WorldWideScience

Sample records for chemical genetics approach

  1. Chapter 7. Management strategies for dwarf mistletoes: Biological, chemical, and genetic approaches

    Science.gov (United States)

    S. F. Shamoun; L. E. DeWald

    2002-01-01

    The opportunity and need for management of mistletoe populations with biological, chemical, and genetic approaches are greatest for application to the dwarf mistletoes. Although much information is available on these management strategies (see reviews by Hawksworth 1972, Knutson 1978), significant research and development are still required for these to become...

  2. New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals

    Directory of Open Access Journals (Sweden)

    RENATA V. VELHO

    2015-08-01

    Full Text Available With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.

  3. New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals.

    Science.gov (United States)

    Velho, Renata V; Sperb-Ludwig, Fernanda; Schwartz, Ida V D

    2015-08-01

    With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.

  4. Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach

    Energy Technology Data Exchange (ETDEWEB)

    Han, Sangjo [Bioinformatics Lab, Healthcare Group, SK Telecom, 9-1, Sunae-dong, Pundang-gu, Sungnam-si, Kyunggi-do 463-784 (Korea, Republic of); Lee, Minho [Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Chang, Hyeshik [Department of Biological Science, Seoul National University, 599 Gwanakro, Gwanak-gu, Seoul 151-747 (Korea, Republic of); Nam, Miyoung [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 (Korea, Republic of); Park, Han-Oh [Bioneer Corp., 8-11 Munpyeongseo-ro, Daedeok-gu, Daejeon 306-220 (Korea, Republic of); Kwak, Youn-Sig [Department of Applied Biology, Gyeongsang National University, 501 Jinju-daero, Jinju, Gyeongnam 660-701 (Korea, Republic of); Ha, Hye-jeong [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-Gu, Daejeon 305-806 (Korea, Republic of); Kim, Dongsup [Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Hwang, Sung-Ook [Department of Obstetrics and Gynecology, Inha University Hospital, 7-206 Sinheung-dong, Jung-gu, Incheon 400-711 (Korea, Republic of); Hoe, Kwang-Lae [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 (Korea, Republic of); Kim, Dong-Uk [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-Gu, Daejeon 305-806 (Korea, Republic of)

    2013-07-12

    Highlights: •The first compendium of chemical-genetic profiles form fission yeast was generated. •The first HTS of drug mode-of-action in fission yeast was performed. •The first comparative chemical genetic analysis between two yeasts was conducted. -- Abstract: Genome-wide chemical genetic profiles in Saccharomyces cerevisiae since the budding yeast deletion library construction have been successfully used to reveal unknown mode-of-actions of drugs. Here, we introduce comparative approach to infer drug target proteins more accurately using two compendiums of chemical-genetic profiles from the budding yeast S. cerevisiae and the fission yeast Schizosaccharomyces pombe. For the first time, we established DNA-chip based growth defect measurement of genome-wide deletion strains of S. pombe, and then applied 47 drugs to the pooled heterozygous deletion strains to generate chemical-genetic profiles in S. pombe. In our approach, putative drug targets were inferred from strains hypersensitive to given drugs by analyzing S. pombe and S. cerevisiae compendiums. Notably, many evidences in the literature revealed that the inferred target genes of fungicide and bactericide identified by such comparative approach are in fact the direct targets. Furthermore, by filtering out the genes with no essentiality, the multi-drug sensitivity genes, and the genes with less eukaryotic conservation, we created a set of drug target gene candidates that are expected to be directly affected by a given drug in human cells. Our study demonstrated that it is highly beneficial to construct the multiple compendiums of chemical genetic profiles using many different species. The fission yeast chemical-genetic compendium is available at (http://pombe.kaist.ac.kr/compendium)

  5. Molecular and Chemical Genetic Approaches to Developmental Origins of Aging and Disease in Zebrafish

    Science.gov (United States)

    Sasaki, Tomoyuki; Kishi, Shuji

    2013-01-01

    The incidence of diseases increases rapidly with age, accompanied by progressive deteriorations of physiological functions in organisms. Aging-associated diseases are sporadic but mostly inevitable complications arising from senescence. Senescence is often considered the antithesis of early development, but yet there may be factors and mechanisms in common between these two phenomena over the dynamic process of aging. The association between early development and late-onset disease with advancing age is thought to come from a consequence of developmental plasticity, the phenomenon by which one genotype can give rise to a range of physiologically and/or morphologically adaptive states in response to different environmental or genetic perturbations. On the one hand, we hypothesized that the future aging process can be predictive based on adaptivity during the early developmental period. Modulating the thresholds of adaptive plasticity by chemical genetic approaches, we have been investigating whether any relationship exists between the regulatory mechanisms that function in early development and in senescence using the zebrafish (Danio rerio), a small freshwater fish and a useful model animal for genetic studies. We have successfully conducted experiments to isolate zebrafish mutants expressing apparently altered senescence phenotypes during embryogenesis (“embryonic senescence”), subsequently showing shortened lifespan in adulthoods. We anticipate that previously uncharacterized developmental genes may mediate the aging process and play a pivotal role in senescence. On the other hand, unexpected senescence-related genes might also be involved in the early developmental process and regulation. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes and small molecular compounds that can be linked to the senescence phenotype, and thereby facilitates searching for the evolutionary and developmental origins

  6. A chemical genetic approach to engineer phototropin kinases for substrate labeling.

    Science.gov (United States)

    Schnabel, Jonathan; Hombach, Peter; Waksman, Thomas; Giuriani, Giovanni; Petersen, Jan; Christie, John M

    2018-04-13

    Protein kinases (PKs) control many aspects of plant physiology by regulating signaling networks through protein phosphorylation. Phototropins (phots) are plasma membrane-associated serine/threonine PKs that control a range of physiological processes that collectively serve to optimize photosynthetic efficiency in plants. These include phototropism, leaf positioning and flattening, chloroplast movement, and stomatal opening. Despite their identification over two decades ago, only a handful of substrates have been identified for these PKs. Progress in this area has been hampered by the lack of a convenient means to confirm the identity of potential substrate candidates. Here we demonstrate that the kinase domain of Arabidopsis phot1 and phot2 can be successfully engineered to accommodate non-natural ATP analogues by substituting the bulky gatekeeper residue threonine for glycine. This approach circumvents the need for radioactivity to track phot kinase activity and follow light-induced receptor autophosphorylation in vitro by incorporating thiophosphate from N 6 -benzyl-ATPγS. Consequently, thiophosphorylation of phot substrate candidates can be readily monitored when added or co-expressed with phots in vitro Furthermore, gatekeeper-modified phot1 retained its functionality and its ability to accommodate N 6 -benzyl-ATPγS as a phosphodonor when expressed in Arabidopsis We therefore anticipate that this chemical genetic approach will provide new opportunities for labeling and identifying substrates for phots and other related AGC kinases under in vitro and near-native in vivo conditions. © 2018 Schnabel et al.

  7. Approaches to chemical synthetic biology.

    Science.gov (United States)

    Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

    2012-07-16

    Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  8. Genetic k-means clustering approach for mapping human vulnerability to chemical hazards in the industrialized city: a case study of Shanghai, China.

    Science.gov (United States)

    Shi, Weifang; Zeng, Weihua

    2013-06-20

    Reducing human vulnerability to chemical hazards in the industrialized city is a matter of great urgency. Vulnerability mapping is an alternative approach for providing vulnerability-reducing interventions in a region. This study presents a method for mapping human vulnerability to chemical hazards by using clustering analysis for effective vulnerability reduction. Taking the city of Shanghai as the study area, we measure human exposure to chemical hazards by using the proximity model with additionally considering the toxicity of hazardous substances, and capture the sensitivity and coping capacity with corresponding indicators. We perform an improved k-means clustering approach on the basis of genetic algorithm by using a 500 m × 500 m geographical grid as basic spatial unit. The sum of squared errors and silhouette coefficient are combined to measure the quality of clustering and to determine the optimal clustering number. Clustering result reveals a set of six typical human vulnerability patterns that show distinct vulnerability dimension combinations. The vulnerability mapping of the study area reflects cluster-specific vulnerability characteristics and their spatial distribution. Finally, we suggest specific points that can provide new insights in rationally allocating the limited funds for the vulnerability reduction of each cluster.

  9. Genetic k-Means Clustering Approach for Mapping Human Vulnerability to Chemical Hazards in the Industrialized City: A Case Study of Shanghai, China

    Directory of Open Access Journals (Sweden)

    Weihua Zeng

    2013-06-01

    Full Text Available Reducing human vulnerability to chemical hazards in the industrialized city is a matter of great urgency. Vulnerability mapping is an alternative approach for providing vulnerability-reducing interventions in a region. This study presents a method for mapping human vulnerability to chemical hazards by using clustering analysis for effective vulnerability reduction. Taking the city of Shanghai as the study area, we measure human exposure to chemical hazards by using the proximity model with additionally considering the toxicity of hazardous substances, and capture the sensitivity and coping capacity with corresponding indicators. We perform an improved k-means clustering approach on the basis of genetic algorithm by using a 500 m × 500 m geographical grid as basic spatial unit. The sum of squared errors and silhouette coefficient are combined to measure the quality of clustering and to determine the optimal clustering number. Clustering result reveals a set of six typical human vulnerability patterns that show distinct vulnerability dimension combinations. The vulnerability mapping of the study area reflects cluster-specific vulnerability characteristics and their spatial distribution. Finally, we suggest specific points that can provide new insights in rationally allocating the limited funds for the vulnerability reduction of each cluster.

  10. 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

  11. Therapeutic approaches to genetic disorders

    African Journals Online (AJOL)

    salah

    Although prevention is the ideal goal for genetic disorders, various types of therapeutic ... The patient being ... pirical or aimed at controlling or mediating signs and symptoms without care. ... plications and gene therapy approaches .... genes family, have opened a wide and .... cancer where nanoparticles are used to.

  12. Quantitative genetic activity graphical profiles for use in chemical evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Waters, M.D. [Environmental Protection Agency, Washington, DC (United States); Stack, H.F.; Garrett, N.E.; Jackson, M.A. [Environmental Health Research and Testing, Inc., Research Triangle Park, NC (United States)

    1990-12-31

    A graphic approach, terms a Genetic Activity Profile (GAP), was developed to display a matrix of data on the genetic and related effects of selected chemical agents. The profiles provide a visual overview of the quantitative (doses) and qualitative (test results) data for each chemical. Either the lowest effective dose or highest ineffective dose is recorded for each agent and bioassay. Up to 200 different test systems are represented across the GAP. Bioassay systems are organized according to the phylogeny of the test organisms and the end points of genetic activity. The methodology for producing and evaluating genetic activity profile was developed in collaboration with the International Agency for Research on Cancer (IARC). Data on individual chemicals were compiles by IARC and by the US Environmental Protection Agency (EPA). Data are available on 343 compounds selected from volumes 1-53 of the IARC Monographs and on 115 compounds identified as Superfund Priority Substances. Software to display the GAPs on an IBM-compatible personal computer is available from the authors. Structurally similar compounds frequently display qualitatively and quantitatively similar profiles of genetic activity. Through examination of the patterns of GAPs of pairs and groups of chemicals, it is possible to make more informed decisions regarding the selection of test batteries to be used in evaluation of chemical analogs. GAPs provided useful data for development of weight-of-evidence hazard ranking schemes. Also, some knowledge of the potential genetic activity of complex environmental mixtures may be gained from an assessment of the genetic activity profiles of component chemicals. The fundamental techniques and computer programs devised for the GAP database may be used to develop similar databases in other disciplines. 36 refs., 2 figs.

  13. Basic Genetics: A Human Approach.

    Science.gov (United States)

    Biological Sciences Curriculum Study, Colorado Springs, CO. Center for Education in Human and Medical Genetics.

    This document (which has the form of a magazine) provides a variety of articles, stories, editorials, letters, interviews, and other types of magazine features (such as book reviews) which focus on human genetics. In addition to providing information about the principles of genetics, nearly all of the sections in the "magazine" address moral,…

  14. Amazing variational approach to chemical reactions

    OpenAIRE

    Fernández, Francisco M.

    2009-01-01

    In this letter we analyse an amazing variational approach to chemical reactions. Our results clearly show that the variational expressions are unsuitable for the analysis of empirical data obtained from chemical reactions.

  15. Engineering and Functional Analysis of Mitotic Kinases Through Chemical Genetics.

    Science.gov (United States)

    Jones, Mathew J K; Jallepalli, Prasad V

    2016-01-01

    During mitosis, multiple protein kinases transform the cytoskeleton and chromosomes into new and highly dynamic structures that mediate the faithful transmission of genetic information and cell division. However, the large number and strong conservation of mammalian kinases in general pose significant obstacles to interrogating them with small molecules, due to the difficulty in identifying and validating those which are truly selective. To overcome this problem, a steric complementation strategy has been developed, in which a bulky "gatekeeper" residue within the active site of the kinase of interest is replaced with a smaller amino acid, such as glycine or alanine. The enlarged catalytic pocket can then be targeted in an allele-specific manner with bulky purine analogs. This strategy provides a general framework for dissecting kinase function with high selectivity, rapid kinetics, and reversibility. In this chapter we discuss the principles and techniques needed to implement this chemical genetic approach in mammalian cells.

  16. Enzyme Technology of Peroxidases: Immobilization, Chemical and Genetic Modification

    Science.gov (United States)

    Longoria, Adriana; Tinoco, Raunel; Torres, Eduardo

    An overview of enzyme technology applied to peroxidases is made. Immobilization on organic, inorganic, and hybrid supports; chemical modification of amino acids and heme group; and genetic modification by site-directed and random mutagenesis are included. Different strategies that were carried out to improve peroxidase performance in terms of stability, selectivity, and catalytic activity are analyzed. Immobilization of peroxidases on inorganic and organic materials enhances the tolerance of peroxidases toward the conditions normally found in many industrial processes, such as the presence of an organic solvent and high temperature. In addition, it is shown that immobilization helps to increase the Total Turnover Number at levels high enough to justify the use of a peroxidase-based biocatalyst in a synthesis process. Chemical modification of peroxidases produces modified enzymes with higher thermostability and wider substrate variability. Finally, through mutagenesis approaches, it is possible to produce modified peroxidases capable of oxidizing nonnatural substrates with high catalytic activity and affinity.

  17. Chemical genetics and strigolactone perception [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Shelley Lumba

    2017-06-01

    Full Text Available Strigolactones (SLs are a collection of related small molecules that act as hormones in plant growth and development. Intriguingly, SLs also act as ecological communicators between plants and mycorrhizal fungi and between host plants and a collection of parasitic plant species. In the case of mycorrhizal fungi, SLs exude into the soil from host roots to attract fungal hyphae for a beneficial interaction. In the case of parasitic plants, however, root-exuded SLs cause dormant parasitic plant seeds to germinate, thereby allowing the resulting seedling to infect the host and withdraw nutrients. Because a laboratory-friendly model does not exist for parasitic plants, researchers are currently using information gleaned from model plants like Arabidopsis in combination with the chemical probes developed through chemical genetics to understand SL perception of parasitic plants. This work first shows that understanding SL signaling is useful in developing chemical probes that perturb SL perception. Second, it indicates that the chemical space available to probe SL signaling in both model and parasitic plants is sizeable. Because these parasitic pests represent a major concern for food insecurity in the developing world, there is great need for chemical approaches to uncover novel lead compounds that perturb parasitic plant infections.

  18. Comparative Approaches to Genetic Discrimination: Chasing Shadows?

    Science.gov (United States)

    Joly, Yann; Feze, Ida Ngueng; Song, Lingqiao; Knoppers, Bartha M

    2017-05-01

    Genetic discrimination (GD) is one of the most pervasive issues associated with genetic research and its large-scale implementation. An increasing number of countries have adopted public policies to address this issue. Our research presents a worldwide comparative review and typology of these approaches. We conclude with suggestions for public policy development. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Dynamic traffic assignment : genetic algorithms approach

    Science.gov (United States)

    1997-01-01

    Real-time route guidance is a promising approach to alleviating congestion on the nations highways. A dynamic traffic assignment model is central to the development of guidance strategies. The artificial intelligence technique of genetic algorithm...

  20. Chemical fingerprints encode mother–offspring similarity, colony membership, relatedness, and genetic quality in fur seals

    Science.gov (United States)

    Stoffel, Martin A.; Caspers, Barbara A.; Forcada, Jaume; Giannakara, Athina; Baier, Markus; Eberhart-Phillips, Luke; Müller, Caroline; Hoffman, Joseph I.

    2015-01-01

    Chemical communication underpins virtually all aspects of vertebrate social life, yet remains poorly understood because of its highly complex mechanistic basis. We therefore used chemical fingerprinting of skin swabs and genetic analysis to explore the chemical cues that may underlie mother–offspring recognition in colonially breeding Antarctic fur seals. By sampling mother–offspring pairs from two different colonies, using a variety of statistical approaches and genotyping a large panel of microsatellite loci, we show that colony membership, mother–offspring similarity, heterozygosity, and genetic relatedness are all chemically encoded. Moreover, chemical similarity between mothers and offspring reflects a combination of genetic and environmental influences, the former partly encoded by substances resembling known pheromones. Our findings reveal the diversity of information contained within chemical fingerprints and have implications for understanding mother–offspring communication, kin recognition, and mate choice. PMID:26261311

  1. Chemical Genetics — A Versatile Method to Combine Science and Higher Level Teaching in Molecular Genetics

    Directory of Open Access Journals (Sweden)

    Björn Sandrock

    2012-10-01

    Full Text Available Phosphorylation is a key event in many cellular processes like cell cycle, transformation of environmental signals to transcriptional activation or polar growth. The chemical genetics approach can be used to analyse the effect of highly specific inhibition in vivo and is a promising method to screen for kinase targets. We have used this approach to study the role of the germinal centre kinase Don3 during the cell division in the phytopathogenic fungus Ustilago maydis. Due to the easy determination of the don3 phenotype we have chosen this approach for a genetic course for M.Sc. students and for IMPRS (International Max-Planck research school students. According to the principle of “problem-based learning” the aim of this two-week course is to transfer knowledge about the broad spectrum of kinases to the students and that the students acquire the ability to design their own analog-sensitive kinase of interest. In addition to these training goals, we benefit from these annual courses the synthesis of basic constructs for genetic modification of several kinases in our model system U. maydis.

  2. The calculus a genetic approach

    CERN Document Server

    Toeplitz, Otto

    2007-01-01

    When first published posthumously in 1963, this book presented a radically different approach to the teaching of calculus.  In sharp contrast to the methods of his time, Otto Toeplitz did not teach calculus as a static system of techniques and facts to be memorized. Instead, he drew on his knowledge of the history of mathematics and presented calculus as an organic evolution of ideas beginning with the discoveries of Greek scholars, such as Archimedes, Pythagoras, and Euclid, and developing through the centuries in the work of Kepler, Galileo, Fermat, Newton, and Leibniz. Through this unique a

  3. Mutagenicity of chemicals in genetically modified animals

    NARCIS (Netherlands)

    Willems MI; van Benthem J; LEO

    2001-01-01

    The strategy for assessing human health risks of chemicals consists of a large number of tests in different research disciplines. Tests include acute and chronic toxicity, genotoxicity, reproduction toxicity and carcinogenicity. Genotoxic properties of chemicals are assessed in short-term in vitro

  4. Genetic approaches in comparative and evolutionary physiology

    Science.gov (United States)

    Bridgham, Jamie T.; Kelly, Scott A.; Garland, Theodore

    2015-01-01

    Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. PMID:26041111

  5. Combined genetic effects of chemicals and radiation

    International Nuclear Information System (INIS)

    Kada, T.; Inoue, T.; Yokoiyama, A.; Russel, L.B.

    1979-01-01

    Interactions of chemicals and radiation are complex and there may exist other unexpected patterns that are not mentioned. We show some examples. Photodynamic mutation induction by fluorescein dyes and Radiosensitization with iodine compounds are classified as Interactions of chemicals and radiation outside of the cell. On the other hand, the Antimutagenic effects of cobaltous chloride is concerned with events taking place in cells that had already been exposed to a mutagenic agent. It is likely that the action of a mutagenic agent is not direct and that cellular functions, such as mutators or repair systems, are involved in the mutagenesis initiated by the agent. Such cellular functions can be affected by a second agent. In sexually reproducing organisms, the two agents can also act on separate cells (male and female germcells) which subsequently fuse. Interaction effects of all types will be useful in future research in shedding light on the main pathways of mutagenesis

  6. Combined genetic effects of chemicals and radiation

    International Nuclear Information System (INIS)

    Kada, T.; Inoue, T.; Yokoiyama, A.; Russell, L.B.

    1979-01-01

    The interactions of chemicals and radiation are complex, and there may exist other unexpected patterns. The photodynamic induction of mutation by fluorescein dyes, and the radiosensitization with iodine compounds are classified as the interactions of chemicals and radiation outside cells. On the other hand, the antimutagenic effects of cobaltous chloride is concerned with the events taking place in the cells that had already been exposed to mutagenic agents. It is likely that the action of mutagenic agents is not direct, and that cellular functions, such as mutators or repair systems, are involved in the mutagenesis initiated by the agents. Such cellular functions can be affected by a second agent. In sexually reproducing organisms, two agents can also act on separate cells (male and female germ cells) which subsequently fuse. In mice, the experiments combining the radiation applied to one sex with the chemicals given to the other sex are only in early stages. Males were irradiated with X-ray (spermatozoa and spermatids sampled) and females (mature oocytes) were treated with caffeine. When the endpoint was dominant lethal, the level of X-ray effect induced in the male genome was independent of the caffeine treatment of the female. However, when the endpoint was sex-chromosome-loss, and a different strain of female was used, the caffeine potentiation was statistically significant at 5% level. (Yamashita, S.)

  7. Genetic and chemical diversity of high mucilaginous plants of Sida complex by ISSR markers and chemical fingerprinting.

    Science.gov (United States)

    Thul, Sanjog T; Srivastava, Ankit K; Singh, Subhash C; Shanker, Karuna

    2011-09-01

    A method was developed based on multiple approaches wherein DNA and chemical analysis was carried out toward differentiation of important species of Sida complex that is being used for commercial preparation. Isolated DNA samples were successfully performed through PCR amplification using ISSR markers and degree of genetic diversity among the different species of Sida is compared with that of chemical diversity. For genetic fingerprint investigation, selected 10 ISSR primers generating reproducible banding patterns were used. Among the total of 63 amplicons, 62 were recorded as polymorphic, genetic similarity index deduced from ISSR profiles ranged from 12 to 51%. Based on similarity index, S. acuta and S. rhombifolia found to be most similar (51%). High number of species-specific bands played pivotal role to delineate species at genetic level. Investigation based on HPTLC fingerprints analysis revealed 23 bands representing to characteristic chemicals and similarity index ranged from 73 to 91%. Prominent distinguishable bands were observed only in S. acuta, while S. cordifolia and S. rhombifolia shared most bands making them difficult to identify on chemical fingerprint basis. This report summarizes the genotypic and chemotypic diversity and the use of profiles for authentication of species of Sida complex.

  8. Genetic susceptibility factors for multiple chemical sensitivity revisited

    DEFF Research Database (Denmark)

    Berg, Nikolaj Drimer; Rasmussen, Henrik Berg; Linneberg, Allan

    2010-01-01

    of this study was to investigate genetic susceptibility factors for MCS and self-reported chemical sensitivity in a population sample. Ninety six MCS patients and 1,207 controls from a general population divided into four severity groups of chemical sensitivity were genotyped for variants in the genes encoding......Multiple chemical sensitivity (MCS) is characterised by adverse effects due to exposure to low levels of chemical substances. Various genes, especially genes of importance to the metabolism of xenobiotic compounds, have been associated with MCS, but findings are inconsistent. The purpose...... significant (OR=1.2, p=0.28). Fast arylamine N-acetyltransferase 2 metaboliser status was associated with severity of chemical sensitivity only in the most severely affected group in the population sample (OR=3.1, p=0.04). The cholecystokinin 2 receptor allele with 21 CT repeats was associated with MCS when...

  9. Genetic engineering and chemical conjugation of potato virus X.

    Science.gov (United States)

    Lee, Karin L; Uhde-Holzem, Kerstin; Fischer, Rainer; Commandeur, Ulrich; Steinmetz, Nicole F

    2014-01-01

    Here we report the genetic engineering and chemical modification of potato virus X (PVX) for the presentation of various peptides, proteins, and fluorescent dyes, or other chemical modifiers. Three different ways of genetic engineering are described and by these means, peptides are successfully expressed not only when the foot and mouth disease virus (FMDV) 2A sequence or a flexible glycine-serine linker is included, but also when the peptide is fused directly to the PVX coat protein. When larger proteins or unfavorable peptide sequences are presented, a partial fusion via the FMDV 2A sequence is preferable. When these PVX chimeras retain the ability to assemble into viral particles and are thus able to infect plants systemically, they can be utilized to inoculate susceptible plants for isolation of sufficient amounts of virus particles for subsequent chemical modification. Chemical modification is required for the display of nonbiological ligands such as fluorophores, polymers, and small drug compounds. We present three methods of chemical bioconjugation. For direct conjugation of small chemical modifiers to solvent exposed lysines, N-hydroxysuccinimide chemistry can be applied. Bio-orthogonal reactions such as copper-catalyzed azide-alkyne cycloaddition or hydrazone ligation are alternatives to achieve more efficient conjugation (e.g., when working with high molecular weight or insoluble ligands). Furthermore, hydrazone ligation offers an attractive route for the introduction of pH-cleavable cargos (e.g., therapeutic molecules).

  10. Engineering electrical properties of graphene: chemical approaches

    International Nuclear Information System (INIS)

    Kim, Yong-Jin; Kim, Yuna; Hong, Byung Hee; Novoselov, Konstantin

    2015-01-01

    To ensure the high performance of graphene-based devices, it is necessary to engineer the electrical properties of graphene with enhanced conductivity, controlled work function, opened or closed bandgaps, etc. This can be performed by various non-covalent chemical approaches, including molecular adsorption, substrate-induced doping, polymerization on graphene, deposition of metallic thin films or nanoparticles, etc. In addition, covalent approaches such as the substitution of carbon atoms with boron or nitrogen and the functionalization with hydrogen or fluorine are useful to tune the bandgaps more efficiently, with better uniformity and stability. In this review, representative examples of chemically engineered graphene and its device applications will be reviewed, and remaining challenges will be discussed. (topical review)

  11. A stochastic approach to chemical evolution

    International Nuclear Information System (INIS)

    Copi, C.J.

    1997-01-01

    Observations of elemental abundances in the Galaxy have repeatedly shown an intrinsic scatter as a function of time and metallicity. The standard approach to chemical evolution does not attempt to address this scatter in abundances since only the mean evolution is followed. In this work, the scatter is addressed via a stochastic approach to solving chemical evolution models. Three simple chemical evolution scenarios are studied using this stochastic approach: a closed box model, an infall model, and an outflow model. These models are solved for the solar neighborhood in a Monte Carlo fashion. The evolutionary history of one particular region is determined randomly based on the star formation rate and the initial mass function. Following the evolution in an ensemble of such regions leads to the predicted spread in abundances expected, based solely on different evolutionary histories of otherwise identical regions. In this work, 13 isotopes are followed, including the light elements, the CNO elements, a few α-elements, and iron. It is found that the predicted spread in abundances for a 10 5 M circle-dot region is in good agreement with observations for the α-elements. For CN, the agreement is not as good, perhaps indicating the need for more physics input for low-mass stellar evolution. Similarly for the light elements, the predicted scatter is quite small, which is in contradiction to the observations of 3 He in HII regions. The models are tuned for the solar neighborhood so that good agreement with HII regions is not expected. This has important implications for low-mass stellar evolution and on using chemical evolution to determine the primordial light-element abundances in order to test big bang nucleosynthesis. copyright 1997 The American Astronomical Society

  12. Chemical and genetic tools to explore S1P biology.

    Science.gov (United States)

    Cahalan, Stuart M

    2014-01-01

    The zwitterionic lysophospholipid Sphingosine 1-Phosphate (S1P) is a pleiotropic mediator of physiology and pathology. The synthesis, transport, and degradation of S1P are tightly regulated to ensure that S1P is present in the proper concentrations in the proper location. The binding of S1P to five G protein-coupled S1P receptors regulates many physiological systems, particularly the immune and vascular systems. Our understanding of the functions of S1P has been aided by the tractability of the system to both chemical and genetic manipulation. Chemical modulators have been generated to affect most of the known components of S1P biology, including agonists of S1P receptors and inhibitors of enzymes regulating S1P production and degradation. Genetic knockouts and manipulations have been similarly engineered to disrupt the functions of individual S1P receptors or enzymes involved in S1P metabolism. This chapter will focus on the development and utilization of these chemical and genetic tools to explore the complex biology surrounding S1P and its receptors, with particular attention paid to the in vivo findings that these tools have allowed for.

  13. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Science.gov (United States)

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

  14. Genetic Approaches to Develop Salt Tolerant Germplasm

    KAUST Repository

    Tester, Mark A.

    2015-08-19

    Forty percent of the world\\'s food is produced under irrigation, and this is directly threatened by over-exploitation and changes in the global environment. One way to address this threat is to develop systems for increasing our ability to use lower quality water, in particular saline water. Low cost partial desalination of brackish water, use of saline water for cooling and increases in the salinity tolerance of crops can all contribute to the development of this new agricultural system. In this talk, the focus will be on the use of forward genetic approaches for discovery of genes related to salinity tolerance in barley and tomatoes. Rather than studying salinity tolerance as a trait in itself, we dissect salinity tolerance into a series of components that are hypothesised to contribute to overall salinity tolerance (following the paradigm of Munns & Tester, 2008). For example, one significant component of tolerance of most crop plants to moderate soil salinity is due to the ability to maintain low concentrations of Na+ in the leaves, and much analysis of this aspect has been done (e.g. Roy et al., 2013, 2014). A major site for the control of shoot Na+ accumulation is at the plasma membrane of the mature stele of the root. Alleles of HKT, a major gene underlying this transport process have been characterized and, in work led by Dr Rana Munns (CSIRO), have now been introgressed into commercial durum wheat and led to significantly increased yields in saline field conditions (Munns et al., 2012). The genotyping of mapping populations is now highly efficient. However, the ability to quantitatively phenotype these populations is now commonly limiting forward progress in plant science. The increasing power of digital imaging and computational technologies offers the opportunity to relieve this phenotyping bottleneck. The Plant Accelerator is a 4500m2 growth facility that provides non-destructive phenotyping of large populations of plants (http

  15. Chemical event chain model of coupled genetic oscillators.

    Science.gov (United States)

    Jörg, David J; Morelli, Luis G; Jülicher, Frank

    2018-03-01

    We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

  16. Chemical event chain model of coupled genetic oscillators

    Science.gov (United States)

    Jörg, David J.; Morelli, Luis G.; Jülicher, Frank

    2018-03-01

    We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

  17. A Chemical Activity Approach to Exposure and Risk Assessment of Chemicals

    DEFF Research Database (Denmark)

    Gobas, Frank A. P. C.; Mayer, Philipp; Parkerton, Thomas F.

    2018-01-01

    activity approach, its strengths and limitations, and provides examples of how this concept may be applied to the management of single chemicals and chemical mixtures. The examples demonstrate that the chemical activity approach provides a useful framework for 1) compiling and evaluating exposure......To support the goals articulated in the vision for exposure and risk assessment in the twenty-first century, we highlight the application of a thermodynamic chemical activity approach for the exposure and risk assessment of chemicals in the environment. The present article describes the chemical...... assessment. The article further illustrates that the chemical activity approach can support an adaptive management strategy for environmental stewardship of chemicals where “safe” chemical activities are established based on toxicological studies and presented as guidelines for environmental quality...

  18. Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge.

    Science.gov (United States)

    Martins, Joana; Vasconcelos, Vitor

    2015-11-13

    Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.

  19. Simulation Approach for Timing Analysis of Genetic Logic Circuits

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2017-01-01

    in a manner similar to electronic logic circuits, but they are much more stochastic and hence much harder to characterize. In this article, we introduce an approach to analyze the threshold value and timing of genetic logic circuits. We show how this approach can be used to analyze the timing behavior...... of single and cascaded genetic logic circuits. We further analyze the timing sensitivity of circuits by varying the degradation rates and concentrations. Our approach can be used not only to characterize the timing behavior but also to analyze the timing constraints of cascaded genetic logic circuits...

  20. Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment.

    Directory of Open Access Journals (Sweden)

    Miyako Kusano

    Full Text Available As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms.

  1. Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

    Science.gov (United States)

    Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

    2011-01-01

    As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

  2. Chemical and genetic defenses against disease in insect societies.

    Science.gov (United States)

    Stow, Adam; Beattie, Andrew

    2008-10-01

    The colonies of ants, bees, wasps and termites, the social insects, consist of large numbers of closely related individuals; circumstances ideal for contagious diseases. Antimicrobial assays of these animals have demonstrated a wide variety of chemical defenses against both bacteria and fungi that can be broadly classified as either external antiseptic compounds or internal immune molecules. Reducing the disease risks inherent in colonies of social insects is also achieved by behaviors, such as multiple mating or dispersal, that lower genetic relatedness both within- and among colonies. The interactions between social insects and their pathogens are complex, as illustrated by some ants that require antimicrobial and behavioral defenses against highly specialized fungi, such as those in the genus Cordyceps that attack larvae and adults and species in the genus Escovopsis that attack their food supplies. Studies of these defenses, especially in ants, have revealed remarkably sophisticated immune systems, including peptides induced by, and specific to, individual bacterial strains. The latter may be the result of the recruitment by the ants of antibiotic-producing bacteria but the extent of such three-way interactions remains unknown. There is strong experimental evidence that the evolution of sociality required dramatic increases in antimicrobial defenses and that microbes have been powerful selective agents. The antimicrobial chemicals and the insect-killing fungi may be useful in medicine and agriculture, respectively.

  3. Computational Approaches to Chemical Hazard Assessment

    Science.gov (United States)

    Luechtefeld, Thomas; Hartung, Thomas

    2018-01-01

    Summary Computational prediction of toxicity has reached new heights as a result of decades of growth in the magnitude and diversity of biological data. Public packages for statistics and machine learning make model creation faster. New theory in machine learning and cheminformatics enables integration of chemical structure, toxicogenomics, simulated and physical data in the prediction of chemical health hazards, and other toxicological information. Our earlier publications have characterized a toxicological dataset of unprecedented scale resulting from the European REACH legislation (Registration Evaluation Authorisation and Restriction of Chemicals). These publications dove into potential use cases for regulatory data and some models for exploiting this data. This article analyzes the options for the identification and categorization of chemicals, moves on to the derivation of descriptive features for chemicals, discusses different kinds of targets modeled in computational toxicology, and ends with a high-level perspective of the algorithms used to create computational toxicology models. PMID:29101769

  4. Mechanisms of Bunyavirus Virulence: A Genetic Approach.

    Science.gov (United States)

    1984-12-01

    of canine parvovirus Type-2, feline panleukopenia virus and mink enteritis virus. Virology 129,401-414. Partner A., Webster, R. G., and Bean W. J...CM, and Webster RG. Procedures for the characterization of the genetic material of candidate vaccine strains. Develop Biol Standard 39:15-24, 1977

  5. A “genetics first” approach to selection

    Science.gov (United States)

    A different approach for using genomic information in genetic improvement is proposed. Past research in population genetics and animal breeding combined with information on sequence variants suggest the possibility that selection might be able to capture a portion of inbreeding and heterosis effect...

  6. 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.

  7. Chemical Facility Preparedness: A Comprehensive Approach

    National Research Council Canada - National Science Library

    Pennington, Daniel

    2006-01-01

    .... Many sites are clustered together in densely populated areas. If terrorists cause catastrophic chemical releases or explosions at these key facilities, large numbers of Americans will be put at risk of injury or death...

  8. Genetic & epigenetic approach to human obesity

    Directory of Open Access Journals (Sweden)

    K Rajender Rao

    2014-01-01

    Full Text Available Obesity is an important clinical and public health challenge, epitomized by excess adipose tissue accumulation resulting from an imbalance in energy intake and energy expenditure. It is a forerunner for a variety of other diseases such as type-2-diabetes (T2D, cardiovascular diseases, some types of cancer, stroke, hyperlipidaemia and can be fatal leading to premature death. Obesity is highly heritable and arises from the interplay of multiple genes and environmental factors. Recent advancements in Genome-wide association studies (GWAS have shown important steps towards identifying genetic risks and identification of genetic markers for lifestyle diseases, especially for a metabolic disorder like obesity. According to the 12 th u0 pdate of Human Obesity Gene Map there are 253 quantity trait loci (QTL for obesity related phenotypes from 61 genome wide scan studies. Contribution of genetic propensity of individual ethnic and racial variations in obesity is an active area of research. Further, understanding its complexity as to how these variations could influence ones susceptibility to become or remain obese will lead us to a greater understanding of how obesity occurs and hopefully, how to prevent and treat this condition. In this review, various strategies adapted for such an analysis based on the recent advances in genome wide and functional variations in human obesity are discussed.

  9. Protein engineering approaches to chemical biotechnology.

    Science.gov (United States)

    Chen, Zhen; Zeng, An-Ping

    2016-12-01

    Protein engineering for the improvement of properties of biocatalysts and for the generation of novel metabolic pathways plays more and more important roles in chemical biotechnology aiming at the production of chemicals from biomass. Although widely used in single-enzyme catalysis process, protein engineering is only being increasingly explored in recent years to achieve more complex in vitro and in vivo biocatalytic processes. This review focuses on major contributions of protein engineering to chemical biotechnology in the field of multi-enzymatic cascade catalysis and metabolic engineering. Especially, we discuss and highlight recent strategies for combining pathway design and protein engineering for the production of novel products. Copyright © 2016. Published by Elsevier Ltd.

  10. Approach to chemical equilibrium in thermal models

    International Nuclear Information System (INIS)

    Boal, D.H.

    1984-01-01

    The experimentally measured (μ - , charged particle)/(μ - ,n) and (p,n/p,p') ratios for the emission of energetic nucleons are used to estimate the time evolution of a system of secondary nucleons produced in a direct interaction of a projectile or captured muon. The values of these ratios indicate that chemical equilibrium is not achieved among the secondary nucleons in noncomposite induced reactions, and this restricts the time scale for the emission of energetic nucleons to be about 0.7 x 10 -23 sec. It is shown that the reason why thermal equilibrium can be reached so rapidly for a particular nucleon species is that the sum of the particle spectra produced in multiple direct reactions looks surprisingly thermal. The rate equations used to estimate the reaction times for muon and nucleon induced reactions are then applied to heavy ion collisions, and it is shown that chemical equilibrium can be reached more rapidly, as one would expect

  11. Chemical toxicity approach for emergency response

    International Nuclear Information System (INIS)

    Bauer, T.

    2009-01-01

    In the event of an airborne release of chemical agent or toxic industrial chemical by accidental or intentional means, emergency responders must have a reasonable estimate of the location and size of the resulting hazard area. Emergency responders are responsible for warning persons downwind of the hazard to evacuate or shelter-in-place and must know where to look for casualties after the hazard has passed or dissipated. Given the same source characterization, modern hazard assessment models provide comparable concentration versus location and time estimates. Even urban hazard assessment models often provide similar predictions. There is a major shortcoming, though, in applying model output to estimating human toxicity effects. There exist a variety of toxicity values for non-lethal effects ranging from short-term to occupational to lifetime exposures. For health and safety purposes, these estimates are all safe-sided in converting animal data to human effects and in addressing the most sensitive subset of the population. In addition, these values are usually based on an assumed 1 hour exposure duration at constant concentration and do not reflect either a passing clouds concentration profile or duration. Emergency responders need expected value toxicity parameters rather than the existing safe-sided ones. This presentation will specify the types of toxicity values needed to provide appropriate chemical hazard estimates to emergency responders and will demonstrate how dramatically their use changes the hazard area.(author)

  12. Designing Genetics Instruction for a Socratic Approach

    Science.gov (United States)

    Idros, Sharifah Norhaidah Syed

    2004-01-01

    Science is at heart a rational activity. Reasoning, being an important component of critical thinking has been successfully taught using Socratic methods. As an approach, the instructor or designer of instruction models an inquiring and probing mind focusing on providing questions and not answers. The main aim has been to allow learners to…

  13. 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

  14. A Comprehensive Approach for Pectin Chemical and Functional Characterization

    DEFF Research Database (Denmark)

    de Sousa, António Felipe Gomes Teixeira

    In this work, a comprehensive approach for the chemical and functional analysis of pectin was used in order to relate the different extraction conditions used to the polymer structure and the final functional (mainly gelling) properties. A wide range of methods were utilized including chemical an...

  15. A multiobjective approach to the genetic code adaptability problem.

    Science.gov (United States)

    de Oliveira, Lariza Laura; de Oliveira, Paulo S L; Tinós, Renato

    2015-02-19

    The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why exactly the canonical code was selected among this huge number of possible genetic codes. Many researchers argue that the organization of the canonical code is a product of natural selection and that the code's robustness against mutations would support this hypothesis. In order to investigate the natural selection hypothesis, some researches employ optimization algorithms to identify regions of the genetic code space where best codes, according to a given evaluation function, can be found (engineering approach). The optimization process uses only one objective to evaluate the codes, generally based on the robustness for an amino acid property. Only one objective is also employed in the statistical approach for the comparison of the canonical code with random codes. We propose a multiobjective approach where two or more objectives are considered simultaneously to evaluate the genetic codes. In order to test our hypothesis that the multiobjective approach is useful for the analysis of the genetic code adaptability, we implemented a multiobjective optimization algorithm where two objectives are simultaneously optimized. Using as objectives the robustness against mutation with the amino acids properties polar requirement (objective 1) and robustness with respect to hydropathy index or molecular volume (objective 2), we found solutions closer to the canonical genetic code in terms of robustness, when compared with the results using only one objective reported by other authors. Using more objectives, more optimal solutions are obtained and, as a consequence, more information can be used to investigate the adaptability of the genetic code. The multiobjective approach

  16. Integrative Chemical-Biological Read-Across Approach for Chemical Hazard Classification

    Science.gov (United States)

    Low, Yen; Sedykh, Alexander; Fourches, Denis; Golbraikh, Alexander; Whelan, Maurice; Rusyn, Ivan; Tropsha, Alexander

    2013-01-01

    Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (”biological” similarity). The Chemical-Biological Read-Across (CBRA) approach infers each compound's toxicity from those of both chemical and biological analogs whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone, or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models. PMID:23848138

  17. A Hybrid Genetic Algorithm Approach for Optimal Power Flow

    Directory of Open Access Journals (Sweden)

    Sydulu Maheswarapu

    2011-08-01

    Full Text Available This paper puts forward a reformed hybrid genetic algorithm (GA based approach to the optimal power flow. In the approach followed here, continuous variables are designed using real-coded GA and discrete variables are processed as binary strings. The outcomes are compared with many other methods like simple genetic algorithm (GA, adaptive genetic algorithm (AGA, differential evolution (DE, particle swarm optimization (PSO and music based harmony search (MBHS on a IEEE30 bus test bed, with a total load of 283.4 MW. Its found that the proposed algorithm is found to offer lowest fuel cost. The proposed method is found to be computationally faster, robust, superior and promising form its convergence characteristics.

  18. Understanding the Science-Learning Environment: A Genetically Sensitive Approach

    Science.gov (United States)

    Haworth, Claire M. A.; Davis, Oliver S. P.; Hanscombe, Ken B.; Kovas, Yulia; Dale, Philip S.; Plomin, Robert

    2013-01-01

    Previous studies have shown that environmental influences on school science performance increase in importance from primary to secondary school. Here we assess for the first time the relationship between the science-learning environment and science performance using a genetically sensitive approach to investigate the aetiology of this link. 3000…

  19. An imaging genetics approach to understanding social influence

    Directory of Open Access Journals (Sweden)

    Emily eFalk

    2012-06-01

    Full Text Available Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain’s reward system. We next review neuroimaging evidence linking social punishment (exclusion to brain systems involved in the experience of pain, as well as evidence linking exclusion to conformity. We suggest that genetic variants that increase sensitivity to social cues may predispose individuals to be more sensitive to either social rewards or punishments (or potentially both, which in turn increases conformity and susceptibility to normative social influences more broadly. To this end, we review evidence for genetic moderators of neurochemical responses in the brain, and suggest ways in which genes and pharmacology may modulate sensitivity to social influences. We conclude by proposing an integrative imaging genetics approach to the study of brain mediators and genetic modulators of a variety of social influences on human attitudes, beliefs, and actions.

  20. An imaging genetics approach to understanding social influence.

    Science.gov (United States)

    Falk, Emily B; Way, Baldwin M; Jasinska, Agnes J

    2012-01-01

    Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain's reward system. We next review neuroimaging evidence linking social punishment (exclusion) to brain systems involved in the experience of pain, as well as evidence linking exclusion to conformity. We suggest that genetic variants that increase sensitivity to social cues may predispose individuals to be more sensitive to either social rewards or punishments (or potentially both), which in turn increases conformity and susceptibility to normative social influences more broadly. To this end, we review evidence for genetic moderators of neurochemical responses in the brain, and suggest ways in which genes and pharmacology may modulate sensitivity to social influences. We conclude by proposing an integrative imaging genetics approach to the study of brain mediators and genetic modulators of a variety of social influences on human attitudes, beliefs, and actions.

  1. WONOEP appraisal: new genetic approaches to study epilepsy

    Science.gov (United States)

    Rossignol, Elsa; Kobow, Katja; Simonato, Michele; Loeb, Jeffrey A.; Grisar, Thierry; Gilby, Krista L.; Vinet, Jonathan; Kadam, Shilpa D.; Becker, Albert J.

    2014-01-01

    Objective New genetic investigation techniques, including next-generation sequencing, epigenetic profiling, cell lineage mapping, targeted genetic manipulation of specific neuronal cell types, stem cell reprogramming and optogenetic manipulations within epileptic networks are progressively unravelling the mysteries of epileptogenesis and ictogenesis. These techniques have opened new avenues to discover the molecular basis of epileptogenesis and to study the physiological impacts of mutations in epilepsy-associated genes on a multilayer level, from cells to circuits. Methods This manuscript reviews recently published applications of these new genetic technologies in the study of epilepsy, as well as work presented by the authors at the genetic session of the XII Workshop on the Neurobiology of Epilepsy in Quebec, Canada. Results Next-generation sequencing is providing investigators with an unbiased means to assess the molecular causes of sporadic forms of epilepsy and have revealed the complexity and genetic heterogeneity of sporadic epilepsy disorders. To assess the functional impact of mutations in these newly identified genes on specific neuronal cell-types during brain development, new modeling strategies in animals, including conditional genetics in mice and in utero knockdown approaches, are enabling functional validation with exquisite cell-type and temporal specificity. In addition, optogenetics, using cell-type specific Cre recombinase driver lines, is enabling investigators to dissect networks involved in epilepsy. Genetically-encoded cell-type labeling is also providing new means to assess the role of the non-neuronal components of epileptic networks such as glial cells. Furthermore, beyond its role in revealing coding variants involved in epileptogenesis, next-generation sequencing can be used to assess the epigenetic modifications that lead to sustained network hyperexcitability in epilepsy, including methylation changes in gene promoters and non

  2. Graphene: chemical approaches to the synthesis and modification

    Energy Technology Data Exchange (ETDEWEB)

    Grayfer, E D; Makotchenko, V G; Nazarov, Albert S; Kim, S J; Fedorov, Vladimir E

    2011-08-31

    Published data on the new carbon nanomaterial, graphene, are described systematically from the chemist's standpoint. The attention is focused on the chemical methods of the synthesis of graphene-like materials from various precursors: natural and expanded graphite, graphite oxide, graphite intercalation compounds, etc. Approaches to the chemical modification of the graphene plane by various reagents and routes for the preparation of colloidal dispersions of graphene are considered. The bibliography includes 220 references.

  3. A probabilistic approach for validating protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

    Wang Bowei; Wang, Yunjun; Wishart, David S.

    2010-01-01

    It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

  4. A genetic ensemble approach for gene-gene interaction identification

    Directory of Open Access Journals (Sweden)

    Ho Joshua WK

    2010-10-01

    Full Text Available Abstract Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA and an ensemble of classifiers (called genetic ensemble. Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR and is slightly better than Polymorphism Interaction Analysis (PIA, which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of

  5. Redirecting adenovirus tropism by genetic, chemical, and mechanical modification of the adenovirus surface for cancer gene therapy.

    Science.gov (United States)

    Yoon, A-Rum; Hong, Jinwoo; Kim, Sung Wan; Yun, Chae-Ok

    2016-06-01

    Despite remarkable advancements, clinical evaluations of adenovirus (Ad)-mediated cancer gene therapies have highlighted the need for improved delivery and targeting. Genetic modification of Ad capsid proteins has been extensively attempted. Although genetic modification enhances the therapeutic potential of Ad, it is difficult to successfully incorporate extraneous moieties into the capsid and the engineering process is laborious. Recently, chemical modification of the Ad surface with nanomaterials and targeting moieties has been found to enhance Ad internalization into the target by both passive and active mechanisms. Alternatively, external stimulus-mediated targeting can result in selective accumulation of Ad in the tumor and prevent dissemination of Ad into surrounding nontarget tissues. In the present review, we discuss various genetic, chemical, and mechanical engineering strategies for overcoming the challenges that hinder the therapeutic efficacy of Ad-based approaches. Surface modification of Ad by genetic, chemical, or mechanical engineering strategies enables Ad to overcome the shortcomings of conventional Ad and enhances delivery efficiency through distinct and unique mechanisms that unmodified Ad cannot mimic. However, although the therapeutic potential of Ad-mediated gene therapy has been enhanced by various surface modification strategies, each strategy still possesses innate limitations that must be addressed, requiring innovative ideas and designs.

  6. Reverse Genetics Approaches for the Development of Influenza Vaccines

    Science.gov (United States)

    Nogales, Aitor; Martínez-Sobrido, Luis

    2016-01-01

    Influenza viruses cause annual seasonal epidemics and occasional pandemics of human respiratory disease. Influenza virus infections represent a serious public health and economic problem, which are most effectively prevented through vaccination. However, influenza viruses undergo continual antigenic variation, which requires either the annual reformulation of seasonal influenza vaccines or the rapid generation of vaccines against potential pandemic virus strains. The segmented nature of influenza virus allows for the reassortment between two or more viruses within a co-infected cell, and this characteristic has also been harnessed in the laboratory to generate reassortant viruses for their use as either inactivated or live-attenuated influenza vaccines. With the implementation of plasmid-based reverse genetics techniques, it is now possible to engineer recombinant influenza viruses entirely from full-length complementary DNA copies of the viral genome by transfection of susceptible cells. These reverse genetics systems have provided investigators with novel and powerful approaches to answer important questions about the biology of influenza viruses, including the function of viral proteins, their interaction with cellular host factors and the mechanisms of influenza virus transmission and pathogenesis. In addition, reverse genetics techniques have allowed the generation of recombinant influenza viruses, providing a powerful technology to develop both inactivated and live-attenuated influenza vaccines. In this review, we will summarize the current knowledge of state-of-the-art, plasmid-based, influenza reverse genetics approaches and their implementation to provide rapid, convenient, safe and more effective influenza inactivated or live-attenuated vaccines. PMID:28025504

  7. Applications of a formal approach to decipher discrete genetic networks.

    Science.gov (United States)

    Corblin, Fabien; Fanchon, Eric; Trilling, Laurent

    2010-07-20

    A growing demand for tools to assist the building and analysis of biological networks exists in systems biology. We argue that the use of a formal approach is relevant and applicable to address questions raised by biologists about such networks. The behaviour of these systems being complex, it is essential to exploit efficiently every bit of experimental information. In our approach, both the evolution rules and the partial knowledge about the structure and the behaviour of the network are formalized using a common constraint-based language. In this article our formal and declarative approach is applied to three biological applications. The software environment that we developed allows to specifically address each application through a new class of biologically relevant queries. We show that we can describe easily and in a formal manner the partial knowledge about a genetic network. Moreover we show that this environment, based on a constraint algorithmic approach, offers a wide variety of functionalities, going beyond simple simulations, such as proof of consistency, model revision, prediction of properties, search for minimal models relatively to specified criteria. The formal approach proposed here deeply changes the way to proceed in the exploration of genetic and biochemical networks, first by avoiding the usual trial-and-error procedure, and second by placing the emphasis on sets of solutions, rather than a single solution arbitrarily chosen among many others. Last, the constraint approach promotes an integration of model and experimental data in a single framework.

  8. Multiobjective genetic algorithm approaches to project scheduling under risk

    OpenAIRE

    Kılıç, Murat; Kilic, Murat

    2003-01-01

    In this thesis, project scheduling under risk is chosen as the topic of research. Project scheduling under risk is defined as a biobjective decision problem and is formulated as a 0-1 integer mathematical programming model. In this biobjective formulation, one of the objectives is taken as the expected makespan minimization and the other is taken as the expected cost minimization. As the solution approach to this biobjective formulation genetic algorithm (GA) is chosen. After carefully invest...

  9. An imaging genetics approach to understanding social influence

    OpenAIRE

    Emily eFalk; Emily eFalk; Baldwin eWay; Agnes eJasinska

    2012-01-01

    Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain’s reward system. We next review neur...

  10. An imaging genetics approach to understanding social influence

    OpenAIRE

    Falk, Emily B.; Way, Baldwin M.; Jasinska, Agnes J.

    2012-01-01

    Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain's reward system. We next review neuro...

  11. Human Genetic Marker for Resistance to Radiation and Chemicals

    International Nuclear Information System (INIS)

    Lieberman, Howard B.

    2001-01-01

    TO characterize the human HRDAD9 gene and evaluate its potential as a biomarker to predict susceptibility to the deleterious health effects potentially caused by exposure to radiations or chemicals present at DOE hazardous waste cleanup sites. HRAD9 is a human gene that is highly conserved throughout evolution. Related genes have been isolated from yeasts and mice, underscoring its biological significance. Most of our previous work involved characterization of the yeast gene cognate, wherein it was determined that the corresponding protein plays a significant role in promoting resistance of cells to radiations and chemicals, and in particular, controlling cell growth in response to DNA damage

  12. Molecular genetics and livestock selection. Approaches, opportunities and risks

    International Nuclear Information System (INIS)

    Williams, J.L.

    2005-01-01

    Following domestication, livestock were selected both naturally through adaptation to their environments and by man so that they would fulfil a particular use. As selection methods have become more sophisticated, rapid progress has been made in improving those traits that are easily measured. However, selection has also resulted in decreased diversity. In some cases, improved breeds have replaced local breeds, risking the loss of important survival traits. The advent of molecular genetics provides the opportunity to identify the genes that control particular traits by a gene mapping approach. However, as with selection, the early mapping studies focused on traits that are easy to measure. Where molecular genetics can play a valuable role in livestock production is by providing the means to select effectively for traits that are difficult to measure. Identifying the genes underpinning particular traits requires a population in which these traits are segregating. Fortunately, several experimental populations have been created that have allowed a wide range of traits to be studied. Gene mapping work in these populations has shown that the role of particular genes in controlling variation in a given trait can depend on the genetic background. A second finding is that the most favourable alleles for a trait may in fact. be present in animals that perform poorly for the trait. In the long term, knowledge of -the genes controlling particular traits, and the way they interact with the genetic background, will allow introgression between breeds and the assembly of genotypes that are best suited to particular environments, producing animals with the desired characteristics. If used wisely, this approach will maintain genetic diversity while improving performance over a wide range of desired traits. (author)

  13. Rationale for an integrated approach to genetic epidemiology.

    Science.gov (United States)

    Laberge, Claude M; Knoppers, Bartha Maria

    1992-10-01

    Genetic knowledge is now in the public domain and its interpretation by the media and the citizens brings the issues into the public forum of discussion for the necessary ethical, legal and socio-cultural evaluation of its application. Science is being perceived by some as dangerous and as requiring international regulation. Others feel that genetic knowledge will be the breakthrough that will permit medical progress and individual autonomy with regards to personal health and lifestyle choices. The mapping of the human genome has already yielded valuable information on an increasing number of diseases and their variants. Prevailing popular and journalistic archetypes ("imaginaires") used in the media are perceived by the producers as slowing down the possible application of genetic knowledge. The answers to these dilemmas are not readily apparent nor are they prescribed by classical philosophy of medicine. Since genetic knowledge eventually resides with the individual who carries the genes of disease and/or susceptibility, a logical approach to integration of this knowledge at a societal level would seem to reside with individual education and decision-making. The politics of the ensuing social debate could transform the current social contract since an individual's interests need to be balanced against those of his or her immediate family in the sharing of information. The ethical foundations of such a contract requires the genetic education of "Everyone" as a matter of urgent priority. Genetic education should not serve ideological power struggles between the medical establishment and the ethical-legal alliance. Instead, it should ensure the transfer of knowledge to physicians, to patients, to users, to planners, to social science and humanities researchers and to politicians, so that they may make "informed" and free decisions....

  14. Mouse genetic approaches applied to the normal tissue radiation response

    International Nuclear Information System (INIS)

    Haston, Christina K.

    2012-01-01

    The varying responses of inbred mouse models to radiation exposure present a unique opportunity to dissect the genetic basis of radiation sensitivity and tissue injury. Such studies are complementary to human association studies as they permit both the analysis of clinical features of disease, and of specific variants associated with its presentation, in a controlled environment. Herein I review how animal models are studied to identify specific genetic variants influencing predisposition to radiation-induced traits. Among these radiation-induced responses are documented strain differences in repair of DNA damage and in extent of tissue injury (in the lung, skin, and intestine) which form the base for genetic investigations. For example, radiation-induced DNA damage is consistently greater in tissues from BALB/cJ mice, than the levels in C57BL/6J mice, suggesting there may be an inherent DNA damage level per strain. Regarding tissue injury, strain specific inflammatory and fibrotic phenotypes have been documented for principally, C57BL/6 C3H and A/J mice but a correlation among responses such that knowledge of the radiation injury in one tissue informs of the response in another is not evident. Strategies to identify genetic differences contributing to a trait based on inbred strain differences, which include linkage analysis and the evaluation of recombinant congenic (RC) strains, are presented, with a focus on the lung response to irradiation which is the only radiation-induced tissue injury mapped to date. Such approaches are needed to reveal genetic differences in susceptibility to radiation injury, and also to provide a context for the effects of specific genetic variation uncovered in anticipated clinical association studies. In summary, mouse models can be studied to uncover heritable variation predisposing to specific radiation responses, and such variations may point to pathways of importance to phenotype development in the clinic.

  15. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs).

    Science.gov (United States)

    Arulandhu, Alfred J; van Dijk, Jeroen P; Dobnik, David; Holst-Jensen, Arne; Shi, Jianxin; Zel, Jana; Kok, Esther J

    2016-07-01

    With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples.

  16. Human exposure assessment: Approaches for chemicals (REACH) and biocides (BPD)

    NARCIS (Netherlands)

    Hemmen, J.J. van; Gerritsen-Ebben, R.

    2008-01-01

    The approaches that are indicated in the various guidance documents for the assessment of human exposure for chemicals and biocides are summarised. This reflects the TNsG (Technical notes for Guidance) version 2: human exposure assessment for biocidal products (1) under the BPD (Biocidal Products

  17. The Conceptual Change Approach to Teaching Chemical Equilibrium

    Science.gov (United States)

    Canpolat, Nurtac; Pinarbasi, Tacettin; Bayrakceken, Samih; Geban, Omer

    2006-01-01

    This study investigates the effect of a conceptual change approach over traditional instruction on students' understanding of chemical equilibrium concepts (e.g. dynamic nature of equilibrium, definition of equilibrium constant, heterogeneous equilibrium, qualitative interpreting of equilibrium constant, changing the reaction conditions). This…

  18. Genetic effects of combined chemical-X-ray treatments in male mouse germ cells

    International Nuclear Information System (INIS)

    Cattanach, B.M.; Rasberry, C.

