protein-protein interaction network, we found that mutations in sticky and dFmr1 resulted in misexpression of common gene networks, and consequently predicted additional specific phenotypes previously not known to be associated with either gene. Further phenotypic analyses validated these predictions. Conclusion These findings establish a functional link between two previously unrelated genes. Microarray analysis indicates that sticky and dFmr1 are both required for regulation of many developmental genes in a variety of cell types. The diversity of transcripts regulated by these two genes suggests a clear cause of the pleiotropy that sticky and dFmr1 mutants display and provides many novel, testable hypotheses about the functions of these genes. As both of these genes are implicated in the development and function of the mammalian brain, these results have relevance to human health as well as to understanding more general biological processes.

Genetic Local Search for Optimum Multiuser Detection Problem in DS-CDMA Systems

Science.gov (United States)

Wang, Shaowei; Ji, Xiaoyong

Optimum multiuser detection (OMD) in direct-sequence code-division multiple access (DS-CDMA) systems is an NP-complete problem. In this paper, we present a genetic local search algorithm, which consists of an evolution strategy framework and a local improvement procedure. The evolution strategy searches the space of feasible, locally optimal solutions only. A fast iterated local search algorithm, which employs the proprietary characteristics of the OMD problem, produces local optima with great efficiency. Computer simulations show the bit error rate (BER) performance of the GLS outperforms other multiuser detectors in all cases discussed. The computation time is polynomial complexity in the number of users.

toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research.

Science.gov (United States)

Rhee, David B; Croken, Matthew McKnight; Shieh, Kevin R; Sullivan, Julie; Micklem, Gos; Kim, Kami; Golden, Aaron

2015-01-01

Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it is still not fully known which genetic or epigenetic factors are involved in regulating virulence traits of T. gondii. There are on-going efforts to elucidate the mechanisms regulating the stage transition process via the application of high-throughput epigenomics, genomics and proteomics techniques. Given the range of experimental conditions and the typical yield from such high-throughput techniques, a new challenge arises: how to effectively collect, organize and disseminate the generated data for subsequent data analysis. Here, we describe toxoMine, which provides a powerful interface to support sophisticated integrative exploration of high-throughput experimental data and metadata, providing researchers with a more tractable means toward understanding how genetic and/or epigenetic factors play a coordinated role in determining pathogenicity of T. gondii. As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward user interaction. Furthermore, toxoMine allows users to define their own parameters during the search process that gives users near-limitless search and query capabilities. The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine complements the major community database ToxoDB by providing a data warehouse that enables more extensive integrative studies for T. gondii. Given all these factors, we believe it will become an indispensable resource to the greater infectious disease research community. © The Author(s) 2015. Published by Oxford University Press.

Supply of genetic information--amount, format, and frequency.

Science.gov (United States)

Misztal, I; Lawlor, T J

1999-05-01

The volume and complexity of genetic information is increasing because of new traits and better models. New traits may include reproduction, health, and carcass. More comprehensive models include the test day model in dairy cattle or a growth model in beef cattle. More complex models, which may include nonadditive effects such as inbreeding and dominance, also provide additional information. The amount of information per animal may increase drastically if DNA marker typing becomes routine and quantitative trait loci information is utilized. In many industries, evaluations are run more frequently. They result in faster genetic progress and improved management and marketing opportunities but also in extra costs and information overload. Adopting new technology and making some organizational changes can help realize all the added benefits of the improvements to the genetic evaluation systems at an acceptable cost. Continuous genetic evaluation, in which new records are accepted and breeding values are updated continuously, will relieve time pressures. An online mating system with access to both genetic and marketing information can result in mating recommendations customized for each user. Such a system could utilize inbreeding and dominance information that cannot efficiently be accommodated in the current sire summaries or off-line mating programs. The new systems will require a new organizational approach in which the task of scientists and technicians will not be simply running the evaluations but also providing the research, design, supervision, and maintenance required in the entire system of evaluation, decision making, and distribution.

Multiple-Active Multiple-Passive Antenna Systems and Applications

DEFF Research Database (Denmark)

Tsakalaki, Elpiniki

2013-01-01

-passive (MAMP) antenna topologies, as explained in Sect. 8.1. Then, Sect. 8.2 proposes MAMP antenna structures with application to reconfigurable MIMO transmission in the presence of antenna mutual coupling under poor scattering channel conditions. For this purpose, the section presents an adaptive MAMP antenna...... system capable of changing its transmission parameters via passive radiators attached to tunable loads, according to the structure of the RF propagation channel. The hybrid MAMP array structure can be tractably analyzed using the active element response vector (instead of the classical steering vector...... adaptive MAMP system can be limited to practical dimensions whereas the passive antennas require no extra RF hardware, thus meeting the cost, space, and power constrains of the users’ mobile terminals. The simulation results show that the adaptive MAMP system, thanks to its “adaptivity”, is able to achieve...

Genetic line comparisons and genetic parameters for endoparasite infections and test-day milk production traits.

Science.gov (United States)

May, Katharina; Brügemann, Kerstin; Yin, Tong; Scheper, Carsten; Strube, Christina; König, Sven

2017-09-01

Keeping dairy cows in grassland systems relies on detailed analyses of genetic resistance against endoparasite infections, including between- and within-breed genetic evaluations. The objectives of this study were (1) to compare different Black and White dairy cattle selection lines for endoparasite infections and (2) the estimation of genetic (co)variance components for endoparasite and test-day milk production traits within the Black and White cattle population. A total of 2,006 fecal samples were taken during 2 farm visits in summer and autumn 2015 from 1,166 cows kept in 17 small- and medium-scale organic and conventional German grassland farms. Fecal egg counts were determined for gastrointestinal nematodes (FEC-GIN) and flukes (FEC-FLU), and fecal larvae counts for the bovine lungworm Dictyocaulus viviparus (FLC-DV). The lowest values for gastrointestinal nematode infections were identified for genetic lines adopted to pasture-based production systems, especially selection lines from New Zealand. Heritabilities were low for FEC-GIN (0.05-0.06 ± 0.04) and FLC-DV (0.05 ± 0.04), but moderate for FEC-FLU (0.33 ± 0.06). Almost identical heritabilities were estimated for different endoparasite trait transformations (log-transformation, square root). The genetic correlation between FEC-GIN and FLC-DV was 1.00 ± 0.60, slightly negative between FEC-GIN and FEC-FLU (-0.10 ± 0.27), and close to zero between FLC-DV and FEC-FLU (0.03 ± 0.30). Random regression test-day models on a continuous time scale [days in milk (DIM)] were applied to estimate genetic relationships between endoparasite and longitudinal test-day production traits. Genetic correlations were negative between FEC-GIN and milk yield (MY) until DIM 85, and between FEC-FLU and MY until DIM 215. Genetic correlations between FLC-DV and MY were negative throughout lactation, indicating improved disease resistance for high-productivity cows. Genetic relationships between FEC-GIN and FEC-FLU with milk

A reliability model of the Angra 1 power system by the device of stages optimized by genetic algorithms

International Nuclear Information System (INIS)

Crossetti, Patricia Guimaraes

2006-01-01

This thesis proposes a probabilistic model to perform the reliability analysis of nuclear power plant systems under aging. This work analyses the Angra 1 power system. Systems subject to aging consist of components whose failure rates are not all constant, thus generating Non-Markovian models. Genetic algorithms were used for optimizing the application of the device of stages. Two approaches were used in the optimization, MCEF and MCEV. The results obtained for the Angra 1 power system show that the probability of a station blackout is negligible. (author)

Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels.