    1987-01-01

    Several studies have shown that the yield of genetic damage induced by radiation in male mouse germ cells can be modified by chemical treatments. Pre-treatments with radio-protecting agents have given contradictory results but this appears to be largely attributable to the different germ cell stages tested and dependent upon the level of radiation damage induced. Pre-treatments which enhance the yield of genetic damage have been reported although, as yet, no tests have been conducted with radio-sensitizers. Another form of interaction between chemicals and radiation is specifically found with spermatogonial stem cells. Chemicals that kill cells can, by population depletion, substantially and predictably modify the genetic response to subsequent radiation exposure over a period of several days, or even weeks. Enhancement and reduction in the genetic yield can be attained, dependent upon the interval between treatments, with the modification also varying with the type of genetic damage scored. Post-treatment with one chemical (TEM) has been shown to reduce the genetic response to radiation exposure. (author)

  19. A Decision Analytic Approach to Exposure-Based Chemical ...

    Science.gov (United States)

    The manufacture of novel synthetic chemicals has increased in volume and variety, but often the environmental and health risks are not fully understood in terms of toxicity and, in particular, exposure. While efforts to assess risks have generally been effective when sufficient data are available, the hazard and exposure data necessary to assess risks adequately are unavailable for the vast majority of chemicals in commerce. The US Environmental Protection Agency has initiated the ExpoCast Program to develop tools for rapid chemical evaluation based on potential for exposure. In this context, a model is presented in which chemicals are evaluated based on inherent chemical properties and behaviorally-based usage characteristics over the chemical’s life cycle. These criteria are assessed and integrated within a decision analytic framework, facilitating rapid assessment and prioritization for future targeted testing and systems modeling. A case study outlines the prioritization process using 51 chemicals. The results show a preliminary relative ranking of chemicals based on exposure potential. The strength of this approach is the ability to integrate relevant statistical and mechanistic data with expert judgment, allowing for an initial tier assessment that can further inform targeted testing and risk management strategies. The National Exposure Research Laboratory′s (NERL′s) Human Exposure and Atmospheric Sciences Division (HEASD) conducts research in suppor

  20. General approaches to the risk assessment of chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, Patrick [Commission of the European Communities, Directorate General XI, Environment, Nuclear Safety and Civil Protection (Belgium)

    1992-07-01

    deciding upon the granting of permits for landfill sites or the discharge of toxic chemicals to water or air and in doing so they must take into account the hydrology, geology and climate of the specific locality. While the basic approach to chemical risk assessment will be the same, irrespective of the specific objective for which the assessment is carried out, the details will vary as a function of: the product type (pharmaceutical, pesticide, industrial chemical, etc.), the target population of interest (patient, environment, consumer, worker, etc.) and the exposure scenario (global, international, national, local)

  1. General approaches to the risk assessment of chemicals

    International Nuclear Information System (INIS)

    Murphy, Patrick

    1992-01-01

    deciding upon the granting of permits for landfill sites or the discharge of toxic chemicals to water or air and in doing so they must take into account the hydrology, geology and climate of the specific locality. While the basic approach to chemical risk assessment will be the same, irrespective of the specific objective for which the assessment is carried out, the details will vary as a function of: the product type (pharmaceutical, pesticide, industrial chemical, etc.), the target population of interest (patient, environment, consumer, worker, etc.) and the exposure scenario (global, international, national, local)

  2. A computational approach to chemical etiologies of diabetes

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Brunak, Søren; Grandjean, Philippe

    2013-01-01

    Computational meta-analysis can link environmental chemicals to genes and proteins involved in human diseases, thereby elucidating possible etiologies and pathogeneses of non-communicable diseases. We used an integrated computational systems biology approach to examine possible pathogenetic...... linkages in type 2 diabetes (T2D) through genome-wide associations, disease similarities, and published empirical evidence. Ten environmental chemicals were found to be potentially linked to T2D, the highest scores were observed for arsenic, 2,3,7,8-tetrachlorodibenzo-p-dioxin, hexachlorobenzene...

  3. An Airborne Conflict Resolution Approach Using a Genetic Algorithm

    Science.gov (United States)

    Mondoloni, Stephane; Conway, Sheila

    2001-01-01

    An airborne conflict resolution approach is presented that is capable of providing flight plans forecast to be conflict-free with both area and traffic hazards. This approach is capable of meeting constraints on the flight plan such as required times of arrival (RTA) at a fix. The conflict resolution algorithm is based upon a genetic algorithm, and can thus seek conflict-free flight plans meeting broader flight planning objectives such as minimum time, fuel or total cost. The method has been applied to conflicts occurring 6 to 25 minutes in the future in climb, cruise and descent phases of flight. The conflict resolution approach separates the detection, trajectory generation and flight rules function from the resolution algorithm. The method is capable of supporting pilot-constructed resolutions, cooperative and non-cooperative maneuvers, and also providing conflict resolution on trajectories forecast by an onboard FMC.

  4. Chemical-genetic profile analysis of five inhibitory compounds in yeast.

    Science.gov (United States)

    Alamgir, Md; Erukova, Veronika; Jessulat, Matthew; Azizi, Ali; Golshani, Ashkan

    2010-08-06

    Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action. These profiles can help elucidate the complex interactions between small bioactive compounds and the cell machinery, and explain putative gene function(s). Colony size reduction was used to investigate the chemical-genetic profile of cycloheximide, 3-amino-1,2,4-triazole, paromomycin, streptomycin and neomycin in the yeast Saccharomyces cerevisiae. These compounds target the process of protein biosynthesis. More than 70,000 strains were analyzed from the array of gene deletion mutant yeast strains. As expected, the overall profiles of the tested compounds were similar, with deletions for genes involved in protein biosynthesis being the major category followed by metabolism. This implies that novel genes involved in protein biosynthesis could be identified from these profiles. Further investigations were carried out to assess the activity of three profiled genes in the process of protein biosynthesis using relative fitness of double mutants and other genetic assays. Chemical-genetic profiles provide insight into the molecular mechanism(s) of the examined compounds by elucidating their potential primary and secondary cellular target sites. Our follow-up investigations into the activity of three profiled genes in the process of protein biosynthesis provided further evidence concerning the usefulness of chemical-genetic analyses for annotating gene functions. We termed these genes TAE2, TAE3 and TAE4 for translation associated elements 2-4.

  5. Chemical-genetic profile analysis of five inhibitory compounds in yeast

    Directory of Open Access Journals (Sweden)

    Alamgir Md

    2010-08-01

    Full Text Available Abstract Background Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action. These profiles can help elucidate the complex interactions between small bioactive compounds and the cell machinery, and explain putative gene function(s. Results Colony size reduction was used to investigate the chemical-genetic profile of cycloheximide, 3-amino-1,2,4-triazole, paromomycin, streptomycin and neomycin in the yeast Saccharomyces cerevisiae. These compounds target the process of protein biosynthesis. More than 70,000 strains were analyzed from the array of gene deletion mutant yeast strains. As expected, the overall profiles of the tested compounds were similar, with deletions for genes involved in protein biosynthesis being the major category followed by metabolism. This implies that novel genes involved in protein biosynthesis could be identified from these profiles. Further investigations were carried out to assess the activity of three profiled genes in the process of protein biosynthesis using relative fitness of double mutants and other genetic assays. Conclusion Chemical-genetic profiles provide insight into the molecular mechanism(s of the examined compounds by elucidating their potential primary and secondary cellular target sites. Our follow-up investigations into the activity of three profiled genes in the process of protein biosynthesis provided further evidence concerning the usefulness of chemical-genetic analyses for annotating gene functions. We termed these genes TAE2, TAE3 and TAE4 for translation associated elements 2-4.

  6. The TSCA interagency testing committee`s approaches to screening and scoring chemicals and chemical groups: 1977-1983

    Energy Technology Data Exchange (ETDEWEB)

    Walker, J.D. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    This paper describes the TSCA interagency testing committee`s (ITC) approaches to screening and scoring chemicals and chemical groups between 1977 and 1983. During this time the ITC conducted five scoring exercises to select chemicals and chemical groups for detailed review and to determine which of these chemicals and chemical groups should be added to the TSCA Section 4(e) Priority Testing List. 29 refs., 1 fig., 2 tabs.

  7. Modeling AEC—New Approaches to Study Rare Genetic Disorders

    Science.gov (United States)

    Koch, Peter J.; Dinella, Jason; Fete, Mary; Siegfried, Elaine C.; Koster, Maranke I.

    2015-01-01

    Ankyloblepharon-ectodermal defects-cleft lip/palate (AEC) syndrome is a rare monogenetic disorder that is characterized by severe abnormalities in ectoderm-derived tissues, such as skin and its appendages. A major cause of morbidity among affected infants is severe and chronic skin erosions. Currently, supportive care is the only available treatment option for AEC patients. Mutations in TP63, a gene that encodes key regulators of epidermal development, are the genetic cause of AEC. However, it is currently not clear how mutations in TP63 lead to the various defects seen in the patients’ skin. In this review, we will discuss current knowledge of the AEC disease mechanism obtained by studying patient tissue and genetically engineered mouse models designed to mimic aspects of the disorder. We will then focus on new approaches to model AEC, including the use of patient cells and stem cell technology to replicate the disease in a human tissue culture model. The latter approach will advance our understanding of the disease and will allow for the development of new in vitro systems to identify drugs for the treatment of skin erosions in AEC patients. Further, the use of stem cell technology, in particular induced pluripotent stem cells (iPSC), will enable researchers to develop new therapeutic approaches to treat the disease using the patient’s own cells (autologous keratinocyte transplantation) after correction of the disease-causing mutations. PMID:24665072

  8. QCD phase transition at real chemical potential with canonical approach

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, Atsushi [RCNP, Osaka University,Osaka, 567-0047 (Japan); Nishina Center, RIKEN,Wako, Saitama 351-0198 (Japan); School of Biomedicine, Far Eastern Federal University,Vladivostok, 690950 (Russian Federation); Oka, Shotaro [Institute of Theoretical Physics, Department of Physics, Rikkyo University,Toshima-ku, Tokyo 171-8501 (Japan); Taniguchi, Yusuke [Graduate School of Pure and Applied Sciences, University of Tsukuba,Tsukuba, Ibaraki 305-8571 (Japan)

    2016-02-08

    We study the finite density phase transition in the lattice QCD at real chemical potential. We adopt a canonical approach and the canonical partition function is constructed for N{sub f}=2 QCD. After derivation of the canonical partition function we calculate observables like the pressure, the quark number density, its second cumulant and the chiral condensate as a function of the real chemical potential. We covered a wide range of temperature region starting from the confining low to the deconfining high temperature; 0.65T{sub c}≤T≤3.62T{sub c}. We observe a possible signal of the deconfinement and the chiral restoration phase transition at real chemical potential below T{sub c} starting from the confining phase. We give also the convergence range of the fugacity expansion.

  9. The terrorist threat nuclear, radiological, biological, chemical - a medical approach

    International Nuclear Information System (INIS)

    Revel, M.C. de; Gourmelon, M.C.S.; Vidal, P.C.; Renaudeau, P.C.S.

    2005-01-01

    Since September 11, 2001, the fear of a large scale nuclear, biological and/or chemical terrorism is taken again into consideration at the highest level of national policies of risk prevention. The advent of international terrorism implies a cooperation between the military defense and the civil defense. The nuclear, radiological, biological and chemical (NRBC) experts of the health service of army and of civil defense will have to work together in case of major terror attack. This book presents this cooperation between civil and military experts in the NRBC domain: risk analysis, national defense plans, crisis management, syndromes and treatments. The different aspects linked with the use of nuclear, biological and chemical weapons are analyzed by the best experts from French medical and research institutes. All topics of each NRBC domain are approached: historical, basic, diagnostic, therapeutic and preventive. (J.S.)

  10. Maximizing lifetime of wireless sensor networks using genetic approach

    DEFF Research Database (Denmark)

    Wagh, Sanjeev; Prasad, Ramjee

    2014-01-01

    The wireless sensor networks are designed to install the smart network applications or network for emergency solutions, where human interaction is not possible. The nodes in wireless sensor networks have to self organize as per the users requirements through monitoring environments. As the sensor......-objective parameters are considered to solve the problem using genetic algorithm of evolutionary approach.......The wireless sensor networks are designed to install the smart network applications or network for emergency solutions, where human interaction is not possible. The nodes in wireless sensor networks have to self organize as per the users requirements through monitoring environments. As the sensor...

  11. A reverse genetics approach to study feline infectious peritonitis.

    Science.gov (United States)

    Tekes, Gergely; Spies, Danica; Bank-Wolf, Barbara; Thiel, Volker; Thiel, Heinz-Jürgen

    2012-06-01

    Feline infectious peritonitis (FIP) is a lethal immunopathological disease caused by feline coronaviruses (FCoVs). Here, we describe a reverse genetics approach to study FIP by assessing the pathogenicity of recombinant type I and type II and chimeric type I/type II FCoVs. All recombinant FCoVs established productive infection in cats, and recombinant type II FCoV (strain 79-1146) induced FIP. Virus sequence analyses from FIP-diseased cats revealed that the 3c gene stop codon of strain 79-1146 has changed to restore a full-length open reading frame (ORF).

  12. Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

    Science.gov (United States)

    Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

    2014-11-12

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

  13. A genetic-neural artificial intelligence approach to resins optimization

    International Nuclear Information System (INIS)

    Cabral, Denise C.; Barros, Marcio P.; Lapa, Celso M.F.; Pereira, Claudio M.N.A.

    2005-01-01

    This work presents a preliminary study about the viability and adequacy of a new methodology for the definition of one of the main properties of ion exchange resins used for isotopic separation. Basically, the main problem is the definition of pelicule diameter in case of pelicular ion exchange resins, in order to achieve the best performance in the shortest time. In order to achieve this, a methodology was developed, based in two classic techniques of Artificial Intelligence (AI). At first, an artificial neural network (NN) was trained to map the existing relations between the nucleus radius and the resin's efficiency associated with the exchange time. Later on, a genetic algorithm (GA) was developed in order to find the best pelicule dimension. Preliminary results seem to confirm the potential of the method, and this can be used in any chemical process employing ion exchange resins. (author)

  14. Dating Antarctic ice sheet collapse: Proposing a molecular genetic approach

    Science.gov (United States)

    Strugnell, Jan M.; Pedro, Joel B.; Wilson, Nerida G.

    2018-01-01

    Sea levels at the end of this century are projected to be 0.26-0.98 m higher than today. The upper end of this range, and even higher estimates, cannot be ruled out because of major uncertainties in the dynamic response of polar ice sheets to a warming climate. Here, we propose an ecological genetics approach that can provide insight into the past stability and configuration of the West Antarctic Ice Sheet (WAIS). We propose independent testing of the hypothesis that a trans-Antarctic seaway occurred at the last interglacial. Examination of the genomic signatures of bottom-dwelling marine species using the latest methods can provide an independent window into the integrity of the WAIS more than 100,000 years ago. Periods of connectivity facilitated by trans-Antarctic seaways could be revealed by dating coalescent events recorded in DNA. These methods allow alternative scenarios to be tested against a fit to genomic data. Ideal candidate taxa for this work would need to possess a circumpolar distribution, a benthic habitat, and some level of genetic structure indicated by phylogeographical investigation. The purpose of this perspective piece is to set out an ecological genetics method to help resolve when the West Antarctic Ice Shelf last collapsed.

  15. Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

    OpenAIRE

    Adrian Jinich; Dmitrij Rappoport; Ian Dunn; Benjamin Sanchez-Lengeling; Roberto Olivares-Amaya; Elad Noor; Arren Bar Even; Alán Aspuru-Guzik

    2014-01-01

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfe...

  16. [DIFFERENT APPROACHES FOR CHEMICAL RISK ASSESSMENT IN LABORATORIES].

    Science.gov (United States)

    Caporossi, Lidia; Papaleo, Bruno; Capanna, Silvia; Calicchia, Sara; Marcellini, Laura; De Rosa, Mariangela; Castellano, Paola

    2015-01-01

    The aim of this study was to compare the different approaches used for chemical risk assessment, in relation to the perception of riskfor operators, in some research laboratories of a hospital in Rome. All information regarding the chemicals used for the application of three algorithmic models for chemical risk assessment ("Movarisch", "Inforisk", "Archimede") were collected. An environmental and biological monitoring and a study on the combined exposure to multiple chemicals using the World Health Organization proposed steps were carried out. A questionnaire was prepared for the identification of risk perception. An estimation of chemical risk with algorithms was compared with data from monitoring: findings showed that estimated risk was higher than those identified with airborne or urine concentrations, always under their limit values. The study of multiple exposure showed a possible cumulative risk, in some cases, but the conditions of use (volume and time) often bring to a reduced one. The perception of risk attributed to the monitored hazardous substances showed a correct perception in all laboratories and for all workers, with regard to the substances manipulated.

  17. Predicting the carcinogenicity of chemicals with alternative approaches: recent advances.

    Science.gov (United States)

    Benigni, Romualdo

    2014-09-01

    Alternative approaches to the rodent bioassay are necessary for early identification of problematic drugs and biocides during the development process, and are the only practicable tool for assessing environmental chemicals with no or adequate safety documentation. This review informs on: i) the traditional prescreening through genotoxicity testing; ii) an integrative approach that assesses DNA-reactivity and ability to disorganize tissues; iii) new applications of omics technologies (ToxCast/Tox21 project); iv) a pragmatic approach aimed at filling data gaps by intrapolating/extrapolating from similar chemicals (read-across, category formation). The review also approaches the issue of the concerns about false-positive and false-negative results that prevents a wider acceptance and use of alternatives. The review addresses strengths and limitations of various proposals, and concludes on the need of differential approaches to the issue of false negatives and false positives. False negatives can be eliminated or reduced below the variability of the animal assay with conservative quantitative structure-activity relationships or in vitro tests; false positives can be cleared with ad hoc mechanistically based follow-ups. This framework can permit a reduction of animal testing and a better protection of human health.

  18. Nuclear power plant maintenance scheduling dilemma: a genetic algorithm approach

    International Nuclear Information System (INIS)

    Mahdavi, M.H.; Modarres, M.

    2004-01-01

    There are huge numbers of components scheduled for maintenance when a nuclear power plant is shut down. Among these components, a number of them are safety related which their operability as well as reliability when plant becomes up is main concerns. Not performing proper maintenance on this class of components/system would impose substantial risk on operating the NPP. In this paper a new approach based on genetic algorithms is presented to optimize the NPP maintenance schedule during shutdown. following this approach the cost incurred by maintenance activities for each schedule is balanced with the risk imposed by the maintenance scheduling plan to the plant operation status when it is up. The risk model implemented in the GA scheduler as its evaluation function is developed on the basis of the probabilistic risk assessment methodology. the Ga optimizers itself is shown to be superior compared to other optimization methods such as the monte carlo technique

  19. A Heuristics Approach for Classroom Scheduling Using Genetic Algorithm Technique

    Science.gov (United States)

    Ahmad, Izah R.; Sufahani, Suliadi; Ali, Maselan; Razali, Siti N. A. M.

    2018-04-01

    Reshuffling and arranging classroom based on the capacity of the audience, complete facilities, lecturing time and many more may lead to a complexity of classroom scheduling. While trying to enhance the productivity in classroom planning, this paper proposes a heuristic approach for timetabling optimization. A new algorithm was produced to take care of the timetabling problem in a university. The proposed of heuristics approach will prompt a superior utilization of the accessible classroom space for a given time table of courses at the university. Genetic Algorithm through Java programming languages were used in this study and aims at reducing the conflicts and optimizes the fitness. The algorithm considered the quantity of students in each class, class time, class size, time accessibility in each class and lecturer who in charge of the classes.

  20. Production of amino acids - Genetic and metabolic engineering approaches.

    Science.gov (United States)

    Lee, Jin-Ho; Wendisch, Volker F

    2017-12-01

    The biotechnological production of amino acids occurs at the million-ton scale and annually about 6milliontons of l-glutamate and l-lysine are produced by Escherichia coli and Corynebacterium glutamicum strains. l-glutamate and l-lysine production from starch hydrolysates and molasses is very efficient and access to alternative carbon sources and new products has been enabled by metabolic engineering. This review focusses on genetic and metabolic engineering of amino acid producing strains. In particular, rational approaches involving modulation of transcriptional regulators, regulons, and attenuators will be discussed. To address current limitations of metabolic engineering, this article gives insights on recent systems metabolic engineering approaches based on functional tools and method such as genome reduction, amino acid sensors based on transcriptional regulators and riboswitches, CRISPR interference, small regulatory RNAs, DNA scaffolding, and optogenetic control, and discusses future prospects. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. A genetic algorithm approach to recognition and data mining

    Energy Technology Data Exchange (ETDEWEB)

    Punch, W.F.; Goodman, E.D.; Min, Pei [Michigan State Univ., East Lansing, MI (United States)] [and others

    1996-12-31

    We review here our use of genetic algorithm (GA) and genetic programming (GP) techniques to perform {open_quotes}data mining,{close_quotes} the discovery of particular/important data within large datasets, by finding optimal data classifications using known examples. Our first experiments concentrated on the use of a K-nearest neighbor algorithm in combination with a GA. The GA selected weights for each feature so as to optimize knn classification based on a linear combination of features. This combined GA-knn approach was successfully applied to both generated and real-world data. We later extended this work by substituting a GP for the GA. The GP-knn could not only optimize data classification via linear combinations of features but also determine functional relationships among the features. This allowed for improved performance and new information on important relationships among features. We review the effectiveness of the overall approach on examples from biology and compare the effectiveness of the GA and GP.

  2. NIF: Impacts of chemical accidents and comparison of chemical/radiological accident approaches

    International Nuclear Information System (INIS)

    Lazaro, M.A.; Policastro, A.J.; Rhodes, M.

    1996-01-01

    The US Department of Energy (DOE) proposes to construct and operate the National Ignition Facility (NIF). The goals of the NIF are to (1) achieve fusion ignition in the laboratory for the first time by using inertial confinement fusion (ICF) technology based on an advanced-design neodymium glass solid-state laser, and (2) conduct high-energy-density experiments in support of national security and civilian applications. The primary focus of this paper is worker-public health and safety issues associated with postulated chemical accidents during the operation of NIF. The key findings from the accident analysis will be presented. Although NIF chemical accidents will be emphasized, the important differences between chemical and radiological accident analysis approaches and the metrics for reporting results will be highlighted. These differences are common EIS facility and transportation accident assessments

  3. Genetic and neural approaches to nuclear transient identification

    International Nuclear Information System (INIS)

    Almeida, Jose Carlos Soares de; Mol, Antonio Carlos de Abreu; Pereira, Claudio Marcio Nascimento Abreu; Lapa, Celso Marcelo Franklin

    2005-01-01

    This work presents two approaches for pattern recognition to the same set of reactor signals. The first one describes a possibilistic approach optimized by genetic algorithm. The use of a possibilistic classification provides a natural and consistent classification rules, leading naturally to a good heuristic to handle the 'don't know' response, in case of unrecognized transient, which is fairly desirable in transient classification systems where safety is critical, since wrong or not reliable classifications can be catastrophic. Application of the proposed approach to a nuclear transient identification problem reveals good capability of the genetic algorithm in learning optimized possibilistic classification rules for efficient diagnosis including 'don't know' response. The second one uses two multilayer neural networks (NN). The first NN is responsible for the dynamic identification. This NN uses, as input, a short set (in a moving time window) of recent measurements of each variable avoiding the necessity of using starting events. The second NN is used to validate the instantaneous identification (from the first net) through the validation of each variable. This net is responsible for allowing the system to provide a 'don't know' response. In order to validate both methods, a Nuclear Power Plant (NPP) transient identification problem comprising postulated accidents, simulated for a pressurized water reactor, was proposed in the validation process it has been considered noisy data in order to evaluate the method robustness. Obtained results reveal the ability of the methods in dealing with both dynamic identification of transients and correct 'don't know' response. (author)

  4. A genetic approach to shape reconstruction in limited data tomography

    International Nuclear Information System (INIS)

    Turcanu, C.; Craciunescu, T.

    2001-01-01

    The paper proposes a new method for shape reconstruction in computerized tomography. Unlike nuclear medicine applications, in physical science problems we are often confronted with limited data sets: constraints in the number of projections or limited view angles . The problem of image reconstruction from projection may be considered as a problem of finding an image (solution) having projections that match the experimental ones. In our approach, we choose a statistical correlation coefficient to evaluate the fitness of any potential solution. The optimization process is carried out by a genetic algorithm. The algorithm has some features common to all genetic algorithms but also some problem-oriented characteristics. One of them is that a chromosome, representing a potential solution, is not linear but coded as a matrix of pixels corresponding to a two-dimensional image. This kind of internal representation reflects the genuine manifestation and slight differences between two points situated in the original problem space give rise to similar differences once they become coded. Another particular feature is a newly built crossover operator: the grid-based crossover, suitable for high dimension two-dimensional chromosomes. Except for the population size and the dimension of the cutting grid for the grid-based crossover, all the other parameters of the algorithm are independent of the geometry of the tomographic reconstruction. The performances of the method are evaluated on a phantom typical for an application with limited data sets: the determination of the neutron energy spectra with time resolution in case of short-pulsed neutron emission. A genetic reconstruction is presented. The qualitative judgement and also the quantitative one, based on some figures of merit, point out that the proposed method ensures an improved reconstruction of shapes, sizes and resolution in the image, even in the presence of noise. (authors)

  5. Human Metabolic Enzymes Deficiency: A Genetic Mutation Based Approach

    Directory of Open Access Journals (Sweden)

    Swati Chaturvedi

    2016-01-01

    Full Text Available One of the extreme challenges in biology is to ameliorate the understanding of the mechanisms which emphasize metabolic enzyme deficiency (MED and how these pretend to have influence on human health. However, it has been manifested that MED could be either inherited as inborn error of metabolism (IEM or acquired, which carries a high risk of interrupted biochemical reactions. Enzyme deficiency results in accumulation of toxic compounds that may disrupt normal organ functions and cause failure in producing crucial biological compounds and other intermediates. The MED related disorders cover widespread clinical presentations and can involve almost any organ system. To sum up the causal factors of almost all the MED-associated disorders, we decided to embark on a less traveled but nonetheless relevant direction, by focusing our attention on associated gene family products, regulation of their expression, genetic mutation, and mutation types. In addition, the review also outlines the clinical presentations as well as diagnostic and therapeutic approaches.

  6. A genetic epidemiology approach to cyber-security.

    Science.gov (United States)

    Gil, Santiago; Kott, Alexander; Barabási, Albert-László

    2014-07-16

    While much attention has been paid to the vulnerability of computer networks to node and link failure, there is limited systematic understanding of the factors that determine the likelihood that a node (computer) is compromised. We therefore collect threat log data in a university network to study the patterns of threat activity for individual hosts. We relate this information to the properties of each host as observed through network-wide scans, establishing associations between the network services a host is running and the kinds of threats to which it is susceptible. We propose a methodology to associate services to threats inspired by the tools used in genetics to identify statistical associations between mutations and diseases. The proposed approach allows us to determine probabilities of infection directly from observation, offering an automated high-throughput strategy to develop comprehensive metrics for cyber-security.

  7. Integrating exposure into chemical alternatives assessment using a qualitative approach

    DEFF Research Database (Denmark)

    Greggs, Bill; Arnold, Scott; Burns, T. E.

    2016-01-01

    , other attributes beyond hazard are also important, including exposure, risk, life-cycle impacts, performance, cost, and social responsibility. Building on the 2014 recommendations by the U.S. National Academy of Sciences to improve AA decisions by including comparative exposure assessment, the HESI...... Sustainable Chemical Alternatives Technical Committee, which consists of scientists from academia, industry, government, and NGOs, has developed a qualitative comparative exposure approach. Conducting such a comparison can screen for alternatives that are expected to have a higher human or environmental...... not necessarily reflect the views or policies of the U.S. Environmental Protection Agency....

  8. Marine Derived Polysaccharides for Biomedical Applications: Chemical Modification Approaches

    Directory of Open Access Journals (Sweden)

    Paola Laurienzo

    2008-09-01

    Full Text Available Polysaccharide-based biomaterials are an emerging class in several biomedical fields such as tissue regeneration, particularly for cartilage, drug delivery devices and gelentrapment systems for the immobilization of cells. Important properties of the polysaccharides include controllable biological activity, biodegradability, and their ability to form hydrogels. Most of the polysaccharides used derive from natural sources; particularly, alginate and chitin, two polysaccharides which have an extensive history of use in medicine, pharmacy and basic sciences, and can be easily extracted from marine plants (algae kelp and crab shells, respectively. The recent rediscovery of poly-saccharidebased materials is also attributable to new synthetic routes for their chemical modification, with the aim of promoting new biological activities and/or to modify the final properties of the biomaterials for specific purposes. These synthetic strategies also involve the combination of polysaccharides with other polymers. A review of the more recent research in the field of chemical modification of alginate, chitin and its derivative chitosan is presented. Moreover, we report as case studies the results of our recent work concerning various different approaches and applications of polysaccharide-based biomaterials, such as the realization of novel composites based on calcium sulphate blended with alginate and with a chemically modified chitosan, the synthesis of novel alginate-poly(ethylene glycol copolymers and the development of a family of materials based on alginate and acrylic polymers of potential interest as drug delivery systems.

  9. AMAZON RAINFOREST COSMETICS: CHEMICAL APPROACH FOR QUALITY CONTROL

    Directory of Open Access Journals (Sweden)

    Mariko Funasaki

    2016-02-01

    Full Text Available The market for natural cosmetics featuring ingredients derived from Amazon natural resources is growing worldwide. However, there is neither enough scientific basis nor quality control of these ingredients. This paper is an account of the chemical constituents and their biological activities of fourteen Amazonian species used in cosmetic industry, including açaí (Euterpe oleracea, andiroba (Carapa guianensis, bacuri (Platonia insignis, Brazil nut (Bertholletia excelsa, buriti (Mauritia vinifera or M. flexuosa, cumaru (Dipteryx odorata, cupuaçu (Theobroma grandiflorum, guarana (Paullinia cupana, mulateiro (Calycophyllum spruceanum, murumuru (Astrocaryum murumuru, patawa (Oenocarpus bataua or Jessenia bataua, pracaxi (Pentaclethra macroloba, rosewood (Aniba rosaeodora, and ucuuba (Virola sebifera. Based on the reviewed articles, we selected chemical markers for the quality control purpose and evaluated analytical methods. Even though chromatographic and spectroscopic methods are major analytical techniques in the studies of these species, molecular approaches will also be important as used in food and medicine traceability. Only a little phytochemical study is available about most of the Amazonian species and some species such as açaí and andiroba have many reports on chemical constituents, but studies on biological activities of isolated compounds and sampling with geographical variation are limited.

  10. A genetic programming approach for Burkholderia Pseudomallei diagnostic pattern discovery

    Science.gov (United States)

    Yang, Zheng Rong; Lertmemongkolchai, Ganjana; Tan, Gladys; Felgner, Philip L.; Titball, Richard

    2009-01-01

    Motivation: Finding diagnostic patterns for fighting diseases like Burkholderia pseudomallei using biomarkers involves two key issues. First, exhausting all subsets of testable biomarkers (antigens in this context) to find a best one is computationally infeasible. Therefore, a proper optimization approach like evolutionary computation should be investigated. Second, a properly selected function of the antigens as the diagnostic pattern which is commonly unknown is a key to the diagnostic accuracy and the diagnostic effectiveness in clinical use. Results: A conversion function is proposed to convert serum tests of antigens on patients to binary values based on which Boolean functions as the diagnostic patterns are developed. A genetic programming approach is designed for optimizing the diagnostic patterns in terms of their accuracy and effectiveness. During optimization, it is aimed to maximize the coverage (the rate of positive response to antigens) in the infected patients and minimize the coverage in the non-infected patients while maintaining the fewest number of testable antigens used in the Boolean functions as possible. The final coverage in the infected patients is 96.55% using 17 of 215 (7.4%) antigens with zero coverage in the non-infected patients. Among these 17 antigens, BPSL2697 is the most frequently selected one for the diagnosis of Burkholderia Pseudomallei. The approach has been evaluated using both the cross-validation and the Jack–knife simulation methods with the prediction accuracy as 93% and 92%, respectively. A novel approach is also proposed in this study to evaluate a model with binary data using ROC analysis. Contact: z.r.yang@ex.ac.uk PMID:19561021

  11. A high‐throughput FTIR spectroscopy approach to assess adaptive variation in the chemical composition of pollen

    OpenAIRE

    Zimmermann, Boris; Bağcıoğlu, Murat; Tafinstseva, Valeria; Kohler, Achim; Ohlson, Mikael; Fjellheim, Siri

    2017-01-01

    Abstract The two factors defining male reproductive success in plants are pollen quantity and quality, but our knowledge about the importance of pollen quality is limited due to methodological constraints. Pollen quality in terms of chemical composition may be either genetically fixed for high performance independent of environmental conditions, or it may be plastic to maximize reproductive output under different environmental conditions. In this study, we validated a new approach for studyin...

  12. Modeling drug- and chemical- induced hepatotoxicity with systems biology approaches

    Directory of Open Access Journals (Sweden)

    Sudin eBhattacharya

    2012-12-01

    Full Text Available We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of ‘toxicity pathways’ is described in the context of the 2007 US National Academies of Science report, Toxicity testing in the 21st Century: A Vision and A Strategy. Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically-based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular virtual tissue model of the liver lobule that combines molecular circuits in individual hepatocytes with cell-cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the AhR toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsymTM to understand drug-induced liver injury (DILI, the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.

  13. Synchronization and Arrest of the Budding Yeast Cell Cycle Using Chemical and Genetic Methods.

    Science.gov (United States)

    Rosebrock, Adam P

    2017-01-03

    The cell cycle of budding yeast can be arrested at specific positions by different genetic and chemical methods. These arrests enable study of cell cycle phase-specific phenotypes that would be missed during examination of asynchronous cultures. Some methods for arrest are reversible, with kinetics that enable release of cells back into a synchronous cycling state. Benefits of chemical and genetic methods include scalability across a large range of culture sizes from a few milliliters to many liters, ease of execution, the absence of specific equipment requirements, and synchronization and release of the entire culture. Of note, cell growth and division are decoupled during arrest and block-release experiments. Cells will continue transcription, translation, and accumulation of protein while arrested. If allowed to reenter the cell cycle, cells will do so as a population of mixed, larger-than-normal cells. Despite this important caveat, many aspects of budding yeast physiology are accessible using these simple chemical and genetic tools. Described here are methods for the block and release of cells in G 1 phase and at the M/G 1 transition using α-factor mating pheromone and the temperature-sensitive cdc15-2 allele, respectively, in addition to methods for arresting the cell cycle in early S phase and at G 2 /M by using hydroxyurea and nocodazole, respectively. © 2017 Cold Spring Harbor Laboratory Press.

  14. Personalized Education Approaches for Chemical Engineering and Relevant Majors

    Directory of Open Access Journals (Sweden)

    Zhao Feng-qing

    2016-01-01

    Full Text Available Personalized education has drawn increasing attention in universities these years. With the purpose of improving the studentss’ comprehensive ability and developing teaching strategies to ensure students’ education is tailored to their needs, we proposed Three-Stage Approach (TSA to enhance personalized education for chemical engineering and relevant majors: professional tutorial system--equipping with professional guidance teachers for freshman students to guide their learning activities and provide professional guidance; open experimental project--setting up open experimental projects for sophomore and junior students to choose freely; individualized education module--setting up 10 different individualized education modules for senior students to select. After years of practice, the personalized education model is improved day by day and proved effective and fruitful.

  15. Management of diabetic complications: a chemical constituents based approach.

    Science.gov (United States)

    Singh, Randhir; Kaur, Navpreet; Kishore, Lalit; Gupta, Girish Kumar

    2013-10-28

    Long term hyperglycemia leads to development of complications associated with diabetes. Diabetic complications are now a global health problem without effective therapeutic approach. Hyperglycemia and oxidative stress are important components for the development of diabetic complications. Over the past few decades, herbal medicines have attracted much attention as potential therapeutic agents in the prevention and treatment of diabetic complications due to their multiple targets and less toxic side effects. This review aims to assess the current available knowledge of medicinal herbs for attenuation and management of diabetic complications and their underlying mechanisms. Bibliographic investigation was carried out by scrutinizing classical text books and peer reviewed papers, consulting worldwide accepted scientific databases (SCOPUS, PUBMED, SCIELO, NISCAIR, Google Scholar) to retrieve available published literature. The inclusion criteria for the selection of plants were based upon all medicinal herbs and their active compounds with attributed potentials in relieving diabetic complications. Moreover, plants which have potential effect in ameliorating oxidative stress in diabetic animals have been included. Overall, 238 articles were reviewed for plant literature and out of the reviewed literature, 127 articles were selected for the study. Various medicinal plants/plant extracts containing flavonoids, alkaloids, phenolic compounds, terpenoids, saponins and phytosterol type chemical constituents were found to be effective in the management of diabetic complications. This effect might be attributed to amelioration of persistent hyperglycemia, oxidative stress and modulation of various metabolic pathways involved in the pathogenesis of diabetic complications. Screening chemical candidate from herbal medicine might be a promising approach for new drug discovery to treat the diabetic complications. There is still a dire need to explore the mechanism of action of

  16. Translation and genetic criticism : genetic and editorial approaches to the 'untranslatable' in Joyce and Beckett

    OpenAIRE

    Hulle, Van, Dirk

    2015-01-01

    Abstract: Genetics of translation may suggest a unidirectional link between two fields of research (genetic criticism applied to translation), but there are many ways in which translation and genetic criticism interact. This article's research hypothesis is that an exchange of ideas between translation studies and genetic criticism can be mutually beneficial in more than one way. The main function of this exchange is to enhance a form of textual awareness, and to realize this enhanced textual...

  17. Genetic approaches to understanding post-traumatic stress disorder

    Science.gov (United States)

    Almli, Lynn M.; Fani, Negar; Smith, Alicia K.; Ressler, Kerry J.

    2015-01-01

    Post-traumatic stress disorder (PTSD) is increasingly recognized as both a disorder of enormous mental health and societal burden, but also as an anxiety disorder that may be particularly understandable from a scientific perspective. Specifically, PTSD can be conceptualized as a disorder of fear and stress dysregulation, and the neural circuitry underlying these pathways in both animals and humans are becoming increasingly well understood. Furthermore, PTSD is the only disorder in psychiatry in which the initiating factor, the trauma exposure, can be identified. Thus, the pathophysiology of the fear and stress response underlying PTSD can be examined and potentially interrupted. Twin studies have shown that the development of PTSD following a trauma is heritable, and that genetic risk factors may account for up to 30–40% of this heritability. A current goal is to understand the gene pathways that are associated with PTSD, and how those genes act on the fear/stress circuitry to mediate risk vs. resilience for PTSD. This review will examine gene pathways that have recently been analysed, primarily through candidate gene studies (including neuroimaging studies of candidate genes), in addition to genome-wide associations and the epigenetic regulation of PTSD. Future and on-going studies are utilizing larger and collaborative cohorts to identify novel gene candidates through genome-wide association and other powerful genomic approaches. Identification of PTSD biological pathways strengthens the hope of progress in the mechanistic understanding of a model psychiatric disorder and allows for the development of targeted treatments and interventions. PMID:24103155

  18. Genetic approaches to understanding post-traumatic stress disorder.

    Science.gov (United States)

    Almli, Lynn M; Fani, Negar; Smith, Alicia K; Ressler, Kerry J

    2014-02-01

    Post-traumatic stress disorder (PTSD) is increasingly recognized as both a disorder of enormous mental health and societal burden, but also as an anxiety disorder that may be particularly understandable from a scientific perspective. Specifically, PTSD can be conceptualized as a disorder of fear and stress dysregulation, and the neural circuitry underlying these pathways in both animals and humans are becoming increasingly well understood. Furthermore, PTSD is the only disorder in psychiatry in which the initiating factor, the trauma exposure, can be identified. Thus, the pathophysiology of the fear and stress response underlying PTSD can be examined and potentially interrupted. Twin studies have shown that the development of PTSD following a trauma is heritable, and that genetic risk factors may account for up to 30-40% of this heritability. A current goal is to understand the gene pathways that are associated with PTSD, and how those genes act on the fear/stress circuitry to mediate risk vs. resilience for PTSD. This review will examine gene pathways that have recently been analysed, primarily through candidate gene studies (including neuroimaging studies of candidate genes), in addition to genome-wide associations and the epigenetic regulation of PTSD. Future and on-going studies are utilizing larger and collaborative cohorts to identify novel gene candidates through genome-wide association and other powerful genomic approaches. Identification of PTSD biological pathways strengthens the hope of progress in the mechanistic understanding of a model psychiatric disorder and allows for the development of targeted treatments and interventions.

  19. Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

    Directory of Open Access Journals (Sweden)

    Julianne M O'Reilly-Wapstra

    Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

  20. Forward Genetic Approaches for Elucidation of Novel Regulators of Lyme Arthritis Severity

    Directory of Open Access Journals (Sweden)

    Kenneth K.C. Bramwell

    2014-06-01

    Full Text Available Patients experiencing natural infection with Borrelia burgdorferi display a spectrum of associated symptoms and severity, strongly implicating the impact of genetically determined host factors in the pathogenesis of Lyme disease. Herein, we provide a summary of the host genetic factors that have been demonstrated to influence the severity and chronicity of Lyme arthritis symptoms, and a review of the resources available, current progress, and added value of a forward genetic approach for identification of novel genetic regulators.

  1. Identification of Methylosome Components as Negative Regulators of Plant Immunity Using Chemical Genetics.

    Science.gov (United States)

    Huang, Shuai; Balgi, Aruna; Pan, Yaping; Li, Meng; Zhang, Xiaoran; Du, Lilin; Zhou, Ming; Roberge, Michel; Li, Xin

    2016-12-05

    Nucleotide-binding leucine-rich repeat (NLR) proteins serve as immune receptors in both plants and animals. To identify components required for NLR-mediated immunity, we designed and carried out a chemical genetics screen to search for small molecules that can alter immune responses in Arabidopsis thaliana. From 13 600 compounds, we identified Ro 8-4304 that was able to specifically suppress the severe autoimmune phenotypes of chs3-2D (chilling sensitive 3, 2D), including the arrested growth morphology and heightened PR (Pathogenesis Related) gene expression. Further, six Ro 8-4304 insensitive mutants were uncovered from the Ro 8-4304-insensitive mutant (rim) screen using a mutagenized chs3-2D population. Positional cloning revealed that rim1 encodes an allele of AtICln (I, currents; Cl, chloride; n, nucleotide). Genetic and biochemical analysis demonstrated that AtICln is in the same protein complex with the methylosome components small nuclear ribonucleoprotein D3b (SmD3b) and protein arginine methyltransferase 5 (PRMT5), which are required for the biogenesis of small nuclear ribonucleoproteins (snRNPs) involved in mRNA splicing. Double mutant analysis revealed that SmD3b is also involved in the sensitivity to Ro 8-4304, and the prmt5-1 chs3-2D double mutant is lethal. Loss of AtICln, SmD3b, or PRMT5 function results in enhanced disease resistance against the virulent oomycete pathogen Hyaloperonospora arabidopsidis Noco2, suggesting that mRNA splicing plays a previously unknown negative role in plant immunity. The successful implementation of a high-throughput chemical genetic screen and the identification of a small-molecule compound affecting plant immunity indicate that chemical genetics is a powerful tool to study whole-organism plant defense pathways. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

  2. Genetic testing in congenital heart disease:A clinical approach

    Institute of Scientific and Technical Information of China (English)

    Marie A Chaix; Gregor Andelfinger; Paul Khairy

    2016-01-01

    Congenital heart disease(CHD) is the most common type of birth defect. Traditionally, a polygenic model defined by the interaction of multiple genes and environmental factors was hypothesized to account for different forms of CHD. It is now understood that the contribution of genetics to CHD extends beyond a single unified paradigm. For example, monogenic models and chromosomal abnormalities have been associated with various syndromic and non-syndromic forms of CHD. In such instances, genetic investigation and testing may potentially play an important role in clinical care. A family tree with a detailed phenotypic description serves as the initial screening tool to identify potentially inherited defects and to guide further genetic investigation. The selection of a genetic test is contingent upon the particular diagnostic hypothesis generated by clinical examination. Genetic investigation in CHD may carry the potential to improve prognosis by yielding valuable information with regards to personalized medical care, confidence in the clinical diagnosis, and/or targeted patient followup. Moreover, genetic assessment may serve as a tool to predict recurrence risk, define the pattern of inheritance within a family, and evaluate the need for further family screening. In some circumstances, prenatal or preimplantation genetic screening could identify fetuses or embryos at high risk for CHD. Although genetics may appear to constitute a highly specialized sector of cardiology, basic knowledge regarding inheritance patterns, recurrence risks, and available screening and diagnostic tools, including their strengths and limitations, could assist the treating physician in providing sound counsel.

  3. Modelling Autistic Features in Mice Using Quantitative Genetic Approaches

    NARCIS (Netherlands)

    Molenhuis, Remco T; Bruining, Hilgo; Kas, Martien J

    2017-01-01

    Animal studies provide a unique opportunity to study the consequences of genetic variants at the behavioural level. Human studies have identified hundreds of risk genes for autism spectrum disorder (ASD) that can lead to understanding on how genetic variation contributes to individual differences in

  4. Genetic testing in congenital heart disease: A clinical approach

    Science.gov (United States)

    Chaix, Marie A; Andelfinger, Gregor; Khairy, Paul

    2016-01-01

    Congenital heart disease (CHD) is the most common type of birth defect. Traditionally, a polygenic model defined by the interaction of multiple genes and environmental factors was hypothesized to account for different forms of CHD. It is now understood that the contribution of genetics to CHD extends beyond a single unified paradigm. For example, monogenic models and chromosomal abnormalities have been associated with various syndromic and non-syndromic forms of CHD. In such instances, genetic investigation and testing may potentially play an important role in clinical care. A family tree with a detailed phenotypic description serves as the initial screening tool to identify potentially inherited defects and to guide further genetic investigation. The selection of a genetic test is contingent upon the particular diagnostic hypothesis generated by clinical examination. Genetic investigation in CHD may carry the potential to improve prognosis by yielding valuable information with regards to personalized medical care, confidence in the clinical diagnosis, and/or targeted patient follow-up. Moreover, genetic assessment may serve as a tool to predict recurrence risk, define the pattern of inheritance within a family, and evaluate the need for further family screening. In some circumstances, prenatal or preimplantation genetic screening could identify fetuses or embryos at high risk for CHD. Although genetics may appear to constitute a highly specialized sector of cardiology, basic knowledge regarding inheritance patterns, recurrence risks, and available screening and diagnostic tools, including their strengths and limitations, could assist the treating physician in providing sound counsel. PMID:26981213

  5. Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: Challenges, opportunities, and research needs

    International Nuclear Information System (INIS)

    Burgess-Herbert, Sarah L.; Euling, Susan Y.

    2013-01-01

    A critical challenge for environmental chemical risk assessment is the characterization and reduction of uncertainties introduced when extrapolating inferences from one species to another. The purpose of this article is to explore the challenges, opportunities, and research needs surrounding the issue of how genomics data and computational and systems level approaches can be applied to inform differences in response to environmental chemical exposure across species. We propose that the data, tools, and evolutionary framework of comparative genomics be adapted to inform interspecies differences in chemical mechanisms of action. We compare and contrast existing approaches, from disciplines as varied as evolutionary biology, systems biology, mathematics, and computer science, that can be used, modified, and combined in new ways to discover and characterize interspecies differences in chemical mechanism of action which, in turn, can be explored for application to risk assessment. We consider how genetic, protein, pathway, and network information can be interrogated from an evolutionary biology perspective to effectively characterize variations in biological processes of toxicological relevance among organisms. We conclude that comparative genomics approaches show promise for characterizing interspecies differences in mechanisms of action, and further, for improving our understanding of the uncertainties inherent in extrapolating inferences across species in both ecological and human health risk assessment. To achieve long-term relevance and consistent use in environmental chemical risk assessment, improved bioinformatics tools, computational methods robust to data gaps, and quantitative approaches for conducting extrapolations across species are critically needed. Specific areas ripe for research to address these needs are recommended

  6. Genetic and chemical knockdown: a complementary strategy for evaluating an anti-infective target

    Directory of Open Access Journals (Sweden)

    Ramachandran V

    2013-02-01

    Full Text Available Vasanthi Ramachandran,1,* Ragini Singh,2,* Xiaoyu Yang,1 Ragadeepthi Tunduguru,1 Subrat Mohapatra,2 Swati Khandelwal,2 Sanjana Patel,2 Santanu Datta21AstraZeneca India R&D, Bangalore, India; 2Cellworks India, Bangalore, India *These authors contributed equally to this workAbstract: The equity of a drug target is principally evaluated by its genetic vulnerability with tools ranging from antisense- and microRNA-driven knockdowns to induced expression of the target protein. In order to upgrade the process of antibacterial target identification and discern its most effective type of inhibition, an in silico toolbox that evaluates its genetic and chemical vulnerability leading either to stasis or cidal outcome was constructed and validated. By precise simulation and careful experimentation using enolpyruvyl shikimate-3-phosphate synthase and its specific inhibitor glyphosate, it was shown that genetic knockdown is distinct from chemical knockdown. It was also observed that depending on the particular mechanism of inhibition, viz competitive, uncompetitive, and noncompetitive, the antimicrobial potency of an inhibitor could be orders of magnitude different. Susceptibility of Escherichia coli to glyphosate and the lack of it in Mycobacterium tuberculosis could be predicted by the in silico platform. Finally, as predicted and simulated in the in silico platform, the translation of growth inhibition to a cidal effect was able to be demonstrated experimentally by altering the carbon source from sorbitol to glucose.Keywords: knockdown, inhibition, in silico, vulnerability

  7. Evolutionary potential of root chemical defense: genetic correlations with shoot chemistry and plant growth.

    Science.gov (United States)

    Parker, J D; Salminen, J-P; Agrawal, Anurag A

    2012-08-01

    Root herbivores can affect plant fitness, and roots often contain the same secondary metabolites that act as defenses in shoots, but the ecology and evolution of root chemical defense have been little investigated. Here, we investigated genetic variance, heritability, and correlations among defensive phenolic compounds in shoot vs. root tissues of common evening primrose, Oenothera biennis. Across 20 genotypes, there were roughly similar concentrations of total phenolics in shoots vs. roots, but the allocation of particular phenolics to shoots vs. roots varied along a continuum of genotype growth rate. Slow-growing genotypes allocated 2-fold more of the potential pro-oxidant oenothein B to shoots than roots, whereas fast-growing genotypes had roughly equivalent above and belowground concentrations. Phenolic concentrations in both roots and shoots were strongly heritable, with mostly positive patterns of genetic covariation. Nonetheless, there was genotype-specific variation in the presence/absence of two major ellagitannins (oenothein A and its precursor oenothein B), indicating two different chemotypes based on alterations in this chemical pathway. Overall, the presence of strong genetic variation in root defenses suggests ample scope for the evolution of these compounds as defenses against root herbivores.

  8. Ethical genetic research in Indigenous communities: challenges and successful approaches.

    Science.gov (United States)

    McWhirter, Rebekah E; Mununggirritj, Djapirri; Marika, Dipililnga; Dickinson, Joanne L; Condon, John R

    2012-12-01

    Indigenous populations, in common with all populations, stand to benefit from the potential of genetic research to lead to improvements in diagnostic and therapeutic tools for a wide range of complex diseases. However, many Indigenous communities, especially ones that are isolated, are not included in genetic research efforts. This situation is largely a consequence of the challenges of ethically conducting genetic research in Indigenous communities and compounded by Indigenous peoples' negative past experiences with genetic issues. To examine ways of addressing these challenges, we review one investigation of a cancer cluster in remote Aboriginal communities in Arnhem Land, Australia. Our experiences demonstrate that genetic research can be both ethically and successfully conducted with Indigenous communities by respecting the authority of the community, involving community members, and including regular community review throughout the research process. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Genetic and chemical diversity of Uncaria tomentosa (Willd. ex. Schult. DC. in the Brazilian Amazon.

    Directory of Open Access Journals (Sweden)

    Isabela Cristina Gomes Honório

    Full Text Available Uncaria tomentosa (Willd. ex Schult. DC., a plant native to the Amazon region, is used widely in popular medicine and by the pharmaceutical industry because of its anti-inflammatory activity. However, the survival of this species is endangered by deforestation and indiscriminate collection, and a preservation plan is urgently required. The objectives of this study were to determine the genetic and chemical variability between and within eight populations of U. tomentosa from the Brazilian states of Acre, Pará and Amapá, and to investigate possible correlations between genetic and geographical distances, and between geographical distances or altitude and the accumulation of bioactive oxindole alkaloids. Three sequence-related amplified polymorphism (SRAP markers were employed to fingerprint genomic DNA, and the amounts of mitraphylline and isomitraphylline in leaf samples were established by high-performance liquid chromatography. Although significant divergence existed between the tested populations (FST = 0.246, the largest genetic diversity and the highest percentage of polymorphism (95.68% was found within the population from Mâncio Lima, Acre. Gene flow was considered rather limited (Nm = 1.57, and no correlations between genetic and geographical distances were detected, suggesting that population structure followed an island model. Accumulations of mitraphylline and isomitraphylline varied in the range 32.94 to 0.57 and 3.75 to 0.36 mg g-1 dry weight, respectively. The concentration of isomitraphylline was positively influenced by altitude, such that the population collected at the site with the highest elevation (Tarauacá, Acre exhibited the greatest alkaloid content. SRAP markers were very efficient in fingerprinting genomic DNA from U. tomentosa populations and clearly showed that genetic variability within populations was greater than between populations. A conservation and management plan should prioritize the creation of germplasm

  10. Chemical and genetic discrimination of Cistanches Herba based on UPLC-QTOF/MS and DNA barcoding.

    Science.gov (United States)

    Zheng, Sihao; Jiang, Xue; Wu, Labin; Wang, Zenghui; Huang, Linfang

    2014-01-01

    Cistanches Herba (Rou Cong Rong), known as "Ginseng of the desert", has a striking curative effect on strength and nourishment, especially in kidney reinforcement to strengthen yang. However, the two plant origins of Cistanches Herba, Cistanche deserticola and Cistanche tubulosa, vary in terms of pharmacological action and chemical components. To discriminate the plant origin of Cistanches Herba, a combined method system of chemical and genetic--UPLC-QTOF/MS technology and DNA barcoding--were firstly employed in this study. The results indicated that three potential marker compounds (isomer of campneoside II, cistanoside C, and cistanoside A) were obtained to discriminate the two origins by PCA and OPLS-DA analyses. DNA barcoding enabled to differentiate two origins accurately. NJ tree showed that two origins clustered into two clades. Our findings demonstrate that the two origins of Cistanches Herba possess different chemical compositions and genetic variation. This is the first reported evaluation of two origins of Cistanches Herba, and the finding will facilitate quality control and its clinical application.

  11. Chemical and genetic discrimination of Cistanches Herba based on UPLC-QTOF/MS and DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Sihao Zheng

    Full Text Available Cistanches Herba (Rou Cong Rong, known as "Ginseng of the desert", has a striking curative effect on strength and nourishment, especially in kidney reinforcement to strengthen yang. However, the two plant origins of Cistanches Herba, Cistanche deserticola and Cistanche tubulosa, vary in terms of pharmacological action and chemical components. To discriminate the plant origin of Cistanches Herba, a combined method system of chemical and genetic--UPLC-QTOF/MS technology and DNA barcoding--were firstly employed in this study. The results indicated that three potential marker compounds (isomer of campneoside II, cistanoside C, and cistanoside A were obtained to discriminate the two origins by PCA and OPLS-DA analyses. DNA barcoding enabled to differentiate two origins accurately. NJ tree showed that two origins clustered into two clades. Our findings demonstrate that the two origins of Cistanches Herba possess different chemical compositions and genetic variation. This is the first reported evaluation of two origins of Cistanches Herba, and the finding will facilitate quality control and its clinical application.

  12. Correlation and regression analyses of genetic effects for different types of cells in mammals under radiation and chemical treatment

    International Nuclear Information System (INIS)

    Slutskaya, N.G.; Mosseh, I.B.

    2006-01-01

    Data about genetic mutations under radiation and chemical treatment for different types of cells have been analyzed with correlation and regression analyses. Linear correlation between different genetic effects in sex cells and somatic cells have found. The results may be extrapolated on sex cells of human and mammals. (authors)

  13. Evidence-Based Approaches to Improving Chemical Equilibrium Instruction

    Science.gov (United States)

    Davenport, Jodi L.; Leinhardt, Gaea; Greeno, James; Koedinger, Kenneth; Klahr, David; Karabinos, Michael; Yaron, David J.

    2014-01-01

    Two suggestions for instruction in chemical equilibrium are presented, along with the evidence that supports these suggestions. The first is to use diagrams to connect chemical reactions to the effects of reactions on concentrations. The second is the use of the majority and minority species (M&M) strategy to analyze chemical equilibrium…

  14. Problems and solutions in the estimation of genetic risks from radiation and chemicals

    International Nuclear Information System (INIS)

    Russell, W.L.

    1980-01-01

    Extensive investigations with mice on the effects of various physical and biological factors, such as dose rate, sex and cell stage, on radiation-induced mutation have provided an evaluation of the genetics hazards of radiation in man. The mutational results obtained in both sexes with progressive lowering of the radiation dose rate have permitted estimation of the mutation frequency expected under the low-level radiation conditions of most human exposure. Supplementing the studies on mutation frequency are investigations on the phenotypic effects of mutations in mice, particularly anatomical disorders of the skeleton, which allow an estimation of the degree of human handicap associated with the occurrence of parallel defects in man. Estimation of the genetic risk from chemical mutagens is much more difficult, and the research is much less advanced. Results on transmitted mutations in mice indicate a poor correlation with mutation induction in non-mammalian organisms

  15. What next for preimplantation genetic screening? A polar body approach!

    NARCIS (Netherlands)

    Geraedts, Joep; Collins, John; Gianaroli, Luca; Goossens, Veerle; Handyside, Alan; Harper, Joyce; Montag, Markus; Repping, Sjoerd; Schmutzler, Andreas

    2010-01-01

    Screening of human preimplantation embryos for numerical chromosome abnormalities has been conducted mostly at the preimplantation stage using fluorescence in situ hybridization. However, it is clear that preimplantation genetic screening (PGS) as it is currently practiced does not improve live

  16. Congenital hydrocephalus in clinical practice : A genetic diagnostic approach

    NARCIS (Netherlands)

    Verhagen, J. M. A.; Schrander-Stumpel, C. T. R. M.; Krapels, P. C.; de Die-Smulders, C. E. M.; van Lint, F. H. M.; Willekes, C.; Weber, J. W.; Gavilanes, A. W. D.; Macville, M. V. E.; Stegmann, A. P. A.; Engelen, J. J. M.; Bakker, J.; Vos, Y. J.; Frints, S. G. M.

    2011-01-01

    Congenital hydrocephalus is a common and often disabling disorder. The etiology is very heterogeneous. Little is known about the genetic causes of congenital hydrocephalus. A retrospective survey was performed including patients with primary congenital hydrocephalus referred to the Department of

  17. Introduction to focus issue: quantitative approaches to genetic networks.

    Science.gov (United States)

    Albert, Réka; Collins, James J; Glass, Leon

    2013-06-01

    All cells of living organisms contain similar genetic instructions encoded in the organism's DNA. In any particular cell, the control of the expression of each different gene is regulated, in part, by binding of molecular complexes to specific regions of the DNA. The molecular complexes are composed of protein molecules, called transcription factors, combined with various other molecules such as hormones and drugs. Since transcription factors are coded by genes, cellular function is partially determined by genetic networks. Recent research is making large strides to understand both the structure and the function of these networks. Further, the emerging discipline of synthetic biology is engineering novel gene circuits with specific dynamic properties to advance both basic science and potential practical applications. Although there is not yet a universally accepted mathematical framework for studying the properties of genetic networks, the strong analogies between the activation and inhibition of gene expression and electric circuits suggest frameworks based on logical switching circuits. This focus issue provides a selection of papers reflecting current research directions in the quantitative analysis of genetic networks. The work extends from molecular models for the binding of proteins, to realistic detailed models of cellular metabolism. Between these extremes are simplified models in which genetic dynamics are modeled using classical methods of systems engineering, Boolean switching networks, differential equations that are continuous analogues of Boolean switching networks, and differential equations in which control is based on power law functions. The mathematical techniques are applied to study: (i) naturally occurring gene networks in living organisms including: cyanobacteria, Mycoplasma genitalium, fruit flies, immune cells in mammals; (ii) synthetic gene circuits in Escherichia coli and yeast; and (iii) electronic circuits modeling genetic networks

  18. AI AND SAR APPROACHES FOR PREDICTING CHEMICAL CARCINOGENICITY: SURVEY AND STATUS REPORT

    Science.gov (United States)

    A wide variety of artificial intelligence (AI) and structure-activity relationship (SAR approaches have been applied to tackling the general problem of predicting rodent chemical carcinogenicity. Given the diversity of chemical structures and mechanisms relative to this endpoin...

  19. Genetic algorithm and neural network hybrid approach for job-shop scheduling

    OpenAIRE

    Zhao, Kai; Yang, Shengxiang; Wang, Dingwei

    1998-01-01

    Copyright @ 1998 ACTA Press This paper proposes a genetic algorithm (GA) and constraint satisfaction adaptive neural network (CSANN) hybrid approach for job-shop scheduling problems. In the hybrid approach, GA is used to iterate for searching optimal solutions, CSANN is used to obtain feasible solutions during the iteration of genetic algorithm. Simulations have shown the valid performance of the proposed hybrid approach for job-shop scheduling with respect to the quality of solutions and ...

  20. A propensity score approach to correction for bias due to population stratification using genetic and non-genetic factors.

    Science.gov (United States)

    Zhao, Huaqing; Rebbeck, Timothy R; Mitra, Nandita

    2009-12-01

    Confounding due to population stratification (PS) arises when differences in both allele and disease frequencies exist in a population of mixed racial/ethnic subpopulations. Genomic control, structured association, principal components analysis (PCA), and multidimensional scaling (MDS) approaches have been proposed to address this bias using genetic markers. However, confounding due to PS can also be due to non-genetic factors. Propensity scores are widely used to address confounding in observational studies but have not been adapted to deal with PS in genetic association studies. We propose a genomic propensity score (GPS) approach to correct for bias due to PS that considers both genetic and non-genetic factors. We compare the GPS method with PCA and MDS using simulation studies. Our results show that GPS can adequately adjust and consistently correct for bias due to PS. Under no/mild, moderate, and severe PS, GPS yielded estimated with bias close to 0 (mean=-0.0044, standard error=0.0087). Under moderate or severe PS, the GPS method consistently outperforms the PCA method in terms of bias, coverage probability (CP), and type I error. Under moderate PS, the GPS method consistently outperforms the MDS method in terms of CP. PCA maintains relatively high power compared to both MDS and GPS methods under the simulated situations. GPS and MDS are comparable in terms of statistical properties such as bias, type I error, and power. The GPS method provides a novel and robust tool for obtaining less-biased estimates of genetic associations that can consider both genetic and non-genetic factors. 2009 Wiley-Liss, Inc.

  1. A Novel Approach: Chemical Relational Databases, and the ...

    Science.gov (United States)

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as

  2. Genes, Culture and Conservatism-A Psychometric-Genetic Approach.

    Science.gov (United States)

    Schwabe, Inga; Jonker, Wilfried; van den Berg, Stéphanie M

    2016-07-01

    The Wilson-Patterson conservatism scale was psychometrically evaluated using homogeneity analysis and item response theory models. Results showed that this scale actually measures two different aspects in people: on the one hand people vary in their agreement with either conservative or liberal catch-phrases and on the other hand people vary in their use of the "?" response category of the scale. A 9-item subscale was constructed, consisting of items that seemed to measure liberalism, and this subscale was subsequently used in a biometric analysis including genotype-environment interaction, correcting for non-homogeneous measurement error. Biometric results showed significant genetic and shared environmental influences, and significant genotype-environment interaction effects, suggesting that individuals with a genetic predisposition for conservatism show more non-shared variance but less shared variance than individuals with a genetic predisposition for liberalism.

  3. Genetic algorithm approach to thin film optical parameters determination

    International Nuclear Information System (INIS)

    Jurecka, S.; Jureckova, M.; Muellerova, J.

    2003-01-01

    Optical parameters of thin film are important for several optical and optoelectronic applications. In this work the genetic algorithm proposed to solve optical parameters of thin film values. The experimental reflectance is modelled by the Forouhi - Bloomer dispersion relations. The refractive index, the extinction coefficient and the film thickness are the unknown parameters in this model. Genetic algorithm use probabilistic examination of promissing areas of the parameter space. It creates a population of solutions based on the reflectance model and then operates on the population to evolve the best solution by using selection, crossover and mutation operators on the population individuals. The implementation of genetic algorithm method and the experimental results are described too (Authors)

  4. Pharmacological profiling of zebrafish behavior using chemical and genetic classification of sleep-wake modifiers.

    Science.gov (United States)

    Nishimura, Yuhei; Okabe, Shiko; Sasagawa, Shota; Murakami, Soichiro; Ashikawa, Yoshifumi; Yuge, Mizuki; Kawaguchi, Koki; Kawase, Reiko; Tanaka, Toshio

    2015-01-01

    Sleep-wake states are impaired in various neurological disorders. Impairment of sleep-wake states can be an early condition that exacerbates these disorders. Therefore, treating sleep-wake dysfunction may prevent or slow the development of these diseases. Although many gene products are likely to be involved in the sleep-wake disturbance, hypnotics and psychostimulants clinically used are limited in terms of their mode of action and are not without side effects. Therefore, there is a growing demand for developing new hypnotics and psychostimulants with high efficacy and few side effects. Toward this end, animal models are indispensable for use in genetic and chemical screens to identify sleep-wake modifiers. As a proof-of-concept study, we performed behavioral profiling of zebrafish treated with chemical and genetic sleep-wake modifiers. We were able to demonstrate that behavioral profiling of zebrafish treated with hypnotics or psychostimulants from 9 to 10 days post-fertilization was sufficient to identify drugs with specific modes of action. We were also able to identify behavioral endpoints distinguishing GABA-A modulators and hypocretin (hcrt) receptor antagonists and between sympathomimetic and non-sympathomimetic psychostimulants. This behavioral profiling can serve to identify genes related to sleep-wake disturbance associated with various neuropsychiatric diseases and novel therapeutic compounds for insomnia and excessive daytime sleep with fewer adverse side effects.

  5. Prediction of Chemical Carcinogenicity in Rodents from in vitro Genetic Toxicity Assays

    Science.gov (United States)

    Tennant, Raymond W.; Margolin, Barry H.; Shelby, Michael D.; Zeiger, Errol; Haseman, Joseph K.; Spalding, Judson; Caspary, William; Resnick, Michael; Stasiewicz, Stanley; Anderson, Beth; Minor, Robert

    1987-05-01

    Four widely used in vitro assays for genetic toxicity were evaluated for their ability to predict the carcinogenicity of selected chemicals in rodents. These assays were mutagenesis in Salmonella and mouse lymphoma cells and chromosome aberrations and sister chromatid exchanges in Chinese hamster ovary cells. Seventy-three chemicals recently tested in 2-year carcinogenicity studies conducted by the National Cancer Institute and the National Toxicology Program were used in this evaluation. Test results from the four in vitro assays did not show significant differences in individual concordance with the rodent carcinogenicity results; the concordance of each assay was approximately 60 percent. Within the limits of this study there was no evidence of complementarity among the four assays, and no battery of tests constructed from these assays improved substantially on the overall performance of the Salmonella assay. The in vitro assays which represented a range of three cell types and four end points did show substantial agreement among themselves, indicating that chemicals positive in one in vitro assay tended to be positive in the other in vitro assays. To help put this project into its proper context, we emphasize certain features of the study: 1) Standard protocols were used to mimic the major use of STTs worldwide--screening for mutagens and carcinogens; no attempt was made to optimize protocols for specific chemicals. 2) The 73 NTP chemicals and their 60% incidence of carcinogenicity are probably not representative of the universe of chemicals but rather reflect the recent chemical selection process for the NTP carcinogenicity assay. 3) The small, diverse group of chemicals precludes a meaningful evaluation of the predictive utility of chemical structure information. 4) The NTP is currently testing these same 73 chemicals in two in vivo STTs for chromosomal effects. 5) Complete data for an additional group of 30 to 40 NTP chemicals will be gathered on

  6. The nuclear terrorist, radiological, biological, chemical threat. Medical approach

    International Nuclear Information System (INIS)

    Gourmelon, P.; Vidal, D.; Renaudeau, C.

    2005-01-01

    This book illustrates the cooperation of the civil and the military experts in the domain of the NBRC (nuclear, biological, radiological and chemical threat). The different aspects bond to the use of nuclear, biological and chemical weapons, are discussed. Al topics of each domains (NRBC) are presented: historical and fundamental aspects, diagnostic, therapeutic and prevention. (A.L.B.)

  7. Genetic and chemical modifiers of a CUG toxicity model in Drosophila.

    Directory of Open Access Journals (Sweden)

    Amparo Garcia-Lopez

    2008-02-01

    Full Text Available Non-coding CUG repeat expansions interfere with the activity of human Muscleblind-like (MBNL proteins contributing to myotonic dystrophy 1 (DM1. To understand this toxic RNA gain-of-function mechanism we developed a Drosophila model expressing 60 pure and 480 interrupted CUG repeats in the context of a non-translatable RNA. These flies reproduced aspects of the DM1 pathology, most notably nuclear accumulation of CUG transcripts, muscle degeneration, splicing misregulation, and diminished Muscleblind function in vivo. Reduced Muscleblind activity was evident from the sensitivity of CUG-induced phenotypes to a decrease in muscleblind genetic dosage and rescue by MBNL1 expression, and further supported by the co-localization of Muscleblind and CUG repeat RNA in ribonuclear foci. Targeted expression of CUG repeats to the developing eye and brain mushroom bodies was toxic leading to rough eyes and semilethality, respectively. These phenotypes were utilized to identify genetic and chemical modifiers of the CUG-induced toxicity. 15 genetic modifiers of the rough eye phenotype were isolated. These genes identify putative cellular processes unknown to be altered by CUG repeat RNA, and they include mRNA export factor Aly, apoptosis inhibitor Thread, chromatin remodelling factor Nurf-38, and extracellular matrix structural component Viking. Ten chemical compounds suppressed the semilethal phenotype. These compounds significantly improved viability of CUG expressing flies and included non-steroidal anti-inflammatory agents (ketoprofen, muscarinic, cholinergic and histamine receptor inhibitors (orphenadrine, and drugs that can affect sodium and calcium metabolism such as clenbuterol and spironolactone. These findings provide new insights into the DM1 phenotype, and suggest novel candidates for DM1 treatments.

  8. A high-throughput FTIR spectroscopy approach to assess adaptive variation in the chemical composition of pollen.

    Science.gov (United States)

    Zimmermann, Boris; Bağcıoğlu, Murat; Tafinstseva, Valeria; Kohler, Achim; Ohlson, Mikael; Fjellheim, Siri

    2017-12-01

    The two factors defining male reproductive success in plants are pollen quantity and quality, but our knowledge about the importance of pollen quality is limited due to methodological constraints. Pollen quality in terms of chemical composition may be either genetically fixed for high performance independent of environmental conditions, or it may be plastic to maximize reproductive output under different environmental conditions. In this study, we validated a new approach for studying the role of chemical composition of pollen in adaptation to local climate. The approach is based on high-throughput Fourier infrared (FTIR) characterization and biochemical interpretation of pollen chemical composition in response to environmental conditions. The study covered three grass species, Poa alpina , Anthoxanthum odoratum , and Festuca ovina . For each species, plants were grown from seeds of three populations with wide geographic and climate variation. Each individual plant was divided into four genetically identical clones which were grown in different controlled environments (high and low levels of temperature and nutrients). In total, 389 samples were measured using a high-throughput FTIR spectrometer. The biochemical fingerprints of pollen were species and population specific, and plastic in response to different environmental conditions. The response was most pronounced for temperature, influencing the levels of proteins, lipids, and carbohydrates in pollen of all species. Furthermore, there is considerable variation in plasticity of the chemical composition of pollen among species and populations. The use of high-throughput FTIR spectroscopy provides fast, cheap, and simple assessment of the chemical composition of pollen. In combination with controlled-condition growth experiments and multivariate analyses, FTIR spectroscopy opens up for studies of the adaptive role of pollen that until now has been difficult with available methodology. The approach can easily be

  9. The statutory approach: the control of chemical products

    International Nuclear Information System (INIS)

    Briens, F.

    1997-01-01

    The evaluation and management of risks linked with chemical products and in particular with petroleum products is now performed using all the available tools developed by the OECD or the European Union in order to harmonize the procedures between member states. This paper describes the statutory liabilities linked to the trade of chemical products of industrial use in the case of new and of existing chemical substances (classification, labelling, risk evaluation and reduction, physico-chemical properties, toxicological and eco-toxicological studies, neutralization, limitation of trade and use, import/export, protection of the ozone layer, etc..). It refers to the legal framework (orders, by-laws, decrees, guidelines..) defined by the OECD and the European Community and recalls the organization and administration of the competent authorities for the control of chemical products. (J.S.)

  10. Investigating an Ethical Approach to Genetically Modified Crops in ...

    African Journals Online (AJOL)

    Genetically modified (GM) crops gained attention in southern Africa in the context of broader debates about the struggle for food security and poverty alleviation to achieve sustainable development. The prospects of GM crops as a technological innovation have provoked numerous debates and environmental concern ...

  11. Genetic bases of the nutritional approach to migraine.

    Science.gov (United States)

    De Marchis, Maria Laura; Guadagni, Fiorella; Silvestris, Erica; Lovero, Domenica; Della-Morte, David; Ferroni, Patrizia; Barbanti, Piero; Palmirotta, Raffaele

    2018-03-08

    Migraine is a common multifactorial and polygenic neurological disabling disorder characterized by a genetic background and associated to environmental, hormonal and food stimulations. A large series of evidence suggest a strong correlation between nutrition and migraine and indicates several commonly foods, food additives and beverages that may be involved in the mechanisms triggering the headache attack in migraine-susceptible persons. There are foods and drinks, or ingredients of the same, that can trigger the migraine crisis as well as some foods play a protective function depending on the specific genetic sensitivity of the subject. The recent biotechnological advances have enhanced the identification of some genetic factors involved in onset diseases and the identification of sequence variants of genes responsible for the individual sensitivity to migraine trigger-foods. Therefore many studies are aimed at the analysis of polymorphisms of genes coding for the enzymes involved in the metabolism of food factors in order to clarify the different ways in which people respond to foods based on their genetic constitution. This review discusses the latest knowledge and scientific evidence of the role of gene variants and nutrients, food additives and nutraceuticals interactions in migraine.

  12. A holistic approach to genetic conservation of Pinus strobiformis

    Science.gov (United States)

    K.M. Waring; R. Sniezko; B.A. Goodrich; C. Wehenkel; J.J. Jacobs

    2017-01-01

    Pinus strobiformis (southwestern white pine) is threatened by both a rapidly changing climate and the tree disease white pine blister rust, caused by an introduced fungal pathogen, Cronartium ribicola. We began a proactive program in ~2009 to sustain P. strobiformis that includes genetic conservation, research, and management strategies. Research...

  13. The characterization of goat genetic diversity : Towards a genomic approach

    NARCIS (Netherlands)

    Ajmone-Marsan, P.; Colli, L.; Han, J. L.; Achilli, A.; Lancioni, H.; Joost, S.; Crepaldi, P.; Pilla, F.; Stella, A.; Taberlet, P.; Boettcher, P.; Negrini, R.; Lenstra, J. A.

    2014-01-01

    The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers

  14. 1 Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    2015-04-14

    Apr 14, 2015 ... Study of genetic diversity is the process by which variation ... diversity tree is available, a core collection can be selected by .... are numerous natural factors, such as hybridization and clinical .... to develop a deeper understanding of the topic .... This can be detected by southern hybridization after running ...

  15. 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

  16. Food Control and a Citizen Science Approach for Improving Teaching of Genetics in Universities

    Science.gov (United States)

    Borrell, Y. J.; Muñoz-Colmenero, A. M.; Dopico, E.; Miralles, L.; Garcia-Vazquez, E.

    2016-01-01

    A Citizen Science approach was implemented in the laboratory practices of Genetics at the University of Oviedo, related with the engaging topic of Food Control. Real samples of food products consumed by students at home ("students as samplers") were employed as teaching material in three different courses of Genetics during the academic…

  17. MycoKey Round Table Discussions of Future Directions in Research on Chemical Detection Methods, Genetics and Biodiversity of Mycotoxins

    Directory of Open Access Journals (Sweden)

    John F. Leslie

    2018-03-01

    Full Text Available MycoKey, an EU-funded Horizon 2020 project, includes a series of “Roundtable Discussions” to gather information on trending research areas in the field of mycotoxicology. This paper includes summaries of the Roundtable Discussions on Chemical Detection and Monitoring of mycotoxins and on the role of genetics and biodiversity in mycotoxin production. Discussions were managed by using the nominal group discussion technique, which generates numerous ideas and provides a ranking for those identified as the most important. Four questions were posed for each research area, as well as two questions that were common to both discussions. Test kits, usually antibody based, were one major focus of the discussions at the Chemical Detection and Monitoring roundtable because of their many favorable features, e.g., cost, speed and ease of use. The second area of focus for this roundtable was multi-mycotoxin detection protocols and the challenges still to be met to enable these protocols to become methods of choice for regulated mycotoxins. For the genetic and biodiversity group, both the depth and the breadth of trending research areas were notable. For some areas, e.g., microbiome studies, the suggested research questions were primarily of a descriptive nature. In other areas, multiple experimental approaches, e.g., transcriptomics, proteomics, RNAi and gene deletions, are needed to understand the regulation of toxin production and mechanisms underlying successful biological controls. Answers to the research questions will provide starting points for developing acceptable prevention and remediation processes. Forging a partnership between scientists and appropriately-placed communications experts was recognized by both groups as an essential step to communicating risks, while retaining overall confidence in the safety of the food supply and the integrity of the food production chain.

  18. MycoKey Round Table Discussions of Future Directions in Research on Chemical Detection Methods, Genetics and Biodiversity of Mycotoxins

    Science.gov (United States)

    Lattanzio, Veronica; Cary, Jeffrey; Chulze, Sofia N.; Gerardino, Annamaria; Liao, Yu-Cai; Maragos, Chris M.; Meca, Giuseppe; Moretti, Antonio; Munkvold, Gary; Mulè, Giuseppina; Njobeh, Patrick; Pecorelli, Ivan; Pietri, Amedeo; Proctor, Robert H.; Rahayu, Endang S.; Ramírez, Maria L.; Samson, Robert; Stroka, Jörg; Sumarah, Mark; Zhang, Qi; Zhang, Hao; Logrieco, Antonio F.

    2018-01-01

    MycoKey, an EU-funded Horizon 2020 project, includes a series of “Roundtable Discussions” to gather information on trending research areas in the field of mycotoxicology. This paper includes summaries of the Roundtable Discussions on Chemical Detection and Monitoring of mycotoxins and on the role of genetics and biodiversity in mycotoxin production. Discussions were managed by using the nominal group discussion technique, which generates numerous ideas and provides a ranking for those identified as the most important. Four questions were posed for each research area, as well as two questions that were common to both discussions. Test kits, usually antibody based, were one major focus of the discussions at the Chemical Detection and Monitoring roundtable because of their many favorable features, e.g., cost, speed and ease of use. The second area of focus for this roundtable was multi-mycotoxin detection protocols and the challenges still to be met to enable these protocols to become methods of choice for regulated mycotoxins. For the genetic and biodiversity group, both the depth and the breadth of trending research areas were notable. For some areas, e.g., microbiome studies, the suggested research questions were primarily of a descriptive nature. In other areas, multiple experimental approaches, e.g., transcriptomics, proteomics, RNAi and gene deletions, are needed to understand the regulation of toxin production and mechanisms underlying successful biological controls. Answers to the research questions will provide starting points for developing acceptable prevention and remediation processes. Forging a partnership between scientists and appropriately-placed communications experts was recognized by both groups as an essential step to communicating risks, while retaining overall confidence in the safety of the food supply and the integrity of the food production chain. PMID:29494529

  19. Ecological consequences, genetic and chemical variations in fragmented populations of a medicinal plant, justicia adhatoda and implications for its conservation

    International Nuclear Information System (INIS)

    Gilani, S.A.; Watanabe, K.N.; Fujii, Y.; Shinwari, Z.K.

    2011-01-01

    Justicia adhatoda from Kohat Plateau was selected for genetic diversity studies, due to its fragmented habitat, importance in traditional and pharmaceutical medicine and a lack of population structure studies. We had two hypotheses: that habitat loss posed a greater threat to populations than loss of genetic diversity, and that chemical diversity would be higher among different populations than within populations. Genetic diversity within and among populations was evaluated using PBA (P450 based analogue) markers. AMOVA analysis revealed that there was higher genetic diversity within populations (90%) than among populations (10%). No genetic drift was observed, i.e., genetic diversity within populations was maintained despite fewer numbers of individuals in fragmented populations. Surveys of J. adhatoda populations revealed that they were growing in harsh conditions and were imperiled due to extensive harvesting for commercial and domestic purposes. Chemical diversity was evaluated by GC-MS (Gas Chromatograph-Mass Spectrometry) analysis of 90% methanol and 1:2 chloroform:methanol extracts. GC-MS analysis of both the extracts showed nine and 18 chemical compounds, respectively, with higher chemical variations among populations. It is therefore recommended that efforts for the conservation of severely fragmented populations of J. adhatoda must be carried out along with sustainable harvesting. (author)

  20. Safety of genetically engineered foods: approaches to assessing unintended health effects

    National Research Council Canada - National Science Library

    Committee on Identifying and Assessing Unintended Effects of Genetically Engineered Foods on Human Health, National Research Council

    2004-01-01

    .... It identifies and recommends several pre- and post-market approaches to guide the assessment of unintended compositional changes that could result from genetically modified foods and research avenues...

  1. From chemical metabolism to life: the origin of the genetic coding process

    Directory of Open Access Journals (Sweden)

    Antoine Danchin

    2017-06-01

    Full Text Available Looking for origins is so much rooted in ideology that most studies reflect opinions that fail to explore the first realistic scenarios. To be sure, trying to understand the origins of life should be based on what we know of current chemistry in the solar system and beyond. There, amino acids and very small compounds such as carbon dioxide, dihydrogen or dinitrogen and their immediate derivatives are ubiquitous. Surface-based chemical metabolism using these basic chemicals is the most likely beginning in which amino acids, coenzymes and phosphate-based small carbon molecules were built up. Nucleotides, and of course RNAs, must have come to being much later. As a consequence, the key question to account for life is to understand how chemical metabolism that began with amino acids progressively shaped into a coding process involving RNAs. Here I explore the role of building up complementarity rules as the first information-based process that allowed for the genetic code to emerge, after RNAs were substituted to surfaces to carry over the basic metabolic pathways that drive the pursuit of life.

  2. Evaluation of an Integrated Approach Involving Chemical and ...

    African Journals Online (AJOL)

    Chemical and bio-remediation measures for the detoxification of pollutants such as cyanide and heavy metals in mine tailings ... in treated effluent released into natural water bodies after bacterial degradation was generally within international ...

  3. Antibodies and isotopes, a chemical approach to tumour targeting

    International Nuclear Information System (INIS)

    Vaughan, A.T.M.; Yankuba, S.C.S.; Anderson, P.

    1986-01-01

    In this study, scandium-47 and yttrium-90 have been used as representatives of potential cytotoxic labels. Both isotopes have a high yield of energetic beta particles and half-lives of the same order as indium-111. In addition they are both members of Group III and so may be used as a base for chemical comparisons in the future with radiotoxic isotopes from other chemical groups

  4. Systems approach to chemical spill response information needs

    Energy Technology Data Exchange (ETDEWEB)

    Parnarouskis, M.C.; Flessner, M.F.; Potts, R.G.

    1980-01-01

    The Chemical Hazards Response Information System (CHRIS) has been specifically designed to meet the emergency needs of US Coast Guard field personnel, currently providing them with information on 900 hazardous chemicals, with methods of predicting hazards resulting from accidental discharges, and with procedures for selecting and implementing response to accident discharges. The major components of CHRIS and the computerized hazard assessment models within the Hazard Assessment Computer System are described in detail.

  5. Genetic approaches refine ex situ lowland tapir (Tapirus terrestris) conservation.

    Science.gov (United States)

    Gonçalves da Silva, Anders; Lalonde, Danielle R; Quse, Viviana; Shoemaker, Alan; Russello, Michael A

    2010-01-01

    Ex situ conservation management remains an important tool in the face of continued habitat loss and global environmental change. Here, we use microsatellite marker variation to evaluate conventional assumptions of pedigree-based ex situ population management and directly inform a captive lowland tapir breeding program within a range country. We found relatively high levels of genetic variation (N(total) = 41; mean H(E) = 0.67 across 10 variable loci) and little evidence for relatedness among founder individuals (N(founders) = 10; mean relatedness = -0.05). Seven of 29 putative parent-offspring relationships were excluded by parentage analysis based on allele sharing, and we identified 2 individuals of high genetic value to the population (mk genetic markers were used to inform kinship. We discuss our results within the context of recent studies that have assessed the utility of neutral molecular markers for ex situ conservation.

  6. Food control and a citizen science approach for improving teaching of Genetics in universities.

    Science.gov (United States)

    Borrell, Y J; Muñoz-Colmenero, A M; Dopico, E; Miralles, L; Garcia-Vazquez, E

    2016-09-10

    A Citizen Science approach was implemented in the laboratory practices of Genetics at the University of Oviedo, related with the engaging topic of Food Control. Real samples of food products consumed by students at home (students as samplers) were employed as teaching material in three different courses of Genetics during the academic year 2014-2015: Experimental Methods in Food Production (MBTA) (Master level), and Applied Molecular Biology (BMA) and Conservation Genetics and Breeding (COMGE) (Bachelor/Degree level). Molecular genetics based on PCR amplification of DNA markers was employed for species identification of 22 seafood products in COMGE and MBTA, and for detection of genetically modified (GM) maize from nine products in BMA. In total six seafood products incorrectly labeled (27%), and two undeclared GM maize (22%) were found. A post-Laboratory survey was applied for assessing the efficacy of the approach for improving motivation in the Laboratory Practices of Genetics. Results confirmed that students that worked on their own samples from local markets were significantly more motivated and better evaluated their Genetic laboratory practices than control students (χ(2)  = 12.11 p = 0.033). Our results suggest that citizen science approaches could not be only useful for improving teaching of Genetics in universities but also to incorporate students and citizens as active agents in food control. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):450-462, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

  7. The practice of genetic counselling: a Ccmparative approach to understanding genetic counselling in China

    NARCIS (Netherlands)

    Suli, S.

    2009-01-01

    This article provides an empirical account of the application of genetic counselling in China based on interviews, clinical observation and literature research during a field study from September 2008 to February 2009, carried out mainly in China and partly in Hong Kong and the United Kingdom.

  8. Invasion success in Cogongrass (Imperata cylindrica): A population genetic approach exploring genetic diversity and historical introductions

    Science.gov (United States)

    Rima D. Lucardi; Lisa E. Wallace; Gary N. Ervin

    2014-01-01

    Propagule pressure significantly contributes to and limits the potential success of a biological invasion, especially during transport, introduction, and establishment. Events such as multiple introductions of foreign parent material and gene flow among them can increase genetic diversity in founding populations, often leading to greater invasion success. We applied...

  9. An approach to fabricating chemical sensors based on ZnO nanorod arrays

    International Nuclear Information System (INIS)

    Park, Jae Young; Song, Dong Eon; Kim, Sang Sub

    2008-01-01

    Vertically and laterally aligned ZnO nanorod arrays were synthesized on Pt-coated Si substrates by catalyst-free metal organic chemical vapor deposition. An approach to fabricating chemical sensors based on the nanorod arrays using a coating-and-etching process with a photo-resist is reported. Tests of the devices as oxygen gas sensors have been performed. Our results demonstrate that the approach holds promise for the realization of sensitive and reliable nanorod array chemical sensors

  10. Physico-Chemical Properties and Biodegradability of Genetically Modified Populus trichocarpa and Pinus taeda

    Science.gov (United States)

    Edmunds, Charles Warren

    Increasing concerns over greenhouse gas emissions and the finite supply of fossil fuels lead to the goal of utilizing lignocellulosic feedstocks for biofuels, platform chemicals, and biocomposites. Lignin is responsible for the recalcitrance of lignocellulosic biomass and is a major barrier to its deconstruction. Great progress has been made in mapping and modifying the lignin biosynthetic pathway. However, the link between the genetic modification, resulting chemical and physical properties of the wood, and how these properties influence the thermomechanical and recalcitrance to biological and chemical degradation needs further investigation. In this dissertation, the study of modified Populus trichocarpa and Pinus taeda were utilized to accomplish this goal. Thermo-mechanical properties of genetically modified P. trichocarpa with altered lignin content and/or lignin structure were measured with a series of tools including; dynamic mechanical analysis, nuclear magnetic resonance, and wet chemistry techniques. Results demonstrated lignin content and lignin structure likely influence the glass transition temperature (Tg), and that decreased lignin content and the corresponding higher proportion of cell wall carbohydrates may contribute to increased molecular mobility in the wood polymer structure. The effect of lignin biosynthetic pathway modification on biological degradation of these transgenic wood specimens was of interest. However, experimental methods for fungal treatment on small young greenhouse-grown wood specimens are not well established. Therefore, a project was undertaken to develop a method for fungal inoculation and incubation for these unique specimens. Several parameters were tested, and a fungal treatment method was identified with sufficient weight loss after decay and significant reduction in variation of weight loss between replicates compared to previous experiments by direct inoculation of wood with liquid malt extract fungal culture

  11. Discovery of chemical oscillatory layering in adarce from Rehai, Tengchong, Yunnan and its genetic mechanism

    International Nuclear Information System (INIS)

    Wang Jianghai; Dong Jinquan

    1994-01-01

    Based on characteristics of mineral assemblages and compositions of sinter in several typical region, Western Yunnan, it is recognized that rhythmic compositional layering is widespread in sinter. According to self-organization theory and fluid dynamic experiments completed by predecessors, the authors have studied dynamic features of fluids in thermo-chamber; and concluded that in which double-diffusive convection layering would imperatively take place on the basis of estimation of dynamic parameters and determination of differences between RT and R0. Finally, a two-stage genetic model has been put forward for explaining the rhythmic layering in sinter, i.e. :1) double-diffusive convection of fluid in chambers was induced by the gradients of temperature and concentration; and 2) the rising of layered fluids and the precipitation of the chemical material occurred. Obviously, rhythmic layering in sinter is a typical self-organizational phenomenon

  12. Optimal Solutions of Multiproduct Batch Chemical Process Using Multiobjective Genetic Algorithm with Expert Decision System

    Science.gov (United States)

    Mokeddem, Diab; Khellaf, Abdelhafid

    2009-01-01

    Optimal design problem are widely known by their multiple performance measures that are often competing with each other. In this paper, an optimal multiproduct batch chemical plant design is presented. The design is firstly formulated as a multiobjective optimization problem, to be solved using the well suited non dominating sorting genetic algorithm (NSGA-II). The NSGA-II have capability to achieve fine tuning of variables in determining a set of non dominating solutions distributed along the Pareto front in a single run of the algorithm. The NSGA-II ability to identify a set of optimal solutions provides the decision-maker DM with a complete picture of the optimal solution space to gain better and appropriate choices. Then an outranking with PROMETHEE II helps the decision-maker to finalize the selection of a best compromise. The effectiveness of NSGA-II method with multiojective optimization problem is illustrated through two carefully referenced examples. PMID:19543537

  13. Computational approaches to the chemical conversion of carbon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Daojian; Negreiros, Fabio R.; Apra, Edoardo; Fortunelli, Alessandro

    2013-06-01

    The conversion of CO2 into fuels and chemicals is viewed as an attractive route for controlling the atmospheric concentration of this greenhouse gas and recycling it, but its industrial application is limited by the low selectivity and activity of the current catalysts. Theoretical modeling, in particular density-functional theory (DFT) simulations, provides a powerful and effective tool to discover chemical reaction mechanisms and design new catalysts for the chemical conversion of CO2, overcoming the repetitious and time/labor consuming trial-and-error experimental processes. In this article we give a comprehensive survey of recent advances on mechanism determination by DFT calculations for the catalytic hydrogenation of CO2 into CO, CH4, CH3OH, and HCOOH, and CO2 methanation, as well as the photo- and electrochemical reduction of CO2. DFT-guided design procedures of new catalytic systems are also reviewed, and challenges and perspectives in this field are outlined.

  14. An approach for assessing human exposures to chemical mixtures in the environment

    International Nuclear Information System (INIS)

    Rice, Glenn; MacDonell, Margaret; Hertzberg, Richard C.; Teuschler, Linda; Picel, Kurt; Butler, Jim; Chang, Young-Soo; Hartmann, Heidi

    2008-01-01

    Humans are exposed daily to multiple chemicals, including incidental exposures to complex chemical mixtures released into the environment and to combinations of chemicals that already co-exist in the environment because of previous releases from various sources. Exposures to chemical mixtures can occur through multiple pathways and across multiple routes. In this paper, we propose an iterative approach for assessing exposures to environmental chemical mixtures; it is similar to single-chemical approaches. Our approach encompasses two elements of the Risk Assessment Paradigm: Problem Formulation and Exposure Assessment. Multiple phases of the assessment occur in each element of the paradigm. During Problem Formulation, analysts identify and characterize the source(s) of the chemical mixture, ensure that dose-response and exposure assessment measures are concordant, and develop a preliminary evaluation of the mixture's fate. During Exposure Assessment, analysts evaluate the fate of the chemicals comprising the mixture using appropriate models and measurement data, characterize the exposure scenario, and estimate human exposure to the mixture. We also describe the utility of grouping the chemicals to be analyzed based on both physical-chemical properties and an understanding of environmental fate. In the article, we also highlight the need for understanding of changes in the mixture composition in the environment due to differential transport, differential degradation, and differential partitioning to other media. The section describes the application of the method to various chemical mixtures, highlighting issues associated with assessing exposures to chemical mixtures in the environment

  15. A Genetic-Algorithms-Based Approach for Programming Linear and Quadratic Optimization Problems with Uncertainty

    Directory of Open Access Journals (Sweden)

    Weihua Jin

    2013-01-01

    Full Text Available This paper proposes a genetic-algorithms-based approach as an all-purpose problem-solving method for operation programming problems under uncertainty. The proposed method was applied for management of a municipal solid waste treatment system. Compared to the traditional interactive binary analysis, this approach has fewer limitations and is able to reduce the complexity in solving the inexact linear programming problems and inexact quadratic programming problems. The implementation of this approach was performed using the Genetic Algorithm Solver of MATLAB (trademark of MathWorks. The paper explains the genetic-algorithms-based method and presents details on the computation procedures for each type of inexact operation programming problems. A comparison of the results generated by the proposed method based on genetic algorithms with those produced by the traditional interactive binary analysis method is also presented.

  16. A New Approach to Tuning Heuristic Parameters of Genetic Algorithms

    Czech Academy of Sciences Publication Activity Database

    Holeňa, Martin

    2006-01-01

    Roč. 3, č. 3 (2006), s. 562-569 ISSN 1790-0832. [AIKED'06. WSEAS International Conference on Artificial Intelligence , Knowledge Engineering and Data Bases. Madrid, 15.02.2006-17.02.2006] R&D Projects: GA ČR(CZ) GA201/05/0325; GA ČR(CZ) GA201/05/0557 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary optimization * genetic algorithms * heuristic parameters * parameter tuning * artificial neural networks * convergence speed * population diversity Subject RIV: IN - Informatics, Computer Science

  17. Theorising Masculinities and Crime: A Genetic-Social Approach

    OpenAIRE

    Owen, Timothy

    2012-01-01

    This paper examines competing notions of ‘masculinities’ in relation to crime, and the global nature of gendered inequalities. It is the contention here that social constructionist theories of male sexualities contain certain theoretical deficits. It is suggested that a post-Postmodern analysis of ‘masculinities’ might incorporate some of the insights from Owen’s Genetic-Social meta-theoretical framework. Owen’s ‘sensitising’ framework has been ‘applied’ to the sociological study of human bio...

  18. Method for accurate determination of dissociation constants of optical ratiometric systems: chemical probes, genetically encoded sensors, and interacting molecules.

    Science.gov (United States)

    Pomorski, Adam; Kochańczyk, Tomasz; Miłoch, Anna; Krężel, Artur

    2013-12-03

    Ratiometric chemical probes and genetically encoded sensors are of high interest for both analytical chemists and molecular biologists. Their high sensitivity toward the target ligand and ability to obtain quantitative results without a known sensor concentration have made them a very useful tool in both in vitro and in vivo assays. Although ratiometric sensors are widely used in many applications, their successful and accurate usage depends on how they are characterized in terms of sensing target molecules. The most important feature of probes and sensors besides their optical parameters is an affinity constant toward analyzed molecules. The literature shows that different analytical approaches are used to determine the stability constants, with the ratio approach being most popular. However, oversimplification and lack of attention to detail results in inaccurate determination of stability constants, which in turn affects the results obtained using these sensors. Here, we present a new method where ratio signal is calibrated for borderline values of intensities of both wavelengths, instead of borderline ratio values that generate errors in many studies. At the same time, the equation takes into account the cooperativity factor or fluorescence artifacts and therefore can be used to characterize systems with various stoichiometries and experimental conditions. Accurate determination of stability constants is demonstrated utilizing four known optical ratiometric probes and sensors, together with a discussion regarding other, currently used methods.

  19. Recent Developments on Genetic Engineering of Microalgae for Biofuels and Bio-Based Chemicals.

    Science.gov (United States)

    Ng, I-Son; Tan, Shih-I; Kao, Pei-Hsun; Chang, Yu-Kaung; Chang, Jo-Shu

    2017-10-01

    Microalgae serve as a promising source for the production of biofuels and bio-based chemicals. They are superior to terrestrial plants as feedstock in many aspects and their biomass is naturally rich in lipids, carbohydrates, proteins, pigments, and other valuable compounds. Due to the relatively slow growth rate and high cultivation cost of microalgae, to screen efficient and robust microalgal strains as well as genetic modifications of the available strains for further improvement are of urgent demand in the development of microalgae-based biorefinery. In genetic engineering of microalgae, transformation and selection methods are the key steps to accomplish the target gene modification. However, determination of the preferable type and dosage of antibiotics used for transformant selection is usually time-consuming and microalgal-strain-dependent. Therefore, more powerful and efficient techniques should be developed to meet this need. In this review, the conventional and emerging genome-editing tools (e.g., CRISPR-Cas9, TALEN, and ZFN) used in editing the genomes of nuclear, mitochondria, and chloroplast of microalgae are thoroughly surveyed. Although all the techniques mentioned above demonstrate their abilities to perform gene editing and desired phenotype screening, there still need to overcome higher production cost and lower biomass productivity, to achieve efficient production of the desired products in microalgal biorefineries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Germ cell toxicity: significance in genetic and fertility effects of radiation and chemicals

    International Nuclear Information System (INIS)

    Oakberg, E.F.

    1983-01-01

    The response of the male and female to radiation and chemicals is different. Any loss of oocytes in the female cannot be replaced, and if severe enough, will result in a shortening of the reproductive span. In the male, a temporary sterile period may be induced owing to destruction of the differentiating spermatogonia, but the stem cells are the most resistant spermatogonial type, are capable of repopulating the seminiferous epithelium, and fertility usually returns. The response of both the male and female changes with development of the embryonic to the adult gonad, and with differentiation and maturation in the adult. The primordial germ cells, early oocytes, and differentiating spermatogonia of the adult male are unusually sensitive to the cytotoxic action of noxious agents, but each agent elicits a specific response owing to the intricate biochemical and physiological changes associated with development and maturation of the gametes. The relationship of germ cell killing to fertility is direct, and long-term fertility effects can be predicted from histological analysis of the gonads. The relationship to genetic effects, on the other hand, is indirect, and acts primarily by limiting the cell stages available for testing, by affecting the distribution of mitotically active stem cells among the different stages of the mitotic cycle, and thereby, changing both the type and frequency of genetic effects observed. 100 references, 38 figures, 7 tables

  1. Protection against genetic hazards from environmental chemical mutagens: experience with ionizing radiation

    International Nuclear Information System (INIS)

    Sankaranarayanan, K.

    1977-01-01

    In radiation protection, the recurrent theme is, and always has been, dose limitation whether it is for occupational workers, individual members of the public or the population as a whole. The key words are 'dose' and 'limitation'. The quantitative system of dose limitation has been achieved because of a number of conceptual developments in our understanding of the mechanism of radiation action, development of radiation dosimetry, the accumulation of a vast body of quantitative information on dose-effect relationships and the effects of various biological and physical variables that affect these relationships of data on patterns and levels of exposures likely to be encountered to make estimates of the effects expected to result from such exposures, and balancing of risks to society against the benefits derived, the latter a matter of informed judgement. The philosophy has always been to avoid all unnecessary exposures and to limit the necessary exposures (justified by the benefits expected) to as low a level as reasonably achievable, social and economic factors being taken into acccount. The introduction of the concept that the system of dose limitation to the population should be based on genetic risks has stressed the need for careful planning to ensure that our genetic heritage is not endangered. Transfer of this knowledge to the field of chemical protection is discussed. (Auth.)

  2. Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review.

    Science.gov (United States)

    Tripathi, Niraj; Khare, Dhirendra

    2016-10-01

    Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and 'omics' research, is provided in this article.

  3. Introduction: integrating genetic and cultural evolutionary approaches to language.

    Science.gov (United States)

    Mesoudi, Alex; McElligott, Alan G; Adger, David

    2011-04-01

    The papers in this special issue of Human Biology address recent research in the field of language evolution, both the genetic evolution of the language faculty and the cultural evolution of specific languages. While both of these areas have received increasing interest in recent years, there is also a need to integrate these somewhat separate efforts and explore the relevant gene-culture coevolutionary interactions. Here we summarize the individual contributions, set them in the context of the wider literature, and identify outstanding future research questions. The first set of papers concerns the comparative study of nonhuman communication in primates and birds from both a behavioral and neurobiological perspective, revealing evidence for several common language-related traits in various nonhuman species and providing clues as to the evolutionary origin and function of the human language faculty. The second set of papers discusses the consequences of viewing language as a culturally evolving system in its own right, including claims that this removes the need for strong genetic biases for language acquisition, and that phylogenetic evolutionary methods can be used to reconstruct language histories. We conclude by highlighting outstanding areas for future research, including identifying the precise selection pressures that gave rise to the language faculty in ancestral hominin species, and determining the strength, domain specificity, and origin of the cultural transmission biases that shape languages as they pass along successive generations of language learners.

  4. A network dynamics approach to chemical reaction networks

    Science.gov (United States)

    van der Schaft, A. J.; Rao, S.; Jayawardhana, B.

    2016-04-01

    A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.

  5. Integrating Exposure into Chemical Alternatives Assessment Using a Qualitative Approach

    Science.gov (United States)

    Most alternatives assessments (AA) published to date are largely hazard-based rankings, and as such may not represent a fully informed consideration of the advantages and disadvantages of possible alternatives. With an assessment goal of identifying an alternative chemical that i...

  6. A network dynamics approach to chemical reaction networks

    NARCIS (Netherlands)

    van der Schaft, Abraham; Rao, S.; Jayawardhana, B.

    2016-01-01

    A treatment of chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a

  7. Small molecules, big players: the National Cancer Institute's Initiative for Chemical Genetics.

    Science.gov (United States)

    Tolliday, Nicola; Clemons, Paul A; Ferraiolo, Paul; Koehler, Angela N; Lewis, Timothy A; Li, Xiaohua; Schreiber, Stuart L; Gerhard, Daniela S; Eliasof, Scott

    2006-09-15

    In 2002, the National Cancer Institute created the Initiative for Chemical Genetics (ICG), to enable public research using small molecules to accelerate the discovery of cancer-relevant small-molecule probes. The ICG is a public-access research facility consisting of a tightly integrated team of synthetic and analytical chemists, assay developers, high-throughput screening and automation engineers, computational scientists, and software developers. The ICG seeks to facilitate the cross-fertilization of synthetic chemistry and cancer biology by creating a research environment in which new scientific collaborations are possible. To date, the ICG has interacted with 76 biology laboratories from 39 institutions and more than a dozen organic synthetic chemistry laboratories around the country and in Canada. All chemistry and screening data are deposited into the ChemBank web site (http://chembank.broad.harvard.edu/) and are available to the entire research community within a year of generation. ChemBank is both a data repository and a data analysis environment, facilitating the exploration of chemical and biological information across many different assays and small molecules. This report outlines how the ICG functions, how researchers can take advantage of its screening, chemistry and informatic capabilities, and provides a brief summary of some of the many important research findings.

  8. Terrestrial ecotoxicity of eight chemicals in a systematic approach

    Energy Technology Data Exchange (ETDEWEB)

    Hund-Rinke, K.; Simon, M. [Fraunhofer Inst. for Molecular Biology and Applied Ecology, Schmallenberg (Germany)

    2005-07-01

    Background and objective. Terrestrial ecotoxicity data are required for many research purposes. The data are derived either from the literature or elaborated by own investigations. As the terrestrial toxicity tests are usually time-consuming and labour intensive, the experiments are performed with a limited number of test organisms and soils. In the context of a project sponsored by CEFIC-LRI (European Chemical Industry Council - Long-Range Research Initiative), EC{sub 50}-values were systematically elaborated for eight chemicals with a wide range of logK{sub ow}-values (CdCl{sub 2}, Trinitrotoluene, 3,4-dichloroaniline, 2,4-dichlorophenol, Tributyltinchloride, Pentachlorophenol, Benzo(a)pyrene, p,p-dichloro-2,2-diphenyl-1,1,1-trichloroethane). The substances were selected covering a broad range of physico-chemical and ecotoxicological properties. As toxicity endpoints, microbial activities, plant germination and growth as well as reproduction of earthworms and collembola were determined. As such systematic investigations are rarely performed and for some substances no data existed, the data pool is made available to the scientific community. Methods. All toxicity tests were conducted on three different soil types (sandy soil, silty soil, loamy soil), according to ISO and OECD guidelines Results, discussion, conclusion and outlook. The different toxicities of the chemicals, the influence of soil properties on bioavailability as well as different sensitivities of test organisms and test parameters are reflected by the EC{sub 50}-values. The results showed that the EC{sub 50}-values calculated on the basis of nominal concentrations can significantly vary from EC{sub 50}-values derived from analytical concentrations for some substances. To avoid false conclusions, this has to be considered especially when concentrations determined in the field are compared with toxicity data obtained from the literature or calculated on the basis of nominal concentrations. Moreover

  9. BP neural network optimized by genetic algorithm approach for titanium and iron content prediction in EDXRF

    International Nuclear Information System (INIS)

    Wang Jun; Liu Mingzhe; Li Zhe; Li Lei; Shi Rui; Tuo Xianguo

    2015-01-01

    The quantitative elemental content analysis is difficult due to the uniform effect, particle effect and the element matrix effect, etc, when using energy dispersive X-ray fluorescence (EDXRF) technique. In this paper, a hybrid approach of genetic algorithm (GA) and back propagation (BP) neural network was proposed without considering the complex relationship between the concentration and intensity. The aim of GA optimized BP was to get better network initial weights and thresholds. The basic idea was that the reciprocal of the mean square error of the initialization BP neural network was set as the fitness value of the individual in GA, and the initial weights and thresholds were replaced by individuals, and then the optimal individual was sought by selection, crossover and mutation operations, finally a new BP neural network model was created with the optimal initial weights and thresholds. The calculation results of quantitative analysis of titanium and iron contents for five types of ore bodies in Panzhihua Mine show that the results of classification prediction are far better than that of overall forecasting, and relative errors of 76.7% samples are less than 2% compared with chemical analysis values, which demonstrates the effectiveness of the proposed method. (authors)

  10. The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.

    Science.gov (United States)

    Zhi, Xiao-Yang; Jiang, Zhao; Yang, Ling-Ling; Huang, Ying

    2017-02-01

    The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach. Genetic variations have occurred throughout the whole evolutionary history of the Corynebacteriaceae. Gene loss has been the primary force causing genetic changes, not only in terms of the number of protein families affected, but also because of its continuity on the time series. The variation in metabolism caused by these genetic changes mainly occurred for membrane transporters, two-component systems, and metabolism related to amino acids and carbohydrates. Interestingly, horizontal gene transfer (HGT) not only caused changes related to pathogenicity, but also triggered the acquisition of antimicrobial resistance. The Darwinian theory of evolution did not adequately explain the effects of dispersive HGT and/or gene loss in the evolution of the Corynebacteriaceae. These findings provide new insight into the evolution and speciation of Corynebacteriaceae and advance our understanding of the genetic innovation in microbial populations. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Genetic Complexity of Episodic Memory: A Twin Approach to Studies of Aging

    Science.gov (United States)

    Kremen, William S.; Spoon, Kelly M.; Jacobson, Kristen C.; Vasilopoulos, Terrie; McCaffery, Jeanne M.; Panizzon, Matthew S.; Franz, Carol E.; Vuoksimaa, Eero; Xian, Hong; Rana, Brinda K.; Toomey, Rosemary; McKenzie, Ruth; Lyons, Michael J.

    2016-01-01

    Episodic memory change is a central issue in cognitive aging, and understanding that process will require elucidation of its genetic underpinnings. A key limiting factor in genetically informed research on memory has been lack of attention to genetic and phenotypic complexity, as if “memory is memory” and all well-validated assessments are essentially equivalent. Here we applied multivariate twin models to data from late-middle-aged participants in the Vietnam Era Twin Study of Aging to examine the genetic architecture of 6 measures from 3 standard neuropsychological tests: the California Verbal Learning Test-2, and Wechsler Memory Scale-III Logical Memory (LM) and Visual Reproductions (VR). An advantage of the twin method is that it can estimate the extent to which latent genetic influences are shared or independent across different measures before knowing which specific genes are involved. The best-fitting model was a higher order common pathways model with a heritable higher order general episodic memory factor and three test-specific subfactors. More importantly, substantial genetic variance was accounted for by genetic influences that were specific to the latent LM and VR subfactors (28% and 30%, respectively) and independent of the general factor. Such unique genetic influences could partially account for replication failures. Moreover, if different genes influence different memory phenotypes, they could well have different age-related trajectories. This approach represents an important step toward providing critical information for all types of genetically informative studies of aging and memory. PMID:24956007

  12. Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.

    Science.gov (United States)

    Bellucci, Michael A; Coker, David F

    2011-07-28

    We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent. © 2011 American Institute of Physics

  13. 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

  14. Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century

    International Nuclear Information System (INIS)

    Mortensen, Holly M.; Euling, Susan Y.

    2013-01-01

    Response to environmental chemicals can vary widely among individuals and between population groups. In human health risk assessment, data on susceptibility can be utilized by deriving risk levels based on a study of a susceptible population and/or an uncertainty factor may be applied to account for the lack of information about susceptibility. Defining genetic susceptibility in response to environmental chemicals across human populations is an area of interest in the NAS' new paradigm of toxicity pathway-based risk assessment. Data from high-throughput/high content (HT/HC), including -omics (e.g., genomics, transcriptomics, proteomics, metabolomics) technologies, have been integral to the identification and characterization of drug target and disease loci, and have been successfully utilized to inform the mechanism of action for numerous environmental chemicals. Large-scale population genotyping studies may help to characterize levels of variability across human populations at identified target loci implicated in response to environmental chemicals. By combining mechanistic data for a given environmental chemical with next generation sequencing data that provides human population variation information, one can begin to characterize differential susceptibility due to genetic variability to environmental chemicals within and across genetically heterogeneous human populations. The integration of such data sources will be informative to human health risk assessment

  15. Genetic Approaches to Appearance and Ancestry : Improving Forensic DNA Analysis

    NARCIS (Netherlands)

    L.C. Chaitanya (Lakshmi)

    2016-01-01

    textabstractTraditionally, routine forensic casework is based on comparative grounds. DNA profiles obtained from crime-scenes are compared with those of potential suspects or DNA profiles deposited in forensic DNA databases. The principal limitation of such comparative approach is that trace

  16. At the brink of supercoloniality: genetic, behavioral and chemical assessments of population structure of the desert ant Cataglyphis niger

    Directory of Open Access Journals (Sweden)

    Maya eSaar

    2014-05-01

    Full Text Available The nesting habits of ants play an important role in structuring ant populations. They vary from monodomy, a colony occupies a single nest, via polydomy, a colony occupies multiple adjacent nests, to supercoloniality, a colony spans over large territories comprising dozen to thousands nests without having any boundaries. The population structure of the desert ant Cataglyphis niger, previously considered to form supercolonies, was studied using genetic, chemical and behavioral tools in plots of 50x50 meters at two distinct populations. At the Palmahim site, the plot comprised 15 nests that according to the genetic analysis constituted three colonies. Likewise at the Rishon Leziyyon site 14 nests constituted 5 genetic colonies. In both sites, both chemical analysis and the behavioral (aggression tests confirmed the colony genetic architecture. The behavioral tests also revealed that aggression between colonies within a population was higher than that exhibited between colonies of different populations, suggesting the occurrence of the nasty neighbor phenomenon. In contrast to supercolony structure previously reported in another population of this species, the presently studied populations were composed of polydomous colonies. However, both the genetic and chemical data revealed that the inter-colonial differences between sites were larger than those within site, suggesting some within-site population viscosity. Thus, C. niger exhibits flexible nesting characteristics, from polydomy to supercoloniality, and can be considered at the brink of supercoloniality. We attribute the differences in population structure among sites to the intensity of intraspecific competition.

  17. Modeling warfare in social animals: a "chemical" approach.

    Science.gov (United States)

    Santarlasci, Alisa; Martelloni, Gianluca; Frizzi, Filippo; Santini, Giacomo; Bagnoli, Franco

    2014-01-01

    We present here a general method for modelling the dynamics of battles among social animals. The proposed method exploits the procedures widely used to model chemical reactions, but still uncommon in behavioural studies. We applied this methodology to the interpretation of experimental observations of battles between two species of ants (Lasius neglectus and Lasius paralienus), but this scheme may have a wider applicability and can be extended to other species as well. We performed two types of experiment labelled as interaction and mortality. The interaction experiments are designed to obtain information on the combat dynamics and lasted one hour. The mortality ones provide information on the casualty rates of the two species and lasted five hours. We modelled the interactions among ants using a chemical model which considers the single ant individuals and fighting groups analogously to atoms and molecules. The mean-field behaviour of the model is described by a set of non-linear differential equations. We also performed stochastic simulations of the corresponding agent-based model by means of the Gillespie event-driven integration scheme. By fitting the stochastic trajectories with the deterministic model, we obtained the probability distribution of the reaction parameters. The main result that we obtained is a dominance phase diagram, that gives the average trajectory of a generic battle, for an arbitrary number of opponents. This phase diagram was validated with some extra experiments. With respect to other war models (e.g., Lanchester's ones), our chemical model considers all phases of the battle and not only casualties. This allows a more detailed description of the battle (with a larger number of parameters), allowing the development of more sophisticated models (e.g., spatial ones), with the goal of distinguishing collective effects from the strategic ones.

  18. Harmonization of risk management approaches: radiation and chemical exposures

    Energy Technology Data Exchange (ETDEWEB)

    Srinivasan, P. [Bhabha Atomic Research Centre, Radiation Safety Systems Div., Mumbai (India)

    2006-07-01

    Assessment of occupational and public risk from the environmental pollutants like chemicals, radiation, etc demands that the effects be considered not only from each individual pollutant, but from the combination of all the pollutants. An integrated risk assessment system needs to be in place to have an overall risk perspective for the benefit of policy makers and decision takers to try to achieve risk reduction in totality. The basis for risk-based radiation dose limits is derived from epidemiological studies, which provide a rich source of data largely unavailable to chemical risk assessors. In addition, use of the principle of optimization as expressed in the ALARA concept has resulted in a safety culture, which is much more than just complying with stipulated limits. The conservative hypothesis of no-threshold dose-effect relation (ICRP) is universally assumed. The end-points and the severity of different classes of pollutants and even different pollutants in a same class vary over a wide range. Hence, it is difficult to arrive at a quantitative value for the net detriment that weighs the various types of end-points and various classes of pollutants. Once the risk due to other pollutants is quantified by some acceptable methodology, it can be expressed in terms of the Risk Equivalent Radiation Dose (R.E.R.D.) for easy comparison with options involving radiation exposure. This paper is an effort to use to quantify and present the risk due to exposure to chemicals and radiation in a common scale for the purpose of easy comparison to facilitate decision taking. (authors)

  19. Modeling Warfare in Social Animals: A "Chemical" Approach

    Science.gov (United States)

    Santarlasci, Alisa; Martelloni, Gianluca; Frizzi, Filippo; Santini, Giacomo; Bagnoli, Franco

    2014-01-01

    We present here a general method for modelling the dynamics of battles among social animals. The proposed method exploits the procedures widely used to model chemical reactions, but still uncommon in behavioural studies. We applied this methodology to the interpretation of experimental observations of battles between two species of ants (Lasius neglectus and Lasius paralienus), but this scheme may have a wider applicability and can be extended to other species as well. We performed two types of experiment labelled as interaction and mortality. The interaction experiments are designed to obtain information on the combat dynamics and lasted one hour. The mortality ones provide information on the casualty rates of the two species and lasted five hours. We modelled the interactions among ants using a chemical model which considers the single ant individuals and fighting groups analogously to atoms and molecules. The mean-field behaviour of the model is described by a set of non-linear differential equations. We also performed stochastic simulations of the corresponding agent-based model by means of the Gillespie event-driven integration scheme. By fitting the stochastic trajectories with the deterministic model, we obtained the probability distribution of the reaction parameters. The main result that we obtained is a dominance phase diagram, that gives the average trajectory of a generic battle, for an arbitrary number of opponents. This phase diagram was validated with some extra experiments. With respect to other war models (e.g., Lanchester's ones), our chemical model considers all phases of the battle and not only casualties. This allows a more detailed description of the battle (with a larger number of parameters), allowing the development of more sophisticated models (e.g., spatial ones), with the goal of distinguishing collective effects from the strategic ones. PMID:25369269

  20. Harmonization of risk management approaches: radiation and chemical exposures

    International Nuclear Information System (INIS)

    Srinivasan, P.