Science.gov (United States)

Srirangan, Kajan; Bruder, Mark; Akawi, Lamees; Miscevic, Dragan; Kilpatrick, Shane; Moo-Young, Murray; Chou, C Perry

2017-09-01

Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].

Organoid Models of Human and Mouse Ductal Pancreatic Cancer

Science.gov (United States)

Boj, Sylvia F.; Hwang, Chang-Il; Baker, Lindsey A.; Chio, Iok In Christine; Engle, Dannielle D.; Corbo, Vincenzo; Jager, Myrthe; Ponz-Sarvise, Mariano; Tiriac, Hervé; Spector, Mona S.; Gracanin, Ana; Oni, Tobiloba; Yu, Kenneth H.; van Boxtel, Ruben; Huch, Meritxell; Rivera, Keith D.; Wilson, John P.; Feigin, Michael E.; Öhlund, Daniel; Handly-Santana, Abram; Ardito-Abraham, Christine M.; Ludwig, Michael; Elyada, Ela; Alagesan, Brinda; Biffi, Giulia; Yordanov, Georgi N.; Delcuze, Bethany; Creighton, Brianna; Wright, Kevin; Park, Youngkyu; Morsink, Folkert H.M.; Molenaar, I. Quintus; Borel Rinkes, Inne H.; Cuppen, Edwin; Hao, Yuan; Jin, Ying; Nijman, Isaac J.; Iacobuzio-Donahue, Christine; Leach, Steven D.; Pappin, Darryl J.; Hammell, Molly; Klimstra, David S.; Basturk, Olca; Hruban, Ralph H.; Offerhaus, George Johan; Vries, Robert G.J.; Clevers, Hans; Tuveson, David A.

2015-01-01

SUMMARY Pancreatic cancer is one of the most lethal malignancies due to its late diagnosis and limited response to treatment. Tractable methods to identify and interrogate pathways involved in pancreatic tumorigenesis are urgently needed. We established organoid models from normal and neoplastic murine and human pancreas tissues. Pancreatic organoids can be rapidly generated from resected tumors and biopsies, survive cryopreservation and exhibit ductal- and disease stage-specific characteristics. Orthotopically transplanted neoplastic organoids recapitulate the full spectrum of tumor development by forming early-grade neoplasms that progress to locally invasive and metastatic carcinomas. Due to their ability to be genetically manipulated, organoids are a platform to probe genetic cooperation. Comprehensive transcriptional and proteomic analyses of murine pancreatic organoids revealed genes and pathways altered during disease progression. The confirmation of many of these protein changes in human tissues demonstrates that organoids are a facile model system to discover characteristics of this deadly malignancy. PMID:25557080

Genetic classes and genetic categories : Protecting genetic groups through data protection law

NARCIS (Netherlands)

Hallinan, Dara; de Hert, Paul; Taylor, L.; Floridi, L.; van der Sloot, B.

2017-01-01

Each person shares genetic code with others. Thus, one individual’s genome can reveal information about other individuals. When multiple individuals share aspects of genetic architecture, they form a ‘genetic group’. From a social and legal perspective, two types of genetic group exist: Those which

Plant Genetic Resources: Selected Issues from Genetic Erosion to Genetic Engineering

Directory of Open Access Journals (Sweden)

Karl Hammer

2008-04-01

Full Text Available Plant Genetic Resources (PGR continue to play an important role in the development of agriculture. The following aspects receive a special consideration:1. Definition. The term was coined in 1970. The genepool concept served as an important tool in the further development. Different approaches are discussed.2. Values of Genetic Resources. A short introduction is highlighting this problem and stressing the economic usfulness of PGR.3. Genetic Erosion. Already observed by E. Baur in 1914, this is now a key issue within PGR. The case studies cited include Ethiopia, Italy, China, S Korea, Greece and S. Africa. Modern approaches concentrate on allelic changes in varieties over time but neglect the landraces. The causes and consequences of genetic erosion are discussed.4. Genetic Resources Conservation. Because of genetic erosion there is a need for conservation. PGR should be consigned to the appropriate method of conservation (ex situ, in situ, on-farm according to the scientific basis of biodiversity (genetic diversity, species diversity, ecosystem diversity and the evolutionary status of plants (cultivated plants, weeds, related wild plants (crop wild relatives.5. GMO. The impact of genetically engineered plants on genetic diversity is discussed.6. The Conclusions and Recommendations stress the importance of PGR. Their conservation and use are urgent necessities for the present development and future survival of mankind.

GeVaDSs – decision support system for novel Genetic Vaccine development process

Directory of Open Access Journals (Sweden)

Blazewicz Jacek

2012-05-01

Full Text Available Abstract Background The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and implemented molecular and immunology methods, and designed support tools for immunization data storage and analyses. Such collection can create a unique opportunity for immunologists to analyse data delivered from their laboratories. Results We designed and implemented GeVaDSs (Genetic Vaccine Decision Support system an interactive system for efficient storage, integration, retrieval and representation of data. Moreover, GeVaDSs allows for relevant association and interpretation of data, and thus for knowledge-based generation of testable hypotheses of vaccine responses. Conclusions GeVaDSs has been tested by several laboratories in Europe, and proved its usefulness in vaccine analysis. Case study of its application is presented in the additional files. The system is available at: http://gevads.cs.put.poznan.pl/preview/(login: viewer, password: password.

TID and I-TD controller design for magnetic levitation system using genetic algorithm

Directory of Open Access Journals (Sweden)

Debdoot Sain

2016-09-01

Full Text Available This article is about the design of controllers for magnetic levitation (Maglev system in both simulation and real time. Local linearization around the equilibrium point has been done for the nonlinear Maglev system to obtain a linearized model transfer function. In this study, the design of integral-tilted-derivative (I-TD controller has been proposed for the Maglev system and its performance is compared with conventional tilted-integral-derivative (TID controller. In this study, TID controller parameters have been optimized through genetic algorithm (GA and those set of values have been employed for the design of I-TD controller. A performance comparison between TID and I-TD controller is then investigated. The analysis shows the superiority of I-TD controller over TID controller in terms of maximum overshoot, gain margin and phase margin. The settling time remains almost same in both the cases. In future, a detailed study of robustness in presence of model uncertainties will be incorporated as a scope of further research.

Statistics for Learning Genetics

Science.gov (United States)

Charles, Abigail Sheena

, although the necessity for infusing these quantitative subjects with genetics and, overall, the biological sciences is growing (topics including synthetic biology, molecular systems biology and phylogenetics) there remains little time in the semester to be dedicated to the consolidation of learning and understanding.

Association of Systemic Lupus Erythematosus Clinical Features with European Population Genetic Substructure

Czech Academy of Sciences Publication Activity Database

Alonso-Perez, E.; Suarez-Gestal, M.; Calaza, M.; Witte, T.; Papasteriades, Ch.; Marchini, M.; Migliaresi, S.; Kovacs, A.; Ordi-Ros, J.; Bijl, M.; Santos, M.J.; Růžičková, Šárka; Pullmann, R.; Carreira, P.; Skopouli, F.N.; D'Alfonso, S.; Sebastiani, G.D.; Suarez, A.; Blanco, F.J.; Gomez-Reino, J.J.; Gonzalez, A.