    2006-01-01

    Assessment of occupational and public risk from the environmental pollutants like chemicals, radiation, etc demands that the effects be considered not only from each individual pollutant, but from the combination of all the pollutants. An integrated risk assessment system needs to be in place to have an overall risk perspective for the benefit of policy makers and decision takers to try to achieve risk reduction in totality. The basis for risk-based radiation dose limits is derived from epidemiological studies, which provide a rich source of data largely unavailable to chemical risk assessors. In addition, use of the principle of optimization as expressed in the ALARA concept has resulted in a safety culture, which is much more than just complying with stipulated limits. The conservative hypothesis of no-threshold dose-effect relation (ICRP) is universally assumed. The end-points and the severity of different classes of pollutants and even different pollutants in a same class vary over a wide range. Hence, it is difficult to arrive at a quantitative value for the net detriment that weighs the various types of end-points and various classes of pollutants. Once the risk due to other pollutants is quantified by some acceptable methodology, it can be expressed in terms of the Risk Equivalent Radiation Dose (R.E.R.D.) for easy comparison with options involving radiation exposure. This paper is an effort to use to quantify and present the risk due to exposure to chemicals and radiation in a common scale for the purpose of easy comparison to facilitate decision taking. (authors)

  1. Modeling warfare in social animals: a "chemical" approach.

    Directory of Open Access Journals (Sweden)

    Alisa Santarlasci

    Full Text Available We present here a general method for modelling the dynamics of battles among social animals. The proposed method exploits the procedures widely used to model chemical reactions, but still uncommon in behavioural studies. We applied this methodology to the interpretation of experimental observations of battles between two species of ants (Lasius neglectus and Lasius paralienus, but this scheme may have a wider applicability and can be extended to other species as well. We performed two types of experiment labelled as interaction and mortality. The interaction experiments are designed to obtain information on the combat dynamics and lasted one hour. The mortality ones provide information on the casualty rates of the two species and lasted five hours. We modelled the interactions among ants using a chemical model which considers the single ant individuals and fighting groups analogously to atoms and molecules. The mean-field behaviour of the model is described by a set of non-linear differential equations. We also performed stochastic simulations of the corresponding agent-based model by means of the Gillespie event-driven integration scheme. By fitting the stochastic trajectories with the deterministic model, we obtained the probability distribution of the reaction parameters. The main result that we obtained is a dominance phase diagram, that gives the average trajectory of a generic battle, for an arbitrary number of opponents. This phase diagram was validated with some extra experiments. With respect to other war models (e.g., Lanchester's ones, our chemical model considers all phases of the battle and not only casualties. This allows a more detailed description of the battle (with a larger number of parameters, allowing the development of more sophisticated models (e.g., spatial ones, with the goal of distinguishing collective effects from the strategic ones.

  2. Speed Bump Detection Using Accelerometric Features: A Genetic Algorithm Approach.

    Science.gov (United States)

    Celaya-Padilla, Jose M; Galván-Tejada, Carlos E; López-Monteagudo, F E; Alonso-González, O; Moreno-Báez, Arturo; Martínez-Torteya, Antonio; Galván-Tejada, Jorge I; Arceo-Olague, Jose G; Luna-García, Huizilopoztli; Gamboa-Rosales, Hamurabi

    2018-02-03

    Among the current challenges of the Smart City, traffic management and maintenance are of utmost importance. Road surface monitoring is currently performed by humans, but the road surface condition is one of the main indicators of road quality, and it may drastically affect fuel consumption and the safety of both drivers and pedestrians. Abnormalities in the road, such as manholes and potholes, can cause accidents when not identified by the drivers. Furthermore, human-induced abnormalities, such as speed bumps, could also cause accidents. In addition, while said obstacles ought to be signalized according to specific road regulation, they are not always correctly labeled. Therefore, we developed a novel method for the detection of road abnormalities (i.e., speed bumps). This method makes use of a gyro, an accelerometer, and a GPS sensor mounted in a car. After having the vehicle cruise through several streets, data is retrieved from the sensors. Then, using a cross-validation strategy, a genetic algorithm is used to find a logistic model that accurately detects road abnormalities. The proposed model had an accuracy of 0.9714 in a blind evaluation, with a false positive rate smaller than 0.018, and an area under the receiver operating characteristic curve of 0.9784. This methodology has the potential to detect speed bumps in quasi real-time conditions, and can be used to construct a real-time surface monitoring system.

  3. Structural modification of polysaccharides: A biochemical-genetic approach

    Science.gov (United States)

    Kern, Roger G.; Petersen, Gene R.

    1991-01-01

    Polysaccharides have a wide range of industrial and biomedical applications. An industry trend is underway towards the increased use of bacteria to produce polysaccharides. Long term goals of this work are the adaptation and enhancement of saccharide properties for electronic and optic applications. In this report we illustrate the application of enzyme-bearing bacteriophage on strains of the enteric bacterium Klebsiella pneumoniae, which produces a polysaccharide with the relatively rare rheological property of drag-reduction. This has resulted in the production of new polysaccharides with enhanced rheological properties. Our laboratory is developing techniques for processing and structurally modifying bacterial polysaccharides and oligosaccharides which comprise their basic polymeric repeat units. Our research has focused on bacteriophage which produce specific polysaccharide degrading enzymes. This has lead to the development of enzymes generated by bacteriophage as tools for polysaccharide modification and purification. These enzymes were used to efficiently convert the native material to uniform-sized high molecular weight polymers, or alternatively into high-purity oligosaccharides. Enzyme-bearing bacteriophage also serve as genetic selection tools for bacteria that produce new families of polysaccharides with modified structures.

  4. Speed Bump Detection Using Accelerometric Features: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Jose M. Celaya-Padilla

    2018-02-01

    Full Text Available Among the current challenges of the Smart City, traffic management and maintenance are of utmost importance. Road surface monitoring is currently performed by humans, but the road surface condition is one of the main indicators of road quality, and it may drastically affect fuel consumption and the safety of both drivers and pedestrians. Abnormalities in the road, such as manholes and potholes, can cause accidents when not identified by the drivers. Furthermore, human-induced abnormalities, such as speed bumps, could also cause accidents. In addition, while said obstacles ought to be signalized according to specific road regulation, they are not always correctly labeled. Therefore, we developed a novel method for the detection of road abnormalities (i.e., speed bumps. This method makes use of a gyro, an accelerometer, and a GPS sensor mounted in a car. After having the vehicle cruise through several streets, data is retrieved from the sensors. Then, using a cross-validation strategy, a genetic algorithm is used to find a logistic model that accurately detects road abnormalities. The proposed model had an accuracy of 0.9714 in a blind evaluation, with a false positive rate smaller than 0.018, and an area under the receiver operating characteristic curve of 0.9784. This methodology has the potential to detect speed bumps in quasi real-time conditions, and can be used to construct a real-time surface monitoring system.

  5. Terrorist threat, chemical, biological, radiological, nuclear medical approach

    International Nuclear Information System (INIS)

    Revel, Th. de; Gourmelon, P.; Vidal, D.; Renaudeau, C.

    2005-01-01

    The different aspects linked to the use of nuclear, radiological, biological and or chemical weapons are gathered in this work. They concern history, fundamental aspect, diagnosis, therapy and prevention. The part devoted to the nuclear aspect concern the accidents in relation with ionizing radiations, the radiation syndrome, the contribution and limits of dosimetry, the treatment of medullary aplasia, the evaluation and treatment of an internal contamination, new perspectives on the use of cytokine for the treatment of accidental irradiated persons, alternative to the blood transfusion. (N.C.)

  6. A functional data analysis approach for genetic association studies

    OpenAIRE

    Reimherr, Matthew; Nicolae, Dan

    2014-01-01

    We present a new method based on Functional Data Analysis (FDA) for detecting associations between one or more scalar covariates and a longitudinal response, while correcting for other variables. Our methods exploit the temporal structure of longitudinal data in ways that are otherwise difficult with a multivariate approach. Our procedure, from an FDA perspective, is a departure from more established methods in two key aspects. First, the raw longitudinal phenotypes are assembled into functio...

  7. New approach for direct chemical synthesis of hexagonal Co nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Abel, Frank M., E-mail: fabel@udel.edu [Physics and Astronomy, University of Delaware (United States); Tzitzios, Vasilis [Institute of Nanoscience and Nanotechnology, NCSR, Demokritos (Greece); Hadjipanayis, George C. [Physics and Astronomy, University of Delaware (United States)

    2016-02-15

    In this paper, we explore the possibility of producing hexagonal Cobalt nanoparticles, with high saturation magnetization by direct chemical synthesis. The nanoparticles were synthesized by reduction of anhydrous cobalt (II) chloride by NaBH{sub 4} in tetraglyme at temperatures in the range of 200–270 °C under a nitrogen–hydrogen atmosphere. The reactions were done at high temperatures to allow for the formation of as-made hexagonal cobalt. The size of the particles was controlled by the addition of different surfactants. The best magnetic properties so far were obtained on spherical hexagonal Co nanoparticles with an average size of 45 nm, a saturation magnetization of 143 emu/g and coercivity of 500 Oe. the saturation magnetization and coercivity were further improved by annealing the Co nanoparticles leading to saturation magnetization of 160 emu/g and coercivity of 540 Oe. - Highlights: • We synthesized hexagonal cobalt nanoparticles by a new wet chemical method. • We considered the effects of different surfactants on particles magnetic properties. • The as-made Co nanoparticles had magnetic properties of 143 emu/g and 500 Oe. • After annealing magnetic properties of 160 emu/g and 540 Oe were obtained.

  8. Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

    Science.gov (United States)

    Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

    2008-06-01

    A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

  9. A genetic programming approach to oral cancer prognosis

    Directory of Open Access Journals (Sweden)

    Mei Sze Tan

    2016-09-01

    Full Text Available Background The potential of genetic programming (GP on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis. Method GP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS. The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM and logistic regression (LR are also done in order to verify the predictive capabilities of the GP. Result The result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341 when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis. Discussion Some of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis.

  10. A genetic programming approach to oral cancer prognosis.

    Science.gov (United States)

    Tan, Mei Sze; Tan, Jing Wei; Chang, Siow-Wee; Yap, Hwa Jen; Abdul Kareem, Sameem; Zain, Rosnah Binti

    2016-01-01

    The potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis. GP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS). The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM) and logistic regression (LR) are also done in order to verify the predictive capabilities of the GP. The result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341) when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis. Some of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis.

  11. Chemical pattern of brazilian apples: a chemometric approach based on the Fuji and Gala varieties

    OpenAIRE

    Vieira,Renato Giovanetti; Prestes,Rosilene Aparecida; Denardi,Frederico; Nogueira,Alessandro; Wosiacki,Gilvan

    2011-01-01

    The chemical composition of apple juices may be used to discriminate between the varieties for consumption and those for raw material. Fuji and Gala have a chemical pattern that can be used for this classification. Multivariate methods correlate independent continuous chemical descriptors with the categorical apple variety. Three main descriptors of apple juice were selected: malic acid, total reducing sugar and total phenolic compounds. A chemometric approach, employing PCA and SIMCA, was us...

  12. A Data-Driven Sparse-Learning Approach to Model Reduction in Chemical Reaction Networks

    OpenAIRE

    Harirchi, Farshad; Khalil, Omar A.; Liu, Sijia; Elvati, Paolo; Violi, Angela; Hero, Alfred O.

    2017-01-01

    In this paper, we propose an optimization-based sparse learning approach to identify the set of most influential reactions in a chemical reaction network. This reduced set of reactions is then employed to construct a reduced chemical reaction mechanism, which is relevant to chemical interaction network modeling. The problem of identifying influential reactions is first formulated as a mixed-integer quadratic program, and then a relaxation method is leveraged to reduce the computational comple...

  13. How effects of chemicals might differ from those of radiations in giving rise to genetic ill-health in man

    International Nuclear Information System (INIS)

    Evans, H.J.

    1980-01-01

    Possible differences between the effects of the two groups of agents are considered. Two types of genetic damage are discussed. The first type involves mutational changes induced in germ cells or germ cell precursors which are then transmitted to the products of conception and to any resultant offspring and their descendants. The second kind is that damage sustained by the genome in somatic cells which is transmitted to daughter cells. Such somatic mutations are not heritable in the familiar sense, but they are transmitted to descendant cells within the body. It is concluded that a greater heterogeneity is expected in mutagenic response to chemical mutagens than to radiations in human populations, that the spectrum of mutations following chemical exposure may be quite different from that following radiation exposure, and that for many chemical agents, and in contrast to ionising radiations, one might expect a greater burden of genetic ill-health due to increased frequencies of mildly deleterious recessive and polygenic mutations. (Auth.)

  14. Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

    Science.gov (United States)

    Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

    2018-01-01

    Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

  15. Application of QRM approach in a chemical company

    Directory of Open Access Journals (Sweden)

    Carolina Belotti Pedroso

    2017-06-01

    Full Text Available The Quick Response Management (QRM has as its main goal lead time reduction in companies that offer a wide range of products. With the evolution of production paradigms and considering the current context in which organizations operate, the necessity of competition based on time is growing increasingly. Due to this, and in order to minimize them, this research focused on investigating the main causes of these long lead times in a company active in the chemical sector. The research started with a bibliographic review about the subject of QRM; the second part of the study consisted of field research and the use of a computer simulation application (MPX. Results from the research show the effectiveness of applying concepts from QRM for lead time reduction, whereby a reduction of around 50% in lead time was possible. This paper outlines contributions to the theories about the subject and collaborates to disseminate this issue, which is relatively scarce in Brazil, more broadly.

  16. Color stabilization of red wines. A chemical and colloidal approach.

    Science.gov (United States)

    Alcalde-Eon, Cristina; García-Estévez, Ignacio; Puente, Victor; Rivas-Gonzalo, Julián C; Escribano-Bailón, M Teresa

    2014-07-23

    The effects of cold treatment and time on CIELAB color parameters and on anthocyanin and anthocyanin-derived pigments composition have been evaluated as has been the effectiveness of either an enological tannin or a mannoprotein (M) on their stabilization. With respect to color, hue (hab) was increased in the wines treated with both enological products. Furthermore, the color changes induced by cold treatment were lessened by the addition of these two enological products, although the protective effect was higher for the wines treated with M. The pigment analysis revealed higher percentages of anthocyanin-derived pigments in tannin and M-treated samples (in both cold treated and not) in relation to control ones. The addition of the enological tannin may favor the synthesis of anthocyanin-derived pigments, which are chemically more stable than native anthocyanins, whereas M seems to stabilize anthocyanin-derived pigments from a colloidal point of view, avoiding their aggregation and further precipitation.

  17. A TIERED APPROACH TO LIFE STAGES TESTING FOR AGRICULTURAL CHEMICAL SAFERY ASSESSMENT

    Science.gov (United States)

    A proposal has been developed by the Agricultural Chemical Safety Assessment (ACSA) Technical Committee of the ILSI Health and Environmental Sciences Institute (HESI) for an improved approach to assessing the safety of crop protection chemicals. The goal is to ensure that studie...

  18. Effectiveness of Instruction Based on the Constructivist Approach on Understanding Chemical Equilibrium Concepts

    Science.gov (United States)

    Akkus, Huseyin; Kadayifci, Hakki; Atasoy, Basri; Geban, Omer

    2003-01-01

    The purpose of this study was to identify misconceptions concerning chemical equilibrium concepts and to investigate the effectiveness of instruction based on the constructivist approach over traditional instruction on 10th grade students' understanding of chemical equilibrium concepts. The subjects of this study consisted of 71 10th grade…

  19. Molecular genetic approaches to the study of cellular senescence.

    Science.gov (United States)

    Goletz, T J; Smith, J R; Pereira-Smith, O M

    1994-01-01

    Cellular senescence is an inability of cells to synthesize DNA and divide, which results in a terminal loss of proliferation despite the maintenance of basic metabolic processes. Senescence has been proposed as a model for the study of aging at the cellular level, and the basis for this model system and its features have been summarized. Although strong experimental evidence exists to support the hypothesis that cellular senescence is a dominant active process, the mechanisms responsible for this phenomenon remain a mystery. Investigators have taken several approaches to gain a better understanding of senescence. Several groups have documented the differences between young and senescent cells, and others have identified changes that occur during the course of a cell's in vitro life span. Using molecular and biochemical approaches, important changes in gene expression and function of cell-cycle-associated products have been identified. The active production of an inhibitor of DNA synthesis has been demonstrated. This may represent the final step in a cascade of events governing senescence. The study of immortal cells which have escaped senescence has also provided useful information, particularly with regard to the genes governing the senescence program. These studies have identified four complementation groups for indefinite division, which suggests that there are at least four genes or gene pathways in the senescence program. Through the use of microcell-mediated chromosome transfer, chromosomes encoding senescence genes have been identified; efforts to clone these genes are ongoing.(ABSTRACT TRUNCATED AT 250 WORDS)

  20. Computational Integration of Human Genetic Data to Evaluate AOP-Specific Susceptibility

    Science.gov (United States)

    There is a need for approaches to efficiently evaluate human genetic variability and susceptibility related to environmental chemical exposure. Direct estimation of the genetic contribution to variability in susceptibility to environmental chemicals is only possible in special ca...

  1. Tactical approach to maneuvering within the chemical contamination labyrinth

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, T.W. [Department of Energy, Oak Ridge, TN (United States)

    1990-12-31

    The Department of Energy (DOE) recognized the need and accepts the responsibility for understanding the reality and mitigating the consequence of the complex chemical contamination legacy it inherited as well as controlling, reducing, and eliminating extant emissions and effluents. The key to maneuvering through this complicated and multifaceted labyrinth of concerns, from which a meaningful, high quality, and cost-effective restoration/mitigation machine is then set in motions, is the ability to perform accurate, factual, and explicit health and environmental/ecological risk assessments. Likewise, the common denominator for carrying out this essential task is to have access to comprehensive and reliable data of known quality with which to perform those analyses. DOE is committed to identifying the data universe; to technically scrutinize and ensure the quality of that data; to develop efficient and cost-effective means to maximize the handling, utilization, and sharing of that universe; and to undertake those assessments. DOE views this as an effort that can only be accomplished through a merging of the technical excellence that exists within federal and state agencies, academia, and industry. The task at hand is so large that only by integrating that intelligence base can we hope to accomplish the goals of establishing meaningful standards, developing functional and effective solutions, and providing quality guidance at a national scale.

  2. Comparison of weighting approaches for genetic risk scores in gene-environment interaction studies.

    Science.gov (United States)

    Hüls, Anke; Krämer, Ursula; Carlsten, Christopher; Schikowski, Tamara; Ickstadt, Katja; Schwender, Holger

    2017-12-16

    Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign weights, the gold standard is to use external weights from an independent study. However, appropriate external weights are not always available. In such situations and in the presence of predominant marginal genetic effects, we have shown in a previous study that GRS with internal weights from marginal genetic effects ("GRS-marginal-internal") are a powerful and reliable alternative to single SNP approaches or the use of unweighted GRS. However, this approach might not be appropriate for detecting predominant interactions, i.e. interactions showing an effect stronger than the marginal genetic effect. In this paper, we present a weighting approach for such predominant interactions ("GRS-interaction-training") in which parts of the data are used to estimate the weights from the interaction terms and the remaining data are used to determine the GRS. We conducted a simulation study for the detection of GxE interactions in which we evaluated power, type I error and sign-misspecification. We compared this new weighting approach to the GRS-marginal-internal approach and to GRS with external weights. Our simulation study showed that in the absence of external weights and with predominant interaction effects, the highest power was reached with the GRS-interaction-training approach. If marginal genetic effects were predominant, the GRS-marginal-internal approach was more appropriate. Furthermore, the power to detect interactions reached by the GRS-interaction-training approach was only slightly lower than the power achieved by GRS with external weights. The power of the GRS-interaction-training approach was confirmed in a real data application to the Traffic, Asthma and Genetics (TAG) Study (N = 4465 observations). When appropriate external weights are unavailable, we

  3. Kinetics of methane fermentation yield in biogas reactors: Genetic variation and association with chemical composition in maize

    International Nuclear Information System (INIS)

    Grieder, Christoph; Mittweg, Greta; Dhillon, Baldev S.; Montes, Juan M.; Orsini, Elena; Melchinger, Albrecht E.

    2012-01-01

    Maize (Zea mays L.) is the most competitive crop for methane production in Germany. Methane fermentation yield per unit of dry matter (MFY) is a determinant of methane yield, but little information is available on this trait. Our objectives were to investigate the kinetics of MFY during fermentation of maize, estimate quantitative-genetic parameters for different traits related to MFY and examine the relationship of MFY with chemical composition and silage quality. Whole-plant material of 16 inbreds and their 32 testcrosses was analyzed for MFY over 35 days of fermentation using a discontinuous laboratory assay. Data were also generated on chemical composition and in vitro digestible organic matter (IVDOM). Significant genotypic variances and high heritabilities were observed for MFY at early fermentation stages (up to 5 days) probably due to different concentrations of easily degradable chemical components. However, genotypic variances and heritability of MFY reduced as fermentation progressed, because of complete or partial degradation of all chemical components. Further, there were strong correlations of MFY with chemical components at early fermentation stages but not at later stages. Therefore, MFY at later stages, which is closer to potential MFY, does not seem to be amenable to selection. High heritability of IVDOM and its strong correlation with MFY in testcrosses indicated its possible use for preliminary or indirect selection. Keeping in view the magnitude of genetic variance that was low for MFY and high for dry matter yield (DMY), the other component of methane yield, more emphasis on breeding for DMY seems appropriate. -- Highlights: ► We investigated methane fermentation yield (MFY) of diverse germplasm of maize. ► The kinetics of MFY and its correlations with chemical composition were examined. ► Genetic variance and heritability for MFY decreased with fermentation time. ► Complete fermentation (35 d) reduced correlations of MFY with chemical

  4. 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.

  5. Genetic Algorithm Based PID Controller Tuning Approach for Continuous Stirred Tank Reactor

    OpenAIRE

    A. Jayachitra; R. Vinodha

    2014-01-01

    Genetic algorithm (GA) based PID (proportional integral derivative) controller has been proposed for tuning optimized PID parameters in a continuous stirred tank reactor (CSTR) process using a weighted combination of objective functions, namely, integral square error (ISE), integral absolute error (IAE), and integrated time absolute error (ITAE). Optimization of PID controller parameters is the key goal in chemical and biochemical industries. PID controllers have narrowed down the operating r...

  6. Population-genetic approach to standardization of radiation and non-radiation factors

    International Nuclear Information System (INIS)

    Telnov, I.

    2006-01-01

    Numerous studies demonstrate the importance of genetic predisposition in the development of wide range of pathologies and unfavorable effects caused by different factors. This prompts to account for genetic factors in the risk assessment of unfavorable effects. Current approaches used to solve this problem are far from perfect. On the one hand, recommendations on occupational selection bas ed on genetic signs are presently considered as human rights violation. On the other hand, to medically inform an individual with certain genetic characteristics about possible unfavorable health effects due to occupational hazard has little effect. Finally, a vast number of polymorphic genes in human genome (at least 30%) hampers accounting for all possible factors of genetic predisposition to the increasing number of environmental factors. Therefore, the current situation proves it appropriate to develop the new approach to account for genetic predisposition of individuals that would be free of flaws considered above. A possible basis for such an approach is the assessment of genotype specific relative risk (G.S.R.R.) that accounts for genetic predisposition (susceptibility) of individuals to the effects of unfavorable factors. The study used results from 65 studies. This effort was undertaken to study the association between 32 diseases and unfavorable effects and 17 genetic polymorphic systems. Data analysis included calculation of relative risk (R.R.) of specific diseases or effects development in individuals with different genotypes. Genotype-specific relative risk (G.S.R.R.) of diseases and unfavorable effects in individuals with 'sensitive' genotypes was calculated. Since about the third of genes in human genome are polymorphic, and therefore, a considerable number of genes can be involved in genetic predisposition of an individual to a specific unfavorable effect, an averaged G.S.R.R. of diseases and unfavorable effects was calculated for integral characteristics on

  7. 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.

  8. An approach to quantitate and control the mutagenic hazards of environmental chemical and radioactive pollutants

    International Nuclear Information System (INIS)

    Murthy, M.S.S.

    1977-01-01

    Human population, both at the occupational and non-occupational levels, is exposed to the environment polluted by man-made chemicals and radiation sources. The parameters required for quantitating mutagenic hazards of any agent are listed and it has been pointed out that though sufficient information of this nature is available in the case of radiations, it is almost impossible to collect similar information for chemical substances due to their number running into astronomical figures. A short-cut approach, therefore, is suggested to quantitate and control the mutagenic hazards of these pollutants. It is to express the mutagenic hazards of a chemical substance in terms of equivalent radiation units. The unit proposed for this purpose is called as Rem-Equivalent Chemical (REC). Total mutagenic burden to the society should take account of exposure from both chemicals and radiations. Advantages and limitation of this approach are discussed. (M.G.B.)

  9. Design of tailor-made chemical blend using a decomposition-based computer-aided approach

    DEFF Research Database (Denmark)

    Yunus, Nor Alafiza; Gernaey, Krist; Manan, Z.A.

    2011-01-01

    Computer aided techniques form an efficient approach to solve chemical product design problems such as the design of blended liquid products (chemical blending). In chemical blending, one tries to find the best candidate, which satisfies the product targets defined in terms of desired product...... methodology for blended liquid products that identifies a set of feasible chemical blends. The blend design problem is formulated as a Mixed Integer Nonlinear Programming (MINLP) model where the objective is to find the optimal blended gasoline or diesel product subject to types of chemicals...... and their compositions and a set of desired target properties of the blended product as design constraints. This blend design problem is solved using a decomposition approach, which eliminates infeasible and/or redundant candidates gradually through a hierarchy of (property) model based constraints. This decomposition...

  10. On Generating Optimal Signal Probabilities for Random Tests: A Genetic Approach

    Directory of Open Access Journals (Sweden)

    M. Srinivas

    1996-01-01

    Full Text Available Genetic Algorithms are robust search and optimization techniques. A Genetic Algorithm based approach for determining the optimal input distributions for generating random test vectors is proposed in the paper. A cost function based on the COP testability measure for determining the efficacy of the input distributions is discussed. A brief overview of Genetic Algorithms (GAs and the specific details of our implementation are described. Experimental results based on ISCAS-85 benchmark circuits are presented. The performance of our GAbased approach is compared with previous results. While the GA generates more efficient input distributions than the previous methods which are based on gradient descent search, the overheads of the GA in computing the input distributions are larger.

  11. Environmental Contamination Genetic Consequences Monitoring on the Former Semipalatinsk Test Site: General Approach

    International Nuclear Information System (INIS)

    Seisebaev, A.T.; Bakhtin, M.M.; Zhapbasov, R.Zh.

    1998-01-01

    genetic monitoring of natural populations of plants and animals and the theoretic approach for their fulfillment. We also consider the main issues of research work on assessment and forecast of the remote genetic consequences of nuclear tests at STS: 1) assessment of the environmental radiation situation; determination of the indicator species of plants and animals and the criteria encompassing the different levels from the molecular one through the genetic to the population one; 2) study of the dose dependence of the genetic effects under the chronic ionizing radiation; 3) analysis of mutation process dynamics in the following generations of population under various exposure condition; 4) study of the possible ways of population adaptation to the chronic impact of various radiation doses; 5) analysis of relation between different genetic changes in exposed population and ecology alterations, etc

  12. Zebrafish Functional Genetics Approach to the Pathogenesis of Well-Differentiated Liposarcoma

    Science.gov (United States)

    2015-12-01

    Roderick JE, LaBelle JL, Bird G, Mathieu R, Bodaar K, Colon D, Pyati U, Stevenson KE, Qi J, Harris M, Silverman LB, Sallan SE, Bradner JL, Neuberg DS...pathogenesis of high-risk T-cell acute lymphoblastic leukemia. Our approach combines human cancer genomics with functional genetics, biochemistry and

  13. An Alternative Educational Approach for an Inorganic Chemistry Laboratory Course in Industrial and Chemical Engineering

    Science.gov (United States)

    Garces, Andres; Sanchez-Barba, Luis Fernando

    2011-01-01

    We describe an alternative educational approach for an inorganic chemistry laboratory module named "Experimentation in Chemistry", which is included in Industrial Engineering and Chemical Engineering courses. The main aims of the new approach were to reduce the high levels of failure and dropout on the module and to make the content match the…

  14. Systematic Approach to Calculate the Concentration of Chemical Species in Multi-Equilibrium Problems

    Science.gov (United States)

    Baeza-Baeza, Juan Jose; Garcia-Alvarez-Coque, Maria Celia

    2011-01-01

    A general systematic approach is proposed for the numerical calculation of multi-equilibrium problems. The approach involves several steps: (i) the establishment of balances involving the chemical species in solution (e.g., mass balances, charge balance, and stoichiometric balance for the reaction products), (ii) the selection of the unknowns (the…

  15. The role of genetic background in susceptibility to chemical warfare nerve agents across rodent and non-human primate models.

    Science.gov (United States)

    Matson, Liana M; McCarren, Hilary S; Cadieux, C Linn; Cerasoli, Douglas M; McDonough, John H

    2018-01-15

    Genetics likely play a role in various responses to nerve agent exposure, as genetic background plays an important role in behavioral, neurological, and physiological responses to environmental stimuli. Mouse strains or selected lines can be used to identify susceptibility based on background genetic features to nerve agent exposure. Additional genetic techniques can then be used to identify mechanisms underlying resistance and sensitivity, with the ultimate goal of developing more effective and targeted therapies. Here, we discuss the available literature on strain and selected line differences in cholinesterase activity levels and response to nerve agent-induced toxicity and seizures. We also discuss the available cholinesterase and toxicity literature across different non-human primate species. The available data suggest that robust genetic differences exist in cholinesterase activity, nerve agent-induced toxicity, and chemical-induced seizures. Available cholinesterase data suggest that acetylcholinesterase activity differs across strains, but are limited by the paucity of carboxylesterase data in strains and selected lines. Toxicity and seizures, two outcomes of nerve agent exposure, have not been fully evaluated for genetic differences, and thus further studies are required to understand baseline strain and selected line differences. Published by Elsevier B.V.

  16. Control of Disease Induced by Tospoviruses in Tomato: An Update of the Genetic Approach

    Directory of Open Access Journals (Sweden)

    J. Cebolla-Cornejo

    2003-12-01

    Full Text Available Advances in the search for genetic resistance to tospoviruses affecting tomato crops are reviewed. The economic losses caused by Tomato spotted wilt tospovirus (TSWV, the great number of hosts it affects and its wide distribution around the world has made TSWV one of the ten most important plant viruses. Other viruses in or related to the same genus also cause severe damage, although their presence in the world is much more localized. Due to the limited effectiveness of physical, chemical and biological control methods, the use of genetic resistance for control is the best management strategy on a medium-long term basis. Given the relative ease with which new TSWV isolates that overcome existing genetic resistance are generated, it is of prime importance to continue the search for new sources of resistance, as well as to promote a better exploitation of available ones. A better understanding of the mechanisms causing resistance and of their genetic control, as well as the identification of molecular markers linked to resistance genes, would enable the pyramiding of different resistance genes. This would be a positive contribution to the development of a greater and more durable resistance. It is also necessary to further the study of genetic resistance to other viruses of the genus Tospovirus, as globalisation can speed up their distribution throughout the world.

  17. Microbial and genetic ecology of tropical Vertisols under intensive chemical farming.

    Science.gov (United States)

    Malhotra, Jaya; Aparna, K; Dua, Ankita; Sangwan, Naseer; Trimurtulu, N; Rao, D L N; Lal, Rup

    2015-01-01

    There are continued concerns on unscientific usage of chemical fertilizers and pesticides, particularly in many developing countries leading to adverse consequences for soil biological quality and agricultural sustainability. In farmers' fields in tropical Vertisols of peninsular India, "high" fertilizer and pesticide usage at about 2.3 times the recommended rates in black gram (Vigna mungo) did not have a deleterious effect on the abundance of culturable microorganisms, associative nitrogen fixers, nitrifiers, and 16S rRNA gene diversity compared to normal rates. However, "very high" application at about five times the fertilizers and 1.5 times pesticides in chilies (Capsicum annuum) adversely affected the populations of fungi, actinomycetes, and ammonifiers, along with a drastic change in the eubacterial community profile and diversity over normal rates. Actinobacteria were dominant in black gram normal (BG1) (47%), black gram high (BG2) (36%), and chili normal (CH1) (30%) and were least in chili very high (CH2) (14%). Geodermatophilus formed 20% of Actinobacteria in BG1 but disappeared in BG2, CH1, and CH2. Asticcacaulis dominated at "very high" input site (CH2). Diversity of nitrogen fixers was completely altered; Dechloromonas and Anaeromyxobacter were absent in BG1 but proliferated well in BG2. There was reduction in rhizobial nifH sequences in BG2 by 46%. Phylogenetic differences characterized by UniFrac and principal coordinate analysis showed that BG2 and CH2 clustered together depicting a common pattern of genetic shift, while BG1 and CH1 fell at different axis. Overall, there were adverse consequences of "very high" fertilizer and pesticide usage on soil microbial diversity and function in tropical Vertisols.

  18. [Genetic diagnostics of pathogenic splicing abnormalities in the clinical laboratory--pitfalls and screening approaches].

    Science.gov (United States)

    Niimi, Hideki; Ogawa, Tomomi; Note, Rhougou; Hayashi, Shirou; Ueno, Tomohiro; Harada, Kenu; Uji, Yoshinori; Kitajima, Isao

    2010-12-01

    In recent years, genetic diagnostics of pathogenic splicing abnormalities are increasingly recognized as critically important in the clinical genetic diagnostics. It is reported that approximately 10% of pathogenic mutations causing human inherited diseases are splicing mutations. Nonetheless, it is still difficult to identify splicing abnormalities in routine genetic diagnostic settings. Here, we studied two different kinds of cases with splicing abnormalities. The first case is a protein S deficiency. Nucleotide analyses revealed that the proband had a previously reported G to C substitution in the invariant AG dinucleotide at the splicing acceptor site of intronl/exon2, which produces multiple splicing abnormalities resulting in protein S deficiency. The second case is an antithrombin (AT) deficiency. This proband had a previously reported G to A substitution, at nucleotide position 9788 in intron 4, 14 bp in front of exon 5, which created a de novo exon 5 splice site and resulted in AT deficiency. From a practical standpoint, we discussed the pitfalls, attentions, and screening approaches in genetic diagnostics of pathogenic splicing abnormalities. Due to the difficulty with full-length sequence analysis of introns, and the lack of RNA samples, splicing mutations may escape identification. Although current genetic testing remains to be improved, to screen for splicing abnormalities more efficiently, it is significant to use an appropriate combination of various approaches such as DNA and/or RNA samples, splicing mutation databases, bioinformatic tools to detect splice sites and cis-regulatory elements, and in vitro and/or in vivo experimentally methods as needed.

  19. Arbitrariness is not enough: towards a functional approach to the genetic code.

    Science.gov (United States)

    Lacková, Ľudmila; Matlach, Vladimír; Faltýnek, Dan

    2017-12-01

    Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about "code" in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign's object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.

  20. Comparison of modeling approaches to prioritize chemicals based on estimates of exposure and exposure potential.

    Science.gov (United States)

    Mitchell, Jade; Arnot, Jon A; Jolliet, Olivier; Georgopoulos, Panos G; Isukapalli, Sastry; Dasgupta, Surajit; Pandian, Muhilan; Wambaugh, John; Egeghy, Peter; Cohen Hubal, Elaine A; Vallero, Daniel A

    2013-08-01

    While only limited data are available to characterize the potential toxicity of over 8 million commercially available chemical substances, there is even less information available on the exposure and use-scenarios that are required to link potential toxicity to human and ecological health outcomes. Recent improvements and advances such as high throughput data gathering, high performance computational capabilities, and predictive chemical inherency methodology make this an opportune time to develop an exposure-based prioritization approach that can systematically utilize and link the asymmetrical bodies of knowledge for hazard and exposure. In response to the US EPA's need to develop novel approaches and tools for rapidly prioritizing chemicals, a "Challenge" was issued to several exposure model developers to aid the understanding of current systems in a broader sense and to assist the US EPA's effort to develop an approach comparable to other international efforts. A common set of chemicals were prioritized under each current approach. The results are presented herein along with a comparative analysis of the rankings of the chemicals based on metrics of exposure potential or actual exposure estimates. The analysis illustrates the similarities and differences across the domains of information incorporated in each modeling approach. The overall findings indicate a need to reconcile exposures from diffuse, indirect sources (far-field) with exposures from directly, applied chemicals in consumer products or resulting from the presence of a chemical in a microenvironment like a home or vehicle. Additionally, the exposure scenario, including the mode of entry into the environment (i.e. through air, water or sediment) appears to be an important determinant of the level of agreement between modeling approaches. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Comparison of modeling approaches to prioritize chemicals based on estimates of exposure and exposure potential

    Science.gov (United States)

    Mitchell, Jade; Arnot, Jon A.; Jolliet, Olivier; Georgopoulos, Panos G.; Isukapalli, Sastry; Dasgupta, Surajit; Pandian, Muhilan; Wambaugh, John; Egeghy, Peter; Cohen Hubal, Elaine A.; Vallero, Daniel A.

    2014-01-01

    While only limited data are available to characterize the potential toxicity of over 8 million commercially available chemical substances, there is even less information available on the exposure and use-scenarios that are required to link potential toxicity to human and ecological health outcomes. Recent improvements and advances such as high throughput data gathering, high performance computational capabilities, and predictive chemical inherency methodology make this an opportune time to develop an exposure-based prioritization approach that can systematically utilize and link the asymmetrical bodies of knowledge for hazard and exposure. In response to the US EPA’s need to develop novel approaches and tools for rapidly prioritizing chemicals, a “Challenge” was issued to several exposure model developers to aid the understanding of current systems in a broader sense and to assist the US EPA’s effort to develop an approach comparable to other international efforts. A common set of chemicals were prioritized under each current approach. The results are presented herein along with a comparative analysis of the rankings of the chemicals based on metrics of exposure potential or actual exposure estimates. The analysis illustrates the similarities and differences across the domains of information incorporated in each modeling approach. The overall findings indicate a need to reconcile exposures from diffuse, indirect sources (far-field) with exposures from directly, applied chemicals in consumer products or resulting from the presence of a chemical in a microenvironment like a home or vehicle. Additionally, the exposure scenario, including the mode of entry into the environment (i.e. through air, water or sediment) appears to be an important determinant of the level of agreement between modeling approaches. PMID:23707726

  2. Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

    KAUST Repository

    Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K.

    2012-01-01

    We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimize data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximizes parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie [14]. In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system's size. © 2006 IEEE.

  3. Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

    KAUST Repository

    Klingbeil, Guido

    2012-02-01

    We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimize data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximizes parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie [14]. In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system\\'s size. © 2006 IEEE.

  4. 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)

  5. Comparing targeted exome and whole exome approaches for genetic diagnosis of neuromuscular disorders

    Directory of Open Access Journals (Sweden)

    Svetlana Gorokhova

    2015-12-01

    Full Text Available Massively parallel sequencing is rapidly becoming a widely used method in genetic diagnostics. However, there is still no clear consensus as to which approach can most efficiently identify the pathogenic mutations carried by a given patient, while avoiding false negative and false positive results. We developed a targeted exome approach (MyoPanel2 in order to optimize genetic diagnosis of neuromuscular disorders. Using this approach, we were able to analyse 306 genes known to be mutated in myopathies as well as in related disorders, obtaining 98.8% target sequence coverage at 20×. Moreover, MyoPanel2 was able to detect 99.7% of 11,467 known mutations responsible for neuromuscular disorders. We have then used several quality control parameters to compare performance of the targeted exome approach with that of whole exome sequencing. The results of this pilot study of 140 DNA samples suggest that targeted exome sequencing approach is an efficient genetic diagnostic test for most neuromuscular diseases.

  6. 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

  7. Controlling organic chemical hazards in food manufacturing: a hazard analysis critical control points (HACCP) approach.

    Science.gov (United States)

    Ropkins, K; Beck, A J

    2002-08-01

    Hazard analysis by critical control points (HACCP) is a systematic approach to the identification, assessment and control of hazards. Effective HACCP requires the consideration of all hazards, i.e., chemical, microbiological and physical. However, to-date most 'in-place' HACCP procedures have tended to focus on the control of microbiological and physical food hazards. In general, the chemical component of HACCP procedures is either ignored or limited to applied chemicals, e.g., food additives and pesticides. In this paper we discuss the application of HACCP to a broader range of chemical hazards, using organic chemical contaminants as examples, and the problems that are likely to arise in the food manufacturing sector. Chemical HACCP procedures are likely to result in many of the advantages previously identified for microbiological HACCP procedures: more effective, efficient and economical than conventional end-point-testing methods. However, the high costs of analytical monitoring of chemical contaminants and a limited understanding of formulation and process optimisation as means of controlling chemical contamination of foods are likely to prevent chemical HACCP becoming as effective as microbiological HACCP.

  8. A systems engineering approach to manage the complexity in sustainable chemical product-process design

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    This paper provides a perspective on model-data based solution approaches for chemical product-process design, which consists of finding the identity of the candidate chemical product, designing the process that can sustainably manufacture it and verifying the performance of the product during...... framework can manage the complexity associated with product-process problems very efficiently. Three specific computer-aided tools (ICAS, Sustain-Pro and VPPDLab) have been presented and their applications to product-process design, highlighted....

  9. Characterization of the pharmacokinetics of gasoline using PBPK modeling with a complex mixtures chemical lumping approach.

    Science.gov (United States)

    Dennison, James E; Andersen, Melvin E; Yang, Raymond S H

    2003-09-01

    Gasoline consists of a few toxicologically significant components and a large number of other hydrocarbons in a complex mixture. By using an integrated, physiologically based pharmacokinetic (PBPK) modeling and lumping approach, we have developed a method for characterizing the pharmacokinetics (PKs) of gasoline in rats. The PBPK model tracks selected target components (benzene, toluene, ethylbenzene, o-xylene [BTEX], and n-hexane) and a lumped chemical group representing all nontarget components, with competitive metabolic inhibition between all target compounds and the lumped chemical. PK data was acquired by performing gas uptake PK studies with male F344 rats in a closed chamber. Chamber air samples were analyzed every 10-20 min by gas chromatography/flame ionization detection and all nontarget chemicals were co-integrated. A four-compartment PBPK model with metabolic interactions was constructed using the BTEX, n-hexane, and lumped chemical data. Target chemical kinetic parameters were refined by studies with either the single chemical alone or with all five chemicals together. o-Xylene, at high concentrations, decreased alveolar ventilation, consistent with respiratory irritation. A six-chemical interaction model with the lumped chemical group was used to estimate lumped chemical partitioning and metabolic parameters for a winter blend of gasoline with methyl t-butyl ether and a summer blend without any oxygenate. Computer simulation results from this model matched well with experimental data from single chemical, five-chemical mixture, and the two blends of gasoline. The PBPK model analysis indicated that metabolism of individual components was inhibited up to 27% during the 6-h gas uptake experiments of gasoline exposures.

  10. An extended risk assessment approach for chemical plants applied to a study related to pipe ruptures

    International Nuclear Information System (INIS)

    Milazzo, Maria Francesca; Aven, Terje

    2012-01-01

    Risk assessments and Quantitative Risk Assessment (QRA) in particular have been used in the chemical industry for many years to support decision-making on the choice of arrangements and measures associated with chemical processes, transportation and storage of dangerous substances. The assessments have been founded on a risk perspective seeing risk as a function of frequency of events (probability) and associated consequences. In this paper we point to the need for extending this approach to place a stronger emphasis on uncertainties. A recently developed risk framework designed to better reflect such uncertainties is presented and applied to a chemical plant and specifically the analysis of accidental events related to the rupture of pipes. Two different ways of implementing the framework are presented, one based on the introduction of probability models and one without. The differences between the standard approach and the extended approaches are discussed from a theoretical point of view as well as from a practical risk analyst perspective.

  11. Neuro-genetic hybrid approach for the solution of non-convex economic dispatch problem

    International Nuclear Information System (INIS)

    Malik, T.N.; Asar, A.U.

    2009-01-01

    ED (Economic Dispatch) is non-convex constrained optimization problem, and is used for both on line and offline studies in power system operation. Conventionally, it is solved as convex problem using optimization techniques by approximating generator input/output characteristic. Curves of monotonically increasing nature thus resulting in an inaccurate dispatch. The GA (Genetic Algorithm) has been used for the solution of this problem owing to its inherent ability to address the convex and non-convex problems equally. This approach brings the solution to the global minimum region of search space in a short time and then takes longer time to converge to near optimal results. GA based hybrid approaches are used to fine tune the near optimal results produced by GA. This paper proposes NGH (Neuro Genetic Hybrid) approach to solve the economic dispatch with valve point effect. The proposed approach combines the GA with the ANN (Artificial Neural Network) using SI (Swarm Intelligence) learning rule. The GA acts as a global optimizer and the neural network fine tunes the GA results to the desired targets. Three machines standard test system has been tested for validation of the approach. Comparing the results with GA and NGH model based on back-propagation learning, the proposed approach gives contrast improvements showing the promise of the approach. (author)

  12. A systems engineering approach to manage the complexity in sustainable chemical product-process design

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    This paper provides a perspective on model-data based solution approaches for chemical product-process design, which consists of finding the identity of the candidate chemical product, designing the process that can sustainably manufacture it and verifying the performance of the product during...... application. The chemical product tree is potentially very large and a wide range of options exist for selecting the product to make, the raw material to use as well as the processing route to employ. It is shown that systematic computer-aided methods and tools integrated within a model-data based design...

  13. Genetic Approaches to Study Meiosis and Meiosis-Specific Gene Expression in Saccharomyces cerevisiae.

    Science.gov (United States)

    Kassir, Yona; Stuart, David T

    2017-01-01

    The budding yeast Saccharomyces cerevisiae has a long history as a model organism for studies of meiosis and the cell cycle. The popularity of this yeast as a model is in large part due to the variety of genetic and cytological approaches that can be effectively performed with the cells. Cultures of the cells can be induced to synchronously progress through meiosis and sporulation allowing large-scale gene expression and biochemical studies to be performed. Additionally, the spore tetrads resulting from meiosis make it possible to characterize the haploid products of meiosis allowing investigation of meiotic recombination and chromosome segregation. Here we describe genetic methods for analysis progression of S. cerevisiae through meiosis and sporulation with an emphasis on strategies for the genetic analysis of regulators of meiosis-specific genes.

  14. Environmental Pollution, Toxicity Profile and Treatment Approaches for Tannery Wastewater and Its Chemical Pollutants.

    Science.gov (United States)

    Saxena, Gaurav; Chandra, Ram; Bharagava, Ram Naresh

    Leather industries are key contributors in the economy of many developing countries, but unfortunately they are facing serious challenges from the public and governments due to the associated environmental pollution. There is a public outcry against the industry due to the discharge of potentially toxic wastewater having alkaline pH, dark brown colour, unpleasant odour, high biological and chemical oxygen demand, total dissolved solids and a mixture of organic and inorganic pollutants. Various environment protection agencies have prioritized several chemicals as hazardous and restricted their use in leather processing however; many of these chemicals are used and discharged in wastewater. Therefore, it is imperative to adequately treat/detoxify the tannery wastewater for environmental safety. This paper provides a detail review on the environmental pollution and toxicity profile of tannery wastewater and chemicals. Furthermore, the status and advances in the existing treatment approaches used for the treatment and/or detoxification of tannery wastewater at both laboratory and pilot/industrial scale have been reviewed. In addition, the emerging treatment approaches alone or in combination with biological treatment approaches have also been considered. Moreover, the limitations of existing and emerging treatment approaches have been summarized and potential areas for further investigations have been discussed. In addition, the clean technologies for waste minimization, control and management are also discussed. Finally, the international legislation scenario on discharge limits for tannery wastewater and chemicals has also been discussed country wise with discharge standards for pollution prevention due to tannery wastewater.

  15. Maternal Smoking During Pregnancy and Offspring Birth Weight: A Genetically-Informed Approach Comparing Multiple Raters

    Science.gov (United States)

    Knopik, Valerie S.; Marceau, Kristine; Palmer, Rohan H. C.; Smith, Taylor F.; Heath, Andrew C.

    2016-01-01

    Maternal smoking during pregnancy (SDP) is a significant public health concern with adverse consequences to the health and well-being of the fetus. There is considerable debate about the best method of assessing SDP, including birth/medical records, timeline follow-back approaches, multiple reporters, and biological verification (e.g., cotinine). This is particularly salient for genetically-informed approaches where it is not always possible or practical to do a prospective study starting during the prenatal period when concurrent biological specimen samples can be collected with ease. In a sample of families (N = 173) specifically selected for sibling pairs discordant for prenatal smoking exposure, we: (1) compare rates of agreement across different types of report—maternal report of SDP, paternal report of maternal SDP, and SDP contained on birth records from the Department of Vital Statistics; (2) examine whether SDP is predictive of birth weight outcomes using our best SDP report as identified via step (1); and (3) use a sibling-comparison approach that controls for genetic and familial influences that siblings share in order to assess the effects of SDP on birth weight. Results show high agreement between reporters and support the utility of retrospective report of SDP. Further, we replicate a causal association between SDP and birth weight, wherein SDP results in reduced birth weight even when accounting for genetic and familial confounding factors via a sibling comparison approach. PMID:26494459

  16. Analysis of stock investment selection based on CAPM using covariance and genetic algorithm approach

    Science.gov (United States)

    Sukono; Susanti, D.; Najmia, M.; Lesmana, E.; Napitupulu, H.; Supian, S.; Putra, A. S.

    2018-03-01

    Investment is one of the economic growth factors of countries, especially in Indonesia. Stocks is a form of investment, which is liquid. In determining the stock investment decisions which need to be considered by investors is to choose stocks that can generate maximum returns with a minimum risk level. Therefore, we need to know how to allocate the capital which may give the optimal benefit. This study discusses the issue of stock investment based on CAPM which is estimated using covariance and Genetic Algorithm approach. It is assumed that the stocks analyzed follow the CAPM model. To do the estimation of beta parameter on CAPM equation is done by two approach, first is to be represented by covariance approach, and second with genetic algorithm optimization. As a numerical illustration, in this paper analyzed ten stocks traded on the capital market in Indonesia. The results of the analysis show that estimation of beta parameters using covariance and genetic algorithm approach, give the same decision, that is, six underpriced stocks with buying decision, and four overpriced stocks with a sales decision. Based on the analysis, it can be concluded that the results can be used as a consideration for investors buying six under-priced stocks, and selling four overpriced stocks.

  17. Landscape genetic approaches to guide native plant restoration in the Mojave Desert

    Science.gov (United States)

    Shryock, Daniel F.; Havrilla, Caroline A.; DeFalco, Lesley; Esque, Todd C.; Custer, Nathan; Wood, Troy E.

    2016-01-01

    Restoring dryland ecosystems is a global challenge due to synergistic drivers of disturbance coupled with unpredictable environmental conditions. Dryland plant species have evolved complex life-history strategies to cope with fluctuating resources and climatic extremes. Although rarely quantified, local adaptation is likely widespread among these species and potentially influences restoration outcomes. The common practice of reintroducing propagules to restore dryland ecosystems, often across large spatial scales, compels evaluation of adaptive divergence within these species. Such evaluations are critical to understanding the consequences of large-scale manipulation of gene flow and to predicting success of restoration efforts. However, genetic information for species of interest can be difficult and expensive to obtain through traditional common garden experiments. Recent advances in landscape genetics offer marker-based approaches for identifying environmental drivers of adaptive genetic variability in non-model species, but tools are still needed to link these approaches with practical aspects of ecological restoration. Here, we combine spatially-explicit landscape genetics models with flexible visualization tools to demonstrate how cost-effective evaluations of adaptive genetic divergence can facilitate implementation of different seed sourcing strategies in ecological restoration. We apply these methods to Amplified Fragment Length Polymorphism (AFLP) markers genotyped in two Mojave Desert shrub species of high restoration importance: the long-lived, wind-pollinated gymnosperm Ephedra nevadensis, and the short-lived, insect-pollinated angiosperm Sphaeralcea ambigua. Mean annual temperature was identified as an important driver of adaptive genetic divergence for both species. Ephedra showed stronger adaptive divergence with respect to precipitation variability, while temperature variability and precipitation averages explained a larger fraction of adaptive

  18. Some chemical influence on genetic effects of ionizing radiation and biodosimetry problems

    International Nuclear Information System (INIS)

    Mosse, I.B.

    2007-01-01

    Complete text of publication follows. Radiation sensitivity is a quantitative character from genetic point of view and the distribution of this character values in populations is characterized by a binomial curve. So, 50% of the population have the mean values of radiosensitivity (x ± 0.67σ), 95% of individuals have radiosensitivity values equal to x ± 1.96σ and 5% of the population have this characters ranged from x ± 1.96σ to x ± 3σ, with division into the supersensitive fraction (2.5%) and the superresistant one (2.5%). Radiosensitivity as well as other quantitative characters is caused by the interaction of some pairs of polymeric genes determining a lot of physiological and biochemical organism features. Thus, irradiation in the same dose can induce different level of mutations or other biological effects in different humans. Besides, radiosensitivity depends to a great degree upon environmental factors. For instance, a level of radiosensitivity depends on physical activity, nervous and psychological state, hormonal balance etc. A diet can change an individual radioresistance - food rich in vitamins, microelements, adaptogens and so on favors the increase in individual radioresistance. Many food stuffs contain radioprotectors or antimutagens. So, tea, coffee, cocoa, chocolate, mushrooms and other products have melanin, which is a very effective radioprotector not only against acute irradiation, but even against chronic one according to out data. On the contrary some substances in our food such as residual amounts of fertilizers or herbicides can be mutagenic or increase mutagenic action of radiation. In the last case we observed synergetic or antagonistic effects. Radioadaptive response is one of the most significant factors which can be responsible for uncorrected radiation dose evaluation by biodosimetry methods. This phenomenon decreases effects of ionizing radiation approximately twice. Adaptive reaction can be induced by low radiation dose as well

  19. Earthquake—explosion discrimination using genetic algorithm-based boosting approach

    Science.gov (United States)

    Orlic, Niksa; Loncaric, Sven

    2010-02-01

    An important and challenging problem in seismic data processing is to discriminate between natural seismic events such as earthquakes and artificial seismic events such as explosions. Many automatic techniques for seismogram classification have been proposed in the literature. Most of these methods have a similar approach to seismogram classification: a predefined set of features based on ad-hoc feature selection criteria is extracted from the seismogram waveform or spectral data and these features are used for signal classification. In this paper we propose a novel approach for seismogram classification. A specially formulated genetic algorithm has been employed to automatically search for a near-optimal seismogram feature set, instead of using ad-hoc feature selection criteria. A boosting method is added to the genetic algorithm when searching for multiple features in order to improve classification performance. A learning set of seismogram data is used by the genetic algorithm to discover a near-optimal feature set. The feature set identified by the genetic algorithm is then used for seismogram classification. The described method is developed to classify seismograms in two groups, whereas a brief overview of method extension for multiple group classification is given. For method verification, a learning set consisting of 40 local earthquake seismograms and 40 explosion seismograms was used. The method was validated on seismogram set consisting of 60 local earthquake seismograms and 60 explosion seismograms, with correct classification of 85%.

  20. Target identification of natural and traditional medicines with quantitative chemical proteomics approaches.

    Science.gov (United States)

    Wang, Jigang; Gao, Liqian; Lee, Yew Mun; Kalesh, Karunakaran A; Ong, Yong Siang; Lim, Jaehong; Jee, Joo-Eun; Sun, Hongyan; Lee, Su Seong; Hua, Zi-Chun; Lin, Qingsong

    2016-06-01

    Natural and traditional medicines, being a great source of drugs and drug leads, have regained wide interests due to the limited success of high-throughput screening of compound libraries in the past few decades and the recent technology advancement. Many drugs/bioactive compounds exert their functions through interaction with their protein targets, with more and more drugs showing their ability to target multiple proteins, thus target identification has an important role in drug discovery and biomedical research fields. Identifying drug targets not only furthers the understanding of the mechanism of action (MOA) of a drug but also reveals its potential therapeutic applications and adverse side effects. Chemical proteomics makes use of affinity chromatography approaches coupled with mass spectrometry to systematically identify small molecule-protein interactions. Although traditional affinity-based chemical proteomics approaches have made great progress in the identification of cellular targets and elucidation of MOAs of many bioactive molecules, nonspecific binding remains a major issue which may reduce the accuracy of target identification and may hamper the drug development process. Recently, quantitative proteomics approaches, namely, metabolic labeling, chemical labeling, or label-free approaches, have been implemented in target identification to overcome such limitations. In this review, we will summarize and discuss the recent advances in the application of various quantitative chemical proteomics approaches for the identification of targets of natural and traditional medicines. Copyright © 2016. Published by Elsevier Inc.

  1. Genetic engineering of industrial Saccharomyces cerevisiae strains using a selection/counter-selection approach.

    Science.gov (United States)

    Kutyna, Dariusz R; Cordente, Antonio G; Varela, Cristian

    2014-01-01

    Gene modification of laboratory yeast strains is currently a very straightforward task thanks to the availability of the entire yeast genome sequence and the high frequency with which yeast can incorporate exogenous DNA into its genome. Unfortunately, laboratory strains do not perform well in industrial settings, indicating the need for strategies to modify industrial strains to enable strain development for industrial applications. Here we describe approaches we have used to genetically modify industrial strains used in winemaking.

  2. Feature Selection using Multi-objective Genetic Algorith m: A Hybrid Approach

    OpenAIRE

    Ahuja, Jyoti; GJUST - Guru Jambheshwar University of Sciecne and Technology; Ratnoo, Saroj Dahiya; GJUST - Guru Jambheshwar University of Sciecne and Technology

    2015-01-01

    Feature selection is an important pre-processing task for building accurate and comprehensible classification models. Several researchers have applied filter, wrapper or hybrid approaches using genetic algorithms which are good candidates for optimization problems that involve large search spaces like in the case of feature selection. Moreover, feature selection is an inherently multi-objective problem with many competing objectives involving size, predictive power and redundancy of the featu...

  3. Developmental psychopathology in an era of molecular genetics and neuroimaging: A developmental neurogenetics approach.

    Science.gov (United States)

    Hyde, Luke W

    2015-05-01

    The emerging field of neurogenetics seeks to model the complex pathways from gene to brain to behavior. This field has focused on imaging genetics techniques that examine how variability in common genetic polymorphisms predict differences in brain structure and function. These studies are informed by other complimentary techniques (e.g., animal models and multimodal imaging) and have recently begun to incorporate the environment through examination of Imaging Gene × Environment interactions. Though neurogenetics has the potential to inform our understanding of the development of psychopathology, there has been little integration between principles of neurogenetics and developmental psychopathology. The paper describes a neurogenetics and Imaging Gene × Environment approach and how these approaches have been usefully applied to the study of psychopathology. Six tenets of developmental psychopathology (the structure of phenotypes, the importance of exploring mechanisms, the conditional nature of risk, the complexity of multilevel pathways, the role of development, and the importance of who is studied) are identified, and how these principles can further neurogenetics applications to understanding the development of psychopathology is discussed. A major issue of this piece is how neurogenetics and current imaging and molecular genetics approaches can be incorporated into developmental psychopathology perspectives with a goal of providing models for better understanding pathways from among genes, environments, the brain, and behavior.

  4. Method of transient identification based on a possibilistic approach, optimized by genetic algorithm

    International Nuclear Information System (INIS)

    Almeida, Jose Carlos Soares de

    2001-02-01

    This work develops a method for transient identification based on a possible approach, optimized by Genetic Algorithm to optimize the number of the centroids of the classes that represent the transients. The basic idea of the proposed method is to optimize the partition of the search space, generating subsets in the classes within a partition, defined as subclasses, whose centroids are able to distinguish the classes with the maximum correct classifications. The interpretation of the subclasses as fuzzy sets and the possible approach provided a heuristic to establish influence zones of the centroids, allowing to achieve the 'don't know' answer for unknown transients, that is, outside the training set. (author)

  5. A probabilistic multi objective CLSC model with Genetic algorithm-ε_Constraint approach

    Directory of Open Access Journals (Sweden)

    Alireza TaheriMoghadam

    2014-05-01

    Full Text Available In this paper an uncertain multi objective closed-loop supply chain is developed. The first objective function is maximizing the total profit. The second objective function is minimizing the use of row materials. In the other word, the second objective function is maximizing the amount of remanufacturing and recycling. Genetic algorithm is used for optimization and for finding the pareto optimal line, Epsilon-constraint method is used. Finally a numerical example is solved with proposed approach and performance of the model is evaluated in different sizes. The results show that this approach is effective and useful for managerial decisions.

  6. A New Approach to Joining Dissimilar Ceramic Oxides for Chemical Sensors

    International Nuclear Information System (INIS)

    Zhuiykov, Serge

    2009-01-01

    Conventional joining of dissimilar oxides for sensing electrodes (SE) of chemical sensors has been pivotal to the development of various sensors and is vital to their further development. However, it is shown that the uncertainty (of a fundamental nature) in the properties of dissimilar oxides in SE causes the determination of their sensing characteristics to be ambiguous. Characteristics are different for such controlled parameters as pyrolysis temperature, crystal structure, particle's morphology and size, chemical and phase composition, the coefficient of thermal expansion (CTE), surface architecture, the bulk and surface stoichiometry and type and conductivity of additives. Here, we provide an alternative approach for joining dissimilar metal-oxides for chemical sensors SE. The approach relies on the development of at least one transient liquid oxide phase on the ceramic-SE interface. These results constitute key points relevant to selection oxides for joining, sintering temperatures and heating/cooling temperature rates.

  7. Chemical treatment of the intra-canal dentin surface: a new approach to modify dentin hydrophobicity

    Directory of Open Access Journals (Sweden)

    Cesar GAITAN-FONSECA

    2013-01-01

    Full Text Available Objective This study evaluated the hydrophobicity of dentin surfaces that were modified through chemical silanization with octadecyltrichlorosilane (OTS. Material and Methods An in vitro experimental study was performed using 40 human permanent incisors that were divided into the following two groups: non-silanized and silanized. The specimens were pretreated and chemically modified with OTS. After the chemical modification, the dentin hydrophobicity was examined using a water contact angle measurement (WCA. The effectiveness of the modification of hydrophobicity was verified by the fluid permeability test (FPT. Results and Conclusions Statistically significant differences were found in the values of WCA and FPT between the two groups. After silanization, the hydrophobic intraradicular dentin surface exhibited in vitro properties that limit fluid penetration into the sealed root canal. This chemical treatment is a new approach for improving the sealing of the root canal system.

  8. An optimized chemical kinetic mechanism for HCCI combustion of PRFs using multi-zone model and genetic algorithm

    International Nuclear Information System (INIS)

    Neshat, Elaheh; Saray, Rahim Khoshbakhti

    2015-01-01

    Highlights: • A new chemical kinetic mechanism for PRFs HCCI combustion is developed. • New mechanism optimization is performed using genetic algorithm and multi-zone model. • Engine-related combustion and performance parameters are predicted accurately. • Engine unburned HC and CO emissions are predicted by the model properly. - Abstract: Development of comprehensive chemical kinetic mechanisms is required for HCCI combustion and emissions prediction to be used in engine development. The main purpose of this study is development of a new chemical kinetic mechanism for primary reference fuels (PRFs) HCCI combustion, which can be applied to combustion models to predict in-cylinder pressure and exhaust CO and UHC emissions, accurately. Hence, a multi-zone model is developed for HCCI engine simulation. Two semi-detailed chemical kinetic mechanisms those are suitable for premixed combustion are used for n-heptane and iso-octane HCCI combustion simulation. The iso-octane mechanism contains 84 species and 484 reactions and the n-heptane mechanism contains 57 species and 296 reactions. A simple interaction between iso-octane and n-heptane is considered in new mechanism. The multi-zone model is validated using experimental data for pure n-heptane and iso-octane. A new mechanism is prepared by combination of these two mechanisms for n-heptane and iso-octane blended fuel, which includes 101 species and 594 reactions. New mechanism optimization is performed using genetic algorithm and multi-zone model. Mechanism contains low temperature heat release region, which decreases with increasing octane number. The results showed that the optimized chemical kinetic mechanism is capable of predicting engine-related combustion and performance parameters. Also after implementing the optimized mechanism, engine unburned HC and CO emissions predicted by the model are in good agreement with the corresponding experimental data

  9. The Effect of a Conceptual Change Approach on Understanding of Students' Chemical Equilibrium Concepts

    Science.gov (United States)

    Atasoy, Basri; Akkus, Huseyin; Kadayifci, Hakki

    2009-01-01

    The purpose of this study was to compare the effects of a conceptual change approach over traditional instruction on tenth-grade students' conceptual achievement in understanding chemical equilibrium. The study was conducted in two classes of the same teacher with participation of a total of 44 tenth-grade students. In this study, a…

  10. A thermal and chemical degradation approach to decipher pristane and phytane precursors in sedimentary organic matter

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Koopmans, M.P.; Rijpstra, W.I.C.; Klapwijk, M.M.; Lewan, M.D.

    1999-01-01

    A thermal and chemical degradation approach was followed to determine the precursors of pristane (Pr) and phytane (Ph) in samples from the Gessoso-solfifera, Ghareb and Green River Formations. Hydrous pyrolysis of these samples yields large amounts of Pr and Ph carbon skeletons, indicating that

  11. APPROACHES FOR INCORPORATING NON-CHEMICAL STRESSORS INTO CUMULATIVE RISK ASSESSMENTS

    Science.gov (United States)

    Over the past twenty years, the risk assessment paradigm has gradually shifted from an individual chemical approach to a community-based model. Inherent in community-based risk assessment is consideration of the totality of stressors affecting a defined population including both ...

  12. Two Experiments to Approach the Boltzmann Factor: Chemical Reaction and Viscous Flow

    Science.gov (United States)

    Fazio, Claudio; Battaglia, Onofrio R.; Guastella, Ivan

    2012-01-01

    In this paper we discuss a pedagogical approach aimed at pointing out the role played by the Boltzmann factor in describing phenomena usually perceived as regulated by different mechanisms of functioning. Experimental results regarding some aspects of a chemical reaction and of the viscous flow of some liquids are analysed and described in terms…

  13. A wet-chemical approach to perovskite and fluorite-type nanoceramics: synthesis and processing

    NARCIS (Netherlands)

    Veldhuis, Sjoerd

    2015-01-01

    In thesis the low-temperature, wet-chemical approach to various functional inorganic oxide materials is described. The main focus of this research is to control the material’s synthesis from liquid precursor to metal oxide powder or thin film; while understanding its formation mechanism. In

  14. Improving Students' Chemical Literacy Levels on Thermochemical and Thermodynamics Concepts through a Context-Based Approach

    Science.gov (United States)

    Cigdemoglu, Ceyhan; Geban, Omer

    2015-01-01

    The aim of this study was to delve into the effect of context-based approach (CBA) over traditional instruction (TI) on students' chemical literacy level related to thermochemical and thermodynamics concepts. Four eleventh-grade classes with 118 students in total taught by two teachers from a public high school in 2012 fall semester were enrolled…

  15. Specific Chemical and Genetic Markers Revealed a Thousands-Year Presence of Toxic Nodularia spumigena in the Baltic Sea.

    Science.gov (United States)

    Cegłowska, Marta; Toruńska-Sitarz, Anna; Kowalewska, Grażyna; Mazur-Marzec, Hanna

    2018-04-04

    In the Baltic Sea, diazotrophic cyanobacteria have been present for thousands of years, over the whole brackish water phase of the ecosystem. However, our knowledge about the species composition of the cyanobacterial community is limited to the last several decades. In the current study, the presence of species-specific chemical and genetic markers in deep sediments were analyzed to increase the existing knowledge on the history of toxic Nodularia spumigena blooms in the Baltic Sea. As chemical markers, three cyclic nonribosomal peptides were applied: the hepatotoxic nodularin, which in the sea was detected solely in N. spumigena , and two anabaenopeptins (AP827 and AP883a) characteristic of two different chemotypes of this species. From the same sediment samples, DNA was isolated and the gene involved in biosynthesis of nodularin, as well as the phycocyanin intergenic spacer region (PC-IGS), were amplified. The results of chemical and genetic analyses proved for the first time the thousands-year presence of toxic N. spumigena in the Baltic Sea. They also indicated that through all this time, the same two sub-populations of the species co-existed.

  16. EDF's approach to determine specifications for nuclear power plant bulk chemicals

    International Nuclear Information System (INIS)

    Basile, Alix; Dijoux, Michel; Le-Calvar, Marc; Gressier, Frederic; Mole, Didier

    2012-09-01

    Chemical impurities in the primary, secondary and auxiliary nuclear power plants circuits generate risks of corrosion of the fuel cladding, steel and nickel based alloys. The PMUC (Products and Materials Used in plants) organization established by EDF intends to limit this risk by specifying maximum levels of impurities in products and materials used for the operation and maintenance of Nuclear Power Plants (NPPs). Bulk chemicals specifications, applied on primary and secondary circuit chemicals and hydrogen and nitrogen gases, are particularly important to prevent chemical species to be involved in the corrosion of the NPPs materials. The application of EDF specifications should lead to reasonably exclude any risk of degradation of the first and second containment barriers and auxiliary circuits Important to Safety (IPS) by limiting the concentrations of chlorides, fluorides, sulfates... The risk of metal embrittlement by elements with low melting point (mercury, lead...) is also included. For the primary circuit, the specifications intend to exclude the risk of activation of impurities introduced by the bulk chemicals. For the first containment barrier, to reduce the risk of deposits like zeolites, PMUC products specifications set limit values for calcium, magnesium, aluminum and silica. EDF's approach for establishing specifications for bulk chemicals is taking also into account the capacity of industrial production, as well as costs, limitations of analytical control methods (detection limits) and environmental releases issues. This paper aims to explain EDF's approach relative to specifications of impurities in bulk chemicals. Also presented are the various parameters taken into account to determine the maximum pollution levels in the chemicals, the theoretical hypothesis to set the specifications and the calculation method used to verify that the specifications are suitable. (authors)

  17. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

    DEFF Research Database (Denmark)

    Bothwell, H.; Bisbing, S.; Therkildsen, Nina Overgaard

    2013-01-01

    It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental...... loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi...... variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major...

  18. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  19. Hereditary breast and ovarian cancer: successful systematic implementation of a group approach to genetic counselling.

    Science.gov (United States)

    Benusiglio, Patrick R; Di Maria, Marina; Dorling, Leila; Jouinot, Anne; Poli, Antoine; Villebasse, Sophie; Le Mentec, Marine; Claret, Béatrice; Boinon, Diane; Caron, Olivier

    2017-01-01

    The increase in referrals to cancer genetics clinics, partially associated with the "Angelina Jolie effect", presents a challenge to existing services, many are already running at full capacity. More efficient ways to deliver genetic counselling are therefore urgently needed. We now systematically offer group instead of standard individual counselling to patients with suspected Hereditary Breast and Ovarian Cancer. Group sessions last 30 min. The first twenty consist of a presentation by the genetic counsellor, the next ten of a discussion involving a cancer geneticist and a psychologist. A short individual consultation ensues, where personal and family issues are addressed and consent obtained. Blood is drawn afterwards. Satisfaction and knowledge are evaluated. We report data for the Oct-2014-Aug-2015 period. 210 patients attended group counselling, up to eight simultaneously. We always fitted them within a 4-h time frame. Mean satisfaction score was 41/43. Knowledge scores increased from 3.1/6 to 4.9/6 post-counselling (p value group counselling, we have withstood increases in referrals without compromising care. The "Angelina Jolie effect" and rapid developments in personalized medicine threaten to overwhelm cancer genetics clinics. In this context, our innovative approach should ensure that all patients have access to approved services.

  20. Usher syndrome: an effective sequencing approach to establish a genetic and clinical diagnosis.

    Science.gov (United States)

    Lenarduzzi, S; Vozzi, D; Morgan, A; Rubinato, E; D'Eustacchio, A; Osland, T M; Rossi, C; Graziano, C; Castorina, P; Ambrosetti, U; Morgutti, M; Girotto, G

    2015-02-01

    Usher syndrome is an autosomal recessive disorder characterized by retinitis pigmentosa, sensorineural hearing loss and, in some cases, vestibular dysfunction. The disorder is clinically and genetically heterogeneous and, to date, mutations in 11 genes have been described. This finding makes difficult to get a precise molecular diagnosis and offer patients accurate genetic counselling. To overcome this problem and to increase our knowledge of the molecular basis of Usher syndrome, we designed a targeted resequencing custom panel. In a first validation step a series of 16 Italian patients with known molecular diagnosis were analysed and 31 out of 32 alleles were detected (97% of accuracy). After this step, 31 patients without a molecular diagnosis were enrolled in the study. Three out of them with an uncertain Usher diagnosis were excluded. One causative allele was detected in 24 out 28 patients (86%) while the presence of both causative alleles characterized 19 patients out 28 (68%). Sixteen novel and 27 known alleles were found in the following genes: USH2A (50%), MYO7A (7%), CDH23 (11%), PCDH15 (7%) and USH1G (2%). Overall, on the 44 patients the protocol was able to characterize 74 alleles out of 88 (84%). These results suggest that our panel is an effective approach for the genetic diagnosis of Usher syndrome leading to: 1) an accurate molecular diagnosis, 2) better genetic counselling, 3) more precise molecular epidemiology data fundamental for future interventional plans. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  2. 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.

  3. Approaches to quality management and accreditation in a genetic testing laboratory

    Science.gov (United States)

    Berwouts, Sarah; Morris, Michael A; Dequeker, Elisabeth

    2010-01-01

    Medical laboratories, and specifically genetic testing laboratories, provide vital medical services to different clients: clinicians requesting a test, patients from whom the sample was collected, public health and medical-legal instances, referral laboratories and authoritative bodies. All expect results that are accurate and obtained in an efficient and effective manner, within a suitable time frame and at acceptable cost. There are different ways of achieving the end results, but compliance with International Organization for Standardization (ISO) 15189, the international standard for the accreditation of medical laboratories, is becoming progressively accepted as the optimal approach to assuring quality in medical testing. We present recommendations and strategies designed to aid genetic testing laboratories with the implementation of a quality management system, including key aspects such as document control, external quality assessment, internal quality control, internal audit, management review, validation, as well as managing the human side of change. The focus is on pragmatic approaches to attain the levels of quality management and quality assurance required for accreditation according to ISO 15189, within the context of genetic testing. Attention is also given to implementing efficient and effective quality improvement. PMID:20720559

  4. The relationships between chemical and genetic differentiation and environmental factors across the distribution of Erigeron breviscapus (Asteraceae).

    Science.gov (United States)

    Li, Xiang; Peng, Li-yan; Zhang, Shu-dong; Zhao, Qin-shi; Yi, Ting-shuang

    2013-01-01

    Erigeron breviscapus (Vant.) Hand.-Mazz. is an important, widely used Chinese herb with scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B being its major active compounds. We aimed to resolve the influence of biotic and abiotic factors on the concentrations of these compounds and to determine appropriate cultivation methods to improve the yields of the four compounds in this herb. In order to detect the major genetic and natural environmental factors affecting the yields of these four compounds, we applied AFLP markers to investigate the population genetic differentiation and HPLC to measure the concentrations of four major active compounds among 23 wild populations which were located across almost the entire distribution of this species in China. The meteorological data including annual average temperature, annual average precipitation and annual average hours of sunshine were collected. The relationships among the concentrations of four compounds and environmental factors and genetic differentiation were studied. Low intraspecific genetic differentiation is detected, and there is no obvious correlation between the genetic differentiation and the contents of the chemical compounds. We investigated the correlation between the concentrationsof four compounds (scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B) and environmental factors. Concentrations of two compounds (1,5-dicaffeoylquinic acid and 3,5-dicaffeoylquinic acid) were correlated with environmental factors. The concentration of 1,5-dicaffeoylquinic acid is positively correlated with latitude, and is negatively correlated with the annual average temperature. The concentration of 3,5-dicaffeoylquinic acid is positively correlated with annual average precipitation. Therefore, changing cultivation conditions may significantly improve the yields of these two compounds. We found the concentration of scutellarin positively correlated with that of

  5. The relationships between chemical and genetic differentiation and environmental factors across the distribution of Erigeron breviscapus (Asteraceae.

    Directory of Open Access Journals (Sweden)

    Xiang Li

    Full Text Available AIMS: Erigeron breviscapus (Vant. Hand.-Mazz. is an important, widely used Chinese herb with scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B being its major active compounds. We aimed to resolve the influence of biotic and abiotic factors on the concentrations of these compounds and to determine appropriate cultivation methods to improve the yields of the four compounds in this herb. METHODS: In order to detect the major genetic and natural environmental factors affecting the yields of these four compounds, we applied AFLP markers to investigate the population genetic differentiation and HPLC to measure the concentrations of four major active compounds among 23 wild populations which were located across almost the entire distribution of this species in China. The meteorological data including annual average temperature, annual average precipitation and annual average hours of sunshine were collected. The relationships among the concentrations of four compounds and environmental factors and genetic differentiation were studied. IMPORTANT FINDINGS: Low intraspecific genetic differentiation is detected, and there is no obvious correlation between the genetic differentiation and the contents of the chemical compounds. We investigated the correlation between the concentrationsof four compounds (scutellarin, 1,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and erigoster B and environmental factors. Concentrations of two compounds (1,5-dicaffeoylquinic acid and 3,5-dicaffeoylquinic acid were correlated with environmental factors. The concentration of 1,5-dicaffeoylquinic acid is positively correlated with latitude, and is negatively correlated with the annual average temperature. The concentration of 3,5-dicaffeoylquinic acid is positively correlated with annual average precipitation. Therefore, changing cultivation conditions may significantly improve the yields of these two compounds. We found the concentration

  6. Coupled sulfur isotopic and chemical mass transfer modeling: Approach and application to dynamic hydrothermal processes

    International Nuclear Information System (INIS)

    Janecky, D.R.

    1988-01-01

    A computational modeling code (EQPSreverse arrowS) has been developed to examine sulfur isotopic distribution pathways coupled with calculations of chemical mass transfer pathways. A post processor approach to EQ6 calculations was chosen so that a variety of isotopic pathways could be examined for each reaction pathway. Two types of major bounding conditions were implemented: (1) equilibrium isotopic exchange between sulfate and sulfide species or exchange only accompanying chemical reduction and oxidation events, and (2) existence or lack of isotopic exchange between solution species and precipitated minerals, parallel to the open and closed chemical system formulations of chemical mass transfer modeling codes. All of the chemical data necessary to explicitly calculate isotopic distribution pathways is generated by most mass transfer modeling codes and can be input to the EQPS code. Routines are built in to directly handle EQ6 tabular files. Chemical reaction models of seafloor hydrothermal vent processes and accompanying sulfur isotopic distribution pathways illustrate the capabilities of coupling EQPSreverse arrowS with EQ6 calculations, including the extent of differences that can exist due to the isotopic bounding condition assumptions described above. 11 refs., 2 figs

  7. An Inverse Analysis Approach to the Characterization of Chemical Transport in Paints

    Science.gov (United States)

    Willis, Matthew P.; Stevenson, Shawn M.; Pearl, Thomas P.; Mantooth, Brent A.

    2014-01-01

    The ability to directly characterize chemical transport and interactions that occur within a material (i.e., subsurface dynamics) is a vital component in understanding contaminant mass transport and the ability to decontaminate materials. If a material is contaminated, over time, the transport of highly toxic chemicals (such as chemical warfare agent species) out of the material can result in vapor exposure or transfer to the skin, which can result in percutaneous exposure to personnel who interact with the material. Due to the high toxicity of chemical warfare agents, the release of trace chemical quantities is of significant concern. Mapping subsurface concentration distribution and transport characteristics of absorbed agents enables exposure hazards to be assessed in untested conditions. Furthermore, these tools can be used to characterize subsurface reaction dynamics to ultimately design improved decontaminants or decontamination procedures. To achieve this goal, an inverse analysis mass transport modeling approach was developed that utilizes time-resolved mass spectroscopy measurements of vapor emission from contaminated paint coatings as the input parameter for calculation of subsurface concentration profiles. Details are provided on sample preparation, including contaminant and material handling, the application of mass spectrometry for the measurement of emitted contaminant vapor, and the implementation of inverse analysis using a physics-based diffusion model to determine transport properties of live chemical warfare agents including distilled mustard (HD) and the nerve agent VX. PMID:25226346

  8. The Genetics of Obsessive-Compulsive Disorder and Tourette Syndrome: An Epidemiological and Pathway-Based Approach for Gene Discovery

    Science.gov (United States)

    Grados, Marco A.

    2010-01-01

    Objective: To provide a contemporary perspective on genetic discovery methods applied to obsessive-compulsive disorder (OCD) and Tourette syndrome (TS). Method: A review of research trends in genetics research in OCD and TS is conducted, with emphasis on novel approaches. Results: Genome-wide association studies (GWAS) are now in progress in OCD…

  9. Dynamic Load Balanced Clustering using Elitism based Random Immigrant Genetic Approach for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    K. Mohaideen Pitchai

    2017-07-01

    Full Text Available Wireless Sensor Network (WSN consists of a large number of small sensors with restricted energy. Prolonged network lifespan, scalability, node mobility and load balancing are important needs for several WSN applications. Clustering the sensor nodes is an efficient technique to reach these goals. WSN have the characteristics of topology dynamics because of factors like energy conservation and node movement that leads to Dynamic Load Balanced Clustering Problem (DLBCP. In this paper, Elitism based Random Immigrant Genetic Approach (ERIGA is proposed to solve DLBCP which adapts to topology dynamics. ERIGA uses the dynamic Genetic Algorithm (GA components for solving the DLBCP. The performance of load balanced clustering process is enhanced with the help of this dynamic GA. As a result, the ERIGA achieves to elect suitable cluster heads which balances the network load and increases the lifespan of the network.

  10. Branch-pipe-routing approach for ships using improved genetic algorithm

    Science.gov (United States)

    Sui, Haiteng; Niu, Wentie

    2016-09-01

    Branch-pipe routing plays fundamental and critical roles in ship-pipe design. The branch-pipe-routing problem is a complex combinatorial optimization problem and is thus difficult to solve when depending only on human experts. A modified genetic-algorithm-based approach is proposed in this paper to solve this problem. The simplified layout space is first divided into threedimensional (3D) grids to build its mathematical model. Branch pipes in layout space are regarded as a combination of several two-point pipes, and the pipe route between two connection points is generated using an improved maze algorithm. The coding of branch pipes is then defined, and the genetic operators are devised, especially the complete crossover strategy that greatly accelerates the convergence speed. Finally, simulation tests demonstrate the performance of proposed method.

  11. [Research progress in chemical communication among insect-resistant genetically modified plants, insect pests and natural enemies].

    Science.gov (United States)

    Liu, Qing-Song; Li, Yun-He; Chen, Xiu-Ping; Peng, Yu-Fa

    2014-08-01

    Semiochemicals released by plants or insects play an important role in the communication among plants, phytophagous insects and their natural enemies. They thus form a chemical information network which regulates intra- and inter-specific behaviors and sustains the composition and structure of plant and insect communities. The application of insect-resistant genetically modified (IRGM) crops may affect the chemical communication within and among the tritrophic levels, and thus cause disturbances to the biotic community structure and the stability of the farmland ecosystem. This has raised concerns about the environmental safety of IRGM crops and triggered research worldwide. In the current article we provided a brief summary of the chemical communication among plants, herbivores and natural enemies; analyzed the potential of IRGM crops to affect the chemical communication between plants and arthropods and the related mechanisms; and discussed the current research progress and the future prospects in this field. We hope that this will promote the research in this field by Chinese scientists and increase our understanding of the potential effects of growing of IRGM crops on the arthropod community structure.

  12. Comparison of gamma radiation and radiomimmetic chemical, bleomycin in leukocytes from certain genetic disorders

    International Nuclear Information System (INIS)

    Saraswathy, Radha

    2004-01-01

    Full text: To compare the frequency and distribution pattern of bleomycin and gamma radiation induced chromosomal aberrations in human genetic disorders. To study if the induced chromosomal break points are specific for specific human genetic disorders. Human genetics disorders such as; retinitis pigmentosa, retinoblastoma, xeroderma pigmentosa and gonadal dysgenesis were used in our study. Suitable controls were maintained. The frequency and distribution pattern of chromosomal break points in individual chromosomes were determined in lymphocytes exposed to 50r of gamma radiation and 10μg/ml of bleomycin for 3h at G2. In normal individuals none of the unirradiated leukocyte cultures of any syndrome showed any accountable number of chromosomal aberrations. The frequency of radiation induced chromosomal break points showed a non random distribution pattern and frequently clustered at some specific chromosome regions to form hot spots. Lack of linear-quadratic dose response was observed in the lymphocyte exposed to bleomycin in normal individual. The frequency of chromosomal aberrations in the whole genome for the genetic disorders were higher than the controls and a varying distribution pattern of bleomycin induced breaks per cell was observed

  13. Genetic Algorithms for the Optimization of Chemical Processes Based on Problem Descriptions

    Czech Academy of Sciences Publication Activity Database

    Holeňa, Martin; Rodemerck, U.; Čukić, T.; Linke, D.; Dingerdissen, U.

    2007-01-01

    Roč. 6, č. 4 (2007), s. 615-621 ISSN 1109-2769 R&D Projects: GA ČR GA201/05/0325 Institutional research plan: CEZ:AV0Z10300504 Keywords : computer applications in chemistry * optimization methods * empirical objective function * genetic algorithms * problem-tailoring * formal description language * program generator Subject RIV: IN - Informatics, Computer Science

  14. Rat reverse genetics : generation and characterization of chemically induced rat mutants

    NARCIS (Netherlands)

    van Boxtel, R.

    2010-01-01

    The use of animal models has been crucial for studying the function of genetic elements in the human genome. Embryonic stem (ES) cell-based homologous recombination (HR) has proven a very efficient technique for gene manipulation. However, this technique is not (yet) available for all model

  15. A Genetic Algorithms-based Approach for Optimized Self-protection in a Pervasive Service Middleware

    DEFF Research Database (Denmark)

    Zhang, Weishan; Ingstrup, Mads; Hansen, Klaus Marius

    2009-01-01

    With increasingly complex and heterogeneous systems in pervasive service computing, it becomes more and more important to provide self-protected services to end users. In order to achieve self-protection, the corresponding security should be provided in an optimized manner considering...... the constraints of heterogeneous devices and networks. In this paper, we present a Genetic Algorithms-based approach for obtaining optimized security configurations at run time, supported by a set of security OWL ontologies and an event-driven framework. This approach has been realized as a prototype for self-protection...... in the Hydra middleware, and is integrated with a framework for enforcing the computed solution at run time using security obligations. The experiments with the prototype on configuring security strategies for a pervasive service middleware show that this approach has acceptable performance, and could be used...

  16. An in vitro approach for prioritization and evaluation of chemical effects on glucocorticoid receptor mediated adipogenesis.

    Science.gov (United States)

    Hartman, Jessica K; Beames, Tyler; Parks, Bethany; Doheny, Daniel; Song, Gina; Efremenko, Alina; Yoon, Miyoung; Foley, Briana; Deisenroth, Chad; McMullen, Patrick D; Clewell, Rebecca A

    2018-05-18

    Rising obesity rates worldwide have socio-economic ramifications. While genetics, diet, and lack of exercise are major contributors to obesity, environmental factors may enhance susceptibility through disruption of hormone homeostasis and metabolic processes. The obesogen hypothesis contends that chemical exposure early in development may enhance adipocyte differentiation, thereby increasing the number of adipocytes and predisposing for obesity and metabolic disease. We previously developed a primary human adipose stem cell (hASC) assay to evaluate the effect of environmental chemicals on PPARG-dependent adipogenesis. Here, the assay was modified to determine the effects of chemicals on the glucocorticoid receptor (GR) pathway. In differentiation cocktail lacking the glucocorticoid agonist dexamethasone (DEX), hASCs do not differentiate into adipocytes. In the presence of GR agonists, adipocyte maturation was observed using phenotypic makers for lipid accumulation, adipokine secretion, and expression of key genes. To evaluate the role of environmental compounds on adipocyte differentiation, progenitor cells were treated with 19 prioritized compounds previously identified by ToxPi as having GR-dependent bioactivity, and multiplexed assays were used to confirm a GR-dependent mode of action. Five chemicals were found to be strong agonists. The assay was also modified to evaluate GR-antagonists, and 8/10 of the hypothesized antagonists inhibited adipogenesis. The in vitro bioactivity data was put into context with extrapolated human steady state concentrations (Css) and clinical exposure data (Cmax). These data support using a human adipose-derived stem cell differentiation assay to test the potential of chemicals to alter human GR-dependent adipogenesis. Copyright © 2017. Published by Elsevier Inc.

  17. A chemical-genetic strategy reveals distinct temporal requirements for SAD-1 kinase in neuronal polarization and synapse formation

    Directory of Open Access Journals (Sweden)

    Shokat Kevan M

    2008-09-01

    Full Text Available Abstract Background Neurons assemble into a functional network through a sequence of developmental processes including neuronal polarization and synapse formation. In Caenorhabditis elegans, the serine/threonine SAD-1 kinase is essential for proper neuronal polarity and synaptic organization. To determine if SAD-1 activity regulates the establishment or maintenance of these neuronal structures, we examined its temporal requirements using a chemical-genetic method that allows for selective and reversible inactivation of its kinase activity in vivo. Results We generated a PP1 analog-sensitive variant of SAD-1. Through temporal inhibition of SAD-1 kinase activity we show that its activity is required for the establishment of both neuronal polarity and synaptic organization. However, while SAD-1 activity is needed strictly when neurons are polarizing, the temporal requirement for SAD-1 is less stringent in synaptic organization, which can also be re-established during maintenance. Conclusion This study reports the first temporal analysis of a neural kinase activity using the chemical-genetic system. It reveals that neuronal polarity and synaptic organization have distinct temporal requirements for SAD-1.

  18. Tailor-made Design of Chemical Blends using Decomposition-based Computer-aided Approach

    DEFF Research Database (Denmark)

    Yunus, Nor Alafiza; Manan, Zainuddin Abd.; Gernaey, Krist

    (properties). In this way, first the systematic computer-aided technique establishes the search space, and then narrows it down in subsequent steps until a small number of feasible and promising candidates remain and then experimental work may be conducted to verify if any or all the candidates satisfy......Computer aided technique is an efficient approach to solve chemical product design problems such as design of blended liquid products (chemical blending). In chemical blending, one tries to find the best candidate, which satisfies the product targets defined in terms of desired product attributes...... is decomposed into two stages. The first stage investigates the mixture stability where all unstable mixtures are eliminated and the stable blend candidates are retained for further testing. In the second stage, the blend candidates have to satisfy a set of target properties that are ranked according...

  19. An approach in building a chemical compound search engine in oracle database.

    Science.gov (United States)

    Wang, H; Volarath, P; Harrison, R

    2005-01-01

    A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

  20. Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population.

    Science.gov (United States)

    Raghavan, Chitra; Mauleon, Ramil; Lacorte, Vanica; Jubay, Monalisa; Zaw, Hein; Bonifacio, Justine; Singh, Rakesh Kumar; Huang, B Emma; Leung, Hei

    2017-06-07

    Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations. Copyright © 2017 Raghavan et al.

  1. Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population

    Directory of Open Access Journals (Sweden)

    Chitra Raghavan

    2017-06-01

    Full Text Available Multi-parent Advanced Generation Intercross (MAGIC populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL mapping. In this study, 1316 S6:8 indica MAGIC (MI lines and the eight founders were sequenced using Genotyping by Sequencing (GBS. As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height, physical (grain length and grain width and cooking properties (amylose content of the rice grain, abiotic stress (submergence tolerance, and biotic stress (brown spot disease were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations.

  2. Optimal planning approaches with multiple impulses for rendezvous based on hybrid genetic algorithm and control method

    Directory of Open Access Journals (Sweden)

    JingRui Zhang

    2015-03-01

    Full Text Available In this article, we focus on safe and effective completion of a rendezvous and docking task by looking at planning approaches and control with fuel-optimal rendezvous for a target spacecraft running on a near-circular reference orbit. A variety of existent practical path constraints are considered, including the constraints of field of view, impulses, and passive safety. A rendezvous approach is calculated by using a hybrid genetic algorithm with those constraints. Furthermore, a control method of trajectory tracking is adopted to overcome the external disturbances. Based on Clohessy–Wiltshire equations, we first construct the mathematical model of optimal planning approaches of multiple impulses with path constraints. Second, we introduce the principle of hybrid genetic algorithm with both stronger global searching ability and local searching ability. We additionally explain the application of this algorithm in the problem of trajectory planning. Then, we give three-impulse simulation examples to acquire an optimal rendezvous trajectory with the path constraints presented in this article. The effectiveness and applicability of the tracking control method are verified with the optimal trajectory above as control objective through the numerical simulation.

  3. Enhancing sewage sludge dewaterability by bioleaching approach with comparison to other physical and chemical conditioning methods.

    Science.gov (United States)

    Liu, Fenwu; Zhou, Jun; Wang, Dianzhan; Zhou, Lixiang

    2012-01-01

    The sewage sludge conditioning process is critical to improve the sludge dewaterability prior to mechanical dewatering. Traditionally, sludge is conditioned by physical or chemical approaches, mostly with the addition of inorganic or organic chemicals. Here we report that bioleaching, an efficient and economical microbial method for the removal of sludge-borne heavy metals, also plays a significant role in enhancing sludge dewaterability. The effects of bioleaching and physical or chemical approaches on sludge dewaterability were compared. The conditioning result of bioleaching by Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans on sludge dewatering was investigated and compared with the effects of hydrothermal (121 degrees C for 2 hr), microwave (1050 W for 50 sec), ultrasonic (250 W for 2 min), and chemical conditioning (24% ferric chloride and 68% calcium oxide; dry basis). The results show that the specific resistance to filtration (SRF) or capillary suction time (CST) of sludge is decreased by 93.1% or 74.1%, respectively, after fresh sludge is conditioned by bioleaching, which is similar to chemical conditioning treatment with ferric chloride and calcium oxide but much more effective than other conditioning approaches including hydrothermal, microwave, and ultrasonic conditioning. Furthermore, after sludge dewatering, bioleached sludge filtrate contains the lowest concentrations of chroma (18 times), COD (542 mg/L), total N (TN, 300 mg/L), NH4(+)-N (208 mg/L), and total P (TP, 2 mg/L) while the hydrothermal process resulted in the highest concentration of chroma (660 times), COD (18,155 mg/L), TN (472 mg/L), NH4(+)-N (381 mg/L), and TP (191 mg/L) among these selected conditioning methods. Moreover, unlike chemical conditioning, sludge bioleaching does not result in a significant reduction of organic matter, TN, and TP in the resulting dewatered sludge cake. Therefore, considering sludge dewaterability and the chemical properties of sludge

  4. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  5. Comparison of Pyrolysis Mass Spectrometry and Near Infrared Spectroscopy for Genetic Analysis of Lignocellulose Chemical Composition in Populus

    Directory of Open Access Journals (Sweden)

    Jianxing Zhang

    2014-03-01

    Full Text Available Genetic analysis of wood chemical composition is often limited by the cost and throughput of direct analytical methods. The speed and low cost of Fourier transform near infrared (FT-NIR overcomes many of these limitations, but it is an indirect method relying on calibration models that are typically developed and validated with small sample sets. In this study, we used >1500 young greenhouse grown trees from a clonally propagated single Populus family, grown at low and high nitrogen, and compared FT-NIR calibration sample sizes of 150, 250, 500 and 750 on calibration and prediction model statistics, and heritability estimates developed with pyrolysis molecular beam mass spectrometry (pyMBMS wood chemical composition. As calibration sample size increased from 150 to 750, predictive model statistics improved slightly. Overall, stronger calibration and prediction statistics were obtained with lignin, S-lignin, S/G ratio, and m/z 144 (an ion from cellulose, than with C5 and C6 carbohydrates, and m/z 114 (an ion from xylan. Although small differences in model statistics were observed between the 250 and 500 sample calibration sets, when predicted values were used for calculating genetic control, the 500 sample set gave substantially more similar results to those obtained with the pyMBMS data. With the 500 sample calibration models, genetic correlations obtained with FT-NIR and pyMBMS methods were similar. Quantitative trait loci (QTL analysis with pyMBMS and FT-NIR predictions identified only three common loci for lignin traits. FT-NIR identified four QTLs that were not found with pyMBMS data, and these QTLs were for the less well predicted carbohydrate traits.

  6. Chemometrical characterization of four italian rice varieties based on genetic and chemical analyses.

    Science.gov (United States)

    Brandolini, Vincenzo; Coïsson, Jean Daniel; Tedeschi, Paola; Barile, Daniela; Cereti, Elisabetta; Maietti, Annalisa; Vecchiati, Giorgio; Martelli, Aldo; Arlorio, Marco

    2006-12-27

    This paper describes a method for achieving qualitative identification of four rice varieties from two different Italian regions. To estimate the presence of genetic diversity among the four rice varieties, we used polymerase chain reaction-randomly amplified polymorphic DNA (PCR-RAPD) markers, and to elucidate whether a relationship exists between the ground and the specific characteristics of the product, we studied proximate composition, fatty acid composition, mineral content, and total antioxidant capacity. Using principal component analysis on genomic and compositional data, we were able to classify rice samples according to their variety and their district of production. This work also examined the discrimination ability of different parameters. It was found that genomic data give the best discrimination based on varieties, indicating that RAPD assays could be useful in discriminating among closely related species, while compositional analyses do not depend on the genetic characters only but are related to the production area.

  7. A Genetic Algorithm-based Antenna Selection Approach for Large-but-Finite MIMO Networks

    KAUST Repository

    Makki, Behrooz

    2016-12-29

    We study the performance of antenna selectionbased multiple-input-multiple-output (MIMO) networks with large but finite number of transmit antennas and receivers. Considering the continuous and bursty communication scenarios with different users’ data request probabilities, we develop an efficient antenna selection scheme using genetic algorithms (GA). As demonstrated, the proposed algorithm is generic in the sense that it can be used in the cases with different objective functions, precoding methods, levels of available channel state information and channel models. Our results show that the proposed GAbased algorithm reaches (almost) the same throughput as the exhaustive search-based optimal approach, with substantially less implementation complexity.

  8. A Genetic Algorithm-based Antenna Selection Approach for Large-but-Finite MIMO Networks

    KAUST Repository

    Makki, Behrooz; Ide, Anatole; Svensson, Tommy; Eriksson, Thomas; Alouini, Mohamed-Slim

    2016-01-01

    We study the performance of antenna selectionbased multiple-input-multiple-output (MIMO) networks with large but finite number of transmit antennas and receivers. Considering the continuous and bursty communication scenarios with different users’ data request probabilities, we develop an efficient antenna selection scheme using genetic algorithms (GA). As demonstrated, the proposed algorithm is generic in the sense that it can be used in the cases with different objective functions, precoding methods, levels of available channel state information and channel models. Our results show that the proposed GAbased algorithm reaches (almost) the same throughput as the exhaustive search-based optimal approach, with substantially less implementation complexity.

  9. Approach to estimation of level of information security at enterprise based on genetic algorithm

    Science.gov (United States)

    V, Stepanov L.; V, Parinov A.; P, Korotkikh L.; S, Koltsov A.

    2018-05-01

    In the article, the way of formalization of different types of threats of information security and vulnerabilities of an information system of the enterprise and establishment is considered. In a type of complexity of ensuring information security of application of any new organized system, the concept and decisions in the sphere of information security are expedient. One of such approaches is the method of a genetic algorithm. For the enterprises of any fields of activity, the question of complex estimation of the level of security of information systems taking into account the quantitative and qualitative factors characterizing components of information security is relevant.

  10. Laboratory evaluation of the in situ chemical treatment approach to soil and groundwater remediation

    International Nuclear Information System (INIS)

    Thorton, E.C.; Trader, D.E.

    1993-10-01

    Results of initial proof of principle laboratory testing activities successfully demonstrated the viability of the in situ chemical treatment approach for remediation of soil and groundwater contaminated by hexavalent chromium. Testing activities currently in progress further indicate that soils contaminated with hexavalent chromium and uranium at concentrations of several hundred parts per million can be successfully treated with 100 ppM hydrogen sulfide gas mixtures. Greater than 90% immobilization of hexavalent chromium and 50% immobilization of uranium have been achieved in these tests after a treatment period of one day. Activities associated with further development and implementation of the in situ chemical treatment approach include conducting additional bench scale tests with contaminated geomedia, and undertaking scale-up laboratory tests and a field demonstration. This report discusses the testing and further development of this process

  11. Chemical Genetic Screens for TDP-43 Modifiers and ALS Drug Discovery

    Science.gov (United States)

    2015-03-01

    Champagne , and Pierre Drapeau. 25th international symposium on ALS/MND (5-7 December 2014) Patten SA, Vaccaro A, Drapeau P, Kabashi E, Parker JA...transgenic mice produced with TDP- 43 genomic fragments. Brain 134, 2610-2626 (2011). 6 Kabashi, E., Champagne , N., Brustein, E. & Drapeau, P. In the...swim of things: recent insights to neurogenetic disorders from zebrafish. Trends Genet 26, 373-381 (2010). 7 Kabashi, E., Brustein, E., Champagne , N

  12. Chemical Genetic Screens for TDP-43 Modifiers and ALS Drug Discovery

    Science.gov (United States)

    2013-10-01

    red. Chlo= Chlorprothixene hydrochloride; Amo= Amoxapine; Mians = Mianserine hydrochloride; Pizo= Pizotifen malate; Pimet= Pimethixene maleate; Cloz...lobar degeneration in transgenic mice produced with TDP-43 genomic fragments. Brain. 32. Li Y, Ray P, Rao EJ, Shi C, Guo W, et al. (2010) A Drosophila...2008) Sirtuin Inhibition Protects from the Polyalanine Muscular Dystrophy Protein PABPN1. Hum Mol Genet. 36. Wang J, Farr GW, Hall DH, Li F, Furtak

  13. New approach to predict photoallergic potentials of chemicals based on murine local lymph node assay.

    Science.gov (United States)

    Maeda, Yosuke; Hirosaki, Haruka; Yamanaka, Hidenori; Takeyoshi, Masahiro

    2018-05-23

    Photoallergic dermatitis, caused by pharmaceuticals and other consumer products, is a very important issue in human health. However, S10 guidelines of the International Conference on Harmonization do not recommend the existing prediction methods for photoallergy because of their low predictability in human cases. We applied local lymph node assay (LLNA), a reliable, quantitative skin sensitization prediction test, to develop a new photoallergy prediction method. This method involves a three-step approach: (1) ultraviolet (UV) absorption analysis; (2) determination of no observed adverse effect level for skin phototoxicity based on LLNA; and (3) photoallergy evaluation based on LLNA. Photoallergic potential of chemicals was evaluated by comparing lymph node cell proliferation among groups treated with chemicals with minimal effect levels of skin sensitization and skin phototoxicity under UV irradiation (UV+) or non-UV irradiation (UV-). A case showing significant difference (P < .05) in lymph node cell proliferation rates between UV- and UV+ groups was considered positive for photoallergic reaction. After testing 13 chemicals, seven human photoallergens tested positive and the other six, with no evidence of causing photoallergic dermatitis or UV absorption, tested negative. Among these chemicals, both doxycycline hydrochloride and minocycline hydrochloride were tetracycline antibiotics with different photoallergic properties, and the new method clearly distinguished between the photoallergic properties of these chemicals. These findings suggested high predictability of our method; therefore, it is promising and effective in predicting human photoallergens. Copyright © 2018 John Wiley & Sons, Ltd.

  14. Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches.

    Science.gov (United States)

    de Luca, Aurélie; Horvath, Dragos; Marcou, Gilles; Solov'ev, Vitaly; Varnek, Alexandre

    2012-09-24

    This work addresses the problem of similarity search and classification of chemical reactions using Neighborhood Behavior (NB) and Condensed Graphs of Reaction (CGR) approaches. The CGR formalism represents chemical reactions as a classical molecular graph with dynamic bonds, enabling descriptor calculations on this graph. Different types of the ISIDA fragment descriptors generated for CGRs in combination with two metrics--Tanimoto and Euclidean--were considered as chemical spaces, to serve for reaction dissimilarity scoring. The NB method has been used to select an optimal combination of descriptors which distinguish different types of chemical reactions in a database containing 8544 reactions of 9 classes. Relevance of NB analysis has been validated in generic (multiclass) similarity search and in clustering with Self-Organizing Maps (SOM). NB-compliant sets of descriptors were shown to display enhanced mapping propensities, allowing the construction of better Self-Organizing Maps and similarity searches (NB and classical similarity search criteria--AUC ROC--correlate at a level of 0.7). The analysis of the SOM clusters proved chemically meaningful CGR substructures representing specific reaction signatures.

  15. Aquatic exposures of chemical mixtures in urban environments: Approaches to impact assessment.

    Science.gov (United States)

    de Zwart, Dick; Adams, William; Galay Burgos, Malyka; Hollender, Juliane; Junghans, Marion; Merrington, Graham; Muir, Derek; Parkerton, Thomas; De Schamphelaere, Karel A C; Whale, Graham; Williams, Richard

    2018-03-01

    Urban regions of the world are expanding rapidly, placing additional stress on water resources. Urban water bodies serve many purposes, from washing and sources of drinking water to transport and conduits for storm drainage and effluent discharge. These water bodies receive chemical emissions arising from either single or multiple point sources, diffuse sources which can be continuous, intermittent, or seasonal. Thus, aquatic organisms in these water bodies are exposed to temporally and compositionally variable mixtures. We have delineated source-specific signatures of these mixtures for diffuse urban runoff and urban point source exposure scenarios to support risk assessment and management of these mixtures. The first step in a tiered approach to assessing chemical exposure has been developed based on the event mean concentration concept, with chemical concentrations in runoff defined by volumes of water leaving each surface and the chemical exposure mixture profiles for different urban scenarios. Although generalizations can be made about the chemical composition of urban sources and event mean exposure predictions for initial prioritization, such modeling needs to be complemented with biological monitoring data. It is highly unlikely that the current paradigm of routine regulatory chemical monitoring alone will provide a realistic appraisal of urban aquatic chemical mixture exposures. Future consideration is also needed of the role of nonchemical stressors in such highly modified urban water bodies. Environ Toxicol Chem 2018;37:703-714. © 2017 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC. © 2017 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

  16. A combined genetic and multi medium approach revels new secondary metabolites in Aspergillus nidulans

    DEFF Research Database (Denmark)

    Klejnstrup, Marie Louise; Nielsen, Morten Thrane; Frisvad, Jens Christian

    Secondary metabolites are a diverse group of metabolites which serve as important natural sources of drugs for treating diseases. The availability of full genome sequences of several filamentous fungi has revealed a large genetic potential for production of secondary metabolites that are not obse......Secondary metabolites are a diverse group of metabolites which serve as important natural sources of drugs for treating diseases. The availability of full genome sequences of several filamentous fungi has revealed a large genetic potential for production of secondary metabolites...... that are not observed under standard laboratory conditions. Genetic approaches have proven a fruitfull strategy towards the production and identification of these unknown metabolites. Examples include deletion of the cclA1 and laeA2 genes in A. nidulans which affects the expression of secondary metabolites including...... monodictyphenone and terrequinone A respectively. We have deleted the cclA gene in A. nidulans and grown the mutants on several complex media to provoke the production of secondary metabolites. This resulted in the production of several metabolites not previously reported from A. nidulans. Some of these have been...

  17. Genetic engineering represents a safe approach for innovations improving nutritional contents of major food crops

    Directory of Open Access Journals (Sweden)

    Werner Arber

    2017-05-01

    Full Text Available About 70 years ago early microbial genetic research revealed that inherited phenotypic traits become determined by DNA filaments composed of 4 different nucleotides that are linearly arranged. In the meantime we know that genes, the determinants of specific life functions, are genomic segments of an average size of about 1000 nucleotides, i.e. a very small part of a genome. Fundamental insights into the structures and functions of selected genes can be reached by sorting out the relevant short DNA segment, splicing this fragment into a natural gene vector such as a viral genome or a fertility plasmid. This allows the researchers to transfer the genetic hybrid into an appropriate host cell in order to produce many copies that can then serve for functional and structural analysis. This research approach became efficient in the 1970s. On the request of involved researchers, safety guidelines became proposed 1975 at the Asilomar Conference on Recombinant DNA (Berg, Baltimore, Brenner, Roblin, & Singer, 1975, then generally introduced and still largely followed nowadays. Carefully carried out genetic engineering by horizontally transferring a selected and functionally well known DNA segment into the genome of another organism has in many published biosafety investigations never shown any unexpected harmful effect. We will present below selected examples of research contributions enabling innovations for the benefit of human life conditions.

  18. The challenges and promises of genetic approaches for ballast water management

    Science.gov (United States)

    Rey, Anaïs; Basurko, Oihane C.; Rodríguez-Ezpeleta, Naiara

    2018-03-01

    Ballast water is a main vector of introduction of Harmful Aquatic Organisms and Pathogens, which includes Non-Indigenous Species. Numerous and diversified organisms are transferred daily from a donor to a recipient port. Developed to prevent these introduction events, the International Convention for the Control and Management of Ships' Ballast Water and Sediments will enter into force in 2017. This international convention is asking for the monitoring of Harmful Aquatic Organisms and Pathogens. In this review, we highlight the urgent need to develop cost-effective methods to: (1) perform the biological analyses required by the convention; and (2) assess the effectiveness of two main ballast water management strategies, i.e. the ballast water exchange and the use of ballast water treatment systems. We have compiled the biological analyses required by the convention, and performed a comprehensive evaluation of the potential and challenges of the use of genetic tools in this context. Following an overview of the studies applying genetic tools to ballast water related research, we present metabarcoding as a relevant approach for early detection of Harmful Aquatic Organisms and Pathogens in general and for ballast water monitoring and port risk assessment in particular. Nonetheless, before implementation of genetic tools in the context of the ballast water management convention, benchmarked tests against traditional methods should be performed, and standard, reproducible and easy to apply protocols should be developed.

  19. An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations.

    Directory of Open Access Journals (Sweden)

    Arunabha Majumdar

    2018-02-01

    Full Text Available Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy. For a locus exhibiting overall pleiotropy, it is important to identify which specific traits underlie this association. We propose a Bayesian meta-analysis approach (termed CPBayes that uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. This method uses a unified Bayesian statistical framework based on a spike and slab prior. CPBayes performs a fully Bayesian analysis by employing the Markov Chain Monte Carlo (MCMC technique Gibbs sampling. It takes into account heterogeneity in the size and direction of the genetic effects across traits. It can be applied to both cohort data and separate studies of multiple traits having overlapping or non-overlapping subjects. Simulations show that CPBayes can produce higher accuracy in the selection of associated traits underlying a pleiotropic signal than the subset-based meta-analysis ASSET. We used CPBayes to undertake a genome-wide pleiotropic association study of 22 traits in the large Kaiser GERA cohort and detected six independent pleiotropic loci associated with at least two phenotypes. This includes a locus at chromosomal region 1q24.2 which exhibits an association simultaneously with the risk of five different diseases: Dermatophytosis, Hemorrhoids, Iron Deficiency, Osteoporosis and Peripheral Vascular Disease. We provide an R-package 'CPBayes' implementing the proposed method.

  20. Evaluation of Average Life Expectancy of Exposed Individuals and their offspring: Population Genetic Approach

    International Nuclear Information System (INIS)

    Telnov, V. I.; Sotnik, N. V.

    2004-01-01

    Average life expectancy (ALE) is a significant integrating indicator of the population health. It can be affected by many factors such as radiation and hereditary ones. A population-genetic analysis of the average life expectancy (ALE) was performed for nuclear workers at the Mayak Production. Association exposed to external and internal radiation over a wide dose range and their offspring. A methodical approach was proposed to determine ALE for individuals with different genotypes and estimate ALE in the population based on genotype distribution. The analysis of a number of genetic markers revealed significant changes in the age-specific pattern of the Hp types in workers over 60 years. Such changes were caused by both radiation and non-radiation (cardiovascular pathology) factors. In the first case ALE decreased as Hp 1-1 > Hp 2-2> Hp2-1 (radiation). In the second case, it decreased as Hp 1-1> Hp-2-1> Hp2-2 (non-radiation). analysis of genetic markers in the workers offspring indicated significant shifts in distribution of the Hp types, especially an increase in the proportion of Hp 2-2 at doses from external γ-rays over 200 cGy to parents by the time of conception. Based on the non-radiation genotype differences in ALE in this group of offspring, the preliminary calculation of ALE was carried out, which indicated its reduction by 0.52 years in comparison with the control. (Author) 21 refs

  1. Leveraging ethnic group incidence variation to investigate genetic susceptibility to glioma: A novel candidate SNP approach

    Directory of Open Access Journals (Sweden)

    Daniel Ian Jacobs

    2012-10-01

    Full Text Available Objectives: Using a novel candidate SNP approach, we aimed to identify a possible genetic basis for the higher glioma incidence in Whites relative to East Asians and African-Americans. Methods: We hypothesized that genetic regions containing SNPs with extreme differences in allele frequencies across ethnicities are most likely to harbor susceptibility variants. We used International HapMap Project data to identify 3,961 candidate SNPs with the largest allele frequency differences in Whites compared to East Asians and Africans and tested these SNPs for association with glioma risk in a set of White cases and controls. Top SNPs identified in the discovery dataset were tested for association with glioma in five independent replication datasets. Results: No SNP achieved statistical significance in either the discovery or replication datasets after accounting for multiple testing. However, the most strongly associated SNP, rs879471, was found to be in linkage disequilibrium with a previously identified risk SNP, rs6010620, in RTEL1. We estimate rs6010620 to account for a glioma incidence rate ratio of 1.34 for Whites relative to East Asians. Conclusions: We explored genetic susceptibility to glioma using a novel candidate SNP method which may be applicable to other diseases with appropriate epidemiologic patterns.

  2. Carcass characteristics, chemical composition and fatty acid profile of longissimus muscle of young bulls from four genetic groups finished in feedlot

    Directory of Open Access Journals (Sweden)

    Roberto Haruyoshi Ito

    2012-02-01

    Full Text Available This experiment was carried out to evaluate the carcass characteristics, chemical composition and fatty acid profile of the longissimus muscle of 32 young bulls from four genetic groups: Caracu; Canchin; Aberdeen Angus × Canchin; and Charolais × Caracu, finished in feedlot and slaughtered at 22 months old. Each group was composed of eight animals. There was no difference for moisture, ash, crude protein or total cholesterol between bulls from different genetic groups. However, total lipids percentage was higher for bulls from Caracu and Aberdeen Angus × Canchin and lower for Canchin and Charolais genetic groups. Polyunsaturated fattty acids and n-6 percentage was higher for Canchin and lower for Caracu, Aberdeen Angus × Canchin and Charolais genetic groups. Canchin and Charolais × Caracu genetic groups presented higher n-3 percentage than Caracu and Aberdeen Angus × Canchin. There was no difference for the n-6/n-3 ratio among the bulls from the four genetic groups.

  3. Tracing Technological Development Trajectories: A Genetic Knowledge Persistence-Based Main Path Approach.

    Directory of Open Access Journals (Sweden)

    Hyunseok Park

    Full Text Available The aim of this paper is to propose a new method to identify main paths in a technological domain using patent citations. Previous approaches for using main path analysis have greatly improved our understanding of actual technological trajectories but nonetheless have some limitations. They have high potential to miss some dominant patents from the identified main paths; nonetheless, the high network complexity of their main paths makes qualitative tracing of trajectories problematic. The proposed method searches backward and forward paths from the high-persistence patents which are identified based on a standard genetic knowledge persistence algorithm. We tested the new method by applying it to the desalination and the solar photovoltaic domains and compared the results to output from the same domains using a prior method. The empirical results show that the proposed method can dramatically reduce network complexity without missing any dominantly important patents. The main paths identified by our approach for two test cases are almost 10x less complex than the main paths identified by the existing approach. The proposed approach identifies all dominantly important patents on the main paths, but the main paths identified by the existing approach miss about 20% of dominantly important patents.

  4. Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing.

    Science.gov (United States)

    Chakravarti, Deboki; Cho, Jang Hwan; Weinberg, Benjamin H; Wong, Nicole M; Wong, Wilson W

    2016-04-18

    Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.

  5. A Parallel Approach To Optimum Actuator Selection With a Genetic Algorithm

    Science.gov (United States)

    Rogers, James L.

    2000-01-01

    Recent discoveries in smart technologies have created a variety of aerodynamic actuators which have great potential to enable entirely new approaches to aerospace vehicle flight control. For a revolutionary concept such as a seamless aircraft with no moving control surfaces, there is a large set of candidate locations for placing actuators, resulting in a substantially larger number of combinations to examine in order to find an optimum placement satisfying the mission requirements. The placement of actuators on a wing determines the control effectiveness of the airplane. One approach to placement Maximizes the moments about the pitch, roll, and yaw axes, while minimizing the coupling. Genetic algorithms have been instrumental in achieving good solutions to discrete optimization problems, such as the actuator placement problem. As a proof of concept, a genetic has been developed to find the minimum number of actuators required to provide uncoupled pitch, roll, and yaw control for a simplified, untapered, unswept wing model. To find the optimum placement by searching all possible combinations would require 1,100 hours. Formulating the problem and as a multi-objective problem and modifying it to take advantage of the parallel processing capabilities of a multi-processor computer, reduces the optimization time to 22 hours.

  6. A systematic approach to assessing the clinical significance of genetic variants.

    Science.gov (United States)

    Duzkale, H; Shen, J; McLaughlin, H; Alfares, A; Kelly, M A; Pugh, T J; Funke, B H; Rehm, H L; Lebo, M S

    2013-11-01

    Molecular genetic testing informs diagnosis, prognosis, and risk assessment for patients and their family members. Recent advances in low-cost, high-throughput DNA sequencing and computing technologies have enabled the rapid expansion of genetic test content, resulting in dramatically increased numbers of DNA variants identified per test. To address this challenge, our laboratory has developed a systematic approach to thorough and efficient assessments of variants for pathogenicity determination. We first search for existing data in publications and databases including internal, collaborative and public resources. We then perform full evidence-based assessments through statistical analyses of observations in the general population and disease cohorts, evaluation of experimental data from in vivo or in vitro studies, and computational predictions of potential impacts of each variant. Finally, we weigh all evidence to reach an overall conclusion on the potential for each variant to be disease causing. In this report, we highlight the principles of variant assessment, address the caveats and pitfalls, and provide examples to illustrate the process. By sharing our experience and providing a framework for variant assessment, including access to a freely available customizable tool, we hope to help move towards standardized and consistent approaches to variant assessment. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. A practical approach to screen for authorised and unauthorised genetically modified plants.

    Science.gov (United States)

    Waiblinger, Hans-Ulrich; Grohmann, Lutz; Mankertz, Joachim; Engelbert, Dirk; Pietsch, Klaus

    2010-03-01

    In routine analysis, screening methods based on real-time PCR are most commonly used for the detection of genetically modified (GM) plant material in food and feed. In this paper, it is shown that the combination of five DNA target sequences can be used as a universal screening approach for at least 81 GM plant events authorised or unauthorised for placing on the market and described in publicly available databases. Except for maize event LY038, soybean events DP-305423 and BPS-CV127-9 and cotton event 281-24-236 x 3006-210-23, at least one of the five genetic elements has been inserted in these GM plants and is targeted by this screening approach. For the detection of these sequences, fully validated real-time PCR methods have been selected. A screening table is presented that describes the presence or absence of the target sequences for most of the listed GM plants. These data have been verified either theoretically according to available databases or experimentally using available reference materials. The screening table will be updated regularly by a network of German enforcement laboratories.