2012-01-01

Roč. 6, č. 12 (2012), e29033 E-ISSN 1932-6203 Institutional research plan: CEZ:AV0Z50520701 Keywords : erythematosus * genetic factors * genotype phenotype correlation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.730, year: 2012

Genetic and nutrition development of indigenous chicken in Africa

DEFF Research Database (Denmark)

Khobondo, J O; Muasya, T K; Miyumo, S

2015-01-01

This review gives insights into genetic and feeding regime development for indigenous chicken genetic resources. We highlight and combine confirming evidence of genetic diversity and variability using morphological and molecular techniques. We further discuss previous past and current genetic...... requirement for indigenous chicken and report nutritive contents of various local feedstuffs under various production systems. Various conservation strategies for sustainable utilization are hereby reviewed...

Modeling life the mathematics of biological systems

CERN Document Server

Garfinkel, Alan; Guo, Yina

2017-01-01

From predator-prey populations in an ecosystem, to hormone regulation within the body, the natural world abounds in dynamical systems that affect us profoundly. This book develops the mathematical tools essential for students in the life sciences to describe these interacting systems and to understand and predict their behavior. Complex feedback relations and counter-intuitive responses are common in dynamical systems in nature; this book develops the quantitative skills needed to explore these interactions. Differential equations are the natural mathematical tool for quantifying change, and are the driving force throughout this book. The use of Euler’s method makes nonlinear examples tractable and accessible to a broad spectrum of early-stage undergraduates, thus providing a practical alternative to the procedural approach of a traditional Calculus curriculum. Tools are developed within numerous, relevant examples, with an emphasis on the construction, evaluation, and interpretation of mathematical models ...

Noise in Genetic Toggle Switch Models

Directory of Open Access Journals (Sweden)

Andrecut M.

2006-06-01

Full Text Available In this paper we study the intrinsic noise effect on the switching behavior of a simple genetic circuit corresponding to the genetic toggle switch model. The numerical results obtained from a noisy mean-field model are compared to those obtained from the stochastic Gillespie simulation of the corresponding system of chemical reactions. Our results show that by using a two step reaction approach for modeling the transcription and translation processes one can make the system to lock in one of the steady states for exponentially long times.

Do species conservation assessments capture genetic diversity?

Directory of Open Access Journals (Sweden)

Malin C. Rivers

2014-12-01

Full Text Available The best known system for classifying threat status of species, the IUCN Red List, currently lacks explicit considerations of genetic diversity, and consequently may not account for potential adaptation of species to future environmental change. To address this gap, we integrate range-wide genetic analysis with IUCN Red List assessments.We calculated the loss of genetic diversity under simulated range loss for species of Delonix (Leguminosae. Simulated range loss involved random loss of populations and was intended to model ongoing habitat destruction. We found a strong relationship between loss of genetic diversity and range. Moreover, we found correspondence between levels of genetic diversity and thresholds for ‘non-threatened’ versus ‘threatened’ IUCN Red List categories.Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved. Keywords: Conservation assessment, Conservation genetics, Extinction risk, Genetic diversity, IUCN Red List, Range

Adults' perceptions of genetic counseling and genetic testing.

Science.gov (United States)

Houfek, Julia Fisco; Soltis-Vaughan, Brigette S; Atwood, Jan R; Reiser, Gwendolyn M; Schaefer, G Bradley

2015-02-01

This study described the perceptions of genetic counseling and testing of adults (N = 116) attending a genetic education program. Understanding perceptions of genetic counseling, including the importance of counseling topics, will contribute to patient-focused care as clinical genetic applications for common, complex disorders evolve. Participants completed a survey addressing: the importance of genetic counseling topics, benefits and negative effects of genetic testing, and sharing test results. Topics addressing practical information about genetic conditions were rated most important; topics involving conceptual genetic/genomic principles were rated least important. The most frequently identified benefit and negative effect of testing were prevention/early detection/treatment and psychological distress. Participants perceived that they were more likely to share test results with first-degree than other relatives. Findings suggest providing patients with practical information about genetic testing and genetic contributions to disease, while also determining whether their self-care abilities would be enhanced by teaching genetic/genomic principles. Copyright © 2014 Elsevier Inc. All rights reserved.

Dynamical systems on networks a tutorial

CERN Document Server

Porter, Mason A

2016-01-01

This volume is a tutorial for the study of dynamical systems on networks. It discusses both methodology and models, including spreading models for social and biological contagions. The authors focus especially on “simple” situations that are analytically tractable, because they are insightful and provide useful springboards for the study of more complicated scenarios. This tutorial, which also includes key pointers to the literature, should be helpful for junior and senior undergraduate students, graduate students, and researchers from mathematics, physics, and engineering who seek to study dynamical systems on networks but who may not have prior experience with graph theory or networks. Mason A. Porter is Professor of Nonlinear and Complex Systems at the Oxford Centre for Industrial and Applied Mathematics, Mathematical Institute, University of Oxford, UK. He is also a member of the CABDyN Complexity Centre and a Tutorial Fellow of Somerville College. James P. Gleeson is Professor of Industrial and Appli...

Multi-objective optimization of an underwater compressed air energy storage system using genetic algorithm

International Nuclear Information System (INIS)

Cheung, Brian C.; Carriveau, Rupp; Ting, David S.K.

2014-01-01

This paper presents the findings from a multi-objective genetic algorithm optimization study on the design parameters of an underwater compressed air energy storage system (UWCAES). A 4 MWh UWCAES system was numerically simulated and its energy, exergy, and exergoeconomics were analysed. Optimal system configurations were determined that maximized the UWCAES system round-trip efficiency and operating profit, and minimized the cost rate of exergy destruction and capital expenditures. The optimal solutions obtained from the multi-objective optimization model formed a Pareto-optimal front, and a single preferred solution was selected using the pseudo-weight vector multi-criteria decision making approach. A sensitivity analysis was performed on interest rates to gauge its impact on preferred system designs. Results showed similar preferred system designs for all interest rates in the studied range. The round-trip efficiency and operating profit of the preferred system designs were approximately 68.5% and $53.5/cycle, respectively. The cost rate of the system increased with interest rates. - Highlights: • UWCAES system configurations were developed using multi-objective optimization. • System was optimized for energy efficiency, exergy, and exergoeconomics • Pareto-optimal solution surfaces were developed at different interest rates. • Similar preferred system configurations were found at all interest rates studied

Non-genetic factors affecting growth performance and carcass ...

African Journals Online (AJOL)

Bekezela

There is a paucity of information on non-genetic ... herds. These data were obtained from the Integrated Recording and Genetic Information Systems .... performance is determined by muscle fibre characteristics (Larzul et al., 1997), which are ...

Molecular – genetic variance of RH blood group system within human population of Bosnia and Herzegovina

Directory of Open Access Journals (Sweden)

Lejla Lasić

2013-02-01

Full Text Available There are two major theories for inheritance of Rh blood group system: Fisher - Race theory and Wiener theory. Aim of this study was identifying frequency of RHDCE alleles in Bosnian - Herzegovinian population and introduction of this method in screening for Rh phenotype in B&H since this type of analysis was not used for blood typing in B&H before. Rh blood group was typed by Polymerase Chain Reaction, using the protocols and primers previously established by other authors, then carrying out electrophoresis in 2-3% agarose gel. Percentage of Rh positive individuals in our sample is 84.48%, while the percentage of Rh negative individuals is 15.52%. Inter-rater agreement statistic showed perfect agreement (K=1 between the results of Rh blood system detection based on serological and molecular-genetics methods. In conclusion, molecular - genetic methods are suitable for prenatal genotyping and specific cases while standard serological method is suitable for high-throughput of samples.

Role of genetics in infection-associated arthritis.

Science.gov (United States)

Benham, Helen; Robinson, Philip C; Baillet, Athan C; Rehaume, Linda M; Thomas, Ranjeny

2015-04-01

Genetic discoveries in arthritis and their associated biological pathways spanning the innate and adaptive immune system demonstrate the strong association between susceptibility to arthritis and control of exogenous organisms. The canonical theory of the aetiology of immune-mediated arthritis and other immune-mediated diseases is that the introduction of exogenous antigenic stimuli to a genetically susceptible host sets up the environment for an abnormal immune response manifesting as disease. A disruption in host-microbe homeostasis driven by disease-associated genetic variants could ultimately provide the source of exogenous antigen triggering disease development. We discuss genetic variants impacting the innate and adaptive arms of the immune system and their relationship to microbial control and arthritic disease. We go on to consider the evidence for a relationship between HLA-B27, infection and arthritis, and then emerging evidence for an interaction between microbiota and rheumatoid arthritis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Inducible and transmissible genetic events and pediatric tumors of the nervous system

International Nuclear Information System (INIS)

Rice, Jerry M.

2006-01-01

Tumors of the nervous system most often occur in both children and adults as sporadic events with no family history of the disease, but they are also among the clinical manifestations of a significant number of familial cancer syndromes, including familial retinoblastoma, neurofibromatosis 1 and 2, tuberous sclerosis, and Cowden, Turcot, Li-Fraumeni and nevoid basal cell carcinoma (Gorlin) syndromes. All of these syndromes involve transmissible genetic risk resulting from loss of a functional allele, or inheritance of a structurally defective allele, of a specific gene. These genes include RB1, NF1, NF2, TSC1, TSC2, TP53, PTEN, APC, hMLH1, hPSM2, and PTCH, most of which function as tumor suppressor genes. The same genes are also observed in mutated and inactive forms, or are deleted, in tumor cells in sporadic cases of the same tumors. The nature of the mutational events that give rise to these inactivated alleles suggests a possible role of environmental mutagens in their causation. However, only external ionizing radiation at high doses is clearly established as an environmental cause of brain, nerve and meningeal tumors in humans. Transplacental carcinogenesis studies in rodents and other species emphasize the extraordinary susceptibility of the developing mammalian nervous system to carcinogenesis, but the inverse relationship of latency to dose suggests that low transplacental exposures to genotoxicants are more likely to result in brain tumors late in life, rather than in childhood. While not all neurogenic tumor-related genes in humans have similar effects in experimental rodents, genetically engineered mice (GEM) increasingly provide useful insights into the combined effects of multiple tumor suppressor genes and of gene-environment interactions in the genesis of brain tumors, especially pediatric brain tumors such as medulloblastoma. (author)

Developmental Systems Theory and the Person-Oriented Approach. Commentary on: "An Interpretation of Part of Gilbert Gottlieb's Legacy: Developmental Systems Theory Contra Developmental Behavior Genetics"

Science.gov (United States)

Bergman, Lars R.

2015-01-01

Molenaar's (2015) article concerns Developmental Systems Theory (DST) in relation to behavior genetics and he presents implications of DST for empirical research, especially the need for subject-specific studies. In this commentary, the article is discussed from a broader developmental science perspective, particularly regarded through the lens of…

The relationship between genetic merit for yield and live weight, condition score, and energy balance of spring calving Holstein Friesian dairy cows on grass based systems of milk production

NARCIS (Netherlands)

Buckley, F.; Dillon, P.; Rath, M.; Veerkamp, R.F.

2000-01-01

The objectives of this study were to estimate the effects of genetic merit for milk yield on energy balance, DM intake (DMI), and fertility for cows managed on three different grass-based feeding systems and to estimate possible interactions between genetic merit and feeding system. Individual

Towards a genetic architecture of cryptic genetic variation

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics; Volume 84; Issue 3. Towards a genetic architecture of cryptic genetic variation and genetic assimilation: the contribution of K. G. Bateman. Ian Dworkin. Commentary on J. Genet. Classic Volume 84 Issue 3 December 2005 pp 223-226 ...

Genetics Home Reference: rhabdoid tumor predisposition syndrome

Science.gov (United States)

... rare type of ovarian cancer called small cell cancer of the ovary hypercalcemic type (SCCOHT). Related Information What does it mean if a disorder seems to run in my family? What is the prognosis of a genetic condition? Genetic ... Cancer Institute: Childhood Central Nervous System Atypical Teratoid/Rhabdoid ...

Analytically tractable climate-carbon cycle feedbacks under 21st century anthropogenic forcing

Science.gov (United States)

Lade, Steven J.; Donges, Jonathan F.; Fetzer, Ingo; Anderies, John M.; Beer, Christian; Cornell, Sarah E.; Gasser, Thomas; Norberg, Jon; Richardson, Katherine; Rockström, Johan; Steffen, Will

2018-05-01

Changes to climate-carbon cycle feedbacks may significantly affect the Earth system's response to greenhouse gas emissions. These feedbacks are usually analysed from numerical output of complex and arguably opaque Earth system models. Here, we construct a stylised global climate-carbon cycle model, test its output against comprehensive Earth system models, and investigate the strengths of its climate-carbon cycle feedbacks analytically. The analytical expressions we obtain aid understanding of carbon cycle feedbacks and the operation of the carbon cycle. Specific results include that different feedback formalisms measure fundamentally the same climate-carbon cycle processes; temperature dependence of the solubility pump, biological pump, and CO2 solubility all contribute approximately equally to the ocean climate-carbon feedback; and concentration-carbon feedbacks may be more sensitive to future climate change than climate-carbon feedbacks. Simple models such as that developed here also provide workbenches for simple but mechanistically based explorations of Earth system processes, such as interactions and feedbacks between the planetary boundaries, that are currently too uncertain to be included in comprehensive Earth system models.

Optimization of Electrical System for Offshore Wind Farms via a Genetic Algorithm Approach

DEFF Research Database (Denmark)

Zhao, Menghua

, and the LTC limitation of transformers, the power generation limits and the voltage operation range are considered as the constraints. The optimization method combined with probabilistic analysis is used to obtain the capacity of a given wind farm site. The OES-OWF is approached by Genetic Algorithm (GA...... to very different costs, system reliability, power quality, and power losses etc. Therefore, the optimization of electrical system design for offshore wind farms becomes more and more necessary. There are two tasks in this project: 1) the first one is to construct an algorithm for finding the capacity......). This platform is based on a knowledge database, and composed of several functional modules such as cost calculation, reliability evaluation, losses calculation, AC-DC integrated load flow algorithm etc. All these modules are based on a spreadsheet database which provides an interface for users to input...

A Real-Coded Genetic Algorithm with System Reduction and Restoration for Rapid and Reliable Power Flow Solution of Power Systems

Directory of Open Access Journals (Sweden)

Hassan Abdullah Kubba

2015-05-01

Full Text Available The paper presents a highly accurate power flow solution, reducing the possibility of ending at local minima, by using Real-Coded Genetic Algorithm (RCGA with system reduction and restoration. The proposed method (RCGA is modified to reduce the total computing time by reducing the system in size to that of the generator buses, which, for any realistic system, will be smaller in number, and the load buses are eliminated. Then solving the power flow problem for the generator buses only by real-coded GA to calculate the voltage phase angles, whereas the voltage magnitudes are specified resulted in reduced computation time for the solution. Then the system is restored by calculating the voltages of the load buses in terms of the calculated voltages of the generator buses, after a derivation of equations for calculating the voltages of the load busbars. The proposed method was demonstrated on 14-bus IEEE test systems and the practical system 362-busbar IRAQI NATIONAL GRID (ING. The proposed method has reliable convergence, a highly accurate solution and less computing time for on-line applications. The method can conveniently be applied for on-line analysis and planning studies of large power systems.