  8. Process planning optimization on turning machine tool using a hybrid genetic algorithm with local search approach

    Directory of Open Access Journals (Sweden)

    Yuliang Su

    2015-04-01

    Full Text Available A turning machine tool is a kind of new type of machine tool that is equipped with more than one spindle and turret. The distinctive simultaneous and parallel processing abilities of turning machine tool increase the complexity of process planning. The operations would not only be sequenced and satisfy precedence constraints, but also should be scheduled with multiple objectives such as minimizing machining cost, maximizing utilization of turning machine tool, and so on. To solve this problem, a hybrid genetic algorithm was proposed to generate optimal process plans based on a mixed 0-1 integer programming model. An operation precedence graph is used to represent precedence constraints and help generate a feasible initial population of hybrid genetic algorithm. Encoding strategy based on data structure was developed to represent process plans digitally in order to form the solution space. In addition, a local search approach for optimizing the assignments of available turrets would be added to incorporate scheduling with process planning. A real-world case is used to prove that the proposed approach could avoid infeasible solutions and effectively generate a global optimal process plan.

  9. A novel approach: chemical relational databases, and the role of the ISSCAN database on assessing chemical carcinogenicity.

    Science.gov (United States)

    Benigni, Romualdo; Bossa, Cecilia; Richard, Ann M; Yang, Chihae

    2008-01-01

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did not contain chemical structures. Concepts and technologies originated from the structure-activity relationships science have provided powerful tools to create new types of databases, where the effective linkage of chemical toxicity with chemical structure can facilitate and greatly enhance data gathering and hypothesis generation, by permitting: a) exploration across both chemical and biological domains; and b) structure-searchability through the data. This paper reviews the main public databases, together with the progress in the field of chemical relational databases, and presents the ISSCAN database on experimental chemical carcinogens.

  10. Estimation of the effects of chemical mutagens: lessons from radiation genetics

    International Nuclear Information System (INIS)

    Wolff, S.; Calfornia Univ., Los Angeles

    1975-01-01

    Years of work with ionizing radiations have produced a wealth of data on radiation-induced mutations. These data, which have given insights regarding the mutational processes, should form the background for all mutagenesis work. In chemical mutagenesis, as in radiation mutagenesis, it is important to know the shape of the dose-effect curve in order to make further interpretations and calculations. It is also important to be on the constant alert for new relations that can be explored

  11. Human genetic marker for resistance to radiations and chemicals. 1998 annual progress report

    International Nuclear Information System (INIS)

    Lieberman, H.B.

    1998-01-01

    'The broad objective of the project is to understand the molecular basis for the response of cells to radiations and chemicals, with the pragmatic goal of being able to identify human subpopulations that are exceptionally sensitive to DNA damaging agents. The project focuses on HRAD9, a human orthologue of the fission yeast Schizosaccharomyces pombe gene rad9. S. pombe rad9::ura4+ mutant cells are highly sensitive to ionizing radiation, UV and many chemicals, such as the DNA synthesis inhibitor hydroxyurea. They also lack the ability to delay cycling transiently in S phase or in G2 following a block in DNA replication or after incurring DNA damage, respectively -i.e., they lack checkpoint controls. The attempt by mutant cells to progress through mitosis in the absence of fully intact DNA accounts at least in part for their sensitivity to DNA damaging agents. Cells bearing rad9::ura4+ also aberrantly regulate UVDE, an enzyme that participates in a secondary DNA excision repair pathway. The key role played by S. pombe rad9 in promoting resistance to chemicals and radiations suggests that the evolutionarily conserved human cognate also has important functions in mammals. The first set of aims in this proposal centers on characterizing the structure and expression of HRAD9, to assess structure/function relationships and potentially link protein activity to a specific tissue. The next set of aims focuses on determining the role of HRAD9 in radio/chemoresponsiveness and cancer.'

  12. Epigenetic and genetic factors in the cellular response to radiations and DNA-damaging chemicals

    International Nuclear Information System (INIS)

    Williams, J.R.; D'Arpa, P.

    1981-01-01

    DNA-damaging agents are widely used as therapeutic tools for a variety of disease states. Many such agents are considered to produce detrimental side effects. Thus, it is important to evaluate both therapeutic efficacy and potential risk. DNA-damaging agents can be so evaluated by comparison to agents whose therapeutic benefit and potential hazards are better known. We propose a framework for such comparison, demonstrating that a simple transformation of cytotoxicity-dose response patterns permits a facile comparison of variation between cells exposed to a single DNA-damaging agent or to different cytotoxic agents. Further, by transforming data from experiments which compare responses of 2 cell populations to an effects ratio, different patterns for the changes in cytotoxicity produced by epigenetic and genetic factors were compared. Using these transformations, we found that there is a wide variation (a factor of 4) between laboratories for a single agent (UVC) and only a slightly larger variation (factor of 6) between normal cell response for different types of DNA-damaging agents (x-ray, UVC, alkylating agents, crosslinking agents). Epigenetic factors such as repair and recovery appear to be a factor only at higher dose levels. Comparison in the cytotoxic effect of a spectrum of DNA-damaging agents in xeroderma pigmentosum, ataxia telangiectasia, and Fanconi's anemia cells indicates significantly different patterns, implying that the effect, and perhaps the nature, of these genetic conditions are quite different

  13. Recognition of chemical entities: combining dictionary-based and grammar-based approaches

    Science.gov (United States)

    2015-01-01

    Background The past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstructured texts. The BioCreative CHEMDNER challenge invites the development of systems for the automatic recognition of chemicals in text (CEM task) and for ranking the recognized compounds at the document level (CDI task). We investigated an ensemble approach where dictionary-based named entity recognition is used along with grammar-based recognizers to extract compounds from text. We assessed the performance of ten different commercial and publicly available lexical resources using an open source indexing system (Peregrine), in combination with three different chemical compound recognizers and a set of regular expressions to recognize chemical database identifiers. The effect of different stop-word lists, case-sensitivity matching, and use of chunking information was also investigated. We focused on lexical resources that provide chemical structure information. To rank the different compounds found in a text, we used a term confidence score based on the normalized ratio of the term frequencies in chemical and non-chemical journals. Results The use of stop-word lists greatly improved the performance of the dictionary-based recognition, but there was no additional benefit from using chunking information. A combination of ChEBI and HMDB as lexical resources, the LeadMine tool for grammar-based recognition, and the regular expressions, outperformed any of the individual systems. On the test set, the F-scores were 77.8% (recall 71.2%, precision 85.8%) for the CEM task and 77.6% (recall 71.7%, precision 84.6%) for the CDI task. Missed terms were mainly due to tokenization issues, poor recognition of formulas, and term conjunctions. Conclusions We developed an ensemble system that combines dictionary-based and grammar-based approaches for chemical named

  14. Recognition of chemical entities: combining dictionary-based and grammar-based approaches.

    Science.gov (United States)

    Akhondi, Saber A; Hettne, Kristina M; van der Horst, Eelke; van Mulligen, Erik M; Kors, Jan A

    2015-01-01

    The past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstructured texts. The BioCreative CHEMDNER challenge invites the development of systems for the automatic recognition of chemicals in text (CEM task) and for ranking the recognized compounds at the document level (CDI task). We investigated an ensemble approach where dictionary-based named entity recognition is used along with grammar-based recognizers to extract compounds from text. We assessed the performance of ten different commercial and publicly available lexical resources using an open source indexing system (Peregrine), in combination with three different chemical compound recognizers and a set of regular expressions to recognize chemical database identifiers. The effect of different stop-word lists, case-sensitivity matching, and use of chunking information was also investigated. We focused on lexical resources that provide chemical structure information. To rank the different compounds found in a text, we used a term confidence score based on the normalized ratio of the term frequencies in chemical and non-chemical journals. The use of stop-word lists greatly improved the performance of the dictionary-based recognition, but there was no additional benefit from using chunking information. A combination of ChEBI and HMDB as lexical resources, the LeadMine tool for grammar-based recognition, and the regular expressions, outperformed any of the individual systems. On the test set, the F-scores were 77.8% (recall 71.2%, precision 85.8%) for the CEM task and 77.6% (recall 71.7%, precision 84.6%) for the CDI task. Missed terms were mainly due to tokenization issues, poor recognition of formulas, and term conjunctions. We developed an ensemble system that combines dictionary-based and grammar-based approaches for chemical named entity recognition, outperforming

  15. Testing of chemicals for genetic activity with Saccharomyces cerevisiae: a report of the U. S. Environmental Protection Agency Gene-Tox Program

    Energy Technology Data Exchange (ETDEWEB)

    Zimmermann, F.K.; von Borstel, R.C.; von Halle, E.S.; Parry, J.M.; Siebert, D.; Zetterberg, G.; Barale, R.; Loprieno, N.

    1984-01-01

    This review article with over 200 references summarizes the results of mutation screening tests with 492 chemicals using saccharomyces cerevisiae as the test organism. In addition, an extensive description of S. cerevisiae as a test organism is given. Yeast can be used to study genetic effects both in mitotic and in meiotic cells because it can be cultured as a stable haploid or a stable diploid. The most commonly used genetic endpoint has been mitotic recombination either as mitotic crossing-over or mitotic gene conversion. Data were available on tests with 492 chemicals, of which 249 were positive, as reported in 173 articles or reports. The genetic test/carcinogenicity accuracy was 0.74, based on the carcinogen listing established in the gene-tox program. The yeast tests supplement the bacterial tests for detecting agents that act via radical formation, antibacterial drugs, and other chemicals interfering with chromosome segregation and recombination processes.

  16. Chemical entity recognition in patents by combining dictionary-based and statistical approaches

    Science.gov (United States)

    Akhondi, Saber A.; Pons, Ewoud; Afzal, Zubair; van Haagen, Herman; Becker, Benedikt F.H.; Hettne, Kristina M.; van Mulligen, Erik M.; Kors, Jan A.

    2016-01-01

    We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistical one. For this purpose the performance of several lexical resources was assessed using Peregrine, our open-source indexing engine. We combined our dictionary-based results on the patent corpus with the results of tmChem, a chemical recognizer using a conditional random field classifier. To improve the performance of tmChem, we utilized three additional features, viz. part-of-speech tags, lemmas and word-vector clusters. When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, the best system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second among nine teams for CPD with an accuracy of 94.23%. The differences in performance between the best ensemble system and the statistical system separately were small. Database URL: http://biosemantics.org/chemdner-patents PMID:27141091

  17. Chemical entity recognition in patents by combining dictionary-based and statistical approaches.

    Science.gov (United States)

    Akhondi, Saber A; Pons, Ewoud; Afzal, Zubair; van Haagen, Herman; Becker, Benedikt F H; Hettne, Kristina M; van Mulligen, Erik M; Kors, Jan A

    2016-01-01

    We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistical one. For this purpose the performance of several lexical resources was assessed using Peregrine, our open-source indexing engine. We combined our dictionary-based results on the patent corpus with the results of tmChem, a chemical recognizer using a conditional random field classifier. To improve the performance of tmChem, we utilized three additional features, viz. part-of-speech tags, lemmas and word-vector clusters. When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, the best system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second among nine teams for CPD with an accuracy of 94.23%. The differences in performance between the best ensemble system and the statistical system separately were small.Database URL: http://biosemantics.org/chemdner-patents. © The Author(s) 2016. Published by Oxford University Press.

  18. A New Spectral Shape-Based Record Selection Approach Using Np and Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Edén Bojórquez

    2013-01-01

    Full Text Available With the aim to improve code-based real records selection criteria, an approach inspired in a parameter proxy of spectral shape, named Np, is analyzed. The procedure is based on several objectives aimed to minimize the record-to-record variability of the ground motions selected for seismic structural assessment. In order to select the best ground motion set of records to be used as an input for nonlinear dynamic analysis, an optimization approach is applied using genetic algorithms focuse on finding the set of records more compatible with a target spectrum and target Np values. The results of the new Np-based approach suggest that the real accelerograms obtained with this procedure, reduce the scatter of the response spectra as compared with the traditional approach; furthermore, the mean spectrum of the set of records is very similar to the target seismic design spectrum in the range of interest periods, and at the same time, similar Np values are obtained for the selected records and the target spectrum.

  19. Pre-emptive resource-constrained multimode project scheduling using genetic algorithm: A dynamic forward approach

    Directory of Open Access Journals (Sweden)

    Aidin Delgoshaei

    2016-09-01

    Full Text Available Purpose: The issue resource over-allocating is a big concern for project engineers in the process of scheduling project activities. Resource over-allocating drawback is frequently seen after scheduling of a project in practice which causes a schedule to be useless. Modifying an over-allocated schedule is very complicated and needs a lot of efforts and time. In this paper, a new and fast tracking method is proposed to schedule large scale projects which can help project engineers to schedule the project rapidly and with more confidence. Design/methodology/approach: In this article, a forward approach for maximizing net present value (NPV in multi-mode resource constrained project scheduling problem while assuming discounted positive cash flows (MRCPSP-DCF is proposed. The progress payment method is used and all resources are considered as pre-emptible. The proposed approach maximizes NPV using unscheduled resources through resource calendar in forward mode. For this purpose, a Genetic Algorithm is applied to solve. Findings: The findings show that the proposed method is an effective way to maximize NPV in MRCPSP-DCF problems while activity splitting is allowed. The proposed algorithm is very fast and can schedule experimental cases with 1000 variables and 100 resources in few seconds. The results are then compared with branch and bound method and simulated annealing algorithm and it is found the proposed genetic algorithm can provide results with better quality. Then algorithm is then applied for scheduling a hospital in practice. Originality/value: The method can be used alone or as a macro in Microsoft Office Project® Software to schedule MRCPSP-DCF problems or to modify resource over-allocated activities after scheduling a project. This can help project engineers to schedule project activities rapidly with more accuracy in practice.

  20. Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters.

    Science.gov (United States)

    Germond, Arno; Fujita, Hideaki; Ichimura, Taro; Watanabe, Tomonobu M

    2016-06-01

    Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from fluorescent proteins. GE sensors are now used to study biological phenomena by facilitating the measurement of biochemical behaviors at various scales, ranging from single molecules to single cells or even whole animals. Here, we review the historical development of GE fluorescent sensors and report on their current status. We specifically focus on the development strategies of the GE sensors used for measuring pH, ion concentrations (e.g., chloride and calcium), redox indicators, membrane potential, temperature, pressure, and molecular crowding. We demonstrate that these fluroescent protein-based sensors have a shared history of concepts and development strategies, and we highlight the most original concepts used to date. We believe that the understanding and application of these various concepts will pave the road for the development of future GE sensors and lead to new breakthroughs in bioimaging.

  1. Genetic interpretations of elemental and chemical differences in a soil chronosequence, California

    Science.gov (United States)

    Harden, J.W.

    1988-01-01

    Soils developed on fluvial terraces in central California have similar parent materials, climatic settings, vegetation cover and slopes but range in age from 40,000 to 3,000,000 years. The soils have chemical compositions that change systematically with increasing age. Such chemical differentiation is most likely the result of long-term weathering and mineralogical transformations that occurred since deposition of terrace fills and stabilization of the geomorphic surfaces. The changes in composition with time closely mimic other studies on mineral weathering, in which alkali and alkali-earth elements are lost more rapidly than transitional elements. The relative rates of element loss were determined by changes in element ratios over time. Net losses and gains of elements in different size fractions were monitored by their concentrations relative to Zr, the most stable constituent. Both sand and finer size fractions have lost considerable amounts of Ca, Mg, Na and K. Aluminum appears to have been lost from the sand fraction and gained in the fine fraction over a 3-million-year-time-span. Although there is no evidence for losses of Fe and Ti from sands, there is a net influx of Fe and Ti into finer fractions, probably gained from undetectable yet significant weathering of sand grains. Etching of sand grains, clay mineralogy, and microprobe analyses also indicate that the soils have undergone these chemical transformations during their formation. Mineralogical analyses also mimic other studies on mineral weathering, in which the pyroxenes weather more rapidly than hornblende, which weathers more rapidly than sphene or zircon. ?? 1988.

  2. Chemical Exposure Assessment Program at Los Alamos National Laboratory: A risk based approach

    International Nuclear Information System (INIS)

    Stephenson, D.J.

    1996-01-01

    The University of California Contract And DOE Order 5480.10 require that Los Alamos National Laboratory (LANL) perform health hazard assessments/inventories of all employee workplaces. In response to this LANL has developed the Chemical Exposure Assessment Program. This program provides a systematic risk-based approach to anticipation, recognition, evaluation and control of chemical workplace exposures. Program implementation focuses resources on exposures with the highest risks for causing adverse health effects. Implementation guidance includes procedures for basic characterization, qualitative risk assessment, quantitative validation, and recommendations and reevaluation. Each component of the program is described. It is shown how a systematic method of assessment improves documentation, retrieval, and use of generated exposure information

  3. A multi target approach to control chemical reactions in their inhomogeneous solvent environment

    International Nuclear Information System (INIS)

    Keefer, Daniel; Thallmair, Sebastian; Zauleck, Julius P P; Vivie-Riedle, Regina de

    2015-01-01

    Shaped laser pulses offer a powerful tool to manipulate molecular quantum systems. Their application to chemical reactions in solution is a promising concept to redesign chemical synthesis. Along this road, theoretical developments to include the solvent surrounding are necessary. An appropriate theoretical treatment is helpful to understand the underlying mechanisms. In our approach we simulate the solvent by randomly selected snapshots from molecular dynamics trajectories. We use multi target optimal control theory to optimize pulses for the various arrangements of explicit solvent molecules simultaneously. This constitutes a major challenge for the control algorithm, as the solvent configurations introduce a large inhomogeneity to the potential surfaces. We investigate how the algorithm handles the new challenges and how well the controllability of the system is preserved with increasing complexity. Additionally, we introduce a way to statistically estimate the efficiency of the optimized laser pulses in the complete thermodynamical ensemble. (paper)

  4. A genetic algorithm approach to optimization for the radiological worker allocation problem

    International Nuclear Information System (INIS)

    Yan Chen; Masakuni Narita; Masashi Tsuji; Sangduk Sa

    1996-01-01

    The worker allocation optimization problem in radiological facilities inevitably involves various types of requirements and constraints relevant to radiological protection and labor management. Some of these goals and constraints are not amenable to a rigorous mathematical formulation. Conventional methods for this problem rely heavily on sophisticated algebraic or numerical algorithms, which cause difficulties in the search for optimal solutions in the search space of worker allocation optimization problems. Genetic algorithms (GAB) are stochastic search algorithms introduced by J. Holland in the 1970s based on ideas and techniques from genetic and evolutionary theories. The most striking characteristic of GAs is the large flexibility allowed in the formulation of the optimal problem and the process of the search for the optimal solution. In the formulation, it is not necessary to define the optimal problem in rigorous mathematical terms, as required in the conventional methods. Furthermore, by designing a model of evolution for the optimal search problem, the optimal solution can be sought efficiently with computational simple manipulations without highly complex mathematical algorithms. We reported a GA approach to the worker allocation problem in radiological facilities in the previous study. In this study, two types of hard constraints were employed to reduce the huge search space, where the optimal solution is sought in such a way as to satisfy as many of soft constraints as possible. It was demonstrated that the proposed evolutionary method could provide the optimal solution efficiently compared with conventional methods. However, although the employed hard constraints could localize the search space into a very small region, it brought some complexities in the designed genetic operators and demanded additional computational burdens. In this paper, we propose a simplified evolutionary model with less restrictive hard constraints and make comparisons between

  5. A nuclear reload optimization approach using a real coded genetic algorithm with random keys

    International Nuclear Information System (INIS)

    Lima, Alan M.M. de; Schirru, Roberto; Medeiros, Jose A.C.C.

    2009-01-01

    The fuel reload of a Pressurized Water Reactor is made whenever the burn up of the fuel assemblies in the nucleus of the reactor reaches a certain value such that it is not more possible to maintain a critical reactor producing energy at nominal power. The problem of fuel reload optimization consists on determining the positioning of the fuel assemblies within the nucleus of the reactor in an optimized way to minimize the cost benefit relationship of fuel assemblies cost per maximum burn up, and also satisfying symmetry and safety restrictions. The fuel reload optimization problem difficulty grows exponentially with the number of fuel assemblies in the nucleus of the reactor. During decades the fuel reload optimization problem was solved manually by experts that used their knowledge and experience to build configurations of the reactor nucleus, and testing them to verify if safety restrictions of the plant are satisfied. To reduce this burden, several optimization techniques have been used, included the binary code genetic algorithm. In this work we show the use of a real valued coded approach of the genetic algorithm, with different recombination methods, together with a transformation mechanism called random keys, to transform the real values of the genes of each chromosome in a combination of discrete fuel assemblies for evaluation of the reload optimization. Four different recombination methods were tested: discrete recombination, intermediate recombination, linear recombination and extended linear recombination. For each of the 4 recombination methods 10 different tests using different seeds for the random number generator were conducted 10 generating, totaling 40 tests. The results of the application of the genetic algorithm are shown with formulation of real numbers for the problem of the nuclear reload of the plant Angra 1 type PWR. Since the best results in the literature for this problem were found by the parallel PSO we will it use for comparison

  6. Physics-based approach to chemical source localization using mobile robotic swarms

    Science.gov (United States)

    Zarzhitsky, Dimitri

    2008-07-01

    Recently, distributed computation has assumed a dominant role in the fields of artificial intelligence and robotics. To improve system performance, engineers are combining multiple cooperating robots into cohesive collectives called swarms. This thesis illustrates the application of basic principles of physicomimetics, or physics-based design, to swarm robotic systems. Such principles include decentralized control, short-range sensing and low power consumption. We show how the application of these principles to robotic swarms results in highly scalable, robust, and adaptive multi-robot systems. The emergence of these valuable properties can be predicted with the help of well-developed theoretical methods. In this research effort, we have designed and constructed a distributed physicomimetics system for locating sources of airborne chemical plumes. This task, called chemical plume tracing (CPT), is receiving a great deal of attention due to persistent homeland security threats. For this thesis, we have created a novel CPT algorithm called fluxotaxis that is based on theoretical principles of fluid dynamics. Analytically, we show that fluxotaxis combines the essence, as well as the strengths, of the two most popular biologically-inspired CPT methods-- chemotaxis and anemotaxis. The chemotaxis strategy consists of navigating in the direction of the chemical density gradient within the plume, while the anemotaxis approach is based on an upwind traversal of the chemical cloud. Rigorous and extensive experimental evaluations have been performed in simulated chemical plume environments. Using a suite of performance metrics that capture the salient aspects of swarm-specific behavior, we have been able to evaluate and compare the three CPT algorithms. We demonstrate the improved performance of our fluxotaxis approach over both chemotaxis and anemotaxis in these realistic simulation environments, which include obstacles. To test our understanding of CPT on actual hardware

  7. Alteration of Asian lacquer: in-depth insight using a physico-chemical multiscale approach.

    Science.gov (United States)

    Le Hô, Anne-Solenn; Duhamel, Chloé; Daher, Céline; Bellot-Gurlet, Ludovic; Paris, Céline; Regert, Martine; Sablier, Michel; André, Guilhem; Desroches, Jean-Paul; Dumas, Paul

    2013-10-07

    Oriental lacquer has been used in Asian countries for thousands of years as a durable and aesthetic coating material for its adhesive, consolidating, protective and decorative properties. Although these objects are made from an unusual material in Occident, Western museum collections host many lacquerwares. Curators, restorers and scientists are daily confronted with questions of their conservation and their alteration. The characterization of their conservation state is usually assessed through visual observations. However deterioration often starts at the microscopic level and cannot be detected by a simple visual inspection. Often, ageing and deterioration of artworks are connected to physical, mechanical and chemical transformations. Thus new insight into alteration of lacquer involves the monitoring of macro-, microscopic and molecular modifications, and this can be assessed from physico-chemical measurements. Non-invasive (microtopography and Scanning Electron Microscopy - SEM) and micro-invasive (infrared micro-spectroscopy using a synchrotron source - SR-μFTIR) investigations were performed to study the degradation processes of lacquers and evaluate their level of alteration. In particular, spectral decomposition and fitting procedure were performed in the 1820-1520 cm(-1) region to follow the shift of the C=O and C=C band positions during lacquer ageing. The present work proves the potential of this physico-chemical approach in conservation studies of lacquers and in the quantification of the state of alteration. It evidences chemical phenomena of alteration such as oxidation and decomposition of a lacquer polymeric network. It also demonstrates for the first time the degradation front of artificially aged lacquer and the chemical imaging of a more than 2000 years old archaeological lacquer by using SR-μFTIR.

  8. Modeling the binding affinity of structurally diverse industrial chemicals to carbon using the artificial intelligence approaches.

    Science.gov (United States)

    Gupta, Shikha; Basant, Nikita; Rai, Premanjali; Singh, Kunwar P

    2015-11-01

    Binding affinity of chemical to carbon is an important characteristic as it finds vast industrial applications. Experimental determination of the adsorption capacity of diverse chemicals onto carbon is both time and resource intensive, and development of computational approaches has widely been advocated. In this study, artificial intelligence (AI)-based ten different qualitative and quantitative structure-property relationship (QSPR) models (MLPN, RBFN, PNN/GRNN, CCN, SVM, GEP, GMDH, SDT, DTF, DTB) were established for the prediction of the adsorption capacity of structurally diverse chemicals to activated carbon following the OECD guidelines. Structural diversity of the chemicals and nonlinear dependence in the data were evaluated using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation procedures performed employing a wide series of statistical checks. In complete dataset, the qualitative models rendered classification accuracies between 97.04 and 99.93%, while the quantitative models yielded correlation (R(2)) values of 0.877-0.977 between the measured and the predicted endpoint values. The quantitative prediction accuracies for the higher molecular weight (MW) compounds (class 4) were relatively better than those for the low MW compounds. Both in the qualitative and quantitative models, the Polarizability was the most influential descriptor. Structural alerts responsible for the extreme adsorption behavior of the compounds were identified. Higher number of carbon and presence of higher halogens in a molecule rendered higher binding affinity. Proposed QSPR models performed well and outperformed the previous reports. A relatively better performance of the ensemble learning models (DTF, DTB) may be attributed to the strengths of the bagging and boosting algorithms which enhance the predictive accuracies. The

  9. [New approaches to early diagnosis of chronic organophosphorus chemicals intoxication in workers at chemical weapons extermination objects].

    Science.gov (United States)

    Babakov, V N; Goncharov, N V; Radilov, A S; Glashkina, E P; Podol'skaia, E P; Ermolaeva, E E; Shilov, V V; Prokof'eva, D S; Voĭtenko, N G; Egorov, N A

    2009-01-01

    Mass spectrum analysis revealed differences in general contents of low-molecular peptides spectrums in chemical weapons extermination object staffers, in comparison with the reference group. Findings are that serum paraoxonase activity in chemical weapons extermination object staffers in significantly increased.

  10. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches

    DEFF Research Database (Denmark)

    Ugelvig, Line; Drijfhout, Falko; Kronauer, Daniel

    2008-01-01

    BACKGROUND: The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 po...

  11. A bayesian approach to inferring the genetic population structure of sugarcane accessions from INTA (Argentina

    Directory of Open Access Journals (Sweden)

    Mariana Inés Pocovi

    2015-06-01

    Full Text Available Understanding the population structure and genetic diversity in sugarcane (Saccharum officinarum L. accessions from INTA germplasm bank (Argentina will be of great importance for germplasm collection and breeding improvement as it will identify diverse parental combinations to create segregating progenies with maximum genetic variability for further selection. A Bayesian approach, ordination methods (PCoA, Principal Coordinate Analysis and clustering analysis (UPGMA, Unweighted Pair Group Method with Arithmetic Mean were applied to this purpose. Sixty three INTA sugarcane hybrids were genotyped for 107 Simple Sequence Repeat (SSR and 136 Amplified Fragment Length Polymorphism (AFLP loci. Given the low probability values found with AFLP for individual assignment (4.7%, microsatellites seemed to perform better (54% for STRUCTURE analysis that revealed the germplasm to exist in five optimum groups with partly corresponding to their origin. However clusters shown high degree of admixture, F ST values confirmed the existence of differences among groups. Dissimilarity coefficients ranged from 0.079 to 0.651. PCoA separated sugarcane in groups that did not agree with those identified by STRUCTURE. The clustering including all genotypes neither showed resemblance to populations find by STRUCTURE, but clustering performed considering only individuals displaying a proportional membership > 0.6 in their primary population obtained with STRUCTURE showed close similarities. The Bayesian method indubitably brought more information on cultivar origins than classical PCoA and hierarchical clustering method.

  12. Intracellular, genetic or congenital immunisation--transgenic approaches to increase disease resistance of farm animals.

    Science.gov (United States)

    Müller, M; Brem, G

    1996-01-26

    Novel approaches to modify disease resistance or susceptibility in livestock are justified not only by economical reasons and with respect to animal welfare but also by recent advancements in molecular genetics. The control or elimination of infectious pathogens in farm animals is historically achieved by the use of vaccines and drugs and by quarantine safeguards and eradication. Currently, research on the improvement of disease resistance based on nucleic acid technology focuses on two main issues: additive gene transfer and the development of nucleic acid vaccines. The strategies aim at the stable or transient expression of components known to influence non-specific or specific host defence mechanisms against infectious pathogens. Thus, candidates for gene transfer experiments include all genes inducing or conferring innate and acquired immunity as well as specific disease resistance genes. Referring to the site and mode of action and the source of the effective agent the strategies are termed 'intracellular', 'genetic' and 'congenital' immunisation. The targeted disruption (deletive gene transfer) of disease susceptibility genes awaits the establishment of totipotential embryonic cell lineages in farm animals. The cytokine network regulates cellular viability, growth and differentiation in physiological and pathophysiological states. The identification of the JAK-STAT pathway used by many cytokines for their intracellular signal propagation has provided not only new target molecules for modulating the immune response but will also permit the further elucidation of host-pathogen interactions and resistance mechanisms.

  13. Pollen Sterility—A Promising Approach to Gene Confinement and Breeding for Genetically Modified Bioenergy Crops

    Directory of Open Access Journals (Sweden)

    Albert P. Kausch

    2012-10-01

    Full Text Available Advanced genetic and biotechnology tools will be required to realize the full potential of food and bioenergy crops. Given current regulatory concerns, many transgenic traits might never be deregulated for commercial release without a robust gene confinement strategy in place. The potential for transgene flow from genetically modified (GM crops is widely known. Pollen-mediated transfer is a major component of gene flow in flowering plants and therefore a potential avenue for the escape of transgenes from GM crops. One approach for preventing and/or mitigating transgene flow is the production of trait linked pollen sterility. To evaluate the feasibility of generating pollen sterility lines for gene confinement and breeding purposes we tested the utility of a promoter (Zm13Pro from a maize pollen-specific gene (Zm13 for driving expression of the reporter gene GUS and the cytotoxic gene barnase in transgenic rice (Oryza sativa ssp. Japonica cv. Nipponbare as a monocot proxy for bioenergy grasses. This study demonstrates that the Zm13 promoter can drive pollen-specific expression in stably transformed rice and may be useful for gametophytic transgene confinement and breeding strategies by pollen sterility in food and bioenergy crops.

  14. A Reverse Genetics Approach for the Design of Methyltransferase-Defective Live Attenuated Avian Metapneumovirus Vaccines.

    Science.gov (United States)

    Zhang, Yu; Sun, Jing; Wei, Yongwei; Li, Jianrong

    2016-01-01

    Avian metapneumovirus (aMPV), also known as avian pneumovirus or turkey rhinotracheitis virus, is the causative agent of turkey rhinotracheitis and is associated with swollen head syndrome in chickens. aMPV belongs to the family Paramyxoviridae which includes many important human pathogens such as human respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and human parainfluenza virus type 3 (PIV3). The family also includes highly lethal emerging pathogens such as Nipah virus and Hendra virus, as well as agriculturally important viruses such as Newcastle disease virus (NDV). For many of these viruses, there is no effective vaccine. Here, we describe a reverse genetics approach to develop live attenuated aMPV vaccines by inhibiting the viral mRNA cap methyltransferase. The viral mRNA cap methyltransferase is an excellent target for the attenuation of paramyxoviruses because it plays essential roles in mRNA stability, efficient viral protein translation and innate immunity. We have described in detail the materials and methods used to generate recombinant aMPVs that lack viral mRNA cap methyltransferase activity. We have also provided methods to evaluate the genetic stability, pathogenesis, and immunogenicity of live aMPV vaccine candidates in turkeys.

  15. Integrating high-content imaging and chemical genetics to probe host cellular pathways critical for Yersinia pestis infection.

    Directory of Open Access Journals (Sweden)

    Krishna P Kota

    Full Text Available The molecular machinery that regulates the entry and survival of Yersinia pestis in host macrophages is poorly understood. Here, we report the development of automated high-content imaging assays to quantitate the internalization of virulent Y. pestis CO92 by macrophages and the subsequent activation of host NF-κB. Implementation of these assays in a focused chemical screen identified kinase inhibitors that inhibited both of these processes. Rac-2-ethoxy-3 octadecanamido-1-propylphosphocholine (a protein Kinase C inhibitor, wortmannin (a PI3K inhibitor, and parthenolide (an IκB kinase inhibitor, inhibited pathogen-induced NF-κB activation and reduced bacterial entry and survival within macrophages. Parthenolide inhibited NF-κB activation in response to stimulation with Pam3CSK4 (a TLR2 agonist, E. coli LPS (a TLR4 agonist or Y. pestis infection, while the PI3K and PKC inhibitors were selective only for Y. pestis infection. Together, our results suggest that phagocytosis is the major stimulus for NF-κB activation in response to Y. pestis infection, and that Y. pestis entry into macrophages may involve the participation of protein kinases such as PI3K and PKC. More importantly, the automated image-based screening platform described here can be applied to the study of other bacteria in general and, in combination with chemical genetic screening, can be used to identify host cell functions facilitating the identification of novel antibacterial therapeutics.

  16. An Interval-Valued Approach to Business Process Simulation Based on Genetic Algorithms and the BPMN

    Directory of Open Access Journals (Sweden)

    Mario G.C.A. Cimino

    2014-05-01

    Full Text Available Simulating organizational processes characterized by interacting human activities, resources, business rules and constraints, is a challenging task, because of the inherent uncertainty, inaccuracy, variability and dynamicity. With regard to this problem, currently available business process simulation (BPS methods and tools are unable to efficiently capture the process behavior along its lifecycle. In this paper, a novel approach of BPS is presented. To build and manage simulation models according to the proposed approach, a simulation system is designed, developed and tested on pilot scenarios, as well as on real-world processes. The proposed approach exploits interval-valued data to represent model parameters, in place of conventional single-valued or probability-valued parameters. Indeed, an interval-valued parameter is comprehensive; it is the easiest to understand and express and the simplest to process, among multi-valued representations. In order to compute the interval-valued output of the system, a genetic algorithm is used. The resulting process model allows forming mappings at different levels of detail and, therefore, at different model resolutions. The system has been developed as an extension of a publicly available simulation engine, based on the Business Process Model and Notation (BPMN standard.

  17. A HYBRID GENETIC ALGORITHM-NEURAL NETWORK APPROACH FOR PRICING CORES AND REMANUFACTURED CORES

    Directory of Open Access Journals (Sweden)

    M. Seidi

    2012-01-01

    Full Text Available

    ENGLISH ABSTRACT:Sustainability has become a major issue in most economies, causing many leading companies to focus on product recovery and reverse logistics. Remanufacturing is an industrial process that makes used products reusable. One of the important aspects in both reverse logistics and remanufacturing is the pricing of returned and remanufactured products (called cores. In this paper, we focus on pricing the cores and remanufactured cores. First we present a mathematical model for this purpose. Since this model does not satisfy our requirements, we propose a simulation optimisation approach. This approach consists of a hybrid genetic algorithm based on a neural network employed as the fitness function. We use automata learning theory to obtain the learning rate required for training the neural network. Numerical results demonstrate that the optimal value of the acquisition price of cores and price of remanufactured cores is obtained by this approach.

    AFRIKAANSE OPSOMMING: Volhoubaarheid het ‘n belangrike saak geword in die meeste ekonomieë, wat verskeie maatskappye genoop het om produkherwinning en omgekeerde logistiek te onder oë te neem. Hervervaardiging is ‘n industriële proses wat gebruikte produkte weer bruikbaar maak. Een van die belangrike aspekte in beide omgekeerde logistiek en hervervaardiging is die prysbepaling van herwinne en hervervaardigde produkte. Hierdie artikel fokus op die prysbepalingsaspekte by wyse van ‘n wiskundige model.

  18. Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach.

    Science.gov (United States)

    Mridula, Meenu R; Nair, Ashalatha S; Kumar, K Satheesh

    2018-02-01

    In this paper, we compared the efficacy of observation based modeling approach using a genetic algorithm with the regular statistical analysis as an alternative methodology in plant research. Preliminary experimental data on in vitro rooting was taken for this study with an aim to understand the effect of charcoal and naphthalene acetic acid (NAA) on successful rooting and also to optimize the two variables for maximum result. Observation-based modelling, as well as traditional approach, could identify NAA as a critical factor in rooting of the plantlets under the experimental conditions employed. Symbolic regression analysis using the software deployed here optimised the treatments studied and was successful in identifying the complex non-linear interaction among the variables, with minimalistic preliminary data. The presence of charcoal in the culture medium has a significant impact on root generation by reducing basal callus mass formation. Such an approach is advantageous for establishing in vitro culture protocols as these models will have significant potential for saving time and expenditure in plant tissue culture laboratories, and it further reduces the need for specialised background.

  19. Plant responses to UV and blue light: biochemical and genetic approaches

    International Nuclear Information System (INIS)

    Jenkins, G.I.; Christie, J.M.; Fuglevand, G.; Long, J.C.; Jackson, J.A.

    1995-01-01

    UV and blue light control many aspects of plant growth and development. It is evident that several different photoreceptors mediate responses to UV and blue light, and there are reports of the functional and biochemical characterisation of a putative photoreceptor for phototropism and of the functional and molecular characterisation of the CRY1 photoreceptor, encoded by the Arabidopsis HY4 gene. The CRY1 photoreceptor mediates extension growth and gene expression responses to UV-A/blue light presumably through different or branching signal transduction pathways. Progress has been made in cell physiological and biochemical studies of UV/blue light signal transduction, but much remains to be done to relate candidate UV/blue signal transduction events to particular photoreceptors and responses. The application of a genetic approach in Arabidopsis has been responsible for many advances in understanding UV/blue responses, but further UV-B, UV-A and blue light response mutants need to be isolated. (author)

  20. Test interval optimization of safety systems of nuclear power plant using fuzzy-genetic approach

    International Nuclear Information System (INIS)

    Durga Rao, K.; Gopika, V.; Kushwaha, H.S.; Verma, A.K.; Srividya, A.

    2007-01-01

    Probabilistic safety assessment (PSA) is the most effective and efficient tool for safety and risk management in nuclear power plants (NPP). PSA studies not only evaluate risk/safety of systems but also their results are very useful in safe, economical and effective design and operation of NPPs. The latter application is popularly known as 'Risk-Informed Decision Making'. Evaluation of technical specifications is one such important application of Risk-Informed decision making. Deciding test interval (TI), one of the important technical specifications, with the given resources and risk effectiveness is an optimization problem. Uncertainty is inherently present in the availability parameters such as failure rate and repair time due to the limitation in assessing these parameters precisely. This paper presents a solution to test interval optimization problem with uncertain parameters in the model with fuzzy-genetic approach along with a case of application from a safety system of Indian pressurized heavy water reactor (PHWR)

  1. 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...

  2. A NAÏVE APPROACH TO SPEED UP PORTFOLIO OPTIMIZATION PROBLEM USING A MULTIOBJECTIVE GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    Baixauli-Soler, J. Samuel

    2012-05-01

    Full Text Available Genetic algorithms (GAs are appropriate when investors have the objective of obtaining mean‑variance (VaR efficient frontier as minimising VaR leads to non‑convex and non‑differential risk‑return optimisation problems. However GAs are a time‑consuming optimisation technique. In this paper, we propose to use a naïve approach consisting of using samples split by quartile of risk to obtain complete efficient frontiers in a reasonable computation time. Our results show that using reduced problems which only consider a quartile of the assets allow us to explore the efficient frontier for a large range of risk values. In particular, the third quartile allows us to obtain efficient frontiers from the 1.8% to 2.5% level of VaR quickly, while that of the first quartile of assets is from 1% to 1.3% level of VaR.

  3. Yeast Augmented Network Analysis (YANA: a new systems approach to identify therapeutic targets for human genetic diseases [v1; ref status: indexed, http://f1000r.es/3gk

    Directory of Open Access Journals (Sweden)

    David J. Wiley

    2014-06-01

    Full Text Available Genetic interaction networks that underlie most human diseases are highly complex and poorly defined. Better-defined networks will allow identification of a greater number of therapeutic targets. Here we introduce our Yeast Augmented Network Analysis (YANA approach and test it with the X-linked spinal muscular atrophy (SMA disease gene UBA1. First, we express UBA1 and a mutant variant in fission yeast and use high-throughput methods to identify fission yeast genetic modifiers of UBA1. Second, we analyze available protein-protein interaction network databases in both fission yeast and human to construct UBA1 genetic networks. Third, from these networks we identified potential therapeutic targets for SMA. Finally, we validate one of these targets in a vertebrate (zebrafish SMA model. This study demonstrates the power of combining synthetic and chemical genetics with a simple model system to identify human disease gene networks that can be exploited for treating human diseases.

  4. An Adaptive Agent-Based Model of Homing Pigeons: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Francis Oloo

    2017-01-01

    Full Text Available Conventionally, agent-based modelling approaches start from a conceptual model capturing the theoretical understanding of the systems of interest. Simulation outcomes are then used “at the end” to validate the conceptual understanding. In today’s data rich era, there are suggestions that models should be data-driven. Data-driven workflows are common in mathematical models. However, their application to agent-based models is still in its infancy. Integration of real-time sensor data into modelling workflows opens up the possibility of comparing simulations against real data during the model run. Calibration and validation procedures thus become automated processes that are iteratively executed during the simulation. We hypothesize that incorporation of real-time sensor data into agent-based models improves the predictive ability of such models. In particular, that such integration results in increasingly well calibrated model parameters and rule sets. In this contribution, we explore this question by implementing a flocking model that evolves in real-time. Specifically, we use genetic algorithms approach to simulate representative parameters to describe flight routes of homing pigeons. The navigation parameters of pigeons are simulated and dynamically evaluated against emulated GPS sensor data streams and optimised based on the fitness of candidate parameters. As a result, the model was able to accurately simulate the relative-turn angles and step-distance of homing pigeons. Further, the optimised parameters could replicate loops, which are common patterns in flight tracks of homing pigeons. Finally, the use of genetic algorithms in this study allowed for a simultaneous data-driven optimization and sensitivity analysis.

  5. A statistical approach to quantification of genetically modified organisms (GMO) using frequency distributions.

    Science.gov (United States)

    Gerdes, Lars; Busch, Ulrich; Pecoraro, Sven

    2014-12-14

    According to Regulation (EU) No 619/2011, trace amounts of non-authorised genetically modified organisms (GMO) in feed are tolerated within the EU if certain prerequisites are met. Tolerable traces must not exceed the so-called 'minimum required performance limit' (MRPL), which was defined according to the mentioned regulation to correspond to 0.1% mass fraction per ingredient. Therefore, not yet authorised GMO (and some GMO whose approvals have expired) have to be quantified at very low level following the qualitative detection in genomic DNA extracted from feed samples. As the results of quantitative analysis can imply severe legal and financial consequences for producers or distributors of feed, the quantification results need to be utterly reliable. We developed a statistical approach to investigate the experimental measurement variability within one 96-well PCR plate. This approach visualises the frequency distribution as zygosity-corrected relative content of genetically modified material resulting from different combinations of transgene and reference gene Cq values. One application of it is the simulation of the consequences of varying parameters on measurement results. Parameters could be for example replicate numbers or baseline and threshold settings, measurement results could be for example median (class) and relative standard deviation (RSD). All calculations can be done using the built-in functions of Excel without any need for programming. The developed Excel spreadsheets are available (see section 'Availability of supporting data' for details). In most cases, the combination of four PCR replicates for each of the two DNA isolations already resulted in a relative standard deviation of 15% or less. The aims of the study are scientifically based suggestions for minimisation of uncertainty of measurement especially in -but not limited to- the field of GMO quantification at low concentration levels. Four PCR replicates for each of the two DNA isolations

  6. Incorporating Functional Genomic Information in Genetic Association Studies Using an Empirical Bayes Approach.

    Science.gov (United States)

    Spencer, Amy V; Cox, Angela; Lin, Wei-Yu; Easton, Douglas F; Michailidou, Kyriaki; Walters, Kevin

    2016-04-01

    There is a large amount of functional genetic data available, which can be used to inform fine-mapping association studies (in diseases with well-characterised disease pathways). Single nucleotide polymorphism (SNP) prioritization via Bayes factors is attractive because prior information can inform the effect size or the prior probability of causal association. This approach requires the specification of the effect size. If the information needed to estimate a priori the probability density for the effect sizes for causal SNPs in a genomic region isn't consistent or isn't available, then specifying a prior variance for the effect sizes is challenging. We propose both an empirical method to estimate this prior variance, and a coherent approach to using SNP-level functional data, to inform the prior probability of causal association. Through simulation we show that when ranking SNPs by our empirical Bayes factor in a fine-mapping study, the causal SNP rank is generally as high or higher than the rank using Bayes factors with other plausible values of the prior variance. Importantly, we also show that assigning SNP-specific prior probabilities of association based on expert prior functional knowledge of the disease mechanism can lead to improved causal SNPs ranks compared to ranking with identical prior probabilities of association. We demonstrate the use of our methods by applying the methods to the fine mapping of the CASP8 region of chromosome 2 using genotype data from the Collaborative Oncological Gene-Environment Study (COGS) Consortium. The data we analysed included approximately 46,000 breast cancer case and 43,000 healthy control samples. © 2016 The Authors. *Genetic Epidemiology published by Wiley Periodicals, Inc.

  7. The genetic origins of biosynthesis and light-responsive control of the chemical UV screen of land plants

    International Nuclear Information System (INIS)

    Jorgensen, R.

    1994-01-01

    Most land plants possess the capacity to protect themselves from UV light, and do so by producing pigments that absorb efficiently in the UV-A and UV-B regions of the spectrum while allowing transmission of nearly all photosynthetically useful wavelengths. These UV-absorbing pigments are mainly phenylpropanoids and flavonoids. This chapter summarizes current understanding of the mechanism of UV protection in higher land plants, evaluates the information available from lower land plants and their green-algal relatives, and then considers the possible evolutionary origins of this use of chemical filters for selectively screening UV light from solar radiation. It is proposed that photo control over the biosynthesis of UV-absorbing phenylpropanoids and flavonoids may have evolved in concert with the evolution of the high biosynthetic activity necessary for UV protection. The toxicity of phenylpropanoids and flavonoids has been postulated to have been a barrier to the evolution of an effective chemical UV screen, and that some means for sequestering these compounds and/or for controlling their synthesis probably evolved prior to, or in concert with, the evolution of high rates of biosynthesis. The original photoreceptor and signal transduction system is speculated to have been based on photo isomerization of a phenylpropanoid ester and a pre-existing product feedback mechanism for controlling phenylpropanoid biosynthesis. Understanding the original mechanism for photo control of the chemical UV screen of land plants could be valuable for understanding the adaptability of extant land plants to rising levels of solar UV-B radiation and may suggest genetic strategies for engineering improved UV tolerance in crop plants. (author)

  8. Modeling of scale-dependent bacterial growth by chemical kinetics approach.

    Science.gov (United States)

    Martínez, Haydee; Sánchez, Joaquín; Cruz, José-Manuel; Ayala, Guadalupe; Rivera, Marco; Buhse, Thomas

    2014-01-01

    We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V) of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

  9. Modeling of Scale-Dependent Bacterial Growth by Chemical Kinetics Approach

    Directory of Open Access Journals (Sweden)

    Haydee Martínez

    2014-01-01

    Full Text Available We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli  JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

  10. Functional, genetic and chemical characterization of biosurfactants produced by plant growth-promoting Pseudomonas putida 267.

    Science.gov (United States)

    Kruijt, Marco; Tran, Ha; Raaijmakers, Jos M

    2009-08-01

    Plant growth-promoting Pseudomonas putida strain 267, originally isolated from the rhizosphere of black pepper, produces biosurfactants that cause lysis of zoospores of the oomycete pathogen Phytophthora capsici. The biosurfactants were characterized, the biosynthesis gene(s) partially identified, and their role in control of Phytophthora damping-off of cucumber evaluated. The biosurfactants were shown to lyse zoospores of Phy. capsici and inhibit growth of the fungal pathogens Botrytis cinerea and Rhizoctonia solani. In vitro assays further showed that the biosurfactants of strain 267 are essential in swarming motility and biofilm formation. In spite of the zoosporicidal activity, the biosurfactants did not play a significant role in control of Phytophthora damping-off of cucumber, since both wild type strain 267 and its biosurfactant-deficient mutant were equally effective, and addition of the biosurfactants did not provide control. Genetic characterization revealed that surfactant biosynthesis in strain 267 is governed by homologues of PsoA and PsoB, two nonribosomal peptide synthetases involved in production of the cyclic lipopeptides (CLPs) putisolvin I and II. The structural relatedness of the biosurfactants of strain 267 to putisolvins I and II was supported by LC-MS and MS-MS analyses. The biosurfactants produced by Ps. putida 267 were identified as putisolvin-like CLPs; they are essential in swarming motility and biofilm formation, and have zoosporicidal and antifungal activities. Strain 267 provides excellent biocontrol activity against Phytophthora damping-off of cucumber, but the lipopeptide surfactants are not involved in disease suppression. Pseudomonas putida 267 suppresses Phy. capsici damping-off of cucumber and provides a potential supplementary strategy to control this economically important oomycete pathogen. The putisolvin-like biosurfactants exhibit zoosporicidal and antifungal activities, yet they do not contribute to biocontrol of Phy

  11. Chemical pattern of brazilian apples: a chemometric approach based on the Fuji and Gala varieties

    Directory of Open Access Journals (Sweden)

    Renato Giovanetti Vieira

    2011-06-01

    Full Text Available The chemical composition of apple juices may be used to discriminate between the varieties for consumption and those for raw material. Fuji and Gala have a chemical pattern that can be used for this classification. Multivariate methods correlate independent continuous chemical descriptors with the categorical apple variety. Three main descriptors of apple juice were selected: malic acid, total reducing sugar and total phenolic compounds. A chemometric approach, employing PCA and SIMCA, was used to classify apple juice samples. PCA was performed with 24 juices from Fuji and Gala, and SIMCA, with 15 juices. The exploratory and predictive models recognized 88% and 64%, respectively, as belonging to a mixed domain. The apple juice from commercial fruits shows a pattern related to cv. Fuji and Gala with boundaries from 0.18 to 0.389 g.100 mL-1 (malic acid, from 8.65 to 15.18 g.100 mL-1 (total reducing sugar and from 100 to 400 mg.L-1 (total phenolic compounds, but such boundaries were slightly shorter in the remaining set of commercial apple juices, specifically from 0.16 to 0.36 g.100 mL-1, from 9.25 to 15.5 g.100 mL-1 and from 180 to 606 mg.L-1 for acidity, reducing sugar and phenolic compounds, respectively, representing the acid, sweet and bitter tastes.

  12. A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity

    Science.gov (United States)

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

  13. Planning additional drilling campaign using two-space genetic algorithm: A game theoretical approach

    Science.gov (United States)

    Kumral, Mustafa; Ozer, Umit

    2013-03-01

    Grade and tonnage are the most important technical uncertainties in mining ventures because of the use of estimations/simulations, which are mostly generated from drill data. Open pit mines are planned and designed on the basis of the blocks representing the entire orebody. Each block has different estimation/simulation variance reflecting uncertainty to some extent. The estimation/simulation realizations are submitted to mine production scheduling process. However, the use of a block model with varying estimation/simulation variances will lead to serious risk in the scheduling. In the medium of multiple simulations, the dispersion variances of blocks can be thought to regard technical uncertainties. However, the dispersion variance cannot handle uncertainty associated with varying estimation/simulation variances of blocks. This paper proposes an approach that generates the configuration of the best additional drilling campaign to generate more homogenous estimation/simulation variances of blocks. In other words, the objective is to find the best drilling configuration in such a way as to minimize grade uncertainty under budget constraint. Uncertainty measure of the optimization process in this paper is interpolation variance, which considers data locations and grades. The problem is expressed as a minmax problem, which focuses on finding the best worst-case performance i.e., minimizing interpolation variance of the block generating maximum interpolation variance. Since the optimization model requires computing the interpolation variances of blocks being simulated/estimated in each iteration, the problem cannot be solved by standard optimization tools. This motivates to use two-space genetic algorithm (GA) approach to solve the problem. The technique has two spaces: feasible drill hole configuration with minimization of interpolation variance and drill hole simulations with maximization of interpolation variance. Two-space interacts to find a minmax solution

  14. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    Science.gov (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Equilibrium approach towards water resource management and pollution control in coal chemical industrial park.

    Science.gov (United States)

    Xu, Jiuping; Hou, Shuhua; Xie, Heping; Lv, Chengwei; Yao, Liming

    2018-08-01

    In this study, an integrated water and waste load allocation model is proposed to assist decision makers in better understanding the trade-offs between economic growth, resource utilization, and environmental protection of coal chemical industries which characteristically have high water consumption and pollution. In the decision framework, decision makers in a same park, each of whom have different goals and preferences, work together to seek a collective benefit. Similar to a Stackelberg-Nash game, the proposed approach illuminates the decision making interrelationships and involves in the conflict coordination between the park authority and the individual coal chemical company stockholders. In the proposed method, to response to climate change and other uncertainties, a risk assessment tool, Conditional Value-at-Risk (CVaR) and uncertainties through reflecting parameters and coefficients using probability and fuzzy set theory are integrated in the modeling process. Then a case study from Yuheng coal chemical park is presented to demonstrate the practicality and efficiency of the optimization model. To reasonable search the potential consequences of different responses to water and waste load allocation strategies, a number of scenario results considering environmental uncertainty and decision maker' attitudes are examined to explore the tradeoffs between economic development and environmental protection and decision makers' objectives. The results are helpful for decision/police makers to adjust current strategies adapting for current changes. Based on the scenario analyses and discussion, some propositions and operational policies are given and sensitive adaptation strategies are presented to support the efficient, balanced and sustainable development of coal chemical industrial parks. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris.

    Directory of Open Access Journals (Sweden)

    Filippo Frizzi

    Full Text Available Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a 'nasty neighbor' effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships.

  17. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

    NARCIS (Netherlands)

    B. Giardine (Belinda); J. Borg (Joseph); D.R. Higgs (Douglas); K.R. Peterson (Kenneth R.); J.N.J. Philipsen (Sjaak); D. Maglott (Donna); B.K. Singleton (Belinda K.); D.J. Anstee (David J.); A.N. Basak (Nazli); B.H. Clark (Bruce); F.C. Costa (Flavia C.); P. Faustino (Paula); H. Fedosyuk (Halyna); A.E. Felice (Alex); A. Francina (Alain); R. Galanello (Renzo); M.V.E. Gallivan (Monica V. E.); M. Georgitsi (Marianthi); R.J. Gibbons (Richard J.); P.C. Giordano (Piero Carlo); C.L. Harteveld (Cornelis); J.D. Hoyer (James D.); M. Jarvis (Martin); P. Joly (Philippe); E. Kanavakis (Emmanuel); P. Kollia (Panagoula); S. Menzel (Stephan); W.G. Miller (William); K. Moradkhani (Kamran); J. Old (John); A. Papachatzpoulou (Adamantia); M.N. Papadakis (Manoussos); P. Papadopoulos (Petros); S. Pavlovic (Sonja); L. Perseu (Lucia); M. Radmilovic (Milena); C. Riemer (Cathy); S. Satta (Stefania); I.A. Schrijver (Ingrid); M. Stojiljkovic (Maja); S.L. Thein; J. Traeger-Synodinos (Joanne); R. Tully (Ray); T. Wada (Takahito); J.S. Waye (John); C. Wiemann (Claudia); B. Zukic (Branka); D.H.K. Chui (David H. K.); H. Wajcman (Henri); R. Hardison (Ross); G.P. Patrinos (George)

    2011-01-01

    textabstractWe developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public

  18. Biotechnological approaches for the genetic improvement of Jatropha curcas L.: A biodiesel plant

    KAUST Repository

    Kumar, Nitish; Singh, Amritpal S.; Kumari, Swati; Reddy, Muppala P.

    2015-01-01

    . In this review, an effort is made to project the current biotechnology and molecular biology tools employed in the direction of, evaluating the genetic diversity and phylogeny revelation of Jatropha spp., identification of genetic markers for desirable traits

  19. Applying new genetic approaches to improve quality of population assessment of green and loggerhead turtles

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — As the NOAA-Fisheries? National Sea Turtle Genetics Lab, the SWFSC Marine Turtle Genetics Program has the lead responsibility for generating, analyzing and...

  20. A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches

    Science.gov (United States)

    Zheng, Xiasheng; Zhang, Peng; Liao, Baosheng; Li, Jing; Liu, Xingyun; Shi, Yuhua; Cheng, Jinle; Lai, Zhitian; Xu, Jiang; Chen, Shilin

    2017-01-01

    Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples. PMID:28955365

  1. A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches

    Directory of Open Access Journals (Sweden)

    Xiasheng Zheng

    2017-09-01

    Full Text Available Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis, to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control.Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.

  2. A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches.

    Science.gov (United States)

    Zheng, Xiasheng; Zhang, Peng; Liao, Baosheng; Li, Jing; Liu, Xingyun; Shi, Yuhua; Cheng, Jinle; Lai, Zhitian; Xu, Jiang; Chen, Shilin

    2017-01-01

    Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight : We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.

  3. Assuring the safety of genetically modified (GM) foods: the importance of an holistic, integrative approach.

    Science.gov (United States)

    Cockburn, Andrew

    2002-09-11

    Genes change continuously by natural mutation and recombination enabling man to select and breed crops having the most desirable traits such as yield or flavour. Genetic modification (GM) is a recent development which allows specific genes to be identified, isolated, copied and inserted into other plants with a high level of specificity. The food safety considerations for GM crops are basically the same as those arising from conventionally bred crops, very few of which have been subject to any testing yet are generally regarded as being safe to eat. In contrast a rigorous safety testing paradigm has been developed for GM crops, which utilises a systematic, stepwise and holistic approach. The resultant science based process, focuses on a classical evaluation of the toxic potential of the introduced novel trait and the wholesomeness of the transformed crop. In addition, detailed consideration is given to the history and safe use of the parent crop as well as that of the gene donor. The overall safety evaluation is conducted under the concept known as substantial equivalence which is enshrined in all international crop biotechnology guidelines. This provides the framework for a comparative approach to identify the similarities and differences between the GM product and its comparator which has a known history of safe use. By building a detailed profile on each step in the transformation process, from parent to new crop, and by thoroughly evaluating the significance from a safety perspective, of any differences that may be detected, a very comprehensive matrix of information is constructed which enables the conclusion as to whether the GM crop, derived food or feed is as safe as its traditional counterpart. Using this approach in the evaluation of more than 50 GM crops which have been approved worldwide, the conclusion has been that foods and feeds derived from genetically modified crops are as safe and nutritious as those derived from traditional crops. The lack of

  4. Time series segmentation: a new approach based on Genetic Algorithm and Hidden Markov Model

    Science.gov (United States)

    Toreti, A.; Kuglitsch, F. G.; Xoplaki, E.; Luterbacher, J.