Introduction to genetic algorithms as a modeling tool

International Nuclear Information System (INIS)

Wildberger, A.M.; Hickok, K.A.

1990-01-01

Genetic algorithms are search and classification techniques modeled on natural adaptive systems. This is an introduction to their use as a modeling tool with emphasis on prospects for their application in the power industry. It is intended to provide enough background information for its audience to begin to follow technical developments in genetic algorithms and to recognize those which might impact on electric power engineering. Beginning with a discussion of genetic algorithms and their origin as a model of biological adaptation, their advantages and disadvantages are described in comparison with other modeling tools such as simulation and neural networks in order to provide guidance in selecting appropriate applications. In particular, their use is described for improving expert systems from actual data and they are suggested as an aid in building mathematical models. Using the Thermal Performance Advisor as an example, it is suggested how genetic algorithms might be used to make a conventional expert system and mathematical model of a power plant adapt automatically to changes in the plant's characteristics

Psychological impact of von Hippel-Lindau genetic screening in patients with a previous history of hemangioblastoma of the central nervous system.

Science.gov (United States)

Rochette, Claire; Baumstarck, Karine; Canoni-Zattara, Hélène; Abdullah, Ahmad Esmaeel; Figarella-Branger, Dominique; Pertuit, Morgane; Barlier, Anne; Castinetti, Frédéric; Pacak, Karel; Metellus, Philippe; Taïeb, David

2018-05-15

Von Hippel-Lindau (VHL) syndrome is a hereditary cancer syndrome characterized by a high risk of developing benign and malignant tumors, including central nervous system hemangioblastomas (CNS HBs). For an early diagnosis of VHL, before the occurrence of cancers (especially renal cell carcinoma), it is of huge importance to initiate VHL genetic testing in at-risk patients. The aim of the study was to assess the psychological impact of VHL genetic testing in patients previously diagnosed with a CNS HB. From 1999 until 2015, 55 patients underwent surgery for CNS HBs. Eleven patients were already screened for VHL mutations and 3 patients deceased before the start of the study. From the remaining 42 patients, 24 were accepted to be enrolled in the study. Assessment of psychological impact of VHL genetic testing was performed by measuring anxiety levels, mood disorders, quality of life, and psychological consequences of genetic screening. Twenty-one of the enrolled 24 patients underwent VHL genetic testing and 12 patients came back for the communication of positive genetic results. The baseline psychological status did not differ between these 2 groups. Patients who attended the visit of communication of genetic results had similar anxiety levels compared to those who had not. Furthermore, they also experienced an improvement in the level of anxiety and two QoL dimension scores compared to their baseline status. In summary, there is no evidence of a negative psychosocial impact of VHL genetic testing in patients with a previous history of CNS HB. We, therefore, recommend the recall of patients who have not been previously screened.

Genetic susceptibility and neurotransmitters in Tourette syndrome.

Science.gov (United States)

Paschou, Peristera; Fernandez, Thomas V; Sharp, Frank; Heiman, Gary A; Hoekstra, Pieter J

2013-01-01

Family studies have consistently shown that Tourette syndrome (TS) is a familial disorder and twin studies have clearly indicated a genetic contribution in the etiology of TS. Whereas early segregation studies of TS suggested a single-gene autosomal dominant disorder, later studies have pointed to more complex models including additive and multifactorial inheritance and likely interaction with genetic factors. While the exact cellular and molecular base of TS is as yet elusive, neuroanatomical and neurophysiological studies have pointed to the involvement of cortico-striato-thalamocortical circuits and abnormalities in dopamine, glutamate, gamma-aminobutyric acid, and serotonin neurotransmitter systems, with the most consistent evidence being available for involvement of dopamine-related abnormalities, that is, a reduction in tonic extracellular dopamine levels along with hyperresponsive spike-dependent dopamine release, following stimulation. Genetic and gene expression findings are very much supportive of involvement of these neurotransmitter systems. Moreover, intriguingly, genetic work on a two-generation pedigree has opened new research pointing to a role for histamine, a so far rather neglected neurotransmitter, with the potential of the development of new treatment options. Future studies should be aimed at directly linking neurotransmitter-related genetic and gene expression findings to imaging studies (imaging genetics), which enables a better understanding of the pathways and mechanisms through which the dynamic interplay of genes, brain, and environment shapes the TS phenotype. © 2013 Elsevier Inc. All rights reserved.

GENETICS ASPECTS OF DIABETIC NEPHROPATHY

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Oana-Elena Sauca

2010-09-01

Full Text Available Diabetic nephropathy is a clinical syndrome characterized by persistent albuminuria, a relentless decline in GFR, raised arterial blood pressure, and increased relative mortality for cardiovascular diseases. The pathogenesis of diabetic nephropathy is multifactorial, with contributions from metabolic abnormalities, hemodynamic alteration, and various growth and genetic factors. The identification of the main genes would allow the detection of those individuals at high risk for diabetic nephropathy and better understanding of its pathophysiologyas well.The present review discusses the main information available in literature regarding some genetic variants (involved in the renin-angiotensin system, glucose and lipid metabolism and some cytoskeleton proteins that reaffirms the importance of genetic factors in diabetic nephropathy.

Optimal hydrogenerator governor tuning with a genetic algorithm

International Nuclear Information System (INIS)

Lansberry, J.E.; Wozniak, L.; Goldberg, D.E.

1992-01-01

Many techniques exist for developing optimal controllers. This paper investigates genetic algorithms as a means of finding optimal solutions over a parameter space. In particular, the genetic algorithm is applied to optimal tuning of a governor for a hydrogenerator plant. Analog and digital simulation methods are compared for use in conjunction with the genetic algorithm optimization process. It is shown that analog plant simulation provides advantages in speed over digital plant simulation. This speed advantage makes application of the genetic algorithm in an actual plant environment feasible. Furthermore, the genetic algorithm is shown to possess the ability to reject plant noise and other system anomalies in its search for optimizing solutions

Genetic privacy.

Science.gov (United States)

Sankar, Pamela

2003-01-01

During the past 10 years, the number of genetic tests performed more than tripled, and public concern about genetic privacy emerged. The majority of states and the U.S. government have passed regulations protecting genetic information. However, research has shown that concerns about genetic privacy are disproportionate to known instances of information misuse. Beliefs in genetic determinacy explain some of the heightened concern about genetic privacy. Discussion of the debate over genetic testing within families illustrates the most recent response to genetic privacy concerns.

Efficacy of a web-based intelligent tutoring system for communicating genetic risk of breast cancer: a fuzzy-trace theory approach.

Science.gov (United States)

Wolfe, Christopher R; Reyna, Valerie F; Widmer, Colin L; Cedillos, Elizabeth M; Fisher, Christopher R; Brust-Renck, Priscila G; Weil, Audrey M

2015-01-01

. Many healthy women consider genetic testing for breast cancer risk, yet BRCA testing issues are complex. . To determine whether an intelligent tutor, BRCA Gist, grounded in fuzzy-trace theory (FTT), increases gist comprehension and knowledge about genetic testing for breast cancer risk, improving decision making. . In 2 experiments, 410 healthy undergraduate women were randomly assigned to 1 of 3 groups: an online module using a Web-based tutoring system (BRCA Gist) that uses artificial intelligence technology, a second group read highly similar content from the National Cancer Institute (NCI) Web site, and a third that completed an unrelated tutorial. . BRCA Gist applied FTT and was designed to help participants develop gist comprehension of topics relevant to decisions about BRCA genetic testing, including how breast cancer spreads, inherited genetic mutations, and base rates. . We measured content knowledge, gist comprehension of decision-relevant information, interest in testing, and genetic risk and testing judgments. . Control knowledge scores ranged from 54% to 56%, NCI improved significantly to 65% and 70%, and BRCA Gist improved significantly more to 75% and 77%, P tutors, such as BRCA Gist, are scalable, cost-effective ways of helping people understand complex issues, improving decision making. © The Author(s) 2014.

Improvements of methanogenesis by genetic techniques

International Nuclear Information System (INIS)

Baresi, L.

1985-01-01

The objective of this research is to characterize the genetic system of one or two strains of methanogenic bacteria. Both ultraviolet exposure and chemical screening will be used to isolate mutant species. These species will be tested for genetic recombination. Bacteriophages and plasmids will be sought. Two species, Methanococcus voltae and Methanobacterium thermoautotrophicum, will be subjected to extensive screening and manipulation. Nutritional mutants of these two strains will be studied to determine uptake rates. Once a set of satisfactory mutants is obtained, two types of genetic recombination experiments (conjugation and DNA transformation) will be carried out

Determination of genetic diversity among some almond accessions

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Pinar Hasan

2015-01-01

Full Text Available More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD and 4 inter-simple sequence repeat (ISSR markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections. The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88% compared to RAPD (74%. RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

Time Delay Systems Methods, Applications and New Trends

CERN Document Server

Vyhlídal, Tomáš; Niculescu, Silviu-Iulian; Pepe, Pierdomenico

2012-01-01

This volume is concerned with the control and dynamics of time delay systems; a research field with at least six-decade long history that has been very active especially in the past two decades. In parallel to the new challenges emerging from engineering, physics, mathematics, and economics, the volume covers several new directions including topology induced stability, large-scale interconnected systems, roles of networks in stability, and new trends in predictor-based control and consensus dynamics. The associated applications/problems are described by highly complex models, and require solving inverse problems as well as the development of new theories, mathematical tools, numerically-tractable algorithms for real-time control. The volume, which is targeted to present these developments in this rapidly evolving field, captures a careful selection of the most recent papers contributed by experts and collected under five parts: (i) Methodology: From Retarded to Neutral Continuous Delay Models, (ii) Systems, S...

Localization of canine brachycephaly using an across breed mapping approach.

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Danika Bannasch

2010-03-01

Full Text Available The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10-30 and control (20-60 samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.

Intelligent DNA-based molecular diagnostics using linked genetic markers

Energy Technology Data Exchange (ETDEWEB)

Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

1994-12-31

This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

Cognitive radio resource allocation based on coupled chaotic genetic algorithm

International Nuclear Information System (INIS)

Zu Yun-Xiao; Zhou Jie; Zeng Chang-Chang

2010-01-01

A coupled chaotic genetic algorithm for cognitive radio resource allocation which is based on genetic algorithm and coupled Logistic map is proposed. A fitness function for cognitive radio resource allocation is provided. Simulations are conducted for cognitive radio resource allocation by using the coupled chaotic genetic algorithm, simple genetic algorithm and dynamic allocation algorithm respectively. The simulation results show that, compared with simple genetic and dynamic allocation algorithm, coupled chaotic genetic algorithm reduces the total transmission power and bit error rate in cognitive radio system, and has faster convergence speed

Learning Management Systems on Blended Learning Courses

DEFF Research Database (Denmark)

Kuran, Mehmet Şükrü; Pedersen, Jens Myrup; Elsner, Raphael

2017-01-01

LMSes, Moodle, Blackboard Learn, Canvas, and Stud.IP with respect to these. We explain how these features were utilized to increase the efficiency, tractability, and quality of experience of the course. We found that an LMS with advanced features such as progress tracking, modular course support...

Genetic Testing between Private and Public Interests: Some Legal and Ethical Reflections.

Science.gov (United States)

Sándor, Judit

2018-01-01

In Europe, there is a wide variety of genetic tests that various private companies offer to patients or to consumers. More and more people have become curious about their genetic predisposition and susceptibility. Most public health-care systems, however, are not adequately prepared for responding to these new demands and to the results of these genetic tests as, quite often, there is no available therapy for the identified genetic condition. This discrepancy between the newly emerging expectations and the insufficient responses contributes to a further rift between the public and private sectors of health care. Individual genetic test results may also trigger the need for personalized medicine and may open up a competition between the two fields in offering further genetic tests and medical exams. Pro-active patients may need a different kind of information on genetic tests and their implications. In this context, how should the public health system deal with the challenges of private testing? Will private genetic testing transform health care from a solidarity-based system to an individualistic one? In this paper, I would like to explore the emerging legal and ethical issues related to genetic testing and the relevant legal framework that has developed so far. In the conclusion, I will examine the possibilities of further legal development.

"Glowing head" mice: a genetic tool enabling reliable preclinical image-based evaluation of cancers in immunocompetent allografts.

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Chi-Ping Day

Full Text Available Preclinical therapeutic assessment currently relies on the growth response of established human cell lines xenografted into immunocompromised mice, a strategy that is generally not predictive of clinical outcomes. Immunocompetent genetically engineered mouse (GEM-derived tumor allograft models offer highly tractable preclinical alternatives and facilitate analysis of clinically promising immunomodulatory agents. Imageable reporters are essential for accurately tracking tumor growth and response, particularly for metastases. Unfortunately, reporters such as luciferase and GFP are foreign antigens in immunocompetent mice, potentially hindering tumor growth and confounding therapeutic responses. Here we assessed the value of reporter-tolerized GEMs as allograft recipients by targeting minimal expression of a luciferase-GFP fusion reporter to the anterior pituitary gland (dubbed the "Glowing Head" or GH mouse. The luciferase-GFP reporter expressed in tumor cells induced adverse immune responses in wildtype mouse, but not in GH mouse, as transplantation hosts. The antigenicity of optical reporters resulted in a decrease in both the growth and metastatic potential of the labeled tumor in wildtype mice as compared to the GH mice. Moreover, reporter expression can also alter the tumor response to chemotherapy or targeted therapy in a context-dependent manner. Thus the GH mice and experimental approaches vetted herein provide concept validation and a strategy for effective, reproducible preclinical evaluation of growth and response kinetics for traceable tumors.

Testing the structure of a hydrological model using Genetic Programming

Science.gov (United States)

Selle, Benny; Muttil, Nitin

2011-01-01

SummaryGenetic Programming is able to systematically explore many alternative model structures of different complexity from available input and response data. We hypothesised that Genetic Programming can be used to test the structure of hydrological models and to identify dominant processes in hydrological systems. To test this, Genetic Programming was used to analyse a data set from a lysimeter experiment in southeastern Australia. The lysimeter experiment was conducted to quantify the deep percolation response under surface irrigated pasture to different soil types, watertable depths and water ponding times during surface irrigation. Using Genetic Programming, a simple model of deep percolation was recurrently evolved in multiple Genetic Programming runs. This simple and interpretable model supported the dominant process contributing to deep percolation represented in a conceptual model that was published earlier. Thus, this study shows that Genetic Programming can be used to evaluate the structure of hydrological models and to gain insight about the dominant processes in hydrological systems.

Genetics Education in Nurse Residency Programs: A Natural Fit.