    2009-04-01

    The subdivision of a time series into homogeneous segments has been performed using various methods applied to different disciplines. In climatology, for example, it is accompanied by the well-known homogenization problem and the detection of artificial change points. In this context, we present a new method (GAMM) based on Hidden Markov Model (HMM) and Genetic Algorithm (GA), applicable to series of independent observations (and easily adaptable to autoregressive processes). A left-to-right hidden Markov model, estimating the parameters and the best-state sequence, respectively, with the Baum-Welch and Viterbi algorithms, was applied. In order to avoid the well-known dependence of the Baum-Welch algorithm on the initial condition, a Genetic Algorithm was developed. This algorithm is characterized by mutation, elitism and a crossover procedure implemented with some restrictive rules. Moreover the function to be minimized was derived following the approach of Kehagias (2004), i.e. it is the so-called complete log-likelihood. The number of states was determined applying a two-fold cross-validation procedure (Celeux and Durand, 2008). Being aware that the last issue is complex, and it influences all the analysis, a Multi Response Permutation Procedure (MRPP; Mielke et al., 1981) was inserted. It tests the model with K+1 states (where K is the state number of the best model) if its likelihood is close to K-state model. Finally, an evaluation of the GAMM performances, applied as a break detection method in the field of climate time series homogenization, is shown. 1. G. Celeux and J.B. Durand, Comput Stat 2008. 2. A. Kehagias, Stoch Envir Res 2004. 3. P.W. Mielke, K.J. Berry, G.W. Brier, Monthly Wea Rev 1981.

  5. Modeling solar radiation of Mediterranean region in Turkey by using fuzzy genetic approach

    International Nuclear Information System (INIS)

    Kisi, Ozgur

    2014-01-01

    The study investigates the ability of FG (fuzzy genetic) approach in modeling solar radiation of seven cities from Mediterranean region of Anatolia, Turkey. Latitude, longitude, altitude and month of the year data from the Adana, K. Maras, Mersin, Antalya, Isparta, Burdur and Antakya cities are used as inputs to the FG model to estimate one month ahead solar radiation. FG model is compared with ANNs (artificial neural networks) and ANFIS (adaptive neruro fuzzzy inference system) models with respect to RMSE (root mean square errors), MAE (mean absolute errors) and determination coefficient (R 2 ) statistics. Comparison results indicate that the FG model performs better than the ANN and ANFIS models. It is found that the FG model can be successfully used for estimating solar radiation by using latitude, longitude, altitude and month of the year information. FG model with RMSE = 6.29 MJ/m 2 , MAE = 4.69 MJ/m 2 and R 2 = 0.905 in the test stage was found to be superior to the optimal ANN model with RMSE = 7.17 MJ/m 2 , MAE = 5.29 MJ/m 2 and R 2 = 0.876 and ANFIS model with RMSE = 6.75 MJ/m 2 , MAE = 5.10 MJ/m 2 and R 2 = 0.892 in estimating solar radiation. - Highlights: • SR (Solar radiation) of seven cities from Mediterranean region of Turkey is predicted. • FG (Fuzzy genetic) models are developed for accurately estimation of SR. • The ability of the FG models used in the study is found to be satisfactory. • FG models are compared with commonly used ANNs (artificial neural networks). • FG models are found to perform better than the ANNs models

  6. From animal models to human disease: a genetic approach for personalized medicine in ALS.

    Science.gov (United States)

    Picher-Martel, Vincent; Valdmanis, Paul N; Gould, Peter V; Julien, Jean-Pierre; Dupré, Nicolas

    2016-07-11

    Amyotrophic Lateral Sclerosis (ALS) is the most frequent motor neuron disease in adults. Classical ALS is characterized by the death of upper and lower motor neurons leading to progressive paralysis. Approximately 10 % of ALS patients have familial form of the disease. Numerous different gene mutations have been found in familial cases of ALS, such as mutations in superoxide dismutase 1 (SOD1), TAR DNA-binding protein 43 (TDP-43), fused in sarcoma (FUS), C9ORF72, ubiquilin-2 (UBQLN2), optineurin (OPTN) and others. Multiple animal models were generated to mimic the disease and to test future treatments. However, no animal model fully replicates the spectrum of phenotypes in the human disease and it is difficult to assess how a therapeutic effect in disease models can predict efficacy in humans. Importantly, the genetic and phenotypic heterogeneity of ALS leads to a variety of responses to similar treatment regimens. From this has emerged the concept of personalized medicine (PM), which is a medical scheme that combines study of genetic, environmental and clinical diagnostic testing, including biomarkers, to individualized patient care. In this perspective, we used subgroups of specific ALS-linked gene mutations to go through existing animal models and to provide a comprehensive profile of the differences and similarities between animal models of disease and human disease. Finally, we reviewed application of biomarkers and gene therapies relevant in personalized medicine approach. For instance, this includes viral delivering of antisense oligonucleotide and small interfering RNA in SOD1, TDP-43 and C9orf72 mice models. Promising gene therapies raised possibilities for treating differently the major mutations in familial ALS cases.

  7. A new generic approach for estimating the concentrations of down-the-drain chemicals at catchment and national scale

    Energy Technology Data Exchange (ETDEWEB)

    Keller, V.D.J. [Centre for Ecology and Hydrology, Hydrological Risks and Resources, Maclean Building, Crowmarsh Gifford, Wallingford OX10 8BB (United Kingdom)]. E-mail: vke@ceh.ac.uk; Rees, H.G. [Centre for Ecology and Hydrology, Hydrological Risks and Resources, Maclean Building, Crowmarsh Gifford, Wallingford OX10 8BB (United Kingdom); Fox, K.K. [University of Lancaster (United Kingdom); Whelan, M.J. [Unilever Safety and Environmental Assurance Centre, Colworth (United Kingdom)

    2007-07-15

    A new generic approach for estimating chemical concentrations in rivers at catchment and national scales is presented. Domestic chemical loads in waste water are estimated using gridded population data. River flows are estimated by combining predicted runoff with topographically derived flow direction. Regional scale exposure is characterised by two summary statistics: PEC{sub works}, the average concentration immediately downstream of emission points, and, PEC{sub area}, the catchment-average chemical concentration. The method was applied to boron at national (England and Wales) and catchment (Aire-Calder) scales. Predicted concentrations were within 50% of measured mean values in the Aire-Calder catchment and in agreement with results from the GREAT-ER model. The concentration grids generated provide a picture of the spatial distribution of expected chemical concentrations at various scales, and can be used to identify areas of potentially high risk. - A new grid-based approach to predict spatially-referenced freshwater concentrations of domestic chemicals.

  8. About the Genetic Mechanisms of Apatites: A Survey on the Methodological Approaches

    Directory of Open Access Journals (Sweden)

    Linda Pastero

    2017-08-01

    Full Text Available Apatites are properly considered as a strategic material owing to the broad range of their practical uses, primarily biomedical but chemical, pharmaceutical, environmental and geological as well. The apatite group of minerals has been the subject of a huge number of papers, mainly devoted to the mass crystallization of nanosized hydroxyapatite (or carboapatite as a scaffold for osteoinduction purposes. Many wet and dry methods of synthesis have been proposed. The products have been characterized using various techniques, from the transmission electron microscopy to many spectroscopic methods like IR and Raman. The experimental approach usually found in literature allows getting tailor made micro- and nano- crystals ready to be used in a wide variety of fields. Despite the wide interest in synthesis and characterization, little attention has been paid to the relationships between bulk structure and corresponding surfaces and to the role plaid by surfaces on the mechanisms involved during the early stages of growth of apatites. In order to improve the understanding of their structure and chemical variability, close attention will be focused on the structural complexity of hydroxyapatite (HAp, on the richness of its surfaces and their role in the interaction with the precursor phases, and in growth kinetics and morphology.

  9. Effects of genetic mutations and chemical exposures on Caenorhabditis elegans feeding: evaluation of a novel, high-throughput screening assay.

    Directory of Open Access Journals (Sweden)

    Windy A Boyd

    2007-12-01

    Full Text Available Government agencies have defined a need to reduce, refine or replace current mammalian-based bioassays with testing methods that use alternative species. Invertebrate species, such as Caenorhabditis elegans, provide an attractive option because of their short life cycles, inexpensive maintenance, and high degree of evolutionary conservation with higher eukaryotes. The C. elegans pharynx is a favorable model for studying neuromuscular function, and the effects of chemicals on neuromuscular activity, i.e., feeding. Current feeding methodologies, however, are labor intensive and only semi-quantitative.Here a high-throughput assay is described that uses flow cytometry to measure C. elegans feeding by determining the size and intestinal fluorescence of hundreds of nematodes after exposure to fluorescent-labeled microspheres. This assay was validated by quantifying fluorescence in feeding-defective C. elegans (eat mutants, and by exposing wild-type nematodes to the neuroactive compounds, serotonin and arecoline. The eat mutations previously determined to cause slow pumping rates exhibited the lowest feeding levels with our assay. Concentration-dependent increases in feeding levels after serotonin exposures were dependent on food availability, while feeding levels decreased in arecoline-exposed nematodes regardless of the presence of food. The effects of the environmental contaminants, cadmium chloride and chlorpyrifos, on wild-type C. elegans feeding were then used to demonstrate an application of the feeding assay. Cadmium exposures above 200 microM led to a sharp drop in feeding levels. Feeding of chlorpyrifos-exposed nematodes decreased in a concentration-dependent fashion with an EC(50 of 2 microM.The C. elegans fluorescence microsphere feeding assay is a rapid, reliable method for the assessment of neurotoxic effects of pharmaceutical drugs, industrial chemicals or environmental agents. This assay may also be applicable to large scale genetic or

  10. A review of genome-wide approaches to study the genetic basis for spermatogenic defects.

    Science.gov (United States)

    Aston, Kenneth I; Conrad, Donald F

    2013-01-01

    Rapidly advancing tools for genetic analysis on a genome-wide scale have been instrumental in identifying the genetic bases for many complex diseases. About half of male infertility cases are of unknown etiology in spite of tremendous efforts to characterize the genetic basis for the disorder. Advancing our understanding of the genetic basis for male infertility will require the application of established and emerging genomic tools. This chapter introduces many of the tools available for genetic studies on a genome-wide scale along with principles of study design and data analysis.

  11. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    International Nuclear Information System (INIS)

    Rosenow, Phil; Tonner, Ralf

    2016-01-01

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H 2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  12. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    Energy Technology Data Exchange (ETDEWEB)

    Rosenow, Phil; Tonner, Ralf, E-mail: tonner@chemie.uni-marburg.de [Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften, Philipps-Universität Marburg, Hans-Meerwein-Straße, Marburg 35032 (Germany)

    2016-05-28

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H{sub 2} desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  13. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    Science.gov (United States)

    Rosenow, Phil; Tonner, Ralf

    2016-05-01

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  14. A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy.

    Science.gov (United States)

    Ramasesha, Krupa; De Marco, Luigi; Horning, Andrew D; Mandal, Aritra; Tokmakoff, Andrei

    2012-04-07

    We present an approach for calculating nonlinear spectroscopic observables, which overcomes the approximations inherent to current phenomenological models without requiring the computational cost of performing molecular dynamics simulations. The trajectory mapping method uses the semi-classical approximation to linear and nonlinear response functions, and calculates spectra from trajectories of the system's transition frequencies and transition dipole moments. It rests on identifying dynamical variables important to the problem, treating the dynamics of these variables stochastically, and then generating correlated trajectories of spectroscopic quantities by mapping from the dynamical variables. This approach allows one to describe non-Gaussian dynamics, correlated dynamics between variables of the system, and nonlinear relationships between spectroscopic variables of the system and the bath such as non-Condon effects. We illustrate the approach by applying it to three examples that are often not adequately treated by existing analytical models--the non-Condon effect in the nonlinear infrared spectra of water, non-Gaussian dynamics inherent to strongly hydrogen bonded systems, and chemical exchange processes in barrier crossing reactions. The methods described are generally applicable to nonlinear spectroscopy throughout the optical, infrared and terahertz regions.

  15. Domino effects within a chemical cluster: a game-theoretical modeling approach by using Nash-equilibrium.

    Science.gov (United States)

    Reniers, Genserik; Dullaert, Wout; Karel, Soudan

    2009-08-15

    Every company situated within a chemical cluster faces domino effect risks, whose magnitude depends on every company's own risk management strategies and on those of all others. Preventing domino effects is therefore very important to avoid catastrophes in the chemical process industry. Given that chemical companies are interlinked by domino effect accident links, there is some likelihood that even if certain companies fully invest in domino effects prevention measures, they can nonetheless experience an external domino effect caused by an accident which occurred in another chemical enterprise of the cluster. In this article a game-theoretic approach to interpret and model behaviour of chemical plants within chemical clusters while negotiating and deciding on domino effects prevention investments is employed.

  16. Evaluation of two-year Jewish genetic disease screening program in Atlanta: insight into community genetic screening approaches.

    Science.gov (United States)

    Shao, Yunru; Liu, Shuling; Grinzaid, Karen

    2015-04-01

    Improvements in genetic testing technologies have led to the development of expanded carrier screening panels for the Ashkenazi Jewish population; however, there are major inconsistencies in current screening practices. A 2-year pilot program was launched in Atlanta in 2010 to promote and facilitate screening for 19 Jewish genetic diseases. We analyzed data from this program, including participant demographics and outreach efforts. This retrospective analysis is based on a de-identified dataset of 724 screenees. Data were obtained through medical chart review and questionnaires and included demographic information, screening results, response to outreach efforts, and follow-up behavior and preferences. We applied descriptive analysis, chi-square tests, and logistic regression to analyze the data and compare findings with published literature. The majority of participants indicated that they were not pregnant or did not have a partner who was pregnant were affiliated with Jewish organizations and reported 100 % AJ ancestry. Overall, carrier frequency was 1 in 3.9. Friends, rabbis, and family members were the most common influencers of the decision to receive screening. People who were older, had a history of pregnancy, and had been previously screened were more likely to educate others (all p influencers who then encouraged screening in the target population. Educating influencers and increasing overall awareness were the most effective outreach strategies.

  17. Is it acceptable to approach colorectal cancer patients at diagnosis to discuss genetic testing? A pilot study

    OpenAIRE

    Porteous, M; Dunckley, M; Appleton, S; Catt, S; Dunlop, M; Campbell, H; Cull, A

    2003-01-01

    In this pilot study, the acceptability of approaching 111 newly diagnosed colorectal cancer patients with the offer of genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC) was assessed. A total of 78% of participants found it highly acceptable to have the information about HNPCC brought to their attention at that time.

  18. An alternative approach to risk rank chemicals on the threat they pose to the aquatic environment.

    Science.gov (United States)

    Johnson, Andrew C; Donnachie, Rachel L; Sumpter, John P; Jürgens, Monika D; Moeckel, Claudia; Pereira, M Gloria

    2017-12-01

    This work presents a new and unbiased method of risk ranking chemicals based on the threat they pose to the aquatic environment. The study ranked 12 metals, 23 pesticides, 11 other persistent organic pollutants (POPs), 13 pharmaceuticals, 10 surfactants and similar compounds and 2 nanoparticles (total of 71) of concern against one another by comparing their median UK river water and median ecotoxicity effect concentrations. To complement this, by giving an assessment on potential wildlife impacts, risk ranking was also carried out by comparing the lowest 10th percentile of the effects data with the highest 90th percentile of the exposure data. In other words, risk was pared down to just toxicity versus exposure. Further modifications included incorporating bioconcentration factors, using only recent water measurements and excluding either lethal or sub-lethal effects. The top ten chemicals, based on the medians, which emerged as having the highest risk to organisms in UK surface waters using all the ecotoxicity data were copper, aluminium, zinc, ethinylestradiol (EE2), linear alkylbenzene sulfonate (LAS), triclosan, manganese, iron, methomyl and chlorpyrifos. By way of contrast, using current UK environmental quality standards as the comparator to median UK river water concentrations would have selected 6 different chemicals in the top ten. This approach revealed big differences in relative risk; for example, zinc presented a million times greater risk then metoprolol and LAS 550 times greater risk than nanosilver. With the exception of EE2, most pharmaceuticals were ranked as having a relatively low risk. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Random Forest Approach to QSPR Study of Fluorescence Properties Combining Quantum Chemical Descriptors and Solvent Conditions.

    Science.gov (United States)

    Chen, Chia-Hsiu; Tanaka, Kenichi; Funatsu, Kimito

    2018-04-22

    The Quantitative Structure - Property Relationship (QSPR) approach was performed to study the fluorescence absorption wavelengths and emission wavelengths of 413 fluorescent dyes in different solvent conditions. The dyes included the chromophore derivatives of cyanine, xanthene, coumarin, pyrene, naphthalene, anthracene and etc., with the wavelength ranging from 250 nm to 800 nm. An ensemble method, random forest (RF), was employed to construct nonlinear prediction models compared with the results of linear partial least squares and nonlinear support vector machine regression models. Quantum chemical descriptors derived from density functional theory method and solvent information were also used by constructing models. The best prediction results were obtained from RF model, with the squared correlation coefficients [Formula: see text] of 0.940 and 0.905 for λ abs and λ em , respectively. The descriptors used in the models were discussed in detail in this report by comparing the feature importance of RF.

  20. Probing the chemical environments of early star formation: A multidisciplinary approach

    Science.gov (United States)

    Hardegree-Ullman, Emily Elizabeth

    Chemical compositions of prestellar and protostellar environments in the dense interstellar medium are best quantified using a multidisciplinary approach. For my dissertation, I completed two projects to measure molecular abundances during the earliest phases of star formation. The first project investigates gas phase CO depletion in molecular cloud cores, the progenitors of star systems, using infrared photometry and molecular line spectroscopy at radio wavelengths. Hydrogenation of CO depleted onto dust is an important first step toward building complex organic molecules. The second project constrains polycyclic aromatic hydrocarbon (PAH) abundances toward young stellar objects (YSO). Band strengths measured from laboratory spectroscopy of pyrene/water ice mixtures were applied to estimate abundances from features attributed to PAHs in observational YSO spectra. PAHs represent a distinct but important component of interstellar organic material that is widely observed but not well quantified in star-forming regions.

  1. Chemical approaches toward graphene-based nanomaterials and their applications in energy-related areas.

    Science.gov (United States)

    Luo, Bin; Liu, Shaomin; Zhi, Linjie

    2012-03-12

    A 'gold rush' has been triggered all over the world for exploiting the possible applications of graphene-based nanomaterials. For this purpose, two important problems have to be solved; one is the preparation of graphene-based nanomaterials with well-defined structures, and the other is the controllable fabrication of these materials into functional devices. This review gives a brief overview of the recent research concerning chemical and thermal approaches toward the production of well-defined graphene-based nanomaterials and their applications in energy-related areas, including solar cells, lithium ion secondary batteries, supercapacitors, and catalysis. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Quantitative NMR Approach to Optimize the Formation of Chemical Building Blocks from Abundant Carbohydrates.

    Science.gov (United States)

    Elliot, Samuel G; Tolborg, Søren; Sádaba, Irantzu; Taarning, Esben; Meier, Sebastian

    2017-07-21

    The future role of biomass-derived chemicals relies on the formation of diverse functional monomers in high yields from carbohydrates. Recently, it has become clear that a series of α-hydroxy acids, esters, and lactones can be formed from carbohydrates in alcohol and water solvents using tin-containing catalysts such as Sn-Beta. These compounds are potential building blocks for polyesters bearing additional olefin and alcohol functionalities. An NMR approach was used to identify, quantify, and optimize the formation of these building blocks in the Sn-Beta-catalyzed transformation of abundant carbohydrates. Record yields of the target molecules can be achieved by obstructing competing reactions through solvent selection. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Controlled low-temperature fabrication of ZnO nanopillars with a wet-chemical approach

    Energy Technology Data Exchange (ETDEWEB)

    Postels, B [Institute of Semiconductor Technology, Technical University of Braunschweig, Hans-Sommer-Strasse 66, D-38106 Braunschweig (Germany); Wehmann, H-H [Institute of Semiconductor Technology, Technical University of Braunschweig, Hans-Sommer-Strasse 66, D-38106 Braunschweig (Germany); Bakin, A [Institute of Semiconductor Technology, Technical University of Braunschweig, Hans-Sommer-Strasse 66, D-38106 Braunschweig (Germany); Kreye, M [Institute of Semiconductor Technology, Technical University of Braunschweig, Hans-Sommer-Strasse 66, D-38106 Braunschweig (Germany); Fuhrmann, D [Institute of Applied Physics, Technical University of Braunschweig, Mendelssohnstrasse 2, D-38106 Braunschweig (Germany); Blaesing, J [Institute of Experimental Physics, Otto-von-Guericke-University Magdeburg, Universitaetsplatz 1, 39016 Magdeburg (Germany); Hangleiter, A [Institute of Applied Physics, Technical University of Braunschweig, Mendelssohnstrasse 2, D-38106 Braunschweig (Germany); Krost, A [Institute of Experimental Physics, Otto-von-Guericke-University Magdeburg, Universitaetsplatz 1, 39016 Magdeburg (Germany); Waag, A [Institute of Semiconductor Technology, Technical University of Braunschweig, Hans-Sommer-Strasse 66, D-38106 Braunschweig (Germany)

    2007-05-16

    Aqueous chemical growth (ACG) is an efficient way to generate wafer-scale and densely packed arrays of ZnO nanopillars on various substrate materials. ACG is a low-temperature growth approach that is only weakly influenced by the substrate and even allows growth on flexible polymer substrates or on conducting materials. The advanced fabrication of wafer-scale and highly vertically aligned arrays of ZnO nanopillars on various substrate materials is demonstrated. Moreover, it is possible to control the morphology in diameter and length by changing the growth conditions. Photoluminescence characterization clearly shows a comparatively strong band-edge luminescence, even at room temperature, that is accompanied by a rather weak visible luminescence in the yellow/orange spectral range.

  4. Non-animal approaches for toxicokinetics in risk evaluations of food chemicals.

    Science.gov (United States)

    Punt, Ans; Peijnenburg, Ad A C M; Hoogenboom, Ron L A P; Bouwmeester, Hans

    2017-01-01

    The objective of the present work was to review the availability and predictive value of non-animal toxicokinetic approaches and to evaluate their current use in European risk evaluations of food contaminants, additives and food contact materials, as well as pesticides and medicines. Results revealed little use of quantitative animal or human kinetic data in risk evaluations of food chemicals, compared with pesticides and medicines. Risk evaluations of medicines provided sufficient in vivo kinetic data from different species to evaluate the predictive value of animal kinetic data for humans. These data showed a relatively poor correlation between the in vivo bioavailability in rats and dogs versus that in humans. In contrast, in vitro (human) kinetic data have been demonstrated to provide adequate predictions of the fate of compounds in humans, using appropriate in vitro-in vivo scalers and by integration of in vitro kinetic data with in silico kinetic modelling. Even though in vitro kinetic data were found to be occasionally included within risk evaluations of food chemicals, particularly results from Caco-2 absorption experiments and in vitro data on gut-microbial conversions, only minor use of in vitro methods for metabolism and quantitative in vitro-in vivo extrapolation methods was identified. Yet, such quantitative predictions are essential in the development of alternatives to animal testing as well as to increase human relevance of toxicological risk evaluations. Future research should aim at further improving and validating quantitative alternative methods for kinetics, thereby increasing regulatory acceptance of non-animal kinetic data.

  5. An external domino effects investment approach to improve cross-plant safety within chemical clusters

    International Nuclear Information System (INIS)

    Reniers, Genserik

    2010-01-01

    Every company situated within a chemical cluster faces the risk of being struck by an escalating accident at one of its neighbouring plants (the so-called external domino effect risks). These cross-plant risks can be reduced or eliminated if neighbouring companies are willing to invest in systems and measures to prevent them. However, since reducing such multi-plant risks does not lead to direct economic benefits, enterprises tend to be reluctant to invest more than needed for meeting minimal legal requirements and they tend to invest without collaborating. The suggested approach in this article indicates what information is required to evaluate the available investment options in external domino effects prevention. To this end, game theory is used as a promising scientific technique to investigate the decision-making process on investments in prevention measures simultaneously involving several plants. The game between two neighbouring chemical plants and their strategic investment behaviour regarding the prevention of external domino effects is described and an illustrative example is provided. Recommendations are formulated to advance cross-plant prevention investments in a two-company cluster.

  6. Quasi-chemical approach for adsorption of mixtures with non-additive lateral interactions

    Energy Technology Data Exchange (ETDEWEB)

    Pinto, O.A. [Instituto de Bionanotecnología (INBIONATEC-CONICET), Universidad Nacional de Santiago de Estero, RN 9 Km 1125 Villa el Zanjón, Santiago del Estero G4206XCP (Argentina); Pasinetti, P.M., E-mail: pmp@unsl.edu.ar [Departamento de Física, Instituto de Física Aplicada (INFAP), Universidad Nacional de San Luis—CONICET, Ejército de los Andes 950, D5700BWS San Luis (Argentina); Ramirez-Pastor, A.J. [Departamento de Física, Instituto de Física Aplicada (INFAP), Universidad Nacional de San Luis—CONICET, Ejército de los Andes 950, D5700BWS San Luis (Argentina)

    2017-01-15

    Highlights: • The classical quasi-chemical approach is generalized to model non-additive mixtures. • The formalism allows to obtain the partial isotherms and the differential heat of adsorption. • A rich variety of low-temperature phases is observed in the adsorbed layer. • Theoretical results show a good agreement with Monte Carlo simulations. - Abstract: The statistical thermodynamics of binary mixtures with non-additive lateral interactions was developed on a generalization in the spirit of the lattice-gas model and the classical quasi-chemical approximation (QCA). The traditional assumption of a strictly pairwise additive nearest-neighbors interaction is replaced by a more general one, namely that the bond linking a certain atom with any of its neighbors depends considerably on how many of them are actually present (or absent) on the sites in the first coordination shell of the atom. The total and partial adsorption isotherms are given for both attractive and repulsive lateral interactions between the adsorbed species. Interesting behaviors are observed and discussed in terms of the low-temperature phases formed in the system. Comparisons with Monte Carlo simulations are performed in order to test the validity of the theoretical model.

  7. An external domino effects investment approach to improve cross-plant safety within chemical clusters.

    Science.gov (United States)

    Reniers, Genserik

    2010-05-15

    Every company situated within a chemical cluster faces the risk of being struck by an escalating accident at one of its neighbouring plants (the so-called external domino effect risks). These cross-plant risks can be reduced or eliminated if neighbouring companies are willing to invest in systems and measures to prevent them. However, since reducing such multi-plant risks does not lead to direct economic benefits, enterprises tend to be reluctant to invest more than needed for meeting minimal legal requirements and they tend to invest without collaborating. The suggested approach in this article indicates what information is required to evaluate the available investment options in external domino effects prevention. To this end, game theory is used as a promising scientific technique to investigate the decision-making process on investments in prevention measures simultaneously involving several plants. The game between two neighbouring chemical plants and their strategic investment behaviour regarding the prevention of external domino effects is described and an illustrative example is provided. Recommendations are formulated to advance cross-plant prevention investments in a two-company cluster. Copyright (c) 2009 Elsevier B.V. All rights reserved.

  8. Management strategies for trace organic chemicals in water - A review of international approaches.

    Science.gov (United States)

    Bieber, Stefan; Snyder, Shane A; Dagnino, Sonia; Rauch-Williams, Tanja; Drewes, Jörg E

    2018-03-01

    To ensure an appropriate management of potential health risks and uncertainties from the release of trace organic chemicals (TOrCs) into the aqueous environment, many countries have evaluated and implemented strategies to manage TOrCs. The aim of this study was to evaluate existing management strategies for TOrCs in different countries to derive and compare underlying core principles and paradigms and to develop suggestions for more holistic management strategies to protect the environment and drinking water supplies from the discharge of undesired TOrCs. The strategies in different industrial countries were summarized and subsequently compared with regards to three particular questions: 1) Do the approaches different countries have implemented manage all or only specific portions of the universe of chemicals; 2) What implementation and compliance strategies are used to manage aquatic and human health risk and what are their pros and cons; and 3) How are site-specific watershed differences being addressed? While management strategies of the different countries target similar TOrCs, the programs differ in several important aspects, including underlying principles, the balance between aquatic or human health protection, implementation methods, and financing mechanisms used to fund regulatory programs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Effectiveness of bone cleaning process using chemical and entomology approaches: time and cost.

    Science.gov (United States)

    Lai, Poh Soon; Khoo, Lay See; Mohd Hilmi, Saidin; Ahmad Hafizam, Hasmi; Mohd Shah, Mahmood; Nurliza, Abdullah; Nazni, Wasi Ahmad

    2015-08-01

    Skeletal examination is an important aspect of forensic pathology practice, requiring effective bone cleaning with minimal artefact. This study was conducted to compare between chemical and entomology methods of bone cleaning. Ten subjects between 20 and 40 years old who underwent uncomplicated medico-legal autopsies at the Institute of Forensic Medicine Malaysia were randomly chosen for this descriptive cross sectional study. The sternum bone was divided into 4 parts, each part subjected to a different cleaning method, being two chemical approaches i.e. laundry detergent and a combination of 6% hydrogen peroxide and powder sodium bicarbonate and two entomology approaches using 2nd instar maggots of Chrysomyia rufifacies and Ophyra spinigera. A scoring system for grading the outcome of cleaning was used. The effectiveness of the methods was evaluated based on average weight reduction per day and median number of days to achieve the average score of less than 1.5 within 12 days of the bone cleaning process. Using maggots was the most time-effective and costeffective method, achieving an average weight reduction of 1.4 gm per day, a median of 11.3 days to achieve the desired score and an average cost of MYR 4.10 per case to reach the desired score within 12 days. This conclusion was supported by blind validation by forensic specialists achieving a 77.8% preference for maggots. Emission scanning electron microscopy evaluation also revealed that maggots especially Chrysomyia rufifacies preserved the original condition of the bones better allowing improved elucidation of bone injuries in future real cases.

  10. Biosafety risk assessment approaches for insect-resistant genetically modified crops

    Directory of Open Access Journals (Sweden)

    Inaam Ullah

    2017-02-01

    Full Text Available Background: Environmental risk assessment (ERA is imperative for commercial release of insect resistant, genetically modified crops (IR-GMCs.An insect specific, spider venom peptideω-HXTX-Hv1a (Hvt was successfully expressed in cotton plants. The cotton plants producing Hvt protein have demonstrated resistance against economically important insect pest species. The study was performed to assess the effects of Hvt producing cotton plants on Honey bees (Apis mellifera. Methods: Three approaches were used to evaluate the effects of Hvt protein on adults of honeybees; whole plant assays in flight cages, in vitro assays with pollen of Hvt-cotton, and assays with elevated levels of purified Hvt protein. Pollens of Bt cotton or purified Bt proteins were used as control. Results: The field experiments did not yield any meaningful data due to high rate of mortality in all treatments including the control. However, the laboratory experiments provided conclusive results in which Hvt, purified or in pollens, did not affect the survival or longevity of the bees compared to the control. During the course of study we were able to compare the quality, effectiveness and economics of different experiments. Conclusions: We conclude that Hvt either purified or produced in cotton plants do not affect the survival or longevity of honey bees. We are also of the view that starting at laboratory level assays not only gives meaningful data but also saves a lot of time and money that can be spent on other important questions regarding safety of a particular transgenic crop. Hence, a purpose-based, tiered approach could be the best choice for pre-release ERA of IR-GMCs.

  11. Chemical Topic Modeling: Exploring Molecular Data Sets Using a Common Text-Mining Approach.

    Science.gov (United States)

    Schneider, Nadine; Fechner, Nikolas; Landrum, Gregory A; Stiefl, Nikolaus

    2017-08-28

    Big data is one of the key transformative factors which increasingly influences all aspects of modern life. Although this transformation brings vast opportunities it also generates novel challenges, not the least of which is organizing and searching this data deluge. The field of medicinal chemistry is not different: more and more data are being generated, for instance, by technologies such as DNA encoded libraries, peptide libraries, text mining of large literature corpora, and new in silico enumeration methods. Handling those huge sets of molecules effectively is quite challenging and requires compromises that often come at the expense of the interpretability of the results. In order to find an intuitive and meaningful approach to organizing large molecular data sets, we adopted a probabilistic framework called "topic modeling" from the text-mining field. Here we present the first chemistry-related implementation of this method, which allows large molecule sets to be assigned to "chemical topics" and investigating the relationships between those. In this first study, we thoroughly evaluate this novel method in different experiments and discuss both its disadvantages and advantages. We show very promising results in reproducing human-assigned concepts using the approach to identify and retrieve chemical series from sets of molecules. We have also created an intuitive visualization of the chemical topics output by the algorithm. This is a huge benefit compared to other unsupervised machine-learning methods, like clustering, which are commonly used to group sets of molecules. Finally, we applied the new method to the 1.6 million molecules of the ChEMBL22 data set to test its robustness and efficiency. In about 1 h we built a 100-topic model of this large data set in which we could identify interesting topics like "proteins", "DNA", or "steroids". Along with this publication we provide our data sets and an open-source implementation of the new method (CheTo) which

  12. Somatic cell and molecular genetics approach to DNA repair and mutagenesis

    International Nuclear Information System (INIS)

    Thompson, L.H.

    1985-01-01

    In the CHO cell line, UV-sensitive mutants representing five genetic complementation groups have been identified. Mutants from each of these groups were shown to be defective in performing the incision step of repair after exposure to UV. The large number of complementation groups of xeroderma pigmentosa mutations has raised the question whether these groups all correspond to single gene loci. The same issue applies to the 5 groups of UV-sensitive CHO mutants. One approach toward answering this question is to localize in the human karyotype the genes that complement the defects in the CHO mutants. Thus, by making CHO/human cell hybrids under the appropriate selective conditions, we have begun to map each of the complementing human genes. The mutation in strain UV20 (Group 2) was complemented by human chromosome 19. Preliminary evidence suggests that UV5 may also be complemented by human chromosome 19 while each of the other 3 groups involves a different human chromosome. Somewhat surprisingly, mutant EM9 is also complemented by a gene on chromosome 19

  13. Control of bovine spongiform encephalopathy by genetic engineering: possible approaches and regulatory considerations

    International Nuclear Information System (INIS)

    Gavora, J.S.; Kochhar, H.P.S.; Gifford, G.A.

    2005-01-01

    Transmissible spongiform encephalopathies (TSE) include bovine spongiform encephalopathy (BSE), scrapie in sheep and Creutzfeldt-Jakob disease (CJD) in humans. A new CJD variant (nvCJD) is believed to be related to consumption of meat from BSE cattle. In TSE individuals, prion proteins (PrP) with approximately 250 amino acids convert to the pathogenic prion PrP Sc , leading to a dysfunction of the central neural system. Research elsewhere with mice has indicated a possible genetic engineering approach to the introduction of BSE resistance: individuals with amino acid substitutions at positions 167 or 218, inoculated with a pathogenic prion protein, did not support PrP Sc replication. This raises the possibility of producing prion-resistant cattle with a single PrP amino acid substitution. Since prion-resistant animals might still harbour acquired prion infectivity, regulatory assessment of the engineered animals would need to ascertain that such possible 'carriers' do not result in a threat to animal and human health. (author)

  14. Molecular genetic approach to human meningioma: loss of genes on chromosome 22

    International Nuclear Information System (INIS)

    Seizinger, B.R.; De La Monte, S.; Atkins, L.; Gusella, J.F.; Martuza, R.L.

    1987-01-01

    A molecular genetic approach employing polymorphic DNA markers has been used to investigate the role of chromosomal aberrations in meningioma, one of the most common tumors of the human nervous system. Comparison of the alleles detected by DNA markers in tumor DNA versus DNA from normal tissue revealed chromosomal alterations present in primary surgical specimens. In agreement with cytogenetic studies of cultured meningiomas, the most frequent alteration detected was loss of heterozygosity on chromosome 22. Forty of 51 patients were constitutionally heterozygous for at least one chromosome 22 DNA marker. Seventeen of the 40 constitutionally heterozygotic patients (43%) displayed hemizygosity for the corresponding marker in their meningioma tumor tissues. Loss of heterozygosity was also detected at a significantly lower frequency for markers on several other autosomes. In view of the striking association between acoustic neuroma and meningioma in bilateral acoustic neurofibromatosis and the discovery that acoustic neuromas display specific loss of genes on chromosome 22, the authors propose that a common mechanism involving chromosome 22 is operative in the development of both tumor types. Fine-structure mapping to reveal partial deletions in meningiomas may provide the means to clone and characterize a gene (or genes) of importance for tumorigenesis in this and possibly other clinically associated tumors of the human nervous system

  15. Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review

    Directory of Open Access Journals (Sweden)

    Ibrahim B. Salisu

    2017-10-01

    Full Text Available As long as the genetically modified crops are gaining attention globally, their proper approval and commercialization need accurate and reliable diagnostic methods for the transgenic content. These diagnostic techniques are mainly divided into two major groups, i.e., identification of transgenic (1 DNA and (2 proteins from GMOs and their products. Conventional methods such as PCR (polymerase chain reaction and enzyme-linked immunosorbent assay (ELISA were routinely employed for DNA and protein based quantification respectively. Although, these Techniques (PCR and ELISA are considered as significantly convenient and productive, but there is need for more advance technologies that allow for high throughput detection and the quantification of GM event as the production of more complex GMO is increasing day by day. Therefore, recent approaches like microarray, capillary gel electrophoresis, digital PCR and next generation sequencing are more promising due to their accuracy and precise detection of transgenic contents. The present article is a brief comparative study of all such detection techniques on the basis of their advent, feasibility, accuracy, and cost effectiveness. However, these emerging technologies have a lot to do with detection of a specific event, contamination of different events and determination of fusion as well as stacked gene protein are the critical issues to be addressed in future.

  16. Combined Simulated Annealing and Genetic Algorithm Approach to Bus Network Design

    Science.gov (United States)

    Liu, Li; Olszewski, Piotr; Goh, Pong-Chai

    A new method - combined simulated annealing (SA) and genetic algorithm (GA) approach is proposed to solve the problem of bus route design and frequency setting for a given road network with fixed bus stop locations and fixed travel demand. The method involves two steps: a set of candidate routes is generated first and then the best subset of these routes is selected by the combined SA and GA procedure. SA is the main process to search for a better solution to minimize the total system cost, comprising user and operator costs. GA is used as a sub-process to generate new solutions. Bus demand assignment on two alternative paths is performed at the solution evaluation stage. The method was implemented on four theoretical grid networks of different size and a benchmark network. Several GA operators (crossover and mutation) were utilized and tested for their effectiveness. The results show that the proposed method can efficiently converge to the optimal solution on a small network but computation time increases significantly with network size. The method can also be used for other transport operation management problems.

  17. A group approach to genetic counselling of cardiomyopathy patients: satisfaction and psychological outcomes sufficient for further implementation.

    Science.gov (United States)

    Otten, Ellen; Birnie, Erwin; Ranchor, Adelita V; van Tintelen, J Peter; van Langen, Irene M

    2015-11-01

    The introduction of next-generation sequencing in everyday clinical genetics practise is increasing the number of genetic disorders that can be confirmed at DNA-level, and consequently increases the possibilities for cascade screening. This leads to a greater need for genetic counselling, whereas the number of professionals available to provide this is limited. We therefore piloted group genetic counselling for symptomatic cardiomyopathy patients at regional hospitals, to assess whether this could be an acceptable alternative to individual counselling. We performed a cohort study with pre- and post-counselling patient measurements using questionnaires, supplemented with evaluations of the group counselling format by the professionals involved. Patients from eight regional hospitals in the northern part of the Netherlands were included. Questionnaires comprised patient characteristics, psychological measures (personal perceived control (PPC), state and trait anxiety inventory (STAI)), and satisfaction with counsellors, counselling content and design. In total, 82 patients (mean age 57.5 year) attended one of 13 group sessions. Median PPC and STAI scores showed significantly higher control and lower anxiety after the counselling. Patients reported they were satisfied with the counsellors, and almost 75% of patients were satisfied with the group counselling. Regional professionals were also, overall, satisfied with the group sessions. The genetics professionals were less satisfied, mainly because of their perceived large time investment and less-than-expected group interaction. Hence, a group approach to cardiogenetic counselling is feasible, accessible, and psychologically effective, and could be one possible approach to counselling the increasing patient numbers in cardiogenetics.

  18. A comparison of mandatory and voluntary approaches to the implementation of Globally Harmonized System of Classification and Labelling of Chemicals (GHS) in the management of hazardous chemicals.

    Science.gov (United States)

    Ta, Goh Choo; Mokhtar, Mazlin Bin; Peterson, Peter John; Yahaya, Nadzri Bin

    2011-01-01

    The European Union (EU) and the World Health Organization (WHO) have applied different approaches to facilitate the implementation of the UN Globally Harmonized System of Classification and Labelling of Chemicals (GHS). The EU applied the mandatory approach by gazetting the EU Regulation 1272/2008 incorporating GHS elements on classification, labelling and packaging of substances and mixtures in 2008; whereas the WHO utilized a voluntary approach by incorporating GHS elements in the WHO guidelines entitled 'WHO Recommended Classification of Pesticides by Hazard' in 2009. We report on an analysis of both the mandatory and voluntary approaches practised by the EU and the WHO respectively, with close reference to the GHS 'purple book'. Our findings indicate that the mandatory approach practiced by the EU covers all the GHS elements referred to in the second revised edition of the GHS 'purple book'. Hence we can conclude that the EU has implemented the GHS particularly for industrial chemicals. On the other hand, the WHO guidelines published in 2009 should be revised to address concerns raised in this paper. In addition, both mandatory and voluntary approaches should be carefully examined because the classification results may be different.

  19. Equilibrium and non-equilibrium concepts in forest genetic modelling: population- and individually-based approaches

    OpenAIRE

    Kramer, Koen; van der Werf, D. C.

    2010-01-01

    The environment is changing and so are forests, in their functioning, in species composition, and in the species’ genetic composition. Many empirical and process-based models exist to support forest management. However, most of these models do not consider the impact of environmental changes and forest management on genetic diversity nor on the rate of adaptation of critical plant processes. How genetic diversity and rates of adaptation depend on management actions is a crucial next step in m...

  20. 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.

  1. Quantitative genetics of Taura syndrome resistance in Pacific (Penaeus vannamei): A cure model approach

    DEFF Research Database (Denmark)

    Ødegård, Jørgen; Gitterle, Thomas; Madsen, Per

    2011-01-01

    cure survival model using Gibbs sampling, treating susceptibility and endurance as separate genetic traits. Results: Overall mortality at the end of test was 28%, while 38% of the population was considered susceptible to the disease. The estimated underlying heritability was high for susceptibility (0....... However, genetic evaluation of susceptibility based on the cure model showed clear associations with standard genetic evaluations that ignore the cure fraction for these data. Using the current testing design, genetic variation in observed survival time and absolute survival at the end of test were most...

  2. Safety of genetically engineered foods: approaches to assessing unintended health effects

    National Research Council Canada - National Science Library

    Committee on Identifying and Assessing Unintended Effects of Genetically Engineered Foods on Human Health, National Research Council

    2004-01-01

    Assists policymakers in evaluating the appropriate scientific methods for detecting unintended changes in food and assessing the potential for adverse health effects from genetically modified products...

  3. Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.

    Science.gov (United States)

    Siegbahn, Per E M; Himo, Fahmi

    2009-06-01

    The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.

  4. The overpressure protection for the chemical reactors: the batch-size approach

    International Nuclear Information System (INIS)

    Dellavedova, M.; Gigante, L.; Lunghi, A.; Pasturenzi, C.; Cardillo, P.; Gerosa, N.P.; Rota, R.

    2008-01-01

    Small and medium enterprises (SMEs) main feature is to run batch and semi-batch processes, working on job orders. They generally have multi propose reactors with an emergency relief system (ERS) already installed. These are normally sized when the reactor is designed, assuming as worst incidental scenario a single phase vapour flow generated by a fire developed outside the apparatus. These assumptions can lead to a big underestimation of the vent area if the actual flow is two-phase and besides generated by a runaway reaction. ERS sizing is particularly hazardous and complex for small mills, as for example fine chemicals and pharmaceutical companies. These factories have usually narrow financial and personal resources, moreover they often use fast processes turnovers. In many cases a complete safety study or the replacement of the ERS is not possible and it can lead to not sustainable costs. The batch-size approach is focused on discontinuous process conditions: aim of this approach is to find the reactor fill level that can lead a vapour single phase flow whether an incident occurs, this condition is considered safe that the ERS installed on the reactor can protect the plant from explosions [it

  5. Poromechanics Parameters of Fluid-Saturated Chemically Active Fibrous Media Derived from a Micromechanical Approach.

    Science.gov (United States)

    Misra, Anil; Parthasarathy, Ranganathan; Singh, Viraj; Spencer, Paulette

    2013-01-01

    The authors have derived macroscale poromechanics parameters for chemically active saturated fibrous media by combining microstructure-based homogenization with Hill's volume averaging. The stress-strain relationship of the dry fibrous media is first obtained by considering the fiber behavior. The constitutive relationships applicable to saturated media are then derived in the poromechanics framework using Hill's Lemmas. The advantage of this approach is that the resultant continuum model assumes a form suited to study porous materials, while retaining the effect of discrete fiber deformation. As a result, the model is able to predict the influence of microscale phenomena such as fiber buckling on the overall behavior, and in particular, on the poromechanics constants. The significance of the approach is demonstrated using the effect of drainage and fiber nonlinearity on monotonic compressive stress-strain behavior. The model predictions conform to the experimental observations for articular cartilage. The method can potentially be extended to other porous materials such as bone, clays, foams, and concrete.

  6. Nanomaterial processing using self-assembly-bottom-up chemical and biological approaches

    International Nuclear Information System (INIS)

    Thiruvengadathan, Rajagopalan; Gangopadhyay, Keshab; Gangopadhyay, Shubhra; Korampally, Venumadhav; Ghosh, Arkasubhra; Chanda, Nripen

    2013-01-01

    Nanotechnology is touted as the next logical sequence in technological evolution. This has led to a substantial surge in research activities pertaining to the development and fundamental understanding of processes and assembly at the nanoscale. Both top-down and bottom-up fabrication approaches may be used to realize a range of well-defined nanostructured materials with desirable physical and chemical attributes. Among these, the bottom-up self-assembly process offers the most realistic solution toward the fabrication of next-generation functional materials and devices. Here, we present a comprehensive review on the physical basis behind self-assembly and the processes reported in recent years to direct the assembly of nanoscale functional blocks into hierarchically ordered structures. This paper emphasizes assembly in the synthetic domain as well in the biological domain, underscoring the importance of biomimetic approaches toward novel materials. In particular, two important classes of directed self-assembly, namely, (i) self-assembly among nanoparticle–polymer systems and (ii) external field-guided assembly are highlighted. The spontaneous self-assembling behavior observed in nature that leads to complex, multifunctional, hierarchical structures within biological systems is also discussed in this review. Recent research undertaken to synthesize hierarchically assembled functional materials have underscored the need as well as the benefits harvested in synergistically combining top-down fabrication methods with bottom-up self-assembly. (review article)

  7. Resolving the chemical nature of nanodesigned silica surface obtained via a bottom-up approach.

    Science.gov (United States)

    Rahma, Hakim; Buffeteau, Thierry; Belin, Colette; Le Bourdon, Gwenaëlle; Degueil, Marie; Bennetau, Bernard; Vellutini, Luc; Heuzé, Karine

    2013-08-14

    The covalent grafting on silica surfaces of a functional dendritic organosilane coupling agent inserted, in a long alkyl chain monolayer, is described. In this paper, we show that depending on experimental parameters, particularly the solvent, it is possible to obtain a nanodesigned surface via a bottom-up approach. Thus, we succeed in the formation of both homogeneous dense monolayer and a heterogeneous dense monolayer, the latter being characterized by a nanosized volcano-type pattern (4-6 nm of height, 100 nm of width, and around 3 volcanos/μm(2)) randomly distributed over the surface. The dendritic attribute of the grafted silylated coupling agent affords enough anchoring sites to immobilize covalently functional gold nanoparticles (GNPs), coated with amino PEG polymer to resolve the chemical nature of the surfaces and especially the volcano type nanopattern structures of the heterogeneous monolayer. Thus, the versatile surface chemistry developed herein is particularly challenging as the nanodesign is straightforward achieved in a bottom-up approach without any specific lithography device.

  8. In silico prediction of toxicity of phenols to Tetrahymena pyriformis by using genetic algorithm and decision tree-based modeling approach.

    Science.gov (United States)

    Abbasitabar, Fatemeh; Zare-Shahabadi, Vahid

    2017-04-01

    Risk assessment of chemicals is an important issue in environmental protection; however, there is a huge lack of experimental data for a large number of end-points. The experimental determination of toxicity of chemicals involves high costs and time-consuming process. In silico tools such as quantitative structure-toxicity relationship (QSTR) models, which are constructed on the basis of computational molecular descriptors, can predict missing data for toxic end-points for existing or even not yet synthesized chemicals. Phenol derivatives are known to be aquatic pollutants. With this background, we aimed to develop an accurate and reliable QSTR model for the prediction of toxicity of 206 phenols to Tetrahymena pyriformis. A multiple linear regression (MLR)-based QSTR was obtained using a powerful descriptor selection tool named Memorized_ACO algorithm. Statistical parameters of the model were 0.72 and 0.68 for R training 2 and R test 2 , respectively. To develop a high-quality QSTR model, classification and regression tree (CART) was employed. Two approaches were considered: (1) phenols were classified into different modes of action using CART and (2) the phenols in the training set were partitioned to several subsets by a tree in such a manner that in each subset, a high-quality MLR could be developed. For the first approach, the statistical parameters of the resultant QSTR model were improved to 0.83 and 0.75 for R training 2 and R test 2 , respectively. Genetic algorithm was employed in the second approach to obtain an optimal tree, and it was shown that the final QSTR model provided excellent prediction accuracy for the training and test sets (R training 2 and R test 2 were 0.91 and 0.93, respectively). The mean absolute error for the test set was computed as 0.1615. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Genetic and Computational Approaches for Studying Plant Development and Abiotic Stress Responses Using Image-Based Phenotyping

    Science.gov (United States)

    Campbell, M. T.; Walia, H.; Grondin, A.; Knecht, A.

    2017-12-01

    The development of abiotic stress tolerant crops (i.e. drought, salinity, or heat stress) requires the discovery of DNA sequence variants associated with stress tolerance-related traits. However, many traits underlying adaptation to abiotic stress involve a suite of physiological pathways that may be induced at different times throughout the duration of stress. Conventional single-point phenotyping approaches fail to fully capture these temporal responses, and thus downstream genetic analysis may only identify a subset of the genetic variants that are important for adaptation to sub-optimal environments. Although genomic resources for crops have advanced tremendously, the collection of phenotypic data for morphological and physiological traits is laborious and remains a significant bottleneck in bridging the phenotype-genotype gap. In recent years, the availability of automated, image-based phenotyping platforms has provided researchers with an opportunity to collect morphological and physiological traits non-destructively in a highly controlled environment. Moreover, these platforms allow abiotic stress responses to be recorded throughout the duration of the experiment, and have facilitated the use of function-valued traits for genetic analyses in major crops. We will present our approaches for addressing abiotic stress tolerance in cereals. This talk will focus on novel open-source software to process and extract biological meaningful data from images generated from these phenomics platforms. In addition, we will discuss the statistical approaches to model longitudinal phenotypes and dissect the genetic basis of dynamic responses to these abiotic stresses throughout development.

  10. A bio-cultural approach to the study of food choice: The contribution of taste genetics, population and culture.

    Science.gov (United States)

    Risso, Davide S; Giuliani, Cristina; Antinucci, Marco; Morini, Gabriella; Garagnani, Paolo; Tofanelli, Sergio; Luiselli, Donata

    2017-07-01

    The study of food choice, one of the most complex human traits, requires an integrated approach that takes into account environmental, socio-cultural and biological diversity. We recruited 183 volunteers from four geo-linguistic groups and highly diversified in terms of both genetic background and food habits from whom we collected genotypes and phenotypes tightly linked to taste perception. We confirmed previous genetic associations, in particular with stevioside perception, and noted significant differences in food consumption: in particular, broccoli, mustard and beer consumption scores were significantly higher (Adjusted P = 0.02, Adjusted P diversity and cultural aspects in taste perception and food consumption. Published by Elsevier Ltd.

  11. Approaches in the risk assessment of genetically modified foods by the Hellenic Food Safety Authority.

    Science.gov (United States)

    Varzakas, Theodoros H; Chryssochoidis, G; Argyropoulos, D

    2007-04-01

    Risk analysis has become important to assess conditions and take decisions on control procedures. In this context it is considered a prerequisite in the evaluation of GM food. Many consumers worldwide worry that food derived from genetically modified organisms (GMOs) may be unhealthy and hence regulations on GMO authorisations and labelling have become more stringent. Nowadays there is a higher demand for non-GM products and these products could be differentiated from GM products using the identity preservation system (IP) that could apply throughout the grain processing system. IP is the creation of a transparent communication system that encompasses HACCP, traceability and related systems in the supply chain. This process guarantees that certain characteristics of the lots of food (non-GM origin) are maintained "from farm to fork". This article examines the steps taken by the Hellenic Food Safety Authority to examine the presence of GMOs in foods. The whole integrated European legislation framework currently in place still needs to be implemented in Greece. Penalties should be enforced to those who import, process GMOs without special licence and do not label those products. Similar penalties should be enforced to those companies that issue false certificates beyond the liabilities taken by the food enterprises for farmers' compensation. We argue that Greece has no serious reasons to choose the use of GMOs due to the fact that the structural and pedologic characteristics of the Greek agriculture favour the biological and integrated cultivation more. Greece is not in favour of the politics behind coexistence of conventional and GM plants and objects to the use of GMOs in the food and the environment because the processor has a big burden in terms of money, time and will suffer a great deal in order to prove that their products are GMO free or that any contamination is adventitious or technically unavoidable. Moreover, Greece owns a large variety of genetic

  12. 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.

  13. A crystal chemical approach to superconductivity. I. A bond-valence sum analysis of inorganic compounds

    International Nuclear Information System (INIS)

    Liebau, Friedrich; Klein, Hans-Joachim; Wang, Xiqu

    2011-01-01

    A crystal-chemical approach to superconductivity is described that is intended to complement the corresponding physical approach. The former approach takes into account the distinction between the stoichiometric valence ( stoich V) and the structural valence ( struct V) which is represented by the bond-valence sums (BVS). Through calculations of BVS values from crystal-structure data determined at ambient temperature and pressure it has been found that in chalcogenides und pnictides of the transition metals Fe, Co, Ni, Mn, Hf, and Zr the atoms of the potential superconducting units yield values of vertical stroke BVS vertical stroke = vertical stroke struct V vertical stroke ≥ 1.11 x vertical stroke stoich V vertical stroke, whereas the atoms of the charge reservoirs have in general values of vertical stroke struct V vertical stroke stoich V vertical stroke. In corresponding compounds which contain the same elements but are not becoming superconducting, nearly all atoms are found to have vertical stroke struct V vertical stroke stoich V vertical stroke. For atoms of oxocuprates that are not becoming superconducting and for atoms of the charge reservoirs of oxocuprates that become superconducting, the relation vertical stroke struct V vertical stroke stoich V vertical stroke seems also to be fulfilled, with the exception of Ba. However, in several oxocuprates the relation vertical stroke struct V vertical stroke = 1.11 x vertical stroke stoich V vertical stroke for the atoms that become superconducting units is violated. These violations seem to indicate that in oxocuprates it is the local bond-valence distribution rather than the bond-valence sums that is essential for superconductivity. The present analysis can possibly be used to predict, by a simple consideration of ambient-T, P structures, whether a compound can become an unconventional superconductor at low T, under high P and/or by doping, or not. (orig.)

  14. The behavior of various chemical forms of nickel in graphite furnace atomic absorption spectrometry under different chemical modification approaches

    International Nuclear Information System (INIS)

    Kowalewska, Zofia

    2012-01-01

    Various organic and inorganic Ni forms were investigated using graphite furnace atomic absorption spectrometry. Experiments without chemical modification showed a wide range of characteristic mass values for Ni (from 6.7 to 29 pg) and the importance of interaction with graphite. With the aim of achieving signal unification of organic Ni forms, different ways of chemical modification were tested. Some rules that govern the behavior of Ni were found and confirmed a significant role of the organic component of the analyte molecule in the analytical process. The application of air as an internal furnace gas in the pyrolysis phase and the Pd modifier injected with the sample solution improved the signal of porphyrins, while the application of iodine and methyltrioctylammonium chloride was required for organic compounds containing oxygen-bound Ni atoms. The Ni signal was strongly diminished when an aqueous solution containing hydrochloric acid was measured with the Pd modifier injected over the sample. Using the developed analytical methods, the range of characteristic mass values for various Ni forms totally dissolved in organic or aqueous solution was 6.5–7.9 pg. - Highlights: ► Some rules that govern behavior of organic Ni forms during GFAAS analysis were found. ► Interaction with graphite can significantly influence evaporation of porphyrins. ► Determination of Ni in form of porphyrins needs Pd organic modifier and air ashing. ► Determination of Ni in O-bound organic compounds needs pretreatment with I2+MTOACl. ► Chemical modification for GFAAS determination of Ni in HCl-containing solution.

  15. Ecological risk assessment of mixtures of radiological and chemical stressors: Methodology to implement an msPAF approach

    International Nuclear Information System (INIS)

    Beaumelle, Léa; Della Vedova, Claire; Beaugelin-Seiller, Karine; Garnier-Laplace, Jacqueline; Gilbin, Rodolphe

    2017-01-01

    A main challenge in ecological risk assessment is to account for the impact of multiple stressors. Nuclear facilities can release both radiological and chemical stressors in the environment. This study is the first to apply species sensitivity distribution (SSD) combined with mixture models (concentration addition (CA) and independent action (IA)) to derive an integrated proxy of the ecological impact of combined radiological and chemical stressors: msPAF (multisubstance potentially affected fraction of species). The approach was tested on the routine liquid effluents from nuclear power plants that contain both radioactive and stable chemicals. The SSD of ionising radiation was significantly flatter than the SSD of 8 stable chemicals (namely Cr, Cu, Ni, Pb, Zn, B, chlorides and sulphates). This difference in shape had strong implications for the selection of the appropriate mixture model: contrarily to the general expectations the IA model gave more conservative (higher msPAF) results than the CA model. The msPAF approach was further used to rank the relative potential impact of radiological versus chemical stressors. - Highlights: • msPAF methodology was applied on mixtures of radiological and chemical stressors. • A consistent set of chronic SSDs was collected for ionising radiation and 8 stable chemicals. • The SSD of ionising radiation had lower steepness than the SSD of stable chemicals. • This resulted in higher msPAF values based on the IA than on the CA mixture model. - The msPAF approach combining SSD and mixture models was used for the first time on mixtures of radiological and chemical stressors.

  16. A new approach to nuclear reactor design optimization using genetic algorithms and regression analysis

    International Nuclear Information System (INIS)

    Kumar, Akansha; Tsvetkov, Pavel V.

    2015-01-01

    Highlights: • This paper presents a new method useful for the optimization of complex dynamic systems. • The method uses the strengths of; genetic algorithms (GA), and regression splines. • The method is applied to the design of a gas cooled fast breeder reactor design. • Tools like Java, R, and codes like MCNP, Matlab are used in this research. - Abstract: A module based optimization method using genetic algorithms (GA), and multivariate regression analysis has been developed to optimize a set of parameters in the design of a nuclear reactor. GA simulates natural evolution to perform optimization, and is widely used in recent times by the scientific community. The GA fits a population of random solutions to the optimized solution of a specific problem. In this work, we have developed a genetic algorithm to determine the values for a set of nuclear reactor parameters to design a gas cooled fast breeder reactor core including a basis thermal–hydraulics analysis, and energy transfer. Multivariate regression is implemented using regression splines (RS). Reactor designs are usually complex and a simulation needs a significantly large amount of time to execute, hence the implementation of GA or any other global optimization techniques is not feasible, therefore we present a new method of using RS in conjunction with GA. Due to using RS, we do not necessarily need to run the neutronics simulation for all the inputs generated from the GA module rather, run the simulations for a predefined set of inputs, build a multivariate regression fit to the input and the output parameters, and then use this fit to predict the output parameters for the inputs generated by GA. The reactor parameters are given by the, radius of a fuel pin cell, isotopic enrichment of the fissile material in the fuel, mass flow rate of the coolant, and temperature of the coolant at the core inlet. And, the optimization objectives for the reactor core are, high breeding of U-233 and Pu-239 in

  17. Responsible genetic approach to stock restoration, sea ranching and stock enhancement of marine fishes and invertebrates

    DEFF Research Database (Denmark)

    Grant, W. Stewart; Jasper, James; Bekkevold, Dorte

    2017-01-01

    of marine fishes and invertebrates have been implemented with various outcomes. A review of the literature indicates that considerable effort has been directed toward culture technologies to maximize production, but scant attention has been given to genetic risks to wild populations. Genetic risks from...