Science.gov (United States)

Hamilton, Nalo M; Stenman, Christina W; Sang, Elaine; Palmer, Christina

2017-08-01

Scientific advances are shedding light on the genetic underpinning of common diseases. With such insight, the entire health care team is faced with the need to address patient questions regarding genetic risk, testing, and the psychosocial aspects of genetics information. Nurses are in a prime position to help with patient education about genetic conditions, yet they often lack adequate genetics education within their nursing curriculum to address patient questions and provide resources. One mechanism to address this knowledge deficit is the incorporation of a genetics-based curriculum into nurse residency programs. This article describes a novel genetics-based curriculum designed and implemented in the UCLA Health System Nurse Residency Program. J Contin Educ Nurs. 2017;48(8):379-384. Copyright 2017, SLACK Incorporated.

An Improved Genetic Algorithm for Optimal Stationary Energy Storage System Locating and Sizing

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Bin Wang

2014-10-01

Full Text Available The application of a stationary ultra-capacitor energy storage system (ESS in urban rail transit allows for the recuperation of vehicle braking energy for increasing energy savings as well as for a better vehicle voltage profile. This paper aims to obtain the best energy savings and voltage profile by optimizing the location and size of ultra-capacitors. This paper firstly raises the optimization objective functions from the perspectives of energy savings, regenerative braking cancellation and installation cost, respectively. Then, proper mathematical models of the DC (direct current traction power supply system are established to simulate the electrical load-flow of the traction supply network, and the optimization objections are evaluated in the example of a Chinese metro line. Ultimately, a methodology for optimal ultra-capacitor energy storage system locating and sizing is put forward based on the improved genetic algorithm. The optimized result shows that certain preferable and compromised schemes of ESSs’ location and size can be obtained, acting as a compromise between satisfying better energy savings, voltage profile and lower installation cost.

Testing the Structure of Hydrological Models using Genetic Programming

Science.gov (United States)

Selle, B.; Muttil, N.

2009-04-01

Genetic Programming is able to systematically explore many alternative model structures of different complexity from available input and response data. We hypothesised that genetic programming can be used to test the structure hydrological models and to identify dominant processes in hydrological systems. To test this, genetic programming was used to analyse a data set from a lysimeter experiment in southeastern Australia. The lysimeter experiment was conducted to quantify the deep percolation response under surface irrigated pasture to different soil types, water table depths and water ponding times during surface irrigation. Using genetic programming, a simple model of deep percolation was consistently evolved in multiple model runs. This simple and interpretable model confirmed the dominant process contributing to deep percolation represented in a conceptual model that was published earlier. Thus, this study shows that genetic programming can be used to evaluate the structure of hydrological models and to gain insight about the dominant processes in hydrological systems.

Accurate crop classification using hierarchical genetic fuzzy rule-based systems

Science.gov (United States)

Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

2014-10-01

This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge.

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Po-Ru Loh

Full Text Available A major goal of large-scale genomics projects is to enable the use of data from high-throughput experimental methods to predict complex phenotypes such as disease susceptibility. The DREAM5 Systems Genetics B Challenge solicited algorithms to predict soybean plant resistance to the pathogen Phytophthora sojae from training sets including phenotype, genotype, and gene expression data. The challenge test set was divided into three subcategories, one requiring prediction based on only genotype data, another on only gene expression data, and the third on both genotype and gene expression data. Here we present our approach, primarily using regularized regression, which received the best-performer award for subchallenge B2 (gene expression only. We found that despite the availability of 941 genotype markers and 28,395 gene expression features, optimal models determined by cross-validation experiments typically used fewer than ten predictors, underscoring the importance of strong regularization in noisy datasets with far more features than samples. We also present substantial analysis of the training and test setup of the challenge, identifying high variance in performance on the gold standard test sets.

An empirical model for independent control of variable speed refrigeration system

International Nuclear Information System (INIS)

Li Hua; Jeong, Seok-Kwon; Yoon, Jung-In; You, Sam-Sang

2008-01-01

This paper deals with an empirical dynamic model for decoupling control of the variable speed refrigeration system (VSRS). To cope with inherent complexity and nonlinearity in system dynamics, the model parameters are first obtained based on experimental data. In the study, the dynamic characteristics of indoor temperature and superheat are assumed to be first-order model with time delay. While the compressor frequency and opening angle of electronic expansion valve are varying, the indoor temperature and the superheat exhibit interfering characteristics each other in the VSRS. Thus, each decoupling model has been proposed to eliminate such interference. Finally, the experiment and simulation results indicate that the proposed model offers more tractable means for describing the actual VSRS comparing to other models currently available

Dynamic state estimation techniques for large-scale electric power systems

International Nuclear Information System (INIS)

Rousseaux, P.; Pavella, M.

1991-01-01

This paper presents the use of dynamic type state estimators for energy management in electric power systems. Various dynamic type estimators have been developed, but have never been implemented. This is primarily because of dimensionality problems posed by the conjunction of an extended Kalman filter with a large scale power system. This paper precisely focuses on how to circumvent the high dimensionality, especially prohibitive in the filtering step, by using a decomposition-aggregation hierarchical scheme; to appropriately model the power system dynamics, the authors introduce new state variables in the prediction step and rely on a load forecasting method. The combination of these two techniques succeeds in solving the overall dynamic state estimation problem not only in a tractable and realistic way, but also in compliance with real-time computational requirements. Further improvements are also suggested, bound to the specifics of the high voltage electric transmission systems

Population Genetics of Identifiler System in Malaysia.

Science.gov (United States)

Nakamura, Yasutaka; Samejima, Michinaga; Minaguchi, Kiyoshi; Nambiar, Phrabhakaran

2016-01-01

Short tandem repeat (STR) polymorphisms were investigated in 341 unrelated Malay individuals (218 males and 123 females) living in or around Kuala Lumpur by using a forensic analysts kit. The following STRs were targeted: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA. The purpose of this study was to elucidate population genetics in Malaysia and calculate statistical parameters for forensic and anthropological research. Data on these STRs in the target population were obtained and subjected to statistical analysis. Accordance with the Hardy-Weinberg equilibrium was proven for all the loci targeted. The combined power of discrimination was greater than 0.9999999999, indicating that this multiplex system is an excellent tool for forensic casework. The allele frequency in the data were weighed against that in four other local populations (Chinese, Iranian, Belgian, and African). The average coefficient of correlation was strongest in the order of Africa (0.092522), Belgium (0.264822), Iran (0.404363), and China (0.706661). These results are consistent with what is known about the anthropological history of and prehistoric human migration in the Malay region. We believe that these data offer a valuable anthropological resource, being applicable to the statistical evaluation of DNA evidence in human identification, as well as the determination of ethnicity in healthy populations.

From Genetics to Genetic Algorithms

Indian Academy of Sciences (India)

Genetic algorithms (GAs) are computational optimisation schemes with an ... The algorithms solve optimisation problems ..... Genetic Algorithms in Search, Optimisation and Machine. Learning, Addison-Wesley Publishing Company, Inc. 1989.

Unfolding neutron spectra with BS-TLD system using genetic algorithms

Energy Technology Data Exchange (ETDEWEB)

Santos, Joelan A.L., E-mail: jasantos@cnen.gov.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear; Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Silva, Everton R. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Centro de Informatica; Ferreira, Tiago A.E. [Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE (Brazil). Dept. de Estatistica e Informatica; Fonseca, Evaldo S. [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Vilela, Eudice C., E-mail: ecvilela@cnen.gov.br [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil)

2011-07-01

Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as function of energy to be characterized. To perform this task, the neutron spectrometer has a primary role in determining the neutron flux ({Phi}{sub E}(E)). Precise information allows radiological quantities establishment related to that spectrum but it is necessary, however, a series of steps with a spectrometric system that can cover a large interval of energy and whose answer is isotropic. The most widely used for accomplishing this task is the spectrometric Bonner spheres system. One of the biggest problems related to neutron spectrometry is the process of data analysis, known as unfolding. Most of the work undertaken to implement new techniques of this process, using data obtained with the scintillator {sup 6}LiI(I). However, characteristics related to the dead time make it not be so effective when used in high flow neutron fields. An alternative to this problem is the use of thermoluminescent detectors (TLD), but the codes used do not provide a more specific response matrix to unfolding the information obtained through these materials, which makes the development of a specific response matrix important to adequately characterize the response obtained by them. This paper proposes using a technique of artificial intelligence called genetic algorithm, which uses bio-inspired mathematical models and through the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a system of Bonner spheres, such as thermal neutron detectors, to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enables of this technique to unfolding neutrons spectra with BS-TLD system. (author)

Unfolding neutron spectra with BS-TLD system using genetic algorithms

International Nuclear Information System (INIS)

Santos, Joelan A.L.; Silva, Everton R.; Vilela, Eudice C.

2011-01-01

Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as function of energy to be characterized. To perform this task, the neutron spectrometer has a primary role in determining the neutron flux (Φ E (E)). Precise information allows radiological quantities establishment related to that spectrum but it is necessary, however, a series of steps with a spectrometric system that can cover a large interval of energy and whose answer is isotropic. The most widely used for accomplishing this task is the spectrometric Bonner spheres system. One of the biggest problems related to neutron spectrometry is the process of data analysis, known as unfolding. Most of the work undertaken to implement new techniques of this process, using data obtained with the scintillator 6 LiI(I). However, characteristics related to the dead time make it not be so effective when used in high flow neutron fields. An alternative to this problem is the use of thermoluminescent detectors (TLD), but the codes used do not provide a more specific response matrix to unfolding the information obtained through these materials, which makes the development of a specific response matrix important to adequately characterize the response obtained by them. This paper proposes using a technique of artificial intelligence called genetic algorithm, which uses bio-inspired mathematical models and through the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a system of Bonner spheres, such as thermal neutron detectors, to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enables of this technique to unfolding neutrons spectra with BS-TLD system. (author)

Genetics, systems, and alcohol.

Science.gov (United States)

McClearn, G E

1993-03-01

Under a variety of rubrics (e.g., complexity, self-constructing systems, dissipative structures), interest has recently burgeoned in applying principles of complex systems to a wide variety of scientific issues. A major concern is with emergent properties of systems not derivable from the properties of components of the systems. In this paper, some elementary aspects of "systems" considerations are applied to phenomena of alcohol pharmacogenetics. It is likely that whole new families of informative phenotypes can be generated by this approach.

Quantum Dynamics in Biological Systems

Science.gov (United States)

Shim, Sangwoo

In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

Codon size reduction as the origin of the triplet genetic code.

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Pavel V Baranov

Full Text Available The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon

An investigation of the genetic toxicology of irradiated foodstuffs using short-term systems

International Nuclear Information System (INIS)

Phillips, B.J.; Kranz, E.; Elias, P.S.; Muenzner, R.

1980-01-01

The genetic toxicology of irradiated foodstuffs has been investigated by the use of a battery of short-term tests for genetic damage. Appropriate methods are discussed for the preparation of food samples for testing by techniques involving micro-organisms and mammalian cells in culture. A new method of sample preparation by enzymatic digestion in vitro is described and its use in the testing of three irradiated foodstuffs by the Salmonella typhimurium reverse mutation test is reported. The results of the mutation tests provide further evidence of the lack of genetic toxicity of irradiated foods. (author)

About Genetic Counselors

Science.gov (United States)

... clinical care in many areas of medicine. Assisted Reproductive Technology/Infertility Genetics Cancer Genetics Cardiovascular Genetics Cystic Fibrosis Genetics Fetal Intervention and Therapy Genetics Hematology Genetics Metabolic Genetics ...

Bioinformatics tools and database resources for systems genetics analysis in mice-a short review and an evaluation of future needs

NARCIS (Netherlands)

Durrant, Caroline; Swertz, Morris A.; Alberts, Rudi; Arends, Danny; Moeller, Steffen; Mott, Richard; Prins, Pjotr; van der Velde, K. Joeri; Jansen, Ritsert C.; Schughart, Klaus

During a meeting of the SYSGENET working group 'Bioinformatics', currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed. The group evaluated interoperability and performed initial feasibility studies. To aid future

Optimization of genetic transformation protocol mediated by biolistic ...

African Journals Online (AJOL)

Abhay Kumar

2013-02-06

Feb 6, 2013 ... We report here an efficient genotype-independent genetic transformation system in wheat. Highly regenerable embryogenic calli obtained from mature seeds were employed as the target tissue for the genetic transformation of three bread wheat varieties viz C306, HDR77 and PBW343 representing.

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system

OpenAIRE

Raimondo, Joseph V.; Joyce, Bradley; Kay, Louise; Schlagheck, Theresa; Newey, Sarah E.; Srinivas, Shankar; Akerman, Colin J.

2013-01-01

Within the nervous system, intracellular Cl− and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission, and network excitability. Cl− and pH are often co-regulated, and network activity results in the movement of both Cl− and H+. Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl− and pH sensors have been described previously, these either l...

Genetic effects of ionizing radiation and repair processes

International Nuclear Information System (INIS)

Tuschl, H.

1986-11-01

Since DNA (=desoxyribonucleic acid) is the largest molecule within the cell it is the most important target for direct and indirect radiation effects. Within DNA the total genetic information is stored, thus damage to DNA in germ cells causes genetic disorders and damage in somatic cells is implicated in cancer and immunodeficiences. Alterations of DNA structure are not only due to ionizing radiation effects, but also to spontaneous DNA modifications and damage from interactions with environmental ultraviolet light and chemical agents. To maintain its genetic integrity, each organism had to develop different repair systems able to recognize and remove DNA damage. Repeated exposure to a DNA damaging agent can even lead to adaptation processes and increased resistance to the same agent. At normal function of repair systems it can be assumed that the capacity of those systems is adequate to scope with the effects of low radiation doses. (Author)

Genetic Testing between Private and Public Interests: Some Legal and Ethical Reflections

Directory of Open Access Journals (Sweden)

Judit Sándor

2018-01-01

Full Text Available In Europe, there is a wide variety of genetic tests that various private companies offer to patients or to consumers. More and more people have become curious about their genetic predisposition and susceptibility. Most public health-care systems, however, are not adequately prepared for responding to these new demands and to the results of these genetic tests as, quite often, there is no available therapy for the identified genetic condition. This discrepancy between the newly emerging expectations and the insufficient responses contributes to a further rift between the public and private sectors of health care. Individual genetic test results may also trigger the need for personalized medicine and may open up a competition between the two fields in offering further genetic tests and medical exams. Pro-active patients may need a different kind of information on genetic tests and their implications. In this context, how should the public health system deal with the challenges of private testing? Will private genetic testing transform health care from a solidarity-based system to an individualistic one? In this paper, I would like to explore the emerging legal and ethical issues related to genetic testing and the relevant legal framework that has developed so far. In the conclusion, I will examine the possibilities of further legal development.

Workable male sterility systems for hybrid rice: Genetics, biochemistry, molecular biology, and utilization.