  18. Minimal approaches to genetic improvement of growth rates in white spruce

    Science.gov (United States)

    D.T. Lester

    1973-01-01

    Several features of central importance to genetic improvement of white spruce have been demonstrated by tree breeders. First, white spruce is genetically a highly variable species and much of the existent variation can be readily incorporated in planting stock (Jeffers 1969, Holst and Teich 1969). Second, local seed often is not the best for rapid growth (Nienstaedt...

  19. A Top-down Approach to Genetic Circuit Synthesis and Optimized Technology Mapping

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2017-01-01

    Genetic logic circuits are becoming popular as an emerging field of technology. They are composed of genetic parts of DNA and work inside a living cell to perform a dedicated boolean function triggered by the presence or absence of certain proteins or other species....

  20. A Powerful Approach to Estimating Annotation-Stratified Genetic Covariance via GWAS Summary Statistics.

    Science.gov (United States)

    Lu, Qiongshi; Li, Boyang; Ou, Derek; Erlendsdottir, Margret; Powles, Ryan L; Jiang, Tony; Hu, Yiming; Chang, David; Jin, Chentian; Dai, Wei; He, Qidu; Liu, Zefeng; Mukherjee, Shubhabrata; Crane, Paul K; Zhao, Hongyu

    2017-12-07

    Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits' genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics. Through theoretical and numerical analyses, we demonstrate that our method provides accurate covariance estimates, thereby enabling researchers to dissect both the shared and distinct genetic architecture across traits to better understand their etiologies. Among 50 complex traits with publicly accessible GWAS summary statistics (N total ≈ 4.5 million), we identified more than 170 pairs with statistically significant genetic covariance. In particular, we found strong genetic covariance between late-onset Alzheimer disease (LOAD) and amyotrophic lateral sclerosis (ALS), two major neurodegenerative diseases, in single-nucleotide polymorphisms (SNPs) with high minor allele frequencies and in SNPs located in the predicted functional genome. Joint analysis of LOAD, ALS, and other traits highlights LOAD's correlation with cognitive traits and hints at an autoimmune component for ALS. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  1. Review of laboratory-based terrestrial bioaccumulation assessment approaches for organic chemicals: Current status and future possibilities.

    Science.gov (United States)

    Hoke, Robert; Huggett, Duane; Brasfield, Sandra; Brown, Becky; Embry, Michelle; Fairbrother, Anne; Kivi, Michelle; Paumen, Miriam Leon; Prosser, Ryan; Salvito, Dan; Scroggins, Rick

    2016-01-01

    In the last decade, interest has been renewed in approaches for the assessment of the bioaccumulation potential of chemicals, principally driven by the need to evaluate large numbers of chemicals as part of new chemical legislation, while reducing vertebrate test organism use called for in animal welfare legislation. This renewed interest has inspired research activities and advances in bioaccumulation science for neutral organic chemicals in aquatic environments. In January 2013, ILSI Health and Environmental Sciences Institute convened experts to identify the state of the science and existing shortcomings in terrestrial bioaccumulation assessment of neutral organic chemicals. Potential modifications to existing laboratory methods were identified, including areas in which new laboratory approaches or test methods could be developed to address terrestrial bioaccumulation. The utility of "non-ecotoxicity" data (e.g., mammalian laboratory data) was also discussed. The highlights of the workshop discussions are presented along with potential modifications in laboratory approaches and new test guidelines that could be used for assessing the bioaccumulation of chemicals in terrestrial organisms. © 2015 SETAC.

  2. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach

    Directory of Open Access Journals (Sweden)

    Amr T. M. Saeb

    2016-01-01

    Full Text Available Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases.

  3. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw (Poland); Gómez-Sicilia, Àngel [Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid (Spain); Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/Faraday 9, 28049 Cantoblanco (Madrid) (Spain)

    2015-12-28

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  4. Chemical characterisation of the whole plant cell wall of archaeological wood: an integrated approach.

    Science.gov (United States)

    Zoia, Luca; Tamburini, Diego; Orlandi, Marco; Łucejko, Jeannette Jacqueline; Salanti, Anika; Tolppa, Eeva-Liisa; Modugno, Francesca; Colombini, Maria Perla

    2017-07-01

    Wood artefacts undergo complex alteration and degradation during ageing, and gaining information on the chemical composition of wood in archaeological artefacts is fundamental to plan conservation strategies. In this work, an integrated analytical approach based on innovative NMR spectroscopy procedures, gel permeation chromatography and analytical pyrolysis coupled with gas chromatography/mass spectrometry (Py-GC-MS) was applied for the first time on archaeological wood from the Oseberg collection (Norway), in order to evaluate the chemical state of preservation of the wood components, without separating them. We adopted ionic liquids (ILs) as non-derivatising solvents, thus obtaining an efficient dissolution of the wood, allowing us to overcome the difficulty of dissolving wood in its native form in conventional molecular solvents. Highly substituted lignocellulosic esters were therefore obtained under mild conditions by reacting the solubilised wood with either acetyl chloride or benzoyl chloride. A phosphytilation reaction was also performed using 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholan. As a result, the functionalised wood developed an enhanced solubility in molecular solvents, thus enabling information about modifications of lignin, depolymerisation of cellulose and structure of lignin-carbohydrate complexes to be obtained by means of spectroscopic (2D-HSQC-NMR and 31 P-NMR) and chromatographic (gel permeation chromatography) techniques. Py-GC-MS was used to investigate the degradation undergone by the lignocellulosic components on the basis of their pyrolysis products, without any pre-treatment of the samples. The application of all these combined techniques enabled a comprehensive characterisation of the whole cell wall of archaeological wood and the evaluation of its state of preservation. High depletion of carbohydrates and high extent of lignin oxidation were highlighted in the alum-treated objects, whereas a good preservation state was found

  5. An approach to enhance self-compensation capability in paper-based devices for chemical sensing.

    Science.gov (United States)

    Lo, Shih-Jie; Chen, Kuan-Hung; Yao, Da-Jeng

    2015-12-01

    This paper describes a simple design for increasing the tolerance of reagent dislocation on a paper-based platform using a combination of wax-treated paper and a vortex mixer. To date, massive budgetary funds are required in the biotechnological industry to develop new applications; a large part of that cost is attributable to the screening of specific chemical compounds. Here, we propose using a liquid-handling robot to automatically deposit selected reagents on a paper-based platform. We also present a preliminary concept approach for developing a reagent placing device with simple and inexpensive features. A defect of inaccuracy was observed between droplet location and test well location after viewing the performance of the liquid-handling robot on our paper-based platform. Because of dislocation error resulting from robotic reagent placement, we decided to apply an external, rotational force following droplet placement in order to compensate for the distance of reagent dislocation. Note, the largest distance of reagent dislocation was determined by examining the results of altering applied reagent volume, but not concentration, in volumes from 5 µL to 30 µL in a series of experiments. As a result of these experiments, we observed that dislocation was positively affected by an increase in applied volume. A colorimetric assay for nitrite detection was also performed to confirm the feasibility of this method. This work, we believe, can minimize the cost of chemical compound screening for the biotechnological industry. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Chemical composition, plant genetic differences, and antifungal activity of the essential oil of Helichrysum italicum G. Don ssp. microphyllum (Willd) Nym.

    Science.gov (United States)

    Angioni, Alberto; Barra, Andrea; Arlorio, Marco; Coisson, Jean Daniel; Russo, Maria T; Pirisi, Filippo M; Satta, Maurizio; Cabras, Paolo

    2003-02-12

    The chemical composition of the essential oil of the Sardinian dwarf curry plant [Helichrysum italicum G. Don ssp. microphyllum (Willd) Nym] was studied. Genetic analysis suggested the presence of two chemotypes; morphological and chemical differences confirmed the presence of two chemotypes (A and B). The maximum yields were 0.18 and 0.04% (v/w) for flowering tops and stems, respectively. The concentrations of nerol and its esters (acetate and propionate), limonene, and linalool reach their highest values during the flowering stage both in flowers and in stems. Besides the essential oil, type B showed an interesting antifungal activity.

  7. Chemical Genetic Analysis and Functional Characterization of Staphylococcal Wall Teichoic Acid 2-Epimerases Reveals Unconventional Antibiotic Drug Targets

    Energy Technology Data Exchange (ETDEWEB)

    Mann, Paul A.; Müller, Anna; Wolff, Kerstin A.; Fischmann, Thierry; Wang, Hao; Reed, Patricia; Hou, Yan; Li, Wenjin; Müller, Christa E.; Xiao, Jianying; Murgolo, Nicholas; Sher, Xinwei; Mayhood, Todd; Sheth, Payal R.; Mirza, Asra; Labroli, Marc; Xiao, Li; McCoy, Mark; Gill, Charles J.; Pinho, Mariana G.; Schneider, Tanja; Roemer, Terry (Merck); (Bonn); (FCT/UNL)

    2016-05-04

    Here we describe a chemical biology strategy performed in Staphylococcus aureus and Staphylococcus epidermidis to identify MnaA, a 2-epimerase that we demonstrate interconverts UDP-GlcNAc and UDP-ManNAc to modulate substrate levels of TarO and TarA wall teichoic acid (WTA) biosynthesis enzymes. Genetic inactivation of mnaA results in complete loss of WTA and dramatic in vitro β-lactam hypersensitivity in methicillin-resistant S. aureus (MRSA) and S. epidermidis (MRSE). Likewise, the β-lactam antibiotic imipenem exhibits restored bactericidal activity against mnaA mutants in vitro and concomitant efficacy against 2-epimerase defective strains in a mouse thigh model of MRSA and MRSE infection. Interestingly, whereas MnaA serves as the sole 2-epimerase required for WTA biosynthesis in S. epidermidis, MnaA and Cap5P provide compensatory WTA functional roles in S. aureus. We also demonstrate that MnaA and other enzymes of WTA biosynthesis are required for biofilm formation in MRSA and MRSE. We further determine the 1.9Å crystal structure of S. aureus MnaA and identify critical residues for enzymatic dimerization, stability, and substrate binding. Finally, the natural product antibiotic tunicamycin is shown to physically bind MnaA and Cap5P and inhibit 2-epimerase activity, demonstrating that it inhibits a previously unanticipated step in WTA biosynthesis. In summary, MnaA serves as a new Staphylococcal antibiotic target with cognate inhibitors predicted to possess dual therapeutic benefit: as combination agents to restore β-lactam efficacy against MRSA and MRSE and as non-bioactive prophylactic agents to prevent Staphylococcal biofilm formation.

  8. Virus fitness differences observed between two naturally occurring isolates of Ebola virus Makona variant using a reverse genetics approach.

    Science.gov (United States)

    Albariño, César G; Guerrero, Lisa Wiggleton; Chakrabarti, Ayan K; Kainulainen, Markus H; Whitmer, Shannon L M; Welch, Stephen R; Nichol, Stuart T

    2016-09-01

    During the large outbreak of Ebola virus disease that occurred in Western Africa from late 2013 to early 2016, several hundred Ebola virus (EBOV) genomes have been sequenced and the virus genetic drift analyzed. In a previous report, we described an efficient reverse genetics system designed to generate recombinant EBOV based on a Makona variant isolate obtained in 2014. Using this system, we characterized the replication and fitness of 2 isolates of the Makona variant. These virus isolates are nearly identical at the genetic level, but have single amino acid differences in the VP30 and L proteins. The potential effects of these differences were tested using minigenomes and recombinant viruses. The results obtained with this approach are consistent with the role of VP30 and L as components of the EBOV RNA replication machinery. Moreover, the 2 isolates exhibited clear fitness differences in competitive growth assays. Published by Elsevier Inc.

  9. Wastewater-based epidemiology, an analytical chemical approach for the investigation of human consumption of lifestyle chemicals

    NARCIS (Netherlands)

    Causanilles Llanes, A.

    2018-01-01

    The research presented in this thesis supports the hypothesis that wastewater-based epidemiology (WBE) approach can be used as an alternative and non-intrusive technique that provides information about a population’s health and lifestyle habits. The focus is in the essential role of analytical

  10. A constrained approach to multiscale stochastic simulation of chemically reacting systems

    KAUST Repository

    Cotter, Simon L.; Zygalakis, Konstantinos C.; Kevrekidis, Ioannis G.; Erban, Radek

    2011-01-01

    Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address

  11. Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution.

    Science.gov (United States)

    Smith, Silvia E; Showers-Corneli, Patrice; Dardenne, Caitlin N; Harpending, Henry H; Martin, Darren P; Beiko, Robert G

    2012-01-01

    The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens is due in part to their ability to rapidly adapt to their changing environment and host. Recombination is the fastest way for bacterial genomes to acquire genetic material, but conflicting results about the extent of recombination in the genus Mycobacterium have been reported. We examined a data set comprising 18 distinct strains from 13 named species for evidence of recombination. Genomic regions common to all strains (accounting for 10% to 22% of the full genomes of all examined species) were aligned and concatenated in the chromosomal order of one mycobacterial reference species. The concatenated sequence was screened for evidence of recombination using a variety of statistical methods, with each proposed event evaluated by comparing maximum-likelihood phylogenies of the recombinant section with the non-recombinant portion of the dataset. Incongruent phylogenies were identified by comparing the site-wise log-likelihoods of each tree using multiple tests. We also used a phylogenomic approach to identify genes that may have been acquired through horizontal transfer from non-mycobacterial sources. The most frequent associated lineages (and potential gene transfer partners) in the Mycobacterium lineage-restricted gene trees are other members of suborder Corynebacterinae, but more-distant partners were identified as well. In two examined cases of potentially frequent and habitat-directed transfer (M. abscessus to Segniliparus and M. smegmatis to Streptomyces), observed sequence distances were small and consistent with a hypothesis of transfer, while in a third case (M. vanbaalenii to Streptomyces) distances were larger. The analyses described here indicate that whereas evidence of recombination in core regions within the genus is

  12. Improved Genetic Profiling of Anthropometric Traits Using a Big Data Approach.

    Directory of Open Access Journals (Sweden)

    Oriol Canela-Xandri

    Full Text Available Genome-wide association studies (GWAS promised to translate their findings into clinically beneficial improvements of patient management by tailoring disease management to the individual through the prediction of disease risk. However, the ability to translate genetic findings from GWAS into predictive tools that are of clinical utility and which may inform clinical practice has, so far, been encouraging but limited. Here we propose to use a more powerful statistical approach, the use of which has traditionally been limited due to computational requirements and lack of sufficiently large individual level genotyped cohorts, but which improve the prediction of multiple medically relevant phenotypes using the same panel of SNPs. As a proof of principle, we used a shared panel of 319,038 common SNPs with MAF > 0.05 to train the prediction models in 114,264 unrelated White-British individuals for height and four obesity related traits (body mass index, basal metabolic rate, body fat percentage, and waist-to-hip ratio. We obtained prediction accuracies that ranged between 46% and 75% of the maximum achievable given the captured heritable component. For height, this represents an improvement in prediction accuracy of up to 68% (184% more phenotypic variance explained over SNPs reported to be robustly associated with height in a previous GWAS meta-analysis of similar size. Across-population predictions in White non-British individuals were similar to those in White-British whilst those in Asian and Black individuals were informative but less accurate. We estimate that the genotyping of circa 500,000 unrelated individuals will yield predictions between 66% and 82% of the SNP-heritability captured by common variants in our array. Prediction accuracies did not improve when including rarer SNPs or when fitting multiple traits jointly in multivariate models.

  13. The development of a nuclear chemical plant human reliability management approach: HRMS and JHEDI

    International Nuclear Information System (INIS)

    Kirwan, Barry

    1997-01-01

    In the late 1980's, amidst the qualitative and quantitative validation of certain Human Reliability Assessment (HRA) techniques, there was a desire for a new technique specifically for a nuclear reprocessing plant being designed. The technique was to have the following attributes: it should be data-based rather than involving pure expert judgement; it was to be flexible, so that it would allow both relatively rapid screening and more detailed assessment; and it was to have sensitivity analysis possibilities, so that Human Factors design-related parameters, albeit at a gross level, could be brought into the risk assessment equation. The techniques and literature were surveyed, and it was decided that no one technique fulfilled these requirements, and so a new approach was developed. Two techniques were devised, the Human Reliability Management System (HRMS), and the Justification of Human Error Data Information (JHEDI) technique, the latter being essentially a quicker screening version of the former. Both techniques carry out task analysis, error analysis, and Performance Shaping Factor-based quantification, but JHEDI involves less detailed assessment than HRMS. Additionally, HRMS can be utilised to determine error reduction mechanisms, based on the way the Performance Shaping Factors are contributing to the assessed error probabilities. Both techniques are fully computerised and assessments are highly documentable and auditable, which was seen as a useful feature both by the company developing the techniques, and by the regulatory authorities assessing the final output risk assessments into which these two techniques fed data. This paper focuses in particular on the quantification process used by these techniques. The quantification approach for both techniques was principally one of extrapolation from real data to the desired Human Error Probability (HEP), based on a comparison between Performance Shaping Factor (PSF) profiles for the real, and the to

  14. Unraveling the genetic landscape of autosomal recessive Charcot-Marie-Tooth neuropathies using a homozygosity mapping approach

    Science.gov (United States)

    Zimoń, Magdalena; Battaloǧlu, Esra; Parman, Yesim; Erdem, Sevim; Baets, Jonathan; De Vriendt, Els; Atkinson, Derek; Almeida-Souza, Leonardo; Deconinck, Tine; Ozes, Burcak; Goossens, Dirk; Cirak, Sebahattin; Van Damme, Philip; Shboul, Mohammad; Voit, Thomas; Van Maldergem, Lionel; Dan, Bernard; El-Khateeb, Mohammed S.; Guergueltcheva, Velina; Lopez-Laso, Eduardo; Goemans, Nathalie; Masri, Amira; Züchner, Stephan; Timmerman, Vincent; Topaloǧlu, Haluk; De Jonghe, Peter

    2016-01-01

    Autosomal recessive forms of Charcot-Marie-Tooth disease (ARCMT) are rare but severe disorders of the peripheral nervous system. Their molecular basis is poorly understood due to the extensive genetic and clinical heterogeneity, posing considerable challenges for patients, physicians, and researchers. We report on the genetic findings from a systematic study of a large collection of 174 independent ARCMT families. Initial sequencing of the three most common ARCMT genes (ganglioside-induced differentiation protein 1—GDAP1, SH3 domain and tetratricopeptide repeats-containing protein 2—SH3TC2, histidine-triad nucleotide binding protein 1—HINT1) identified pathogenic mutations in 41 patients. Subsequently, 87 selected nuclear families underwent single nucleotide polymorphism (SNP) genotyping and homozygosity mapping, followed by targeted screening of known ARCMT genes. This strategy provided molecular diagnosis to 22 % of the families. Altogether, our unbiased genetic approach identified pathogenic mutations in ten ARCMT genes in a total of 41.3 % patients. Apart from a newly described founder mutation in GDAP1, the majority of variants constitute private molecular defects. Since the gene testing was independent of the clinical phenotype of the patients, we identified mutations in patients with unusual or additional clinical features, extending the phenotypic spectrum of the SH3TC2 gene. Our study provides an overview of the ARCMT genetic landscape and proposes guidelines for tackling the genetic heterogeneity of this group of hereditary neuropathies. PMID:25231362

  15. A Novel Approach of Understanding and Incorporating Error of Chemical Transport Models into a Geostatistical Framework

    Science.gov (United States)

    Reyes, J.; Vizuete, W.; Serre, M. L.; Xu, Y.

    2015-12-01

    The EPA employs a vast monitoring network to measure ambient PM2.5 concentrations across the United States with one of its goals being to quantify exposure within the population. However, there are several areas of the country with sparse monitoring spatially and temporally. One means to fill in these monitoring gaps is to use PM2.5 modeled estimates from Chemical Transport Models (CTMs) specifically the Community Multi-scale Air Quality (CMAQ) model. CMAQ is able to provide complete spatial coverage but is subject to systematic and random error due to model uncertainty. Due to the deterministic nature of CMAQ, often these uncertainties are not quantified. Much effort is employed to quantify the efficacy of these models through different metrics of model performance. Currently evaluation is specific to only locations with observed data. Multiyear studies across the United States are challenging because the error and model performance of CMAQ are not uniform over such large space/time domains. Error changes regionally and temporally. Because of the complex mix of species that constitute PM2.5, CMAQ error is also a function of increasing PM2.5 concentration. To address this issue we introduce a model performance evaluation for PM2.5 CMAQ that is regionalized and non-linear. This model performance evaluation leads to error quantification for each CMAQ grid. Areas and time periods of error being better qualified. The regionalized error correction approach is non-linear and is therefore more flexible at characterizing model performance than approaches that rely on linearity assumptions and assume homoscedasticity of CMAQ predictions errors. Corrected CMAQ data are then incorporated into the modern geostatistical framework of Bayesian Maximum Entropy (BME). Through cross validation it is shown that incorporating error-corrected CMAQ data leads to more accurate estimates than just using observed data by themselves.

  16. Thermodynamic approach to the conditions of chemical deposition of boron by contact with an inert substrate

    International Nuclear Information System (INIS)

    Thebault, J.; Naslain, R.; Hagenmuller, P.; Bernard, C.

    1978-01-01

    The optimum conditions for the synthesis of boron by chemical vapour deposition (CVD) from BCl 3 -H 2 or BBr 3 -H 2 mixtures onto an inert substrate (boron or boronized metals) have been studied by a thermodynamic approach. This approach, which postulates that states close to equilibrium are reached in the vicinity of the hot substrate, is based on the minimization of the total Gibbs free energy of the system. Between 1200 and 1900 K and under a total pressure of 1 atm, the hydrogen reduction of BCl 3 can lead to two types of by-products: BHCl 2 at all temperatures, and BCl 2 or BCl subhalides at high temperatures; BHCl 2 is the main product of the reduction at the lowest temperatures. The hydrogen reduction of BCl 3 is never complete for the conditions commonly used for the synthesis of boron. The amount of by-products and of BBr 3 which must be recycled can be minimized by utilizing BCl 3 -H 2 mixtures rich in hydrogen. The amount of boron deposited exhibits a maximum for a temperature close to 1700 K. Similar results have been obtained for BBr 3 . However, between 1000 and 1500 K and under a total pressure of 1 atm the amount of by-products (BHBr 2 and BBr 2 ) is smaller than in the case of BCl 3 . The boron yield from the reduction of BBr 3 is higher than that from BCl 3 and the percentage of boron halide which must be recycled is lower in the case of BBr 3 . Thus, BBr 3 appears to be a better source than BCl 3 for the CVD of boron. (Auth.)

  17. Chemical and Enzymatic Approaches to Carbohydrate-Derived Spiroketals: Di-D-Fructose Dianhydrides (DFAs

    Directory of Open Access Journals (Sweden)

    José M. García Fernández

    2008-08-01

    Full Text Available Di-D-fructose dianhydrides (DFAs comprise a unique family of stereoisomeric spiro-tricyclic disaccharides formed upon thermal and/or acidic activation of sucroseand/ or D-fructose-rich materials. The recent discovery of the presence of DFAs in food products and their remarkable nutritional features has attracted considerable interest from the food industry. DFAs behave as low-caloric sweeteners and have proven to exert beneficial prebiotic nutritional functions, favouring the growth of Bifidobacterium spp. In the era of functional foods, investigation of the beneficial properties of DFAs has become an important issue. However, the complexity of the DFA mixtures formed during caramelization or roasting of carbohydrates by traditional procedures (up to 14 diastereomeric spiroketal cores makes evaluation of their individual properties a difficult challenge. Great effort has gone into the development of efficient procedures to obtain DFAs in pure form at laboratory and industrial scale. This paper is devoted to review the recent advances in the stereoselective synthesis of DFAs by means of chemical and enzymatic approaches, their scope, limitations, and complementarities.

  18. An approach to develop chemical intuition for atomistic electron transport calculations using basis set rotations

    Energy Technology Data Exchange (ETDEWEB)

    Borges, A.; Solomon, G. C. [Department of Chemistry and Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø (Denmark)

    2016-05-21

    Single molecule conductance measurements are often interpreted through computational modeling, but the complexity of these calculations makes it difficult to directly link them to simpler concepts and models. Previous work has attempted to make this connection using maximally localized Wannier functions and symmetry adapted basis sets, but their use can be ambiguous and non-trivial. Starting from a Hamiltonian and overlap matrix written in a hydrogen-like basis set, we demonstrate a simple approach to obtain a new basis set that is chemically more intuitive and allows interpretation in terms of simple concepts and models. By diagonalizing the Hamiltonians corresponding to each atom in the molecule, we obtain a basis set that can be partitioned into pseudo-σ and −π and allows partitioning of the Landuaer-Büttiker transmission as well as create simple Hückel models that reproduce the key features of the full calculation. This method provides a link between complex calculations and simple concepts and models to provide intuition or extract parameters for more complex model systems.

  19. A Genetic Algorithms Based Approach for Identification of Escherichia coli Fed-batch Fermentation

    Directory of Open Access Journals (Sweden)

    Olympia Roeva

    2004-10-01

    Full Text Available This paper presents the use of genetic algorithms for identification of Escherichia coli fed-batch fermentation process. Genetic algorithms are a directed random search technique, based on the mechanics of natural selection and natural genetics, which can find the global optimal solution in complex multidimensional search space. The dynamic behavior of considered process has known nonlinear structure, described with a system of deterministic nonlinear differential equations according to the mass balance. The parameters of the model are estimated using genetic algorithms. Simulation examples for demonstration of the effectiveness and robustness of the proposed identification scheme are included. As a result, the model accurately predicts the process of cultivation of E. coli.

  20. 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.

  1. The Third International Meeting on Genetic Disorders in the RAS/MAPK Pathway: Toward a Therapeutic Approach

    OpenAIRE

    Korf, Bruce; Ahmadian, Reza; Allanson, Judith; Aoki, Yoko; Bakker, Annette; Wright, Emma Burkitt; Denger, Brian; Elgersma, Ype; Gelb, Bruce D.; Gripp, Karen W.; Kerr, Bronwyn; Kontaridis, Maria; Lazaro, Conxi; Linardic, Corinne; Lozano, Reymundo

    2015-01-01

    "The Third International Meeting on Genetic Disorders in the RAS/MAPK Pathway: Towards a Therapeutic Approach" was held at the Renaissance Orlando at SeaWorld Hotel (August 2-4, 2013). Seventy-one physicians and scientists attended the meeting, and parallel meetings were held by patient advocacy groups (CFC International, Costello Syndrome Family Network, NF Network and Noonan Syndrome Foundation). Parent and patient advocates opened the meeting with a panel discussion to set the stage regard...

  2. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

    DEFF Research Database (Denmark)

    Manning, Alisa K; Hivert, Marie-France; Scott, Robert A

    2012-01-01

    pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci...... associated with fasting insulin at P triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci...

  3. Genetic shifting: a novel approach for controlling vector-borne diseases

    OpenAIRE

    Powell, Jeffrey R.; Tabachnick, Walter J.

    2014-01-01

    Rendering populations of vectors of diseases incapable of transmitting pathogens through genetic methods has long been a goal of vector geneticists. We outline a method to achieve this goal that does not involve introduction of any new genetic variants to the target population. Rather we propose that shifting the frequencies of naturally occurring alleles that confer refractoriness to transmission can reduce transmission below a sustainable level. The program employs methods successfully used...

  4. The thermodynamic approach to boron chemical vapour deposition based on a computer minimization of the total Gibbs free energy

    International Nuclear Information System (INIS)

    Naslain, R.; Thebault, J.; Hagenmuller, P.; Bernard, C.

    1979-01-01

    A thermodynamic approach based on the minimization of the total Gibbs free energy of the system is used to study the chemical vapour deposition (CVD) of boron from BCl 3 -H 2 or BBr 3 -H 2 mixtures on various types of substrates (at 1000 < T< 1900 K and 1 atm). In this approach it is assumed that states close to equilibrium are reached in the boron CVD apparatus. (Auth.)

  5. Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

    International Nuclear Information System (INIS)

    Kustova, Elena V.; Kremer, Gilberto M.

    2014-01-01

    Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N 2 flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure

  6. Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

    Energy Technology Data Exchange (ETDEWEB)

    Kustova, Elena V., E-mail: e.kustova@spbu.ru [Department of Mathematics and Mechanics, Saint Petersburg State University, 198504 Universitetskiy pr. 28, Saint Petersburg (Russian Federation); Kremer, Gilberto M., E-mail: kremer@fisica.ufpr.br [Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba (Brazil)

    2014-12-05

    Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N{sub 2} flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure.

  7. Identifying Associations Between Brain Imaging Phenotypes and Genetic Factors via A Novel Structured SCCA Approach.

    Science.gov (United States)

    Du, Lei; Zhang, Tuo; Liu, Kefei; Yan, Jingwen; Yao, Xiaohui; Risacher, Shannon L; Saykin, Andrew J; Han, Junwei; Guo, Lei; Shen, Li

    2017-06-01

    Brain imaging genetics attracts more and more attention since it can reveal associations between genetic factors and the structures or functions of human brain. Sparse canonical correlation analysis (SCCA) is a powerful bi-multivariate association identification technique in imaging genetics. There have been many SCCA methods which could capture different types of structured imaging genetic relationships. These methods either use the group lasso to recover the group structure, or employ the graph/network guided fused lasso to find out the network structure. However, the group lasso methods have limitation in generalization because of the incomplete or unavailable prior knowledge in real world. The graph/network guided methods are sensitive to the sign of the sample correlation which may be incorrectly estimated. We introduce a new SCCA model using a novel graph guided pairwise group lasso penalty, and propose an efficient optimization algorithm. The proposed method has a strong upper bound for the grouping effect for both positively and negatively correlated variables. We show that our method performs better than or equally to two state-of-the-art SCCA methods on both synthetic and real neuroimaging genetics data. In particular, our method identifies stronger canonical correlations and captures better canonical loading profiles, showing its promise for revealing biologically meaningful imaging genetic associations.

  8. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci

    Science.gov (United States)

    Shen, Changbing; Gao, Jing; Sheng, Yujun; Dou, Jinfa; Zhou, Fusheng; Zheng, Xiaodong; Ko, Randy; Tang, Xianfa; Zhu, Caihong; Yin, Xianyong; Sun, Liangdan; Cui, Yong; Zhang, Xuejun

    2016-01-01

    Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association study (GWAS). More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWAS. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo. Many susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in the development of vitiligo. PMID:26870082

  9. A possibilistic approach for transient identification with 'don't know' response capability optimized by genetic algorithm

    International Nuclear Information System (INIS)

    Almeida, Jose Carlos S. de; Schirru, Roberto; Pereira, Claudio M.N.A.; Universidade Federal, Rio de Janeiro, RJ

    2002-01-01

    This work describes a possibilistic approach for transient identification based on the minimum centroids set method, proposed in previous work, optimized by genetic algorithm. The idea behind this method is to split the complex classification problem into small and simple ones, so that the performance in the classification can be increased. In order to accomplish that, a genetic algorithm is used to learn, from realistic simulated data, the optimized time partitions, which the robustness and correctness in the classification are maximized. The use of a possibilistic classification approach propitiates natural and consistent classification rules, leading naturally to a good heuristic to handle the 'don't know 'response, in case of unrecognized transient, which is fairly desirable in transient classification systems where safety is critical. Application of the proposed approach to a nuclear transient indentification problem reveals good capability of the genetic algorithm in learning optimized possibilistic classification rules for efficient diagnosis including 'don't know' response. Obtained results are shown and commented. (author)

  10. Chemical and genetic diversity among some wild stands of Calligonum polygonoides (Polygonaceae from the Thar Desert of Rajasthan

    Directory of Open Access Journals (Sweden)

    Govind K. Vyas

    2012-09-01

    Full Text Available The arid Western Rajasthan, where the Thar Desert of India is immersed, is mostly covered by sand dunes, a common landscape. The region has confronted with fragilities of natural resources, low, erratic and ill-distributed rainfall, and is covered up with many perennial hardy shrubs. Calligonum polygonoides, the most common perennial shrub, is widely present in some localities of this Thar Desert. In this study, we evaluated the diversity present among 54 wild Calligonum polygonoides plants, sampled from eight different locations within the Thar Desert. Our methods included chemical/nutritional characteristics and random amplified polymorphic DNA (RAPD. Both chemical and molecular methods produced wider range of diversity, however, RAPD detected comparatively more diversity. A total of 163 band positions were produced by ten RAPD primers, of which 147 were found polymorphic with 90.18% polymorphism. RAPD-based Jaccard’s similarity coefficients ranged from 0.43-0.89. The analysis of various chemical and mineral constituents revealed that phog is an excellent source of calcium, potassium and phosphorous while relatively poor in zinc. Among minerals, average potassium content was found maximum (2 430mg/100g with 0.14 CV. Zinc was observed comparably less in quantity while highest variable with CV 0.73. The chemical-based Manhattan dissimilarity coefficient values ranged from 0.01-0.22 with an average of 0.12. The comparison of the clusters obtained based on the chemical and mineral parameters with those of the RAPD data showed that the groups formed in both cases showed different patterns of relationships among the samples. Broader range of diversity might be due to the out breeding behavior of C. polygonoides and indicates the good adaptability of the plants in the region studied. However, low diversity observed in the Bikaner province is alarming and suggests that anthropogenic activities leading to heavy population disturbances can affect the

  11. Studying Air Quality Dynamics using A Linear Genetic Programming Approach over Remotely Sensed Atmospheric Parameters: case study (Cairo, Egypt)

    Science.gov (United States)

    El-Askary, H. M.; Sheta, W.; Prasad, A. K.; Ali, H.; Abdel rahman, M.; El-Desouki, A.; Kafatos, M.

    2011-12-01

    Water Vapor Low Mean, Atmospheric Water Vapor Mean, Mass Concentration Land Mean, Optical Depth Ratio Small Land and Ocean Mean, Small Mode Optical Depth Land and Ocean Mean, Cloud Top Pressure Day Mean, Cloud Top Pressure Mean, Cloud Top Temperature Mean. The suggested linear Genetic approach detected hidden anomalies and relationships that cannot be observed from the conventional statistical methods. A well-established model as an important contribution to show the relationships between particle size and the physical and chemical aerosols properties has been designed. Such coupling will provide insight into the micro physics of the phenomenon. The proposed research will reveal previously uncharacterized yet fundamental relations and dependencies among aerosols, cloud and meteorological related parameters. Moreover, it would aid in filling gaps of missing satellite parameters using other available ones.

  12. Chemical and engineering approaches to enable organic field-effect transistors for electronic skin applications.

    Science.gov (United States)

    Sokolov, Anatoliy N; Tee, Benjamin C-K; Bettinger, Christopher J; Tok, Jeffrey B-H; Bao, Zhenan

    2012-03-20

    Skin is the body's largest organ and is responsible for the transduction of a vast amount of information. This conformable material simultaneously collects signals from external stimuli that translate into information such as pressure, pain, and temperature. The development of an electronic material, inspired by the complexity of this organ is a tremendous, unrealized engineering challenge. However, the advent of carbon-based electronics may offer a potential solution to this long-standing problem. In this Account, we describe the use of an organic field-effect transistor (OFET) architecture to transduce mechanical and chemical stimuli into electrical signals. In developing this mimic of human skin, we thought of the sensory elements of the OFET as analogous to the various layers and constituents of skin. In this fashion, each layer of the OFET can be optimized to carry out a specific recognition function. The separation of multimodal sensing among the components of the OFET may be considered a "divide and conquer" approach, where the electronic skin (e-skin) can take advantage of the optimized chemistry and materials properties of each layer. This design of a novel microstructured gate dielectric has led to unprecedented sensitivity for tactile pressure events. Typically, pressure-sensitive components within electronic configurations have suffered from a lack of sensitivity or long mechanical relaxation times often associated with elastomeric materials. Within our method, these components are directly compatible with OFETs and have achieved the highest reported sensitivity to date. Moreover, the tactile sensors operate on a time scale comparable with human skin, making them ideal candidates for integration as synthetic skin devices. The methodology is compatible with large-scale fabrication and employs simple, commercially available elastomers. The design of materials within the semiconductor layer has led to the incorporation of selectivity and sensitivity within

  13. Evaluation of the applicability of the Benchmark approach to existing toxicological data. Framework: Chemical compounds in the working place

    NARCIS (Netherlands)

    Appel MJ; Bouman HGM; Pieters MN; Slob W; Adviescentrum voor chemische; CSR

    2001-01-01

    Five chemicals used in workplace, for which a risk assessment had already been carried out, were selected and the relevant critical studies re-analyzed by the Benchmark approach. The endpoints involved included continuous, and ordinal data. Dose-response modeling could be reasonablyapplied to the

  14. The Effect of Cooperative Learning Approach Based on Conceptual Change Condition on Students' Understanding of Chemical Equilibrium Concepts

    Science.gov (United States)

    Bilgin, Ibrahim; Geban, Omer

    2006-01-01

    The purpose of this study is to investigate the effects of the cooperative learning approach based on conceptual change conditions over traditional instruction on 10th grade students' conceptual understanding and achievement of computational problems related to chemical equilibrium concepts. The subjects of this study consisted of 87 tenth grade…

  15. Systematic documentation and analysis of human genetic variation using the microattribution approach

    Science.gov (United States)

    Giardine, Belinda; Borg, Joseph; Higgs, Douglas R.; Peterson, Kenneth R.; Maglott, Donna; Basak, A. Nazli; Clark, Barnaby; Faustino, Paula; Felice, Alex E.; Francina, Alain; Gallivan, Monica V. E.; Georgitsi, Marianthi; Gibbons, Richard J.; Giordano, Piero C.; Harteveld, Cornelis L.; Joly, Philippe; Kanavakis, Emmanuel; Kollia, Panagoula; Menzel, Stephan; Miller, Webb; Moradkhani, Kamran; Old, John; Papachatzopoulou, Adamantia; Papadakis, Manoussos N.; Papadopoulos, Petros; Pavlovic, Sonja; Philipsen, Sjaak; Radmilovic, Milena; Riemer, Cathy; Schrijver, Iris; Stojiljkovic, Maja; Thein, Swee Lay; Traeger-Synodinos, Jan; Tully, Ray; Wada, Takahito; Waye, John; Wiemann, Claudia; Zukic, Branka; Chui, David H. K.; Wajcman, Henri; Hardison, Ross C.; Patrinos, George P.

    2013-01-01

    We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to these disorders, and then implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories 1. A total of 1,941 unique genetic variants in 37 genes, encoding globins (HBA2, HBA1, HBG2, HBG1, HBD, HBB) and other erythroid proteins (ALOX5AP, AQP9, ARG2, ASS1, ATRX, BCL11A, CNTNAP2, CSNK2A1, EPAS1, ERCC2, FLT1, GATA1, GPM6B, HAO2, HBS1L, KDR, KL, KLF1, MAP2K1, MAP3K5, MAP3K7, MYB, NOS1, NOS2, NOS3, NOX3, NUP133, PDE7B, SMAD3, SMAD6, and TOX) are currently documented in these databases with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants and now provides a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The large repository of previously reported data, together with more recent data, acquired by microattribution, demonstrates how the comprehensive documentation of human variation will provide key insights into normal biological processes and how these are perturbed in human genetic disease. Using the microattribution process set out here, datasets which took decades to accumulate for the globin genes could be assembled rapidly for other genes and disease systems. The principles established here for the globin gene system will serve as a model for other systems and the analysis of other common and/or complex human genetic diseases. PMID:21423179

  16. Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity.

    Directory of Open Access Journals (Sweden)

    J R Managbanag

    Full Text Available BACKGROUND: Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of

  17. Interaction between visual and chemical cues in a Liolaemus lizard: a multimodal approach.

    Science.gov (United States)

    Vicente, Natalin S; Halloy, Monique

    2017-12-01

    Multimodal communication involves the use of signals and cues across two or more sensory modalities. The genus Liolaemus (Iguania: Liolaemidae) offers a great potential for studies on the ecology and evolution of multimodal communication, including visual and chemical signals. In this study, we analyzed the response of male and female Liolaemus pacha to chemical, visual and combined (multimodal) stimuli. Using cue-isolation tests, we registered the number of tongue flicks and headbob displays from exposure to signals in each modality. Number of tongue flicks was greater when a chemical stimulus was presented alone than in the presence of visual or multimodal stimuli. In contrast, headbob displays were fewer in number with visual and chemical stimuli alone, but significantly higher in number when combined. Female signallers triggered significantly more tongue flicks than male signallers, suggesting that chemical cues are involved in sexual recognition. We did not find an inhibition between chemical and visual cues. On the contrary, we observed a dominance of the chemical modality, because when presented with visual stimuli, lizards also responded with more tongue flicks than headbob displays. The total response produced by multimodal stimuli was similar to that of the chemical stimuli alone, possibly suggesting non-redundancy. We discuss whether the visual component of a multimodal signal could attract attention at a distance, increasing the effectiveness of transmission and reception of the information in chemical cues. Copyright © 2017 Elsevier GmbH. All rights reserved.

  18. Mammalian genetics and biostatistics

    International Nuclear Information System (INIS)

    Grahn, D.; Carnes, B.A.; Farrington, B.H.; Lee, C.H.

    1985-01-01

    This program seeks to assess genetic hazards of single, weekly, and continuous doses of 60 Co gamma rays and single and weekly doses of fission neutrons to provide a basis for estimating relative biological effectiveness (RBE) of fission neutrons, to develop detailed dose-response data at low doses as a basis for studying relationships between linear energy transfer (LET) and the sensitivity of various cell stages, and to develop improved statistical approaches to analytical issues in chemical and radiation toxicology. 3 refs

  19. New approaches to evaluating the genetic effects of the atomic bombs

    International Nuclear Information System (INIS)

    Neel, J.V.

    1995-01-01

    In the aftermath of the atomic bombings of Hiroshima and Nagasaki fifty years ago, one of the compelling biomedical questions that arose concerned the genetic effects of this exposure. More recently, revelations of the extent of industrial or accidental exposures in the former Soviet Union and charges that employment in the Sellafield Nuclear Reprocessing Plant in West Cumbria, England has resulted in a gene-mediated increase in children of plant employees have served to keep in the public mind the issue of the genetic risks of exposure to ionizing radiation. The study of the genetic effects of the atomic bombs has moved from the gross morphological level of congenital malformations to the examination of DNA. However, were the need for such genetic studies to arise in the foreseeable future, despite this impressive progress in DNA-oriented systems, the documentation of congenital defect, genetic disease and child survival would still be an essential component of any future study. Whatever the geneticists may think, the phenotypic well-being and survival of children are still the primary indicators on which the public, who ultimately supports these studies, will base its judgement of risk. 28 refs

  20. Genetic diversity among Korean bermudagrass (Cynodon spp.) ecotypes characterized by morphological, cytological and molecular approaches.

    Science.gov (United States)

    Kang, Si-Yong; Lee, Geung-Joo; Lim, Ki Byung; Lee, Hye Jung; Park, In Sook; Chung, Sung Jin; Kim, Jin-Baek; Kim, Dong Sub; Rhee, Hye Kyung

    2008-04-30

    The genus Cynodon comprises ten species. The objective of this study was to evaluate the genetic diversity of Korean bermudagrasses at the morphological, cytological and molecular levels. Morphological parameters, the nuclear DNA content and ploidy levels were observed in 43 bermudagrass ecotypes. AFLP markers were evaluated to define the genetic diversity, and chromosome counts were made to confirm the inferred cytotypes. Nuclear DNA contents were in the ranges 1.42-1.56, 1.94-2.19, 2.54, and 2.77-2.85 pg/2C for the triploid, tetraploid, pentaploid, and hexaploid accessions, respectively. The inferred cytotypes were triploid (2n = 3x = 27), tetraploid (2n = 4x = 36), pentaploid (2n = 5x = 45), and hexaploid (2n = 6x = 54), but the majority of the collections were tetraploid (81%). Mitotic chromosome counts verified the corresponding ploidy levels. The fast growing fine-textured ecotypes had lower ploidy levels, while the pentaploids and hexaploids were coarse types. The genetic similarity ranged from 0.42 to 0.94 with an average of 0.64. UPGMA cluster analysis and principle coordinate analysis separated the ecotypes into 6 distinct groups. The genetic similarity suggests natural hybridization between the different cytotypes, which could be useful resources for future breeding and genetic studies.

  1. Isolation and genetic analysis of pure cells from forensic biological mixtures: The precision of a digital approach.

    Science.gov (United States)

    Fontana, F; Rapone, C; Bregola, G; Aversa, R; de Meo, A; Signorini, G; Sergio, M; Ferrarini, A; Lanzellotto, R; Medoro, G; Giorgini, G; Manaresi, N; Berti, A

    2017-07-01

    Latest genotyping technologies allow to achieve a reliable genetic profile for the offender identification even from extremely minute biological evidence. The ultimate challenge occurs when genetic profiles need to be retrieved from a mixture, which is composed of biological material from two or more individuals. In this case, DNA profiling will often result in a complex genetic profile, which is then subject matter for statistical analysis. In principle, when more individuals contribute to a mixture with different biological fluids, their single genetic profiles can be obtained by separating the distinct cell types (e.g. epithelial cells, blood cells, sperm), prior to genotyping. Different approaches have been investigated for this purpose, such as fluorescent-activated cell sorting (FACS) or laser capture microdissection (LCM), but currently none of these methods can guarantee the complete separation of different type of cells present in a mixture. In other fields of application, such as oncology, DEPArray™ technology, an image-based, microfluidic digital sorter, has been widely proven to enable the separation of pure cells, with single-cell precision. This study investigates the applicability of DEPArray™ technology to forensic samples analysis, focusing on the resolution of the forensic mixture problem. For the first time, we report here the development of an application-specific DEPArray™ workflow enabling the detection and recovery of pure homogeneous cell pools from simulated blood/saliva and semen/saliva mixtures, providing full genetic match with genetic profiles of corresponding donors. In addition, we assess the performance of standard forensic methods for DNA quantitation and genotyping on low-count, DEPArray™-isolated cells, showing that pure, almost complete profiles can be obtained from as few as ten haploid cells. Finally, we explore the applicability in real casework samples, demonstrating that the described approach provides complete

  2. Chitosan and thiolated chitosan: Novel therapeutic approach for preventing corneal haze after chemical injuries.

    Science.gov (United States)

    Zahir-Jouzdani, Forouhe; Mahbod, Mirgholamreza; Soleimani, Masoud; Vakhshiteh, Faezeh; Arefian, Ehsan; Shahosseini, Saeed; Dinarvand, Rasoul; Atyabi, Fatemeh

    2018-01-01

    Corneal haze, commonly caused by deep physical and chemical injuries, can greatly impair vision. Growth factors facilitate fibroblast proliferation and differentiation, which leads to haze intensity. In this study, the potential effect of chitosan (CS) and thiolated-chitosan (TCS) nanoparticles and solutions on inhibition of fibroblast proliferation, fibroblast to myofibroblast differentiation, neovascularization, extracellular matrix (ECM) deposition, and pro-fibrotic cytokine expression was examined. Transforming growth factor beta-1 (TGFβ 1 ) was induced by interleukin-6 (IL6) in human corneal fibroblasts and expression levels of TGFβ 1 , Platelet-derived growth factor (PDGF), α-smooth muscle actins (α-SMA), collagen type I (Col I), fibronectin (Fn) and vascular endothelial growth factor (VEGF) were quantified using qRT-PCR. To assess wound-healing capacity, TCS-treated mice were examined for α-SMA positive cells, collagen deposition, inflammatory cells and neovascularization through pathological immunohistochemistry. The results revealed that CS and TCS could down-regulate the expression levels of TGFβ 1 and PDGF comparable to that of TGFβ 1 knockdown experiment. However, down-regulation of TGFβ 1 was not regulated through miR29b induction. Neovascularization along with α-SMA and ECM deposition were significantly diminished. According to these findings, CS and TCS can be considered as potential anti-fibrotic and anti-angiogenic therapeutics. Furthermore, TCS, thiolated derivative of CS, will increase mucoadhesion of the polymer at the corneal surface which makes the polymer efficient and non-toxic therapeutic approach for corneal injuries. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Characterization of Whole Grain Pasta: Integrating Physical, Chemical, Molecular, and Instrumental Sensory Approaches.

    Science.gov (United States)

    Marti, Alessandra; Cattaneo, Stefano; Benedetti, Simona; Buratti, Susanna; Abbasi Parizad, Parisa; Masotti, Fabio; Iametti, Stefania; Pagani, Maria Ambrogina

    2017-11-01

    The consumption of whole-grain food-including pasta-has been increasing steadily. In the case of whole-grain pasta, given the many different producers, it seems important to have some objective parameters to define its overall quality. In this study, commercial whole-grain pasta samples representative of the Italian market have been characterized from both molecular and electronic-senses (electronic nose and electronic tongue) standpoint in order to provide a survey of the properties of different commercial samples. Only 1 pasta product showed very low levels of heat damage markers (furosine and pyrraline), suggesting that this sample underwent to low temperature dry treatment. In all samples, the furosine content was directly correlated to protein structural indices, since protein structure compactness increased with increasing levels of heat damage markers. Electronic senses were able to discriminate among pasta samples according to the intensity of heat treatment during the drying step. Pasta sample with low furosine content was discriminated by umami taste and by sensors responding to aliphatic and inorganic compounds. Data obtained with this multidisciplinary approach are meant to provide hints for identifying useful indices for pasta quality. As observed for semolina pasta, objective parameters based on heat-damage were best suited to define the overall quality of wholegrain pasta, almost independently of compositional differences among commercial samples. Drying treatments of different intensity also had an impact on instrumental sensory traits that may provide a reliable alternative to analytical determination of chemical markers of heat damage in all cases where there is a need for avoiding time-consuming procedures. © 2017 Institute of Food Technologists®.

  4. Chemical analysis of incense smokes used in Shaxi, Southwest China: a novel methodological approach in ethnobotany.

    Science.gov (United States)

    Staub, Peter O; Schiestl, Florian P; Leonti, Marco; Weckerle, Caroline S

    2011-10-31

    Characterization and comparative analysis of the main VOCs (volatile organic compounds) present in the smoke of 11 experimentally combusted plant species used as incense in Shaxi, Southwest China. Substances which may be responsible for the pleasant smell of the smokes as well as substances with a potential pharmacological activity are discussed. We adopt the dynamic headspace sorption method for the collection of smoke samples as a novel methodological approach in ethnobotany. The VOCs were identified using gas chromatography-mass spectrometry (GC-MS). Principal component analysis and canonical discriminant analysis were performed using PASW statistics (Version 18.0.2). Among the identified compounds were 10 monoterpenoids, 7 sesquiterpenoids, 6 linear hydrocarbons, 6 methoxy phenolics, 2 benzenoids, 2 polycyclic aromatic hydrocarbons, and 2 fatty acids. Based on their volatile profiles, the species are well clustered intraspecifically and separated interspecifically. The most abundant among the compounds potentially responsible for the pleasant smells of the smokes are methyl salicylate (12.28±3.90%) for Gaultheria fragrantissima leaves, δ-cadinene (15.58±2.29%) for Juniperus squamata wood, and α-Pinene for Cupressus funebris branches (9.16±7.73%) and Pistacia weinmanniifolia branches (19.52±8.66%). A couple of substances found are known for pharmacological activity, such as methylsalycilate, beta-caryophyllene and cedrol. The species used by the local people in Shaxi for incense differ clearly with respect to the chemical compounds of their smoke. Further, incense contains substances, which are of pharmacological interest and might support medicinal uses of smoke. Cedrol with its pleasant smell and sedative properties may be an important factor why specific plants are chosen as incense. Our findings support the idea that the effects of the use of incense as well as medicinal smoke depend on both, the cultural as well as the pharmacological context

  5. Merging data from genetic and epigenetic approaches to better understand autistic spectrum disorder.

    Science.gov (United States)

    Grayson, Dennis R; Guidotti, Alessandro

    2016-01-01

    Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that is characterized by a wide range of cognitive and behavioral abnormalities. Genetic research has identified large numbers of genes that contribute to ASD phenotypes. There is compelling evidence that environmental factors contribute to ASD through influences that differentially impact the brain through epigenetic mechanisms. Both genetic mutations and epigenetic influences alter gene expression in different cell types of the brain. Mutations impact the expression of large numbers of genes and also have downstream consequences depending on specific pathways associated with the mutation. Environmental factors impact the expression of sets of genes by altering methylation/hydroxymethylation patterns, local histone modification patterns and chromatin remodeling. Herein, we discuss recent developments in the research of ASD with a focus on epigenetic pathways as a complement to current genetic screening.

  6. Genetic shifting: a novel approach for controlling vector-borne diseases.

    Science.gov (United States)

    Powell, Jeffrey R; Tabachnick, Walter J

    2014-06-01

    Rendering populations of vectors of diseases incapable of transmitting pathogens through genetic methods has long been a goal of vector geneticists. We outline a method to achieve this goal that does not involve the introduction of any new genetic variants to the target population. Rather we propose that shifting the frequencies of naturally occurring alleles that confer refractoriness to transmission can reduce transmission below a sustainable level. The program employs methods successfully used in plant and animal breeding. Because no artificially constructed genetically modified organisms (GMOs) are introduced into the environment, the method is minimally controversial. We use Aedes aegypti and dengue virus (DENV) for illustrative purposes but point out that the proposed program is generally applicable to vector-borne disease control. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. 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)

  8. Advances on a Decision Analytic Approach to Exposure-Based Chemical Prioritization.

    Science.gov (United States)

    Wood, Matthew D; Plourde, Kenton; Larkin, Sabrina; Egeghy, Peter P; Williams, Antony J; Zemba, Valerie; Linkov, Igor; Vallero, Daniel A

    2018-05-11

    The volume and variety of manufactured chemicals is increasing, although little is known about the risks associated with the frequency and extent of human exposure to most chemicals. The EPA and the recent signing of the Lautenberg Act have both signaled the need for high-throughput methods to characterize and screen chemicals based on exposure potential, such that more comprehensive toxicity research can be informed. Prior work of Mitchell et al. using multicriteria decision analysis tools to prioritize chemicals for further research is enhanced here, resulting in a high-level chemical prioritization tool for risk-based screening. Reliable exposure information is a key gap in currently available engineering analytics to support predictive environmental and health risk assessments. An elicitation with 32 experts informed relative prioritization of risks from chemical properties and human use factors, and the values for each chemical associated with each metric were approximated with data from EPA's CP_CAT database. Three different versions of the model were evaluated using distinct weight profiles, resulting in three different ranked chemical prioritizations with only a small degree of variation across weight profiles. Future work will aim to include greater input from human factors experts and better define qualitative metrics. © 2018 Society for Risk Analysis.

  9. A Computer Algebra Approach to Solving Chemical Equilibria in General Chemistry

    Science.gov (United States)

    Kalainoff, Melinda; Lachance, Russ; Riegner, Dawn; Biaglow, Andrew

    2012-01-01

    In this article, we report on a semester-long study of the incorporation into our general chemistry course, of advanced algebraic and computer algebra techniques for solving chemical equilibrium problems. The method presented here is an alternative to the commonly used concentration table method for describing chemical equilibria in general…

  10. A scalable machine-learning approach to recognize chemical names within large text databases

    Directory of Open Access Journals (Sweden)

    Wren Jonathan D

    2006-09-01

    Full Text Available Abstract Motivation The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. Results A first-order Markov Model (MM was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid.

  11. Innovation in Integrated Chemical Product-Process Design - Development through a Model-based Systems Approach

    DEFF Research Database (Denmark)

    Conte, Elisa

    The ‘consumer oriented chemicals based products’ such as shampoos, sunscreens, insect repellents are used everyday by millions of people. They are structured products, constituted of numerous chemicals. This complexity gives the reason for which mainly experimental techniques are still employed...

  12. Y chromosome microdeletions and alterations of spermatogenesis, patient approach and genetic counseling.

    Science.gov (United States)

    Rives, Nathalie

    2014-05-01

    Infertility affects 15% of couples at reproductive age and human male infertility appears frequently idiopathic. The main genetic causes of spermatogenesis defect responsible for non-obstructive azoospermia and severe oligozoospermia are constitutional chromosomal abnormalities and microdeletions in the azoospermia factor region of the Y chromosome. The improvement of the Yq microdeletion screening method gave new insights in the mechanism responsible for the genesis of Yq microdeletions and for the consequences of the management of male infertility and genetic counselling in case of assisted reproductive technology. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  13. Autism and genetics: Clinical approach and association study with two markers of HRAS gene

    Energy Technology Data Exchange (ETDEWEB)

    Herault, J.; Petit, E.; Cherpi, C. [Laboratoire de Biochimie Medicale, Tours (France)] [and others

    1995-08-14

    Twin studies and familial aggregation studies indicate that genetic factors could play a role in infantile autism. In an earlier study, we identified a possible positive association between autism and a c-Harvey-ras (HRAS) oncogene marker at the 3{prime} end of the coding region. In an attempt to confirm this finding, we studied a larger population, well-characterized clinically and genetically. We report a positive association between autism and two HRAS markers, the 3{prime} marker used in the initial study and an additional marker in exon 1. 46 refs., 1 fig., 2 tabs.

  14. Bodies in skin: a philosophical and theological approach to genetic skin diseases.

    Science.gov (United States)

    Walser, Angelika

    2010-03-01

    This contribution evolved from my work in a European network and is dedicated to the rare genetic skin diseases. To gain a deeper knowledge about the question, what it means to suffer from a genetic skin disease, I have discussed the concepts of skin in philosophical and theological anthropology. Presuming that ancient interpretations of skin diseases (moral and cultical impurity) are still relevant today, feminist Christian theology shows the ways of deconstructing stigmatizing paradigma by using the body as a hermeneutic category. Skin becomes the "open borderline" of the human being, pointing out both the social vulnerability and the transcendent capacity of the human person.

  15. Electromagnetic energy as a bridge between atomic and cellular levels in the genetics approach to cancer treatment.

    Science.gov (United States)

    Tofani, Santi

    2015-01-01

    Literature on magnetic fields (MF) and gene expression, as well as on DNA damage, supports the hypothesis that electromagnetic energy may act at atomic level influencing genetic stability. According to quantum physics, MF act on the interconversion of singlet and triplet spin states, and therefore on genetic instability, activating oxidative processes connected to biological free radicals formation, particularly ROS. In the above frame, the results of in vitro and in vivo laboratory trials have been analyzed. The use of a static MF amplitude modulated by 50 Hz MF, with a time average total intensity of 5.5 mT, has been shown to influence tumor cell functions such as cell proliferation, apoptosis, p53 expression, inhibition of tumor growth and prolongation of survival in animals, evidence that MF can be more effective than chemotherapy (cyclophosphamide) in inhibiting metastatic spread and growth, having synergistic activity with chemotherapy (Cis-platin), and no observable side effects or toxicity in animals or in humans. The beneficial biological/clinical effects observed, without any adverse effects, have been confirmed by various authors and augur well for the potentiality of this new approach to treat genetically based diseases like cancer. Further studies are needed to develop a quantum physics approach to biology, allowing a stable bridge to be built between atomic and cellular levels, therefore developing quantum biology.